New Medical Study Results: AIP Can Change Gene Expression

We’ve been waiting and waiting . . . and waiting to share the newest and absolutely incredible AIP medical study results. Every time AIP medical study results come in we have a hard time keeping our mouths shut here at Autoimmune Wellness! The results of a sub-study focused on gene expression, conducted under the original AIP medical study on the Autoimmune Protocol and inflammatory bowel disease (Crohn’s and ulcerative colitis), are out, published by the journal Crohn’s & Colitis 360, and available for everyone to read for free! If you’d like to read the full article now, you can find it here.

How did we get involved in this AIP medical study?

In December of 2015, we were contacted by Dr. Gauree Konijeti, the Director of the Inflammatory Bowel Disease Program Division of Gastroenterology at Scripps Clinic in La Jolla, California. Dr. Konijeti explained that she’d like to undertake a medical study of AIP to evaluate its potential efficacy for patients with Crohn’s and ulcerative colitis. She asked if Angie’s online group health coaching program, SAD to AIP in SIX, could be used to help the study participants transition to AIP. Our answer, of course, was, “YES!!”

Medical studies take lots of time, planning, and money to get off the ground, but those original results were finally published in 2017. From that original study, Dr. Konijeti and her team undertook several sub-studies to extend the data that was collected, including the one we are sharing here on whether dietary changes could influence genetic expression.

What was studied?

This study focused on four participants who were part of the original study and who all had active ulcerative colitis. Before the study began, each participant underwent procedures to take colon tissue biopsies from the outer layer of the intestine known as the mucosa. Using the specialized tissue biopsies, the scientists then assessed the level of expression of specific genes known as RNA expression to see if there were any unique patterns amongst the individuals with ulcerative colitis. Following the completion of the AIP intervention, the scientists collected a second set of mucosal tissue biopsies in order to evaluate any changes in genetic expression from the beginning to the end of the study. To the knowledge of the research team, this was the first study ever conducted looking at changes in mucosal RNA expression during dietary therapy in patients with active IBD.

What were the results of this gene expression study?

The language and study of gene expression is by no means a simple matter, but the long and short of it is that AIP modifies intestinal RNA expression in IBD! Incredible! Here are some highlights on what was found:

  1. A total of 324 significant differentially regulated genes were found following the AIP intervention.
  2. Of those 324 differentially regulated genes, 167 were downregulated, showing signs of decreased genetic expression while 157 were upregulated, showing signs of increased genetic expression.
  3. There were genetic changes associated with downregulation of inflammatory T-cell-mediated responses that likely represented a decreased autoimmune inflammatory response.
  4. There were genetic changes associated with an increased regulatory T-cell response that likely represented positive modulation of the autoimmune inflammatory response.
  5. There was also upregulation of transcriptional pathways associated with the inflammatory response involving mucosal healing including DNA repair that suggested positive restoration of cellular integrity and function.
  6. These results suggest dietary elimination with an emphasis on nutrient-density, can positively modulate inflammation and reduce symptoms in IBD.

To learn in-depth about the study methods, measures, analysis, and results, you can access the full article here.

What does this mean?

Many of you have likely heard that “genes are not your destiny” and it is actually gene expression which truly reflects the health of an organism. This groundbreaking study is scientific validation that dietary and lifestyle protocols, like AIP, can influence our genetic expression! In the future, with even greater research addressing some of the limitations of these promising early findings, we will be able to change the standard of care for those with autoimmune disease. Your voice and support of this research is making it a reality.

About Angie Alt

Angie Alt is a co-founder here at Autoimmune Wellness. She helps others take charge of their health the same way she took charge of her own after suffering with celiac disease, endometriosis, and lichen sclerosis; one nutritious step at a time. Her special focus is on mixing “data with soul” by looking at the honest heart of the autoimmune journey (which sometimes includes curse words). She is a Certified Health Coach through the Institute for Integrative Nutrition, Nutritional Therapy Consultant through The Nutritional Therapy Association and author of The Alternative Autoimmune Cookbook: Eating for All Phases of the Paleo Autoimmune Protocol and The Autoimmune Wellness Handbook. You can also find her on Instagram.


  • Stephanie says

    Yes! I am 34 and since starting AIP years ago, I noticed a small cleft in my chin appear. My grandparents and great grandparents had cleft chins. I never before have had a cleft chin, until now. It is very slight and I only notice it if I move my face or smile a certain way, but it is interesting!

    • Angie Alt says

      Whoa! Really interesting, Stephanie!

    • Mickey Trescott says

      Stephanie – this is so interesting! Thanks for sharing!

  • Heidi H says

    Thank you Angie!
    This was very encouraging since I have been experiencing ibs symptoms and also for the first time high cholesterol. I’m hoping with Real Meal plans as well as AIP, I’ll be able to get my health back and maybe keep it that way!!
    Thank you for all that you and Micky do for the community!!

  • Barbara says

    Hi Ladies,
    I have Mixed Connective Tissue Disease. My primary symptoms are from systemic scleroderma, and polymyositis. My question is about collagen and bone broth………in both AIP and Paleo, both of these are highly praised for autoimmune disease and healing of the gut. However, do you still recommend this for those of us with scleroderma? Our bodies overproduce this substance and create scar tissue with it. Just wondering about your take on it as I’ve never seen it addressed before.
    Thank you!

    • Mickey Trescott says

      Hi Barbara! Thanks for the question! We don’t have any specific guidance in this situation, but many folks customize AIP to work with specifics of their conditions (for instance, lower protein for kidney issues). It is best to have a chat with a doctor or knowledgeable practitioner about your specific case, but I could see running a trial of no/low collagen/broth to see if it expands healing for you. My gut is that lowering inflammation and dampening the autoimmune response may be more productive than depriving your body of the raw materials that are needed to create tissue (and needed by other systems and processes in the body!), but I am not a doctor so I can’t give that specific advice. At any rate, let us know what you learn as I am sure you are not the only one out there with this idea!

Leave a Comment