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IntroductionPatients who had a mild ischaemic stroke who present with subtle or resolving symptoms sometimes go undiagnosed, are excluded from treatment and in some cases clinically worsen. Circulating immune cells are potential biomarkers that can assist with diagnosis in ischaemic stroke. Understanding the transcriptomic changes of each cell population caused by ischaemic stroke is critical because they work closely in a complicated relationship. In this study, we investigated peripheral blood mononuclear cells (PBMCs) transcriptomics of patients who had a stroke using a single-cell RNA sequencing to understand peripheral immune response after mild stroke based on the gene expression in an unbiased way.MethodsTranscriptomes of PBMCsfrom 10 patients who had an acute ischaemic stroke within 24 hours after stroke onset were compared with 9 race-matched/age-matched/gender-matched controls. Individual PBMCs were prepared with ddSeqTM (Illumina-BioRad) and sequenced on the Illumina NovaSeq 6000 platform.ResultsNotable population changes were observed in patients who had a stroke, especially in NK cells and CD14+ monocytes. The number of NK cells was increased, which was further confirmed by flow cytometry. Functional analysis implied that the activity of NK cells also is enhanced in patients who had a stroke. CD14+ monocytes were clustered into two groups; dendritic cell-related CD14+ monocytes and NK cell-related CD14+ monocytes. We found CD14+ monocyte subclusters were dramatically reduced in patients who had a stroke.DiscussionThis is the first study demonstrating the increased number of NK cells and new monocyte subclusters of mild ischaemic stroke based on the transcriptomic analysis. Our findings provide the dynamics of circulating immune response that could assist diagnosis and potential therapeutic development of mild ischaemic stroke.

Diabetic peripheral neuropathy (DPN) is characterized by spontaneous pain in the extremities. Incidence of DPN continues to rise with the global diabetes epidemic. However, there remains a lack of safe, effective analgesics to control this chronic painful condition. Dorsal root ganglia (DRG) contain soma of sensory neurons and modulate sensory signal transduction into the central nervous system. In this study, we aimed to gain a deeper understanding of changes in molecular pathways in the DRG of DPN patients with chronic pain. We recently reported transcriptomic changes in the DRG with DPN. Here, we expand upon those results with integrated metabolomic, proteomic, and phospho-proteomic analyses to compare the molecular profiles of DRG from DPN donors and DRG from control donors without diabetes or chronic pain. Our analyses identified decreases of select amino acids and phospholipid metabolites in the DRG from DPN donors, which are important for cellular maintenance. Additionally, our analyses revealed changes suggestive of extracellular matrix (ECM) remodeling and altered mRNA processing. These results reveal new insights into changes in the molecular profiles associated with DPN.

CHARGE syndrome is a complex developmental disorder caused by mutations in the chromodomain helicase DNA-binding protein-7 (CHD7) and characterized by retarded growth and malformations in the heart and nervous system. Despite the public health relevance of this disorder, relevant cellular pathways and targets of CHD7 that relate to disease pathology are still poorly understood. Here we report that chd-7, the nematode ortholog of Chd7, is required for dauer morphogenesis, lifespan determination, stress response, and body size determination. Consistent with our discoveries, we found chd-7 to be allelic to scd-3, a previously identified dauer suppressor from the DAF-7/ tumor growth factor-β (TGF-β) pathway. Epistatic analysis places CHD-7 at the level of the DAF-3/DAF-5 complex, but we found that CHD-7 also directly impacts the expression of multiple components of this pathway. Transcriptomic analysis revealed that chd-7 mutants fail to repress daf-9 for execution of the dauer program. In addition, CHD-7 regulates the DBL-1/BMP pathway components and shares roles in male tail development and cuticle synthesis. To explore a potential conserved function for chd-7 in vertebrates, we used Xenopus laevis embryos, an established model to study craniofacial development. Morpholino-mediated knockdown of Chd7 led to a reduction in col2a1 messenger RNA (mRNA) levels, a collagen whose expression depends on TGF-β signaling. Both embryonic lethality and craniofacial defects in Chd7-depleted tadpoles were partially rescued by overexpression of col2a1 mRNA. We suggest that Chd7 has conserved roles in regulation of the TGF-β signaling pathway and pathogenic Chd7 could lead to a defective extracellular matrix deposition.

