mini research paper

How to Write a Mini Research Paper Outline

Published 16 October, 2023

A mini research paper outline is a great way to organize your thoughts and get started on an assignment. This blog post is going to walk you through the process of writing a mini-research paper outline. It will not only help you with your own work but also give insight into what professors are looking for from their students.

What is the Outline & Significance of Writing it in a mini-research paper?

An outline is significant for all types of research papers . It serves to arrange your thoughts and your entire work prior to writing a research paper . This kind of paper is aimed at scientific research that will prove you to be a scholar that has technical aptitudes to solve core issues and is all set to convey your ideas using scientific approaches and processes. An outline will be a reminder for you to comprise all the necessary subtleties in it. It is “a frame” of the real research paper that will lead you through the whole procedure but how to write a research paper outline ?

Writing a research paper outline for your mini research paper can give a good direction to the students in writing a research paper. But many students do not have the exact idea about the format of the research paper and that is why they fail to write a good outline during mini research paper submission. The structure of the research paper outline could easily be understood by the students with the help of reliable research paper writers of My Research Topics. All the important steps that are part of a research paper outline could easily be written the Outline of Research Paper by students with the help of these experts.

By preliminary dividing your paper into all its basic parts, you will be far more ordered & will not be concerned that you forgot something. In addition, appear at your outline, you will be calmer as after splitting your work into numerous parts. It will not seem so irresistible & perplexing. You can approach all parts during different days & plan your preparations successively which will assist you to meet even tight time limits!

Get professional research paper writing help from expert writers who can help you in scoring high in college & university. Students across the globe can take guidance in writing research paper outlines, research paper introductions , or even complete research paper writing. So if you are not in a motivation to complete your research paper outline in different subjects like sciences, information technology, Economics, Law and Business studies, etc. Take reliable help in research paper writing from My Research Topics Experts.

Why outline writing is a must for a mini research paper

If you are a student who is used to have research paper writing work on a regular basis, it is not a big deal for you to understand the importance of a research paper outline. Sometimes even professors ask their students to write a mini research paper outline before starting the actual research paper.

The major purpose behind writing a research paper outline is to get an idea about the major points of the topic that you have researched that could be included in the research paper. The majority of the time students forget many significant aspects of the research paper due to a lack of a research paper outline. That is why it is very significant to write a little research paper outline for this purpose.

Mini research paper outlines structure tips

If you are asked by your professors to write a mini research paper outline here are some tips that you must follow for this purpose. My Research Topics Experts have given these tips to the students for their outline of the short research paper.

• Always carry out some research on the topic of your research paperwork before starts writing the outline.
• Make sure to use simple vocabulary and plagiarism-free ideas in your research paper.
• Do not write about the things that are written millions of times already, nobody is interested in reading such research papers.
• Be unique and be innovative along with correct sequences of the arguments in your research paper outline.

It can seem quite difficult to cope with this chore, & in such a case, you can constantly rely on an online writing service. But if you have chosen to write on your own keep reading this piece of writing. To be more capable in the details of the structure look through instances for elementary scholars. The outline for a Literary Essay will also assist you. Anyway, the major parts are as follows:

• Introduction

Seems not that tough, right?! But the fact is that all of the points include a broad range of information for you to arrange in your research outline regarding animals, for example.

The Introduction part is one of the most significant ones. Since it presents the reader with the topic of your paper and it is like a hook that draws the reader’s interest. Here you are supposed to talk about the top necessary components like the thesis statement, the clarification of the topic (some major points, general information), and an explanation of the core terms associated with your learning

The Body part is the amplest one and consists of numerous paragraphs or subparts. Here you bring the opinion to support your report. The research methodology is what follows the introduction segment. It provides insight into the means you carried out the research and must comprise the investigation kind and the questionnaire you have fulfilled. Never forget the aims of the investigation that must be also stated in the introduction.

Make certain to comprise the literature overview. Here mention the creative writing you used as a backup to your hypothesis & theories. This part will demonstrate how you can work the terms, theory, and existing evidence. Your chief theme and the selected literature should be adjacent. Demonstrate how your input develops & distends the active works.

Data and analysis generally go after methods and literature. Here present your results & other variables that you have got in the procedure of the survey. Use tables or graphs if required to be more precise and ordered. Interpret your results. Remember to tell the spectators whether your outcomes bring diversity to the whole topic. Outline the drawbacks of the research & its benefits.

The conclusion part generally does not present the spectators with the new information but gives the cursory look at the whole work by summarizing major points in it. Do not forget to talk about the thesis statement again. Formulate the viewpoint for potential research as well.

Read Also: A Guide to Start Research Process  

How to write a mini research paper outline?

Here is the guide to writing the University research paper outline by experts to the students. Those who want to write a perfect research paper outline can follow these points.

• Begin with the topic of research and understand it by multiple dimensions.
• Write down the important points that you noticed from the topic.
• If possible try to sift out the issues and problems that are associated with that topic and how to solve them.
• Also, try to research the reasons which are obstructing these solutions to work on practical grounds.
• Now start writing your research paper outline by giving the abstract or reason why you are writing your research paper.
• Also, discuss the main points that you will raise through your research paper and the way to reach the solutions for these problems.
• Finally, mention the way that you are going to follow to know the reality of these problems and why they exist.

This is how a good research paper outline could be written by the students easily. Students can show this outline to their professors and teachers as well.

As mentioned above a mini research paper talks about the main issues that the writer is going to deal with in his research paper. Apart from that, it also discusses the way and strategies that will be used to reach up to the solution of these problems. Resources that students are going to use in writing a research paper are sometimes also disclosed to the professors.

To cap it all we can say that a mini research paper outline is helpful to the students in keeping all the points in mind while writing a research paper so that any points do not go missing which should be there. Research paper guidance from the experts of My Research Topics also assists the students to write a supreme quality research paper. So students can take the assistance of these experts in their assignments in the form of assistance in research paper writing.

Research paper writing help to The scholars by My Research Topics at a reasonable cost is given round the clock. Those who do not have the idea about writing a good outline for a mini research paper can effortlessly approach for the assistance of experts. The moment you ask for assistance in your assignment of the research paper, a team of professionals from My Research Topics will actively start work upon your academic assignment work.

The research paper writing services are given to the students by an expert at a very cheap cost-effective and budget-friendly price. Every type of student whether he or she belongs to a poor financial background or rich background can have access to this help.

Stuck During Your Dissertation

Our top dissertation writing experts are waiting 24/7 to assist you with your university project,from critical literature reviews to a complete PhD dissertation.

Other Related Guides

• Research Project Questions
• Types of Validity in Research – Explained With Examples
• Schizophrenia Sample Research Paper
• Quantitative Research Methods – Definitive Guide
• Research Paper On Homelessness For College Students
• How to Study for Biology Final Examination
• Textual Analysis in Research / Methods of Analyzing Text

A Guide to Start Research Process – Introduction, Procedure and Tips

Research findings – objectives , importance and techniques.

• Topic Sentences in Research Paper – Meaning, Parts, Importance, Procedure and Techniques

Recent Research Guides for 2023

Get 15% off your first order with My Research Topics

Connect with a professional writer within minutes by placing your first order. No matter the subject, difficulty, academic level or document type, our writers have the skills to complete it.

My Research Topics is provides assistance since 2004 to Research Students Globally. We help PhD, Psyd, MD, Mphil, Undergrad, High school, College, Masters students to compete their research paper & Dissertations. Our Step by step mentorship helps students to understand the research paper making process.

Research Topics & Ideas

• Sociological Research Paper Topics & Ideas For Students 2023
• Nurses Research Paper Topics & Ideas 2023
• Nursing Capstone Project Research Topics & Ideas 2023
• Unique Research Paper Topics & Ideas For Students 2023
• Teaching Research Paper Topics & Ideas 2023
• Literary Research Paper Topics & Ideas 2023
• Nursing Ethics Research Topics & Ideas 2023

Research Guide

Disclaimer: The Reference papers provided by the Myresearchtopics.com serve as model and sample papers for students and are not to be submitted as it is. These papers are intended to be used for reference and research purposes only.

How To Write A Research Paper

Step-By-Step Tutorial With Examples + FREE Template

By: Derek Jansen (MBA) | Expert Reviewer: Dr Eunice Rautenbach | March 2024

For many students, crafting a strong research paper from scratch can feel like a daunting task – and rightly so! In this post, we’ll unpack what a research paper is, what it needs to do , and how to write one – in three easy steps. 🙂 

Overview: Writing A Research Paper

What (exactly) is a research paper.

• How to write a research paper
• Stage 1 : Topic & literature search
• Stage 2 : Structure & outline
• Stage 3 : Iterative writing
• Key takeaways

Let’s start by asking the most important question, “ What is a research paper? ”.

Simply put, a research paper is a scholarly written work where the writer (that’s you!) answers a specific question (this is called a research question ) through evidence-based arguments . Evidence-based is the keyword here. In other words, a research paper is different from an essay or other writing assignments that draw from the writer’s personal opinions or experiences. With a research paper, it’s all about building your arguments based on evidence (we’ll talk more about that evidence a little later).

Now, it’s worth noting that there are many different types of research papers , including analytical papers (the type I just described), argumentative papers, and interpretative papers. Here, we’ll focus on analytical papers , as these are some of the most common – but if you’re keen to learn about other types of research papers, be sure to check out the rest of the blog .

With that basic foundation laid, let’s get down to business and look at how to write a research paper .

Overview: The 3-Stage Process

While there are, of course, many potential approaches you can take to write a research paper, there are typically three stages to the writing process. So, in this tutorial, we’ll present a straightforward three-step process that we use when working with students at Grad Coach.

These three steps are:

• Finding a research topic and reviewing the existing literature
• Developing a provisional structure and outline for your paper, and
• Writing up your initial draft and then refining it iteratively

Let’s dig into each of these.

Need a helping hand?

Step 1: Find a topic and review the literature

As we mentioned earlier, in a research paper, you, as the researcher, will try to answer a question . More specifically, that’s called a research question , and it sets the direction of your entire paper. What’s important to understand though is that you’ll need to answer that research question with the help of high-quality sources – for example, journal articles, government reports, case studies, and so on. We’ll circle back to this in a minute.

The first stage of the research process is deciding on what your research question will be and then reviewing the existing literature (in other words, past studies and papers) to see what they say about that specific research question. In some cases, your professor may provide you with a predetermined research question (or set of questions). However, in many cases, you’ll need to find your own research question within a certain topic area.

Finding a strong research question hinges on identifying a meaningful research gap – in other words, an area that’s lacking in existing research. There’s a lot to unpack here, so if you wanna learn more, check out the plain-language explainer video below.

Once you’ve figured out which question (or questions) you’ll attempt to answer in your research paper, you’ll need to do a deep dive into the existing literature – this is called a “ literature search ”. Again, there are many ways to go about this, but your most likely starting point will be Google Scholar .

If you’re new to Google Scholar, think of it as Google for the academic world. You can start by simply entering a few different keywords that are relevant to your research question and it will then present a host of articles for you to review. What you want to pay close attention to here is the number of citations for each paper – the more citations a paper has, the more credible it is (generally speaking – there are some exceptions, of course).

Ideally, what you’re looking for are well-cited papers that are highly relevant to your topic. That said, keep in mind that citations are a cumulative metric , so older papers will often have more citations than newer papers – just because they’ve been around for longer. So, don’t fixate on this metric in isolation – relevance and recency are also very important.

Beyond Google Scholar, you’ll also definitely want to check out academic databases and aggregators such as Science Direct, PubMed, JStor and so on. These will often overlap with the results that you find in Google Scholar, but they can also reveal some hidden gems – so, be sure to check them out.

Once you’ve worked your way through all the literature, you’ll want to catalogue all this information in some sort of spreadsheet so that you can easily recall who said what, when and within what context. If you’d like, we’ve got a free literature spreadsheet that helps you do exactly that.

Step 2: Develop a structure and outline

With your research question pinned down and your literature digested and catalogued, it’s time to move on to planning your actual research paper .

It might sound obvious, but it’s really important to have some sort of rough outline in place before you start writing your paper. So often, we see students eagerly rushing into the writing phase, only to land up with a disjointed research paper that rambles on in multiple

Now, the secret here is to not get caught up in the fine details . Realistically, all you need at this stage is a bullet-point list that describes (in broad strokes) what you’ll discuss and in what order. It’s also useful to remember that you’re not glued to this outline – in all likelihood, you’ll chop and change some sections once you start writing, and that’s perfectly okay. What’s important is that you have some sort of roadmap in place from the start.

At this stage you might be wondering, “ But how should I structure my research paper? ”. Well, there’s no one-size-fits-all solution here, but in general, a research paper will consist of a few relatively standardised components:

• Introduction
• Literature review
• Methodology

Let’s take a look at each of these.

First up is the introduction section . As the name suggests, the purpose of the introduction is to set the scene for your research paper. There are usually (at least) four ingredients that go into this section – these are the background to the topic, the research problem and resultant research question , and the justification or rationale. If you’re interested, the video below unpacks the introduction section in more detail. 

The next section of your research paper will typically be your literature review . Remember all that literature you worked through earlier? Well, this is where you’ll present your interpretation of all that content . You’ll do this by writing about recent trends, developments, and arguments within the literature – but more specifically, those that are relevant to your research question . The literature review can oftentimes seem a little daunting, even to seasoned researchers, so be sure to check out our extensive collection of literature review content here .

With the introduction and lit review out of the way, the next section of your paper is the research methodology . In a nutshell, the methodology section should describe to your reader what you did (beyond just reviewing the existing literature) to answer your research question. For example, what data did you collect, how did you collect that data, how did you analyse that data and so on? For each choice, you’ll also need to justify why you chose to do it that way, and what the strengths and weaknesses of your approach were.

Now, it’s worth mentioning that for some research papers, this aspect of the project may be a lot simpler . For example, you may only need to draw on secondary sources (in other words, existing data sets). In some cases, you may just be asked to draw your conclusions from the literature search itself (in other words, there may be no data analysis at all). But, if you are required to collect and analyse data, you’ll need to pay a lot of attention to the methodology section. The video below provides an example of what the methodology section might look like.

By this stage of your paper, you will have explained what your research question is, what the existing literature has to say about that question, and how you analysed additional data to try to answer your question. So, the natural next step is to present your analysis of that data . This section is usually called the “results” or “analysis” section and this is where you’ll showcase your findings.

Depending on your school’s requirements, you may need to present and interpret the data in one section – or you might split the presentation and the interpretation into two sections. In the latter case, your “results” section will just describe the data, and the “discussion” is where you’ll interpret that data and explicitly link your analysis back to your research question. If you’re not sure which approach to take, check in with your professor or take a look at past papers to see what the norms are for your programme.

Alright – once you’ve presented and discussed your results, it’s time to wrap it up . This usually takes the form of the “ conclusion ” section. In the conclusion, you’ll need to highlight the key takeaways from your study and close the loop by explicitly answering your research question. Again, the exact requirements here will vary depending on your programme (and you may not even need a conclusion section at all) – so be sure to check with your professor if you’re unsure.

Step 3: Write and refine

Finally, it’s time to get writing. All too often though, students hit a brick wall right about here… So, how do you avoid this happening to you?

Well, there’s a lot to be said when it comes to writing a research paper (or any sort of academic piece), but we’ll share three practical tips to help you get started.

First and foremost , it’s essential to approach your writing as an iterative process. In other words, you need to start with a really messy first draft and then polish it over multiple rounds of editing. Don’t waste your time trying to write a perfect research paper in one go. Instead, take the pressure off yourself by adopting an iterative approach.

Secondly , it’s important to always lean towards critical writing , rather than descriptive writing. What does this mean? Well, at the simplest level, descriptive writing focuses on the “ what ”, while critical writing digs into the “ so what ” – in other words, the implications. If you’re not familiar with these two types of writing, don’t worry! You can find a plain-language explanation here.

Last but not least, you’ll need to get your referencing right. Specifically, you’ll need to provide credible, correctly formatted citations for the statements you make. We see students making referencing mistakes all the time and it costs them dearly. The good news is that you can easily avoid this by using a simple reference manager . If you don’t have one, check out our video about Mendeley, an easy (and free) reference management tool that you can start using today.

Recap: Key Takeaways

We’ve covered a lot of ground here. To recap, the three steps to writing a high-quality research paper are:

• To choose a research question and review the literature
• To plan your paper structure and draft an outline
• To take an iterative approach to writing, focusing on critical writing and strong referencing

Remember, this is just a b ig-picture overview of the research paper development process and there’s a lot more nuance to unpack. So, be sure to grab a copy of our free research paper template to learn more about how to write a research paper.

You Might Also Like:

Submit a Comment Cancel reply

Your email address will not be published. Required fields are marked *

Save my name, email, and website in this browser for the next time I comment.

• Print Friendly

Want to create or adapt books like this? Learn more about how Pressbooks supports open publishing practices.

13.1 Formatting a Research Paper

Learning objectives.

• Identify the major components of a research paper written using American Psychological Association (APA) style.
• Apply general APA style and formatting conventions in a research paper.

In this chapter, you will learn how to use APA style , the documentation and formatting style followed by the American Psychological Association, as well as MLA style , from the Modern Language Association. There are a few major formatting styles used in academic texts, including AMA, Chicago, and Turabian:

• AMA (American Medical Association) for medicine, health, and biological sciences
• APA (American Psychological Association) for education, psychology, and the social sciences
• Chicago—a common style used in everyday publications like magazines, newspapers, and books
• MLA (Modern Language Association) for English, literature, arts, and humanities
• Turabian—another common style designed for its universal application across all subjects and disciplines

While all the formatting and citation styles have their own use and applications, in this chapter we focus our attention on the two styles you are most likely to use in your academic studies: APA and MLA.

If you find that the rules of proper source documentation are difficult to keep straight, you are not alone. Writing a good research paper is, in and of itself, a major intellectual challenge. Having to follow detailed citation and formatting guidelines as well may seem like just one more task to add to an already-too-long list of requirements.

Following these guidelines, however, serves several important purposes. First, it signals to your readers that your paper should be taken seriously as a student’s contribution to a given academic or professional field; it is the literary equivalent of wearing a tailored suit to a job interview. Second, it shows that you respect other people’s work enough to give them proper credit for it. Finally, it helps your reader find additional materials if he or she wishes to learn more about your topic.

Furthermore, producing a letter-perfect APA-style paper need not be burdensome. Yes, it requires careful attention to detail. However, you can simplify the process if you keep these broad guidelines in mind:

• Work ahead whenever you can. Chapter 11 “Writing from Research: What Will I Learn?” includes tips for keeping track of your sources early in the research process, which will save time later on.
• Get it right the first time. Apply APA guidelines as you write, so you will not have much to correct during the editing stage. Again, putting in a little extra time early on can save time later.
• Use the resources available to you. In addition to the guidelines provided in this chapter, you may wish to consult the APA website at http://www.apa.org or the Purdue University Online Writing lab at http://owl.english.purdue.edu , which regularly updates its online style guidelines.

General Formatting Guidelines

This chapter provides detailed guidelines for using the citation and formatting conventions developed by the American Psychological Association, or APA. Writers in disciplines as diverse as astrophysics, biology, psychology, and education follow APA style. The major components of a paper written in APA style are listed in the following box.

These are the major components of an APA-style paper:

Body, which includes the following:

• Headings and, if necessary, subheadings to organize the content
• In-text citations of research sources
• References page

All these components must be saved in one document, not as separate documents.

The title page of your paper includes the following information:

• Title of the paper
• Author’s name
• Name of the institution with which the author is affiliated
• Header at the top of the page with the paper title (in capital letters) and the page number (If the title is lengthy, you may use a shortened form of it in the header.)

List the first three elements in the order given in the previous list, centered about one third of the way down from the top of the page. Use the headers and footers tool of your word-processing program to add the header, with the title text at the left and the page number in the upper-right corner. Your title page should look like the following example.

The next page of your paper provides an abstract , or brief summary of your findings. An abstract does not need to be provided in every paper, but an abstract should be used in papers that include a hypothesis. A good abstract is concise—about one hundred fifty to two hundred fifty words—and is written in an objective, impersonal style. Your writing voice will not be as apparent here as in the body of your paper. When writing the abstract, take a just-the-facts approach, and summarize your research question and your findings in a few sentences.

In Chapter 12 “Writing a Research Paper” , you read a paper written by a student named Jorge, who researched the effectiveness of low-carbohydrate diets. Read Jorge’s abstract. Note how it sums up the major ideas in his paper without going into excessive detail.

Write an abstract summarizing your paper. Briefly introduce the topic, state your findings, and sum up what conclusions you can draw from your research. Use the word count feature of your word-processing program to make sure your abstract does not exceed one hundred fifty words.

Depending on your field of study, you may sometimes write research papers that present extensive primary research, such as your own experiment or survey. In your abstract, summarize your research question and your findings, and briefly indicate how your study relates to prior research in the field.

Margins, Pagination, and Headings

APA style requirements also address specific formatting concerns, such as margins, pagination, and heading styles, within the body of the paper. Review the following APA guidelines.

Use these general guidelines to format the paper:

• Set the top, bottom, and side margins of your paper at 1 inch.
• Use double-spaced text throughout your paper.
• Use a standard font, such as Times New Roman or Arial, in a legible size (10- to 12-point).
• Use continuous pagination throughout the paper, including the title page and the references section. Page numbers appear flush right within your header.
• Section headings and subsection headings within the body of your paper use different types of formatting depending on the level of information you are presenting. Additional details from Jorge’s paper are provided.

Begin formatting the final draft of your paper according to APA guidelines. You may work with an existing document or set up a new document if you choose. Include the following:

• Your title page
• The abstract you created in Note 13.8 “Exercise 1”
• Correct headers and page numbers for your title page and abstract

APA style uses section headings to organize information, making it easy for the reader to follow the writer’s train of thought and to know immediately what major topics are covered. Depending on the length and complexity of the paper, its major sections may also be divided into subsections, sub-subsections, and so on. These smaller sections, in turn, use different heading styles to indicate different levels of information. In essence, you are using headings to create a hierarchy of information.

The following heading styles used in APA formatting are listed in order of greatest to least importance:

• Section headings use centered, boldface type. Headings use title case, with important words in the heading capitalized.
• Subsection headings use left-aligned, boldface type. Headings use title case.
• The third level uses left-aligned, indented, boldface type. Headings use a capital letter only for the first word, and they end in a period.
• The fourth level follows the same style used for the previous level, but the headings are boldfaced and italicized.
• The fifth level follows the same style used for the previous level, but the headings are italicized and not boldfaced.

Visually, the hierarchy of information is organized as indicated in Table 13.1 “Section Headings” .

Table 13.1 Section Headings

A college research paper may not use all the heading levels shown in Table 13.1 “Section Headings” , but you are likely to encounter them in academic journal articles that use APA style. For a brief paper, you may find that level 1 headings suffice. Longer or more complex papers may need level 2 headings or other lower-level headings to organize information clearly. Use your outline to craft your major section headings and determine whether any subtopics are substantial enough to require additional levels of headings.

Working with the document you developed in Note 13.11 “Exercise 2” , begin setting up the heading structure of the final draft of your research paper according to APA guidelines. Include your title and at least two to three major section headings, and follow the formatting guidelines provided above. If your major sections should be broken into subsections, add those headings as well. Use your outline to help you.

Because Jorge used only level 1 headings, his Exercise 3 would look like the following:

Citation Guidelines

In-text citations.

Throughout the body of your paper, include a citation whenever you quote or paraphrase material from your research sources. As you learned in Chapter 11 “Writing from Research: What Will I Learn?” , the purpose of citations is twofold: to give credit to others for their ideas and to allow your reader to follow up and learn more about the topic if desired. Your in-text citations provide basic information about your source; each source you cite will have a longer entry in the references section that provides more detailed information.

In-text citations must provide the name of the author or authors and the year the source was published. (When a given source does not list an individual author, you may provide the source title or the name of the organization that published the material instead.) When directly quoting a source, it is also required that you include the page number where the quote appears in your citation.

This information may be included within the sentence or in a parenthetical reference at the end of the sentence, as in these examples.

Epstein (2010) points out that “junk food cannot be considered addictive in the same way that we think of psychoactive drugs as addictive” (p. 137).

Here, the writer names the source author when introducing the quote and provides the publication date in parentheses after the author’s name. The page number appears in parentheses after the closing quotation marks and before the period that ends the sentence.

Addiction researchers caution that “junk food cannot be considered addictive in the same way that we think of psychoactive drugs as addictive” (Epstein, 2010, p. 137).

Here, the writer provides a parenthetical citation at the end of the sentence that includes the author’s name, the year of publication, and the page number separated by commas. Again, the parenthetical citation is placed after the closing quotation marks and before the period at the end of the sentence.

As noted in the book Junk Food, Junk Science (Epstein, 2010, p. 137), “junk food cannot be considered addictive in the same way that we think of psychoactive drugs as addictive.”

Here, the writer chose to mention the source title in the sentence (an optional piece of information to include) and followed the title with a parenthetical citation. Note that the parenthetical citation is placed before the comma that signals the end of the introductory phrase.

David Epstein’s book Junk Food, Junk Science (2010) pointed out that “junk food cannot be considered addictive in the same way that we think of psychoactive drugs as addictive” (p. 137).

Another variation is to introduce the author and the source title in your sentence and include the publication date and page number in parentheses within the sentence or at the end of the sentence. As long as you have included the essential information, you can choose the option that works best for that particular sentence and source.

Citing a book with a single author is usually a straightforward task. Of course, your research may require that you cite many other types of sources, such as books or articles with more than one author or sources with no individual author listed. You may also need to cite sources available in both print and online and nonprint sources, such as websites and personal interviews. Chapter 13 “APA and MLA Documentation and Formatting” , Section 13.2 “Citing and Referencing Techniques” and Section 13.3 “Creating a References Section” provide extensive guidelines for citing a variety of source types.

Writing at Work

APA is just one of several different styles with its own guidelines for documentation, formatting, and language usage. Depending on your field of interest, you may be exposed to additional styles, such as the following:

• MLA style. Determined by the Modern Languages Association and used for papers in literature, languages, and other disciplines in the humanities.
• Chicago style. Outlined in the Chicago Manual of Style and sometimes used for papers in the humanities and the sciences; many professional organizations use this style for publications as well.
• Associated Press (AP) style. Used by professional journalists.

References List

The brief citations included in the body of your paper correspond to the more detailed citations provided at the end of the paper in the references section. In-text citations provide basic information—the author’s name, the publication date, and the page number if necessary—while the references section provides more extensive bibliographical information. Again, this information allows your reader to follow up on the sources you cited and do additional reading about the topic if desired.

The specific format of entries in the list of references varies slightly for different source types, but the entries generally include the following information:

• The name(s) of the author(s) or institution that wrote the source
• The year of publication and, where applicable, the exact date of publication
• The full title of the source
• For books, the city of publication
• For articles or essays, the name of the periodical or book in which the article or essay appears
• For magazine and journal articles, the volume number, issue number, and pages where the article appears
• For sources on the web, the URL where the source is located

The references page is double spaced and lists entries in alphabetical order by the author’s last name. If an entry continues for more than one line, the second line and each subsequent line are indented five spaces. Review the following example. ( Chapter 13 “APA and MLA Documentation and Formatting” , Section 13.3 “Creating a References Section” provides extensive guidelines for formatting reference entries for different types of sources.)

In APA style, book and article titles are formatted in sentence case, not title case. Sentence case means that only the first word is capitalized, along with any proper nouns.

Key Takeaways

• Following proper citation and formatting guidelines helps writers ensure that their work will be taken seriously, give proper credit to other authors for their work, and provide valuable information to readers.
• Working ahead and taking care to cite sources correctly the first time are ways writers can save time during the editing stage of writing a research paper.
• APA papers usually include an abstract that concisely summarizes the paper.
• APA papers use a specific headings structure to provide a clear hierarchy of information.
• In APA papers, in-text citations usually include the name(s) of the author(s) and the year of publication.
• In-text citations correspond to entries in the references section, which provide detailed bibliographical information about a source.

Writing for Success Copyright © 2015 by University of Minnesota is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License , except where otherwise noted.

• Privacy Policy

Home » Research Paper – Structure, Examples and Writing Guide

Research Paper – Structure, Examples and Writing Guide

Table of Contents

Research Paper

Definition:

Research Paper is a written document that presents the author’s original research, analysis, and interpretation of a specific topic or issue.

It is typically based on Empirical Evidence, and may involve qualitative or quantitative research methods, or a combination of both. The purpose of a research paper is to contribute new knowledge or insights to a particular field of study, and to demonstrate the author’s understanding of the existing literature and theories related to the topic.

