Genetic Research in IBD: the Keys to a 'Cure'

Genetic Research in IBD: the keys to a ‘cure’

Dermot McGovern MD, PhD, FRCP

Director, Translational Medicine Joshua L and Lisa Z Greer Endowed Chair in IBD Genetics Inflammatory Bowel and Immunobiology Research Institute Cedars-Sinai Medical Center Familial occurrences of ulcerative colitis, regional enteritis and ileocolitis

1875

1913

1932 1933

1950 1952

1960 1963

1988

1996 2001 Post 2001 Professor Joseph B. Kirsner Annals of internal medicine 1963:59:133 ‘Genetics 101’

Human Genome

Book ‘Genetics 101’

23 Chapters

23 Chromosomes ‘Genetics 101’

Each chapter contains ‘Genes’ several thousand stories

Each story is made up of paragraphs ‘Exons’

Interrupted by commercials ‘Introns’ ‘Genetics 101’

Each paragraph is made up of words Codons Each word is written in letters Bases What is a polymorphism?

Also known as a SNP – Single Nucleotide Polymorphism

CD Genetics 2010 – 71 Loci 1q24 8q24 1q32 TAGAP Linkage 6q21 BACH2 7p12 6p25 8q24 CPEB4 Initial GWAS 10p11 NDFIP1 13q14 ERAP2 ICAM1/3 2008 meta-analysis 19p13 5q13 CCL2/7 21q21 3p24 EIF3C/CD19 ITLN1 SP140 YDJC Individual GWAS/candidate gene PTPN22 PLCL1 SMAD3 IL12B VAMP3 GALC 2010 meta-analysis CDKAL1 C2orf74 ZFP36L1 CCR6 THADA TNFSF11 MAP3K7IP1 NKX2-3 JAK2 GCKR MTMR3 PTPN2 C11orf30 19q13 DNMT3A TNFRSF6B ZNF365 LRRK2/MUC19 IL27 IL10 PRDX5/ESRRA NOD2 IRGM ORMDL3 ZMIZ1 DENND1B UBE2D1

5q31 IL23R PTGER4 STAT3 CARD9 SCAMP3/MUC1 IL2RA MHC TNFSF15 ATG16L1 MST1 ICOSLG IL18RAP FUT2 FADS1 Prior 2005 2006 2007 20082009 2010 47 Confirmed UC Loci

21q11 TYK2

RTEL1 STAT3 16q24 IL7R 13q13 DAP 13q12 IL8RA/B 11q23 SATB2 ETS1 IL1R2/1 PRKRIR 1q32 LSP1 CREM FCGR2A Ip36 HNF4A TNFRSF9 TNFRSF14 CDH1 CARD9 TNFSF15 LAMB1 REL JAK2 MST1 21q22 6q23 KIF1A ORMDL3 GNA12 IL2/IL21 NKX2-3 PRDM1 12q15 5p15 5q31 IL23R 7q22 IL12B MHC IL10 1p36 IL17REL PTGER4 2008 2009 2010 New loci bring the count from 99... IBD Genetics 2011 …to ~160 IBD associated loci IBD Genetics 2012 Utility of single ‘gene’ tests for diagnosing CD

Smoking NOD2 CARD8 IBD5 TNFS15

100

20 Carriage of risk allele (%) allele risk of Carriage 0

Controls CD McGovern et al Gastro 2006 IBD - A complex trait ?

Lung Cancer Blood Group Car crash IBD Eye Colour

Diabetes Cystic Fibrosis

Malaria

100% Environment 100% Genetic IBD - A complex trait ?

UC IBDU CD Background:Shared genes immune-mediated diseases

Lees et al Gut 2011 Population ‘Structure’ How will genetics help in IBD? • Diagnosis?

• Increased understanding of underlying causes – Novel therapeutic pathways

• Molecular classification

• Development of Biomarkers – Disease severity – Response to therapy

• ? CURE ‘An estimate, based on currently available information, on whether your genetic risk of Crohn's Disease is higher or lower than average.’

