Multi-ethnic GWAS and meta-analysis of sleep quality identify MPP6 as a novel gene that functions in sleep center neurons

Abstract

Poor sleep quality can have harmful health consequences. Although many aspects of sleep are heritable, the understandings of genetic factors involved in its physiology remain limited. Here, we performed a genome-wide association study (GWAS) using the Pittsburgh Sleep Quality Index (PSQI) in a multi-ethnic discovery cohort (n = 2868) and found two novel genome-wide loci on chromosomes 2 and 7 associated with global sleep quality. A meta-analysis in 12 independent cohorts (100 000 individuals) replicated the association on chromosome 7 between NPY and MPP6. While NPY is an important sleep gene, we tested for an independent functional role of MPP6. Expression data showed an association of this locus with both NPY and MPP6 mRNA levels in brain tissues. Moreover, knockdown of an orthologue of MPP6 in Drosophila melanogaster sleep center neurons resulted in decreased sleep duration. With convergent evidence, we describe a new locus impacting human variability in sleep quality through known NPY and novel MPP6 sleep genes.

Keywords: MPP6; genome-wide association study; sleep centers; sleep quality.

Figure 1.

Regional association plots of discovery GWAS for PSQI global score in OPPERA. (a–b) Regional association plots for genome-wide significant loci at chromosome 7 using EUR as a reference panel (a) and AFR panel (b). (c–d) Regional association plot at chromosome 2 using EUR as reference panel (c) and AFR panel (d). (e–f) Regional association plots for suggestive loci at chromosome 13 using EUR as reference panel (e) and AFR panel (f) Chromosomal position (Mb) is indicated on the x axis, and the –log10 p-value is indicated on the y axis. Each SNP is plotted as filled circle and the lead SNP is shown in purple. The genes within each region are shown in the lower panel. Recombination sites and rates are shown in blue. Additional SNPs in the locus are colored according to linkage disequilibrium (r2) with the lead SNP. rs78633772 instead of rs376585198 as the latter is not in the reference panel.

Figure 2.

Pathway analysis of sleep GWAS using Gene ontology’s biological process. Horizontal bar plots represent –log10 p-value enrichment of pathways. The red line represents Bonferroni threshold for statistical significance.

Figure 3.

Forest plots in meta-analysis. Forest plots of standardized effect size with 95% confidence interval for each replication study as well as for the fixed-effect meta-analysis for genome-wide significant SNPs. Higher effect sizes represent worse sleep quality. The discovery cohort was excluded from the meta-analysis calculation. The test of heterozygosity for each SNP was Q(df 11) = 16.29 p = 0.13 for rs11976703; Q(df 10) = 20.52 p = 0.03 for rs73284230 and Q(df 8) = 6.74 p = 0.57 for rs60869707. The sample sizes for the meta-analysis is 100659, 99931, and 96386 for rs11575542, rs73284230, and rs60869707, respectively.

Figure 4.

LNv-specific knockdowns of varicose in D melanogaster. PDF-Gal4 is a neuron-specific driver. UAS-IR represents transgenic RNAi inverted repeats. PDF-Gal4/+, UAS-VariIR1-2/+ are parental control flies. PDF-Gal4>UAS-variIR1-2 are varicose knockdown flies within LNv neurons. (a) Circadian pattern of sleep (n = 28–32). (b) Percentage of sleep in day time and night time (n = 28–32). (c) Number of sleep episode in day time and night time (n = 28–32). (d) Sleep episode duration in minutes in day time and night time (n = 28–32). Data presented as mean ± SEM. Statistics were determined one-way ANOVA with Tukey’s multiple comparisons test. n.s., not significant, *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.001.