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ARTICLE

NATURE COMMUNICATIONS | DOI: 10.1038/ncomms10448

Table 3 | Top five morningness-associated pathways analysed by MAGENTA.
Database

Gene set*

KEGG

Circadian rhythm

REACTOME

REACTOME

REACTOME

REACTOME

13

Gene set
P value
2.0 10 4

0.059

Circadian clock

53

4.0 10 4

0.20

BMAL1, CLOCK, NPAS2 activates
circadian expression

36

1.9 10 3

Tetrahydrobiopterin BH4 synthesis
recycling salvage and regulation

Phospholipase C b-mediated events

# Of genes

13

43

3.1 10 3

4.3 10 3

FDR

Gene level
P valuew
1.6 10 8
1.4 10 7
1.2 10 3
3.7 10 3
5.2 10 3
1.6 10 8
9.4 10 8
1.2 10 3
3.7 10 3
5.2 10 3
1.5 10 2
2.6 10 2
3.0 10 2
3.9 10 2
4.3 10 2
1.6 10 8

Variant

0.42

Gene
name
PER2
PER3
ARNTL
CRY1
CRY2
PER2
FBXL3
ARNTL
CRY1
CRY2
NCOA6
MEF2C
NR3C1
ATF2
SERPINE1
PER2

rs150174970
rs11121022
rs12805304
rs12298001
rs7127456
rs150174970
rs9565309
rs12805304
rs12298001
rs7127456
rs140865084
rs13155750
rs10482700
rs7554 8314
rs75413959
rs150174970

Variant specific
P value
7.8 10 9
2.0 10 8
9.3 10 6
3.1 10 5
5.5 10 5
7.8 10 9
3.5 10 8
9.3 10 6
3.1 10 5
5.5 10 5
1.7 10 4
1.9 10 4
1.8 10 4
3.1 10 4
3.5 10 4
7.8 10 9

0.22

ARNTL
CRY1
CRY2
NCOA6
NR3C1
SERPINE1
GCHFR

1.2 10 3
3.7 10 3
5.2 10 3
1.5 10 2
3.0 10 2
4.3 10 2
2.3 10 2

rs12805304
rs12298001
rs7127456
rs140865084
rs10482700
rs75413959
rs8036891

9.3 10 6
3.1 10 5
5.5 10 5
1.7 10 4
1.8 10 4
3.5 10 4
2.9 10 4

GCH1
AKT1
NOS3
GNAO1
PRKAR2A
GNAT2
GNAI3
ADCY3
GNAT1
GNAI2
PRKACG

2.4 10 2
3.8 10 2
3.9 10 2
6.2 10 4
1.4 10 3
5.1 10 3
5.5 10 3
8.7 10 3
1.0 10 2
1.1 10 2
4.7 10 2

rs998259
rs117725127
rs3800779
rs2398144
rs56411893
rs72705206
rs72705206
rs4665746
rs62263597
rs2282749
rs10118146

2.0 10 4
3.1 10 4
3.1 10 4
5.5 10 6
3.2 10 5
6.9 10 5
6.9 10 5
5.6 10 5
1.7 10 4
1.7 10 4
3.3 10 4

0.52

FDR, false discovery rate.
*The gene set is from the database of canonical pathways of 1,320 biologically defined gene sets (http://www.broadinstitute.org/gsea/msigdb/index.jsp).
wFor each pathway, we only include genes with a P valueo0.05.

results (Table 3). The top three pathways are circadian related
and share four genes: PER2 (gene based P value ¼ 1.6 10 8),
ARNTL (P ¼ 1.2 10 3), CRY1 (P ¼ 3.7 10 3) and CRY2
(P ¼ 5.2 10 3). In addition, PER3 (P ¼ 1.4 10 7), in the
KEGG circadian rhythm pathway, and FBXL3 (P ¼ 9.4 10 8),
in the REACTOME circadian clock pathway, have strong effects
and were implicated in our GWAS. Other circadian genes also
contribute to the enrichment of circadian pathways, but less
significantly (Table 3). The BH4 related pathway (gene set
P ¼ 3.1 10 3) has a major role in the biosynthesis of melatonin, serotonin and dopamine, which are important hormones
involved in circadian rhythm regulation and brain function. The
phospholipase C (PLC) b-mediated events pathway (P ¼ 4.3
10 3) includes GNAO1 (P ¼ 6.2 10 4), GNAI3 (P ¼ 5.5
10 3), GNAT1 (P ¼ 1.0 10 2) and many other G protein
related genes involved in visual phototransduction. GNAT1 is
related to night blindness45 and GNAI3 is known to interact with
RGS16 (ref. 46). Interestingly, RGS16 is close to our GWAS top
hit. This pathway also includes PRKAR2A (P ¼ 1.4 10 3) and
PRKACG (P ¼ 0.047), which relate to cAMP dependent protein
kinase A, known to regulate critical processes in the circadian
negative feedback loops47. Notably, except for the KEGG
circadian rhythm pathway, which has a false discovery rate

0.06, all other associated pathways have false discovery rate
40.2, meaning the statistical evidence of the association is not
strong.
We assessed correlations between morningness and related
phenotypes with adjustment for potential confounders by regression with covariates for age, gender and ancestry (Table 4). The
covariate-adjusted odds of having insomnia for morning people is
55% of that for night people (P ¼ 1.5 10 140) and the adjusted
odds of having sleep apnoea for morning people is 64% of that for
night people (P ¼ 4.0 10 54). Morning people are also less
likely to require 48 h of sleep (OR ¼ 0.69, P ¼ 6.3 10 53), to
sleep soundly (OR ¼ 0.81, P ¼ 6.8 10 24), to have restless leg
syndrome (OR ¼ 0.71, P ¼ 4.1 10 15) and sweat while sleeping
(OR ¼ 0.90, P ¼ 7.9 10 6) after adjusting for covariates.
Sleepwalking and actual amount of sleep do not correlate with
morningness (P40.1) in the full model. These associations are
consistent with previous studies of insomnia48, sleep apnoea49
and sleep needed50. We calculated the association between the 15
GWAS identified SNPs and these eight sleep phenotypes
(Supplementary Table 4) but found no significant associations.
In addition, we looked up the SNPs and their proxies in the latest
BMI GWAS from the GIANT consortium51 and the latest major
depressive disorder GWAS from the CONVERGE Consortium52.

NATURE COMMUNICATIONS | 7:10448 | DOI: 10.1038/ncomms10448 | www.nature.com/naturecommunications

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