A distinctive DNA methylation pattern in insufficient sleep
Tóm tắt
Short sleep duration or insomnia may lead to an increased risk of various psychiatric and cardio-metabolic conditions. Since DNA methylation plays a critical role in the regulation of gene expression, studies of differentially methylated positions (DMPs) might be valuable for understanding the mechanisms underlying insomnia. We performed a cross-sectional genome-wide analysis of DNA methylation in relation to self-reported insufficient sleep in individuals from a community-based sample (79 men, aged 39.3 ± 7.3), and in relation to shift work disorder in an occupational cohort (26 men, aged 44.9 ± 9.0). The analysis of DNA methylation data revealed that genes corresponding to selected DMPs form a distinctive pathway: “Nervous System Development” (FDR
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Pallesen, S., Sivertsen, B., Nordhus, I. H. & Bjorvatn, B. A 10-year trend of insomnia prevalence in the adult Norwegian population. Sleep Med. 15, 173–179 (2014).
Kronholm, E. et al. Prevalence of insomnia-related symptoms continues to increase in the Finnish working-age population. J. Sleep Res. 25, 454–457 (2016).
Kronholm, E. et al. Self-reported sleep duration, all-cause mortality, cardiovascular mortality and morbidity in Finland. Sleep Med. 12, 215–221 (2011).
Porkka-Heiskanen, T., Zitting, K. M. & Wigren, H. K. Sleep, its regulation and possible mechanisms of sleep disturbances. Acta Physiol. (Oxf) 208, 311–328 (2013).
American Academy of Sleep Medicine International Classification of Sleep Disorders, 3rd edn (2014).
Waage, S. et al. Shift work disorder among oil rig workers in the North Sea. Sleep 32, 558–565 (2009).
Flo, E. et al. Shift work disorder in nurses–assessment, prevalence and related health problems. PLoS One 7, e33981 (2012).
Di Milia, L., Waage, S., Pallesen, S. & Bjorvatn, B. Shift work disorder in a random population sample–prevalence and comorbidities. PLoS One 8, e55306 (2013).
Cirelli, C. & Tononi, G. Gene expression in the brain across the sleep-waking cycle. Brain Res. 885, 303–321 (2000).
Benedict, C. et al. Acute sleep deprivation increases serum levels of neuron-specific enolase (NSE) and S100 calcium binding protein B (S-100B) in healthy young men. Sleep 37, 195–198 (2014).
Massart, R. et al. The genome-wide landscape of DNA methylation and hydroxymethylation in response to sleep deprivation impacts on synaptic plasticity genes. Translational Psychiatry 4 (2014).
Cedernaes, J. et al. Acute Sleep Loss Induces Tissue-Specific Epigenetic and Transcriptional Alterations to Circadian Clock Genes in Men. J. Clin. Endocrinol. Metab. 100, E1255–61 (2015).
Ventskovska, O., Porkka-Heiskanen, T. & Karpova, N. N. Spontaneous sleep-wake cycle and sleep deprivation differently induce Bdnf1, Bdnf4 and Bdnf9a DNA methylation and transcripts levels in the basal forebrain and frontal cortex in rats. J. Sleep Res. 24, 124–130 (2015).
Skuladottir, G. V., Nilsson, E. K., Mwinyi, J. & Schiöth, H. B. One-night sleep deprivation induces changes in the DNA methylation and serum activity indices of stearoyl-CoA desaturase in young healthy men. Lipids in Health and Disease 15 (2016).
Cirelli, C., Gutierrez, C. M. & Tononi, G. Extensive and divergent effects of sleep and wakefulness on brain gene expression. Neuron 41, 35–43 (2004).
Archer, S. N. et al. Mistimed sleep disrupts circadian regulation of the human transcriptome. Proc. Natl. Acad. Sci. USA 111, E682–91 (2014).
Bhatti, P. et al. Nightshift work and genome-wide DNA methylation. Chronobiol. Int. 32, 103–112 (2015).
Sulkava, S. et al. Common genetic variation near melatonin receptor 1A gene linked to job-related exhaustion in shift workers. Sleep 40 (2017).
Polo-Kantola, P. et al. Gender differences in actual and preferred nocturnal sleep duration among Finnish employed population. Maturitas 94, 77–83 (2016).
Greenberg, F. et al. Multi-disciplinary clinical study of Smith-Magenis syndrome (deletion 17p11.2). Am. J. Med. Genet. 62, 247–254 (1996).
De Leersnyder, H. et al. Inversion of the circadian rhythm of melatonin in the Smith-Magenis syndrome. J. Pediatr. 139, 111–116 (2001).
Williams, S. R., Zies, D., Mullegama, S. V., Grotewiel, M. S. & Elsea, S. H. Smith-Magenis syndrome results in disruption of CLOCK gene transcription and reveals an integral role for RAI1 in the maintenance of circadian rhythmicity. Am. J. Hum. Genet. 90, 941–949 (2012).
Edelman, E. A. et al. Gender, genotype, and phenotype differences in Smith-Magenis syndrome: a meta-analysis of 105 cases. Clin. Genet. 71, 540–550 (2007).
