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Publications Using GEM Project Data

Gut Microbiome Composition Is Associated With Future Onset of Crohn’s Disease in Healthy First-Degree Relatives

Research has established that the composition of bacteria residing in the gut is altered in patients with Crohn’s Disease (CD), however, whether these changes to the bacterial populations are associated with CD onset or occur as direct result of the disease or disease treatment remained unknown. To answer this question, gut bacteria populations were characterized using a machine learning approach in the healthy first-degree relatives of the GEM Project cohort. This study found that the gut bacteria composition is associated with the future onset of CD, and suggested that the bacteria residing in the gut may contribute to disease development. With this understanding, a microbiome risk score (MRS) was developed, which ranks individuals according to their risk of developing CD based on the analysis of their gut bacteria.

Raygoza Garay JA, Turpin W, Lee SH, Smith MI, Goethel A, Griffiths AM, Moayyedi P, Espin-Garcia O, Abreu M, Aumais GL, Bernstein CN, Biron IA, Cino M, Deslandres C, Dotan I, El-Matary W, Feagan B, Guttman DS, Huynh H, Dieleman LA, Hyams JS, Jacobson K, Mack D, Marshall JK, Otley A, Panaccione R, Ropeleski M, Silverberg MS, Steinhart AH, Turner D, Yerushalmi B, Paterson AD, Xu W; CCC GEM Project Research Consortium; Croitoru K. Gut Microbiome Composition is associated with future onset of Crohn’s Disease in Healthy First-Degree Relatives. Gastroenterology. 2023 May 30:S0016-5085(23)00805-3. doi: 10.1053/j.gastro.2023.05.032.


Immune response and barrier dysfunction-related proteomic signatures in preclinical phase of Crohn’s disease highlight earliest events of pathogenesis.

This study set out to elucidate the biological pathways involved in the development of Crohn’s disease (CD). In this study, proteins in the blood of healthy first-degree relatives from the GEM Project cohort were measured to see if any serum proteins were associated with future risk of CD onset. The results showed that 25 out of 466 serum proteins were significantly associated with the future development of CD, and interestingly, many of these proteins were important for immune function and gut barrier function. Taken together, this study identified serum protein signatures which are associated with future CD development and provided insight into the earliest events of disease development.

Leibovitzh H, Lee SH, Raygoza Garay JA, Espin-Garcia O, Xue M, Neustaeter A, Goethel A, Huynh HQ, Griffiths AM, Turner D, Madsen KL, Moayyedi P, Steinhart AH, Silverberg MS, Deslandres C, Bitton A, Mack DR, Jacobson K, Cino M, Aumais G, Bernstein CN, Panaccione R, Weiss B, Halfvarson J, Xu W, Turpin W, Croitoru K; Crohn’s and Colitis Canada (CCC) Genetic, Environmental, Microbial (GEM) Project Research Consortium. Immune response and barrier dysfunction-related proteomic signatures in preclinical phase of Crohn’s disease highlight earliest events of pathogenesis. Gut. 2023 Feb 14:gutjnl-2022-328421. doi: 10.1136/gutjnl-2022-328421.


Anti-Integrin αvβ6 Autoantibodies Are a Novel Biomarker That Antedate Ulcerative Colitis

There is an on-going need to identify biomarkers that can predict the occurrence and severity of IBD. Previous work reported that a molecule called anti-integrin αvβ6 (anti-αvβ6) autoantibodies are elevated in the blood of patients with ulcerative colitis (UC) compared with non-IBD individuals. In a collaboration with Dr. Livanos and Mehandru’s research team the GEM project samples were used to validate whether anti-αvβ6 autoantibodies were elevated in blood samples collected from participants before they went on to develop UC. The results showed that anti-αvβ6 autoantibodies were significantly higher in individuals who go on to develop UC compared to those who did not, and that higher levels of this molecule in the blood were associated with more severe UC outcomes. Importantly, the presence of anti-αvβ6 autoantibodies could be seen in the blood up to 10 years before a UC diagnosis. Taken together, anti-αvβ6 autoantibodies are present in the pre-clinical phase of UC and are associated with the development and worse severity of UC. This suggests that anti-αvβ6 autoantibodies are a pre-clinical and prognostic biomarker for UC.

