Understanding the Next Steps in Determining the
Role of the Genome in IBD
Judy H. Cho, M.D.
Ward-Coleman Professor of Translational Genetics and Medicine, Icahn
School of Medicine at Mount Sinai
December 6th, 2014
Questions
 What naturally occurring genetic polymorphisms are
associated with IBD?
What naturally occurring genetic
polymorphisms are associated with IBD?
Assessment
 Value: molecular insight profoundly shaped the
landscape of IBD research
 What’s worked and what hasn’t
 Family-based: linkage NOD2. Otherwise, family-based studies have not
worked—re-vist with microbiome-based studies & genetic counseling
 Case-control:  163 loci and counting
 Surprises & advances
 Magnitude of sample sizes required unexpected: NOD2 (Nature 2001)
involved 416 CD samples - > 30,000 cases
 Number of significant loci larger than expected: 163 and counting
 Advances: autophagy, IL-23 pathway, M1-M2 macrophage subsets
 Challenges: long journey from genes biology drug targeting  new
drugs
Questions
 What naturally occurring genetic polymorphisms are
associated with IBD?
 What are the functional consequences of IBDassociated polymorphisms?
What are the functional consequences of IBDassociated polymorphisms?
 Altered cytokine responses to microbial stimulation :
NOD2, XIAP (direct); many indirect effects
 Genotype-dependent variable bacterial clearance:
autophagy, NADPH oxidase
 Direct ex vivo analyses
 IL23R and Th17/Tc17 cells (Sarin et al., PNAS 2011)
 NOD2 & Paneth cell morphologies (Van Dussen
Gastroenterology 2014)
 Altered regulation of gene expression
What are the functional consequences of IBDassociated polymorphisms?
 Altered cytokine responses to microbial stimulation :
NOD2, XIAP
 Genotype-dependent variable bacterial clearance:
autophagy, NADPH oxidase
 Direct ex vivo analyses
 IL23R and Th17/Tc17 cells (Sarin et al., PNAS 2011)
 NOD2 & Paneth cell morphologies (Van Dussen
Gastroenterology 2014)
 Altered regulation of gene expression
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
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 CD loci genes in open chromatin
regions of Th17 cells, but not monocytes
Category (N)
Th17 cell
DNase I HS
site
Monocyte
DNase I HS
site
Yes (14,267)
No (10,195)
Yes (16,317)
No (8145)
CD loci
non CD loci
log OR
(#gene=1328) (#gene=23,134)
(95% CI)
945 (71.2%) 13,322 (57.6%)
0.6
(0.48, 0.72)
383 (28.8%) 9812 (42.4%)
862 (64.9%) 15,455 (66.8%)
-0.08
466 (35.1%) 7679 (33.2%) (-0.20, 0.032)
p-value
5.90E-22
 Apples to oranges: Th17 cells vs. monocytes
 Pending: tissue-specific enhancer landscape of
organ- and context-specific tissue macrophages
0.15
From co-expression to (genetic) causal
networks
aka NRAMP
NOD2
SLC11A1
IL10
VDR
HCK
CARD9
DOK3
Highly correlated RNA expression
between NOD2, IL10 & HCK
(hematopoietic cell kinase)
 HCK: key for differentiation of
M2 macrophages
LGALS9
Gene in IBDassociated locus
 Cis eQTL in HCK: variable HCK
expression is driving variable
NOD2 & IL10 expression
Eric Schadt
Jostins et al, Nature 2012
Primary value of direct ex-vivo analyses:
pathogenic & protective cells
Defining innate cell hierarchies by high-dimensional Cytof analysis
Uninflamed
CD14
HLADR
BDCA3
Inflamed
 High dimensional analyses
needs to be matched to
deep clinical information
 Basic science questions
 Cellular plasticity and
diffentiation
 DNA-RNA-protein
What are the functional consequences of IBDassociated polymorphisms?
 Altered cytokine responses to microbial stimulation :
NOD2, XIAP
 Genotype-dependent variable bacterial clearance:
autophagy, NADPH oxidase
 Direct ex vivo analyses
 IL23R and Th17/Tc17 cells (Sarin et al., PNAS 2011)
 NOD2 & Paneth cell morphologies (Van Dussen
Gastroenterology 2014)
 Altered regulation of gene expression
Acceleration of in vitro & in vivo studies with CRISPR/CAS9 technologies:
refined genetic & molecular definition will improve modeling
Questions
 What naturally occurring genetic polymorphisms are
associated with IBD?
 What are the functional consequences of IBDassociated polymorphisms?
 Why do Ashkenazi Jewish populations have a higher
IBD prevalence?
 Rare variants
 Common variants
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
Ashkenazi Jews with a higher composite burden
score than non-Jewish European ancestry
IBD Genetic Burden Score
Developing integrative models
of common variant risk?
Striking overlap between IBD & mycobacterial
susceptibility
NOD2
RIPK2
**TNFSF15
163 IBD loci
LRRK2
IL23R
7/9
6/7
C13orf31
7 multigenic
leprosy
GWAS loci
IL12B
STAT1
IRF8
TYK2
STAT3
IFNGR2
IFNGR1
9 single gene
mycobacterial (Tb) genes
Anti-TNF treatment of IBD associated with re-activation
of latent mycobacterial disease
NEJM 2001; 345: 1098
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.
Polygenic adaptation: positive
selection at scores to hundreds of
genes that confer selective advantage
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
Questions
 What naturally occurring genetic polymorphisms are
associated with IBD?
 What are the functional consequences of IBDassociated polymorphisms?
 Why do Ashkenazi Jewish populations have a higher
IBD prevalence?
 What factors are genetic and what are nongenetic/stochastic/developmental?
 Better modeling of genetic contributions
 More frequent modeling of environmental/stochastic
factors
Systematic analysis of rare variants
via enteroids
Biopsy
Add growth factors
Stem cells
Stem cells
> Ascertaining by genotypes
> CRISPR-CAS9
Bank of rare variants
broadly amenable for study
IgA-coating enriches for colitogenic bacteria
 Stool-based collections: IgA enrichment may identify
functionally important bacteria—reducing microbial
complexity
 Frequent sampling
Palm et al., Cell 2014
Questions
 What naturally occurring genetic polymorphisms are
associated with IBD?
 What are the functional consequences of IBDassociated polymorphisms?
 Why do Ashkenazi Jewish populations have a higher
IBD prevalence?
 What factors are genetic and what are nongenetic/stochastic/developmental?
 UC: limited vs. extensive disease
 CD: ileal post-op—modeling first steps of disease
recurrence
 Age-dependent effects: disease severity & age of onset
Acknowledgements
 Cho lab

NIDDK IBD Genetics Consortium
 Steve Brant
 Richard Duerr
 Dermot McGovern
 John Rioux
 Mark Silverberg
 Mark Daly
 Phil Schumm

Thad Stappenbeck-Wash U: enteroids

Yale University
 Clara Abraham
 Richard Flavell

RISK Pediatric Consortium
 Subra Kugathasan
 Ted Denson
 Ken Hui
 Monica Bowen
 Kyle Gettler
 Kaida Ning
 Nai-Yun Hsu
 Felix Chuang
 Yashoda Sharma
 Mount Sinai collaborators
 Inga Peter
 Eric Schadt
 Miriam Merad
 Bruce Sands
 Jean-Fred Colombel