Understanding the interplay between gut microbiota, gut function and host genes in the generation of gastrointestinal symptoms and disease

Abstract

Irritable bowel syndrome (IBS) is a multifactorial and complex disease categorized in the functional gastrointestinal disorders (FGIDs) with an intricate pathogenesis yet far from understood. The prevalence and burden of the FGIDs has urged the need to improve our understanding of them and recent findings have led us to realize that there are biochemical and structural alterations playing roles in their etiology. This thesis has concentrated on a number of factors including altered intestinal motility, pain perception, genetic predisposition, and gut microbiota in order to obtain a better understanding of the interplay between these factors in the generation of gastrointestinal (GI) symptoms.

To achieve this, we have carried out five studies exploiting data from a Swedish data-rich general population-based cohort, namely PopCol, and some other cohorts. In the first study, to investigate the link between gut microbiota and gut transit time (as an objective means to quantify GI functional abnormalities) we studied the association between different indices of fecal microbiota composition with stool consistency and stool frequency (as surrogates for gut transit time) in the PopCol cohort. The obtained results provide more support for the already reported association between gut microbiota and stool consistency and also revealed an even stronger association between the composition of fecal microbiota and stool frequency. To study the association between one of the most common symptoms of FGIDs, i.e. abdominal pain, and gut microbiota in the second study, data of 159 individuals from PopCol cohort (including 52 individuals who reported pain) was inspected. Results indicated an association between fecal microbiota composition and abdominal pain occurrence as well as its frequency, duration, and severity. Also, we could provide more evidence for the negative association of Prevotella with pain in the general population.

In the third study, to investigate the genetic biology of stool frequency, we exploited data from two general population-based cohorts, PopCol and LifeLines-Deep, and carried out a genome-wide association study (GWAS) followed by a meta-analysis. Gene set enrichment analysis was performed on the resulting gene list. Although, possibly due to limited sample size, none of the association tests revealed genome-wide significant results, we could identify excellent functional candidate genes and more interestingly, the results from the post-GWAS analysis suggested xenobiotic metabolism and ion channel activity as two plausible underlying mechanisms for regulation of the stool frequency. This result pointing at the link between ion channel activity and bowel function in addition to the results of another study which revealed that 2.2% of IBS patients carry a mutation in a voltage-gated channel gene (SCN5A), led us to the fourth study. In this study, 14 single nucleotide polymorphisms (SNPs) spread over TRPM8 (a gene involved in GI-related ion channel activity) were investigated in association to IBS and its subtypes in a cohort of IBS cases and controls followed by a meta-analysis of the results of this study and the GWAS of IBS (already published by our lab). Subsequently, PopCol data was used to study the association between TRPM8 genotype variants and stool consistency. Logistic regression analysis revealed significant associations between different variants of TRPM8 gene and predisposition to IBS, which was restricted to the constipation-related subtypes of IBS (IBS-C and IBS-M). This result was confirmed by the meta-analysis. Moreover, a negative correlation between all IBS-C/M predisposing risk alleles and stool consistency was obtained from investigating the PopCol cohort.

Finally, considering the importance of genes and diet in the susceptibility to IBS, in a nutrigenetic approach, we studied the sucrase-isomaltase (SI) gene variants (congenital defective form of this gene results from rare mutations and is characterized by abdominal pain, diarrhea, and bloating) for their potential relevance to IBS in the fifth study. To do this, the four most known congenital sucrase-isomaltase deficiency (CSID) mutations in addition to a SI coding SNP (p.Val15Phe) were screened in a multicenter cohort of IBS cases and controls. The effect of this SNP on the function of SI was also inspected in vitro. Finally, we analyzed p.Val15Phe genotype in association to fecal microbiota and stool frequency in PopCol cohort. Our results indicated that the four CSID mutations and the common variant were more common in patients than asymptomatic controls. The in vitro study indicated 35% reduced enzymatic activity for the SI protein with 15Phe compared to 15Val. Investigating PopCol samples, 15Phe copies correlated with stool frequency and the abundance of fecal Parabacteroides.

In summary, in this thesis we succeeded in providing additional strong evidence for the importance of human genes (TRPM8 and SI) in the development of IBS and its symptoms. Moreover, we demonstrated a link between some of the important IBS symptoms, i.e. abdominal pain and altered stool frequency with gut microbiota composition in the general population. Taken together, this thesis contributes to a better understanding of the interplay between several factors in the generation of GI symptoms. The information we report here may contribute to translational opportunities for the stratification and eventual management of individuals with IBS and other FGIDs.