Recent progress in our understanding of IBD genetics
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Transcript Recent progress in our understanding of IBD genetics
State of the Art: Recent Progress in Understanding
of IBD Genetics
Judy H. Cho, M.D.
Ward-Coleman Professor of Translational Genetics and Medicine, Icahn
School of Medicine at Mount Sinai
December 5, 2014
Concepts
Rare vs. Common genetic variants
Rare variation
Age of onset & population considerations
When to sequence & sequence annotation
Common genetic variants & GWAS studies
Population differences
Non-coding functional variation
Rare vs. common human polymorphisms
Rare
Common
1. Often population-specific
1. Present across populations
2. Most missense alleles are rare
2. Large majority are non-coding
3. Selection: negative selection
3. Selection: balancing , positive
4. Association signals: greater
effect sizes (e.g. OR > 1.5) for
nominally associated variants
4. GWAS-identified significant loci
have modest effects (i.e., odds
ratios)—most less than 1.1
5. Less power—most samples
are homozygous wild-type
5. Greater power to detect
association
Monogenic Early-onset IBD
Mendelian IBD: IL10
deficiency--neonatal
Immunodeficiencies with
variable age of onset
FOXP3: IPEX
WAS: Wiscott-Aldrich
LRBA: LPS-responsive, CVID8
Chronic granulomatous disease
XIAP: X-linked inhibitor of
apoptosis
10 years old
Uhlig et al., Gastroenterology 2014
XIAP, NOD2 and Crohn’s disease
XIAP: X-linked inhibitor of apoptosis
Many XIAP missense mutations—extremely rare
XLP2: X-linked lymphoproliferative immunodeficiency
CD-unique private mutations: (potentially) as high as 4% of
pediatric male IBD cases
Ileocolonic plus perianal disease
NOD2-signaling deficiency
Variable disease course—majority responsive to
traditional therapy
Numbers small, but XIAP-deficiency appears to have a
higher penetrance than NOD2-deficiency
Zeissig et al, Gut 2014
When to consider sequencing
Research? Clinical?
Eventually all of us!!!
Early onset IBD—especially males
Consanguineous
Immunodeficiency plus IBD
ATG16L1 & sequence annotation
ATG16L1 T300A variant: alanine CD risk
Caspase-3 & -7 cleavage sequence: -D-X-X-D-(T/A)Alanine variant increased ATG16L1 degradation
Clearly establishes that CD risk allele is correlated
with impaired autophagy
Sequence annotation: prediction of new/altered
covalent modifications
Murthy et al., Nature 2014
Lassen et al., PNAS 2014
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
AJ-specific frameshift mutation in CSF2RB
associated to IBD
Gene
Function
IBD
Freq
CSF2RB
GMCSF
receptor
0.032
control
odds
P-value
type group
freq
ratios
AJ0.02 0.00104 1.6 IBD
specific
CSF2RB: common subunit to GMCSF, IL3, IL5
Truncation mutation: ~200 aa in cytoplasmic tail
Common variants in this region nominally
associated—also NCF4 (Rioux et al., Nature Genetics 2007)
GMCSF & IBD
Anti-GMCSF antibodies
CD patients with elevated anti-GMCSF Ab
NOD2-deficient mice + neutralizing anti-GMCSF +
piroxicam ileitis
Anti-GMCSF Ab levels correlate with increased disease
complications
GMCSF cytokine
Induces IL10, retinoic acid
Potential therapeutic benefit
Han et al., Gastroenterology 2009, 1261
Gathungu et al., IBD 2013, 1671
Mortha et al., Science 2014
Korzenik et al., NEJM 2005
Concepts
Rare vs. Common genetic variants
Rare variation
Age of onset & population considerations
When to sequence & sequence annotation
Common genetic variants & GWAS studies
Population differences
Non-coding functional variation
Distinct genetic architecture for dominant loci:
European ancestry vs. Japanese Crohn’s disease GWAS
European ancestry
Arg381Gln
Japanese
MHC
TNFSF15
Yamazaki, et al,
Gastroenterology
2013; 781
GWAS/common alleles: vast majority demonstrate
similar direction & effect sizes across populations
Exceptions—biggest effect loci
European ancestry
Asian
Alleles
NOD2
R702W, G908R, fs1007
uncommon risk
monomorphic
IL23R
R381Q
uncommon protective monomorphic
non-coding IL23R
associated
associated
different alleles
ATG16L1
T300A
Risk is LOF
Smaller/no effect
TNFSF15
non-coding TNFSF15
Smaller effects
Risk is GOF
same alleles
Yang et al., IBD 2009
Kim et al., Gut 2014
Hedl et al., PNAS 2014
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
Diseases examined by GWAS
21 different autoimmune diseases
Comparative diseases
Metabolic traits
Neurologic diseases
Most correlated: UC-CD-Ankylosing
spondylitis-psoriasis-Behcet’s disease
Navy blue: no correlation
Maroon red: highest correlation
Farh et al., Nature 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 GWAS signals in cell
type specific enhancers (H3K27ac)
T cells
B cells
Colonic
mucosa
T cell enrichment: RA,
MS, IBD, celiac disease
B cell enrichment: RA>
IBD
Monocyte signal: largely
absent except CRP
Tissue-macrophage
specific signals?
Marked enrichment of
colonic mucosa in UC
RA
CD-UC
Y-axis: 33 cell type H3K27ac
X-axis: 39 diseases
Farh et al., Nature 2014
GWAS and eQTL SNPs show (apparently)
different molecular distributions
eQTL dataset: peripheral blood RNA from twins
BUT: eQTL distribution for stimulated (LPS, IFNg)
gene expression is likely quite different
Value of eQTLs-risk allele alignment: implies
directionality—gain/loss of function
Wright et al., Nature Genetics 2014
Farh et al., Nature 2014
Conclusions
Sequencing and rare variant-associated IBD
Younger, severe, select populations
Establishing genome-wide significance is
challenging—need for early functional analysis
Common variant fine-mapping
“Single” causal allele identifiable statistically in only a
minority of cases
Greatest enrichment of GWAS signals in H3K27ac
active enhancer regions—near, but not in consensus
transcription factor binding sites
Imperfect molecular matching of GWAS and eQTLs:
need to define cell and activation state specificities
Power of genetics: earliest pathophysiologic
mechanisms, precise therapeutic targeting
Acknowledgements
Cho lab
Ken Hui
NIDDK IBD Genetics Consortium
Steve Brant
Monica Bowen
Richard Duerr
Kyle Gettler
Dermot McGovern
Nicole Villaverde
John Rioux
Nai-Yun Hsu
Mark Silverberg
Mark Daly
Felix Chuang
Phil Schumm
Yashoda Sharma
Mount Sinai collaborators
Clara Abraham
Inga Peter
Eric Schadt
Miriam Merad
Bruce Sands
Jean-Fred Colombel
Yale University
Richard Flavell
The Ashkenazi Jewish Consortium
Itsik Pe’er
Todd Lencz