DNA methylation pattern for insufficient sleep and recovery

Chronic insufficient sleep affects basic physiological processes and increases risk for various mental and somatic disorders. Despite the growing number of omics-studies, sleep laboratory studies conducted in human samples, as well as various experiments in animals, the biological mechanisms underlying the health consequences of curtailed sleep are not fully understood. This thesis was inspired by the hypothesis that the consequences of sleep loss may be reflected as changes in the epigenetic processes, with DNA methylation (DNAm) selected as the most feasible to study. The aim of this thesis was to elucidate biological pathways associated with chronic insufficient sleep, as well as to explore how transient and reversible DNAm changes triggered by sleep loss are. In the first study, a cross sectional genome-wide DNAm analysis (Epigenome-wide Association Analysis, EWAS) was performed in relation to self-reported insufficient sleep in individuals from a population-based sample and in relation to insufficient sleep (shift work disorder) among shift-workers from an occupational cohort. No genome-wide significant differences in DNAm were observed in cases versus controls. The study revealed that insufficient sleep was accompanied by the loss of methylation and DNAm alterations in genes enriched in nervous system development pathway. The karyoplot evidenced for several clusters of CpGs on various chromosomes, including a cluster of 12 CpGs on chromosome 17. The genes corresponding to these CpGs were previously associated with a rare genetic condition accompanied by disturbed sleep and inverted circadian rhythm. The second study examined dynamic DNAm changes in relation to recovery from a shift work disorder in the occupational cohort of shift workers across the genome. The results indicated that recovery during vacation leads to the restoration of DNAm and specifically affects genes involved in the activity of N-methyl-d-aspartate (NMDA) glutamate receptors. These findings provide evidence for the dynamic nature of human methylome and suggest CpG sites in genes Glutamate Ionotropic Receptor NMDA Type Subunit 2C (GRIN2C), cAMP Responsive Element Binding Protein 1 (CREB1), and Calcium/calmodulin Dependent Protein Kinase II Beta (CAMK2B) as putative indicators of recovery in a shift worker with shift work disorder. In the third study, we studied the effect of depressed sleep on DNAm in a sample of adolescents with comorbid depression and insomnia as compared to healthy controls. No genome-wide significant differences in DNAm appeared in cases versus controls. However, the top findings of DNAm analyses were enriched in the synaptic long-term depression (LTD) pathway, emphasizing the role of sleep in synaptic plasticity and the widespread physiological consequences of disturbed sleep. Based on these findings, it can be concluded that chronic insufficient sleep is associated with a specific DNAm pattern in blood leukocytes, evidencing for the systemic physiological wide-spread consequences of curtailed sleep. Some of these specific DNAm alterations appeared to be reversible, once individuals restored sleep during two weeks of vacation. Altogether, this thesis contributes to an understanding of the changes triggered by sleep loss in a highly complex and dynamic regulatory mechanism, human DNA methylome.Univaje on terveydelle haitallista ja lisää pitkäaikaisena psykiatristen ja somaattisten sairauksien riskiä. Univajeen patofysiologisia mekanismeja on tutkittu erilaisissa tutkimusasetelmissa ja kokeellisissa malleissa, mutta sen aiheuttamien terveyshaittojen taustalla olevat molekyylibiologiset mekanismit ovat vielä pitkälti tuntemattomia. Tämän väitöskirjan kantavana hypoteesina oli, että univaje johtaa epigeneettisten prosessien – erityisesti DNA:n metylaation – muutoksiin. Selvitimme ensimmäisessä osatyössä riittämättömän unen ja veren valkosolujen DNA-metylaation välisiä yhteyksiä yleisväestössä ja vuorotyötä tekevillä. Tutkimus osoitti, että riittämättömään yöuneen liittyy matalampia DNA:n metylaatiotasoja ja metylaatiotasojen muutoksia hermoston kehitykseen ja toimintaan liittyvissä geeneissä. Osa poikkeavasti metyloituneista geeneistä on liitetty aiemmin sellaisiin harvinaisiin perinnöllisiin sairauksiin, joiden oireina on unen ja vuorokausirytmin häiriöitä. Tarkastelimme toisessa osatyössä valkosolujen DNA:n metylaation dynaamisia muutoksia vuorotyötä tekevillä työjakson aikana sekä vuosiloman jälkeen. Tulokset osoittivat, että vuorotyö-unihäiriöstä kärsivillä oireiden väistyminen ja palautuminen lomajakson aikana johti myös DNA-metylaatiomuutosten palautumiseen. Työssä osoitettiin DNA:n metylaation dynaaminen luonne erityisesti NMDA-glutamaattireseptorien kohdalla ja siten niiden mahdollinen merkitys vuorotyöunihäiriön synty- ja palautumismekanismeissa. Selvitimme kolmannessa tutkimuksessa DNA-metylaatiomuutoksia nuorilla masennuksesta ja unettomuudesta kärsivillä potilailla. Polkuanalyysit antoivat viitteitä siitä, että muistimekanismeihin liittyvän synaptisen polun geenien metylaatiotasot olivat potilailla poikkeavat terveisiin verrokkeihin verrattuna. Löydös sopii hyvin siihen, että riittävä yöuni on tärkeää muistin ja oppimisen toiminnan kannalta. Tulosten perusteella voidaan päätellä, että pitkäaikaiseen univajeeseen liittyy veren valkosolujen DNA-metylaation muutoksia, jotka voivat välittää univajeeseen liittyviä laajoja fysiologisia seuraamuksia. Osa muutoksista oli palautuvia lepojakson jälkeen. Kaiken kaikkiaan väitöskirjatutkimus lisää osaltaan ymmärrystä siitä, kuinka univajeen fysiologiset vaikutukset välittyvät epigeneettisten mekanismien ja erityisesti DNA:n metylaation kautta