Structure of Research Paper

The structure of a research paper typically follows a standard format, consisting of several sections that convey specific information about the research study. The following is a detailed explanation of the structure of a research paper:

The title page contains the title of the paper, the name(s) of the author(s), and the affiliation(s) of the author(s). It also includes the date of submission and possibly, the name of the journal or conference where the paper is to be published.

The abstract is a brief summary of the research paper, typically ranging from 100 to 250 words. It should include the research question, the methods used, the key findings, and the implications of the results. The abstract should be written in a concise and clear manner to allow readers to quickly grasp the essence of the research.

Introduction

The introduction section of a research paper provides background information about the research problem, the research question, and the research objectives. It also outlines the significance of the research, the research gap that it aims to fill, and the approach taken to address the research question. Finally, the introduction section ends with a clear statement of the research hypothesis or research question.

Literature Review

The literature review section of a research paper provides an overview of the existing literature on the topic of study. It includes a critical analysis and synthesis of the literature, highlighting the key concepts, themes, and debates. The literature review should also demonstrate the research gap and how the current study seeks to address it.

The methods section of a research paper describes the research design, the sample selection, the data collection and analysis procedures, and the statistical methods used to analyze the data. This section should provide sufficient detail for other researchers to replicate the study.

The results section presents the findings of the research, using tables, graphs, and figures to illustrate the data. The findings should be presented in a clear and concise manner, with reference to the research question and hypothesis.

The discussion section of a research paper interprets the findings and discusses their implications for the research question, the literature review, and the field of study. It should also address the limitations of the study and suggest future research directions.

The conclusion section summarizes the main findings of the study, restates the research question and hypothesis, and provides a final reflection on the significance of the research.

The references section provides a list of all the sources cited in the paper, following a specific citation style such as APA, MLA or Chicago.

How to Write Research Paper

You can write Research Paper by the following guide:

• Choose a Topic: The first step is to select a topic that interests you and is relevant to your field of study. Brainstorm ideas and narrow down to a research question that is specific and researchable.
• Conduct a Literature Review: The literature review helps you identify the gap in the existing research and provides a basis for your research question. It also helps you to develop a theoretical framework and research hypothesis.
• Develop a Thesis Statement : The thesis statement is the main argument of your research paper. It should be clear, concise and specific to your research question.
• Plan your Research: Develop a research plan that outlines the methods, data sources, and data analysis procedures. This will help you to collect and analyze data effectively.
• Collect and Analyze Data: Collect data using various methods such as surveys, interviews, observations, or experiments. Analyze data using statistical tools or other qualitative methods.
• Organize your Paper : Organize your paper into sections such as Introduction, Literature Review, Methods, Results, Discussion, and Conclusion. Ensure that each section is coherent and follows a logical flow.
• Write your Paper : Start by writing the introduction, followed by the literature review, methods, results, discussion, and conclusion. Ensure that your writing is clear, concise, and follows the required formatting and citation styles.
• Edit and Proofread your Paper: Review your paper for grammar and spelling errors, and ensure that it is well-structured and easy to read. Ask someone else to review your paper to get feedback and suggestions for improvement.
• Cite your Sources: Ensure that you properly cite all sources used in your research paper. This is essential for giving credit to the original authors and avoiding plagiarism.

Research Paper Example

Note : The below example research paper is for illustrative purposes only and is not an actual research paper. Actual research papers may have different structures, contents, and formats depending on the field of study, research question, data collection and analysis methods, and other factors. Students should always consult with their professors or supervisors for specific guidelines and expectations for their research papers.

Research Paper Example sample for Students:

Title: The Impact of Social Media on Mental Health among Young Adults

Abstract: This study aims to investigate the impact of social media use on the mental health of young adults. A literature review was conducted to examine the existing research on the topic. A survey was then administered to 200 university students to collect data on their social media use, mental health status, and perceived impact of social media on their mental health. The results showed that social media use is positively associated with depression, anxiety, and stress. The study also found that social comparison, cyberbullying, and FOMO (Fear of Missing Out) are significant predictors of mental health problems among young adults.

Introduction: Social media has become an integral part of modern life, particularly among young adults. While social media has many benefits, including increased communication and social connectivity, it has also been associated with negative outcomes, such as addiction, cyberbullying, and mental health problems. This study aims to investigate the impact of social media use on the mental health of young adults.

Literature Review: The literature review highlights the existing research on the impact of social media use on mental health. The review shows that social media use is associated with depression, anxiety, stress, and other mental health problems. The review also identifies the factors that contribute to the negative impact of social media, including social comparison, cyberbullying, and FOMO.

Methods : A survey was administered to 200 university students to collect data on their social media use, mental health status, and perceived impact of social media on their mental health. The survey included questions on social media use, mental health status (measured using the DASS-21), and perceived impact of social media on their mental health. Data were analyzed using descriptive statistics and regression analysis.

Results : The results showed that social media use is positively associated with depression, anxiety, and stress. The study also found that social comparison, cyberbullying, and FOMO are significant predictors of mental health problems among young adults.

Discussion : The study’s findings suggest that social media use has a negative impact on the mental health of young adults. The study highlights the need for interventions that address the factors contributing to the negative impact of social media, such as social comparison, cyberbullying, and FOMO.

Conclusion : In conclusion, social media use has a significant impact on the mental health of young adults. The study’s findings underscore the need for interventions that promote healthy social media use and address the negative outcomes associated with social media use. Future research can explore the effectiveness of interventions aimed at reducing the negative impact of social media on mental health. Additionally, longitudinal studies can investigate the long-term effects of social media use on mental health.

Limitations : The study has some limitations, including the use of self-report measures and a cross-sectional design. The use of self-report measures may result in biased responses, and a cross-sectional design limits the ability to establish causality.

Implications: The study’s findings have implications for mental health professionals, educators, and policymakers. Mental health professionals can use the findings to develop interventions that address the negative impact of social media use on mental health. Educators can incorporate social media literacy into their curriculum to promote healthy social media use among young adults. Policymakers can use the findings to develop policies that protect young adults from the negative outcomes associated with social media use.

References :

• Twenge, J. M., & Campbell, W. K. (2019). Associations between screen time and lower psychological well-being among children and adolescents: Evidence from a population-based study. Preventive medicine reports, 15, 100918.
• Primack, B. A., Shensa, A., Escobar-Viera, C. G., Barrett, E. L., Sidani, J. E., Colditz, J. B., … & James, A. E. (2017). Use of multiple social media platforms and symptoms of depression and anxiety: A nationally-representative study among US young adults. Computers in Human Behavior, 69, 1-9.
• Van der Meer, T. G., & Verhoeven, J. W. (2017). Social media and its impact on academic performance of students. Journal of Information Technology Education: Research, 16, 383-398.

Appendix : The survey used in this study is provided below.

Social Media and Mental Health Survey

• How often do you use social media per day?
• Less than 30 minutes
• 30 minutes to 1 hour
• 1 to 2 hours
• 2 to 4 hours
• More than 4 hours
• Which social media platforms do you use?
• Others (Please specify)
• How often do you experience the following on social media?
• Social comparison (comparing yourself to others)
• Cyberbullying
• Fear of Missing Out (FOMO)
• Have you ever experienced any of the following mental health problems in the past month?
• Do you think social media use has a positive or negative impact on your mental health?
• Very positive
• Somewhat positive
• Somewhat negative
• Very negative
• In your opinion, which factors contribute to the negative impact of social media on mental health?
• Social comparison
• In your opinion, what interventions could be effective in reducing the negative impact of social media on mental health?
• Education on healthy social media use
• Counseling for mental health problems caused by social media
• Social media detox programs
• Regulation of social media use

Thank you for your participation!

Applications of Research Paper

Research papers have several applications in various fields, including:

• Advancing knowledge: Research papers contribute to the advancement of knowledge by generating new insights, theories, and findings that can inform future research and practice. They help to answer important questions, clarify existing knowledge, and identify areas that require further investigation.
• Informing policy: Research papers can inform policy decisions by providing evidence-based recommendations for policymakers. They can help to identify gaps in current policies, evaluate the effectiveness of interventions, and inform the development of new policies and regulations.
• Improving practice: Research papers can improve practice by providing evidence-based guidance for professionals in various fields, including medicine, education, business, and psychology. They can inform the development of best practices, guidelines, and standards of care that can improve outcomes for individuals and organizations.
• Educating students : Research papers are often used as teaching tools in universities and colleges to educate students about research methods, data analysis, and academic writing. They help students to develop critical thinking skills, research skills, and communication skills that are essential for success in many careers.
• Fostering collaboration: Research papers can foster collaboration among researchers, practitioners, and policymakers by providing a platform for sharing knowledge and ideas. They can facilitate interdisciplinary collaborations and partnerships that can lead to innovative solutions to complex problems.

When to Write Research Paper

Research papers are typically written when a person has completed a research project or when they have conducted a study and have obtained data or findings that they want to share with the academic or professional community. Research papers are usually written in academic settings, such as universities, but they can also be written in professional settings, such as research organizations, government agencies, or private companies.

Here are some common situations where a person might need to write a research paper:

• For academic purposes: Students in universities and colleges are often required to write research papers as part of their coursework, particularly in the social sciences, natural sciences, and humanities. Writing research papers helps students to develop research skills, critical thinking skills, and academic writing skills.
• For publication: Researchers often write research papers to publish their findings in academic journals or to present their work at academic conferences. Publishing research papers is an important way to disseminate research findings to the academic community and to establish oneself as an expert in a particular field.
• To inform policy or practice : Researchers may write research papers to inform policy decisions or to improve practice in various fields. Research findings can be used to inform the development of policies, guidelines, and best practices that can improve outcomes for individuals and organizations.
• To share new insights or ideas: Researchers may write research papers to share new insights or ideas with the academic or professional community. They may present new theories, propose new research methods, or challenge existing paradigms in their field.

Purpose of Research Paper

The purpose of a research paper is to present the results of a study or investigation in a clear, concise, and structured manner. Research papers are written to communicate new knowledge, ideas, or findings to a specific audience, such as researchers, scholars, practitioners, or policymakers. The primary purposes of a research paper are:

• To contribute to the body of knowledge : Research papers aim to add new knowledge or insights to a particular field or discipline. They do this by reporting the results of empirical studies, reviewing and synthesizing existing literature, proposing new theories, or providing new perspectives on a topic.
• To inform or persuade: Research papers are written to inform or persuade the reader about a particular issue, topic, or phenomenon. They present evidence and arguments to support their claims and seek to persuade the reader of the validity of their findings or recommendations.
• To advance the field: Research papers seek to advance the field or discipline by identifying gaps in knowledge, proposing new research questions or approaches, or challenging existing assumptions or paradigms. They aim to contribute to ongoing debates and discussions within a field and to stimulate further research and inquiry.
• To demonstrate research skills: Research papers demonstrate the author’s research skills, including their ability to design and conduct a study, collect and analyze data, and interpret and communicate findings. They also demonstrate the author’s ability to critically evaluate existing literature, synthesize information from multiple sources, and write in a clear and structured manner.

Characteristics of Research Paper

Research papers have several characteristics that distinguish them from other forms of academic or professional writing. Here are some common characteristics of research papers:

• Evidence-based: Research papers are based on empirical evidence, which is collected through rigorous research methods such as experiments, surveys, observations, or interviews. They rely on objective data and facts to support their claims and conclusions.
• Structured and organized: Research papers have a clear and logical structure, with sections such as introduction, literature review, methods, results, discussion, and conclusion. They are organized in a way that helps the reader to follow the argument and understand the findings.
• Formal and objective: Research papers are written in a formal and objective tone, with an emphasis on clarity, precision, and accuracy. They avoid subjective language or personal opinions and instead rely on objective data and analysis to support their arguments.
• Citations and references: Research papers include citations and references to acknowledge the sources of information and ideas used in the paper. They use a specific citation style, such as APA, MLA, or Chicago, to ensure consistency and accuracy.
• Peer-reviewed: Research papers are often peer-reviewed, which means they are evaluated by other experts in the field before they are published. Peer-review ensures that the research is of high quality, meets ethical standards, and contributes to the advancement of knowledge in the field.
• Objective and unbiased: Research papers strive to be objective and unbiased in their presentation of the findings. They avoid personal biases or preconceptions and instead rely on the data and analysis to draw conclusions.

Advantages of Research Paper

Research papers have many advantages, both for the individual researcher and for the broader academic and professional community. Here are some advantages of research papers:

• Contribution to knowledge: Research papers contribute to the body of knowledge in a particular field or discipline. They add new information, insights, and perspectives to existing literature and help advance the understanding of a particular phenomenon or issue.
• Opportunity for intellectual growth: Research papers provide an opportunity for intellectual growth for the researcher. They require critical thinking, problem-solving, and creativity, which can help develop the researcher’s skills and knowledge.
• Career advancement: Research papers can help advance the researcher’s career by demonstrating their expertise and contributions to the field. They can also lead to new research opportunities, collaborations, and funding.
• Academic recognition: Research papers can lead to academic recognition in the form of awards, grants, or invitations to speak at conferences or events. They can also contribute to the researcher’s reputation and standing in the field.
• Impact on policy and practice: Research papers can have a significant impact on policy and practice. They can inform policy decisions, guide practice, and lead to changes in laws, regulations, or procedures.
• Advancement of society: Research papers can contribute to the advancement of society by addressing important issues, identifying solutions to problems, and promoting social justice and equality.

Limitations of Research Paper

Research papers also have some limitations that should be considered when interpreting their findings or implications. Here are some common limitations of research papers:

• Limited generalizability: Research findings may not be generalizable to other populations, settings, or contexts. Studies often use specific samples or conditions that may not reflect the broader population or real-world situations.
• Potential for bias : Research papers may be biased due to factors such as sample selection, measurement errors, or researcher biases. It is important to evaluate the quality of the research design and methods used to ensure that the findings are valid and reliable.
• Ethical concerns: Research papers may raise ethical concerns, such as the use of vulnerable populations or invasive procedures. Researchers must adhere to ethical guidelines and obtain informed consent from participants to ensure that the research is conducted in a responsible and respectful manner.
• Limitations of methodology: Research papers may be limited by the methodology used to collect and analyze data. For example, certain research methods may not capture the complexity or nuance of a particular phenomenon, or may not be appropriate for certain research questions.
• Publication bias: Research papers may be subject to publication bias, where positive or significant findings are more likely to be published than negative or non-significant findings. This can skew the overall findings of a particular area of research.
• Time and resource constraints: Research papers may be limited by time and resource constraints, which can affect the quality and scope of the research. Researchers may not have access to certain data or resources, or may be unable to conduct long-term studies due to practical limitations.

About the author

Muhammad Hassan

Researcher, Academic Writer, Web developer

You may also like

How to Cite Research Paper – All Formats and...

Data Collection – Methods Types and Examples

Delimitations in Research – Types, Examples and...

Research Paper Format – Types, Examples and...

Research Process – Steps, Examples and Tips

Research Design – Types, Methods and Examples

Research Paper Examples

Research paper examples are of great value for students who want to complete their assignments timely and efficiently. If you are a student in the university, your first stop in the quest for research paper examples will be the campus library where you can get to view the research sample papers of lecturers and other professionals in diverse fields plus those of fellow students who preceded you in the campus. Many college departments maintain libraries of previous student work, including large research papers, which current students can examine.

Embark on a journey of academic excellence with iResearchNet, your premier destination for research paper examples that illuminate the path to scholarly success. In the realm of academia, where the pursuit of knowledge is both a challenge and a privilege, the significance of having access to high-quality research paper examples cannot be overstated. These exemplars are not merely papers; they are beacons of insight, guiding students and scholars through the complex maze of academic writing and research methodologies.

At iResearchNet, we understand that the foundation of academic achievement lies in the quality of resources at one’s disposal. This is why we are dedicated to offering a comprehensive collection of research paper examples across a multitude of disciplines. Each example stands as a testament to rigorous research, clear writing, and the deep understanding necessary to advance in one’s academic and professional journey.

Access to superior research paper examples equips learners with the tools to develop their own ideas, arguments, and hypotheses, fostering a cycle of learning and discovery that transcends traditional boundaries. It is with this vision that iResearchNet commits to empowering students and researchers, providing them with the resources to not only meet but exceed the highest standards of academic excellence. Join us on this journey, and let iResearchNet be your guide to unlocking the full potential of your academic endeavors.

Academic Writing, Editing, Proofreading, And Problem Solving Services

Get 10% off with 24start discount code, what is a research paper.

• Anthropology
• Communication
• Criminal Justice
• Criminal Law
• Criminology
• Mental Health
• Political Science

Importance of Research Paper Examples

• Research Paper Writing Services

A Sample Research Paper on Child Abuse

A research paper represents the pinnacle of academic investigation, a scholarly manuscript that encapsulates a detailed study, analysis, or argument based on extensive independent research. It is an embodiment of the researcher’s ability to synthesize a wealth of information, draw insightful conclusions, and contribute novel perspectives to the existing body of knowledge within a specific field. At its core, a research paper strives to push the boundaries of what is known, challenging existing theories and proposing new insights that could potentially reshape the understanding of a particular subject area.

The objective of writing a research paper is manifold, serving both educational and intellectual pursuits. Primarily, it aims to educate the author, providing a rigorous framework through which they engage deeply with a topic, hone their research and analytical skills, and learn the art of academic writing. Beyond personal growth, the research paper serves the broader academic community by contributing to the collective pool of knowledge, offering fresh perspectives, and stimulating further research. It is a medium through which scholars communicate ideas, findings, and theories, thereby fostering an ongoing dialogue that propels the advancement of science, humanities, and other fields of study.

Research papers can be categorized into various types, each with distinct objectives and methodologies. The most common types include:

• Analytical Research Paper: This type focuses on analyzing different viewpoints represented in the scholarly literature or data. The author critically evaluates and interprets the information, aiming to provide a comprehensive understanding of the topic.
• Argumentative or Persuasive Research Paper: Here, the author adopts a stance on a contentious issue and argues in favor of their position. The objective is to persuade the reader through evidence and logic that the author’s viewpoint is valid or preferable.
• Experimental Research Paper: Often used in the sciences, this type documents the process, results, and implications of an experiment conducted by the author. It provides a detailed account of the methodology, data collected, analysis performed, and conclusions drawn.
• Survey Research Paper: This involves collecting data from a set of respondents about their opinions, behaviors, or characteristics. The paper analyzes this data to draw conclusions about the population from which the sample was drawn.
• Comparative Research Paper: This type involves comparing and contrasting different theories, policies, or phenomena. The aim is to highlight similarities and differences, thereby gaining a deeper understanding of the subjects under review.
• Cause and Effect Research Paper: It explores the reasons behind specific actions, events, or conditions and the consequences that follow. The goal is to establish a causal relationship between variables.
• Review Research Paper: This paper synthesizes existing research on a particular topic, offering a comprehensive analysis of the literature to identify trends, gaps, and consensus in the field.

Understanding the nuances and objectives of these various types of research papers is crucial for scholars and students alike, as it guides their approach to conducting and writing up their research. Each type demands a unique set of skills and perspectives, pushing the author to think critically and creatively about their subject matter. As the academic landscape continues to evolve, the research paper remains a fundamental tool for disseminating knowledge, encouraging innovation, and fostering a culture of inquiry and exploration.

Browse Sample Research Papers

iResearchNet prides itself on offering a wide array of research paper examples across various disciplines, meticulously curated to support students, educators, and researchers in their academic endeavors. Each example embodies the hallmarks of scholarly excellence—rigorous research, analytical depth, and clear, precise writing. Below, we explore the diverse range of research paper examples available through iResearchNet, designed to inspire and guide users in their quest for academic achievement.

Anthropology Research Paper Examples

Our anthropology research paper examples delve into the study of humanity, exploring cultural, social, biological, and linguistic variations among human populations. These papers offer insights into human behavior, traditions, and evolution, providing a comprehensive overview of anthropological research methods and theories.

• Archaeology Research Paper
• Forensic Anthropology Research Paper
• Linguistics Research Paper
• Medical Anthropology Research Paper
• Social Problems Research Paper

Art Research Paper Examples

The art research paper examples feature analyses of artistic expressions across different cultures and historical periods. These papers cover a variety of topics, including art history, criticism, and theory, as well as the examination of specific artworks or movements.

• Performing Arts Research Paper
• Music Research Paper
• Architecture Research Paper
• Theater Research Paper
• Visual Arts Research Paper

Cancer Research Paper Examples

Our cancer research paper examples focus on the latest findings in the field of oncology, discussing the biological mechanisms of cancer, advancements in diagnostic techniques, and innovative treatment strategies. These papers aim to contribute to the ongoing battle against cancer by sharing cutting-edge research.

• Breast Cancer Research Paper
• Leukemia Research Paper
• Lung Cancer Research Paper
• Ovarian Cancer Research Paper
• Prostate Cancer Research Paper

Communication Research Paper Examples

These examples explore the complexities of human communication, covering topics such as media studies, interpersonal communication, and public relations. The papers examine how communication processes affect individuals, societies, and cultures.

• Advertising Research Paper
• Journalism Research Paper
• Media Research Paper
• Public Relations Research Paper
• Public Speaking Research Paper

Crime Research Paper Examples

The crime research paper examples provided by iResearchNet investigate various aspects of criminal behavior and the factors contributing to crime. These papers cover a range of topics, from theoretical analyses of criminality to empirical studies on crime prevention strategies.

• Computer Crime Research Paper
• Domestic Violence Research Paper
• Hate Crimes Research Paper
• Organized Crime Research Paper
• White-Collar Crime Research Paper

Criminal Justice Research Paper Examples

Our criminal justice research paper examples delve into the functioning of the criminal justice system, exploring issues related to law enforcement, the judiciary, and corrections. These papers critically examine policies, practices, and reforms within the criminal justice system.

• Capital Punishment Research Paper
• Community Policing Research Paper
• Corporal Punishment Research Paper
• Criminal Investigation Research Paper
• Criminal Justice System Research Paper
• Plea Bargaining Research Paper
• Restorative Justice Research Paper

Criminal Law Research Paper Examples

These examples focus on the legal aspects of criminal behavior, discussing laws, regulations, and case law that govern criminal proceedings. The papers provide an in-depth analysis of criminal law principles, legal defenses, and the implications of legal decisions.

• Actus Reus Research Paper
• Gun Control Research Paper
• Insanity Defense Research Paper
• International Criminal Law Research Paper
• Self-Defense Research Paper

Criminology Research Paper Examples

iResearchNet’s criminology research paper examples study the causes, prevention, and societal impacts of crime. These papers employ various theoretical frameworks to analyze crime trends and propose effective crime reduction strategies.

• Cultural Criminology Research Paper
• Education and Crime Research Paper
• Marxist Criminology Research Paper
• School Crime Research Paper
• Urban Crime Research Paper

Culture Research Paper Examples

The culture research paper examples examine the beliefs, practices, and artifacts that define different societies. These papers explore how culture shapes identities, influences behaviors, and impacts social interactions.

• Advertising and Culture Research Paper
• Material Culture Research Paper
• Popular Culture Research Paper
• Cross-Cultural Studies Research Paper
• Culture Change Research Paper

Economics Research Paper Examples

Our economics research paper examples offer insights into the functioning of economies at both the micro and macro levels. Topics include economic theory, policy analysis, and the examination of economic indicators and trends.

• Budget Research Paper
• Cost-Benefit Analysis Research Paper
• Fiscal Policy Research Paper
• Labor Market Research Paper

Education Research Paper Examples

These examples address a wide range of issues in education, from teaching methods and curriculum design to educational policy and reform. The papers aim to enhance understanding and improve outcomes in educational settings.

• Early Childhood Education Research Paper
• Information Processing Research Paper
• Multicultural Education Research Paper
• Special Education Research Paper
• Standardized Tests Research Paper

Health Research Paper Examples

The health research paper examples focus on public health issues, healthcare systems, and medical interventions. These papers contribute to the discourse on health promotion, disease prevention, and healthcare management.

• AIDS Research Paper
• Alcoholism Research Paper
• Disease Research Paper
• Health Economics Research Paper
• Health Insurance Research Paper
• Nursing Research Paper

History Research Paper Examples

Our history research paper examples cover significant events, figures, and periods, offering critical analyses of historical narratives and their impact on present-day society.

• Adolf Hitler Research Paper
• American Revolution Research Paper
• Ancient Greece Research Paper
• Apartheid Research Paper
• Christopher Columbus Research Paper
• Climate Change Research Paper
• Cold War Research Paper
• Columbian Exchange Research Paper
• Deforestation Research Paper
• Diseases Research Paper
• Earthquakes Research Paper
• Egypt Research Paper

Leadership Research Paper Examples

These examples explore the theories and practices of effective leadership, examining the qualities, behaviors, and strategies that distinguish successful leaders in various contexts.

• Implicit Leadership Theories Research Paper
• Judicial Leadership Research Paper
• Leadership Styles Research Paper
• Police Leadership Research Paper
• Political Leadership Research Paper
• Remote Leadership Research Paper

Mental Health Research Paper Examples

The mental health research paper examples provided by iResearchNet discuss psychological disorders, therapeutic interventions, and mental health advocacy. These papers aim to raise awareness and improve mental health care practices.

• ADHD Research Paper
• Anxiety Research Paper
• Autism Research Paper
• Depression Research Paper
• Eating Disorders Research Paper
• PTSD Research Paper
• Schizophrenia Research Paper
• Stress Research Paper

Political Science Research Paper Examples

Our political science research paper examples analyze political systems, behaviors, and ideologies. Topics include governance, policy analysis, and the study of political movements and institutions.

• American Government Research Paper
• Civil War Research Paper
• Communism Research Paper
• Democracy Research Paper
• Game Theory Research Paper
• Human Rights Research Paper
• International Relations Research Paper
• Terrorism Research Paper

Psychology Research Paper Examples

These examples delve into the study of the mind and behavior, covering a broad range of topics in clinical, cognitive, developmental, and social psychology.

• Artificial Intelligence Research Paper
• Assessment Psychology Research Paper
• Biological Psychology Research Paper
• Clinical Psychology Research Paper
• Cognitive Psychology Research Paper
• Developmental Psychology Research Paper
• Discrimination Research Paper
• Educational Psychology Research Paper
• Environmental Psychology Research Paper
• Experimental Psychology Research Paper
• Intelligence Research Paper
• Learning Disabilities Research Paper
• Personality Psychology Research Paper
• Psychiatry Research Paper
• Psychotherapy Research Paper
• Social Cognition Research Paper
• Social Psychology Research Paper

Sociology Research Paper Examples

The sociology research paper examples examine societal structures, relationships, and processes. These papers provide insights into social phenomena, inequality, and change.

• Family Research Paper
• Demography Research Paper
• Group Dynamics Research Paper
• Quality of Life Research Paper
• Social Change Research Paper
• Social Movements Research Paper
• Social Networks Research Paper

Technology Research Paper Examples

Our technology research paper examples address the impact of technological advancements on society, exploring issues related to digital communication, cybersecurity, and innovation.

• Computer Forensics Research Paper
• Genetic Engineering Research Paper
• History of Technology Research Paper
• Internet Research Paper
• Nanotechnology Research Paper

Other Research Paper Examples

• Abortion Research Paper
• Adoption Research Paper
• Animal Testing Research Paper
• Bullying Research Paper
• Diversity Research Paper
• Divorce Research Paper
• Drugs Research Paper
• Environmental Issues Research Paper
• Ethics Research Paper
• Evolution Research Paper
• Feminism Research Paper
• Food Research Paper
• Gender Research Paper
• Globalization Research Paper
• Juvenile Justice Research Paper
• Law Research Paper
• Management Research Paper
• Philosophy Research Paper
• Public Health Research Paper
• Religion Research Paper
• Science Research Paper
• Social Sciences Research Paper
• Statistics Research Paper
• Other Sample Research Papers

Each category of research paper examples provided by iResearchNet serves as a valuable resource for students and researchers seeking to deepen their understanding of a specific field. By offering a comprehensive collection of well-researched and thoughtfully written papers, iResearchNet aims to support academic growth and encourage scholarly inquiry across diverse disciplines.

Sample Research Papers: To Read or Not to Read?

When you get an assignment to write a research paper, the first question you ask yourself is ‘Should I look for research paper examples?’ Maybe, I can deal with this task on my own without any help. Is it that difficult?

Thousands of students turn to our service every day for help. It does not mean that they cannot do their assignments on their own. They can, but the reason is different. Writing a research paper demands so much time and energy that asking for assistance seems to be a perfect solution. As the matter of fact, it is a perfect solution, especially, when you need to work to pay for your studying as well.