• NOD2, ATG16L1, IL23R, NKX2, IBD5, PTPN2

‘One's lifetime odds of getting Crohn's Disease range between 0% and 1%, based on genotype. ’

• ? Useful in – General population – FHx – Symptomatic individual ‘…..sort of the modern version of genetic ‘snake oil ’ Francis Collins How will genetics help in IBD? • Diagnosis?

• Increased understanding of underlying causes – Novel therapeutic pathways

• Molecular classification

• Development of Biomarkers – Disease severity – Response to therapy

• ? CURE Genetic heterogeneity Epithelial integrity IL23/IL17

Autophagy Innate Immunity IIBDGC Meta-Analysis Identifies 30 CD Loci

Barrett et al (2008) Nat. Genet. Aug;40(8):955-62

Autophagy

IL23R Signaling T cell Regulation

Transcription Factors

23 CD Genetics 2010 1q24 8q24 1q32 TAGAP Linkage 6q21 BACH2 7p12 6p25 8q24 CPEB4 Initial GWAS 10p11 NDFIP1 13q14 ERAP2 ICAM1/3 2008 meta-analysis 19p13 5q13 CCL2/7 21q21 3p24 EIF3C/CD19 ITLN1 SP140 YDJC Individual GWAS/candidate gene PTPN22 PLCL1 SMAD3 IL12B VAMP3 GALC 2010 meta-analysis CDKAL1 C2orf74 ZFP36L1 CCR6 THADA TNFSF11 MAP3K7IP1 NKX2-3 JAK2 GCKR MTMR3 PTPN2 C11orf30 19q13 DNMT3A TNFRSF6B ZNF365 LRRK2/MUC19 IL27 IL10 PRDX5/ESRRA NOD2 IRGM ORMDL3 ZMIZ1 DENND1B UBE2D1

5q31 IL23R PTGER4 STAT3 CARD9 SCAMP3/MUC1 IL2RA MHC TNFSF15 ATG16L1 MST1 ICOSLG IL18RAP FUT2 FADS1 Prior 2005 2006 2007 20082009 2010 Over-Expression of TNFSF15 in Mouse Generates Severe SB/Colonic Disease with Strictures

Normal Expression Over-Expression

Small Bowel Strictures

Strictures Colon

Is TNFSF15 a target to alter disease progression?

Barrett, R. ... Shih, D. DDW 2011, Abstract #925 TNFSF15 Antibody Healed Histologic Inflammation Day 32 Day 56 Day 56

Rectum

Mid-Colon

Cecum

Before Treatment Isotype Ab TNFSF15 Ab Efficacy (%) 100 25 50 75 0 All Subjects Hypothetical TNFSF15 Trial TNFSF15 Hypothetical 19 %19 anti-TNFSF15 Therapeutic Low TNFSF15 Producers as defined by antibodies and genes 5 %5 High High TNFSF15 50-80 % 50-80 Producers How will genetics help in IBD? • Diagnosis?

• Increased understanding of underlying causes – Novel therapeutic pathways

• Molecular classification

• Development of Biomarkers – Disease severity – Response to therapy

• ? CURE IBD – How many diseases ? “We propose to describe, in its pathologic and clinical details, a disease of the terminal ileum, affecting mainly young adults, characterized by subacute or chronic necrotizing inflammation.”