Kinase Inhibitors in the Treatment of Ovarian Cancer: Current State and Future Promises

Ovarian cancer is the deadliest gynecological cancer, the high-grade serous ovarian carcinoma (HGSC) being its most common and most aggressive form. Despite the latest therapeutical advancements following the introduction of vascular endothelial growth factor receptor (VEGFR) targeting angiogenesis inhibitors and poly-ADP-ribose-polymerase (PARP) inhibitors to supplement the standard platinum- and taxane-based chemotherapy, the expected overall survival of HGSC patients has not improved significantly from the five-year rate of 42%. This calls for the development and testing of more efficient treatment options. Many oncogenic kinase-signaling pathways are dysregulated in HGSC. Since small-molecule kinase inhibitors have revolutionized the treatment of many solid cancers due to the generality of the increased activation of protein kinases in carcinomas, it is reasonable to evaluate their potential against HGSC. Here, we present the latest concluded and on-going clinical trials on kinase inhibitors in HGSC, as well as the recent work concerning ovarian cancer patient organoids and xenograft models. We discuss the potential of kinase inhibitors as personalized treatments, which would require comprehensive assessment of the biological mechanisms underlying tumor spread and chemoresistance in individual patients, and their connection to tumor genome and transcriptome to establish identifiable subgroups of patients who are most likely to benefit from a given therapy

Conditionally Exponential Prior in Focal Near- and Far-Field EEG Source Localization via Randomized Multiresolution Scanning (RAMUS)

In this paper, we focus on the inverse problem of reconstructing distributional brain activity with cortical and weakly detectable deep components in non-invasive Electroencephalography. We consider a recently introduced hybrid reconstruction strategy combining a hierarchical Bayesian model to incorporate a priori information and the advanced randomized multiresolution scanning (RAMUS) source space decomposition approach to reduce modelling errors, respectively. In particular, we aim to generalize the previously extensively used conditionally Gaussian prior (CGP) formalism to achieve distributional reconstructions with higher focality. For this purpose, we introduce as a hierarchical prior, a general exponential distribution, which we refer to as conditionally exponential prior (CEP). The first-degree CEP corresponds to focality enforcing Laplace prior, but it also suffers from strong depth bias, when applied in numerical modelling, making the deep activity unrecoverable. We sample over multiple resolution levels via RAMUS to reduce this bias as it is known to depend on the resolution of the source space. Moreover, we introduce a procedure based on the physiological a priori knowledge of the brain activity to obtain the shape and scale parameters of the gamma hyperprior that steer the CEP. The posterior estimates are calculated using iterative statistical methods, expectation maximization and iterative alternating sequential algorithm, which we show to be algorithmically similar and to have a close resemblance to the iterative ℓ1 and ℓ2 reweighting methods. The performance of CEP is compared with the recent sampling-based dipole localization method Sequential semi-analytic Monte Carlo estimation (SESAME) in numerical experiments of simulated somatosensory evoked potentials related to the human median nerve stimulation. Our results obtained using synthetic sources suggest that a hybrid of the first-degree CEP and RAMUS can achieve an accuracy comparable to the second-degree case (CGP) while being more focal. Further, the proposed hybrid is shown to be robust to noise effects and compares well with the dipole reconstructions obtained with SESAME.publishedVersionPeer reviewe

