Recent progress in our understanding of IBD genetics
advertisement
State of the Art: Recent Progress in Understanding of IBD Genetics Judy H. Cho, M.D. Ward-Coleman Professor of Translational Genetics and Medicine, Icahn School of Medicine at Mount Sinai December 5, 2014 Concepts Rare vs. Common genetic variants Rare variation Age of onset & population considerations When to sequence & sequence annotation Common genetic variants & GWAS studies Population differences Non-coding functional variation Rare vs. common human polymorphisms Rare Common 1. Often population-specific 1. Present across populations 2. Most missense alleles are rare 2. Large majority are non-coding 3. Selection: negative selection 3. Selection: balancing , positive 4. Association signals: greater effect sizes (e.g. OR > 1.5) for nominally associated variants 4. GWAS-identified significant loci have modest effects (i.e., odds ratios)—most less than 1.1 5. Less power—most samples are homozygous wild-type 5. Greater power to detect association Monogenic Early-onset IBD Mendelian IBD: IL10 deficiency--neonatal Immunodeficiencies with variable age of onset FOXP3: IPEX WAS: Wiscott-Aldrich LRBA: LPS-responsive, CVID8 Chronic granulomatous disease XIAP: X-linked inhibitor of apoptosis 10 years old Uhlig et al., Gastroenterology 2014 XIAP, NOD2 and Crohn’s disease XIAP: X-linked inhibitor of apoptosis Many XIAP missense mutations—extremely rare XLP2: X-linked lymphoproliferative immunodeficiency CD-unique private mutations: (potentially) as high as 4% of pediatric male IBD cases Ileocolonic plus perianal disease NOD2-signaling deficiency Variable disease course—majority responsive to traditional therapy Numbers small, but XIAP-deficiency appears to have a higher penetrance than NOD2-deficiency Zeissig et al, Gut 2014 When to consider sequencing Research? Clinical? Eventually all of us!!! Early onset IBD—especially males Consanguineous Immunodeficiency plus IBD ATG16L1 & sequence annotation ATG16L1 T300A variant: alanine CD risk Caspase-3 & -7 cleavage sequence: -D-X-X-D-(T/A)Alanine variant increased ATG16L1 degradation Clearly establishes that CD risk allele is correlated with impaired autophagy Sequence annotation: prediction of new/altered covalent modifications Murthy et al., Nature 2014 Lassen et al., PNAS 2014 Rare variants are “less rare” in AJs AJ Flemish 128 whole genome sequenced in AJs Rare variants are “less rare” in AJs compared to Flemish Profound population bottleneck in AJs Derived allele frequency Carmi et al., Nature Commun 2014 AJ-specific frameshift mutation in CSF2RB associated to IBD Gene Function IBD Freq CSF2RB GMCSF receptor 0.032 control odds P-value type group freq ratios AJ0.02 0.00104 1.6 IBD specific CSF2RB: common subunit to GMCSF, IL3, IL5 Truncation mutation: ~200 aa in cytoplasmic tail Common variants in this region nominally associated—also NCF4 (Rioux et al., Nature Genetics 2007) GMCSF & IBD Anti-GMCSF antibodies CD patients with elevated anti-GMCSF Ab NOD2-deficient mice + neutralizing anti-GMCSF + piroxicam ileitis Anti-GMCSF Ab levels correlate with increased disease complications GMCSF cytokine Induces IL10, retinoic acid Potential therapeutic benefit Han et al., Gastroenterology 2009, 1261 Gathungu et al., IBD 2013, 1671 Mortha et al., Science 2014 Korzenik et al., NEJM 2005 Concepts Rare vs. Common genetic variants Rare variation Age of onset & population considerations When to sequence & sequence annotation Common genetic variants & GWAS studies Population differences Non-coding functional variation Distinct genetic architecture for dominant loci: European ancestry vs. Japanese Crohn’s disease GWAS European ancestry Arg381Gln Japanese MHC TNFSF15 Yamazaki, et al, Gastroenterology 2013; 781 GWAS/common alleles: vast majority demonstrate similar direction & effect sizes across populations Exceptions—biggest effect loci European ancestry Asian Alleles NOD2 R702W, G908R, fs1007 uncommon risk monomorphic IL23R R381Q uncommon protective monomorphic non-coding IL23R associated associated different alleles ATG16L1 T300A Risk is LOF Smaller/no effect TNFSF15 non-coding TNFSF15 Smaller effects Risk is GOF same alleles Yang et al., IBD 2009 Kim et al., Gut 2014 Hedl et al., PNAS 2014 Expression quantitative trait loci (eQTL) mapping mRNA expression as a continous trait Heritable Mappable to specific SNPs Cell lines, tissues and contextspecificity Presently defined eQTLs likely only a subset of genuine eQTLs LPS- & IFNg stimulated monocytes define more eQTLs 80% of transcripts with eQTLs Morley, et al., Nature 2004; 430: 743 Dixon, et al., Nature Genetics 3007; 39: 1202 Fairfax et al., Science 2014 Diseases examined by GWAS 21 different autoimmune diseases Comparative diseases Metabolic traits Neurologic diseases Most correlated: UC-CD-Ankylosing spondylitis-psoriasis-Behcet’s disease Navy blue: no correlation Maroon red: highest correlation Farh et al., Nature 2014 Fine-mapping in autoimmunity Fine-mapped autoimmune loci 90% are non-coding 60% map to immune enhancers Histone marks: greatest enrichment seen for H3K27ac—active/stimulated enhancers Disease-associated SNPs in enhancers are near, but not within consensus transcription factor binding sites Farh et al., Nature 2014 Enrichment of GWAS signals in cell type specific enhancers (H3K27ac) T cells B cells Colonic mucosa T cell enrichment: RA, MS, IBD, celiac disease B cell enrichment: RA> IBD Monocyte signal: largely absent except CRP Tissue-macrophage specific signals? Marked enrichment of colonic mucosa in UC RA CD-UC Y-axis: 33 cell type H3K27ac X-axis: 39 diseases Farh et al., Nature 2014 GWAS and eQTL SNPs show (apparently) different molecular distributions eQTL dataset: peripheral blood RNA from twins BUT: eQTL distribution for stimulated (LPS, IFNg) gene expression is likely quite different Value of eQTLs-risk allele alignment: implies directionality—gain/loss of function Wright et al., Nature Genetics 2014 Farh et al., Nature 2014 Conclusions Sequencing and rare variant-associated IBD Younger, severe, select populations Establishing genome-wide significance is challenging—need for early functional analysis Common variant fine-mapping “Single” causal allele identifiable statistically in only a minority of cases Greatest enrichment of GWAS signals in H3K27ac active enhancer regions—near, but not in consensus transcription factor binding sites Imperfect molecular matching of GWAS and eQTLs: need to define cell and activation state specificities Power of genetics: earliest pathophysiologic mechanisms, precise therapeutic targeting Acknowledgements Cho lab Ken Hui NIDDK IBD Genetics Consortium Steve Brant Monica Bowen Richard Duerr Kyle Gettler Dermot McGovern Nicole Villaverde John Rioux Nai-Yun Hsu Mark Silverberg Mark Daly Felix Chuang Phil Schumm Yashoda Sharma Mount Sinai collaborators Clara Abraham Inga Peter Eric Schadt Miriam Merad Bruce Sands Jean-Fred Colombel Yale University Richard Flavell The Ashkenazi Jewish Consortium Itsik Pe’er Todd Lencz