Crohn, Ginzburg and Oppenheimer JAMA 1932 NOD2 & ileal disease

Relative risk ileal disease

Any variant allele 4.1 (2.7-6.1)

Simple 2.8 (1.8-4.3) heterozygote

Homozygote 30.3 (7.1-129.3)

PAR ileal disease 40%

Ahmad et al Gastroenterology 2002 Crohn’s (‘Segmental’) colitis

“I am prepared to believe that this segmental colitis is a colonic form of Crohn’s disease. Crohn himself does not sanction this extension of the entity to which we give his name…”

“Ulcerative colitis and Crohn’s disease” Lecture delivered to the Royal College of Surgeons of England by Charles Wells, FRCS, October 1952 HLA & IBD phenotype

Colonic CD - HLA

A1B8DR3DQ2 RR=3.2

DRB1*0103 RR=5.1

Ahmad et al Tissue Antigens 2003 Defining IBD: 1996 vs 2016?

‘‘NamesNames’’ vs Molecular Mechanisms UC CD

IBD1 IBD2 IBD3 IBD4

Disease location and behavior How will genetics help in IBD? • Diagnosis?

• Increased understanding of underlying causes – Novel therapeutic pathways

• Molecular classification

• Development of Biomarkers – Disease severity – Response to therapy

• ? CURE Higher Risk Score Associated with need for surgery in UC (MR-UC)

Non-MR-UC p-value < 10 -16 Chi-squared test for trend MR-UC 100

ProportionProportion(%) (%) 20

0 28-38 39-45 46-52 53-60 Risk Score Categories CD Genetics 2010 1q24 8q24 1q32 TAGAP Linkage 6q21 BACH2 7p12 6p25 8q24 CPEB4 Initial GWAS 10p11 NDFIP1 13q14 ERAP2 ICAM1/3 2008 meta-analysis 19p13 5q13 CCL2/7 21q21 3p24 EIF3C/CD19 ITLN1 SP140 YDJC Individual GWAS/candidate gene PTPN22 PLCL1 SMAD3 IL12B VAMP3 GALC 2010 meta-analysis CDKAL1 C2orf74 ZFP36L1 CCR6 THADA TNFSF11 MAP3K7IP1 NKX2-3 JAK2 GCKR MTMR3 PTPN2 C11orf30 19q13 DNMT3A TNFRSF6B ZNF365 LRRK2/MUC19 IL27 IL10 PRDX5/ESRRA NOD2 IRGM ORMDL3 ZMIZ1 DENND1B UBE2D1

5q31 IL23R PTGER4 STAT3 CARD9 SCAMP3/MUC1 IL2RA MHC TNFSF15 ATG16L1 MST1 ICOSLG IL18RAP FUT2 FADS1 Prior 2005 2006 2007 20082009 2010 How will genetics help in IBD? • Diagnosis?

• Increased understanding of underlying causes – Novel therapeutic pathways

• Molecular classification

• Development of Biomarkers – Disease severity – Response to therapy

• ? CURE TPMT activity

Common genetic polymorphism • Trimodal distribution of TPMT activity Immune Response Genes Predict Non- Response to Infliximab in UC ** ** ** 1.8 ** 0.9 ** 0.9 ** 1.6 0.8 0.8 1.4 0.7 0.7 1.2 0.6 0.6 1.0 0.5 0.5 0.8 0.4 0.4 0.6 95% sensitivity0.3 and 85% specificity 0.3 0.4 0.2 0.2 (normalized for beta-actin) for (normalized (normalized for beta-actin) for (normalized (normalized for beta-actin) for (normalized 0.2 0.1 0.1 Relative STC1 mRNA mRNA mRNA expression expression STC1 STC1 Relative Relative Relative PTGS2 mRNA mRNA expression PTGS2 Relative Relative PTGS2 mRNA mRNA expression PTGS2 Relative

Relative TNFRSF11B mRNA mRNA TNFRSF11B TNFRSF11B expression expression Relative Relative 0.0 0.0 0.0 UCR UCR UCR (n=8) (n=8) (n=8) (n=6) (n=16) (n=16) (n=16) (n=6) (n=6) UC NR UC UC NR UC UC NR UC Controls Controls * Controls * 1.8 ** 0.9 ** 1.6 0.8 1.4 0.7 1.2 0.6 1.0 0.5 0.8 0.4 0.6 0.3 0.4 0.2 (normalized for beta-actin) for (normalized (normalized for beta-actin) for (normalized

0.2 mRNA expression IL11 Relative 0.1 Relative IL13RA2 mRNA mRNA expression IL13RA2 Relative 0.0 0.0 UCR UCR (n=8) (n=8) (n=9) (n=3) (n=10) (n=6) UC NR UC UC NR UC Arijs, et al. Gut 2009 Controls Controls Qin et al, Nature 2010 How will genetics help in IBD? • Diagnosis?

