Model of IBD pathogenesis, 2002
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1 Model of IBD pathogenesis, 2002
2 Model of IBD pathogenesis, 2012
3
4 Applying an ecosystem of microbial community analysis tools Curtis Huttenhower, Rob Knight, Dirk Gevers With Rob Beiko 4
5 The microbiome in IBD: a complex microbial disease The gut microbiota varies in IBD Diversity is almost certainly reduced Specific clades are o;en over/under enriched IBD subsets (coli>s, ileal CD, etc.) are differen>ally affected Like disease alleles: infec>ous disease ç è one microbe complex disease ç è many microbes Which structural changes might be causal? (If any) (In each subset) And which are instead associated with treatment/environment? And why: what microbial func>ons might be involved in these changes?
6 The IBD microbiome in the OSCCAR and PRISM cohorts Total Healthy CD UC M F < >65 OSCCAR PRISM Treatments: An>bio>cs Immunosup. Mesalamine Steroids LocaLon: Mucosal (biopsy) Luminal (stool) GeneLcs: ~200 loci, IBD- targeted ~1-4K 16S reads/sample
7 Environment and disease: You are your microbes environment: age, sampling, and treatment MaAsLin: Mul>variate Analysis by Linear Models (Tim Tickle) ~200 OSCCAR+PRISM individuals Gammaproteobacteria Firmicutes Mesalamine Stool vs. biopsy Dorea Bifidobacterium AnLbioLcs Age We can use linear models to tease apart parlally confounded effects
8 What about IBD? MaAsLin: Mul>variate Analysis by Linear Models (Tim Tickle) Enterobacteriaceeae Roseburia Ruminococcus Main effects agree with previous findings Roseburia (Lachnospiraceae) down Ruminococcus down Enterobacteriaceae up Also correctly classify environment Bifidobacterium down (age) Anaeros>pes down (smoking) Faecalibacterium down (ileal) What about diet? sample handling? genelcs?
9 What about IBD? MaAsLin: Mul>variate Analysis by Linear Models (Tim Tickle) Roseburia Ruminococcus Main effects agree with previous findings Roseburia (Lachnospiraceae) down Ruminococcus down Enterobacteriaceae up Also correctly classify environment Bifidobacterium down (age) Anaeros>pes down (smoking) Faecalibacterium down (ileal) What about diet? sample handling? genelcs? Enterobacteriaceeae Faecalibacterium Ileal involvement
10 ReconstrucLng funclonal differences MaAsLin: Mul>variate Analysis by Linear Models (Tim Tickle) Microbial metabolism is differenlally abundant in IBD IBD icd Starch+sugar met. ê /é Amino acid met. ê DNA maint. ê Sec. and invasion é Rela>ve abundance
11 DNA maintenance CC + growth But what about functional detail? IBD in the MetaHIT cohort MetaHIT seqs. HUMAnN pathway abundances Up in CD Down in CD Sugar utilization Signaling + secretion Iron + drug transport UC 11
12 Not who, but why: the IBD microbiome is defined by adaptalon to oxidalve stress
13 Dysbiosis implicated in disease in human and animal models
14 Maslowski et al. Nature 2009 Commensal Bacterial metabolism modulates Inflammatory Response Commensal bacterial metabolism short- chain fa_y acids (SCFA) GPR43 Neutrophil chemotaxis # cells migrated Phagocytosis MFI of phagocytes WT WT Gpr43 / [Acetate](mM) Gpr43 / % cells annexinv +, PI + Apoptosis ROS produc>on MFI of ROS (fold change) WT Gpr43 / - control Inflamma>on of intes>nal mucosa SCFA
15 Experimental approach to idenlfy educalon pathways Gut metabolites bugs/bioac>ves S>mulate cells Transcrip>onal and metabolomic assays T cells Macrophages SFB Prevotella Bioac>ves Epithelial cells L1000 Metabolomics Pathways for immune educa>on
16 Severe Crohn s ColiLs Reprinted by permission of Blackwell Science, Inc. Marion JF et al. In: Di Marino AJ, Benjamin SB (eds). Gastrointes/nal Disease: An Endoscopic Approach. 1997:511.
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18 IL23R isoforms and suscep>bility loci implicated in Crohn's disease Xavier & Podolsky, Nature (2007)
19 Iden>fica>on of autophagy in CD pathogenesis Among the genes conclusively associated to Crohn s, 2 major autophagy genes have been associated ATG16L1, non- synonymous coding SNP (T300A) IRGM, synonymous coding SNP, in perfect LD (r 2 =1) with promoter dele>on
20 Why is autophagy important? Cons>tu>ve and conserved Disease- associated Crohn s Disease Neurodegenera>on Tuberculosis, leprosy, viral infec>on Other roles Inflamma>on ini>a>on and resolu>on An>gen presenta>on Cancer Longevity
21 Core machinery is highly conserved Two ubiqui>n- like conjuga>on systems Atg5/12/16 membrane associa>on is transient Atg16 mediates Atg5/12 membrane targe>ng Atg8 / LC3 conjuga>on occurs on both sides of the membrane LC3 is the favored autophagosome marker
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