Firstly, if you search for research paper examples before you start writing, you can save your time significantly. You look at the example and you understand the gist of your assignment within several minutes. Secondly, when you examine some sample paper, you get to know all the requirements. You analyze the structure, the language, and the formatting details. Finally, reading examples helps students to overcome writer’s block, as other people’s ideas can motivate you to discover your own ideas.

The significance of research paper examples in the academic journey of students cannot be overstated. These examples serve not only as a blueprint for structuring and formatting academic papers but also as a beacon guiding students through the complex landscape of academic writing standards. iResearchNet recognizes the pivotal role that high-quality research paper examples play in fostering academic success and intellectual growth among students.

Blueprint for Academic Success

Research paper examples provided by iResearchNet are meticulously crafted to demonstrate the essential elements of effective academic writing. These examples offer clear insights into how to organize a paper, from the introductory paragraph, through the development of arguments and analysis, to the concluding remarks. They showcase the appropriate use of headings, subheadings, and the integration of tables, figures, and appendices, which collectively contribute to a well-organized and coherent piece of scholarly work. By studying these examples, students can gain a comprehensive understanding of the structure and formatting required in academic papers, which is crucial for meeting the rigorous standards of academic institutions.

Sparking Ideas and Providing Evidence

Beyond serving as a structural guide, research paper examples act as a source of inspiration for students embarking on their research projects. These examples illuminate a wide array of topics, methodologies, and analytical frameworks, thereby sparking ideas for students’ own research inquiries. They demonstrate how to effectively engage with existing literature, frame research questions, and develop a compelling thesis statement. Moreover, by presenting evidence and arguments in a logical and persuasive manner, these examples illustrate the art of substantiating claims with solid research, encouraging students to adopt a similar level of rigor and depth in their work.

Enhancing Research Skills

Engagement with high-quality research paper examples is instrumental in improving research skills among students. These examples expose students to various research methodologies, from qualitative case studies to quantitative analyses, enabling them to appreciate the breadth of research approaches applicable to their fields of study. By analyzing these examples, students learn how to critically evaluate sources, differentiate between primary and secondary data, and apply ethical considerations in research. Furthermore, these papers serve as a model for effectively citing sources, thereby teaching students the importance of academic integrity and the avoidance of plagiarism.

In essence, research paper examples are a fundamental resource that can significantly enhance the academic writing and research capabilities of students. iResearchNet’s commitment to providing access to a diverse collection of exemplary papers reflects its dedication to supporting academic excellence. Through these examples, students are equipped with the tools necessary to navigate the challenges of academic writing, foster innovative thinking, and contribute meaningfully to the scholarly community. By leveraging these resources, students can elevate their academic pursuits, ensuring their research is not only rigorous but also impactful.

Custom Research Paper Writing Services

In the academic journey, the ability to craft a compelling and meticulously researched paper is invaluable. Recognizing the challenges and pressures that students face, iResearchNet has developed a suite of research paper writing services designed to alleviate the burden of academic writing and research. Our services are tailored to meet the diverse needs of students across all academic disciplines, ensuring that every research paper not only meets but exceeds the rigorous standards of scholarly excellence. Below, we detail the multifaceted aspects of our research paper writing services, illustrating how iResearchNet stands as a beacon of support in the academic landscape.

At iResearchNet, we understand the pivotal role that research papers play in the academic and professional development of students. With this understanding at our core, we offer comprehensive writing services that cater to the intricate process of research paper creation. Our services are designed to guide students through every stage of the writing process, from initial research to final submission, ensuring clarity, coherence, and scholarly rigor.

The Need for Research Paper Writing Services

Navigating the complexities of academic writing and research can be a daunting task for many students. The challenges of identifying credible sources, synthesizing information, adhering to academic standards, and articulating arguments cohesively are significant. Furthermore, the pressures of tight deadlines and the high stakes of academic success can exacerbate the difficulties faced by students. iResearchNet’s research paper writing services are crafted to address these challenges head-on, providing expert assistance that empowers students to achieve their academic goals with confidence.

Why Choose iResearchNet

Selecting the right partner for research paper writing is a pivotal decision for students and researchers aiming for academic excellence. iResearchNet stands out as the premier choice for several compelling reasons, each designed to meet the diverse needs of our clientele and ensure their success.

• Expert Writers : At iResearchNet, we pride ourselves on our team of expert writers who are not only masters in their respective fields but also possess a profound understanding of academic writing standards. With advanced degrees and extensive experience, our writers bring depth, insight, and precision to each paper, ensuring that your work is informed by the latest research and methodologies.
• Top Quality : Quality is the cornerstone of our services. We adhere to rigorous quality control processes to ensure that every paper we deliver meets the highest standards of academic excellence. Our commitment to quality means thorough research, impeccable writing, and meticulous proofreading, resulting in work that not only meets but exceeds expectations.
• Customized Solutions : Understanding that each research project has its unique challenges and requirements, iResearchNet offers customized solutions tailored to your specific needs. Whether you’re grappling with a complex research topic, a tight deadline, or specific formatting guidelines, our team is equipped to provide personalized support that aligns with your objectives.
• Affordable Prices : We believe that access to high-quality research paper writing services should not be prohibitive. iResearchNet offers competitive pricing structures designed to provide value without compromising on quality. Our transparent pricing model ensures that you know exactly what you are paying for, with no hidden costs or surprises.
• Timely Delivery : Meeting deadlines is critical in academic writing, and at iResearchNet, we take this seriously. Our efficient processes and dedicated team ensure that your paper is delivered on time, every time, allowing you to meet your academic deadlines with confidence.
• 24/7 Support : Our commitment to your success is reflected in our round-the-clock support. Whether you have a question about your order, need to communicate with your writer, or require assistance with any aspect of our service, our friendly and knowledgeable support team is available 24/7 to assist you.
• Money-Back Guarantee : Your satisfaction is our top priority. iResearchNet offers a money-back guarantee, ensuring that if for any reason you are not satisfied with the work delivered, you are entitled to a refund. This policy underscores our confidence in the quality of our services and our dedication to your success.

Choosing iResearchNet for your research paper writing needs means partnering with a trusted provider committed to excellence, innovation, and customer satisfaction. Our unparalleled blend of expert writers, top-quality work, customized solutions, affordability, timely delivery, 24/7 support, and a money-back guarantee makes us the ideal choice for students and researchers seeking to elevate their academic performance.

How It Works: iResearchNet’s Streamlined Process

Navigating the process of obtaining a top-notch research paper has never been more straightforward, thanks to iResearchNet’s streamlined approach. Our user-friendly system ensures that from the moment you decide to place your order to the final receipt of your custom-written paper, every step is seamless, transparent, and tailored to your needs. Here’s how our comprehensive process works:

• Place Your Order : Begin your journey to academic success by visiting our website and filling out the order form. Here, you’ll provide details about your research paper, including the topic, academic level, number of pages, formatting style, and any specific instructions or requirements. This initial step is crucial for us to understand your needs fully and match you with the most suitable writer.
• Make Payment : Once your order details are confirmed, you’ll proceed to the payment section. Our platform offers a variety of secure payment options, ensuring that your transaction is safe and hassle-free. Our transparent pricing policy means you’ll know exactly what you’re paying for upfront, with no hidden fees.
• Choose Your Writer : After payment, you’ll have the opportunity to choose a writer from our team of experts. Our writers are categorized based on their fields of expertise, academic qualifications, and customer feedback ratings. This step empowers you to select the writer who best matches your research paper’s requirements, ensuring a personalized and targeted approach to your project.
• Receive Your Work : Our writer will commence work on your research paper, adhering to the specified guidelines and timelines. Throughout this process, you’ll have the ability to communicate directly with your writer, allowing for updates, revisions, and clarifications to ensure the final product meets your expectations. Once completed, your research paper will undergo a thorough quality check before being delivered to you via your chosen method.
• Free Revisions : Your satisfaction is our priority. Upon receiving your research paper, you’ll have the opportunity to review the work and request any necessary revisions. iResearchNet offers free revisions within a specified period, ensuring that your final paper perfectly aligns with your academic requirements and expectations.

Our process is designed to provide you with a stress-free experience and a research paper that reflects your academic goals. From placing your order to enjoying the success of a well-written paper, iResearchNet is here to support you every step of the way.

Our Extras: Enhancing Your iResearchNet Experience

At iResearchNet, we are committed to offering more than just standard research paper writing services. We understand the importance of providing a comprehensive and personalized experience for each of our clients. That’s why we offer a range of additional services designed to enhance your experience and ensure your academic success. Here are the exclusive extras you can benefit from:

• VIP Service : Elevate your iResearchNet experience with our VIP service, offering you priority treatment from the moment you place your order. This service ensures your projects are given first priority, with immediate attention from our team, and direct access to our top-tier writers and editors. VIP clients also benefit from our highest level of customer support, available to address any inquiries or needs with utmost urgency and personalized care.
• Plagiarism Report : Integrity and originality are paramount in academic writing. To provide you with peace of mind, we offer a detailed plagiarism report with every research paper. This report is generated using advanced plagiarism detection software, ensuring that your work is unique and adheres to the highest standards of academic honesty.
• Text Messages : Stay informed about your order’s progress with real-time updates sent directly to your phone. This service ensures you’re always in the loop, providing immediate notifications about key milestones, writer assignments, and any changes to your order status. With this added layer of communication, you can relax knowing that you’ll never miss an important update about your research paper.
• Table of Contents : A well-organized research paper is key to guiding readers through your work. Our service includes the creation of a detailed table of contents, meticulously structured to reflect the main sections and subsections of your paper. This not only enhances the navigability of your document but also presents your research in a professional and academically appropriate format.
• Abstract Page : The abstract page is your research paper’s first impression, summarizing the essential points of your study and its conclusions. Crafting a compelling abstract is an art, and our experts are skilled in highlighting the significance, methodology, results, and implications of your research succinctly and effectively. This service ensures that your paper makes a strong impact from the very beginning.
• Editor’s Check : Before your research paper reaches you, it undergoes a final review by our team of experienced editors. This editor’s check is a comprehensive process that includes proofreading for grammar, punctuation, and spelling errors, as well as ensuring that the paper meets all your specifications and academic standards. This meticulous attention to detail guarantees that your paper is polished, professional, and ready for submission.

To ensure your research paper is of the highest quality and ready for submission, it undergoes a rigorous editor’s check. This final review process includes a thorough examination for any grammatical, punctuation, or spelling errors, as well as a verification that the paper meets all your specified requirements and academic standards. Our editors’ meticulous approach guarantees that your paper is polished, accurate, and exemplary.

By choosing iResearchNet and leveraging our extras, you can elevate the quality of your research paper and enjoy a customized, worry-free academic support experience.

A research paper is an academic piece of writing, so you need to follow all the requirements and standards. Otherwise, it will be impossible to get the high results. To make it easier for you, we have analyzed the structure and peculiarities of a sample research paper on the topic ‘Child Abuse’.

The paper includes 7300+ words, a detailed outline, citations are in APA formatting style, and bibliography with 28 sources.

To write any paper you need to write a great outline. This is the key to a perfect paper. When you organize your paper, it is easier for you to present the ideas logically, without jumping from one thought to another.

In the outline, you need to name all the parts of your paper. That is to say, an introduction, main body, conclusion, bibliography, some papers require abstract and proposal as well.

A good outline will serve as a guide through your paper making it easier for the reader to follow your ideas.

I. Introduction

Ii. estimates of child abuse: methodological limitations, iii. child abuse and neglect: the legalities, iv. corporal punishment versus child abuse, v. child abuse victims: the patterns, vi. child abuse perpetrators: the patterns, vii. explanations for child abuse, viii. consequences of child abuse and neglect, ix. determining abuse: how to tell whether a child is abused or neglected, x. determining abuse: interviewing children, xi. how can society help abused children and abusive families, introduction.

An introduction should include a thesis statement and the main points that you will discuss in the paper.

A thesis statement is one sentence in which you need to show your point of view. You will then develop this point of view through the whole piece of work:

‘The impact of child abuse affects more than one’s childhood, as the psychological and physical injuries often extend well into adulthood.’

Child abuse is a very real and prominent social problem today. The impact of child abuse affects more than one’s childhood, as the psychological and physical injuries often extend well into adulthood. Most children are defenseless against abuse, are dependent on their caretakers, and are unable to protect themselves from these acts.

Childhood serves as the basis for growth, development, and socialization. Throughout adolescence, children are taught how to become productive and positive, functioning members of society. Much of the socializing of children, particularly in their very earliest years, comes at the hands of family members. Unfortunately, the messages conveyed to and the actions against children by their families are not always the positive building blocks for which one would hope.

In 2008, the Children’s Defense Fund reported that each day in America, 2,421 children are confirmed as abused or neglected, 4 children are killed by abuse or neglect, and 78 babies die before their first birthday. These daily estimates translate into tremendous national figures. In 2006, caseworkers substantiated an estimated 905,000 reports of child abuse or neglect. Of these, 64% suffered neglect, 16% were physically abused, 9% were sexually abused, 7% were emotionally or psychologically maltreated, and 2% were medically neglected. In addition, 15% of the victims experienced “other” types of maltreatment such as abandonment, threats of harm to the child, and congenital drug addiction (National Child Abuse and Neglect Data System, 2006). Obviously, this problem is a substantial one.

In the main body, you dwell upon the topic of your paper. You provide your ideas and support them with evidence. The evidence include all the data and material you have found, analyzed and systematized. You can support your point of view with different statistical data, with surveys, and the results of different experiments. Your task is to show that your idea is right, and make the reader interested in the topic.

In this example, a writer analyzes the issue of child abuse: different statistical data, controversies regarding the topic, examples of the problem and the consequences.

Several issues arise when considering the amount of child abuse that occurs annually in the United States. Child abuse is very hard to estimate because much (or most) of it is not reported. Children who are abused are unlikely to report their victimization because they may not know any better, they still love their abusers and do not want to see them taken away (or do not themselves want to be taken away from their abusers), they have been threatened into not reporting, or they do not know to whom they should report their victimizations. Still further, children may report their abuse only to find the person to whom they report does not believe them or take any action on their behalf. Continuing to muddy the waters, child abuse can be disguised as legitimate injury, particularly because young children are often somewhat uncoordinated and are still learning to accomplish physical tasks, may not know their physical limitations, and are often legitimately injured during regular play. In the end, children rarely report child abuse; most often it is an adult who makes a report based on suspicion (e.g., teacher, counselor, doctor, etc.).

Even when child abuse is reported, social service agents and investigators may not follow up or substantiate reports for a variety of reasons. Parents can pretend, lie, or cover up injuries or stories of how injuries occurred when social service agents come to investigate. Further, there is not always agreement about what should be counted as abuse by service providers and researchers. In addition, social service agencies/agents have huge caseloads and may only be able to deal with the most serious forms of child abuse, leaving the more “minor” forms of abuse unsupervised and unmanaged (and uncounted in the statistical totals).

While most laws about child abuse and neglect fall at the state levels, federal legislation provides a foundation for states by identifying a minimum set of acts and behaviors that define child abuse and neglect. The Federal Child Abuse Prevention and Treatment Act (CAPTA), which stems from the Keeping Children and Families Safe Act of 2003, defines child abuse and neglect as, at minimum, “(1) any recent act or failure to act on the part of a parent or caretaker which results in death, serious physical or emotional harm, sexual abuse, or exploitation; or (2) an act or failure to act which presents an imminent risk or serious harm.”

Using these minimum standards, each state is responsible for providing its own definition of maltreatment within civil and criminal statutes. When defining types of child abuse, many states incorporate similar elements and definitions into their legal statutes. For example, neglect is often defined as failure to provide for a child’s basic needs. Neglect can encompass physical elements (e.g., failure to provide necessary food or shelter, or lack of appropriate supervision), medical elements (e.g., failure to provide necessary medical or mental health treatment), educational elements (e.g., failure to educate a child or attend to special educational needs), and emotional elements (e.g., inattention to a child’s emotional needs, failure to provide psychological care, or permitting the child to use alcohol or other drugs). Failure to meet needs does not always mean a child is neglected, as situations such as poverty, cultural values, and community standards can influence the application of legal statutes. In addition, several states distinguish between failure to provide based on financial inability and failure to provide for no apparent financial reason.

Statutes on physical abuse typically include elements of physical injury (ranging from minor bruises to severe fractures or death) as a result of punching, beating, kicking, biting, shaking, throwing, stabbing, choking, hitting (with a hand, stick, strap, or other object), burning, or otherwise harming a child. Such injury is considered abuse regardless of the intention of the caretaker. In addition, many state statutes include allowing or encouraging another person to physically harm a child (such as noted above) as another form of physical abuse in and of itself. Sexual abuse usually includes activities by a parent or caretaker such as fondling a child’s genitals, penetration, incest, rape, sodomy, indecent exposure, and exploitation through prostitution or the production of pornographic materials.

Finally, emotional or psychological abuse typically is defined as a pattern of behavior that impairs a child’s emotional development or sense of self-worth. This may include constant criticism, threats, or rejection, as well as withholding love, support, or guidance. Emotional abuse is often the most difficult to prove and, therefore, child protective services may not be able to intervene without evidence of harm to the child. Some states suggest that harm may be evidenced by an observable or substantial change in behavior, emotional response, or cognition, or by anxiety, depression, withdrawal, or aggressive behavior. At a practical level, emotional abuse is almost always present when other types of abuse are identified.

Some states include an element of substance abuse in their statutes on child abuse. Circumstances that can be considered substance abuse include (a) the manufacture of a controlled substance in the presence of a child or on the premises occupied by a child (Colorado, Indiana, Iowa, Montana, South Dakota, Tennessee, and Virginia); (b) allowing a child to be present where the chemicals or equipment for the manufacture of controlled substances are used (Arizona, New Mexico); (c) selling, distributing, or giving drugs or alcohol to a child (Florida, Hawaii, Illinois, Minnesota, and Texas); (d) use of a controlled substance by a caregiver that impairs the caregiver’s ability to adequately care for the child (Kentucky, New York, Rhode Island, and Texas); and (e) exposure of the child to drug paraphernalia (North Dakota), the criminal sale or distribution of drugs (Montana, Virginia), or drug-related activity (District of Columbia).

One of the most difficult issues with which the U.S. legal system must contend is that of allowing parents the right to use corporal punishment when disciplining a child, while not letting them cross over the line into the realm of child abuse. Some parents may abuse their children under the guise of discipline, and many instances of child abuse arise from angry parents who go too far when disciplining their children with physical punishment. Generally, state statutes use terms such as “reasonable discipline of a minor,” “causes only temporary, short-term pain,” and may cause “the potential for bruising” but not “permanent damage, disability, disfigurement or injury” to the child as ways of indicating the types of discipline behaviors that are legal. However, corporal punishment that is “excessive,” “malicious,” “endangers the bodily safety of,” or is “an intentional infliction of injury” is not allowed under most state statutes (e.g., state of Florida child abuse statute).

Most research finds that the use of physical punishment (most often spanking) is not an effective method of discipline. The literature on this issue tends to find that spanking stops misbehavior, but no more effectively than other firm measures. Further, it seems to hinder rather than improve general compliance/obedience (particularly when the child is not in the presence of the punisher). Researchers have also explained why physical punishment is not any more effective at gaining child compliance than nonviolent forms of discipline. Some of the problems that arise when parents use spanking or other forms of physical punishment include the fact that spanking does not teach what children should do, nor does it provide them with alternative behavior options should the circumstance arise again. Spanking also undermines reasoning, explanation, or other forms of parental instruction because children cannot learn, reason, or problem solve well while experiencing threat, pain, fear, or anger. Further, the use of physical punishment is inconsistent with nonviolent principles, or parental modeling. In addition, the use of spanking chips away at the bonds of affection between parents and children, and tends to induce resentment and fear. Finally, it hinders the development of empathy and compassion in children, and they do not learn to take responsibility for their own behavior (Pitzer, 1997).

One of the biggest problems with the use of corporal punishment is that it can escalate into much more severe forms of violence. Usually, parents spank because they are angry (and somewhat out of control) and they can’t think of other ways to discipline. When parents are acting as a result of emotional triggers, the notion of discipline is lost while punishment and pain become the foci.

In 2006, of the children who were found to be victims of child abuse, nearly 75% of them were first-time victims (or had not come to the attention of authorities prior). A slight majority of child abuse victims were girls—51.5%, compared to 48% of abuse victims being boys. The younger the child, the more at risk he or she is for child abuse and neglect victimization. Specifically, the rate for infants (birth to 1 year old) was approximately 24 per 1,000 children of the same age group. The victimization rate for children 1–3 years old was 14 per 1,000 children of the same age group. The abuse rate for children aged 4– 7 years old declined further to 13 per 1,000 children of the same age group. African American, American Indian, and Alaska Native children, as well as children of multiple races, had the highest rates of victimization. White and Latino children had lower rates, and Asian children had the lowest rates of child abuse and neglect victimization. Regarding living arrangements, nearly 27% of victims were living with a single mother, 20% were living with married parents, while 22% were living with both parents but the marital status was unknown. (This reporting element had nearly 40% missing data, however.) Regarding disability, nearly 8% of child abuse victims had some degree of mental retardation, emotional disturbance, visual or hearing impairment, learning disability, physical disability, behavioral problems, or other medical problems. Unfortunately, data indicate that for many victims, the efforts of the child protection services system were not successful in preventing subsequent victimization. Children who had been prior victims of maltreatment were 96% more likely to experience another occurrence than those who were not prior victims. Further, child victims who were reported to have a disability were 52% more likely to experience recurrence than children without a disability. Finally, the oldest victims (16–21 years of age) were the least likely to experience a recurrence, and were 51% less likely to be victimized again than were infants (younger than age 1) (National Child Abuse and Neglect Data System, 2006).

Child fatalities are the most tragic consequence of maltreatment. Yet, each year, children die from abuse and neglect. In 2006, an estimated 1,530 children in the United States died due to abuse or neglect. The overall rate of child fatalities was 2 deaths per 100,000 children. More than 40% of child fatalities were attributed to neglect, but physical abuse also was a major contributor. Approximately 78% of the children who died due to child abuse and neglect were younger than 4 years old, and infant boys (younger than 1) had the highest rate of fatalities at 18.5 deaths per 100,000 boys of the same age in the national population. Infant girls had a rate of 14.7 deaths per 100,000 girls of the same age (National Child Abuse and Neglect Data System, 2006).

One question to be addressed regarding child fatalities is why infants have such a high rate of death when compared to toddlers and adolescents. Children under 1 year old pose an immense amount of responsibility for their caretakers: they are completely dependent and need constant attention. Children this age are needy, impulsive, and not amenable to verbal control or effective communication. This can easily overwhelm vulnerable parents. Another difficulty associated with infants is that they are physically weak and small. Injuries to infants can be fatal, while similar injuries to older children might not be. The most common cause of death in children less than 1 year is cerebral trauma (often the result of shaken-baby syndrome). Exasperated parents can deliver shakes or blows without realizing how little it takes to cause irreparable or fatal damage to an infant. Research informs us that two of the most common triggers for fatal child abuse are crying that will not cease and toileting accidents. Both of these circumstances are common in infants and toddlers whose only means of communication often is crying, and who are limited in mobility and cannot use the toilet. Finally, very young children cannot assist in injury diagnoses. Children who have been injured due to abuse or neglect often cannot communicate to medical professionals about where it hurts, how it hurts, and so forth. Also, nonfatal injuries can turn fatal in the absence of care by neglectful parents or parents who do not want medical professionals to possibly identify an injury as being the result of abuse.

Estimates reveal that nearly 80% of perpetrators of child abuse were parents of the victim. Other relatives accounted for nearly 7%, and unmarried partners of parents made up 4% of perpetrators. Of those perpetrators that were parents, over 90% were biological parents, 4% were stepparents, and 0.7% were adoptive parents. Of this group, approximately 58% of perpetrators were women and 42% were men. Women perpetrators are typically younger than men. The average age for women abusers was 31 years old, while for men the average was 34 years old. Forty percent of women who abused were younger than 30 years of age, compared with 33% of men being under 30. The racial distribution of perpetrators is similar to that of victims. Fifty-four percent were white, 21% were African American, and 20% were Hispanic/Latino (National Child Abuse and Neglect Data System, 2006).

There are many factors that are associated with child abuse. Some of the more common/well-accepted explanations are individual pathology, parent–child interaction, past abuse in the family (or social learning), situational factors, and cultural support for physical punishment along with a lack of cultural support for helping parents here in the United States.

The first explanation centers on the individual pathology of a parent or caretaker who is abusive. This theory focuses on the idea that people who abuse their children have something wrong with their individual personality or biological makeup. Such psychological pathologies may include having anger control problems; being depressed or having post-partum depression; having a low tolerance for frustration (e.g., children can be extremely frustrating: they don’t always listen; they constantly push the line of how far they can go; and once the line has been established, they are constantly treading on it to make sure it hasn’t moved. They are dependent and self-centered, so caretakers have very little privacy or time to themselves); being rigid (e.g., having no tolerance for differences—for example, what if your son wanted to play with dolls? A rigid father would not let him, laugh at him for wanting to, punish him when he does, etc.); having deficits in empathy (parents who cannot put themselves in the shoes of their children cannot fully understand what their children need emotionally); or being disorganized, inefficient, and ineffectual. (Parents who are unable to manage their own lives are unlikely to be successful at managing the lives of their children, and since many children want and need limits, these parents are unable to set them or adhere to them.)

Biological pathologies that may increase the likelihood of someone becoming a child abuser include having substance abuse or dependence problems, or having persistent or reoccurring physical health problems (especially health problems that can be extremely painful and can cause a person to become more self-absorbed, both qualities that can give rise to a lack of patience, lower frustration tolerance, and increased stress).

The second explanation for child abuse centers on the interaction between the parent and the child, noting that certain types of parents are more likely to abuse, and certain types of children are more likely to be abused, and when these less-skilled parents are coupled with these more difficult children, child abuse is the most likely to occur. Discussion here focuses on what makes a parent less skilled, and what makes a child more difficult. Characteristics of unskilled parents are likely to include such traits as only pointing out what children do wrong and never giving any encouragement for good behavior, and failing to be sensitive to the emotional needs of children. Less skilled parents tend to have unrealistic expectations of children. They may engage in role reversal— where the parents make the child take care of them—and view the parent’s happiness and well-being as the responsibility of the child. Some parents view the parental role as extremely stressful and experience little enjoyment from being a parent. Finally, less-skilled parents tend to have more negative perceptions regarding their child(ren). For example, perhaps the child has a different shade of skin than they expected and this may disappoint or anger them, they may feel the child is being manipulative (long before children have this capability), or they may view the child as the scapegoat for all the parents’ or family’s problems. Theoretically, parents with these characteristics would be more likely to abuse their children, but if they are coupled with having a difficult child, they would be especially likely to be abusive. So, what makes a child more difficult? Certainly, through no fault of their own, children may have characteristics that are associated with child care that is more demanding and difficult than in the “normal” or “average” situation. Such characteristics can include having physical and mental disabilities (autism, attention deficit hyperactivity disorder [ADHD], hyperactivity, etc.); the child may be colicky, frequently sick, be particularly needy, or cry more often. In addition, some babies are simply unhappier than other babies for reasons that cannot be known. Further, infants are difficult even in the best of circumstances. They are unable to communicate effectively, and they are completely dependent on their caretakers for everything, including eating, diaper changing, moving around, entertainment, and emotional bonding. Again, these types of children, being more difficult, are more likely to be victims of child abuse.

Nonetheless, each of these types of parents and children alone cannot explain the abuse of children, but it is the interaction between them that becomes the key. Unskilled parents may produce children that are happy and not as needy, and even though they are unskilled, they do not abuse because the child takes less effort. At the same time, children who are more difficult may have parents who are skilled and are able to handle and manage the extra effort these children take with aplomb. However, risks for child abuse increase when unskilled parents must contend with difficult children.

Social learning or past abuse in the family is a third common explanation for child abuse. Here, the theory concentrates not only on what children learn when they see or experience violence in their homes, but additionally on what they do not learn as a result of these experiences. Social learning theory in the context of family violence stresses that if children are abused or see abuse (toward siblings or a parent), those interactions and violent family members become the representations and role models for their future familial interactions. In this way, what children learn is just as important as what they do not learn. Children who witness or experience violence may learn that this is the way parents deal with children, or that violence is an acceptable method of child rearing and discipline. They may think when they become parents that “violence worked on me when I was a child, and I turned out fine.” They may learn unhealthy relationship interaction patterns; children may witness the negative interactions of parents and they may learn the maladaptive or violent methods of expressing anger, reacting to stress, or coping with conflict.

