Ground Zero – the impact of the gut microbiome on host epithelial functions and responses.

http://phenomena.nationalgeographic.com/2013/05/13

Eugene B. Chang, M.D. Human Microbiome Science: A Vision for the Future

July 24, 2013

Examples of critical gut epithelial functions that are impacted by microbes

• Barrier function – Intestinal permeability (TJ mediated) – Mucus, AMPs

• Development and Adaptation • Wound healing • Innate immune functions • Cytoprotection • Nutrient/electrolyte/water transport • Autophagy • Proliferation/apoptosis

Small intestine

Colon

Gut microbes regulate mucosal development, proliferation, and apoptosis

(Reikvam, et al PlosOne 2011)

Ki67 immunostaining (green) LGG-derived peptides (p40, p75) Prevent TNF-induced apoptosis

(Yan, et al Gastroenterology 2007)

Conditioned media from Bifidobacterium breve protects against ROS-induced barrier dysfunction

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Caco2BBE Mouse Jejunum

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Hsp25 immunostaining (brown)

Physiological expression of inducible Hsps by surface colonocytes is maintained by gut microbes

GF mice

Metagenomic profiles of mucosa-associated microbiota from the healthy human colon

Wang, et al. Appl Microbiol Biotechnol 2010

In Hsp70 KO mice, otherwise acute DSS colitis becomes chronic

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Wild Type - normal Hsp70 KO – chronic-like colitis

Identified molecular mediators that affect gut epithelial function

• QSM (e.g. CSF of B. subtilis) • Innate ligands (PAMPs, MAMPs)

– PG, MDP – LPS, dsRNA

• SCFAs, Lactic acid • H2S • Chemotactic peptides (nFMLP) • Metabolites

Gaps in our knowledge of gut microbial-epithelial interactions

• Rudimentary knowledge and inventories of bioactive microbe-derived factors

• Incomplete understanding of the complexity and heterogeneity of gut epithelial functions, particularly as they relate to microbial selection, assemblage and region-specific interactions.

• Incomplete vetting and understanding of the above in the context of human biology and pathobiology

Challenges and Needs Human Studies: • Observational and associative • People are different and difficult to study • Disease classifiers are inadequate • Technology-driven • Bottom-up approach

Technical: • Sampling, QC, SOPs • Insufficient vetting (metatranscriptomes, metagenomes, etc)

– Better toolbox

Experimental/data analysis • Animal and experimental models of the human condition • Integration of data sets (host and microbe, location). • Incomplete inventories of microbial transcriptomes,

proteomes, metabolomes, etc.

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IBD are progressive diseases and natural histories differ among patients

Cosnes J et al. Inflamm Bowel Dis. 2002;8:244.

240 228 216 204 192 180 168 156 144 132 120 108 96 84 72 60 48 36 24 12 0 0

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T-0 T-1 T2

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Location, location, location

Half empty, half full?

There is a solution to every problem

Surgical treatment of severe ulcerative colitis – total colectomy with ileal-anal pouch

anastomosis

http://www.gastrolab.net/ku01.htm

• Unique to UC • Microbe-dependent • >50% pts will develop it • Prospective design • Easy to sample • Pts as their own controls

Why study pouchitis?

Developing a model that recapitulates conditions of the human ileal pouch

Self-Emptying (SE)

Self-Filling (SF)

Proximal Small Intestine

Loop

Cecum

Colon

Does stasis promote a colonic-like microbiota?

If UC never involves the small intestinal mucosa, why does pouchitis occurs?

Ileum Emptying Loop

Colon Filling Loop

H&E mucosal histology Microarray heat map

Are colonic microbiota and metaplasia sufficient to cause disease?

IL-10-/- mouse Self-filling loop

Il-10-/- mouse Self-emptying loop

Working model for UC pathogenesis: The perfect storm

Colonic Microbiota (dysbiosis?)

Genetic Susceptibility

Colonic metaplasia

Ulcerative colitis and pouchitis

Challenge: The gut mucosa is a multicellular

Laser capture microdissetion

Enteroid

Folker Meyer Dionysios Antonopoulos Eugene Chang

Vincent Young, Thomas Schmidt

James Tiedje

Mitchell Sogin

Acknowledgements

NIH HMP, NIDDK, Helmsley Trust