Differential DNA methylation in recovery from shift work disorder

The human DNA methylome is responsive to our environment, but its dynamics remain underexplored. We investigated the temporal changes to DNA methylation (DNAme) in relation to recovery from a shift work disorder (SWD) by performing a paired epigenome-wide analysis in an occupational cohort of 32 shift workers (25 men, age=43.8 +/- 8.8 years, 21 SWD cases). We found that the effect of vacation on DNAme was more prominent in the SWD-group as compared to controls, with respect to the amount of significantly differentially methylated positions (DMPs; P-unadjPeer reviewe

Pharmacoepigenetics of hypertension : genome-wide methylation analysis of responsiveness to four classes of antihypertensive drugs using a double-blind crossover study design

Essential hypertension remains the leading risk factor of global disease burden, but its treatment goals are often not met. We investigated whether DNA methylation is associated with antihypertensive responses to a diuretic, a beta-blocker, a calcium channel blocker or an angiotensin receptor antagonist. In addition, since we previously showed an SNP at the transcription start site (TSS) of the catecholamine biosynthesis-related ACY3 gene to associate with blood pressure (BP) response to beta-blockers, we specifically analysed the association of methylation sites close to the ACY3 TSS with BP responses to beta-blockers. We conducted an epigenome-wide association study between leukocyte DNA methylation and BP responses to antihypertensive monotherapies in two hypertensive Finnish cohorts: the GENRES (; amlodipine 5 mg, bisoprolol 5 mg, hydrochlorothiazide 25 mg, or losartan 50 mg daily) and the LIFE-Fin studies (; atenolol 50 mg or losartan 50 mg daily). The monotherapy groups consisted of approximately 200 individuals each. We identified 64 methylation sites to suggestively associate (P < 1E-5) with either systolic or diastolic BP responses to a particular study drug in GENRES. These associations did not replicate in LIFE-Fin . Three methylation sites close to the ACY3 TSS were associated with systolic BP responses to bisoprolol in GENRES but not genome-wide significantly (P < 0.05). No robust associations between DNA methylation and BP responses to four different antihypertensive drugs were identified. However, the findings on the methylation sites close to the ACY3 TSS may support the role of ACY3 genetic and epigenetic variation in BP response to bisoprolol.Peer reviewe

A distinctive DNA methylation pattern in insufficient sleep

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 P value <0.05). We found that 78% of the DMPs were hypomethylated in cases in both cohorts, suggesting that insufficient sleep may be associated with loss of DNA methylation. A karyoplot revealed clusters of DMPs at various chromosomal regions, including 12 DMPs on chromosome 17, previously associated with Smith-Magenis syndrome, a rare condition comprising disturbed sleep and inverse circadian rhythm. Our findings give novel insights into the DNA methylation patterns associated with sleep loss, possibly modifying processes related to neuroplasticity and neurodegeneration. Future prospective studies are needed to confirm the observed associations.Peer reviewe

Common Genetic Variation Near Melatonin Receptor 1A Gene Linked to Job-Related Exhaustion in Shift Workers

Study Objectives: Tolerance to shift work varies; only some shift workers suffer from disturbed sleep, fatigue, and job-related exhaustion. Our aim was to explore molecular genetic risk factors for intolerance to shift work. Methods: We assessed intolerance to shift work with job-related exhaustion symptoms in shift workers using the emotional exhaustion subscale of the Maslach Burnout Inventory-General Survey, and carried out a genome-wide association study (GWAS) using Illumina's Human610-Quad BeadChip (n = 176). The most significant findings were further studied in three groups of Finnish shift workers (n = 577). We assessed methylation in blood cells with the Illumina HumanMethylation450K BeadChip, and examined gene expression levels in the publicly available eGWAS Mayo data. Results: The second strongest signal identified in the GWAS (p = 2.3 x 10E-6) was replicated in two of the replication studies with p Conclusions: These findings suggest that a variant near MTNR1A may be associated with job-related exhaustion in shift workers. The risk variant may exert its effect via epigenetic mechanisms, potentially leading to reduced melatonin signaling in the brain. These results could indicate a link between melatonin signaling, a key circadian regulatory mechanism, and tolerance to shift work.Peer reviewe