What is equally as important, though, is that they are unlikely to learn more acceptable and nonviolent ways of rearing children, interacting with family members, and working out conflict. Here it may happen that an adult who was abused as a child would like to be nonviolent toward his or her own children, but when the chips are down and the child is misbehaving, this abused-child-turned-adult does not have a repertoire of nonviolent strategies to try. This parent is more likely to fall back on what he or she knows as methods of discipline.

Something important to note here is that not all abused children grow up to become abusive adults. Children who break the cycle were often able to establish and maintain one healthy emotional relationship with someone during their childhoods (or period of young adulthood). For instance, they may have received emotional support from a nonabusing parent, or they received social support and had a positive relationship with another adult during their childhood (e.g., teacher, coach, minister, neighbor, etc.). Abused children who participate in therapy during some period of their lives can often break the cycle of violence. In addition, adults who were abused but are able to form an emotionally supportive and satisfying relationship with a mate can make the transition to being nonviolent in their family interactions.

Moving on to a fourth familiar explanation for child abuse, there are some common situational factors that influence families and parents and increase the risks for child abuse. Typically, these are factors that increase family stress or social isolation. Specifically, such factors may include receiving public assistance or having low socioeconomic status (a combination of low income and low education). Other factors include having family members who are unemployed, underemployed (working in a job that requires lower qualifications than an individual possesses), or employed only part time. These financial difficulties cause great stress for families in meeting the needs of the individual members. Other stress-inducing familial characteristics are single-parent households and larger family size. Finally, social isolation can be devastating for families and family members. Having friends to talk to, who can be relied upon, and with whom kids can be dropped off occasionally is tremendously important for personal growth and satisfaction in life. In addition, social isolation and stress can cause individuals to be quick to lose their tempers, as well as cause people to be less rational in their decision making and to make mountains out of mole hills. These situations can lead families to be at greater risk for child abuse.

Finally, cultural views and supports (or lack thereof) can lead to greater amounts of child abuse in a society such as the United States. One such cultural view is that of societal support for physical punishment. This is problematic because there are similarities between the way criminals are dealt with and the way errant children are handled. The use of capital punishment is advocated for seriously violent criminals, and people are quick to use such idioms as “spare the rod and spoil the child” when it comes to the discipline or punishment of children. In fact, it was not until quite recently that parenting books began to encourage parents to use other strategies than spanking or other forms of corporal punishment in the discipline of their children. Only recently, the American Academy of Pediatrics has come out and recommended that parents do not spank or use other forms of violence on their children because of the deleterious effects such methods have on youngsters and their bonds with their parents. Nevertheless, regardless of recommendations, the culture of corporal punishment persists.

Another cultural view in the United States that can give rise to greater incidents of child abuse is the belief that after getting married, couples of course should want and have children. Culturally, Americans consider that children are a blessing, raising kids is the most wonderful thing a person can do, and everyone should have children. Along with this notion is the idea that motherhood is always wonderful; it is the most fulfilling thing a woman can do; and the bond between a mother and her child is strong, glorious, and automatic—all women love being mothers. Thus, culturally (and theoretically), society nearly insists that married couples have children and that they will love having children. But, after children are born, there is not much support for couples who have trouble adjusting to parenthood, or who do not absolutely love their new roles as parents. People look askance at parents who need help, and cannot believe parents who say anything negative about parenthood. As such, theoretically, society has set up a situation where couples are strongly encouraged to have kids, are told they will love kids, but then society turns a blind or disdainful eye when these same parents need emotional, financial, or other forms of help or support. It is these types of cultural viewpoints that increase the risks for child abuse in society.

The consequences of child abuse are tremendous and long lasting. Research has shown that the traumatic experience of childhood abuse is life changing. These costs may surface during adolescence, or they may not become evident until abused children have grown up and become abusing parents or abused spouses. Early identification and treatment is important to minimize these potential long-term effects. Whenever children say they have been abused, it is imperative that they be taken seriously and their abuse be reported. Suspicions of child abuse must be reported as well. If there is a possibility that a child is or has been abused, an investigation must be conducted.

Children who have been abused may exhibit traits such as the inability to love or have faith in others. This often translates into adults who are unable to establish lasting and stable personal relationships. These individuals have trouble with physical closeness and touching as well as emotional intimacy and trust. Further, these qualities tend to cause a fear of entering into new relationships, as well as the sabotaging of any current ones.

Psychologically, children who have been abused tend to have poor self-images or are passive, withdrawn, or clingy. They may be angry individuals who are filled with rage, anxiety, and a variety of fears. They are often aggressive, disruptive, and depressed. Many abused children have flashbacks and nightmares about the abuse they have experienced, and this may cause sleep problems as well as drug and alcohol problems. Posttraumatic stress disorder (PTSD) and antisocial personality disorder are both typical among maltreated children. Research has also shown that most abused children fail to reach “successful psychosocial functioning,” and are thus not resilient and do not resume a “normal life” after the abuse has ended.

Socially (and likely because of these psychological injuries), abused children have trouble in school, will have difficulty getting and remaining employed, and may commit a variety of illegal or socially inappropriate behaviors. Many studies have shown that victims of child abuse are likely to participate in high-risk behaviors such as alcohol or drug abuse, the use of tobacco, and high-risk sexual behaviors (e.g., unprotected sex, large numbers of sexual partners). Later in life, abused children are more likely to have been arrested and homeless. They are also less able to defend themselves in conflict situations and guard themselves against repeated victimizations.

Medically, abused children likely will experience health problems due to the high frequency of physical injuries they receive. In addition, abused children experience a great deal of emotional turmoil and stress, which can also have a significant impact on their physical condition. These health problems are likely to continue occurring into adulthood. Some of these longer-lasting health problems include headaches; eating problems; problems with toileting; and chronic pain in the back, stomach, chest, and genital areas. Some researchers have noted that abused children may experience neurological impairment and problems with intellectual functioning, while others have found a correlation between abuse and heart, lung, and liver disease, as well as cancer (Thomas, 2004).

Victims of sexual abuse show an alarming number of disturbances as adults. Some dislike and avoid sex, or experience sexual problems or disorders, while other victims appear to enjoy sexual activities that are self-defeating or maladaptive—normally called “dysfunctional sexual behavior”—and have many sexual partners.

Abused children also experience a wide variety of developmental delays. Many do not reach physical, cognitive, or emotional developmental milestones at the typical time, and some never accomplish what they are supposed to during childhood socialization. In the next section, these developmental delays are discussed as a means of identifying children who may be abused.

There are two primary ways of identifying children who are abused: spotting and evaluating physical injuries, and detecting and appraising developmental delays. Distinguishing physical injuries due to abuse can be difficult, particularly among younger children who are likely to get hurt or receive injuries while they are playing and learning to become ambulatory. Nonetheless, there are several types of wounds that children are unlikely to give themselves during their normal course of play and exploration. These less likely injuries may signal instances of child abuse.

While it is true that children are likely to get bruises, particularly when they are learning to walk or crawl, bruises on infants are not normal. Also, the back of the legs, upper arms, or on the chest, neck, head, or genitals are also locations where bruises are unlikely to occur during normal childhood activity. Further, bruises with clean patterns, like hand prints, buckle prints, or hangers (to name a few), are good examples of the types of bruises children do not give themselves.

Another area of physical injury where the source of the injury can be difficult to detect is fractures. Again, children fall out of trees, or crash their bikes, and can break limbs. These can be normal parts of growing up. However, fractures in infants less than 12 months old are particularly suspect, as infants are unlikely to be able to accomplish the types of movement necessary to actually break a leg or an arm. Further, multiple fractures, particularly more than one on a bone, should be examined more closely. Spiral or torsion fractures (when the bone is broken by twisting) are suspect because when children break their bones due to play injuries, the fractures are usually some other type (e.g., linear, oblique, compacted). In addition, when parents don’t know about the fracture(s) or how it occurred, abuse should be considered, because when children get these types of injuries, they need comfort and attention.

Head and internal injuries are also those that may signal abuse. Serious blows to the head cause internal head injuries, and this is very different from the injuries that result from bumping into things. Abused children are also likely to experience internal injuries like those to the abdomen, liver, kidney, and bladder. They may suffer a ruptured spleen, or intestinal perforation. These types of damages rarely happen by accident.

Burns are another type of physical injury that can happen by accident or by abuse. Nevertheless, there are ways to tell these types of burn injuries apart. The types of burns that should be examined and investigated are those where the burns are in particular locations. Burns to the bottom of the feet, genitals, abdomen, or other inaccessible spots should be closely considered. Burns of the whole hand or those to the buttocks are also unlikely to happen as a result of an accident.

Turning to the detection and appraisal of developmental delays, one can more readily assess possible abuse by considering what children of various ages should be able to accomplish, than by noting when children are delayed and how many milestones on which they are behind schedule. Importantly, a few delays in reaching milestones can be expected, since children develop individually and not always according to the norm. Nonetheless, when children are abused, their development is likely to be delayed in numerous areas and across many milestones.

As children develop and grow, they should be able to crawl, walk, run, talk, control going to the bathroom, write, set priorities, plan ahead, trust others, make friends, develop a good self-image, differentiate between feeling and behavior, and get their needs met in appropriate ways. As such, when children do not accomplish these feats, their circumstances should be examined.

Infants who are abused or neglected typically develop what is termed failure to thrive syndrome. This syndrome is characterized by slow, inadequate growth, or not “filling out” physically. They have a pale, colorless complexion and dull eyes. They are not likely to spend much time looking around, and nothing catches their eyes. They may show other signs of lack of nutrition such as cuts, bruises that do not heal in a timely way, and discolored fingernails. They are also not trusting and may not cry much, as they are not expecting to have their needs met. Older infants may not have developed any language skills, or these developments are quite slow. This includes both verbal and nonverbal means of communication.

Toddlers who are abused often become hypervigilant about their environments and others’ moods. They are more outwardly focused than a typical toddler (who is quite self-centered) and may be unable to separate themselves as individuals, or consider themselves as distinct beings. In this way, abused toddlers cannot focus on tasks at hand because they are too concerned about others’ reactions. They don’t play with toys, have no interest in exploration, and seem unable to enjoy life. They are likely to accept losses with little reaction, and may have age-inappropriate knowledge of sex and sexual relations. Finally, toddlers, whether they are abused or not, begin to mirror their parents’ behaviors. Thus, toddlers who are abused may mimic the abuse when they are playing with dolls or “playing house.”

Developmental delays can also be detected among abused young adolescents. Some signs include the failure to learn cause and effect, since their parents are so inconsistent. They have no energy for learning and have not developed beyond one- or two-word commands. They probably cannot follow complicated directions (such as two to three tasks per instruction), and they are unlikely to be able to think for themselves. Typically, they have learned that failure is totally unacceptable, but they are more concerned with the teacher’s mood than with learning and listening to instruction. Finally, they are apt to have been inadequately toilet trained and thus may be unable to control their bladders.

Older adolescents, because they are likely to have been abused for a longer period of time, continue to get further and further behind in their developmental achievements. Abused children this age become family nurturers. They take care of their parents and cater to their parents’ needs, rather than the other way around. In addition, they probably take care of any younger siblings and do the household chores. Because of these default responsibilities, they usually do not participate in school activities; they frequently miss days at school; and they have few, if any, friends. Because they have become so hypervigilant and have increasingly delayed development, they lose interest in and become disillusioned with education. They develop low self-esteem and little confidence, but seem old for their years. Children this age who are abused are still likely to be unable to control their bladders and may have frequent toileting accidents.

Other developmental delays can occur and be observed in abused and neglected children of any age. For example, malnutrition and withdrawal can be noticed in infants through teenagers. Maltreated children frequently have persistent or untreated illnesses, and these can become permanent disabilities if medical conditions go untreated for a long enough time. Another example can be the consequences of neurological damage. Beyond being a medical issue, this type of damage can cause problems with social behavior and impulse control, which, again, can be discerned in various ages of children.

Once child abuse is suspected, law enforcement officers, child protection workers, or various other practitioners may need to interview the child about the abuse or neglect he or she may have suffered. Interviewing children can be extremely difficult because children at various stages of development can remember only certain parts or aspects of the events in their lives. Also, interviewers must be careful that they do not put ideas or answers into the heads of the children they are interviewing. There are several general recommendations when interviewing children about the abuse they may have experienced. First, interviewers must acknowledge that even when children are abused, they likely still love their parents. They do not want to be taken away from their parents, nor do they want to see their parents get into trouble. Interviewers must not blame the parents or be judgmental about them or the child’s family. Beyond that, interviews should take place in a safe, neutral location. Interviewers can use dolls and role-play to help children express the types of abuse of which they may be victims.

Finally, interviewers must ask age-appropriate questions. For example, 3-year-olds can probably only answer questions about what happened and who was involved. Four- to five-year-olds can also discuss where the incidents occurred. Along with what, who, and where, 6- to 8-year-olds can talk about the element of time, or when the abuse occurred. Nine- to 10-year-olds are able to add commentary about the number of times the abuse occurred. Finally, 11-year-olds and older children can additionally inform interviewers about the circumstances of abusive instances.

A conclusion is not a summary of what a writer has already mentioned. On the contrary, it is the last point made. Taking every detail of the investigation, the researcher makes the concluding point. In this part of a paper, you need to put a full stop in your research. You need to persuade the reader in your opinion.

Never add any new information in the conclusion. You can present solutions to the problem and you dwell upon the results, but only if this information has been already mentioned in the main body.

Child advocates recommend a variety of strategies to aid families and children experiencing abuse. These recommendations tend to focus on societal efforts as well as more individual efforts. One common strategy advocated is the use of public service announcements that encourage individuals to report any suspected child abuse. Currently, many mandatory reporters (those required by law to report abuse such as teachers, doctors, and social service agency employees) and members of communities feel that child abuse should not be reported unless there is substantial evidence that abuse is indeed occurring. Child advocates stress that this notion should be changed, and that people should report child abuse even if it is only suspected. Public service announcements should stress that if people report suspected child abuse, the worst that can happen is that they might be wrong, but in the grander scheme of things that is really not so bad.

Child advocates also stress that greater interagency cooperation is needed. This cooperation should be evident between women’s shelters, child protection agencies, programs for at-risk children, medical agencies, and law enforcement officers. These agencies typically do not share information, and if they did, more instances of child abuse would come to the attention of various authorities and could be investigated and managed. Along these lines, child protection agencies and programs should receive more funding. When budgets are cut, social services are often the first things to go or to get less financial support. Child advocates insist that with more resources, child protection agencies could hire more workers, handle more cases, conduct more investigations, and follow up with more children and families.

Continuing, more educational efforts must be initiated about issues such as punishment and discipline styles and strategies; having greater respect for children; as well as informing the community about what child abuse is, and how to recognize it. In addition, Americans must alter the cultural orientation about child bearing and child rearing. Couples who wish to remain child-free must be allowed to do so without disdain. And, it must be acknowledged that raising children is very difficult, is not always gloriously wonderful, and that parents who seek help should be lauded and not criticized. These kinds of efforts can help more children to be raised in nonviolent, emotionally satisfying families, and thus become better adults.

Bibliography

When you write a paper, make sure you are aware of all the formatting requirements. Incorrect formatting can lower your mark, so do not underestimate the importance of this part.

Organizing your bibliography is quite a tedious and time-consuming task. Still, you need to do it flawlessly. For this reason, analyze all the standards you need to meet or ask professionals to help you with it. All the comas, colons, brackets etc. matter. They truly do.

Bibliography:

• American Academy of Pediatrics: https://www.aap.org/
• Bancroft, L., & Silverman, J. G. (2002). The batterer as parent. Thousand Oaks, CA: Sage.
• Child Abuse Prevention and Treatment Act, 42 U.S.C.A. § 5106g (1998).
• Childhelp: Child Abuse Statistics: https://www.childhelp.org/child-abuse-statistics/
• Children’s Defense Fund: https://www.childrensdefense.org/
• Child Stats.gov: https://www.childstats.gov/
• Child Welfare League of America: https://www.cwla.org/
• Crosson-Tower, C. (2008). Understanding child abuse and neglect (7th ed.). Boston: Allyn & Bacon.
• DeBecker, G. (1999). Protecting the gift: Keeping children and teenagers safe (and parents sane). New York: Bantam Dell.
• Family Research Laboratory at the University of New Hampshire: https://cola.unh.edu/family-research-laboratory
• Guterman, N. B. (2001). Stopping child maltreatment before it starts: Emerging horizons in early home visitation services. Thousand Oaks, CA: Sage.
• Herman, J. L. (2000). Father-daughter incest. Cambridge, MA: Harvard University Press.
• Medline Plus, Child Abuse: https://medlineplus.gov/childabuse.html
• Myers, J. E. B. (Ed.). (1994). The backlash: Child protection under fire. Newbury Park, CA: Sage.
• National Center for Missing and Exploited Children: https://www.missingkids.org/home
• National Child Abuse and Neglect Data System. (2006). Child maltreatment 2006: Reports from the states to the National Child Abuse and Neglect Data System. Washington, DC: U.S. Department of Health and Human Services, Administration for Children and Families.
• New York University Silver School of Social Work: https://socialwork.nyu.edu/
• Pitzer, R. L. (1997). Corporal punishment in the discipline of children in the home: Research update for practitioners. Paper presented at the National Council on Family Relations Annual Conference, Washington, DC.
• RAND, Child Abuse and Neglect: https://www.rand.org/topics/child-abuse-and-neglect.html
• Richards, C. E. (2001). The loss of innocents: Child killers and their victims. Wilmington, DE: Scholarly Resources.
• Straus, M. A. (2001). Beating the devil out of them: Corporal punishment in American families and its effects on children. Edison, NJ: Transaction.
• Thomas, P. M. (2004). Protection, dissociation, and internal roles: Modeling and treating the effects of child abuse. Review of General Psychology, 7(15).
• U.S. Department of Health and Human Services, Administration for Children and Families: https://www.acf.hhs.gov/

Your Pathway to Academic Excellence with iResearchNet

Embarking on your academic journey with iResearchNet not only sets the foundation for your success but also ensures you navigate the complexities of research paper writing with ease and confidence. Our comprehensive suite of services, from expertly crafted research papers to an array of exclusive extras, is designed with your academic needs and aspirations in mind. By choosing iResearchNet, you’re not just securing a service; you’re investing in your future, in a partnership that values excellence, integrity, and your personal academic goals.

We invite you to take the first step towards transforming your academic challenges into opportunities for growth and learning. Starting is simple, and the benefits are immense. With iResearchNet, you gain access to a world of expertise, personalized support, and resources tailored to elevate your research and writing to the highest standard. Our commitment to quality, alongside our promise of customization, affordability, and timely delivery, ensures that every paper we deliver meets and exceeds your expectations.

Whether you’re seeking to inspire your academic journey with our diverse research paper examples, require the specialized assistance of our expert writers, or wish to enhance your experience with our additional services, iResearchNet is here to support you every step of the way. Our process is streamlined for your convenience, ensuring that from the moment you place your order to the final receipt of your paper, your journey is smooth, transparent, and fully aligned with your academic objectives.

Embrace the opportunity to excel, to stand out, and to make your academic work truly remarkable. Choose iResearchNet today, and let us be your partner in achieving academic excellence. Begin your journey by placing your order, and experience firsthand the impact of professional support and exceptional writing on your academic endeavors. Your success is our priority, and with iResearchNet, it’s within reach.

English 201 - Fincham : Mini Research Paper

• IF I APPLY - source evaluation
• Research logs
• Mini Exploratory Essay
• Mini Annotated Bibliography
• Mini Rough Draft of Research Paper and Mini Revision Assignment
• Mini Research Paper
• Ask A Librarian page

Assignment description

1) To investigate an aspect of  ‘banning books in public schools’ using a Supreme Court decision from the provided list as a starting point;

2) to begin with a question then investigate it through research to arrive at a better understanding of the topic;

3) to strengthen your understanding of Supreme Court First Amendment rulings and their precedents for the full Research Paper;

4) to compose a formal writing that will fully explain and support your thesis.

Components :

- Typed, in a Word document

- Formatting to meet MLA manuscript guidelines, including a Words Cited page not part of the length

- No length requirement

- Must incorporate in text citations for sources

Requirements :

- Typed, in a Word document, following the MLA manuscript formatting.

- Cite at least four sources

- Include a Works Cited page

Use the Writing Center for more help!

The Marshall University Writing Center is a free tutoring service for all Marshall students who want help with their writing. The Writing Center is staffed with graduate and undergraduate students ready to help you at any stage of the writing process. Tutors can be consulted on any writing assignment from any discipline.

Click HERE to go to the Writing Center page and make an appointment!

• << Previous: Mini Rough Draft of Research Paper and Mini Revision Assignment
• Next: Ask A Librarian page >>
• Last Updated: Jan 29, 2024 12:18 PM
• URL: https://libguides.marshall.edu/ENG201Fincham

• help_outline help

iRubric: Mini-Research Paper rubric

• Mini-Research Paper

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

• View all journals
• My Account Login
• Explore content
• About the journal
• Publish with us
• Sign up for alerts
• Open access
• Published: 24 April 2024

Spatiotemporally resolved colorectal oncogenesis in mini-colons ex vivo

• L. Francisco Lorenzo-Martín   ORCID: orcid.org/0000-0003-4717-9338 1   na1 ,
• Tania Hübscher   ORCID: orcid.org/0000-0002-2376-712X 1   na1 ,
• Amber D. Bowler   ORCID: orcid.org/0000-0002-9439-2839 2 , 3 ,
• Nicolas Broguiere   ORCID: orcid.org/0000-0001-9934-4505 1 ,
• Jakob Langer   ORCID: orcid.org/0000-0002-0095-1936 1 ,
• Lucie Tillard 1 ,
• Mikhail Nikolaev   ORCID: orcid.org/0000-0001-5955-900X 4 ,
• Freddy Radtke   ORCID: orcid.org/0000-0003-4315-4045 2 , 3 &
• Matthias P. Lutolf   ORCID: orcid.org/0000-0002-5898-305X 1 , 4  

Nature ( 2024 ) Cite this article

12k Accesses

1 Citations

377 Altmetric

Metrics details

• Cancer models
• Gastrointestinal cancer
• Lab-on-a-chip
• Tissue engineering

Three-dimensional organoid culture technologies have revolutionized cancer research by allowing for more realistic and scalable reproductions of both tumour and microenvironmental structures 1 , 2 , 3 . This has enabled better modelling of low-complexity cancer cell behaviours that occur over relatively short periods of time 4 . However, available organoid systems do not capture the intricate evolutionary process of cancer development in terms of tissue architecture, cell diversity, homeostasis and lifespan. As a consequence, oncogenesis and tumour formation studies are not possible in vitro and instead require the extensive use of animal models, which provide limited spatiotemporal resolution of cellular dynamics and come at a considerable cost in terms of resources and animal lives. Here we developed topobiologically complex mini-colons that are able to undergo tumorigenesis ex vivo by integrating microfabrication, optogenetic and tissue engineering approaches. With this system, tumorigenic transformation can be spatiotemporally controlled by directing oncogenic activation through blue-light exposure, and emergent colon tumours can be tracked in real-time at the single-cell resolution for several weeks without breaking the culture. These induced mini-colons display rich intratumoural and intertumoural diversity and recapitulate key pathophysiological hallmarks displayed by colorectal tumours in vivo. By fine-tuning cell-intrinsic and cell-extrinsic parameters, mini-colons can be used to identify tumorigenic determinants and pharmacological opportunities. As a whole, our study paves the way for cancer initiation research outside living organisms.

Similar content being viewed by others

Optogenetic control of mRNA condensation reveals an intimate link between condensate material properties and functions

Shell buckling for programmable metafluids

Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations

Cancer arises through the accumulation of genetic lesions that confer unrestrained cell growth potential. Over the past 70 years, both two-dimensional (2D) and three-dimensional (3D) in vitro culture models have been developed to make simplified, animal-free versions of cancers readily available for research 4 . These models successfully portray and dissect a wide range of relatively simple cancer cell behaviours, such as proliferation, motility, invasiveness, survival, cell–cell and cell–stroma interactions, and drug responses, among others 1 , 2 , 4 . However, modelling more complex processes that involve multiple cell (sub)types and tissue-level organization remains a challenge, as is the case for cancer initiation.

The cellular transition from healthy to cancerous is an intricate evolutionary process that is still largely obscure due to the insufficient topobiological complexity of the available in vitro cell culture systems, which precludes de novo tumour generation and the establishment of pathophysiologically relevant tumorigenic models 5 , 6 . Even the current gold-standard organoid-based 3D models, which are often postulated as a bridge between in vitro and in vivo 1 , 3 , 7 , are too simplified for modelling cancer development ex vivo. This is mostly due to (1) their closed cystic structure instead of an in vivo-like apically open architecture 8 ; (2) their short lifespan that requires breaking up the culture every few days for passaging 9 ; (3) their lack of topobiological stability and consistency owing to their stochastic growth in 3D matrices 8 ; and (4) their inability to generate hybrid tissues composed of healthy and cancer cells in a balanced and integrated manner 10 . Various next-generation approaches such as bioprinting and microfabrication technologies have been recently implemented to partially address some of these issues 11 , 12 ; however, none have been able to fully recreate intratumour and intertumour complexity. Consequently, cancer research is still inevitably bound to animal experimentation, which provides a pathophysiologically relevant setting, but forbids high-resolution and real-time analyses of cellular dynamics during oncogenesis. Moreover, these models are economically and ethically costly. Thus, while there is the widespread consensus that animal use in research should be reduced, replaced and refined (the 3 Rs 13 ), this commitment is severely hindered by the insufficient physiological complexity displayed by classical in vitro systems.

Here we postulated that a 3D system able to solve the existing limitations of in vitro cultures could be engineered by leveraging scaffold-guided organoid morphogenesis and optogenetics. Specifically, we developed miniature colon tissues in which cells could (1) be cultured for long durations (several weeks) without the need for breaking the culture through passaging; (2) reproduce the stem-differentiated cell patterning axis in a stable and anatomically relevant topology; (3) be easily mutated and tracked in a spatiotemporally controlled manner; and (4) create a biomechanically dynamic system that allows for tumour emergence while preserving the integrity of the surrounding healthy tissue. These features permit the development of biologically complex tumours ex vivo, bridging the gap between in vitro and in vivo models by providing a high-resolution system that can be used to dissect the molecular factors orchestrating cancer initiation.

Spatiotemporally regulated tumorigenesis

We focused on colorectal cancer (CRC) as it is one of the most prominent cancer types worldwide and its malignant transformation can be readily engineered genetically 14 , 15 . To first achieve spatiotemporal control of oncogenic DNA recombination, we developed a doxycycline-sensitive blue-light-regulated Cre system (hereafter, OptoCre), which we then introduced into inducible Apc fl/fl Kras LSL-G12D/+ Trp53 fl/fl (AKP) healthy colon organoids (Extended Data Fig. 1a–c ). A fluorescent Cre reporter was also incorporated to track cells that undergo oncogenic recombination (Extended Data Fig. 1b,c ). We initially tested the system in conventional organoid cultures, in which OptoCre efficiently induced recombination in the presence of blue light and doxycycline (Extended Data Fig. 1d,e ). Dosage optimization prevented unwanted activation by coupling high efficiency with low leakiness (~1.6%) (Extended Data Fig. 1d,e ). To confirm successful oncogenic transformation, we removed growth factors (EGF, noggin, R-spondin, WNT3A) from the organoid medium and observed that only cells with an activated OptoCre were able to grow, a well-known hallmark of mutated AKP colon organoids 16 (Extended Data Fig. 1f ). The presence of the expected mutations at the Apc, Kras and Trp53 loci was confirmed by PCR and exome sequencing (see below; Extended Data Fig. 3f,g ).

On the basis of previous evidence that small intestine cells can form stable tube-shaped epithelia through scaffold-guided organoid morphogenesis in microfluidic devices 9 , we next aimed to establish a ‘mini-colon’ constituted by OptoCre-AKP cells. By seeding colon cell suspensions in hydrogel-patterned microfluidic devices, we generated single-layered colonic epithelia spatially arranged into crypt- and lumen-like domains (Extended Data Fig. 2a ). This spatial arrangement recapitulated the spatial distribution found in vivo, with stem and progenitor (SOX9 + ) cells located at the bottom of the crypt domains and more differentiated colonocytes (FABP1 + ) located in the upper crypt and lumen areas 17 , 18 (Extended Data Fig. 2b ). In contrast to conventional colon organoids, the lumen of these mini-colons was readily perfusable with fresh medium, enabling the removal of cell debris and extending their lifespan to several weeks without the need for passaging or tissue disruption (Extended Data Fig. 2a ).

