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GEM Study //


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; in press.

The measure of serum proteome in the preclinical state of Crohn's disease may provide insight into biological pathways involved in Crohn's disease pathogenesis. We aimed to assess associations of serum proteins with future Crohn's disease onset and with other biomarkers predicting Crohn's disease risk in a healthy at-risk cohort. In a nested case-control study within the Crohn's and Colitis Canada Genetics Environment Microbial Project (CCC-GEM) cohort, which prospectively follows healthy first-degree relatives (FDRs), subjects who developed Crohn's disease (n=71) were matched with four first-degree relatives remaining healthy (n=284). Using samples at recruitment, serum protein profiles using the Olink Proximity Extension Assay platform was assessed for association with future development of Crohn’s disease and with other baseline biomarkers as follows: serum antimicrobial antibodies (AS: positive antibody sum) (Prometheus); faecal calprotectin (FCP); gut barrier function using the fractional excretion of lactulose-to-mannitol ratio (LMR) assay. Results: We identified 25 of 446 serum proteins significantly associated with future development of Crohn’s disease. C-X-C motif chemokine 9 (CXCL9) had the highest odds ratio with future risk of Crohn’s disease (Odds ratio=2.07 per SD, 95% CI 1.58 to 2.73, q=7.9e-5), whereas matrix extracellular phosphoglycoprotein had the lowest odds ratio (Odds ratio 0.44, 95% CI 0.29 to 0.66, q=0.02). Notably, CXCL9 was the only analyte significantly associated with all other Crohn’s disease-risk biomarkers with consistent direction of effect (FCP: Odds ratio=2.21; LMR: Odds ratio=1.67; AS: Odds ratio=1.59) (q<0.05 for all). Conclusion: We identified serum proteomic signatures associated with future Crohn’s disease development, reflecting potential early biological processes of immune and barrier dysfunction.


Leibovitzh H, Lee SH, Xue M, Raygoza Garay JA, Hernandez-Rocha C, Madsen KL, Meddings JB, Guttman DS, Espin-Garcia O, Smith M, Goethel M, Griffiths AM, Moayyedi P, Steinhart AH, Panancionne R, Huynh H, Jacobson K, Aumais G, Mack D, Abreu M, Bernstein CN, Marshall JK, Turner D, Xu W, Turpin W, Croitoru K, on behalf of the Crohn’s and Colitis Canada Genetics Environment Microbial Project Research Consortium. Altered gut microbiome composition and function are associated with gut barrier dysfunction in healthy relatives of patients with Crohn’s disease. Gastroenterology 2022; 163:1364-1376

The gut microbiome has been suggested to play a role in gut barrier hemostasis, but data are scarce and limited to animal studies. We therefore aimed to assess whether alterations in gut microbial composition and functional pathways are associated with gut barrier function in a cohort of healthy first-degree relatives of patients with Crohn's disease. Methods: We used the Crohn's and Colitis Canada Genetic Environmental Microbial (CCC-GEM) cohort of healthy first-degree relatives of patients with Crohn's disease. Gut barrier function was assessed using the urinary fractional excretion of lactulose-to-mannitol ratio (LMR). Microbiome composition was assessed by sequencing fecal 16S ribosomal RNA. The cohort was divided into a discovery cohort (n = 2472) and a validation cohort (n = 655). A regression model was used to assess microbial associations with the LMR. A random forest classifier algorithm was performed to assess microbial community contribution to barrier function. Results: Individuals with impaired barrier function (LMR >0.025) had reduced alpha-diversity (Chao1 index, P = 4.0e-4) and altered beta-diversity (Bray-Curtis dissimilarity index, R2 = 0.001, P = 1.0e-3) compared with individuals with an LMR ≤0.025. When taxa were assessed individually, we identified 8 genera and 52 microbial pathways associated with an LMR >0.025 (q < 0.05). Four genera (decreased prevalence of Adlercreutzia, Clostridia UCG 014, and Clostridium sensu stricto 1 and increased abundance of Colidextribacter) and 8 pathways (including decreased biosynthesis of glutamate, tryptophan, and threonine) were replicated in the validation cohort. The random forest approach revealed that the bacterial community is associated with gut barrier function (area under the curve, 0.63; P = 1.4e-6). Conclusions: The gut microbiome community and pathways are associated with changes in gut barrier function. These findings may identify potential microbial targets to modulate gut barrier.

Turpin W, Dong M, Sasson G, Garay JAR, Espin-Garcia O, Lee SH, Neustaeter A, Smith MI, Lebovic H, Guttman DS, Griffiths AM, Huynh H, Dieleman L, Panaccione R, Steinhart AH, Silverberg MS, Aumais G, Jacobson K, Mack D, Murthy S, Marshall JK, Bernstein CN, Abreu M, Moayyedi P, Xu W, Paterson AD, The CCC GEM Project Research Consortium, Croitoru K. Mediterranean-like dietary pattern associations with gut microbiome composition and sub-clinical gastrointestinal inflammation.Gastroenterology 2022; 163: 685-698.