Objectives Arterial stiffness is recognized as an important predictor of cardiovascular disease morbidity and mortality, independent of traditional cardiovascular disease risk factors. Given that arterial tissue is not easily accessible, most gene expression studies on arterial stiffness have been conducted on animals or on patients who have undergone by-pass surgeries. In order to obtain a deeper understanding of early changes of arterial stiffness, this study compared transcriptome profiles between healthy adults with higher and lower arterial stiffness. Methods The sample included 20 healthy female adults without cardiovascular disease. Arterial stiffness was measured by carotid-femoral pulse wave velocity, the “gold-standard” measure of central arterial stiffness. Peripheral blood samples collected to PAXgene™ RNA tubes were used for RNA sequencing (RNA-seq). The potential confounding effects of age, body mass index, and mean arterial pressure were controlled for in RNA-seq analysis. To validate RNA-seq results, quantitative real-time PCR (qRT-PCR) was performed for six selected genes. Results The findings demonstrated that genes including CAPN9, IL32, ERAP2, RAB6B, MYBPH, and miRNA626 were down-regulated, and that MOCS1 gene was up-regulated among the people with higher arterial stiffness. Real-time PCR showed that the changes of CAPN9, IL32, ERAP2, and RAB6B were in concordance with RNA-seq data, and confirmed the validity of the gene expression profiles obtained by RNA-seq analysis. Conclusions Previous studies have suggested the potential roles of CAPN9, IL32, and ERAP2 in structural changes of the arterial wall through up-regulation of metalloproteinases. However, the current study showed that CAPN9, IL32, and ERAP2 were down-regulated in the individuals with higher arterial stiffness, compared with those with lower arterial stiffness. The unexpected directions of expression of these genes may indicate an effort to maintain vascular homeostasis during increased arterial stiffness among healthy individuals. Further studies are guaranteed to investigate the roles of CAPN9, IL32, and ERAP2 in regulating arterial stiffness in people with and without cardiovascular disease.

Current protein biomarkers are only moderately predictive at identifying individuals with mild traumatic brain injury or concussion. Therefore, more accurate diagnostic markers are needed for sport-related concussion.This was a multicenter, prospective, case-control study of athletes who provided blood samples and were diagnosed with a concussion or were a matched non-concussed control within the National Collegiate Athletic Association-Department of Defense Concussion Assessment, Research, and Education Consortium conducted between 2015 and 2019. The blood was collected within 48 h of injury to identify protein abnormalities at the acute and subacute timepoints. Athletes with concussion were divided into 6 h post-injury (0-6 h post-injury) and after 6 h post-injury (7-48 hours post-injury) groups. We applied a highly multiplexed proteomic technique that used a DNA aptamers assay to target 1305 proteins in plasma samples from athletes with and without sport-related concussion.A total of 140 athletes with concussion (79.3% male; aged 18.71 ± 1.10 years, mean ± SD) and 21 non-concussed athletes (76.2% male; 19.14 ± 1.10 years) were included in this study. We identified 338 plasma proteins that significantly differed in abundance (319 upregulated and 19 downregulated) in concussed athletes compared to non-concussed athletes. The top 20 most differentially abundant proteins discriminated concussed athletes from non-concussed athletes with an area under the curve of 0.954 (95% confidence interval: 0.922‒0.986). Specifically, after 6 h of injury, the individual area under the curve of plasma erythrocyte membrane protein band 4.1 (EPB41) and alpha-synuclein were 0.956 and 0.875, respectively. The combination of EPB41 and alpha-synuclein provided the best area under the curve (1.000), which suggests this combination of candidate plasma biomarkers is best for diagnosing concussion in athletes after 6 h of injury.Our data suggest that proteomic profiling may provide novel diagnostic protein markers and that a combination of EPB41 and alpha-synuclein is the most predictive biomarker of concussion after 6 h of injury.

Pathological sensations caused by peripheral painful neuropathy occurring in Type 2 diabetes mellitus (T2DM) are often described as 'sharp' and 'burning' and are commonly spontaneous in origin. Proposed etiologies implicate dysfunction of nociceptive sensory neurons in dorsal root ganglia (DRG) induced by generation of reactive oxygen species, microvascular defects, and ongoing axonal degeneration and regeneration. To investigate the molecular mechanisms contributing to diabetic pain, DRGs were acquired postmortem from patients who had been experiencing painful diabetic peripheral neuropathy (DPN) and subjected to transcriptome analyses to identify genes contributing to pathological processes and neuropathic pain. DPN occurs in distal extremities resulting in the characteristic "glove and stocking" pattern. Accordingly, the L4 and L5 DRGs, which contain the perikarya of primary afferent neurons innervating the foot, were analyzed from five DPN patients and compared with seven controls. Transcriptome analyses identified 844 differentially expressed genes. We observed increases in levels of inflammation-associated transcripts from macrophages in DPN patients that may contribute to pain hypersensitivity and, conversely, there were frequent decreases in neuronally-related genes. The elevated inflammatory gene profile and the accompanying downregulation of multiple neuronal genes provide new insights into intraganglionic pathology and mechanisms causing neuropathic pain in DPN patients with T2DM.

