Perturbation of the insomnia WDR90 GWAS locus pinpoints rs3752495 as a causal variant influencing distal expression of neighboring gene, PIG-Q

Although genome wide association studies (GWAS) have identified loci for sleep-related traits, they do not directly uncover the underlying causal variants and corresponding effector genes. The majority of such variants reside in non-coding regions and are therefore presumed to impact cis-regulatory elements. Our previously reported 'variant-to-gene mapping' effort in human induced pluripotent stem cell (iPSC)-derived neural progenitor cells (NPCs), combined with validation in both Drosophila and zebrafish, implicated PIG-Q as a functionally relevant gene at the insomnia 'WDR90' GWAS locus. However, importantly that effort did not characterize the corresponding underlying causal variant. Specifically, our previous 3D genomic datasets nominated a shortlist of three neighboring single nucleotide polymorphisms (SNPs) in strong linkage disequilibrium within an intronic enhancer region of WDR90 that contacted the open PIG-Q promoter. We sought to investigate the influence of these SNPs collectively and then individually on PIG-Q modulation to pinpoint the causal "regulatory" variant. Starting with gross level perturbation, deletion of the entire region in NPCs via CRISPR-Cas9 editing and subsequent RNA sequencing revealed expression changes in specific PIG-Q transcripts. Results from individual luciferase reporter assays for each SNP in iPSCs revealed that the region with the rs3752495 risk allele induced a ~2.5-fold increase in luciferase expression. Importantly, rs3752495 also exhibited an allele specific effect, with the risk allele increasing the luciferase expression by ~2-fold versus the non-risk allele. In conclusion, our variant-to-function approach and in vitro validation implicates rs3752495 as a causal insomnia variant embedded within WDR90 while modulating the expression of the distally located PIG-Q.

Perturbation of the insomnia WDR90 GWAS locus pinpoints rs3752495 as a causal variant influencing distal expression of neighboring gene, PIG-Q

Although genome wide association studies (GWAS) have been crucial for the identification of loci associated with sleep traits and disorders, the method itself does not directly uncover the underlying causal variants and corresponding effector genes. The overwhelming majority of such variants reside in non-coding regions and are therefore presumed to impact the activity of cis-regulatory elements, such as enhancers. Our previously reported 'variant-to-gene mapping' effort in human induced pluripotent stem cell (iPSC)-derived neural progenitor cells (NPCs), combined with validation in both Drosophila and zebrafish, implicated PIG-Q as a functionally relevant gene at the insomnia 'WDR90' locus. However, importantly that effort did not characterize the corresponding underlying causal variant at this GWAS signal. Specifically, our genome-wide ATAC-seq and high-resolution promoter-focused Capture C datasets generated in this cell setting brought our attention to a shortlist of three tightly neighboring single nucleotide polymorphisms (SNPs) in strong linkage disequilibrium in a candidate intronic enhancer region of WDR90 that contacted the open PIG-Q promoter. The objective of this study was to investigate the influence of the proxy SNPs collectively and then individually on PIG-Q modulation and to pinpoint the causal "regulatory" variant among the three SNPs. Starting at a gross level perturbation, deletion of the entire region harboring all three SNPs in human iPSC-derived neural progenitor cells via CRISPR-Cas9 editing and subsequent RNA sequencing revealed expression changes in specific PIG-Q transcripts. Results from more refined individual luciferase reporter assays for each of the three SNPs in iPSCs revealed that the intronic region with the rs3752495 risk allele induced a ~2.5-fold increase in luciferase expression (n=10). Importantly, rs3752495 also exhibited an allele specific effect, with the risk allele increasing the luciferase expression by ~2-fold compared to the non-risk allele. In conclusion, our variant-to-function approach and subsequent in vitro validation implicates rs3752495 as a causal insomnia risk variant embedded at the WDR90-PIG-Q locus.

