Transcriptome-wide association study of schizophrenia and ... · METabolic Syndrome In Men...
Transcript of Transcriptome-wide association study of schizophrenia and ... · METabolic Syndrome In Men...
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Transcriptome-wide association study of schizophrenia and
chromatin phenotypes
Alexander (Sasha) Gusev
Harvard TH Chan School of Public Health
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Challenges of studying complex disease
• Goal: specific mechanistic hypotheses.
• Schizophrenia is highly polygenic, with up to 70% of 1MB regions harboring an association
• For an associated SNP, causal mechanism often not through nearest gene [… or mediated by CNV / TFBS / etc]
• Relevant molecular features (RNA-seq/ChIP-seq in brain) are difficult to collect
Loh et al. 2015b Nat. Genet.; Sekar et al. 2016 Nature
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Methods for molecular + GWAS data:
Gusev et al. 2016 Nat. Genet.
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Outline
1. TWAS: [cis] molecular features can be predicted into un-assayed samples
2. TWAS to find expression associated with schizophrenia
3. TWAS to find expression associated with ChIP-Seq chromatin activity
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Outline
1. TWAS: [cis] molecular features can be predicted into un-assayed samples
2. TWAS to find expression associated with schizophrenia
3. TWAS to find expression associated with ChIP-Seq chromatin activity
![Page 6: Transcriptome-wide association study of schizophrenia and ... · METabolic Syndrome In Men (METSIM): 600 adipose RNA-seq Young Finns Study (YFS): 1,300 blood array 4 Expression Reference](https://reader030.fdocuments.us/reader030/viewer/2022040622/5d28761888c9939b378da7ab/html5/thumbnails/6.jpg)
TWAS using individual-level data
C T G T A
G T C A A
C A G T C
~
C A G T C
C A G T C
C A C A A
G T G A C
~
individual GWAS data
β1 β2 β3 β4 β5
C A C T C
G T C T A
Linear genetic
predictor
60-80% prediction
accuracy
expression reference
Gamazon et al. 2015 Nat Genet; Gusev et al. 2016 Nat Genet
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TWAS using summary-level data
2 1 2 5 1
7
R2 > 0.9 w/
individual-level
prediction
summary GWAS data
C T G T A
G T C A A
C A G T C
~
β1 β2 β3 β4 β5
Linear genetic
predictor
60-80% prediction
accuracy
expression reference
Gusev et al. 2016 Nat Genet; Barbeira et al. biorxiv
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Outline
1. TWAS: [cis] molecular features can be predicted into un-assayed samples
2. TWAS to find expression associated with schizophrenia
3. TWAS to find expression associated with ChIP-Seq chromatin activity
![Page 9: Transcriptome-wide association study of schizophrenia and ... · METabolic Syndrome In Men (METSIM): 600 adipose RNA-seq Young Finns Study (YFS): 1,300 blood array 4 Expression Reference](https://reader030.fdocuments.us/reader030/viewer/2022040622/5d28761888c9939b378da7ab/html5/thumbnails/9.jpg)
TWAS for schizophrenia
CommonMind Consortium (CMC) 1: 500 brain RNA-seq alternative splice variants 2 Netherlands Twin Registry (NTR)3: 1,200 blood array METabolic Syndrome In Men (METSIM): 600 adipose RNA-seq Young Finns Study (YFS): 1,300 blood array
4 Expression Reference Panels
GWAS: Psychiatric Genetics Consortium ~80,000 SCZ samples [PGC 2014 Nature]
[1] Fromer et al. 2016 Nat Neuro; [2] Li et al 2016 Science; [3] Wright et al. 2014 Nat Genet
C T G T A
G T C A A
C A G T C
~
2 1 2 5 1
7 TWAS
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157 gene associations (45 in novel loci) 80 splice-variant associations
conditioning on expression explains all genome-wide significant effect at known loci
TWAS for schizophrenia Z-
sco
re
chromosomes
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polygenic effects across thousands of genes
5e−0
8
1e−0
6
1e−0
4
0.00
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0.01
0.05 0.
1
0.2
0.5 1
CMC/brain genes
P−value threshold
liabi
lity−
scal
e R
2
0.00
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8
1e−0
6
1e−0
4
0.00
1
0.01
0.05 0.