Post-traumatic stress disorder (PTSD) and major depressive disorder (MDD) are commonly experienced after exposure to highly stressful events, including physical trauma, yet, biological predictors remain elusive. Methylation of DNA may provide key insights, as it likely is reflective of factors that may increase the risk in trauma patients, as DNA methylation is altered by previous stressors. Here, we compared DNA methylation patterns using bisulfite sequencing in patients with a physical trauma that required more than a 24-h hospitalization (n = 33). We then compared DNA methylation in patients who developed and compared the following groups (1) PTSD and MDD; n = 12), (2) MDD (patients with MDD only; n = 12), and (3) control (patients who did not have PTSD or MDD; n = 9), determined by the PTSD Checklist (PCL-5) and Quick Inventory of Depressive Symptomatology (QIDS) at 6-months follow-up. We identified 17 genes with hypermethylated cytosine sites and 2 genes with hypomethylated sites in comparison between PTSD and control group. In comparison between MDD and control group, we identified 12 genes with hypermethylated cytosine sites and 6 genes with hypomethylated sites. Demethylation of these genes altered the CREB signaling pathway in neurons and may represent a promising therapeutic development target for PTSD and MDD. Our findings suggest that epigenetic changes in these gene regions potentially relate to the onset and symptomology of PTSD and MDD and could be used as potential biomarkers in predicting the onset of PTSD or MDD following traumatic events.

Pathological sensations caused by peripheral painful neuropathy occurring in Type 2 diabetes mellitus (T2DM) are often described as ‘sharp’ and ‘burning’ and are commonly spontaneous in origin. Proposed etiologies implicate dysfunction of nociceptive sensory neurons in dorsal root ganglia (DRG) induced by generation of reactive oxygen species, microvascular defects, and ongoing axonal degeneration and regeneration. To investigate the molecular mechanisms contributing to diabetic pain, DRGs were acquired postmortem from patients who had been experiencing painful diabetic peripheral neuropathy (DPN) and subjected to transcriptome analyses to identify genes contributing to pathological processes and neuropathic pain. DPN occurs in distal extremities resulting in the characteristic “glove and stocking” pattern. Accordingly, the L4 and L5 DRGs, which contain the perikarya of primary afferent neurons innervating the foot, were analyzed from five DPN patients and compared with seven controls. Transcriptom e analyses identified 844 differentially expressed genes. We observed increases in levels of inflammation-associated genes from macrophages in DPN patients that may contribute to increased pain hypersensitivity and, conversely, there were frequent decreases in neuronally-related genes. The elevated inflammatory gene profile and the accompanying downregulation of multiple neuronal genes provide new insights into intraganglionic pathology and mechanisms causing neuropathic pain in DPN patients with T2DM.

CHARGE syndrome is a complex developmental disorder caused by mutations in the chromodomain helicase DNA-binding protein7 (CHD7) and characterized by retarded growth and malformations in the heart and nervous system. Despite the public health relevance of this disorder, relevant targets of CHD7 that relate to disease pathology are still poorly understood. Here we report thatchd-7, the nematode ortholog of Chd7, is required for dauer morphogenesis, lifespan determination, and stress response. Consistent with our discoveries, we foundchd-7to be allelic toscd-3, a previously identified dauer suppressor from the TGF-β pathway. Notably, DAF-12 promotedchd-7 expression, which is necessary to repressdaf-9for execution of the dauer program. Transcriptomic analysis comparingchd-7–defective and normal dauers showed enrichment of collagen genes, consistent with a conserved role for the TGF-β pathway in formation of the extracellular matrix. To validate a conserved function forchd-7in vertebrates, we usedXenopus laevisembryos, an established model to study craniofacial development. Morpholino mediated knockdown of Chd7 led to a reduction incol2a1mRNA levels. Both embryonic lethality and craniofacial defects in Chd7-depleted tadpoles were partially rescued by over-expression ofcol2a1mRNA. We suggest that pathogenic features of CHARGE syndrome caused by Chd7 mutations, such as craniofacial malformations, result from the reduction of collagen levels, implying that the extracellular matrix might represent a critical target of Chd7 in CHARGE development.SIGNIFICANCE STATEMENTCHARGE Syndrome is a complex developmental disorder caused by mutations in the chromodomain helicase DNA-binding protein-7 (CHD7). Unfortunately, the cellular events that lead to CHARGE syndrome are still poorly understood. InC. elegans, we identifiedchd-7in a screen for suppressors of dauer formation, an alternative larval stage that develops in response to sensory signals of a harsh environment. We found thatchd-7regulates expression of collagens, which constitute the worm’s cuticle, a specialized extracellular matrix. In frog’s embryos, we show that Chd7 inhibition leads to poor Col2a1, which is necessary and sufficient to exhibit CHARGE features. These studies establishC. elegansas an amenable animal model to study the etiology of the developmental defects associated with pathogenic Chd7.