Variant-to-gene mapping followed by cross-species genetic screening identifies GPI-anchor biosynthesis as a regulator of sleep

Genome-wide association studies (GWAS) in humans have identified loci robustly associated with several heritable diseases or traits, yet little is known about the functional roles of the underlying causal variants in regulating sleep duration or quality. We applied an ATAC-seq/promoter focused Capture C strategy in human iPSC-derived neural progenitors to carry out a "variant-to-gene" mapping campaign that identified 88 candidate sleep effector genes connected to relevant GWAS signals. To functionally validate the role of the implicated effector genes in sleep regulation, we performed a neuron-specific RNA interference screen in the fruit fly, Drosophila melanogaster, followed by validation in zebrafish. This approach identified a number of genes that regulate sleep including a critical role for glycosylphosphatidylinositol (GPI)-anchor biosynthesis. These results provide the first physical variant-to-gene mapping of human sleep genes followed by a model organism-based prioritization, revealing a conserved role for GPI-anchor biosynthesis in sleep regulation.

0462 Identifying and Characterizing Insomnia Symptom Groups Across the Deployment Cycle in Current Army Soldiers

Introduction

Most research conducted on insomnia and its development in military personnel focuses on cross-sectional data, precluding examination of the course of sleep changes over time. The present study characterized Army Soldiers based on insomnia symptom status trajectory from pre to post-deployment and explored baseline factors predictive of these trajectories in a sample of 7,245 soldiers across 3 Brigade Combat Teams.

Methods

Data were analyzed from the Army Study to Assess Risk and Resilience in Service members (STARRS)-All-Army Study (AAS) Pre Post Deployment Study, using surveys that captured 1-2 months pre-deployment, during deployment, and 6-months post-deployment. Insomnia symptom status was defined at each timepoint as insomnia symptoms that interfered with one or more domains of functioning at least some of the time in the past month. Theoretically-derived variables linked to sleep disturbance were selected as predictors of insomnia symptom trajectory and evaluated using a general linear selection model.

Results

Four trajectories characterized the majority of the sample: ‘good sleepers’ (no insomnia symptoms across time; 44.4%), ‘non-remitting new onset insomnia’ (no pre-deployment insomnia, developed insomnia symptoms during deployment that remained at 6 months; 22.8%), ‘deployment-only insomnia symptoms’ (no pre-deployment insomnia, developed insomnia during deployment but recovered by follow-up; 12.8%), and ‘chronic insomnia’ (insomnia both pre- and post-deployment; 7.4%). Several pre-deployment factors predicted insomnia trajectory, the strongest of which were past six-month attention deficit disorder symptoms, number of lifetime exposures to potentially traumatic events, and past month depression symptoms.

Conclusion

Insomnia is one of the most common reasons that military personnel seek behavioral health treatment and is associated with poorer military readiness. Better characterization and identification of insomnia symptoms over time can improve intervention during post-deployment transitions, particularly for those with new onset insomnia that does not remit.

Support

Cooperative agreement U01MH087981 (Department of the Army; U.S. Department of Health and Human Services, National Institutes of Health, National Institute of Mental Health); U.S. Department of Veterans Affairs, Clinical Science Research and Development-IK2CX001874-PI:Katherine E. Miller, IK2CX001501-PI:Elaine M. Boland; Rehabilitation Research and Development-1IK2RX001836-PI:Elizabeth A. Klingaman. The views expressed here are those of the authors and do not represent the Department of Veterans Affairs.

Estimating sleep parameters using an accelerometer without sleep diary

Wrist worn raw-data accelerometers are used increasingly in large-scale population research. We examined whether sleep parameters can be estimated from these data in the absence of sleep diaries. Our heuristic algorithm uses the variance in estimated z-axis angle and makes basic assumptions about sleep interruptions. Detected sleep period time window (SPT-window) was compared against sleep diary in 3752 participants (range = 60-82 years) and polysomnography in sleep clinic patients (N = 28) and in healthy good sleepers (N = 22). The SPT-window derived from the algorithm was 10.9 and 2.9 minutes longer compared with sleep diary in men and women, respectively. Mean C-statistic to detect the SPT-window compared to polysomnography was 0.86 and 0.83 in clinic-based and healthy sleepers, respectively. We demonstrated the accuracy of our algorithm to detect the SPT-window. The value of this algorithm lies in studies such as UK Biobank where a sleep diary was not used.

