The genetic galaxy: stars, planets and asteroids Sverine Vermeire - PowerPoint PPT Presentation

The genetic galaxy: stars, planets and asteroids Séverine Vermeire MD, PhD Department of Gastroenterology and Catholic University of Leuven Belgium

Concering the universe … where IBD genetics really started

International IBD Genetics Consortium 1997 Oxford - 1999 Canberra - 2001 Paris - 2003 Orlando – 2004 Rome – 2006 Amsterdam

The stars

The stars NOD2/CARD15

NOD2/CARD15 (16q12) Caspase Recruitment Domain Family member 15 Protein/protein Protein PAMP recognition interactions Oligomerisation CARD 1 CARD 2 NBD LRR 1 28 124 127 220 273 577 744 1020 1040 Arg702Trp Gly908Arg SNP8 SNP12 Leu1007fsinsC 3020insC Blau syndrome SNP13

NOD2 pointed out the concept of impaired innate immunity in Crohn’s disease

NOD2 mutation prevalance 100 effect size one mutation RR 2.5 80 60 % 40 20 0 controls CD

NOD2/CARD15 associated with stricturing ileal Crohn’s Lala S et al; Gastroenterology 2003; 125: 47-57 Ogura et al; Gut 2003; 52: 1591-1597

Defensins in the gut are impaired in patients carrying NOD2 mutations Kobayashi et al Science 2005;307:731-734 Wehkamp J Gut 2004; 53: 1658-64

Genome-wide Association Scan  99 loci IBD

The planets

The planets of “ autophagy ”: IRGM and ATG16L1

Autophagy and IBD Mycobacteria Salmonella Shigella Listeria Toxoplasma Herpes simplex …

The planets of “ autophagy ”: IRGM and ATG16L1 • ATG16L1 (sensor for invading pathogens) • IRGM (Immunity-related GTPase family M protein; regulates autophagy induction in response to intracellular pathogens) • ULK1 (kinase required for induction of autophagy; regulated by mTOR) • MTMR3 (PI3P fosfatase; regulates initiation of autophagy; unknown whether positive or negative) • LRRK2 (kinase, GTPase; relation with autophagy; unknown whether positive or negative)

CD patients homozygous for the disease risk allele of ATG16L1 display Paneth cell abnormalities ATG16L1 Risk Allele Wild type Cadwell K et al Nature 2008

Sirolimus as therapy for Crohn’s ? before After 16 weeks Massey DC et al Gut. 2008;57:1294-6

The “ER stress” planets (XBP1, ORMDL3 ) neurodegenerative diseases developmental disorders Cancer Diabetes cystic fibrosis IBD McGuckin M A et al. Am J Physiol Gastrointest Liver Physiol 2010;298:G820-G832

Increased AIEC in ER-stressed Paneth cells (GRP78 scoring) from ATG16L1 patients DNA and biopsies from 78 CD and 12 controls ER stress (+) ER stress (−) CD N (%) Controls N (%) CD N (%) Controls N (%) Total number 8 4 13 4 AIEC fimH 8 (100) 0 (0) 1 (7.7) 0 (0) AIEC eaeA 8 (100) 0 (0) 1 (7.7) 0 (0) Listeria 2 (25) 0 (0) 1 (7.7) 0 (0) monocytogenes MAP 1 (12.5) 0 (0) 0 (0) 0 (0) Salmonella spp. 2 (25) 0 (0) 0 (0) 0 (0) Deuring JJ et al Gut 2013 August

Microbial sensing, autophagy and ER stress pathways in CD 30.0 Hoefkens E & Nys K et al Autophagy 2013 in press 25.0 Percentage of individuals 20.0 Healthy controls 15.0 CD patients UC patients 10.0 5.0 0.0 0 1 2 3 4 5 6 7 8 9 10 11 12 Number of risk alleles

ORMDL3 The (LPS-induced) cytokine response is increasingly induced in carriers of higher # of risk alleles in susceptibility SNPs

… and the asteroids

Crohn’s disease Overlapping genes Ulcerative colitis Lupus Erythematosus Multiple Sclerosis PRDM1/ATG5 PTGER4, STAT3, IL2RA, IL17R, FCGR2A IL10 PTPN22 Rheumatoid arthritis Ankylosing Spondylitis FCGR2A IRF5 IL23R PRDM1 FCGR2A REL IL2/IL21 ERAP2 PTPN22 TNFRSF14 CCR6 IRF5 Psoriasis IL23R IL2RA IL12B Atopic Dermatitis CDKAL1 PTPN22 C11Orf30 IBD Behcet’s IL23R, IL10 NOD2 Leprosy LRRK2 Alopecia TNFSF15 PRDX5 IL2RA IL2RA PTPN22 IL2/IL21 Asthma CCR6 ZMIZ1 ZMIZ1 vitiligo ICOSLG PTPN2 ORMDL3 REL IL18RAP SMAD3 KIF21B VAMP3 PTPN2 IL18RAP 5q31 (IBD5) YDJC BACH2 ORMDL3 PTPN22 DENND1B TNFRSF14 TAGAP IL10 IL27 Type II Diabetes IL2/IL21 ZFP36L1 TYK2 BACH2 CDKAL1 FCGR2A ILR2A Coeliac disease GCKR CAPN10 Type II diabetes THADA HNF4A (MODY)

the Immunochip project • 12 IMISs Other replication: ~6000 SNPs – IBD, coeliac disease, T1D, AS, MS, PSC, RA, psoriasis,… Deep replication: • 196.524 variants ~50,000 SNPs • 38.565 IBD cases 186 fine-mapping regions: • 37.747 controls ~130,000 SNPs HLA region: ~8000 SNPs Nature 2012 491:119-124

iChip increased the number of IBD loci to 163 25/30 risk allele has 18/23 same direction of risk allele has same effect in UC (p < 10 -3 ) direction of effect in CD (p < 0.01) Nature 2012 491:119-124

