Integrative Analysis of the Microbiome and Human Intestinal Transcriptome: Implications for the Pathogenesis of Diverticulitis
Open Access
- Author:
- Schieffer, Kathleen Marie
- Graduate Program:
- Biomedical Sciences
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- August 22, 2017
- Committee Members:
- Walter Alex Koltun, Dissertation Advisor/Co-Advisor
Walter Alex Koltun, Committee Chair/Co-Chair
Shannon Leanne Kelleher, Committee Member
Gregory Steven Yochum, Committee Member
Regina Lamendella, Outside Member
Matam Vijay Kumar, Committee Member - Keywords:
- RNA-seq
Microbiome
Diverticular disease
Immune system
16S rRNA - Abstract:
- The formation of diverticula, or herniations of the colonic mucosa and submucosa through the bowel wall, is prevalent in the sigmoid colon of aged individuals in Western countries. Individuals with diverticula have diverticulosis, a condition which is usually asymptomatic. However, in 4-25% of individuals with diverticulosis, inflammation of the diverticula results in diverticulitis. Acute diverticulitis is commonly treated with empiric antibiotics and increased dietary fiber. Despite the high prevalence of disease in the United States, the pathophysiology of diverticulitis is largely unknown. Previous data suggests that the immune system may play a role in diverticulitis pathogenesis. A key function of the intestinal immune system is to discriminate pathogens from commensal microorganisms. Microbial dysbiosis contributes to the pathogenesis of inflammatory bowel disease; however, whether the microbiome is also involved in diverticulitis pathogenesis is unknown. Therefore, we hypothesized that deregulation of the innate immune system contributes to diverticulitis pathogenesis by promoting a dysbiotic microbial ecosystem. To test this hypothesis, we used RNA-seq, an unbiased and genome-wide approach, to globally survey the intestinal transcriptome of full-thickness sigmoid colon tissue collected adjacent to areas chronically affected by diverticulitis compared to controls. Gene Ontology pathway analysis found increased expression of genes associated with the innate immune response. Expanding on these findings, we identified an increased number of macrophages expressing the scavenger receptor CD163L1 in diverticulitis tissues. In diverticulitis patients, CD163L1+ macrophages localized at the sub-epithelium and co-expressed the chemokine CXCL10. Furthermore, heightened serum CXCL10 was found in diverticulitis patients relative to controls. As the intestinal microbiome influences immune homeostasis, bacterial 16S rRNA and fungal ITS sequencing was performed from chronically diseased tissue and adjacent tissue in diverticulitis patients. We found distinct microbial interactions segregated chronically diseased tissue from adjacent tissue within the same colonic segments. The findings from this dissertation propose that deregulation of the innate immune response to an altered microbial ecosystem results in chronic inflammation and the development of diverticulitis. There are currently no prognostic or diagnostic biomarkers or targeted therapeutic options for diverticulitis; thus this work may help drive development of such targets within molecular pathways of disease relevance.