Sleep and daily functioning during androgen deprivation therapy for prostate cancer

A limited body of evidence suggests that sleep problems are common in prostate cancer patients undergoing androgen deprivation therapy, yet little is known about sleep characteristics and the effects of poor sleep on daily functioning in this population. This study assessed sleep in 60 prostate cancer patients taking androgen deprivation therapy with wrist actigraphy and daily diaries for 7 days. The Epworth Sleepiness Scale and the general version of the Functional Assessment of Cancer Therapy scale were also administered. On average, total sleep time was 5.9 (SD = 1.4) h, and sleep efficiency was 75% (SD = 12.0) as assessed by actigraphy. There was generally poor concordance between actigraphy and daily diary for most sleep metrics. Subjects reported awakening, on average, 2.7 times per night, most commonly for nocturia and hot flashes. Assessment of daily functioning showed that participants had mild daytime sleepiness, which was predicted by total sleep time (F(1,47) = 4.5, P= 0.04) General quality of life was not impaired. This study supports more research on the predictors of poor sleep in order to identify effective interventions.

Cigarette smoking, ambulatory cardiovascular monitoring, and mood in Vietnam veterans with and without chronic posttraumatic stress disorder

This study investigated the association among cigarette smoking, posttraumatic stress disorder (PTSD), and ambulatory cardiovascular and mood monitoring in 117 male Vietnam combat veterans (61 with PTSD and 56 without PTSD). Positive smoking status was associated with higher systolic blood pressure (SBP) and heart rate (HR), as well as greater diastolic blood pressure (DBP) variability. Compared to individuals without PTSD, PTSD patients had higher HR, anger/hostility ratings, and depression/anxiety ratings. Significant diagnosis by smoking status interactions were found indicating that compared to nonsmokers with PTSD, smokers with PTSD had higher DBP, mean arterial pressure (MAP), and positive affect. Ad lib cigarette smoking during the previous 30 min did not have a significant effect on mood or cardiovascular parameters, except in non-PTSD smokers who reported lower depression/anxiety ratings after smoking. Findings suggest that the effect of smoking on cardiovascular parameters may be amplified in smokers in PTSD. Findings suggest that the interrelationships among cardiovascular parameters, cigarette smoking, and PTSD deserve more research attention.

Sleep in the elderly

Older adults frequently experience difficulties with sleep that can be caused by specific sleep disorders (such as sleep-disordered breathing or periodic limb movements in sleep) and circadian rhythm disturbances. These all can be effectively treated. Medical illnesses and medications also can have a negative affect on sleep and effective management of these can significantly improve sleep in older adults. Sleep in institutionalized older adults is even more disturbed than sleep of community-dwelling older people and special considerations can be made to improve the quality of sleep in institutional settings.

Rapid eye movement sleep changes during the adaptation night in combat veterans with posttraumatic stress disorder

BACKGROUND

Hyperarousal in posttraumatic stress disorder (PTSD) is manifested during sleep as well as waking. Elevated rapid eye movement sleep (REMS) phasic activity, likely signifying central nervous system alerting, has been identified in PTSD. The authors reasoned that PTSD compared to control subjects would show particularly increased REMS phasic activity on the first night of polysomnography, with adaptation to a novel environment.

METHODS

First-night polysomnograms of 17 veterans with PTSD were compared with those of 11 control subjects. Sleep was also studied in subsets of both groups over two nights.

RESULTS

On the first night, the PTSD subjects had a higher density of rapid eye movements in the first REMS period. This measure was increased on the first compared to the second night, but there was no interaction effect between night and group.

CONCLUSIONS

REMS changes are again demonstrated in veterans with PTSD. Introduction to a novel environment activated a REMS phasic process, but not differentially in PTSD compared to control subjects.