Once the healthy mini-colon system was established, we investigated its potential to capture tumour biology by inducing oncogenic recombination through blue-light illumination (Fig. 1a ). To mimic the scenario found in vivo, we fine-tuned OptoCre activation to mutate only a small number of cells (<0.5% of the total population). Due to the stability and defined topology of the mini-colon, we easily detected the acquisition of AKP mutations at the single-cell level (GFP + cells) and tracked their evolution over time (Extended Data Fig. 2c,d ). This revealed that cell death is one of the earliest responses to oncogenic recombination, as mutated mini-colons displayed higher cell shedding rates compared with the controls (Extended Data Fig. 2e ), with a large fraction of the mutated cells undergoing apoptosis (Supplementary Video  1 ). Nevertheless, some mutated cells escaped apoptosis and, after a quiescent period (24–72 h), started dividing at an accelerated pace (Extended Data Fig. 2d ). In conventional organoid cultures, these fast-proliferating mutated cells did not lead to any overt tissular rearrangements (Fig. 1b ), whereas, in the mini-colon system, they developed neoplastic structures over 5–10 days (Fig. 1b ). Furthermore, these mini-colon neoplasias evolved from polyp-like to full-blown tumours, recapitulating in vivo tumorigenesis (Fig. 1b,c and Supplementary Videos  2 and 3 ).

a , Schematic of the experimental workflow followed to induce tumorigenesis in mini-colons. CC, colonocyte; ISC, intestinal stem cell; TA, transit-amplifying cell. b , Bright-field and fluorescence images of time-course tumorigenesis experiments in conventional organoids and mini-colons. Fluorescence signal indicates oncogenic recombination. Scale bars, 200 μm (left) and 75 μm (right). c , Bright-field and fluorescence close-up images of a mini-colon tumour. The red and green signals correspond to healthy and mutated cells, respectively. Scale bar, 25 μm. d , Immunofluorescence images of a mini-colon tumour showing the presence of CD44 (top, green), FABP1 (top, magenta) and nuclei (bottom). Scale bar, 35 μm. e , Multiplicity of tumours emerged in mini-colons of the indicated genotypes after light-mediated oncogenic induction. Statistical analysis was performed using two-way analysis of variance (ANOVA) with Sidak’s multiple-comparison test; ** P  = 0.024 (day 6, AKP), ** P  = 0.0021 (day 24, A), *** P  < 0.0001 (all other conditions). n  = 5, 4, 3 and 10 mini-colons for the control, light-induced A, light-induced AK and light-induced AKP conditions, respectively. Data are mean ± s.e.m.

Source Data

Immunostaining analyses revealed that these tumours stemmed from CD44 high cells—a bona fide marker for cancer stem cells in vivo 19 —at the base of the epithelium (Fig. 1d , Extended Data Fig. 2f and Supplementary Video  4 ). Conversely, the bulk of the tumours was composed of cells with different degrees of differentiation, as revealed by the downregulation and upregulation of CD44 and FABP1, respectively (Fig. 1d and Supplementary Video  5 ). This indicated the existence of intratumour heterogeneity in the mini-colon, resembling the in vivo scenario 20 . Consistent with this, histopathological studies showed that these tumours displayed the histological organization characteristic of tubular adenomas (Extended Data Fig. 3a ). To validate their cancerous nature, we performed transplantation experiments in immunodeficient mice and found that mini-colon-derived cancer cells formed tumours in vivo with undistinguishable efficiency from bona fide tumour-derived cancer cells (Extended Data Fig. 3b,c ). Moreover, their histopathological structure was also comparable to the one displayed by primary tumours developed in the colon of AKP mice (Extended Data Fig. 3d ) and included the presence of locally invasive nodules and areas with adenocarcinoma-like features (Extended Data Fig. 3e ).

We confirmed through PCR and exome sequencing that tumour development in the mini-colon was directly associated with the expected mutations at the Apc, Kras and Trp53 loci (Extended Data Fig. 3f,g ). Consistent with this, using organoid lines with a reduced mutational burden ( Apc fl/fl Kras LSL-G12D/+ (hereafter, AK) and Apc fl/fl (hereafter, A)) produced longer latencies in tumour development in a dosage-dependent manner (Fig. 1e and Extended Data Fig. 3h ), demonstrating that mini-colon tumorigenesis can be modulated by the number of oncogenic driver mutations. Collectively, these data show that the mini-colon system enables spatiotemporally controlled in vitro modelling of CRC tumorigenesis with a considerable degree of topobiological complexity.

Context-dependent tumorigenic plasticity

Careful examination of induced mini-colons revealed consistent morphological differences among tumours according to their initiation site, with prominent dense or cystic internal structures arising from the crypt and the luminal epithelium, respectively (see below; Fig. 2b (top)). As mini-colons comprise different types of cells along the crypt–lumen axis (Extended Data Fig. 2b ), we leveraged the spatial resolution provided by OptoCre to investigate whether the initiating cell niche conditioned the morphological and functional features of nascent tumours. To spatially control AKP mutagenesis, we coupled the mini-colon to a photomask restricting blue-light exposure to specific regions of the colonic epithelium (Fig. 2a ), which provided low off-target recombination rates (around 8.5%) (Fig. 2b,c and Extended Data Fig. 4a ). Here again, dense and cystic tumours developed when crypt and lumen epithelia, respectively, were mutationally targeted by blue light (Fig. 2b ). To confirm that this was associated with the differentiation status of the tumour-initiating cell, we cultured mini-colons in either low- or high-differentiation medium before oncogenic induction to shift the proportions of (un)differentiated cells. Low-differentiation conditions produced mini-colons with thicker epithelia, early tumour development and a reduced fraction of cystic tumours (Fig. 2d and Extended Data Fig. 4b,c ). Conversely, high-differentiation conditions produced mini-colons with thinner epithelia, delayed tumour formation and increased cystic tumour frequency (Fig. 2d and Extended Data Fig. 4b,c ). These results indicate that the different environments of the mini-colon can shape tumour fate.

a , Schematic of the experimental workflow followed to spatiotemporally target tumorigenesis in mini-colons. b , Bright-field images of mini-colons that have undergone untargeted (top), crypt-targeted (middle) and lumen-targeted (bottom) tumorigenesis. Targeted areas are indicated by dashed blue lines. The black and white arrows indicate tumours with compact and cystic morphologies, respectively. Scale bar, 75 μm. c , The oncogenic recombination efficiency in targeted and off-target areas in mini-colons. Statistical analysis was performed using two-tailed t -tests; *** P  < 0.0001. n  = 6 mini-colons per condition. Each point represents one mini-colon. d , Bright-field images of induced mini-colons cultured in low-differentiation (top, WENRNi) and high-differentiation (bottom, ENR) conditions. The black and white arrows indicate tumours with compact and cystic morphologies, respectively. Scale bar, 75 μm. e , Schematic of the different colon organoid lines generated in this work. f , Bright-field images of the indicated colon organoid lines cultured for 2 days in basal medium. Scale bar, 200 μm. g , Metabolic activity (measured using resazurin) of the indicated colon organoid lines cultured in basal medium for the indicated time. Numerical labelling (1–8) was used to facilitate cell line identification. Statistical analysis was performed using two-way ANOVA with Sidak’s multiple-comparison test; *** P  = 0.0004 (control), *** P  < 0.0001 (all other conditions). n  = 3 cultures for each line. For c and g , data are mean ± s.e.m.

To evaluate the functional repercussions of the tumour-initiating niche, we isolated cancer cells from mini-colons enriched in either crypt- or lumen-derived tumours and established organoid cell lines (termed mini-colon AKP) (Fig. 2e ). As a control, we generated AKP mutant organoids by shining blue light onto inducible organoids and kept these mutants in parallel with their mini-colon equivalents, doing the required passages on confluency (termed organoid AKP) (Fig. 2e ). We also established organoid cultures from AKP colon tumours extracted from tamoxifen-treated Cdx2-cre ERT2 AKP mice (termed in vivo AKP) (Fig. 2e ). Notably, in contrast to mini-colons, none of these three types of mutant AKP lines were morphologically distinguishable from healthy non-mutated cells when cultured as organoids (Fig. 1b and Extended Data Fig. 4d ). When we cultured these organoids in basal medium depleted of growth factors (BM;  Methods ), both in vivo and crypt tumour-derived mini-colon AKP organoids preserved their proliferative potential (Fig. 2f,g ). Conversely, organoid and lumen tumour-enriched mini-colon AKP lines displayed significantly reduced proliferation rates (Fig. 2f,g ). This was not due to intrinsic cycling defects in any of the organoid lines tested, as these differences were not observed in standard cancer organoid medium (BMGF; Methods and Extended Data Fig. 4e ). As expected, healthy organoids did not grow in any of these conditions (Fig. 2f,g and Extended Data Fig. 4e ). Collectively, these results show that there are context-dependent factors aside from the founding AKP mutations that condition the growth potential of AKP cells. They also indicate that the cells derived from mini-colon crypt tumours recapitulate the growth properties of in vivo CRC cells more faithfully than conventional organoids.

To investigate the molecular programs underpinning these observations, we profiled the transcriptome of the different AKP lines using RNA sequencing (RNA-seq). We first characterized the differences between the two AKP lines derived from conventional systems, in vivo and organoid AKP cells, which also had the biggest disparity in growth potential (Fig. 2g ). According to our previous experiments, in vivo AKP cells upregulated many genes involved in canonical cancer pathways and the promotion of cell growth (Extended Data Fig. 4f,g ). Conversely, these cells downregulated genes associated with cell differentiation, patterning and transcriptional regulation (Extended Data Fig. 4f,g ). To evaluate whether mini-colon AKP cells recapitulated this in vivo AKP transcriptional signature, we performed single-sample gene set enrichment analysis (GSEA) across all of the cell lines. Here, most of the mini-colon AKP lines outscored their organoid AKP counterparts, especially those derived from crypt tumours (Extended Data Fig. 4h ). To investigate the transcriptional divergence between crypt- and lumen-enriched mini-colon AKP cells, we compared the lines with the highest (#v, crypt-enriched) and lowest (#i, lumen-enriched) in vivo AKP signature score (Extended Data Fig. 4h ). These analyses revealed that crypt-derived mini-colon AKP cells upregulated genes involved in WNT signalling, stem cell pluripotency, lipid metabolism and other pathways involved in cancer (Extended Data Fig. 4i ). To identify the potential drivers of growth factor independence among these, we searched for overlaps between AKP lines with high growth potential in BM (in vivo AKP, mini-colon AKP #v). We found that the latter overexpressed a collection of genes that is involved in the activation of MAPK cascades, including receptor tyrosine kinases (RTKs), G-protein-coupled receptors and soluble factors (Extended Data Fig. 5a ). We therefore theorized that these cells were engaging a surplus of MAPK signalling that gave them a greater fitness under growth-factor-poor conditions. To validate this idea, we tested their response to a panel of inhibitors, which confirmed that the growth of AKP lines in BM heavily relied on signals from RTKs (Extended Data Fig. 5b,c ; regorafenib), including KIT (Extended Data Fig. 5b,c ; ripretinib) and FGF receptors (Extended Data Fig. 5b,c ; infigratinib). Corroborating this, the ligands for these RTKs (SCF, FGF2) and others involved in colonocyte clonogenicity (IGF1) 21 could enhance the growth of the AKP lines with poor proliferation potential in BM (Extended Data Fig. 5d,e ). Importantly, all of these dependencies were either reduced or not detectable in conventional CRC organoid medium (BMGF) (Extended Data Figs. 4e and 5b,c ). Taken together, these data indicate that the mini-colon is a plastic system in which context-dependent factors can drive different functional features in CRC cells, including the engagement of ancillary RTK signals that boost their growth potential in challenging environments.

Intra- and intertumour heterogeneity

We hypothesized that the diversity observed in tumour morphology and growth potential reflected clonally distinct tumour types being initiated in the mini-colon. To validate this idea, we performed single-cell transcriptomic profiling of tumour-bearing mini-colons incorporating a genetic cell barcoding system 22 to preserve clonal information (Fig. 3a ). On the basis of bona fide transcriptional markers, mini-colons comprised eight major cell types that were segregated into undifferentiated, absorptive and secretory lineages (Fig. 3b ). Undifferentiated ( Krt20 − ) cells included stem ( Lgr 5 + ), actively proliferating ( Mki67 + ) and progenitor ( Sox9 + Cd44 + ) cells (Fig. 3b,c and Extended Data Fig. 6a ). Mature ( Krt20 + ) absorptive colonocytes constituted the largest fraction of the mini-colon, and included bottom, middle and top colonocytes based on zonation markers 23 (such as Aldob , Iqgap2 and Clca4a ) (Fig. 3b,c and Extended Data Fig. 6a ). Mucus-producing goblet cells ( Muc2 + ) and hormone-releasing enteroendocrine cells ( Neurod1 + ) constituted the secretory compartment (Fig. 3b,c and Extended Data Fig. 6a ). Collectively, this diverse in vivo-like cell composition indicates that mini-colons provide a physiologically relevant context for conducting oncogenesis studies.

a , Schematic of the experimental workflow followed for single-cell and lineage-tracing analysis of mini-colons. b , Unsupervised uniform manifold approximation and projection (UMAP) clustering of the main cell types in mini-colons 7 days after tumorigenic induction. c , The expression (Exp.) of representative cell-type-specific markers in the different cell populations comprising mini-colons. d , Unsupervised clustering (UMAP) of healthy (top) and tumour (bottom) clonal populations in mini-colons. The cell type (left; colour coded as in b ) and clonal identity (right) are indicated. e , The relative cell type abundance in healthy and tumour mini-colon clonal populations. Data are mean ± s.e.m. n  = 16 and 18 for healthy and tumour clones, respectively. f , Healthy and tumour mini-colon clonal population sizes. Statistical analysis was performed using two-tailed Mann–Whitney U -tests; ** P  = 0.0011. n  = 16 and 18 for healthy and tumour clones, respectively. The box plots show the median (centre lines), the first and third quartiles (box limits) and the minimum and maximum values (whiskers). Each point represents one clonal population. g , The correlation between Gpx2 expression and cancer stem cell transcriptional signature enrichment ( Cd44 , Lgr5 , Sox9 ). Statistical analysis was performed using two-sided Pearson correlation tests; P  < 0.0001. n  = 540 cells. Each point represents one cell. CSC, cancer stem cell; ES, enrichment score. h , Bright-field and immunofluorescence images showing the abundance of GPX2 (magenta) and nuclei (cyan) in healthy (right) and tumour (left, indicated by arrows) crypts in a mini-colon. Scale bar, 35 μm. i , Expression of the indicated genes in the indicated tumour clones. Statistical analysis was performed using two-sided Wilcoxon rank-sum tests; *** P  = 1.77 × 10 −17 ( Il1a , clone 1), 1.00 × 10 −78 ( Cdkn2a , clone 14), 3.67 × 10 −22 ( Cdkn2a , clone 48). n  = 540 cells. Each point represents one cell.

To determine the clonal identities across the mini-colon, we compared the genetic barcodes among cells and detected 83 clonal populations. We then discarded small (<5 cells) clones and identified cells containing reads corresponding to the mutated versions of Apc and Trp53 (Extended Data Fig. 6b,c ). These bona fide tumour cells distinguished tumour clonal populations (18 classified) from healthy counterparts (16 classified) ( Methods and Extended Data Fig. 6d ). On average, healthy clonal populations consisted of around 18% undifferentiated cells, which gave rise to the remaining approximately 82% of absorptive colonocytes and secretory cells (Fig. 3d,e ). Conversely, mini-colon tumours were mostly formed by undifferentiated cells (~92%), with sparsely present colonocytes and secretory cells (Fig. 3d,e ). Tumour cells also formed larger clonal populations compared with their healthy counterparts (Fig. 3f ). These cell proportions are well aligned with the ones commonly observed in vivo 24 , 25 .

Analyses of the internal structure of single clonal tumours showed that they comprised a non-homogeneous collection of cells with diverse proliferation, stemness and differentiation markers (Extended Data Fig. 7a ). Such intratumour heterogeneity reflects the complexity of mini-colon tumours, consistent with our immunostaining data (Fig. 1d ). To investigate the mechanisms orchestrating cancer stemness and tumour development, we analysed the transcriptional differences between differentiated ( Krt20 + Apoc2 + Fabp2 + ) and stem ( Lgr5 + Cd44 + Sox9 + ) cancer cells within tumours. We found that Gpx2 , a glutathione peroxidase recently linked to CRC malignant transformation 24 , strongly correlated with the stemness potential of mini-colon cancer cells (Fig. 3g ). Consistent with this, we observed that GPX2 protein was particularly enriched in the basal cells of mini-colon tumours (Fig. 3h ).

To examine whether mini-colons could produce different types of tumours, we next compared the transcriptional profiles of the different tumour clones. Even though all tumour-initiating cells carried the same founding AKP mutations and shared many molecular features, we found clear diversity across mini-colon tumours (Extended Data Fig. 7b ). For example, the expression of the interleukin Il1a and leukocyte peptidase inhibitor Slpi revealed the presence of tumours with an inflammatory-like profile (Fig. 3i and Extended Data Fig. 7b,c ). Cdkn2a (encoding tumour suppressors p14 and p16) and Prdm16 were exclusively expressed by tumours seemingly insensitive to these cell cycle arrest genes given their Ki67 + nature (Fig. 3i and Extended Data Figs. 6a and 7b,c ). Aqp5 , an aquaporin inductor of gastric and colon carcinogenesis 26 , marked specific tumours able to produce the oncogenesis-promoting fibroblast growth factor FGF13 (Extended Data Fig. 7b,c ). Together with other markers (Extended Data Fig. 7b ) and corroborations at the protein level (Extended Data Fig. 7d ), these data indicate that a variety of tumour subtypes can be generated in the mini-colon, arguably due to tumour-niche-intrinsic and/or environmental factors. This probably accounts for the observed differences among mini-colon AKP cell lines (Fig. 2g and Extended Data Fig. 4h ). Importantly, we found that this diversity was relatable to the human context. For example, mini-colons generated tumours with transcriptional profiles representing both iCMS2- and iCMS3-like subtypes 27 (Extended Data Fig. 8a,b ) that were associated with a wide range of aggressiveness profiles (Extended Data Fig. 8c ) and correlated with different extents of lymph node colonization (Extended Data Fig. 8d,e ) when cross-compared with transcriptomic data from the TCGA collection of patients with CRC. Collectively, these findings demonstrate that the mini-colon is a complex cellular ecosystem that recreates both healthy and cancer cell diversity.

Screening of tumorigenic factors

The longevity, experimental flexibility and tumour formation dynamics of mini-colons provides an unparalleled in vitro set-up for conducting tumorigenesis assays. We therefore next used mini-colons as screening tools for identifying molecules with a prominent role in tumour development. As our single-cell RNA-seq (scRNA-seq) analyses revealed Gpx2 overexpression in cancer stem cells (Fig. 3g,h ), we probed its functional relevance by adding the glutathione peroxidase inhibitor tiopronin 28 to the basal medium reservoirs of mini-colons right after blue-light-induced AKP mutagenesis (Fig. 4a ). Basal application of the drug provides ubiquitous exposure on the mini-colon basolateral domain, mimicking a systemic therapy model (Fig. 4a ). By the time control mini-colons developed full-blown tumours, tiopronin-treated counterparts were largely tumour-free with a healthy colonic epithelium (Fig. 4b and Extended Data Fig. 9a ). This was not due to the mere reduction in proliferative activity, as tiopronin had a minor impact on organoid growth (Extended Data Fig. 9b,c ). As tiopronin targets several glutathione peroxidases, we corroborated the specific implication of GPX2 in tumour initiation by knocking down its transcript (Extended Data Fig. 9d ). These knockdown cells showed no detectable defects in terms of organoid morphology or proliferation in unchallenged conditions (Extended Data Fig. 9e,f ). However, after blue-light-mediated oncogenic recombination, GPX2-deficient mini-colons developed tumours with reduced kinetics and multiplicity (Fig. 4c and Extended Data Fig. 9g ), recapitulating the results obtained with tiopronin (Fig. 4b and Extended Data Fig. 9a ). Importantly, mini-colons were instrumental for these findings, as conventional organoid cultures cannot reveal differences in tumour-forming abilities (Extended Data Fig. 9b,h ).

a , The experimental workflow for systemic therapy modelling. b , Bright-field images of mini-colons treated with vehicle or tiopronin after tumorigenic recombination. Images correspond to 6 days after induction. Scale bar, 75 μm. c , The multiplicity of tumours emerged in mini-colons of the indicated genotype after oncogenic induction. Statistical analysis was performed using two-way ANOVA with Sidak’s multiple-comparison test; ** P  = 0.0034, *** P  = 0.0007 (days 6 and 9, sh Gpx2 1), *** P  < 0.0001 (all other conditions). n  = 5, 5 and 4 mini-colons for control, shGpx2 1 and shGpx2 3, respectively. d , Differentially expressed genes after Gpx2 knockdown in light-induced AKP tumour cells. e , Expression of the indicated genes in colonocytes of the indicated genotypes before and after oncogenic recombination. The colour scale shows the z score. f , The main enriched functional terms after Gpx2 knockdown in light-induced AKP tumour cells. Significant terms are highlighted in blue or red, as determined using one-sided Fisher’s exact tests, with gene expression adjusted P -values (Benjamini-Hochberg correction). g , The multiplicity of tumours emerged in mini-colons of the indicated genotype under the indicated pretreatment (2 days before oncogenic induction). Statistical analysis was performed using two-way ANOVA with Sidak’s multiple-comparison test; * P  = 0.0274, ** P  = 0.0033 (days 9 and 10), *** P  < 0.0001 (days 7 and 8). n  = 3 mini-colons for each condition. h , The experimental workflow for microbiota and dietary pattern modelling. BL, blue light. i , Bright-field images of mini-colons treated with the indicated metabolites. Images correspond to 7 days after tumorigenic induction. Scale bar, 75 μm. j , The multiplicity of tumours emerged in mini-colons treated with the indicated metabolites. Statistical analysis was performed using two-way ANOVA with Sidak’s multiple-comparison test; ** P  = 0.0080, *** P  = 0.0008 (days 7 and 8), *** P  < 0.0001 (day 6). n  = 3 mini-colons for each condition. For c , g and j , data are mean ± s.e.m.

To gain molecular insights into the mechanism engaged by GPX2, we performed RNA-seq analysis of Gpx2 -knockdown cells both before and after oncogenic recombination. These analyses revealed that GPX2 deficiency remodels the colonocyte transcriptome in both healthy (Extended Data Fig. 9i ) and tumorigenic (Fig. 4d ) conditions (Supplementary Tables 1 and 2 ). This included the downmodulation of canonical markers associated with both healthy and cancer cell stemness, such as Lgr5 and Cd44 (Fig. 4e ). By contrast, markers of proliferative progenitor cells, such as Sox9 , remained unchanged (Fig. 4e ). Consistent with this, Gpx2 abrogation led to the repression of transcriptional programs implicated in stem cell pluripotency, including the WNT, Hippo–YAP and TGFβ pathways, as well as epithelial–mesenchymal transition and other processes involved in cancer cell fitness (Fig. 4f and Extended Data Fig. 9j,k ). Conversely, transcriptional programs associated with proliferation were not affected, consistent with our observations in cell culture (Extended Data Fig. 9e,f,k ). These findings indicate that the inhibition of GPX2 downmodulates colonocyte stemness, which probably accounts for the reduced tumorigenic potential observed in the mini-colon after oncogenic recombination. Supporting this, we found that non-transformed GPX2-deficient cells displayed reduced clonogenic capacity in medium deprived of exogenous WNT signals (Extended Data Fig. 9l,m ). Furthermore, the enhancement of WNT signalling through pretreatment of mini-colons with CHIR99021 for 2 days before oncogenic induction rescued the tumorigenic potential of Gpx2- knockdown cells (Fig. 4g and Extended Data Fig. 9n ). Collectively, these data uncover GPX2 as a key regulator of colon stemness and tumorigenesis, shedding light on lingering questions spurred by the recent discovery of its association with the malignant progression of human CRC 24 .

Besides cell-intrinsic factors, colon tumorigenesis in vivo is heavily modulated by a myriad of environmental molecules that continuously contact the luminal side of colonocytes, such as the metabolites produced by colon-residing microbiota 29 . The impact of these molecules cannot be faithfully evaluated in conventional organoid cultures, as their lumen is not accessible. As mini-colons address this limitation, we also investigated whether they could model the role of bacterial metabolites of which the tumorigenic function has been corroborated in vivo. To that end, we administered specific metabolites exclusively in the luminal side of healthy mini-colons and, after a conditioning period of 2 days, induced oncogenic recombination (Fig. 4h ). When luminally exposed to deoxycholic acid, a tumour-promoting metabolite 29 , 30 , 31 , mini-colons developed tumours with fast kinetics and high multiplicity (Fig. 4i,j ). Conversely, both tumour-suppressive butyrate 29 , 32 and β-hydroxybutyrate 33 slowed tumour development and reduced multiplicity (Fig. 4i,j ). These results demonstrate that mini-colons faithfully recapitulate the in vivo pathophysiological responses to bacterial metabolites, whereas conventional organoid cultures do not provide informative data on their tumorigenic relevance (Extended Data Fig. 10a ).

Dietary components also constitute a relevant source of luminal factors conditioning colon tumorigenesis 34 . We therefore performed analogous experiments modelling diets with different caloric contents (Fig. 4h and Extended Data Fig. 10b ). These revealed that calorie restriction in the luminal space effectively reduced tumour burden when compared to calorie-enriched medium (Extended Data Fig. 10c,d ), consistent with in vivo evidence 35 . To show the relevance of luminal accessibility, we placed the same amount of dietary medium in the basal medium reservoirs instead of the luminal space (Extended Data Fig. 10b ). Here, no differences were observed between the two dietary patterns (Extended Data Fig. 10e,f ), therefore indicating that an accessible lumen—a forbidden feature in conventional organoids—is decisive for the physiologically relevant modelling of colon biology. Collectively, these findings demonstrate that the mini-colon is a versatile tool that enables faithful in vitro recapitulation of CRC tumorigenesis and its environmental determinants.

Here we show that the mini-colon model shifts the paradigm of cancer initiation research, allowing ex vivo tumorigenesis with unparalleled pathophysiological intricacy. Coupled with spatiotemporal control of oncogenesis, real-time single-cell resolution and broad experimental flexibility, this system opens new perspectives for in vitro screening of cellular and molecular determinants of cancer development. Supporting this, mini-colons faithfully reflect in vivo-like responses to microbiota-derived metabolites and dietary patterns. Likewise, our model can help in the discovery and validation of genetic targets and tumour-suppressive drugs, as illustrated by the finding that glutathione peroxidase inhibition abrogates CRC tumour development. This constitutes a major advance over conventional 3D culture systems like organoids and Transwell models, which can recapitulate isolated aspects of colon biology such as histopathological features 36 or apical accessibility 37 , respectively, but lack the all-round topobiological complexity required to allow tumour formation ex vivo. Although such complexity demands bioengineering expertise to generate mini-colons, we have provided a detailed protocol that makes this system widely adoptable across laboratories that are already familiar with conventional organoid cultures (Protocol Exchange 38 ; see  Methods ).

As for most genetic models of CRC, our system is based on the simultaneous acquisition of several mutations, which does not fully recapitulate the sequential tumorigenic process that occurs in vivo 39 . We therefore acknowledge that adopting a stepwise mutational system will enhance the relevance of the mini-colon as a cancer initiation model. We are also aware that spatial transcriptomics approaches will improve our understanding of tumour heterogeneity in the mini-colon. In the same lines, we envision the incorporation of additional regulatory layers in our OptoCre system, such as the fusion with the oestrogen receptor ligand-binding domain for subcellular localization control 40 , as a promising way to achieve finer spatiotemporal regulation of recombination.

Although mini-colons cannot be considered to be a general replacement for animals in all contexts of cancer research, they offer the possibility to reduce animal use in a wide range of experimental applications. Importantly, the pathophysiological relevance of the mini-colon can be readily enhanced by including stromal cells in the surrounding biomimetic extracellular matrix, which condition both tumour dynamics and invasiveness (Extended Data Fig. 10g–k ). Current lines of work that will be made available in ensuing publications have also proved that this model can be applied to patient-derived colorectal cancer specimens. Lastly, we anticipate that, by adapting its biomechanical properties, topology and culture conditions, it will be possible to expand the system to other prominent epithelial cancer types, such as lung, breast or prostate, bringing an important experimental resource to multiple fields.

