State of the Art in IBD Genetics

Judy H. Cho, M.D.

Ward-Coleman Professor of Medicine and Genetics, Icahn School of Medicine at Mount Sinai

Central importance of human genetics

Germline DNA variants disease susceptibility Primary causality Immediate molecular insight—genes,

increased/decreased function Humans as your experimental system—natural

pertubagens relevance for patients

Genome-wide genetic approaches are unbiased Novel, unexpected insight—autophagy

Promise of new therapy development—major challenge for the field

Genetics: enormous impact on IBD research—autophagy & Paneth cells

Cell 2010

Nature 2013

Critical role for the Paneth cell

Genetics impact: IL-23 pathway & treatment

Science 2006

PNAS 2011

Nature 2013

Salt increases IL23R expression

NEJM 2012

IBD Immunochip: 163 loci associated to IBD

50

Cum

ulat

ive

IBD

loci

100

0

150

2000 2002 2004 2006 2008 2010 2012Year

MHC in UC

NOD2 Single-center GWAS

GWAS meta-analyses Immunochip

163 loci

Nature, 2012

Major genetics concepts: functional variants and evolutionary selection

Overlap of major loci between related diseases—motivation for development of Immunochip

Most GWAS-identified variants are non-coding and affect gene expression (eQTLs)

Immune-mediated disease loci: evolved in response to historically significant pathogens

Population differences: may provide major insight

Common vs. rare variants

Crohn’s disease

Ulcerative colitis

IL23R in both MHC major in UC Crohn’s disease-

uniquely lacks a dominant MHC signal Instead, innate immune

defects: NOD2 & ATG16L1

Genetic architecture: Crohn’s disease vs. ulcerative colitis in European ancestry cohorts

Science 2006;314:1461Nature 2001;411:603

**Nat Genet. 2011;43:246**Nat Genet. 2010;42:1118

Nat Genet. 2009;41:216

Nat Genet. 2011;43:1066

Arg381Gln

The Immunochip effort in IBD: international collaboration on a grand scale

38,565 cases & 37,747 controls Combined 15 separate European ancestry IBD GWAS

25,075 SNPs with p < 0.01 Meta-analysis:

GWAS + New cases genotyped on Immunochip

14,763 CD cases 10,920 UC cases 15,977 controls genotyped

71 new loci163 genome-wide significant loci

Defining the genetic architecture of CD vs. UC

IBD

vs.

con

trol

odd

s ra

tio >1.5

1.3

1.4

1.2

1.1

0.67 1.0 >1.5

IL23R

NOD2

PTPN22

CD vs. UC odds ratio

30 CD specific

loci

23 UC specific

loci

110 IBD loci

MHC

Inflammatory bowel disease: 163 loci genes & alleles

Annotation approaches for “hit SNPs”: cSNPs: 24 loci (15%) eQTLs: 64 loci (39%)** Dapple (protein-protein interaction): 30 loci Grail (literature mining): 87 loci Bayesian network analysis: 43 loci

52 loci contain genes implicated by two or more annotation approaches

Striking overlap of IBD loci between diseases

v

IBD loci

Immune-mediated diseases

82

82

53

82Primary immune

deficiencies

MSMD

Mycobacterial diseaseChronic mucocutaneous candidiasis (CMC): CARD9, STAT3

CMC

Striking overlap between IBD & mycobacterial susceptibility

163 IBD loci

6/7

7 leprosy GWAS loci

7/9

9 single gene mycobacterial (Tb) genes

NOD2RIPK2

TNFSF15LRRK2IL23R

C13orf31

IL12B STAT1 IRF8 TYK2 STAT3

IFNGR2IFNGR1

*

Why the specificity between IBD & mycobacterial infection?

NOD2 & glycolyl MDP: mycobacteria & Actinomycetes contain enzyme (NamH) which converts acetyl MDP to glycolyl MDP (Coulombe, JEM 2009)

TNF & IBD: Over-expression of TNF ileitis & arthritis

(Kontoyiannis, Immunity 1999) Anti-TNF highly effective in the treatment of Crohn’s

disease & ulcerative colitis Anti-TNF treatment reactivation of latent Tb (Keane

et al, NEJM 2001) Ashkenazim, Crohn’s disease & mycobacterial

susceptibility

Epidemiologic support for the Jewish-Tb hypothesis

Population Deaths per 100,000

Mussulman Arabs 1130

Europeans 513

Jews 75

Deaths from tuberculosis, London 1894-1900 Population NY Brooklyn

African-American 774.21 531.35

Ireland 645.73 452.79

Bohemia 499.13 347.22

Russia and Poland (mostly Jews) 98.21 76.72

Scotland 384.12 269.24

Scandinavia 357.00 218.92

Canada 352.32 266.27

Germany 328.80 295.61

France 394.98 252.82

England and Wales 322.50 233.78

Italy 233.85 123.00

United States (White) 205.14 180.79

Hungary (mostly Jews) 155.05 120.77

Jacobs J. The Jewish Encyclopedia; a guide to its contents, an aid to its use. New York, London: Funk & Wagnalls company; 1906.

NYC, 6 years before 1890 per 100,000

Tissue-based co-expression modules define genes with correlated gene expression

Gene in IBD-associated locus

Module with greatest enrichment for IBD genes: 523 module from adipose tissue

NOD2

Highly correlated RNA expression between NOD2, IL10 & HCK (hematopoietic cell kinase)

- HCK: key for differentiation of M2 macrophages

NOD2

HCK

IL10VDR

SLC11A1

DOK3

CARD9

LGALS9

Unexpected relationship between abdominal fat and IBD

Transmural disease complications

Creeping fat

Adipose tissue an abundant source of TNF

Rare variants--less power to detect association, but greater effect sizes (i.e., odds ratios, OR)

Magnitude of effect

Freq

uenc

y of

ge

netic

var

iatio

n

Uncommon variation of large effect (Mendelian)

Common variation of small effects

Not typically present

Not identifiable

0.50

1 (baseline risk)

RiskProtective

GWASMost associations with small effects, OR < 1.1

1% vs. 0.3% OR ~3

Negative selection: deleterious alleles are low frequency

At least 3 of 4 components of Mendelian susceptibility to Mycobacterial diseases (MSMD) genes also associated to IBD

Key components: 1. IL12/23 signaling2. IFNg signaling3. CD40-CD40L interaction 4. NADPH oxidase system **

*

*

**

** ***

**

** *IBD-associated gene

Casanova et al., Immunity 2012 36: 515

*

What about the NADPH oxidase system??

NADPH oxidase deficiency & IBD Autosomal recessive mutations in NCF2 (p67phox)

associated with chronic granulomatous disease NCF4: nominal association to IBD by GWAS

(association signal stronger in AJs) NCF2 mutations at Arg38

Arg38Gln: 0.5% allele in very-early onset IBD with 24x increased risk (Muise et al, Gut 2012)

Ashkenazi Jewish exome sequencing: identified an AJ-specific, distinct mutation Arg38Trp (0.51% allele, 4.4x increased risk)

Both mutations, Arg38Gln, Arg38Trp impaired binding to RAC2 Implicates impaired NADPH oxidase function in adolescent/adult-

onset IBD as well as very-early onset IBD

Conclusions & future directions IBD genetics: foundation for many of the most

impactful publications in IBD research Genetic architecture of IBD shaped in response to

mycobacterial infections—implications Host-microbiome interactions Can leverage the enormous existing biologic understanding of

innate responses to mycobacteria Leverage evolution and population differences

Rare mutations have higher effect sizes and may provide a more direct route to new therapies Early onset Population differences