The genetic architecture of CD vs. UC IBD vs. control odds ratio IL23R >1.5 NOD2 110 IBD 1.4 23 UC loci specific loci 1.3 30 CD specific loci 1.2 MHC 1.1 PTPN22 0.67 1.0 >1.5 CD vs. UC odds ratio Jostins L et al, Nature 2012 491:119-124

Major themes of interest highlighted by iChip • 18% in LD with missense mutations • 40% in LD with variants regulating gene expression • 69% shared with other IMIDs (x 8,6 as expected by chance) • Role of Th17 cells: new RORC (master transcription factor) association • De/ubiquitination: 15 loci involved (p < 0.001) • NF-kB: REL, RELA, NFKB1 • Degradation of TGFb signaling components: – SMURF1, FURIN, SMAD7 (implicated in CRC) • Susceptibility to infectious diseases

Host-microbe interactions shape genetic architecture of IBD IBD loci 6/7 leprosy loci also IBD loci 6/8 MSMD* genes NOD2 within IBD loci IL23R IL12B 82 TNFSF15 STAT1 RIPK2 IRF8 LRRK2 TYK2 C13ORF31 53 STAT3 IFNGR2 MSMD 82 82 Immune-mediated diseases Primary immune deficiencies *MSMD, Mendelian susceptibility to mycobacterial disease

Yet another universe: epigenetics Nicholas T. Ventham , Nicholas A. Kennedy , Elaine R. Nimmo , Jack Satsangi. Gastroenterology 2013; 145: 293-308

Back to earth … How do we use these fantastic findings in our patients?

Examples where genotyping enters the clinic Gene Drug EMA advice TPMT Thiopurines None EGFR Gefitinib in NSCLC Mandatory KRAS Cetuximab, Panitumumab in CRC Mandatory SLCO1B1 Statin induced myopathy None HLA B*5701 Abacavir in HIV Mandatory CYP2D6 Tamoxifen – Breast cancer None CYP2C19 Clopidogrel None

Genetic predisposition to anti-TNF induced skin lesions? Odds ratio Gene SNP ID [95% CI] IL23R rs114657791 0.53 [0.28-1.02] IL12B * rs3181225 0.57 [0.38-0.85] COG6 * rs7993214 1.54 [1.06-2.23] IL12RB2 rs12131065 1.45 [1.02-2.07] Cleynen I & Vermeire S. Nat Rev Gastroenterol Hepatol 2012

Genetic panel to predict colectomy in ASUC HLA DRB*103 MDR1 C3435T MEKK1 Asp643Asn 6 5 RR for colectomy 4 3.21 3 2.59 2 1 1 0 no or 1 at risk 2 or more at risk 3 or more at risk genotype genotypes genotypes McGovern Gastroenterol Suppl 2004;126: A68

Explaining or predicting the subphenotypes of IBD Disease severity Disease location & behaviour Extra-intestinal disease manifestations

CD disease location (conditional on disease behavior and age at diagnosis) N=19.881 NOD2 MHC

CD disease behaviour (conditional on disease location and age at diagnosis) N=19.881

90 UC 80 D’ 70 -log 10 P value 60 50 40 r 2 30 CD location CD UC extent 20 10 0 30,500,000 31,000,000 31,500,000 32,000,000 32,500,000 33,000,000 33,500,000 Class I Class III Class II BTNL DQA HSPA1B DRB5 HLA-A HLA-C 2 2 DRA HLA-B C6orf48 rs9276427 rs9268969 rs6930777 rs3117577 1.90e-17 5.99e-02 6.37e-01 3.96e-07 CD 0.87[0.84-0.90] 1.03 [0.99-1.07] 1.01 [0.96-1.07] 0.86 [0.81-0.91] 1.59e-03 5.52e-85 3.55e-17 6.98e-03 UC 0.95 [0.91-0.98] 0.68 [0.65-0.70] 1.26 [1.19-1.33] 0.95 [0.69-1.00] 2.25e-01 3.86e-07 4.02e-22 4.11e-03 CD location 0.97 [0.91-1.02] 1.16 [1.10-1.23] 0.66 [0.61-0.72] 0.87 [0.78-0.96] 1.06e-01 1.07e-07 6.30e-01 2.27e-16 UC extent 1.05 [0.99-1.10] 0.84 [0.79-0.90] 1.02 [0.94-1.11] 1.46 [1.33-1.59]

Conclusions • Collaborative efforts since 1997 have made IBD genetics a successful project: – GWAS, their meta-analyses & iChip : 163 associated IBD regions • NOD2 and HLA confer the major genetic effect on disease phenotype in CD and UC – But different HLA signals for susceptibility and phenotype • Genetic findings support the hypothesis that UC, colonic CD and ileal CD could be considered as part of a continuous spectrum