Girirajan, S. et al. 17p11.2p12 Triplication and Del(17)q11.2q12 in a Severely Affected Child with Dup(17)p11.2p12 Syndrome. Clin. Genet. 72, 47–58 (2007).
Goh, E. S., Banwell, B., Stavropoulos, D. J., Shago, M. & Yoon, G. Mosaic microdeletion of 17p11.2-p12 and duplication of 17q22-q24 in a girl with Smith-Magenis phenotype and peripheral neuropathy. Am. J. Med. Genet. A. 164A, 748–752 (2014).
Foster, J. G., Wong, S. C. & Sharp, T. V. The hypoxic tumor microenvironment: driving the tumorigenesis of non-small-cell lung cancer. Future Oncol. 10, 2659–2674 (2014).
Li, J., Nanayakkara, A., Jun, J., Savransky, V. & Polotsky, V. Y. Effect of deficiency in SREBP cleavage-activating protein on lipid metabolism during intermittent hypoxia. Physiol. Genomics 31, 273–280 (2007).
Yanagida, J. et al. Accelerated elimination of ultraviolet-induced DNA damage through apoptosis in CDC25A-deficient skin. Carcinogenesis 33, 1754–1761 (2012).
Busque, S. M. & Wagner, C. A. Potassium restriction, high protein intake, and metabolic acidosis increase expression of the glutamine transporter SNAT3 (Slc38a3) in mouse kidney. Am. J. Physiol. Renal Physiol. 297, F440–50 (2009).
Nguyen, C. L. et al. Nek4 regulates entry into replicative senescence and the response to DNA damage in human fibroblasts. Mol. Cell. Biol. 32, 3963–3977 (2012).
Trivedi, M. S., Holger, D., Bui, A. T., Craddock, T. J. A. & Tartar, J. L. Short-term sleep deprivation leads to decreased systemic redox metabolites and altered epigenetic status. PLoS One 12, e0181978 (2017).
Hirotsu, C., Matos, G., Tufik, S. & Andersen, M. L. Changes in gene expression in the frontal cortex of rats with pilocarpine-induced status epilepticus after sleep deprivation. Epilepsy Behav. 27, 378–384 (2013).
Nakamura, K. et al. Genetic and expression analyses reveal elevated expression of syntaxin 1A (STX1A) in high functioning autism. Int. J. Neuropsychopharmacol. 11, 1073–1084 (2008).
Young, E. J. et al. Reduced fear and aggression and altered serotonin metabolism in Gtf2ird1-targeted mice. Genes Brain Behav. 7, 224–234 (2008).
Zhang, N. et al. S-SCAM, a rare copy number variation gene, induces schizophrenia-related endophenotypes in transgenic mouse model. J. Neurosci. 35, 1892–1904 (2015).
Aho, V. et al. Prolonged sleep restriction induces changes in pathways involved in cholesterol metabolism and inflammatory responses. Sci. Rep. 6, 24828 (2016).
Higashide, T. & Inana, G. Characterization of the gene for HRG4 (UNC119), a novel photoreceptor synaptic protein homologous to unc-119. Genomics 57, 446–450 (1999).
Jones, S. E. et al. Genome-Wide Association Analyses in 128,266 Individuals Identifies New Morningness and Sleep Duration Loci. PLoS Genet. 12, e1006125 (2016).
Spada, J. et al. Genome-wide association analysis of actigraphic sleep phenotypes in the LIFE Adult Study. J. Sleep Res. 25, 690–701 (2016).
tom Dieck, S. et al. Deletion of the presynaptic scaffold CAST reduces active zone size in rod photoreceptors and impairs visual processing. J. Neurosci. 32, 12192–12203 (2012).
Kim, E., Grover, L. M., Bertolotti, D. & Green, T. L. Growth hormone rescues hippocampal synaptic function after sleep deprivation. Am. J. Physiol. Regul. Integr. Comp. Physiol. 298, R1588–96 (2010).
Grunder, T., Kohler, K. & Guenther, E. Alterations in NMDA receptor expression during retinal degeneration in the RCS rat. Vis. Neurosci. 18, 781–787 (2001).
Partinen, M. et al. Genetic and environmental determination of human sleep. Sleep 6(3), 179–85 (1983).
Dashti, H. et al. GWAS in 446,118 European adults identifies 78 genetic loci for self-reported habitual sleep duration supported by accelerometer-derived estimates. bioRxiv, https://doi.org/10.1101/274977.
Inouye, M. et al. An immune response network associated with blood lipid levels. PLoS Genet. 6, e1001113 (2010).
Karlsson Linnér, R. et al. An epigenome-wide association study meta-analysis of educational attainment. Mol. Psychiatry (2017).
Aryee, M. J. et al. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics 30, 1363–1369 (2014).
Maksimovic, J., Gordon, L. & Oshlack, A. SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips. Genome Biol. 13, R44-2012-13-6-r44 (2012).
Chen, Y. A. et al. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics 8, 203–9 (2013).