Apc fl/fl mice (a gift from T. Petrova) were crossed to Cdx2-cre ERT2 mice (The Jackson Laboratory). Apc fl/fl Cdx2-cre ERT2 mice (termed A) were then crossed with Kras LSL-G12D/+ Trp53 fl/fl mice (a gift from E. Meylan) to generate Apc fl/fl Kras LSL-G12D/+ Trp53 fl/fl Cdx2-cre ERT2 mice (termed AKP). AKP mice were then back-crossed with C57BL6/J (The Jackson Laboratory) to generate Apc fl/fl Kras LSL-G12D/+ Cdx2-cre ERT2 mice (termed AK).

To induce tumorigenesis in vivo, Cre ERT2 recombinase was activated at the age of 8–10 weeks by a single intraperitoneal injection of 18 mg kg –1 tamoxifen (Sigma-Aldrich, T5648) in sunflower oil. Tumours were allowed to develop for 6 weeks. Mice were then sacrificed for tissue and cell isolation. See also below the specific section for transplantation of organoids in immunocompromised mice.

All animal work was conducted in accordance with Swiss national guidelines, reviewed and approved by the Service Veterinaire Cantonal of Etat de Vaud (VD3035.1 and VD3823). These regulations established 800 mm 3 as the maximal subcutaneous tumour volume allowed, which was not exceeded in any of the experiments. In experiments in which tumorigenesis was induced in vivo, the locomotion, appearance, body condition and intestinal function of the mice were monitored twice weekly and assigned numerical scores to allow quantitative decision making in case humane end points were necessary before the predefined end point of the experiment (6 weeks). All of the mice in this study reached the predefined end point. Mice were kept in the animal facility under EPFL animal care regulations. They were housed in individual cages at 23 ± 1 °C and 55 ± 10% humidity under a 12 h–12 h light–dark cycle. All of the animals were supplied with food and water ad libitum.

OptoCre module plasmid generation

The OptoCre module was designed by integrating the following constructs: (1) FUW-M2rtTA, which constitutively expresses the reverse tetracycline transactivator (rtTA); (2) FUW-tetO-GAVPO, which expresses the light-switchable trans-activator GAVPO after rtTA binding in the presence of doxycycline; and (3) FUW-OptoCre, which expresses Cre recombinase after GAVPO binding in the presence of blue light (Extended Data Fig. 1a ). FUW-M2rtTA was purchased from Addgene (20342). Vectors containing GAVPO and the GAVPO-binding promoter (UASG) 5 -P min , developed previously 41 , were a gift from M. Thomson 42 . For FUW-tetO-GAVPO generation, GAVPO was subcloned into the doxycycline-responsive FUW-TetO backbone (Wernig Lab, Stanford) using the EcoRI and NheI restriction sites (Extended Data Fig. 1a ). For FUW-OptoCre generation, (UASG) 5 -P min was inserted into the FUW-TetO backbone from which the TetO promoter had been removed (Wernig Lab, Stanford) using the BstBI and BamHI restriction sites. We then introduced the Cre recombinase (Addgene, 25997) downstream of (UASG) 5 -P min using the Pac1 restriction sites (Extended Data Fig. 1a ).

Isolation of colon cells

Healthy colon or tumour pieces were finely chopped using a scalpel and transferred to a gentle-MACS C-tube (Miltenyi, 130-093-237) containing 4 ml of digestion medium (RPMI (Thermo Fisher Scientific, 22400089), 1 mg ml –1 collagenase type IV (Life Technologies, 9001-12-1), 0.5 mg ml –1 dispase II (Life Technologies, 17105041) and 10 μg ml –1 DNase I (Applichem, A3778)). Tissues were then digested using the 37C_m_TDK_1 program on the gentle-MACS Octo Dissociator with heaters (Miltenyi). After the program was complete, the cell suspension was passed through a 70-μm strainer (Corning, 431751) and centrifugated at 400 g for 5 min.

Organoid and stromal cell culture

To establish organoids, colon cells were embedded in growth-factor-reduced Matrigel (Corning, 356231) (~2 × 10 4 cells per 20 μl dome) and cultured in Advanced DMEM/F-12 (Thermo Fisher Scientific, 12634028) supplemented with 1× GlutaMax (Thermo Fisher Scientific, 35050038), 10 mM HEPES (Thermo Fisher Scientific, 15630056), 100 μg ml −1 penicillin–streptomycin (Thermo Fisher Scientific, 15140122), 1× B-27 supplement (Thermo Fisher Scientific, 17504001), 1× N2 supplement (Thermo Fisher Scientific, 17502001), 1 mM N -acetylcysteine (Sigma-Aldrich, A9165), 50 μg ml −1 primocin (InvivoGen, ant-pm-2), 50 ng ml −1 EGF (Peprotech, 315-09), 100 ng ml −1 noggin (produced at EPFL Protein Production and Structure Core Facility), 500 ng ml −1 R-spondin (produced at EPFL Protein Production and Structure Core Facility), 50 ng ml –1 WNT3A (Time Bioscience, rmW3aL-010), 10 mM nicotinamide (Calbiochem, 481907) and 2.5 μM Thiazovivin (Stemgen, AMS.04-0017). This full medium is termed ‘WENRNi’. The base version of this medium without EGF, noggin, R-spondin, WNT3A and nicotinamide is referred to as BMGF and was used for the expansion of colon tumour organoids since they do not require the additional growth factors. The base version of BMGF without B-27, N2 and N -acetylcysteine is termed BM or basal medium, and was used for growth-factor deprivation experiments. A detailed protocol describing organoid culture can be found elsewhere 9 . Where indicated, organoids were treated with the following compounds or growth factors: regorafenib (8 μM, Selleckchem, S1178), ripretinib (1 μM, Selleckchem, S8757), infigratinib (1 μM, Selleckchem, S2183), SCF (100 ng ml –1 , PeproTech, 250-03), FGF2 (50 ng ml –1 , Thermo Fisher Scientific, PMG0035) and IGF1 (100 ng ml –1 , R&D Systems, 291-G1-200). Stromal cells were derived from cell suspensions from the primary tissue cultured in EGM-2 MV Microvascular Endothelial Cell Growth Medium-2 (Lonza, CC-3202) on conventional cell culture flasks. This medium selection strategy was followed by magnetic-activated cell sorting (MACS) on EPCAM (Miltenyi Biotec, 130-105-958) according to the manufacturer’s instructions to discard epithelial cells. The presence of stromal cells was further confirmed by immunofluorescence analyses of vimentin expression (see below). Cells were tested for mycoplasma before cryopreservation and in randomized routine checks using the MycoAlert PLUS Mycoplasma Detection Kit (Lonza, LT07-705).

Generation of light-inducible cells

Lentiviral particles carrying the three components of the OptoCre module (see above; Extended Data Fig. 1b ) and a Cre recombination reporter were produced at the EPFL Gene Therapy Platform by transfecting HEK293 cells with each plasmid of the OptoCre module and pLV-CMV-LoxP-DsRed-LoxP-eGFP (Addgene, 65726) plasmids. Lentivirus-containing supernatants were collected and concentrated by centrifugation (1,500 g for 1 h at 4 °C). Lentiviral titration was performed using the p24-antigen ELISA (ZeptoMetrix, 0801111). For transduction, colon organoids (around 2 × 10 5 cells) were dissociated into single cells by incubating in TrypLE Express Enzyme (Thermo Fisher Scientific, 12605028) at 37 °C for 5 min. Cells were then washed with basal medium supplemented with 10% fetal bovine serum (FBS) (Thermo Fisher Scientific, 10500064) and resuspended in WENRNi medium containing 8 μg ml −1 polybrene (Sigma-Aldrich, TR-1003-G) and the following amounts of viral particles: ~10 ng of p24 FUW-M2rtTA per ml, ~80 ng of p24 FUW-tetO-GAVPO per ml, ~80 ng of p24 FUW-OptoCre per ml and ~1,000 ng of p24 CMV-LoxP-DsRed-LoxP-eGFP per ml. These cells were plated in a 24-well plate, centrifuged at 600 g for 60 min at room temperature, and incubated for 6 h at 37 °C. After incubation, the cells were collected, centrifuged, plated in 20 μl Matrigel domes in a 24-well plate and cultured in WENRNi medium. Cells expressing the Cre recombination reporter were selected by supplementing WENRNi medium with 8 μg ml −1 puromycin (InvivoGen, ant-pr-1).

Light-mediated oncogenic recombination

The OptoCre module requires (1) doxycycline to induce rtTA-mediated GAVPO expression and (2) blue light to induce GAVPO-mediated Cre recombinase expression (Extended Data Fig. 1a,b ). At the desired time of oncogenic induction, 2 μg ml −1 doxycycline hydrochloride (Sigma-Aldrich, D3072) was added to the culture medium of either the organoids or mini-colons. Light induction was then performed using a custom-made LightBox built by Baur SA and the Instant Lab at EPFL. The LightBox consisted of an Acqua A5 System (Acme Systems) that could be remotely parametrized using a custom-made web-based application. Communication between the Acqua A5 System and the microcontroller (PJRC, Teensy 3.2) was done through Blocky programming, which allowed for control of the LED drivers (Sparkfun, PicoDuck). The LEDs (Cree LEDs, XLamp XP-C Blue LEDs) were placed into a custom multilayer 24-well plate holder made of black anodized aluminium and polyphenylsulfone; the height was optimized for homogeneous light distribution within each well. The entire LightBox, plate-holder, LEDs and cables were made to be placed in the incubator (watertight and heat resistant). Diffusive elements (Luminit, Light Shaping Diffuser 80°) were used to render the illumination more homogeneous inside each well. The intensity of the blue light (450–465 nm, peak at 455 nm) was optimized, set to 100 μW cm −2 and shined on the cells for 3 h. After blue-light exposure, doxycycline was removed by washing the cultures with fresh medium. In experiments targeting the light to specific regions of the mini-colon, work was carried out in the dark using a near infrared light (Therabulb, NIR-A) to prevent leaky Cre expression. Light-targeting was performed using a photomask that was adapted to the dimensions of the mini-colon and that was created from a photoresist and chrome-coated standard 5 × 5 inch silica plate (Nanofilm) with an automated machine (VPG200 Heidelberg Instrument, 2.0 µm resolution). Once the exposed photoresist was developed, the chrome layer was wet-etched and the remaining photoresist was stripped using a mask processor (Hamatech HMR900) 9 .

Microdevice design, fabrication and loading

The microfluidic device used for mini-colon cultures was designed using Clewin 3.1 (Phoenix Software) and fabricated as previously described 9 . It was composed of three main compartments: (1) a hydrogel chamber for cell growth in the centre; (2) two basal medium reservoirs flanking the hydrogel compartment; and (3) inlet and outlet channels for luminal perfusion 9 . An extracellular matrix containing 80% (v/v) type I collagen (5 mg ml −1 , Reprocell, KKN-IAC-50) and 20% (v/v) growth–factor-reduced Matrigel was loaded into the hydrogel compartment. The microchannels constituting the mini-colon architecture within the hydrogel were designed using Adobe Illustrator CC 2019 and Wolfram Mathematica 11.3. They were then read by PALM RoboSoftware 4.6 (Zeiss) and ablated using a nanosecond laser system (1 ns pulses, 100 Hz frequency, 355 nm; PALM Micro-Beam laser microdissection system, Zeiss). The dimensions of the mini-colon architecture were described previously 9 . A detailed description of all the key steps required for the generation and maintenance of mini-guts is available at Protocol Exchange ( https://doi.org/10.21203/rs.3.pex-903/v1 ) 38 .

Mini-colon culture, development and tumorigenesis

Colon organoids were dissociated into single cells by incubating in TrypLE Express Enzyme for 5 min at 37 °C followed by vigorous pipetting. This cell suspension was washed in 5 volumes of Advanced DMEM/F-12 supplemented with 10% FBS and passed through 40 μm cell strainers (Corning, 431750). After centrifugation at 400 g for 5 min, cells were resuspended in WENRNi medium at around 10 6 cells per ml. The mini-colon luminal microchannel was filled with 10 μl of this cell suspension. Cells were allowed to settle down in the mini-colon crypt-shaped cavities for 5 min, and the leftover unadhered cells were washed out from the microchannel by medium perfusion. The basal medium reservoirs were filled with 100 μl of WENRNi. Unless otherwise indicated, once the healthy colonic epithelium was fully formed (around 2 days after seeding), the medium in the luminal channel was switched to BM, while WENRNi was kept in the basal medium reservoirs. This gradient of growth factor from basal medium reservoirs to luminal space favours colonocyte differentiation across the crypt–lumen axis. For low-differentiation conditions of the differentiation experiments, WENRNi was kept in both the lumen and basal medium reservoirs. Conversely, high-differentiation mini-colons were cultured in WENRNi medium without WNT3A and nicotinamide (termed ENR). Unless otherwise stated, once the colonic epithelium was fully formed, oncogenic induction in the mini-colons was performed as stated above. Where indicated, tiopronin (5 mM, Selleckchem, S2062) or CHIR99021 (3 μM, StemCell Technologies, 100-1042) was added to the basal medium reservoirs after or before oncogenic induction, respectively. For co-culture experiments, ~500 stromal cells were seeded in each hydrogel before the laser-mediated ablation of the mini-colon pattern. The rest of the culture conditions and procedures remained unchanged. To avoid potential unspecific results derived from the small (but non-zero; Extended Data Fig. 1d,e ) leakiness of the optogenetic system, each replication across all studies was performed using independent OptoCre organoid lines freshly generated before each experiment. In all cases, the mini-colons were incubated at 37 °C in 5% CO 2 humidified air, with daily luminal perfusions and medium changes every other day.

Mini-colon whole-mount immunofluorescence staining

Mini-colons were rinsed with phosphate-buffered saline (PBS) and fixed in 4% paraformaldehyde (Thermo Fisher Scientific, 15434389) overnight at 4 °C. After rinsing with PBS, the hydrogels were extracted from the PDMS scaffold using a scalpel, placed into a 48-well plate, permeabilized with 0.1% Tween-20 (Sigma-Aldrich, P9416) in PBS (10 min at 4 °C) and blocked in 2 mg ml −1 bovine serum albumin (Sigma-Aldrich, A3059) in PBS containing 0.1% Triton X-100 (Sigma-Aldrich, T8787) (blocking buffer) for at least 45 min at 4 °C. The samples were subsequently incubated overnight at 4 °C in blocking buffer with the corresponding following primary antibodies: CD44 (1:200; Abcam, ab157107), FABP1 (1:100; R&D Systems, AF1565), SOX9 (1:200; Abcam, ab185966), GPX2 (1:200; Bioss Antibodies, BS-13396R), IL-1α (1:200; R&D Systems, AF-400-SP), CDKN2A (1:100; Abcam, ab211542), E-cadherin (1:100; Abcam, ab11512) and vimentin (1:200; Abcam, ab92547). After three washes in blocking buffer for a total of 6 h at room temperature, the samples were incubated overnight at 4 °C in blocking buffer with the following corresponding secondary antibodies: Alexa Fluor 488 anti-goat (1:400, Thermo Fisher Scientific, A-11055), Alexa Fluor 488 anti-rat (1:400, Thermo Fisher Scientific, A-21208) and Alexa Fluor 647 anti-rabbit (1:400, Thermo Fisher Scientific, A-31573). After 3 washes in blocking buffer for a total of 6 h at room temperature, the samples were incubated with DAPI (1 μg ml −1 ; Tocris Bioscience, 5748) for 10 min at room temperature in blocking buffer. Before imaging, the hydrogels were mounted onto 35 mm glass bottom dishes (Ibidi, 81218-200) in Fluoromount-G (SouthernBiotech, 0100-01).

Mini-colon sectioning and histochemistry

Mini-colons were fixed and extracted from the PDMS scaffold as indicated above and were prepared for cryosectioning by incubating in 30% (w/v) sucrose (Sigma-Aldrich, S1888) in PBS until the sample sank. Subsequently, the samples were incubated for 12 h in a mixture of Cryomatrix (Epredia, 6769006) and 30% sucrose (mixing ratio 50/50) followed by a 12 h incubation in pure Cryomatrix. The samples were then embedded in a tissue mould, frozen on dry ice, and cut into 40-µm-thick sections at −20 °C using the CM3050S cryostat (Leica). Haematoxylin and eosin staining was performed at the EPFL Histology Core Facility using the Ventana Discovery Ultra automated slide preparation system (Roche).

Microscopy and image analysis

Bright-field and fluorescence imaging of living organoids and mini-colons was performed using the Nikon Eclipse Ti2 inverted microscope with ×4/0.13 NA, ×10/0.30 NA and ×40/0.3 NA air objectives and a DS-Qi2 camera (Nikon Corporation). Time lapses were taken in a Nikon Eclipse Ti inverted microscope system equipped with ×4/0.20 NA and ×10/0.30 NA air objectives and DS-Qi2 (Nikon Corporation) and Andor iXon Ultra 888 (Oxford Instruments) cameras. Both systems were controlled using the NIS-Elements AR software (Nikon Corporation). The extended depth of field (EDF) of bright-field images was calculated using a built-in NIS-Elements function. Fluorescence confocal imaging of fixed mini-colons was performed using the Leica SP8 STED 3X inverted microscope system equipped with ×10/0.30 NA air and ×25/0.95 NA water objectives, 405 nm diode and supercontinuum 470–670 nm lasers, and the system was controlled by the Leica LAS-X software (v.3.5.7, Leica microsystems). Histological sections were imaged using a Leica DM5500 upright microscope with ×10/0.30 NA and ×20/0.75 NA air objectives, a ×40/1.0 NA oil objective and a DMC 2900 Color camera, and the system was controlled by the Leica LAS-X software. Image processing was performed using standard contrast- and intensity-level adjustments in ImageJ (NIH). For oncogenic recombination analyses, the GFP-positive area was measured from 16-bit EDF images by subtracting the background, sharpening the images, and applying a signal threshold and a mask. The ratio between GFP-positive area and total organoid area was used for analyses. Recombined cells were segmented using StarDist with the default parameters ( https://github.com/stardist ) on the GFP channel of mini-colon images. Cell debris was discarded from segmentation analyses by setting an empirically established size threshold. For tumour quantification in the mini-colon, neoplastic structures with at least three times the thickness of the surrounding healthy epithelium were considered to be tumours. Videos of immunostainings were rendered using Imaris (Oxford Instruments).

Mini-colon shedding evaluation

The medium from the luminal compartments of the mini-colons, together with an additional luminal perfusion of 10 μl of basal medium, was collected every day for 4 days after the blue-light-induced oncogenic recombination. The protein content in these extracts was analysed using conventional Bradford assays (Bio-Rad, 5000006) and used as an indicator of cell shedding.

Mini-colon cell line derivation

Mini-colon-containing hydrogels were extracted from their microfluidic devices with a scalpel as indicated above and incubated with 0.1% (w/v) collagenase I (Thermo Fisher Scientific, 17100-017) at 37 °C for 10 min. Once the hydrogel was fully digested, the mini-colon was washed with PBS and digested with TrypLE Express Enzyme for 5 min at 37 °C. The resulting cell suspension was washed with Advanced DMEM/F-12 supplemented with 10% FBS, pelleted, embedded in Matrigel and cultured as indicated above for regular colon organoids.

Transplantation of organoids in immunocompromised mice

Organoid lines were established as indicated above from either in vivo colon tumours (reference AKP) or tumour-bearing mini-colons (mini-colon AKP). These organoids were dissociated into single cells using TrypLE Express Enzyme for 5 min at 37 °C, washed with Advanced DMEM/F-12 supplemented with 10% FBS, pelleted and embedded in Matrigel at 2.5 × 10 6 cells per ml. A total of 100 μl of this suspension was inoculated by subcutaneous injection into the right flank of NOD. Cd-Prkdz scid Il2rg tm1Wjl /Szj (NSG) mice (Jackson laboratories). Tumour growth was monitored using callipers twice per week until the end point at 18 days after inoculation. Length ( L ) and width ( W ) were measured and used to approximate the volume ( V ) of the tumour in mm 3 using the modified ellipsoid formula: V  = ( L  ×  W 2 )/2. After euthanasia, tumours were resected from the graft location and measured once more with callipers.

Graft sectioning and histochemistry

Tumour samples were fixed overnight in 4% paraformaldehyde at 4 °C, dehydrated in graded ethanol baths, cleared with xylene, embedded in paraffin and cut into 4-µm-thick sections using the HM 325 Rotary Microtome (Thermo Fisher Scientific). These sections were mounted onto Superfrost plus slides (Epredia, J1800AMNZ) and allowed to dry for 2 days at room temperature. Haematoxylin and eosin staining was performed at the EPFL Histology Core Facility using the Ventana Discovery Ultra automated slide preparation system (Roche).

Mutational screening in colon organoids

Genomic DNA was isolated from colon cells using the PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific, K182001) according to the manufacturer’s instructions. Recombination of the LSL (LoxP-Stop-LoxP) cassette controlling Kras G12D expression was confirmed by PCR using the protocol and oligos described by the Tyler Jacks laboratory ( https://jacks-lab.mit.edu/ , Kras G12D Conditional PCR). Apc and Trp53 recombinations were confirmed through exome sequencing performed at BGI Genomics at 100× coverage using DNBSEQ sequencing technology. DNA reads were mapped to the mouse GRCm39 genome assembly using BWA-MEM (v.0.7.17), filtered using samtools (v.1.9) and visualized using IGV (Integrative Genomics Viewer, Broad Institute, v.2.12.3).

Organoid proliferation assays

Single-cell suspensions of colon cells were generated as indicated above and embedded in 10 μl Matrigel domes at around 10 4 cells per dome in a 48-well plate. For each of the following 4 days, 220 μM resazurin (Sigma-Aldrich, R7017) was added to the culture medium and incubated for 4 h at 37 °C. Next, the resazurin-containing medium was collected and replaced with regular medium. Organoid proliferation was estimated by measuring the reduction of resazurin to fluorescent resorufin in the medium each day using the Tecan Infinite F500 microplate reader (Tecan) with 560 nm excitation and 590 nm emission filters. In the case of colony-formation assays, seeding was performed at around 10 3 cells per dome and the resulting colonies were counted after 3 days.

Organoid RNA extraction and bulk transcriptome profiling

Before RNA isolation, organoids were cultured for 3 days as indicated above and starved for 24 h in BM for the evaluation of growth-factor dependence. In the case of the Gpx2- knockdown experiments, 2 timepoints were analysed: 0 and 2 weeks after blue-light-induced activation (before and after oncogenic recombination, respectively). In all cases, cells were collected using TrypLE Express Enzyme as indicated above and lysed in RLT buffer (Qiagen, 74004), and the RNA was extracted using the QIAGEN RNeasy Micro Kit (Qiagen, 74004) according to the manufacturer’s instructions. Purified RNA was quality checked using a TapeStation 4200 (Agilent), and 500 ng was used for QuantSeq 3′ mRNA-seq library construction according to the manufacturer’s instructions (Lexogen, 015.96). Libraries were quality checked using a Fragment Analyzer (Agilent) and were sequenced in the NextSeq 500 (Illumina) system using NextSeq vm2.5 chemistry with Illumina protocol 15048776. Reads were aligned to the mouse genome (GRCm39) using star (v.2.7.0e) 43 . R (v.4.1.2) was used to perform the differential expression analyses. Count values were imported and processed using edgeR 44 . Expression values were normalized using the trimmed mean of M values (TMM) method 45 and low-expressed genes (<1 counts per million) were filtered out. Differentially expressed genes were identified using linear models (Limma-Voom) 46 and P values were adjusted for multiple comparisons using the Benjamini–Hochberg correction method 47 . Volcano plots and heat maps were generated using the EnhancedVolcano ( https://github.com/kevinblighe/EnhancedVolcano ) and heatmap3 ( https://github.com/slzhao/heatmap3 ) packages, respectively. The in vivo AKP signature was established from the differentially expressed genes between in vivo and organoid AKP lines with a log 2 -transformed fold change of at least |2|. To evaluate the enrichment of the in vivo AKP gene expression program across samples, the enrichment scores for both the upregulated and downregulated signatures were calculated using single-sample GSEA (ssGSEA) 48 . The difference between the two normalized enrichment scores yielded the fit score. ssGSEA was also used to analyse the enrichment of the MSigDB curated Hallmark gene set 49 in Gpx2 -knockdown organoids. Functional annotation was performed using DAVID 50 on the genes with a log 2 -transformed fold change of at least |1|. GOplot 51 was used for the integration of expression and functional annotation data. Known functional interactions among relevant genes were obtained through STRING 52 . Cytoscape 53 was used to perform network data integration and visualization.

Single-cell transcriptome profiling and lineage tracing

Lineage tracing was performed using the CellTag system 22 (V1 pooled barcode library, Addgene, 115643-LVC). In brief, we co-transduced inducible colon organoids with the CellTag barcode library (multiplicity of infection of around 5) and the OptoCre module as indicated above. These cells were then introduced and induced in the mini-colon system as indicated before. After 7 days in the system and when mini-colon tumours were clearly visible, we extracted the cells from mini-colons as indicated above. After pooling and filtering (40 μm) the cell suspensions from two mini-colons, the single-cell sequencing library was constructed using 10x Genomics Chromium 3′ reagents v3.1 according to the manufacturer’s instructions (10x Genomics, PN-1000269, PN-1000127, PN-1000215). Sequencing was performed using NovaSeq 6000 v1.5 reagents (Illumina protocol #1000000106351 v03) for around 100,000 reads per cell. The reads were aligned using Cell Ranger (v.6.1.2) 54 to the mouse genome (mm10) carrying artificial chromosomes for both GFP and CellTag UTR genes, as recommended by CellTag developers for facilitating barcode identification 55 . Raw count matrices were imported into R and analysed using Seurat (v.4.2.0) 56 . Dead cells were discarded on the basis of the number of detected genes (less than 3,000) and the percentage of mitochondrial genes (more than 20%), leading to 2,429 cells after filtering. The data were log-normalized and scaled, and dimensionality reduction was conducted using UMAP with 10 dimensions. Louvain clustering yielded 17 clusters that were merged and named on the basis of canonical cell type markers. Stem, cycling, progenitor, goblet and enteroendocrine cell scoring was based on published signatures in mini-intestines and in vivo 9 . Gene sets highlighting bottom, middle and top colonocytes were taken from enterocyte zonation studies 23 . Cancer stemness was scored based on the expression of Lgr5 , Cd44 and Sox9 . Intrinsic consensus molecular subtype (iCMS) signatures for colorectal cancer were obtained from published work 27 . Signature scoring was performed using burgertools ( https://github.com/nbroguiere/burgertools ). Visual representations of the data were generated using Seurat internal functions. For lineage-tracing analyses, CellTag detection, quantification and clone calling were performed as indicated by CellTag developers 55 , excluding cells expressing fewer than 2 or more than 30 CellTags. After filtering, 83 clonal populations were identified, from which only those with a minimum size of 5 cells were considered for further analyses. To identify clonal populations belonging to tumour cells, we looked for cells expressing transcripts carrying the genetically engineered Apc and Trp53 mutations, that is, deletions of exons 15 and 2–10, respectively (Extended Data Figs. 3g and 6b,c ). Note that this approach could not be performed for Kras , as the mutation is also present in the transcripts from WT cells (but not expressed). As scRNA-seq provides low coverage on exon junctions and therefore the presence of mutations can be assessed only in a small fraction of cells, we used both the cell-type composition and size distributions of bona fide mutationally confirmed tumour clonal populations to classify the rest of clones. Those falling within plus or minus 2 s.d. of the mean cell composition and size of bona fide tumours were classified as tumour clonal populations. Healthy clones were defined as those with a clearly distinct (outside the aforementioned range) cell type composition and the same upper limit size as was observed for tumour clones. After filtering and classification, 16 healthy and 18 tumour clonal populations were obtained and used for further analyses (Extended Data Fig. 6d ). To define the most robust tumour-clone-specific markers, the gene expression from cells in each clone was compared to that from cells in each other clone using the Wilcoxon rank-sum test. We considered only the positive markers and selected those with adjusted P  < 10 −5 . The association of these markers with clinical parameters in patients with CRC (survival, lymph node staging) was performed through cBioPortal ( https://www.cbioportal.org/ ) using the 640-sample CRC TCGA dataset ( https://www.cancer.gov/tcga ) and a differential expression threshold equal or greater than |2 |. Further information is provided in the Data availability and Code availability sections.

shRNA-mediated transcript knockdown

Organoids were transduced as indicated above with lentiviral particles encoding Gpx2 shRNAs obtained from Sigma-Aldrich (TRCN0000076529, TRCN0000076531 and TRCN0000076532; sh Gpx2 1, sh Gpx2 2 and sh Gpx2 3, respectively) or, as a control, shRNA-free counterparts (Addgene, 65726). Transduced cells were selected with puromycin (5 μg ml −1 ; InvivoGen, ant-pr-1). Proper transcript knockdown was assessed using quantitative PCR with reverse transcription (RT–qPCR) and RNA-seq.

