AI and the Future of IBD Treatment Under the Microscope
Harnessing Artificial Intelligence for be er patient outcomes
Foundation at the Forefront of Machine Learning
Artificial intelligence (AI) and machine learning aren’t just tech tools, they’re transformative forces in IBD research helping the Foundation extract insights from vast amounts of data that, before today, would’ve been too daunting and expensive for humans alone to make meaning of.
Alan Moss, MD, chief scientific officer at the Foundation, has seen it happen in practice with IBD Plexus®, the Foundation’s revolutionary research pla orm that gathers and shares data from IBD patients to help scientists and researchers accelerate treatment discoveries. IBD Plexus is capable of collecting a patient’s medical record, but it’s currently very labor-intensive to hand-search medical records to extract targeted data such as whether a patient on drug X had pneumonia at a greater rate than a patient on drug Y.
“But with AI—particularly the language models—we have the opportunity to basically scrape the entire record and say, ‘Here are all the people who had pneumonia, and here’s a pa ern of pneumonia and drug exposure,’” says Moss of information that would otherwise go missed. “We’ve already spoken with partners who have shown us that they can do it, so it’s not just a hypothetical. It’s entirely within our reach.”
The Crohn’s & Colitis Foundation has been leveraging AI across research initiatives for the past six years. From our new IBD Plexus partnership with CytoReason, to the Foundation’s AI-driven biomarker discoveries, to investing in personalized nutrition research, to making it easier to evaluate colonoscopy images, AI in IBD research is exciting and filled with promise. The following highlights showcase our commitment to AI and machine learning-driven innovation as we advance IBD research.
Alan Moss
PRECISION MEDICINE
Data + AI Answers Patient Question, ‘Which Treatment Might Work For Me?’
Our new IBD Plexus® strategic collaboration with CytoReason represents an important milestone in the Foundation’s commitment to play a larger role in advancing life-changing precision medicine strategies. According to Angela Dobes, senior vice president of IBD Plexus, combining CytoReason’s AIpowered disease models with IBD Plexus’ extensive real-world longitudinal data will help ignite the development of smarter therapies, creating a more effective treatment “playbook” for IBD by be er stratifying and subtyping patients based on their disease characteristics and detailed biological information.
“IBD Plexus offers researchers a nuanced understanding of IBD activity,” says Dobes. “With over a decade of comprehensive clinical data on the patient journey linked to molecular data generated from biosamples, we are be er equipped to understand flare-ups and disease progression, which helps doctors provide more effective medication management strategies for patients.”
“The power of AI in drug discovery and development is o en limited by the scarcity of high-quality, relevant data needed to understand complex disease mechanisms,” continues Dobes. “By equipping AI-powered disease models with IBD Plexus’ superior data, we empower researchers to advance discoveries that could alleviate patients’ symptoms, restore their gut health, and prevent their disease from progressing. It’s a precision approach that could help answer the elusive patient question, ‘Which treatment might work for me?’”
AI Predicts Complications and Treatment Response In Pediatric Crohn’s PRECLINICAL HUMAN MECHANISMS
A five-year study led by the Foundation’s Andrés Hurtado-Lorenzo, Ph.D., senior vice president of Translational Research and IBD Ventures, is demonstrating how AI and machine learning can revolutionize research by identifying biomarkers that predict complicated disease course and treatment response in pediatric Crohn’s disease patients.
As Hurtado-Lorenzo explains, following on the success of the Foundation’s funded RISK study that developed a model for prognosis of complications in pediatric Crohn’s disease merging clinical and genetic data, we have now re-analyzed the RISK data using machine learning methods. “We were able to identify 13 novel genes in gut biopsies that can prognosticate the likelihood of a child newly diagnosed with Crohn’s disease to develop complications like fistulas and fibrosis, with higher accuracy. We also identified 13 genes that predict response to anti-TNF drugs,” he adds.
Hurtado-Lorenzo says that “AI-based analysis of proteins in the blood of children from the RISK cohort led to identifying 14 proteins that can also predict future complications, making the prognostic process minimally invasive and highly accurate. We have developed a prototype test integrating these proteins in a single panel and we are in the process of submi ing patents for these discoveries to develop them into clinical tests.”
ENVIRONMENTAL TRIGGERS
AI-Driven Diet Analysis for IBD
As part of the Foundation’s precision nutrition initiative, Pieter Dorrestein, Ph.D., a professor at UC San Diego, has made groundbreaking strides in understanding the relationship between a patient’s diet and its impact on their microbiome by using AI and machine learning to identify dietary pa erns from clinical samples such as blood and stool...a process traditionally dependent on food logs, questionnaires, and dietitian-provided meals.
“We developed an approach to provide a proportional dietary readout of the samples we’re studying,” Dorrestein explains. “This is important because, within 15 minutes of consuming a meal, we can detect its signatures in the bloodstream.”
Dorrestein says machine learning plays a crucial role in this research. “We have all this biological information—sex, age, disease type, and severity— and we use machine learning to analyze it.” This analysis helps identify dietary pa erns and their relationship to a patient’s disease state (e.g., the study found that a higher diversity of fruits and vegetables correlates with a higher diversity of gut microbes, which benefits IBD patients.)
While still observational, the research offers new insights into how a patient’s diet could affect their IBD while supporting the Crohn’s & Colitis Foundation’s mission: By leveraging AI, the Foundation can work toward developing personalized nutrition plans for patients, enhancing their overall treatment and quality of life. This study is generously supported by the Leona M. and Harry B. Helmsley Charitable Trust.