Livanos AE, Dunn A, Fischer J, Ungaro RC, Turpin W, Lee SH, Rui S, Del Valle DM, Jougon JJ, Martinez-Delgado G, Riddle MS, Murray JA, Laird RM, Torres J, Agrawal M, Magee JS, Dervieux T, Gnjatic S, Sheppard D, Sands BE, Porter CK, Croitoru K, Petralia F; CCC-GEM Project Research Consortium; OSCCAR Consortium; Colombel JF, Mehandru S. Anti-integrin αvβ6 autoantibodies are a novel biomarker that antedate ulcerative colitis. Gastroenterology. 2023 Jan 9: S0016-5085(23)00010-0. Epub ahead of print.


Altered Gut Microbiome Composition and Function Are Associated With Gut Barrier Dysfunction in Healthy Relatives of Patients With Crohn’s Disease

This study investigated the relationship between the bacteria in the gut and their association with altered gut barrier function in healthy first-degree relatives of patients with Crohn’s disease (CD). The gut barrier plays an essential role as both a physical and functional barrier between the external environment and the host, thus regulating the entry of potentially harmful macro- and microorganisms as well as nutrients. Our research group has reported that alterations to gut barrier function is present before CD develops, but little is known about why these changes occur. This study demonstrated that in the GEM cohort, individuals with impaired gut barrier function had a different gut bacteria population compared to those with normal gut barrier function. This study is the first to find an association between the gut bacteria population and the gut barrier function in humans. We hope these findings may help to identify potential microbial targets to modulate the gut barrier.

Leibovitzh H, Lee SH, Xue M, Raygoza Garay JA, Hernandez-Rocha C, Madsen KL, Meddings JB, Guttman DS, Espin-Garcia O, Smith MI, Goethel A, Griffiths AM, Moayyedi P, Steinhart AH, Panancionne R, Huynh H, Jacobson K, Aumais G, Mack DR, Abreu M, Bernstein CN, Marshall JK, Turner D, Xu W; CCC GEM Project Research Consortium, Turpin W, Croitoru K. Altered gut microbiome composition and function are associated with gut barrier dysfunction in healthy relatives of patients with Crohn’s disease. Gastroenterology. 2022 Jul 15: 163(5):163(5):1364-1376.e10. Advance online publication.


Mediterranean-Like Dietary Pattern Associations With Gut Microbiome Composition and Subclinical Gastrointestinal Inflammation

This study assessed whether long term dietary patterns could be associated with changes in the gut bacteria composition and gut inflammation in a cohort of first-degree relatives of patients with Crohn’s disease. The results showed that a Mediterranean-like dietary pattern were associated with a distinct gut bacteria composition which had increased abundance of fibre degrading bacteria, as well as lower gut inflammation as defined by fecal-calprotectin. It was determined that the reduction in gut inflammation was due to a direct effect of the Mediterranean-like dietary pattern, as well as indirectly through the diet induced changes to the gut bacteria population.

Turpin, W., Dong, M., Sasson, G., Raygoza Garay, J. A., Espin-Garcia, O., Lee, S. H., Neustaeter, A., Smith, M. I., Leibovitzh, H., Guttman, D. S., Goethel, A., Griffiths, A. M., Huynh, H. Q., Dieleman, L. A., Panaccione, R., Steinhart, A. H., Silverberg, M. S., Aumais, G., Jacobson, K., Mack, D., … Croitoru, K. (2022). Mediterranean-Like Dietary Pattern Associations With Gut Microbiome Composition and Subclinical Gastrointestinal Inflammation. Gastroenterology163(3), 685–698.


Results of the Seventh Scientific Workshop of ECCO: Precision Medicine in IBD-Prediction and Prevention of Inflammatory Bowel Disease

This review highlights the on-going need for IBD prevention and prediction and the current limitations. It is argued here that data from large cohort studies such as the GEM project, among others, support the concept that IBD has a pre-clinical period wherein biological changes occur prior to the clinical manifestation of the disease. As such, it is important that the pre-clinical period is clearly defined as it may reveal the triggers of disease that may be amenable to early intervention. Using data from pre-clinical cohorts, known risk factors, and known pre-clinical biomarkers, this review defines the 4 stages of disease initiation and progression: Stage 1 – At risk, Stage 2 – Disease initiation, Stage 3 – Disease expansion, and Stage 4- Diagnosis.

