Detecting Allelic Imbalance in Inflammatory Bowel Disease

Report
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
Critical role for the Paneth cell
Nature 2013
Genetics impact: IL-23 pathway & treatment
Science 2006
PNAS 2011
Salt increases
IL23R expression
Nature 2013
NEJM 2012
IBD Immunochip: 163 loci associated
to IBD
Cumulative IBD loci
150
100
GWAS metaanalyses
NOD2
Singlecenter
GWAS
Immunochip
163 loci
MHC in
50
UC
0
2000 2002 2004 2006 2008 2010 2012
Nature, 2012
Year
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
Genetic architecture: Crohn’s disease vs.
ulcerative colitis in European ancestry cohorts
Crohn’s disease
Arg381Gln
Ulcerative
colitis
 IL23R in both
 MHC major in UC
 Crohn’s diseaseuniquely lacks a
dominant MHC signal
 Instead, innate immune
defects: NOD2 &
ATG16L1
Nature 2001;411:603
Science 2006;314:1461
Nat Genet. 2009;41:216
**Nat Genet. 2011;43:246
**Nat Genet. 2010;42:1118
Nat Genet. 2011;43:1066
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 loci163 genome-wide significant loci
IBD vs. control odds ratio
Defining the genetic architecture of CD
vs. UC
IL23R
>1.5
1.4
1.3
1.2
23 UC
specific
loci
110 IBD
loci
NOD2
30 CD
specific
loci
MHC
1.1
PTPN22
0.67
1.0
CD vs. UC odds ratio
>1.5
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
IBD loci
82
53
82
Immune-mediated
diseases
MSMD
Primary
82 immune
CMC
deficiencies
Chronic mucocutaneous candidiasis (CMC): CARD9, STAT3
Mycobacterial disease
Striking overlap between IBD & mycobacterial
susceptibility
NOD2
RIPK2
TNFSF15
LRRK2
IL23R
C13orf31
*
163 IBD loci
6/7
7 leprosy
GWAS loci
7/9
IL12B
STAT1
IRF8
TYK2
STAT3
IFNGR2
IFNGR1
9 single gene
mycobacterial (Tb) genes
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
NYC, 6 years before 1890 per 100,000
Deaths from tuberculosis, London 1894-1900
Population
Deaths per 100,000
Mussulman Arabs
1130
Europeans
513
Jews
75
Jacobs J. The Jewish Encyclopedia; a guide to
its contents, an aid to its use. New York, London:
Funk & Wagnalls company; 1906.
Population
NY
Brooklyn
African-American
774.21
531.35
Ireland
645.73
452.79
Bohemia
499.13
347.22
Russia and Poland
98.21
(mostly Jews)
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
Tissue-based co-expression modules define
genes with correlated gene expression
Module with greatest enrichment for IBD
genes: 523 module from adipose tissue
NOD2
SLC11A1
IL10
VDR
NOD2
HCK
CARD9
DOK3
LGALS9
Gene in IBDassociated locus
Highly correlated RNA expression
between NOD2, IL10 & HCK
(hematopoietic cell kinase)
- HCK: key for differentiation of
M2 macrophages
Unexpected relationship between abdominal
fat and IBD
Transmural disease
complications
Adipose tissue an
abundant source of TNF
Creeping fat
Rare variants--less power to detect association,
but greater effect sizes (i.e., odds ratios, OR)
Frequency of
genetic variation
0.50
Protective
Common variation
of small effects
GWAS
Most associations with
small effects, OR < 1.1
Not typically
present
Negative selection: deleterious
alleles are low frequency
1% vs. 0.3% OR ~3
Not
identifiable
1
(baseline risk)
Uncommon variation
of large effect
(Mendelian)
Risk
Magnitude of effect
At least 3 of 4 components of Mendelian susceptibility to
Mycobacterial diseases (MSMD) genes also associated to IBD
*
*
**
*
*
* *
*
* **
**
Key components:
1. IL12/23 signaling
2. IFNg signaling
3. CD40-CD40L interaction
4. NADPH oxidase system
What about the NADPH
oxidase system??
*
*
*IBD-associated gene
Casanova et al., Immunity 2012 36: 515
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

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