• Increased understanding of underlying causes – Novel therapeutic pathways

• Molecular classification

• Development of Biomarkers – Disease severity – Response to therapy

• ? CURE

42 year old pt, 1 st surgery 42 year old pt, different genetics Same patient, now a current smoker ‘Pathway’ & Candidate Diagnosis ? genes Exome Chip GWAS Behaviour

Immunochip

Clinical, Biochemical

Risk scoring Serology system Response to therapy

Color Key Complications

-2 0 2 Row Z-Score

HOOK2 TPGPEP1 NFRSF10B DHRS4L2DENND1A CNKSR3DHRS4 LAMA3BEND7 SLC28A1CRIP1 MSRAT IAM2 PFKFB4ADCY9 OSBPL6GAT S SLC5A4NCKAP5 PDZD3SOAT 2 GRAMD1BT ESK2 BSTACOX2 1 ASPACDHR1 SLC17A9C9orf71 ZBP1MSI2 SSR4ICAM3 FCRL5SLC15A2 LRP8PNOC ASNSMEI1 SEMA4ASLC1A4 GLCCI1LAX1 FAM46CPRDM1 DERL3IRF4 KIAA0125MGC29506 SLC39A8PIM2 CKAP4MTHFD2 EIF2AK3SRPRB CD24EDEM1 PDK1EAF2 ST6GAL1IGLV6-57 PARM1FNDC3B FAM38B_2GLP2R ING2FGF9 RIPK4ZNF704 C20orf46EEPD1 LOC100131796MYOM3 ABCA8LRAT WDR49PIK3C2G ESR2SLC38A5 STON2FBXO16 RALYLFAM38B MLLTDAPK2 4 TRAPH1 RAK1 Expression OPTRALGPS1 N RAB17DENND5B SFXN3AKR7L MLXIPLDNMBP CHRNA7SEMA5A MATCYP4F12 N2 ARHGAP21GABRE AHNAKSMURF2 DOCK5PTPRJ MAFCDC14A TGUCA2B OR1AIP2 FLVCR1MTMR11 APOA1_2RPS5 PLB1APOA1 TNTS RPM6 GDAPCSK5 APOA4FAT 1 SCINT MIGD1 SLC2A2GOLIM4 SLC13A1CUBN SLC15A1APOA4_2 APOC3_2T MED4 RPLP0APOC3 SLC38A1XBP1 IGKC_2SEL1L3 PMP22IGKC APOBLOC652493 and R00221 R00409 R00191 R00097 R00099 R00061 R00408 R00038 R00004 R00313 R00315 R00095 R00094 R00098 R00145 R00314 R00121 R00108 R00334 R00054 R00350 R00026 R00003 R00050 R00184 R00203 R00037 R00190 R00335 R00025 R00115 R00210 R00005 R00222 R00039 R00120 R00333 R00062 R00349 R00088 R00372 R00366 R00096 R00312 R00194 R00107 R00060 R00053 R00144 R00049 R00126 R00217 R00141 ‘microbiome data The environment matters too! "It isn't pollution that's harming the environment. It's the impurities in our air and water that are doing it." - George W. Bush

Genetic interactions with – Smoking Bacteria NSAIDs etc “I can only regret that the aetiology of this condition remains in obscurity, but I trust that ere long further consideration will clear up the difficulty…”

Dalziel BMJ 1913