DNA methylation pathway associated with insufficient sleep

The need to sleep is physiologically regulated and lack of sleep results in impaired daily performance and feeling of tiredness. If sleep disturbance persists for a long time, the risk of many somatic and mental disorders increases. The study of the key molecular processes triggered by insufficient sleep could foster the assessment and enhance the methods of prevention and cure of these long-term health risks. Both insufficient and mistimed sleep have been shown to strongly affect cell transcriptome in animal models and in the studies of selected human cohorts. However, our understanding of the epigenetic modifications, particularly DNA methylation, triggered by the sleep loss remains limited. Here, we performed an epigenome-wide association study in the whole blood samples of men from the general population reporting lack of sleep and of men diagnosed with a shift work disorder. We combined the results from the two independent samples and identified a set of differentially methylated positions (DMPs) common for both cohorts. We further analyzed this set of DMPs by various computational tools, in order to explore altered biological pathways in individuals suffering from lack of sleep. As a result, we discovered a neurological pathway enriched for genes with DMPs, suggesting that curtailed sleep may result in the changes in processes related to synaptic plasticity. We also observed the loss of methylation in the majority of DMPs, in agreement with an earlier observation on the night shift workers. In order to investigate the effect of DNA methylation on gene expression, we performed correlational analyses of M values of the DMPs and the levels of corresponding gene expression. Since methylation levels might fluctuate according to the time of the blood sampling, we also studied the correlation of the DMPs with the time of the sampling. The analysis of genomic locations of the DMPs revealed enrichment of genomic loci involved in syndromes with symptoms of disturbances in visual processing and regulation of circadian rhythm. Our findings suggest that there is a distinctive pattern of genes showing diversity of epigenetic modifications in relation to insufficient sleep in men. The molecular mechanisms behind the observed associations require further investigation, both in general population based samples comprising both genders or occupational cohorts, and in experimental data

Kinase Inhibitors in the Treatment of Ovarian Cancer: Current State and Future Promises

Ovarian cancer is the deadliest gynecological cancer, the high-grade serous ovarian carcinoma (HGSC) being its most common and most aggressive form. Despite the latest therapeutical advancements following the introduction of vascular endothelial growth factor receptor (VEGFR) targeting angiogenesis inhibitors and poly-ADP-ribose-polymerase (PARP) inhibitors to supplement the standard platinum- and taxane-based chemotherapy, the expected overall survival of HGSC patients has not improved significantly from the five-year rate of 42%. This calls for the development and testing of more efficient treatment options. Many oncogenic kinase-signaling pathways are dysregulated in HGSC. Since small-molecule kinase inhibitors have revolutionized the treatment of many solid cancers due to the generality of the increased activation of protein kinases in carcinomas, it is reasonable to evaluate their potential against HGSC. Here, we present the latest concluded and on-going clinical trials on kinase inhibitors in HGSC, as well as the recent work concerning ovarian cancer patient organoids and xenograft models. We discuss the potential of kinase inhibitors as personalized treatments, which would require comprehensive assessment of the biological mechanisms underlying tumor spread and chemoresistance in individual patients, and their connection to tumor genome and transcriptome to establish identifiable subgroups of patients who are most likely to benefit from a given therapy

Effect of molecule branching and glycosidic linkage on the degradation of polydextrose by gut microbiota.

Polydextrose is a randomly linked complex glucose oligomer that is widely used as a sugar replacer, bulking agent, dietary fiber and prebiotic. Polydextrose is poorly utilized by the host and, during gastrointestinal transit, it is slowly degraded by intestinal microbes, although it is not known which parts of the complex molecule are preferred by the microbes. The microbial degradation of polydextrose was assessed by using a simulated model of colonic fermentation. The degradation products and their glycosidic linkages were measured by combined gas chromatography and mass spectrometry, and compared to those of intact polydextrose. Fermentation resulted in an increase in the relative abundance of non-branched molecules with a concomitant decrease in single-branched glucose molecules and a reduced total number of branching points. A detailed analysis showed a preponderance of 1,6 pyranose linkages. The results of this study demonstrate how intestinal microbes selectively degrade polydextrose, and provide an insight into the preferences of gut microbiota in the presence of different glycosidic linkages