identifying dysregulated genes in autoimmune disease

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Identifying Dysregulated Genes in Autoimmune DiseaseChris Cotsapas PhD Yale Neurology/Genetics
Broad Institute [email protected]
Broad Institute [email protected]
47 new   hit15,000 Immunochip 200,000 SNPs   (targeted)  10,000 25 new   hits
WTCCC2 8000 650,000 SNPs  
MS 6000 Subjects Meta-­Analysis 3 new   hits
2.6 million  SNPs  4000 Meta v2.5 6 new   hits 2.6 million  SNPs  IMSGC GWAS 1 new   hit
2000 345,000 SNPs   ANZ  GWAS2 hits
550,000 SNPs   IMSGC NEJM 2007
De Jager et al. Nat Genet 2009 2007 2008 2009 2010 2011 2012 Rubio et al. Nat Genet 2009
IMSGC Nature 2011
Date of comple/on  
Meta-­Analysis v3.0… and that’s not all! 16K MS cases / 26K controls
Replica;on 18K MS cases / 18K controls
100 new  hits
47 new   hit15,000 Immunochip 200,000 SNPs   (targeted)  10,000 25 new   hits
WTCCC2 8000 650,000 SNPs  
MS 6000 Subjects Meta-­Analysis 3 new   hits
2.6 million  SNPs  4000 Meta v2.5 6 new   hits 2.6 million  SNPs  IMSGC GWAS 1 new   hit
2000 345,000 SNPs   ANZ  GWAS2 hits
550,000 SNPs   IMSGC NEJM 2007
De Jager et al. Nat Genet 2009 2007 2008 2009 2010 2011 2012 Rubio et al. Nat Genet 2009
IMSGC Nature 2011 Date of comple/on   Patsopoulos et al. Ann Neurol 2011
GWAS signals are enriched in regulatory DNA
Maurano et al Science 2012
MS GWAS hits enriched in transcription factor binding sites
Farh et al Nature 2015
Plotted SNPs
8
6
4
2
0
103.4 103.5 103.6 103.7
Position on chr4 (Mb) IMSGC, Nat Genet, 2013 Housley et al STM 2015
0
20
40
60
80
100
Supplementary File
B
IMSGC, Nat Genet, 2013
Regulatory posterior RP = Σ(PPADHS)
Problem 1: DHS-gene correlations
CD 3 CD 14 CD 34 Thymus Kidney Lung Heart Brain
Gene 1 Gene 2
CD 3 CD 14 CD 34 Thymus Kidney Lung Heart Brain
Parisa Shooshtari
Align over 57 tissue replicates from REP
C1 1 C1 2 Tissues Hotspot peaks C2
C3 1 1
C2 C3
2 1
T1-Rep1 C4 0 C4 0 T1-Rep2 2 C5 0 C5 0
T2-Rep1 T2-Rep2 1
T4-Rep1 T4-Rep2 2
Cover 8% of genome (cf. 14% of all DHS) T5-Rep2
T6-Rep1 2 T6-Rep2 NB singletons, low power
Scenario 1
1 1
Proportion of Heritability QC+ DHS clusters capture most MS heritability
Caveat DHS clusters are
Parisa Shooshtari Hilary Finucane Alkes Price
Pr op
or tio
n of
h 2g
Correction
Challenge 2: Gene expression correlation QQ plot for P Value of Correlation Between
One DHS and 14000 Genes
Correlation Structure of the Gene Expression Data
Before Correction After
Regulatory posterior RP = Σ(PPADHS)
GABRR2 0.106 RRAGD 0.065 GJA10 0.029
MAP3K7 0.028
72
B
Supplementary File
IKZF3/ORMDL3 locus Gene GP
Chr 17 ORMDL3 0.029 34.5-35.5Mb PIP4K2B 0.022 RP = 0.295 IGFBP4 0.018
IKZF3 0.015 GSDMB 0.014
ZPBP2 0.009 MED1 0.009
MED24 0.009 KRT24 0.009 PNMT 0.008 CDK12 0.007 RPL23 0.007 PSMD3 0.007 PLXDC1 0.006 TOP2A 0.006 RARA 0.006
MS GWAS hits enriched in transcription factor binding sites
Farh et al Nature 2015
MS GWAS risk effect: NFKB1 locus
MS patients show altered NFκB signaling in CD4+ T cells
Figure 1. Naïve CD4 cells from patients with MS exhibit increased phospho-p65 NFκB. Flow cytometry of PBMCs from age-matched healthy control (HC) and relapsing-remitting MS (RRMS) patients stained for CD4, CD45RA, CD45RO, and pS529 p65 NFκB. MFI of p65 results are shown gated on naïve CD4+CD45RA+CD45RO- T-cells.
CD4+ T cells from MS patients proliferate more rapidly after
stimulus (Kofler et al JCI 2014)
ex vivo CD4+ T cells show higher p-p65 (Housley et al, STM 2015)
0 15 30 0
ti o
TNF-α PMA
a b
MS risk effect near NFKB1 alters signaling in CD4+ cells
Housley, unpublished
GWAS loci harbor many NFκB genes
Housley, unpublished
p50
P-p50
Systematic dissection I
0 exposure
3d cell phenotype
25 NFKB1 risk variant homozygotes 25 NFKB1 non-risk variant homozygotes
Acknowledgements • IMSGC
– David Hafler – Phil De Jager – Steve Hauser – Adrian Ivinson – Nikos Patsopoulos – Many, many others
• Partners – David Hafler – Phil De Jager – Brad Bernstein – John Stamatoyannopoulos
• Yale labs – Parisa Shooshtari – Mitja Mitrovic – Alex Casparino – Will Housley
8.6e-09 1.6e-08 3.2e-09 1.5e-08 1.5e-08
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