1
0.2
0.5 1
CMC/brain splicing
P−value threshold
liabi
lity−
scal
e R
2
0.00
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5e−0
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1e−0
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1e−0
4
0.00
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0.05 0.
1
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0.5 1
METSIM/adipose
P−value threshold
liabi
lity−
scal
e R
2
0.00
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0.05
5e−0
8
1e−0
6
1e−0
4
0.00
1
0.01
0.05 0.
1
0.2
0.5 1
YFS/blood
P−value threshold
liabi
lity−
scal
e R
2
0.00
0.01
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0.03
0.04
0.05
5e−0
8
1e−0
6
1e−0
4
0.00
1
0.01
0.05 0.
1
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0.5 1
NTR/blood
P−value threshold
liabi
lity−
scal
e R
2
0.00
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8
1e−0
6
1e−0
4
0.00
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0.01
0.05 0.
1
0.2
0.5 1
ALL jointly
P−value threshold
liabi
lity−
scal
e R
2
0.00
0.01
0.02
0.03
0.04
0.05brain 0.05
0.04
0.03
0.02
0.01
polygenic score using predicted expression, evaluated in independent SCZ cohort
P-value threshold
R2
w/ SCZ status
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more associations with brain and splicing
5e−0
8
1e−0
6
1e−0
4
0.00
1
0.01
0.05 0.
1
0.2
0.5 1
CMC/brain genes
P−value threshold
liabi
lity−
scal
e R
2
0.00
0.01
0.02
0.03
0.04
0.05
5e−0
8
1e−0
6
1e−0
4
0.00
1
0.01
0.05 0.
1
0.2
0.5 1
CMC/brain splicing
P−value threshold
liabi
lity−
scal
e R
2
0.00
0.01
0.02
0.03
0.04
0.05
5e−0
8
1e−0
6
1e−0
4
0.00
1
0.01
0.05 0.
1
0.2
0.5 1
METSIM/adipose
P−value threshold
liabi
lity−
scal
e R
2
0.00
0.01
0.02
0.03
0.04
0.05
5e−0
8
1e−0
6
1e−0
4
0.00
1
0.01
0.05 0.
1
0.2
0.5 1
YFS/blood
P−value threshold
liabi
lity−
scal
e R
2
0.00
0.01
0.02
0.03
0.04
0.05
5e−0
8
1e−0
6
1e−0
4
0.00
1
0.01
0.05 0.
1
0.2
0.5 1
NTR/blood
P−value threshold
liabi
lity−
scal
e R
2
0.00
0.01
0.02
0.03
0.04
0.05
5e−0
8
1e−0
6
1e−0
4
0.00
1
0.01
0.05 0.
1
0.2
0.5 1
ALL jointly
P−value threshold
liabi
lity−
scal
e R
2
0.00
0.01
0.02
0.03
0.04
0.05brain brain splice-var
adipose blood blood 0.05
0.04
0.03
0.02
0.01
P-value threshold
all predicted cis-expression explain 26% of total SCZ SNP-heritability (upper bound on mediated effect)
R2
w/ SCZ status
polygenic score using predicted expression, evaluated in independent SCZ cohort
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Outline
1. TWAS: [cis] molecular features can be predicted into un-assayed samples
2. TWAS to find expression associated with schizophrenia
3. TWAS to find expression associated with ChIP-Seq chromatin activity
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Chromatin variation is under genetic control
[CEU] Waszak et al. 2015 Cell:
Local chromatin-expression interactions form modules.