Torres J, Halfvarson J, Rodríguez-Lago I, Hedin CR, Jess T, Dubinsky M, Croitoru K, & Colombel J-F. Results of the Seventh Scientific Workshop of ECCO: Precision Medicine in IBD—Prediction and Prevention of Inflammatory Bowel Disease. Journal of Crohn’s and Colitis. 2021 Mar; 15(9): 1443–1454.


Anti-Microbial Antibody Response is Associated With Future Onset of Crohn’s Disease Independent of Biomarkers of Altered Gut Barrier Function, Subclinical Inflammation, and Genetic Risk 

This study aimed to assess whether an altered host immune reactivity to microbial antigens could trigger the onset of Crohn’s Disease (CD). Findings from the study suggest that, even after adjusting for confounding factors, an increased anti-microbial antibody response was associated with the risk of future onset of CD, proposing that anti-microbial antibody responses may potentially be an early pre-disease event.  In comparison to the samples from healthy controls, the pre-CD samples showed significantly elevated levels of all 6 individual antibodies against bacterial and fungal antigens, thus demonstrating the differences in anti-microbial reactivity responses.

Lee SH et al. “Anti-Microbial Antibody Response is Associated With Future Onset of Crohn’s Disease Independent of Biomarkers of Altered Gut Barrier Function, Subclinical Inflammation, and Genetic Risk” . Gastroenterology, 2021. doi: 10.1053/j.gastro.2021.07.009.

Novel Fecal Biomarkers that Precede Clinical Diagnosis of Ulcerative Colitis

In a collaboration between the Farncombe Institute, McMaster University and the GEM Project, researchers compared the fecal microbiota composition and activity levels of protein breakdown of samples from 48 subjects for remained healthy with 13 subjects who provided stool sample before and after developing Ulcerative Colitis . Pre-disease fecal samples exhibited increased elastase activity and protein breakdown that is seen in the fecal samples collected after they have developed UC. The researchers further studied the bacterial contribution and functional relevance of this discovered signature through the colonization of germ-free mice using the control, the pre- and post-disease fecal samples. Mice colonized with the pre- and post-disease samples showed higher activity of protein breakdown than those colonized with the control samples.

Galipeau HJ et al. “Novel fecal biomarkers that precede clinical diagnosis of ulcerative colitis”. Gastroenterology. 2020. Doi: 10.1053/j.gastro.2020.12.004


Increased Intestinal Permeability is Associated with Later Development of Crohn’s Disease

In this study, researchers examined if increased intestinal permeability, or leakiness of the gut, was associated with the future development of Crohn’s Disease (CD). They determined the leakiness by comparing the Lactulose Mannitol (LacMan) ratios of 1420 GEM subjects, with 50 of those who had gone on to develop CD. For more information on why scientists use the LacMan Ratio as a measure of intestinal permeability, please see below. Having an abnormally high LacMan ratio significantly increased the odds of developing CD. Ultimately finding that abnormal gut barrier function might serve as a biomarker for risk of CD onset.

Turpin, Williams et al. “Increased Intestinal Permeability Is Associated With Later Development Of Crohn’s Disease”. Gastroenterology, 2020. Elsevier BV, doi:10.1053/j.gastro.2020.08.005.


Analysis of Genetic Association of Intestinal Permeability in Healthy First-degree Relatives of Patients with Crohn’s Disease.

This study was looking to see if there are any genes that are linked to differences in intestinal permeability. The results suggest that specific genes have a limited  impact on intestinal permeability.

Turpin, W et al. “Analysis of Genetic Association of Intestinal Permeability in Healthy First-degree Relatives of Patients With Crohn’s Disease.” Journal Of The Canadian Association Of Gastroenterology, vol 1, no. 2, 2018, pp. 59-60. Oxford University Press (OUP), doi:10.1093/jcag/gwy009.035.


FUT2 genotype and secretory status are not associated with fecal microbial composition and inferred function in healthy subjects.

FUT2 is a gene that is associated with a healthy intestinal function, and can regulate microbiota population. The gene is responsible for the formation of specific motifs present in the mucus that selectively allows the growth of certain microbes and limit foreign invaders to enter the body. This matters especially since individuals with CD are more likely not to have the correct version of the FUT2 gene and thus are not capable of producing protective motif of the mucus. In this study the GEM Project Scientists found that FUT2 is NOT associated with changes in diversity, composition, or function, of the bacteria of the gut microbiome. This suggests that FUT2 is contributing to the risk of CD independently of the gut microbiota.