AI Improves Endoscopic Diagnosis for Ulcerative Colitis
In a pilot study, funded by the Foundation’s clinical research networks and led by Ryan Stidham, MD, at the University of Michigan, researchers investigated the potential of using AI-driven technologies during colonoscopies to automate the assessment of the severity of ulcerative colitis (UC) in patients. Because the traditional method of visually inspecting the colon mucosa is subjective and can vary widely depending on healthcare providers’ experience, the study used AI models trained on extensive datasets of colonoscopy images annotated with established scoring systems, such as the Mayo endoscopic score.
The study tested whether AI could provide more consistent, objective, and readily available assessments than human experts, who sometimes have different opinions. By automating the analysis of colonoscopy videos, AI models were tested in multiple sites (Michigan and North Carolina) to predict disease severity scores accurately. This approach aimed to validate the reliability of AI-generated assessments against expert human scoring and to correlate these assessments with patient outcomes.
The findings suggested that AI-based automated scoring has the potential to standardize disease assessment practices, improve patient care, and facilitate more informed treatment decisions, particularly in regions where access to experienced IBD specialists is limited. The study represents a significant step toward integrating AI technologies into clinical practice to be er diagnose and manage UC.
Foundation Announces Five-Year Research Priorities
This spring, the Crohn’s & Colitis Foundation unveiled its new five-year research agenda , a strategic roadmap developed to set research priorities in inflammatory bowel disease (IBD) not only for the Foundation but for the entire IBD research community. Developed through a year-long collaboration between 100 researchers, clinicians, industry leaders, patients, and caregivers, our research priorities span five key areas: be er understanding IBD’s biology, identifying environmental triggers, developing personalized treatments, leveraging novel technologies, and optimizing real-world care. However, “What’s entirely novel in this new iteration of our research agenda is that we introduced two new focuses: prevention— which centers on preventing the disease in the first place—and restoration, which aims to get patients back to as close to normal functioning as possible,” says Alan Moss, MD, the Foundation’s chief scientific officer. “These additions expand our scope beyond the typical patient journey, striving to improve patient outcomes from before diagnosis to achieving a state of normalcy.”
Patients can expect an expanded research emphasis in these areas (for instance, moving beyond dietary influences to include environmental triggers like air pollution and microplastics). This shi extends from diagnostic technologies (i.e., wearables) to pioneering
Patient Story: Myisha Malone-King
Pragmatic Clinical Research
Precision Medicine
Preclinical Human IBD Mechanisms
Environmental Triggers
Novel Technologies
treatments (i.e., nano-robots aimed at tissue repair) to improve patient care through precise therapeutic approaches.
The Foundation’s research roadmap is published in our Challenges in IBD Research report, which is available on our website, crohnscolitisfoundation.org.
At the Foundation, we put patients first…involving them in everything we do and ensuring their voices are heard. Their input on our research workgroups was integral to developing our research priorities.
Myisha Malone-King is a nurse in Baltimore, Md., who brought her vibrant energy to the Foundation’s Pragmatic Clinical Research workgroup, which explores how research can use real-world observations to understand IBD be er.
“This was an exhilarating experience: I never would have imagined I would have been this involved in something so important to patients,” says
Malone-King.
Excited to learn about and provide her perspective on research that could one day help the IBD community, Malone-King shared her observations on barriers to care for patients from diverse communities. “Between my husband and me, we represent three nationalities,” she says. “I witness how different people are treated and listened to....”
More than a patient advisor, Malone-King is also a moderator in the Foundation’s online forum, a hub for patients and experts to connect, ask questions, and share stories. “I believe this experience is also shaping me into a be er patient advocate,” she says, reflecting on her journey.
Myisha Malone-King
Our Next Breakthrough Is In Your Hands
The game-changing work described in this issue of Under the Microscope is just part of how the Foundation plays a critical role in major IBD breakthroughs. Every day, we strive to redefine how scientists study IBD and accelerate the discovery of innovative therapies that offer real hope to people suffering from IBD. While our long-game vision is a world without IBD, we’re equally commi ed to supporting patients who struggle with the daily physical and emotional toll of IBD...but we can’t do any of it without you. Your gi today to the Crohn’s & Colitis Foundation will help us change the lives of those with IBD.
To contribute, please visit crohnscolitisfoundation.org/microscope.
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President’s Corporate Circle
Nothing says more about your commitment to supporting and strengthening the Crohn’s & Colitis Foundation’s vision than including us in your estate planning. As a member of the Founders Society, you will be listed in our Impact Report and receive inside information and updates on our mission advancement and research progress. If you’re interested in making a planned gi (or you have questions about how to do it), contact Susan Carriker at scarriker@crohnscolitisfoundation.org or visit crohnscolitisfoundation.org/freewill to access a free tool to help you plan your legacy gi to the Foundation.
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Thanks to all the members of our President’s Corporate Circle for their dedicated support to our mission:
AbbVie
Amgen Inc.
AstraZeneca
Boehringer Ingelheim Pharmaceuticals Inc.
Bristol Myers Squibb Company
Celltrion USA
Eli Lilly & Company
Johnson & Johnson
Merck
Pfizer
Sanofi
Takeda Pharmaceuticals USA
Teva Pharmaceuticals
The Crohn’s & Colitis Foundation is the leading nonprofit organization focused on research, education, and support for the millions of Americans affected by inflammatory bowel disease (IBD). We have played a role in every major research breakthrough in IBD and are the trusted source for IBD patients and caregivers, educating, guiding, and supporting them every step of the way.