Analysis of mRNA abundance

Organoids were cultured and collected as indicated above. Cells were then lysed in RLT buffer and RNA was extracted using the QIAGEN RNeasy Micro Kit as indicated above. RT–qPCR was performed using the iTaq Universal SYBR Green One-Step Kit (Bio-Rad Laboratories, 1725150) and the QuantStudio 7 Flex Real-Time PCR System (Thermo Fisher Scientific, 4485701). Raw data were analysed using Design & Analysis Software (v.2.6.0, Thermo Fisher Scientific). We used the abundance of the endogenous Gapdh mRNA as internal normalization control. The following primers were used for transcript quantification: 5′-AGTTCGGACATCAGGAGAACTG-3′ (forward, Gpx2 ), 5′-GATGCTCGTTCTGCCCATTG-3′ (reverse, Gpx2 ), 5′-ATCCTGCACCACCAACTGCT-3′ (forward, Gapdh ) and 5′-GGGCCATCCACAGTCTTCTG-3′ (reverse, Gapdh ).

Microbiota and diet modelling

Inducible mini-colons were generated as indicated above. Once the epithelium was formed and before oncogenic induction, mini-colons were subjected to a conditioning period of 2 days in which luminal medium was (1) supplemented with 100 μM deoxycholate (Sigma-Aldrich, D2510), 10 mM butyrate (Sigma-Aldrich, B5887) or 10 mM β-hydroxybutyrate (Sigma-Aldrich, 54965); or (2) replaced with MEMα (calorie-restricted condition, Thermo Fisher Scientific, 22561-021) or Advanced DMEM/F12 supplemented with 30 μM palmitic acid (calorie-enriched condition, Sigma-Aldrich, P0500). The same concentrations were used in organoid control experiments, but these were added to the full culture medium as the luminal compartment is not accessible in organoids. To assess the relevance of luminal exposure to these factors in the mini-colon, the same total amounts were added in the basal medium reservoirs instead of the luminal channel. In all cases, after conditioning, oncogenic recombination was performed and the mini-colon was cultured as indicated above. The different medium compositions were replenished every day during luminal perfusion.

Statistics and reproducibility

The number of biological replicates ( n ), the type of statistical tests performed and the statistical significance for each experiment are indicated in the corresponding figure legend. For images associated with quantification charts (Fig. 1b,c with Fig. 1e ; Fig. 2b with Fig. 2c ; Fig. 2d with Extended Data Fig. 4b ; Fig. 2f with Fig. 2g ; Fig. 4b with Extended Data Fig. 9a ; Fig. 4i with Fig. 4j ; Extended Data Fig. 2a with Fig. 1e ; Extended Data Fig. 3d,e with Extended Data Fig. 3b ; Extended Data Fig. 3h with Fig. 1e ; Extended Data Fig. 5b with Extended Data Fig. 5c ; Extended Data Fig. 5d with Extended Data Fig. 5e ; Extended Data Fig. 9b with Extended Data Fig. 9c ; Extended Data Fig. 9e with Extended Data Fig. 9f ; Extended Data Fig. 9g with Fig. 4c ; Extended Data Fig. 9l with Extended Data Fig. 9m ; Extended Data Fig. 9n with Fig. 4g ; Extended Data Fig. 10c with Extended Data Fig. 10d ; Extended Data Fig. 10e with Extended Data Fig. 10f ), the number of replicates is the same as for the corresponding chart and is indicated in the figure legend of the latter. For the rest of representative images (Figs. 1d and 3h and Extended Data Figs. 1f , 2b,c,f , 3a , 4a , 7d , 9h and 10a,g–k ), three independent experiments were performed. scRNA-seq (Fig. 3a ) and exome sequencing with matched PCR (Extended Data Fig. 3f,g ) were performed with two independent sets of samples. Bulk RNA-seq was performed with at least three independent sets of samples. Unless otherwise indicated, statistical analyses were performed using GraphPad Prism v.9 (GraphPad). Data normality and equality of variances were analysed with Shapiro–Wilk and Bartlett’s tests, respectively. Parametric distributions were analysed using the Student’s t -test (when comparing two experimental groups) or ANOVA followed by either Dunnett’s test (when comparing more than two experimental groups with a single control group) or Tukey’s HSD test (when comparing more than two experimental groups with every other group). Nonparametric distributions were analysed using either Mann–Whitney U -tests (for comparisons of two experimental groups) or the Kruskal–Wallis followed by Dunn’s test (for comparisons of three or more than three experimental groups) tests. Sidak’s multiple-comparison test was used when comparing different sets of means. χ 2 tests were used to determine the significance of the differences between expected and observed frequencies. In all cases, values were considered to be significant when P  ≤ 0.05. Data obtained are given as the mean ± s.e.m.

Reporting summary

Further information on research design is available in the  Nature Portfolio Reporting Summary linked to this article.

Data availability

Bulk and single-cell RNA-seq data reported in this paper have been deposited at the Gene Expression Omnibus (GEO) public repository under accession number GSE221163 . The association analysis with clinical parameters in patients with CRC was performed through cBioPortal ( https://cbioportal.org ) using the 640-sample CRC TCGA dataset ( https://cancer.gov/tcga ).  Source data are provided with this paper.

Code availability

The code used for data analysis is available at GitHub ( https://github.com/LorenzoLF/Mini-colon_bioengineering ) 57 and Zenodo ( https://doi.org/10.5281/zenodo.10057882 ) 58 .

Drost, J. & Clevers, H. Organoids in cancer research. Nat. Rev. Cancer 18 , 407–418 (2018).

Article   CAS   PubMed   Google Scholar  

Rodrigues, J., Heinrich, M. A., Teixeira, L. M. & Prakash, J. 3D in vitro model (r)evolution: unveiling tumor-stroma interactions. Trends Cancer 7 , 249–264 (2021).

Tuveson, D. & Clevers, H. Cancer modeling meets human organoid technology. Science 364 , 952–955 (2019).

Article   ADS   CAS   PubMed   Google Scholar  

Katt, M. E., Placone, A. L., Wong, A. D., Xu, Z. S. & Searson, P. C. In vitro tumor models: advantages, disadvantages, variables, and selecting the right platform. Front. Bioeng. Biotechnol. 4 , 12 (2016).

Article   PubMed   PubMed Central   Google Scholar  

Lee-Six, H. et al. The landscape of somatic mutation in normal colorectal epithelial cells. Nature 574 , 532–537 (2019).

Vendramin, R., Litchfield, K. & Swanton, C. Cancer evolution: Darwin and beyond. EMBO J. 40 , e108389 (2021).

Article   CAS   PubMed   PubMed Central   Google Scholar  

Kim, J., Koo, B. K. & Knoblich, J. A. Human organoids: model systems for human biology and medicine. Nat. Rev. Mol. Cell Biol. 21 , 571–584 (2020).

Sato, T. et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature 459 , 262–265 (2009).

Nikolaev, M. et al. Homeostatic mini-intestines through scaffold-guided organoid morphogenesis. Nature 585 , 574–578 (2020).

Article   ADS   PubMed   Google Scholar  

Krotenberg Garcia, A. et al. Active elimination of intestinal cells drives oncogenic growth in organoids. Cell Rep 36 , 109307 (2021).

Liu, X. et al. Tumor-on-a-chip: from bioinspired design to biomedical application. Microsyst. Nanoeng. 7 , 50 (2021).

Article   ADS   PubMed   PubMed Central   Google Scholar  

Augustine, R. et al. 3D bioprinted cancer models: revolutionizing personalized cancer therapy. Transl. Oncol. 14 , 101015 (2021).

Hubrecht, R. C. & Carter, E. The 3Rs and humane experimental technique: implementing change. Animals https://doi.org/10.3390/ani9100754 (2019).

Keum, N. & Giovannucci, E. Global burden of colorectal cancer: emerging trends, risk factors and prevention strategies. Nat. Rev. Gastroenterol. Hepatol. 16 , 713–732 (2019).

Article   PubMed   Google Scholar  

Bürtin, F., Mullins, C. S. & Linnebacher, M. Mouse models of colorectal cancer: past, present and future perspectives. World J. Gastroenterol. 26 , 1394–1426 (2020).

Drost, J. et al. Sequential cancer mutations in cultured human intestinal stem cells. Nature 521 , 43–47 (2015).

Gehart, H. & Clevers, H. Tales from the crypt: new insights into intestinal stem cells. Nat. Rev. Gastroenterol. Hepatol. 16 , 19–34 (2019).

Levy, E. et al. Localization, function and regulation of the two intestinal fatty acid-binding protein types. Histochem. Cell Biol. 132 , 351–367 (2009).

Du, L. et al. CD44 is of functional importance for colorectal cancer stem cells. Clin. Cancer Res. 14 , 6751–6760 (2008).

Fleming, M., Ravula, S., Tatishchev, S. F. & Wang, H. L. Colorectal carcinoma: pathologic aspects. J. Gastrointest. Oncol. 3 , 153–173 (2012).

PubMed   PubMed Central   Google Scholar  

Fujii, M. et al. Human intestinal organoids maintain self-renewal capacity and cellular diversity in niche-inspired culture condition. Cell Stem Cell 23 , 787–793 (2018).

Biddy, B. A. et al. Single-cell mapping of lineage and identity in direct reprogramming. Nature 564 , 219–224 (2018).

Article   ADS   CAS   PubMed   PubMed Central   Google Scholar  

Moor, A. E. et al. Spatial reconstruction of single enterocytes uncovers broad zonation along the intestinal villus axis. Cell 175 , 1156–1167 (2018).

Becker, W. R. et al. Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer. Nat. Genet. 54 , 985–995 (2022).

Snippert, H. J. et al. Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells. Cell 143 , 134–144 (2010).

Kang, S. K. et al. Role of human aquaporin 5 in colorectal carcinogenesis. Am. J. Pathol. 173 , 518–525 (2008).

Joanito, I. et al. Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer. Nat. Genet. 54 , 963–975 (2022).

Hall, M. D. et al. Inhibition of glutathione peroxidase mediates the collateral sensitivity of multidrug-resistant cells to tiopronin. J. Biol. Chem. 289 , 21473–21489 (2014).

Louis, P., Hold, G. L. & Flint, H. J. The gut microbiota, bacterial metabolites and colorectal cancer. Nat. Rev. Microbiol. 12 , 661–672 (2014).

Bernstein, C. et al. Carcinogenicity of deoxycholate, a secondary bile acid. Arch. Toxicol. 85 , 863–871 (2011).

Fu, T. et al. FXR regulates intestinal cancer stem cell proliferation. Cell 176 , 1098–1112 (2019).

Wu, X. et al. Effects of the intestinal microbial metabolite butyrate on the development of colorectal cancer. J. Cancer 9 , 2510–2517 (2018).

Dmitrieva-Posocco, O. et al. β-Hydroxybutyrate suppresses colorectal cancer. Nature 605 , 160–165 (2022).

Veettil, S. K. et al. Role of diet in colorectal cancer incidence: umbrella review of meta-analyses of prospective observational studies. JAMA Netw. Open 4 , e2037341 (2021).

Castejón, M. et al. Energy restriction and colorectal cancer: a call for additional research. Nutrients https://doi.org/10.3390/nu12010114 (2020).

van de Wetering, M. et al. Prospective derivation of a living organoid biobank of colorectal cancer patients. Cell 161 , 933–945 (2015).

Blutt, S. E. et al. Use of human tissue stem cell-derived organoid cultures to model enterohepatic circulation. Am. J. Physiol. Gastrointest. Liver Physiol. 321 , G270–G279 (2021).

Nikolaev, N. et al. Bioengineering microfluidic organoids-on-a-chip. Protocol Exchange https://doi.org/10.21203/rs.3.pex-903/v1 (2024).

Cho, K. R. & Vogelstein, B. Genetic alterations in the adenoma–carcinoma sequence. Cancer 70 , 1727–1731 (1992).

Meador, K. et al. Achieving tight control of a photoactivatable Cre recombinase gene switch: new design strategies and functional characterization in mammalian cells and rodent. Nucleic Acids Res. 47 , e97 (2019).

Wang, X., Chen, X. & Yang, Y. Spatiotemporal control of gene expression by a light-switchable transgene system. Nat. Methods 9 , 266–269 (2012).

Sokolik, C. et al. Transcription factor competition allows embryonic stem cells to distinguish authentic signals from noise. Cell Syst. 1 , 117–129 (2015).

Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29 , 15–21 (2013).

Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26 , 139–140 (2010).

Robinson, M. D. & Oshlack, A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11 , R25 (2010).

Law, C. W., Chen, Y., Shi, W. & Smyth, G. K. voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 15 , R29 (2014).

Reiner, A., Yekutieli, D. & Benjamini, Y. Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 19 , 368–375 (2003).

Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102 , 15545–15550 (2005).

Liberzon, A. et al. The Molecular Signatures Database (MSigDB) Hallmark gene set collection. Cell Syst. 1 , 417–425 (2015).

Dennis, G. et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4 , P3 (2003).

Walter, W., Sánchez-Cabo, F. & Ricote, M. GOplot: an R package for visually combining expression data with functional analysis. Bioinformatics 31 , 2912–2914 (2015).

Szklarczyk, D. et al. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 43 , D447–D452 (2015).

Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13 , 2498–2504 (2003).

Zheng, G. X. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8 , 14049 (2017).

Kong, W. et al. CellTagging: combinatorial indexing to simultaneously map lineage and identity at single-cell resolution. Nat. Protoc. 15 , 750–772 (2020).

Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184 , 3573–3587 (2021).

Lorenzo-Martín, L. F. et al. Code for ‘Spatiotemporally resolved colorectal oncogenesis in mini-colons ex vivo’. GitHub github.com/LorenzoLF/Mini-colon_bioengineering (2024).

Lorenzo-Martín, L. F. et al. Code for ‘Spatiotemporally resolved colorectal oncogenesis in mini-colons ex vivo’. Zenodo https://doi.org/10.5281/zenodo.10057882 (2024).

Download references

Acknowledgements

We thank M. Thomson for the original light-inducible plasmids; M. Wernig and G. Neumayer for the initial idea and work on the doxycycline- and light-inducible system; C. Baur for discussing, designing and building the custom illumination device; A. Chrisnandy for assistance on photomask fabrication; O. Mitrofanova, B. Elci and Y. Tinguely for assistance on microdevice fabrication; D. Dutta and S. Li for input on organoid work; and J. Prébandier for administrative assistance. We acknowledge support from the following EPFL core facilities: CMi, CPG, PTBTG, HCF, BIOP, FCCF, BSF and GECF. This work was funded by the Swiss Cancer League (KFS-5103-08-2020), the Personalized Health and Related Technologies (PHRT) Initiative from the ETH Board and the EPFL.

Open access funding provided by EPFL Lausanne.

Author information

These authors contributed equally: L. Francisco Lorenzo-Martín, Tania Hübscher

Authors and Affiliations

Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland

L. Francisco Lorenzo-Martín, Tania Hübscher, Nicolas Broguiere, Jakob Langer, Lucie Tillard & Matthias P. Lutolf

Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland

Amber D. Bowler & Freddy Radtke

Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland

Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland

Mikhail Nikolaev & Matthias P. Lutolf

You can also search for this author in PubMed   Google Scholar

Contributions

L.F.L.-M. conceived the study, designed experiments, performed the experimental and bioinformatic work, analysed the data, performed artwork design and wrote the manuscript. T.H. generated the OptoCre module and blue-light-associated systems, designed experiments, performed experimental work and analysed data. A.D.B. performed mouse-related work and isolated primary cells. N.B. performed bioinformatic work and analysed data. J.L. produced the microfluidic devices, optimized hydrogel patterning and generated mini-colon histological sections. L.T. performed experimental work. M.N. designed and developed the first mini-gut system. F.R. helped to conceive the work. M.P.L. conceived the work, designed experiments and edited the manuscript.

Corresponding authors

Correspondence to L. Francisco Lorenzo-Martín or Matthias P. Lutolf .

Ethics declarations

Competing interests.

The EPFL has filed for patent protection (EP16199677.2, PCT/EP2017/079651, US20190367872A1) on the scaffold-guided organoid technology used here, and M.P.L. and M.N. are named as inventors on those patents. M.P.L. is shareholder in Doppl, which is commercializing those patents. The other authors declare no competing interests.

Peer review

Peer review information.

Nature thanks Bradley Lega and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

Extended data fig. 1 generation of blue–light-inducible akp colon organoids..

a , Schematic of the plasmids comprising the OptoCre module. The promoter, gene, and restriction sites used to generate the plasmids are indicated. b , Schematic of the integration of the different genetic elements that allow spatiotemporal control of oncogenic recombination in colon organoids. c , Schematic of the experimental workflow used to test and optimize the OptoCre system. d , Brightfield and fluorescence images of OptoCre-carrying inducible colon organoids exposed to the indicated conditions. Red and green signals correspond to healthy and mutated cells, respectively. Images were taken 48 h after induction. Scale bar, 200 μm. e , Recombination efficiency in inducible colon organoid exposed to the conditions indicated in panel d. *** P  = 0.0001 (Kruskal-Wallis and Dunn’s multiple comparisons test; n  = 9 cultures for each condition). Each point represents one well of organoids. Data represent mean ± SEM. f , Brightfield and fluorescence images of inducible colon organoids exposed to control (top) and activation (bottom) conditions, dissociated into single cells and replated in the absence of growth factors (BMGF medium). Green signal corresponds to mutated cells. Images were taken 24 h after replating. Scale bar, 200 μm.

Extended Data Fig. 2 Oncogenic mutations induce neoplastic growth in mini-colons.

a , Time-course brightfield and fluorescence images of non-induced healthy colon cells grown as conventional organoids and mini-colons. Absence of fluorescence signal indicates absence of oncogenic recombination. Scale bars, 200 μm (organoids) and 75 μm (mini-colons). b , Immunofluorescence images showing the expression of Fabp1 (left, green), and Sox9 (right, magenta) in healthy mini-colons cultured for 7 days. Scale bar, 100 μm. c , Fluorescence image (left) showing the presence of mutated cells 36 h after the blue–light-mediated induction of a mini-colon. The segmentation of each mutated cell is shown (right). Scale bar, 120 μm. d , Evolution of the number of mutated cells in an inducible mini-colon after blue–light-mediated activation. Each dot represents a measurement every 15 min. The 2 nd order smoothing of the data is shown. e , Time-course quantitation of cell shedding (total protein content) into the lumen of OptoCre and control mini-colons after blue-light induced oncogenic recombination. * P  = 0.0156; ** P  = 0.0033; *** P  = 0.0003 (24 h), <0.0001 (96 h) (two-way ANOVA and Sidak’s multiple comparisons test; n  = 3 mini-colons for each condition). Each point represents one mini-colon. Data represent mean ± SEM. f , Low- (left) and high-magnification (right) immunofluorescence images showing the presence of CD44 (magenta) and nuclei (blue) in a tumour-bearing mini-colon. White and grey arrowheads indicate early and advanced tumorigenic events, respectively. Scale bars, 120 μm (left) and 50 μm (right).

Extended Data Fig. 3 Oncogenic mutations induce full blown tumours in mini-colons.

a , Hematoxylin and eosin staining of a mini-colon tumour section. Scale bar, 25 μm. b , Time-course growth of tumours produced by cells derived from mini-colon tumours upon subcutaneous transplantation in immunodeficient mice ( n  = 5 mice). As a reference, bona fide cancer cells from primary colon tumours are included. c , Image of the tumours at the endpoint of the experiment shown in panel b. d , Hematoxylin and eosin stainings of sections from the indicated tumour types. Zoomed-in areas (right) are indicated with a dashed square (left). Scale bar, 100 μm. e , Hematoxylin and eosin stainings of sections from mini-colon AKP implant tumours showing the presence of invading cancer cells (left, black arrowheads) and areas of cellular atypia (right, white arrowhead). Scale bar, 200 μm. f , Electrophoretic separation of PCR-amplified KRAS LSL locus in the indicated samples. See  Methods for more details on PCR design. g , Whole exome sequencing coverage in the indicated loci and cells. Missing exons in recombined cells are indicated. h , Brightfield images of mini-colons of the indicated genotypes 23 days after blue light exposure. Neoplastic and tumour structures are indicated with black and white arrowheads in A and AK mini-colons, respectively. By that time tumours have extended throughout the whole mini-colon tissue in the case of the AKP model, forming a dense mass of cancer cells. Scale bar, 75 μm.

Extended Data Fig. 4 Mini-colon tumours display in vivo -like functional and transcriptional features.

a , Brightfield and fluorescence images of a mini-colon where blue light exposure has been targeted to a specific area (dashed blue line). Red and green signals correspond to healthy and mutated cells, respectively. Images were taken 36 h after induction. Scale bar, 75 μm. b , Multiplicity of tumours emerged in mini-colons cultured in the indicated conditions. * P  = 0.0122; ** P  = 0.0035; *** P  = 0.0002 (two-way ANOVA and Sidak’s multiple comparisons test; n  = 4 mini-colons for each condition). c , Distribution of tumour morphologies in mini-colons cultured in the indicated conditions. ** P  = 0.0024 (two-way ANOVA and Sidak’s multiple comparisons test; n  = 4 mini-colons for each condition). d , Brightfield images of the indicated colon organoid lines cultured for 3 days in full organoid medium. Scale bar, 200 μm. e , Metabolic activity (measured using resazurin) of the indicated colon organoid lines cultured in BMGF medium for the indicated time. Numeric labelling (1-8) is used to facilitate cell line identification. *** P  = 0.0002 (mini-colon AKP #iii), <0.0001 (all other conditions) (two-way ANOVA and Sidak’s multiple comparisons test; n  = 3 cultures for each line). f , Volcano plot of the differentially expressed genes between “in vivo” and “organoid AKP” cell lines. g , Top enriched functional clusters in the differentially expressed genes identified in panel f. h , Enrichment of the “in vivo AKP” transcriptional signature identified in panel f across the different “mini-colon” and “organoid AKP” lines. * P  = 0.0137; ** P  = 0.0032 (#iii), 0.0075 (#iv); *** P  = 0.0001 (Brown-Forsythe ANOVA and Dunnett’s T3 multiple comparisons test (two-sided), n  = 6 and 3 cultures for “organoid AKP” and the rest of cell lines, respectively). Each dot represents one culture. i , Main enriched functional terms in the differentially expressed genes between “mini-colon AKP” lines # i and # v. Significant terms are highlighted in red (one-sided Fisher’s exact test, adjusted P values). In b , c , e , and h , data represent mean ± SEM. GPL, glycerophospholipid; EL, ether lipid; PG, proteoglycans; SC, stem cell.

Extended Data Fig. 5 Tumorigenesis in the mini-colon leads to enhanced RTK signalling promoting growth factor independence.

a , Gene interaction network of the overlapping genes that are upregulated in AKP lines with high-proliferation potential in BM (“in vivo AKP”, “mini-colon AKP” #v) when compared to low-growth counterparts (“organoid AKP”, “mini-colon AKP” #i). Network hubs are highlighted with circles. b , Brightfield images of “mini-colon AKP” #v organoids cultured for 3 days with the indicated media and compounds. Scale bar, 200 μm. c , Metabolic activity (measured using resazurin) of “mini-colon AKP” #v organoids cultured in the indicated conditions. * P  = 0.0236; *** P  < 0.0001 (two-way ANOVA and Sidak’s multiple comparisons test; n  = 4 cultures for infigranib and 8 for the rest of conditions). d , Brightfield images of “organoid AKP” cells cultured for 3 days in BM with the indicated growth factors. Scale bar, 200 μm. e , Metabolic activity (measured using resazurin) of “organoid AKP” cells cultured in the indicated conditions. *** P  < 0.0001 (two-way ANOVA and Sidak’s multiple comparisons test; n  = 8 cultures for each condition). In c and e , each point represents one well of organoids and data represent mean ± SEM.

Extended Data Fig. 6 Mini-colons comprise a complex cellular ecosystem.

a , Expression distribution of cell–type-specific markers across mini-colon cells. Cell-type labels can be found in Fig. 3b . b , Examples of single-cell RNA reads capturing exon-exon junctions that reveal the expected oncogenic recombination in Apc . c , Examples of single-cell RNA reads capturing exon-exon junctions that reveal the expected oncogenic recombination in Trp53 . d , Unsupervised UMAP clustering of the main cell types found in each of the healthy and tumour clonal populations found within the mini-colon. Tumour clones carry the “CRC” label. UMAP structure corresponds to the one shown in Fig. 3b .

Extended Data Fig. 7 Mini-colons display intra- and inter-tumour diversity.

a , Expression distribution of proliferation ( Mki67 ), stemness ( Cd44 ), and differentiation ( Krt20 ) markers within a single clonal tumour population. b , Heatmap of the genes showing the strongest ( P  < 10 −5 ) differential expression across mini-colon tumours. The tumour clonal population is indicated on top. c , Expression of the indicated genes in the indicated tumour clones. *** P  = 2.74·10 −14 ( Slpi , clone #1), 4.06·10 −50 ( Prdm16 , clone #14), 1.05·10 −13 ( Aqp5 , clone #25) (two-sided Wilcoxon rank-sum test; n  = 540 cells). Each point represents one cell. d , Immunofluorescence images showing the expression of Il1a (left, green), Cdkn2a (right, red), and the presence of nuclei (cyan) in tumour-bearing and control mini-colons. White and grey arrowheads indicate positive and negative tumours, respectively, in terms of marker expression. Scale bar, 100 μm.

Extended Data Fig. 8 The tumour heterogeneity in the mini-colon is relatable to the human context.

a , Expression distribution of intrinsic consensus molecular subtype (iCMS) signatures across tumour cells in the mini-colon. Cell-type labels can be found in Fig. 3d . Exp, expression. b , Fraction of cells within each tumour clone in the mini-colon classified in each iCMS group. c , Survival of CRC patients from the TCGA database according to the expression of the indicated tumour clone-specific markers. The logrank test P value is indicated ( n  = 375 patients). d , Presence of cancer cells in lymph nodes from CRC patients from the TCGA database according to the expression of the indicated tumour clone-specific markers. *** P  = 2.714·10 −5 (two-sided Wilcoxon test; n  = 375 patients). e , Lymph node staging in CRC patients from the TCGA database according to the expression of the indicated tumour clone-specific markers. * P  = 0.0222; ** P  = 4.923·10 −3 (two-sided Chi-squared test; n  = 375 patients).

Extended Data Fig. 9 Gpx2 regulates colonocyte stemness and tumorigenesis.

a , Multiplicity of tumours emerged in mini-colons treated with the indicated compound upon oncogenic induction. *** P  = 0.0001 (day 5), <0.0001 (all other conditions) (two-way ANOVA and Sidak’s multiple comparisons test; n  = 6 mini-colons for each condition). b , Brightfield images of colon organoids treated with the indicated compound after tumorigenic recombination. Images correspond to 3 days after induction. Scale bar, 200 μm. c , Metabolic activity (measured using resazurin) of organoids cultured in the indicated conditions and times after oncogenic recombination. No significant differences (two-way ANOVA and Sidak’s multiple comparisons test; n  = 4 cultures for each condition). d , qRT-PCR based quantitation of Gpx2 mRNA in the indicated cell lines. *** P  < 0.0001 (one-way ANOVA and Tukey’s multiple comparisons test; n  = 6, 4, and 3 organoid cultures for parental, sh Gpx2 #1, and the rest of the lines, respectively). e , Brightfield images of non-induced colon organoids of the indicated genotypes after 3 days of culture. Scale bar, 200 μm. f , Metabolic activity (measured using resazurin) of non-induced colon organoids of the indicated genotypes at the indicated times. No significant differences (two-way ANOVA and Sidak’s multiple comparisons test; n  = 6 cultures for each condition). g , Brightfield images of mini-colons of the indicated genotypes after tumorigenic recombination. Images correspond to 6 days after induction. Scale bar, 75 μm. h , Brightfield images of colon organoids of the indicated genotypes after tumorigenic recombination. Images correspond to 6 days after induction. Scale bar, 200 μm. i , Volcano plot showing the differentially expressed genes upon Gpx2 knockdown in non-transformed colon cells. j , Bubble plot showing the main enriched functional terms in the differentially expressed genes upon Gpx2 knockdown in non-transformed colon cells. Significant terms are highlighted in either blue (downmodulated) or red (upmodulated) (one-sided Fisher’s exact test, adjusted P values). k , Enrichment of the indicated hallmark signatures from the MSigDB in the indicated cell lines. ** P  = 0.0013; *** P  = 0.0008 (Wnt), 0.0003 (EMT, before recombination), <0.0001 (all other conditions); NS, not significant (one-way ANOVA and Tukey’s multiple comparisons test; n  = 3 cultures for each condition). l , Colony assay images of non-induced colon organoids of the indicated genotypes after 3 days of culture in the indicated media conditions. Scale bar, 200 μm. m , Clonogenic capacity of non-induced colon organoids of the indicated genotypes after 3 days of culture in the indicated media conditions. * P  = 0.0219; ** P  = 0.0012 (EN, sh Gpx2 #3), 0.0036 (BMGF, sh Gpx2 #1); *** P  < 0.0001 (two-way ANOVA and Dunnet’s multiple comparisons test; n  = 3 cultures for each condition). n , Brightfield images of Gpx2 knockdown mini-colons that had undergone the indicated pre-treatment before tumorigenic recombination. Images correspond to 7 days after tumour induction. Scale bar, 75 μm. In a , c , d , f , k , and m , each point represents one well of organoids and data represent mean ± SEM.