Turpin, W et al. “FUT2 Genotype and Secretory Status Are Not Associated With Fecal Microbial Composition And Inferred Function In Healthy Subjects”. Gut Microbes, 2018, pp. 1-12. Informa UK Limited, doi:10.1080/19490976.2018.1445956.


Meta-analysis of Human Genome-Microbiome Association Studies: The MiBioGen Consortium Initiative.

The GEM Project contributed to the effort of identifying the influence of our genes on the composition of the microbiome. We participated in the MiBioGen Consortium Initiative comprised of 25 studies spread around the globe where similar types of samples were collected. A specific statistical tool was developed to better understand the relationship between genetics and the bacteria living in the intestines. With this collective effort, we hope to identify additional genetic signals that can explain the existing diversity of microbiota across different subject.

Wang, Jun et al. “Meta-Analysis Of Human Genome-Microbiome Association Studies: The Mibiogen Consortium Initiative”. Microbiome, vol 6, no. 1, 2018. Springer Science And Business Media LLC, doi:10.1186/s40168-018-0479-3.


Association of host genome with intestinal microbial composition in a large healthy cohort.

The intestinal bacteria (microbiota) are known to be influenced by the outside world, our environments, and our own bodies; the hosts. This study looks at the relationship between the intestinal microbiota (representing all bacteria living in our intestines), and the relationship these may have with our genes. Intestinal microbiota are known to be important in health and disease. Our study found that one third of the bacteria in the microbiota is heritable. This means that these heritable bacteria are more likely to be present in two individuals that are related. Our study found that 58 specific mutations in the subjects DNA were contributing to this heritability. Their influence was observed in 33 types of the intestinal bacteria. Four of these discoveries have been confirmed in another group of Subjects. This study was able to show that there are associations between specific genes and the bacteria lining the microbiome.

Turpin, W et al. “Association Of Host Genome With Intestinal Microbial Composition In A Large Healthy Cohort”. Nature Genetics, vol 48, no. 11, 2016, pp. 1413-1417. Springer Science And Business Media LLC, doi:10.1038/ng.3693.


Determinants of intestinal permeability in healthy first-degree relatives of individuals with Crohn’s disease.

In this study researchers were looking for genetic, environmental, and microbial factors that may be influence the intestinal permeability of our healthy subjects.

Why was intestinal permeability looked at? Intestinal permeability is a measure of “leakiness” of the gut. Increased intestinal permeability, or leakiness, may thus allow passage of gut contents (food, bacteria etc.) which can trigger an intestinal inflammatory response. Several studies have documented that changes in intestinal permeability can predict the course of IBD.

What is the LacMan Ratio? It is a tool used to assess intestinal permeability. To find this ratio, Subjects drink a solution that contains a large molecule (lactulose) that can only cross the gut barrier when it is damage. The solution also contains a small molecule (mannitol) that always crosses the barrier, independent of any damage to the gut barrier. So, by measuring the ratio of the two molecules (LacMan ratio), scientist can tells us how well the intestines are doing their job.

What did this study find? The LacMan ratio was found to not be heritable, meaning that genetics may only play a small role in healthy intestinal permeability. The ratio was also not affected by microbial composition. From this we can postulate that other factors such as the environment, would then likely have a greater impact on the deterioration of healthy intestinal permeability.

Kevans, D et al. “Determinants Of Intestinal Permeability In Healthy First-Degree Relatives Of Individuals With Crohnʼs Disease”. Inflammatory Bowel Diseases, vol 21, no. 4, 2015, pp. 879-887. Oxford University Press (OUP), doi:10.1097/mib.0000000000000323.


IBD Genetic Risk Profile in Healthy First-Degree Relatives of Crohn’s Disease Patients

This study compared the genetic composition of  healthy individuals, those diagnosed with CD, and  first-degree relatives of those with CD from the GEM Project.  The results of this study show that first-degree relatives of those with CD have a greater genetic risk of CD in comparison to healthy individuals.

Kevans, D et al. “IBD Genetic Risk Profile In Healthy First-Degree Relatives Of Crohn’S Disease Patients”. Journal Of Crohn’s And Colitis, vol 10, no. 2, 2015, pp. 209-215. Oxford University Press (OUP), doi:10.1093/ecco-jcc/jjv197.