[YRI] Grubert et al. 2015 Cell:
Chromatin variation and expression under shared genetic control,
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genome
connecting genes to chromatin peaks with top hits
for every gene:
expression - QTLs
for every peak
chromatin - QTLs
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TWAS for expression-chromatin associations
C T G T A
G T C A A
C A G T C
~
C A G T C
C A G T C
C A C A A
G T G A C
~
individual epigenomic data
β1 β2 β3 β4 β5
C A C T C
G T C T A
linear genetic
predictor
expression reference
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TWAS identifies 10x more gene/chromatin associations than eQTL overlap approach
0 100 200 300 400 500
0.0
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1.0
Power to detect gene−mark association
# chromatin samples
Pow
er
A
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TWAS
eQTL/cQTL overlap
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TWAS
eQTL/cQTL overlap
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European TWAS
Max distance to gene boundar y# s
ign
ific
an
t a
sso
cia
tio
ns
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100bp 1kb 2kb 10kb 50kb 100kb 250kb 500kb
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H3K4ME1
H3K4ME3
H3K27AC
PU1
RPB2
B
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0
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European QTL
Max distance to gene boundar y
# s
ign
ific
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t a
sso
cia
tio
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100bp 1kb 2kb 10kb 50kb 100kb 250kb 500kb
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H3K4ME1
H3K4ME3
H3K27AC
PU1
RPB2
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Yoruban TWAS
Max distance to gene boundar y
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H3K4ME3
H3K27AC
DHS
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Yoruban QTL
Max distance to gene boundar y#
sig
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t a
sso
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100bp 1kb 2kb 10kb 50kb 100kb 250kb 500kb
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H3K4ME1
H3K4ME3
H3K27AC
DHS
chromatin-TWAS overlapping top hits
distance to the gene TSS
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Validating TWAS gene-chromatin associations
brain/blood reference
expression
Discovery: TWAS gene–chromatin
associations
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Validating TWAS gene-chromatin associations
brain/blood reference
expression
blood target expression
Discovery: TWAS gene–chromatin
associations Replication: measured LCL RNA-seq
expression in chromatin samples
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Chromatin variation is highly associated with expression at predicted gene-peak associations
replication R2 ≈ total expression cis-hg2
ChIP-seq and expression from Waszak et al. 2015 Cell
NTR CMC
PU1
R2(m
ark
,GE
)
0.0
0.1
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TWAS−linked peaks
all nearby peaks
random
* *
NTR CMC
RPB2
R2(m
ark
,GE
)
0.0
0.1
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TWAS−linked peaks
all nearby peaks
random
****
**** ****
NTR CMC
H3K4ME1
R2(m
ark
,GE
)
0.0
0.1
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TWAS−linked peaks
all nearby peaks
random
** *** ** ***
NTR CMC
H3K4ME3
R2(m
ark
,GE
)
0.0
0.1
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0.3
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TWAS−linked peaks
all nearby peaks
random
**
*
***
**
NTR CMC
H3K27AC
R2
(ma
rk,G
E)
0.0
0.1
0.2
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0.5
TWAS−linked peaks
all nearby peaks
random
** **** ** ****
R2 chromatin-expression
(in LCLs)
blood brain
0.5
0.3
0.0
predicted gene-mark pairs background genes
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Enrichment for chromatin associations with SCZ TWAS genes
157 SCZ TWAS genes 42 with chromatin TWAS associations
4x background (P=1x10-11)
significant enrichment for SCZ splice variants with chromatin associations
2 1 2 5 1
7
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TWAS provides mechanistic hypotheses
108 SCZ loci 26/108 have TWAS splicing association
48/108 have TWAS splicing or gene association (76% not nearest gene)
34/48 also have chromatin association
(85% not in the promoter)
N=80,000
N=3,500
N=150
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TWAS provides mechanistic hypotheses
108 SCZ loci 26/108 have TWAS splicing association
48/108 have TWAS splicing or gene association (76% not nearest gene)
34/48 also have chromatin association
(85% not in the promoter)
N=80,000
N=3,500
N=150
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TWAS provides mechanistic hypotheses
108 SCZ loci 26/108 have TWAS splicing association
48/108 have TWAS splicing or gene association (76% not nearest gene)
34/48 also have chromatin association
(85% not in the promoter)
N=80,000
N=3,500
N=150
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Conclusion / Future Work
• TWAS implicates specific genes and their regulators.
• Epigenetic mediators can be a common disease mechanism
• Yields zozens of mechanistic hypotheses for schizophrenia loci (following up with experimental validation)
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Nick Mancuso Hilary Finucane Yakir Reshef Lingyun Song Alexias Safi Edwin Oh Steve McCarroll Ben Neale Mick O’Donovan Roel Ophoff
recruiting in new lab at Dana Farber Cancer Institute &
Harvard Medical School
gusevlab.org
Gregory Crawford Nicholas Katsanis Patrick F Sullivan Bogdan Pasaniuc Alkes L Price
Psychiatric Genomics Consortium CommonMind Consortium PsychENCODE 1000 Genomes
pre-print on biorxiv