Extended Data Fig. 10 Mini-colons provide experimental versatility and resolution to tumorigenic studies.

a , Brightfield images of colon organoids treated with the indicated bacterial metabolites. Images correspond to 5 days after oncogenic induction. Scale bar, 200 μm. b , Schematic of the experimental setup used to evaluate the relevance of luminal access in tumorigenic studies. c , Brightfield images of mini-colons treated with the indicated diets according to experimental setup displayed in panel b (left). Images correspond to 6 days after tumorigenic induction. Scale bar, 75 μm. d , Multiplicity of tumours emerged in mini-colons treated with the indicated diets according to experimental setup displayed in panel b (left). *** P  = 0.0001 (day 7), <0.0001 (days 6 and 8) (two-way ANOVA and Sidak’s multiple comparisons test; n  = 4 and 3 mini-colons for calorie-restricted and -enriched diets, respectively). e , Brightfield images of mini-colons treated with the indicated diets according to experimental setup displayed in panel b (right). Images correspond to 6 days after tumorigenic induction. Scale bar, 75 μm. f , Multiplicity of tumours emerged in mini-colons treated with the indicated diets according to experimental setup displayed in panel b (right). Differences are not significant (two-way ANOVA and Sidak’s multiple comparisons test; n  = 4 and 3 mini-colons for calorie-restricted and -enriched diets, respectively). g , Brightfield image of a healthy (non-transformed) mini-colon with integrated stromal cells in the extracellular matrix. Scale bar, 75 μm. h , Immunofluorescence image showing the presence of E-cadherin (green) and Vimentin (magenta) in the mini-colon shown in panel g. Scale bar, 75 μm. i , Brightfield images of mini-colons in the indicated mono- (left) and co-culture (right) setups. Images correspond to 6 days after tumorigenic induction. Scale bar, 75 μm. j , Brightfield image of an invasive front (arrowhead) formed in response to the presence of stromal cells in a mini-colon. The image corresponds to 6 days after tumorigenic induction (zoomed-in from panel i). Scale bar, 30 μm. k , Immunofluorescence image showing the presence of E-cadherin (green) and Vimentin (magenta) in the invasive front from panel j 23 days after tumorigenic induction. Scale bar, 20 μm. In d and f , data represent mean ± SEM.

Supplementary information

Reporting summary, supplementary table 1.

Differentially expressed genes in shGpx2 colon organoids before oncogenic recombination.

Supplementary Table 2

Differentially expressed genes in shGpx2 colon organoids after oncogenic recombination

Supplementary Video 1

Early response to oncogenic activation within a mini-colon. 46 h time-lapse video of mutated cells in a mini-colon 24 h after oncogenic recombination.

Supplementary Video 2

Hyperplasia and early tumour development in a mini-colon. 36 h time-lapse video of a mini-colon with multiple tumour-initiating events 5 days after oncogenic recombination.

Supplementary Video 3

Ex vivo tumour development in a mini-colon. 38 h time-lapse video of tumour development in a mini-colon 9 days after oncogenic recombination.

Supplementary Video 4

Cancer stem cells initiate tumour development in mini-colons. 3D visualization of cancer stem cell marker CD44 overexpression in early tumorigenic sites.

Supplementary Video 5

Intratumour complexity in mini-colons. 3D visualization of CD44 (cancer stem cell marker) and FABP1 (mature colonocyte marker) expression in mini-colon tumours and epithelium.

Source data

Source data fig. 1, source data fig. 2, source data fig. 3, source data fig. 4, source data extended data fig. 1, source data extended data fig. 2, source data extended data fig. 3, source data extended data fig. 4, source data extended data fig. 5, source data extended data fig. 8, source data extended data fig. 9, source data extended data fig. 10, rights and permissions.

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ .

Reprints and permissions

About this article

Cite this article.

Lorenzo-Martín, L.F., Hübscher, T., Bowler, A.D. et al. Spatiotemporally resolved colorectal oncogenesis in mini-colons ex vivo. Nature (2024). https://doi.org/10.1038/s41586-024-07330-2

Download citation

Received : 02 February 2023

Accepted : 18 March 2024

Published : 24 April 2024

DOI : https://doi.org/10.1038/s41586-024-07330-2

Share this article

Anyone you share the following link with will be able to read this content:

Sorry, a shareable link is not currently available for this article.

Provided by the Springer Nature SharedIt content-sharing initiative

This article is cited by

Mini-colon and brain 'organoids' shed light on cancer and other diseases.

• Sara Reardon

Nature (2024)

By submitting a comment you agree to abide by our Terms and Community Guidelines . If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Quick links

• Explore articles by subject
• Guide to authors
• Editorial policies

Sign up for the Nature Briefing: Cancer newsletter — what matters in cancer research, free to your inbox weekly.

• Category: AI

Tiny but mighty: The Phi-3 small language models with big potential

• Sally Beatty

Sometimes the best way to solve a complex problem is to take a page from a children’s book. That’s the lesson Microsoft researchers learned by figuring out how to pack more punch into a much smaller package.

Last year, after spending his workday thinking through potential solutions to machine learning riddles, Microsoft’s Ronen Eldan was reading bedtime stories to his daughter when he thought to himself, “how did she learn this word? How does she know how to connect these words?” 

That led the Microsoft Research machine learning expert to wonder how much an AI model could learn using only words a 4-year-old could understand – and ultimately to an innovative training approach that’s produced a new class of more capable small language models that promises to make AI more accessible to more people.

Large language models (LLMs) have created exciting new opportunities to be more productive and creative using AI.  But their size means they can require significant computing resources to operate. 

While those models will still be the gold standard for solving many types of complex tasks, Microsoft has been developing a series of small language models (SLMs) that offer many of the same capabilities found in LLMs but are smaller in size and are trained on smaller amounts of data.

The company announced today the Phi-3 family of open models , the most capable and cost-effective small language models available. Phi-3 models outperform models of the same size and next size up across a variety of benchmarks that evaluate language, coding and math capabilities, thanks to training innovations developed by Microsoft researchers.

Microsoft is now making the first in that family of more powerful small language models publicly available: Phi-3-mini , measuring 3.8 billion parameters, which performs better than models twice its size, the company said.

Starting today, it will be available in the Microsoft Azure AI Model Catalog and on Hugging Face , a platform for machine learning models, as well as Ollama , a lightweight framework for running models on a local machine. It will also be available as an NVIDIA NIM  microservice with a standard API interface that can be deployed anywhere. 

Microsoft also announced additional models to the Phi-3 family are coming soon to offer more choice across quality and cost. Phi-3-small (7 billion parameters) and Phi-3-medium (14 billion parameters) will be available in the Azure AI Model Catalog and other model gardens shortly. 

Small language models are designed to perform well for simpler tasks, are more accessible and easier to use for organizations with limited resources and they can be more easily fine-tuned to meet specific needs. 

“What we’re going to start to see is not a shift from large to small, but a shift from a singular category of models to a portfolio of models where customers get the ability to make a decision on what is the best model for their scenario,” said Sonali Yadav, principal product manager for Generative AI at Microsoft.

“Some customers may only need small models, some will need big models and many are going to want to combine both in a variety of ways,” said Luis Vargas, vice president of AI at Microsoft.

Choosing the right language model depends on an organization’s specific needs, the complexity of the task and available resources. Small language models are well suited for organizations looking to build applications that can run locally on a device (as opposed to the cloud) and where a task doesn’t require extensive reasoning or a quick response is needed.

Large language models are more suited for applications that need orchestration of complex tasks involving advanced reasoning, data analysis and understanding of context.  

Small language models also offer potential solutions for regulated industries and sectors that encounter situations where they need high quality results but want to keep data on their own premises, said Yadav. 

Vargas and Yadav are particularly excited about the opportunities to place more capable SLMs on smartphones and other mobile devices that operate “at the edge,” not connected to the cloud. (Think of car computers, PCs without Wi-Fi, traffic systems, smart sensors on a factory floor, remote cameras or devices that monitor environmental compliance.) By keeping data within the device, users can “minimize latency and maximize privacy,” said Vargas. 

Latency refers to the delay that can occur when LLMs communicate with the cloud to retrieve information used to generate answers to users prompts. In some instances, high-quality answers are worth waiting for while in other scenarios speed is more important to user satisfaction.

Because SLMs can work offline, more people will be able to put AI to work in ways that haven’t previously been possible, Vargas said. 

For instance, SLMs could also be put to use in rural areas that lack cell service. Consider a farmer inspecting crops who finds signs of disease on a leaf or branch. Using a SLM with visual capability, the farmer could take a picture of the crop at issue and get immediate recommendations on how to treat pests or disease.  

“If you are in a part of the world that doesn’t have a good network,” said Vargas, “you are still going to be able to have AI experiences on your device.”    

The role of high-quality data  

Just as the name implies, compared to LLMs, SLMs are tiny, at least by AI standards. Phi-3-mini has “only” 3.8 billion parameters – a unit of measure that refers to the algorithmic knobs on a model that help determine its output. By contrast, the biggest large language models are many orders of magnitude larger.

The huge advances in generative AI ushered in by large language models were largely thought to be enabled by their sheer size. But the Microsoft team was able to develop small language models that can deliver outsized results in a tiny package. This breakthrough was enabled by a highly selective approach to training data – which is where children’s books come into play.

To date, the standard way to train large language models has been to use massive amounts of data from the internet. This was thought to be the only way to meet this type of model’s huge appetite for content, which it needs to “learn” to understand the nuances of language and generate intelligent answers to user prompts. But Microsoft researchers had a different idea.

“Instead of training on just raw web data, why don’t you look for data which is of extremely high quality?” asked Sebastien Bubeck, Microsoft vice president of generative AI research who has led the company’s efforts to develop more capable small language models. But where to focus?

Inspired by Eldan’s nightly reading ritual with his daughter, Microsoft researchers decided to create a discrete dataset starting with 3,000 words – including a roughly equal number of nouns, verbs and adjectives. Then they asked a large language model to create a children’s story using one noun, one verb and one adjective from the list – a prompt they repeated millions of times over several days, generating millions of tiny children’s stories.

They dubbed the resulting dataset “TinyStories” and used it to train very small language models of around 10 million parameters. To their surprise, when prompted to create its own stories, the small language model trained on TinyStories generated fluent narratives with perfect grammar.

Next, they took their experiment up a grade, so to speak. This time a bigger group of researchers used carefully selected publicly-available data that was filtered based on educational value and content quality to train Phi-1. After collecting publicly available information into an initial dataset, they used a prompting and seeding formula inspired by the one used for TinyStories, but took it one step further and made it more sophisticated, so that it would capture a wider scope of data. To ensure high quality, they repeatedly filtered the resulting content before feeding it back into a LLM for further synthesizing. In this way, over several weeks, they built up a corpus of data large enough to train a more capable SLM.

“A lot of care goes into producing these synthetic data,” Bubeck said, referring to data generated by AI, “looking over it, making sure it makes sense, filtering it out. We don’t take everything that we produce.” They dubbed this dataset “CodeTextbook.” 

The researchers further enhanced the dataset by approaching data selection like a teacher breaking down difficult concepts for a student. “Because it’s reading from textbook-like material, from quality documents that explain things very, very well,” said Bubeck, “you make the task of the language model to read and understand this material much easier.”

Distinguishing between high- and low-quality information isn’t difficult for a human, but sorting through more than a terabyte of data that Microsoft researchers determined they would need to train their SLM would be impossible without help from a LLM. 

“The power of the current generation of large language models is really an enabler that we didn’t have before in terms of synthetic data generation,” said Ece Kamar, a Microsoft vice president who leads the Microsoft Research AI Frontiers Lab, where the new training approach was developed. 

Starting with carefully selected data helps reduce the likelihood of models returning unwanted or inappropriate responses, but it’s not sufficient to guard against all potential safety challenges. As with all generative AI model releases, Microsoft’s product and responsible AI teams used a multi-layered approach to manage and mitigate risks in developing Phi-3 models.

For instance, after initial training they provided additional examples and feedback on how the models should ideally respond, which builds in an additional safety layer and helps the model generate high-quality results. Each model also undergoes assessment, testing and manual red-teaming, in which experts identify and address potential vulnerabilities.

Finally, developers using the Phi-3 model family can also take advantage of a suite of tools available in Azure AI  to help them build safer and more trustworthy applications.  

Choosing the right-size language model for the right task

But even small language models trained on high quality data have limitations. They are not designed for in-depth knowledge retrieval, where large language models excel due to their greater capacity and training using much larger data sets.

LLMs are better than SLMs at complex reasoning over large amounts of information due to their size and processing power. That’s a function that could be relevant for drug discovery, for example, by helping to pore through vast stores of scientific papers, analyze complex patterns and understand interactions between genes, proteins or chemicals. 

“Anything that involves things like planning where you have a task, and the task is complicated enough that you need to figure out how to partition that task into a set of sub tasks, and sometimes sub-sub tasks, and then execute through all of those to come with a final answer … are really going to be in the domain of large models for a while,” said Vargas.

Based on ongoing conversations with customers, Vargas and Yadav expect to see some companies “offloading” some tasks to small models if the task is not too complex. 

For instance, a business could use Phi-3 to summarize the main points of a long document or extract relevant insights and industry trends from market research reports. Another organization might use Phi-3 to generate copy, helping create content for marketing or sales teams such as product descriptions or social media posts. Or, a company might use Phi-3 to power a support chatbot to answer customers’ basic questions about their plan, or service upgrades.    

Internally, Microsoft is already using suites of models, where large language models play the role of router, to direct certain queries that require less computing power to small language models, while tackling other more complex requests itself.

“The claim here is not that SLMs are going to substitute or replace large language models,” said Kamar. Instead, SLMs “are uniquely positioned for computation on the edge, computation on the device, computations where you don’t need to go to the cloud to get things done. That’s why it is important for us to understand the strengths and weaknesses of this model portfolio.”

And size carries important advantages. There’s still a gap between small language models and the level of intelligence that you can get from the big models on the cloud, said Bubeck. “And maybe there will always be a gap because you know – the big models are going to keep making progress.”

Related links:

• Read more: Introducing Phi-3, redefining what’s possible with SLMs
• Learn more: Azure AI
• Read more: Phi-3 Technical Report: A Highly Capable Language Model Locally on Your Phone

Top image: Sebastien Bubeck, Microsoft vice president of Generative AI research who has led the company’s efforts to develop more capable small language models. (Photo by Dan DeLong for Microsoft)

Help | Advanced Search

Computer Science > Computation and Language

Title: phi-3 technical report: a highly capable language model locally on your phone.

Abstract: We introduce phi-3-mini, a 3.8 billion parameter language model trained on 3.3 trillion tokens, whose overall performance, as measured by both academic benchmarks and internal testing, rivals that of models such as Mixtral 8x7B and GPT-3.5 (e.g., phi-3-mini achieves 69% on MMLU and 8.38 on MT-bench), despite being small enough to be deployed on a phone. The innovation lies entirely in our dataset for training, a scaled-up version of the one used for phi-2, composed of heavily filtered web data and synthetic data. The model is also further aligned for robustness, safety, and chat format. We also provide some initial parameter-scaling results with a 7B and 14B models trained for 4.8T tokens, called phi-3-small and phi-3-medium, both significantly more capable than phi-3-mini (e.g., respectively 75% and 78% on MMLU, and 8.7 and 8.9 on MT-bench).

Submission history

Access paper:.

• HTML (experimental)
• Other Formats

References & Citations

• Google Scholar
• Semantic Scholar

BibTeX formatted citation

Bibliographic and Citation Tools

Code, data and media associated with this article, recommenders and search tools.

• Institution

arXivLabs: experimental projects with community collaborators

arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website.

Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them.

Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs .

AI + Machine Learning , Announcements , Azure AI , Azure AI Studio

Introducing Phi-3: Redefining what’s possible with SLMs

By Misha Bilenko Corporate Vice President, Microsoft GenAI

Posted on April 23, 2024 4 min read

• Tag: Copilot
• Tag: Generative AI

We are excited to introduce Phi-3, a family of open AI models developed by Microsoft. Phi-3 models are the most capable and cost-effective small language models (SLMs) available, outperforming models of the same size and next size up across a variety of language, reasoning, coding, and math benchmarks. This release expands the selection of high-quality models for customers, offering more practical choices as they compose and build generative AI applications.

Starting today, Phi-3-mini , a 3.8B language model is available on Microsoft Azure AI Studio , Hugging Face , and Ollama . 

• Phi-3-mini is available in two context-length variants—4K and 128K tokens. It is the first model in its class to support a context window of up to 128K tokens, with little impact on quality.
• It is instruction-tuned, meaning that it’s trained to follow different types of instructions reflecting how people normally communicate. This ensures the model is ready to use out-of-the-box.
• It is available on Azure AI to take advantage of the deploy-eval-finetune toolchain, and is available on Ollama for developers to run locally on their laptops.
• It has been optimized for ONNX Runtime with support for Windows DirectML along with cross-platform support across graphics processing unit (GPU), CPU, and even mobile hardware.
• It is also available as an NVIDIA NIM microservice with a standard API interface that can be deployed anywhere. And has been optimized for NVIDIA GPUs . 

In the coming weeks, additional models will be added to Phi-3 family to offer customers even more flexibility across the quality-cost curve. Phi-3-small (7B) and Phi-3-medium (14B) will be available in the Azure AI model catalog and other model gardens shortly.   

Microsoft continues to offer the best models across the quality-cost curve and today’s Phi-3 release expands the selection of models with state-of-the-art small models.

Azure AI Studio

Phi-3-mini is now available

Groundbreaking performance at a small size 

Phi-3 models significantly outperform language models of the same and larger sizes on key benchmarks (see benchmark numbers below, higher is better). Phi-3-mini does better than models twice its size, and Phi-3-small and Phi-3-medium outperform much larger models, including GPT-3.5T.  

All reported numbers are produced with the same pipeline to ensure that the numbers are comparable. As a result, these numbers may differ from other published numbers due to slight differences in the evaluation methodology. More details on benchmarks are provided in our technical paper . 

Note: Phi-3 models do not perform as well on factual knowledge benchmarks (such as TriviaQA) as the smaller model size results in less capacity to retain facts.  

Safety-first model design 

Responsible ai principles

Phi-3 models were developed in accordance with the Microsoft Responsible AI Standard , which is a company-wide set of requirements based on the following six principles: accountability, transparency, fairness, reliability and safety, privacy and security, and inclusiveness. Phi-3 models underwent rigorous safety measurement and evaluation, red-teaming, sensitive use review, and adherence to security guidance to help ensure that these models are responsibly developed, tested, and deployed in alignment with Microsoft’s standards and best practices.  

Building on our prior work with Phi models (“ Textbooks Are All You Need ”), Phi-3 models are also trained using high-quality data. They were further improved with extensive safety post-training, including reinforcement learning from human feedback (RLHF), automated testing and evaluations across dozens of harm categories, and manual red-teaming. Our approach to safety training and evaluations are detailed in our technical paper , and we outline recommended uses and limitations in the model cards. See the model card collection .  

Unlocking new capabilities 

Microsoft’s experience shipping copilots and enabling customers to transform their businesses with generative AI using Azure AI has highlighted the growing need for different-size models across the quality-cost curve for different tasks. Small language models, like Phi-3, are especially great for: 

• Resource constrained environments including on-device and offline inference scenarios.
• Latency bound scenarios where fast response times are critical.
• Cost constrained use cases, particularly those with simpler tasks.

For more on small language models, see our Microsoft Source Blog .

Thanks to their smaller size, Phi-3 models can be used in compute-limited inference environments. Phi-3-mini, in particular, can be used on-device, especially when further optimized with ONNX Runtime for cross-platform availability. The smaller size of Phi-3 models also makes fine-tuning or customization easier and more affordable. In addition, their lower computational needs make them a lower cost option with much better latency. The longer context window enables taking in and reasoning over large text content—documents, web pages, code, and more. Phi-3-mini demonstrates strong reasoning and logic capabilities, making it a good candidate for analytical tasks. 

Customers are already building solutions with Phi-3. One example where Phi-3 is already demonstrating value is in agriculture, where internet might not be readily accessible. Powerful small models like Phi-3 along with Microsoft copilot templates are available to farmers at the point of need and provide the additional benefit of running at reduced cost, making AI technologies even more accessible.  

ITC, a leading business conglomerate based in India, is leveraging Phi-3 as part of their continued collaboration with Microsoft on the copilot for Krishi Mitra, a farmer-facing app that reaches over a million farmers.

“ Our goal with the Krishi Mitra copilot is to improve efficiency while maintaining the accuracy of a large language model. We are excited to partner with Microsoft on using fine-tuned versions of Phi-3 to meet both our goals—efficiency and accuracy! ”    Saif Naik, Head of Technology, ITCMAARS

Originating in Microsoft Research, Phi models have been broadly used, with Phi-2 downloaded over 2 million times. The Phi series of models have achieved remarkable performance with strategic data curation and innovative scaling. Starting with Phi-1, a model used for Python coding, to Phi-1.5, enhancing reasoning and understanding, and then to Phi-2, a 2.7 billion-parameter model outperforming those up to 25 times its size in language comprehension. 1 Each iteration has leveraged high-quality training data and knowledge transfer techniques to challenge conventional scaling laws. 

Get started today 

To experience Phi-3 for yourself, start with playing with the model on Azure AI Playground . You can also find the model on the Hugging Chat playground . Start building with and customizing Phi-3 for your scenarios using the  Azure AI Studio . Join us to learn more about Phi-3 during a special  live stream of the AI Show.  

1 Microsoft Research Blog, Phi-2: The surprising power of small language models, December 12, 2023 .

Let us know what you think of Azure and what you would like to see in the future.

Provide feedback

Build your cloud computing and Azure skills with free courses by Microsoft Learn.

Explore Azure learning

Related posts

AI + Machine Learning , Azure AI , Azure AI Content Safety , Azure Cognitive Search , Azure Kubernetes Service (AKS) , Azure OpenAI Service , Customer stories

AI-powered dialogues: Global telecommunications with Azure OpenAI Service   chevron_right

AI + Machine Learning , Azure AI , Azure AI Content Safety , Azure OpenAI Service , Customer stories

Generative AI and the path to personalized medicine with Microsoft Azure   chevron_right

AI + Machine Learning , Azure AI , Azure AI Services , Azure AI Studio , Azure OpenAI Service , Best practices

AI study guide: The no-cost tools from Microsoft to jump start your generative AI journey   chevron_right

AI + Machine Learning , Azure AI , Azure VMware Solution , Events , Microsoft Copilot for Azure , Microsoft Defender for Cloud

Get ready for AI at the Migrate to Innovate digital event   chevron_right

First ever 2nd Year Symposium is complete!

Congratulations to our 2nd year graduate students on their presentations in our first ever 2nd Year Symposium. The event offers the students an opportunity to present and receive feedback on the research for their theses/2nd year papers. Topics included experiences of Black women in healthcare, public education activism, LGBTQ+ victimhood, medical avoidance after incarceration, responses to masculinity challenges, Bangladeshi women's clothing decisions and racial gray zones.

All of us in Sociology are proud of the effort and hard work Liv, Natalia, Ben, Dereika, Emily, Saifa and Maddy have been putting in!

Google Map Phone: (706) 542-2421  

Mini-colons revolutionize colorectal cancer research

As our battle against cancer rages on, the quest for more sophisticated and realistic models to study tumor development has never been more critical. Until now, research has relied on animal models and simplified cell culture methods, which are valuable but cannot fully capture the complex interplay of factors involved in tumor development.

Even newer, more advanced models for studying cancer, such as organoids -- tiny, lab-grown versions of organs -- do not faithfully replicate the cell behaviors and tissue architectures seen in actual tumors.

This gap has significantly hindered our understanding of the intricate processes underlying cancer initiation, progression, and response to treatment, and calls for more sophisticated models to accurately mimic the disease's complexity.

In a significant leap forward for cancer modeling, scientists have combined microfabrication and tissue engineering techniques to develop miniature colon tissues that can simulate the complex process of tumorigenesis outside the body with high fidelity, giving rise to tumors that closely resemble those found in vivo .

The breakthrough, now published in Nature , was made by Luis Francisco Lorenzo Martín, Tania Hübscher and other members of the group of Matthias Lütolf at EPFL, with input from the group of Freddy Radtke (EPFL) and colleagues at Roche's Institute of Human Biology.

The mini-colons are topobiologically complex, meaning that they not only replicate the physical structure of colon tissue, including its distinctive crypt-and-lumen architecture, but they also mimic the cellular diversity present in the actual colon tissue during healthy and diseased states.

Optogenetics: Turning cancer "on"

Another important feature of the mini-colons is that they can be induced to develop tumors "at will" and in targeted areas -- a massive advantage for cancer research. The researchers were able to turn inducible oncogenic genes on using "optogenetics." This cutting-edge technique uses light to control biological processes such as gene expression.

By integrating a blue-light-responsive system into the mini-colons, the researchers made them undergo controlled oncogenic mutations, which can reveal tumor evolution with unprecedented details. This optogenetic approach allowed the scientists to induce targeted changes in specific cell populations within the mini-colons, mimicking the localized onset of colorectal cancer in the body.

"In essence, we used light to trigger tumorigenesis by turning on oncogenic driver mutations in a spatiotemporally controlled manner in healthy bioengineered colon epithelial organoids," says Matthias Lütolf, who is also the founding director of Roche's new Institute of Human Biology. "This basically allows you to watch tumor formation in real-time and do very detailed analyses of a process that's very difficult to study in a mouse."

The ability to trigger these genetic changes with light in the miniature colons not only allows more controlled and more precise activation of the oncogenes, but also provides a powerful tool to study the dynamic processes of tumor development and the cellular response to these mutations in real-time. This innovative use of optogenetics opens up new possibilities for dissecting the molecular and cellular mechanisms of cancer.

By manipulating genetic and environmental conditions, the researchers were also able to replicate and observe a range of tumor behaviors in the mini-colons, and even identified key factors influencing cancer progression -- for example, the protein GPX2, which associated with stem cell characteristics and tumor growth.

This groundbreaking research offers a potent new tool for exploring the underlying mechanisms of colorectal cancer and testing potential therapies, particularly when applied to human patient-derived tissues. The mini-colons' ability to mimic tumor dynamics can reduce our reliance on animal models, which can accelerate the discovery and development of effective treatments.

• Colon Cancer
• Brain Tumor
• Lung Cancer
• Ovarian Cancer
• Breast Cancer
• Prostate Cancer
• Colorectal cancer
• Stem cell treatments
• Esophageal cancer
• Double blind
• Positron emission tomography
• Breast cancer

Story Source:

Materials provided by Ecole Polytechnique Fédérale de Lausanne . Original written by Nik Papageorgiou. The original text of this story is licensed under Creative Commons CC BY-SA 4.0 . Note: Content may be edited for style and length.

Journal Reference :

• L. Francisco Lorenzo-Martín, Tania Hübscher, Amber D. Bowler, Nicolas Broguiere, Jakob Langer, Lucie Tillard, Mikhail Nikolaev, Freddy Radtke, Matthias P. Lutolf. Spatiotemporally resolved colorectal oncogenesis in mini-colons ex vivo . Nature , 2024; DOI: 10.1038/s41586-024-07330-2

Cite This Page :

Explore More

• Mice Given Mouse-Rat Brains Can Smell Again
• New Circuit Boards Can Be Repeatedly Recycled
• Collisions of Neutron Stars and Black Holes
• Advance in Heart Regenerative Therapy
• Bioluminescence in Animals 540 Million Years Ago
• Profound Link Between Diet and Brain Health
• Loneliness Runs Deep Among Parents
• Food in Sight? The Liver Is Ready!
• Acid Reflux Drugs and Risk of Migraine
• Do Cells Have a Hidden Communication System?

Trending Topics

Strange & offbeat.