Case-control studies have shown that patients with Crohn's disease have a microbial composition different from healthy individuals. Although the causes of Crohn's disease are unknown, epidemiologic studies suggest that diet is an important contributor to CD risk, potentially via modulation of bacterial composition and gut inflammation. We hypothesized that long-term dietary clusters are associated with gut microbiome compositions and gut inflammation. Our objectives were to identify dietary patterns and assess whether they are associated with alterations in specific gut microbial compositions and subclinical levels of gut inflammation in a cohort of healthy first-degree relatives of patients with Crohn's disease. As part of the Genetic, Environmental, Microbial (GEM) Project, we recruited a cohort of 2289 healthy first-degree relatives of patients with Crohn's disease. Individuals provided stool samples and answered a validated food frequency questionnaire reflecting their habitual diet during the year before sample collection. Unsupervised analysis identified 3 dietary and 3 microbial composition clusters. Results: DC3, resembling the Mediterranean diet, was strongly associated with a defined microbial composition, with an increased abundance of fiber-degrading bacteria, such as Ruminococcus, as well as taxa such as Faecalibacterium. The DC3 diet was also significantly associated with lower levels of subclinical gut inflammation, defined by fecal calprotectin, compared with other dietary patterns. No significant associations were found between individual food items and fecal calprotectin, suggesting that long-term dietary patterns rather than individual food items contribute to subclinical gut inflammation. Additionally, mediation analysis demonstrated that DC3 had a direct effect on subclinical inflammation that was partially mediated by the microbiota. Conclusions: Overall, these results indicated that Mediterranean-like dietary patterns are associated with microbiome and lower intestinal inflammation. This study will help guide future dietary strategies that affect microbial composition and host gut inflammation to prevent diseases.


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;165(3):670-681.

The cause of Crohn's disease is unknown, but the current hypothesis is that microbial or environmental factors induce gut inflammation in genetically susceptible individuals, leading to chronic intestinal inflammation. Case-control studies of patients with Crohn's disease have cataloged alterations in the gut microbiome composition; however, these studies fail to distinguish whether the altered gut microbiome composition is associated with initiation of Crohn's disease or is the result of inflammation or drug treatment. In this prospective cohort study, 3483 healthy first-degree relatives of patients with Crohn's disease were recruited to identify the gut microbiome composition that precedes the onset of CD and to what extent this composition predicts the risk of developing Crohn's disease. We applied a machine learning approach to the analysis of the gut microbiome composition (based on 16S ribosomal RNA sequencing) to define a microbial signature that associates with future development of Crohn's disease. The performance of the model was assessed in an independent validation cohort. Results: In the validation cohort, the microbiome risk score model yielded a hazard ratio of 2.24 (95% confidence interval, 1.03-4.84; P = .04), using the median of the microbiome risk score from the discovery cohort as the threshold. The microbiome risk score demonstrated a temporal validity by capturing individuals that developed CD up to 5 years before disease onset (area under the curve > 0.65). The 5 most important taxa contributing to the MRS included Ruminococcus torques, Blautia, Colidextribacter, an uncultured genus-level group from Oscillospiraceae, and Roseburia. Conclusion: This study is the first to demonstrate that gut microbiome composition is associated with future onset of CD and suggests that gut microbiome is a contributor in the pathogenesis of CD.


Turpin W, Lee SH, Raygoza Garay JA, Madsen KL, Meddings JB, Bedrani L, Power N, Espin-Garcia O, Xu W, Smith MI, Griffiths AM, Moayyedi P, Turner D, Seidman EG, Steinhart HA, Marshall JK, Jacobson K, Mack D, Huynh H, Bernstein CN, Paterson AD, Croitoru K; CCC GEM Project Research Consortium. Increased Intestinal Permeability is Associated with Later Development of Crohn's Disease.  Gastroenterology 2020; 159;2092-2100. 

This study was from the Crohns and Colitis Canada sponsored GEM study. Increased intestinal permeability has been associated with Crohn's disease, but it is not clear whether it is a cause or result of the disease. We performed a prospective study to determine whether increased intestinal permeability is associated with future development of Crohn's disease. We assessed the intestinal permeability, measured by the urinary fractional excretion of lactulose-to-mannitol ratio at recruitment in 1420 asymptomatic first-degree relatives (6-35 years old) of patients with Crohn's disease (collected from 2008 through 2015). Participants were then followed up for a diagnosis of Crohn's disease from 2008 to 2017, with a median follow-up time of 7.8 years. We analyzed data from 50 participants who developed Crohn's disease after a median of 2.7 years during the study period, along with 1370 individuals who remained asymptomatic until October 2017. We used the Cox proportional hazards model to evaluate time-related risk of Crohn's disease based on the baseline lactulose-to-mannitol ratio. An abnormal lactulose-to-mannitol ratio (>0.03) was associated with a diagnosis of Crohn's disease during the follow-up period (hazard ratio, 3.03; 95% CI, 1.64-5.63; P = 3.97 × 10-4). This association remained significant even when the test was performed more than 3 years before the diagnosis of Crohn's disease (hazard ratio, 1.62; 95% CI, 1.051-2.50; P = .029).

We concluded that increased intestinal permeability is associated with later development of CD; these findings support a model in which altered intestinal barrier function contributes to pathogenesis. Abnormal gut barrier function might serve as a biomarker for risk of CD onset.

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