Insomnia is a highly prevalent condition that is associated with negative health outcomes, yet little is known about the underlying molecular mechanisms.RNA sequencing was conducted using blood samples from 15 individuals with primary insomnia and 15 age- and gender-matched good sleeper controls. The RNA library was sequenced with 150 base pair paired-ends on the Illumina NovaSeq-6000 platform. Alignment was performed using human reference genome hg38. Differential gene expression analysis was performed using DESeq2 following alignment, using log fold change ±0.50, and had a false discovery rate p-value0.05. Pathway analysis was performed using Ingenuity Pathway Analysis.We found 288 differentially expressed genes in insomnia patients when compared to controls. Upregulated genes included LINC02224 (Long Intergenic Non-Protein Coding RNA 2224), DUX4L9 (Double Homeobox 4 Like 9), and TUSC3 (Tumor Suppressor Candidate 3) and down regulated genes included CTXN2 (Cortexin 2), CSMD1 (CUB And Sushi Multiple Domains 1), and SLC12A1 (Solute Carrier Family 12 Member 1). Ingenuity® Pathway Analysis (IPA) revealed 3 associated networks (score40) with genes and hubs related to inflammation (nuclear factor-kB), oxidative stress (Mitochondrial complex 1) and ubiquitination.Differentially expressed genes in this analysis are functionally associated with inflammation and immune response, mitochondrial and metabolic processes. Further research into the transcriptomic changes in insomnia is needed to understand related pathways to the disorder and provide new avenues for diagnostics and therapeutics.

The Mediterranean diet (MD) has been reported to have beneficial effects on breast cancer and cardiovascular diseases. Recently, microRNAs (miRNAs) have been suggested as biomarkers for the diagnosis and disease prognosis in cancer and cardiovascular diseases. We evaluated the influence of the MD on the plasma-derived extracellular vesicle miRNA signature of overweight breast cancer survivors. Sixteen participants instructed to adhere to the MD for eight weeks were included in this study. To curate differentially expressed miRNAs after MD intervention, we employed two methods: significance analysis of microarrays and DESeq2. The selected miRNAs were analyzed using ingenuity pathway analysis. After an eight-week intervention, body mass index, waist circumference, fasting glucose, fasting insulin, and homeostatic model assessment for insulin resistance were significantly improved. Expression levels of 798 miRNAs were comprehensively analyzed, and 42 extracellular vesicle miRNAs were significantly differentially regulated after the eight-week MD (36 were up and 6 were down-regulated). We also identified enriched pathways in genes regulated by differentially expressed 42 miRNAs, which include signaling associated with breast cancer, energy metabolism, glucose metabolism, and insulin. Our study indicates that extracellular vesicle miRNAs differentially expressed as a result of the MD might be involved in the mechanisms that relate to cardiometabolic risk factors in overweight breast cancer survivors.

Study Objectives Posttraumatic stress disorder (PTSD) is a common condition for military personnel and veterans. PTSD has been shown to impact gene expression, however, to date no study has examined comorbid conditions which may also impact gene expression, for example, excessive daytime sleepiness (EDS). As such, this study sought to examine gene expression using RNA sequencing across three group comparisons of military personnel and veterans: (1) PTSD with EDS (PTSDwEDS) versus PTSD without EDS (PTSDw/outEDS), (2) Controls (no PTSD or EDS) versus PTSDwEDS, and (3) Controls versus PTSDw/outEDS. Methods We performed experimental RNA-seq using Illumina’s HiSeq 2500 Sequencing System. We also used Ingenuity Pathway Analysis (IPA), a bioinformatics application, to identify gene pathways and networks which may be disrupted. Results There were only two genes that were significantly dysregulated between the Controls and PTSDw/outEDS, therefore IPA analysis was not conducted. However, comparisons revealed that there was significant gene dysregulation between Controls and the PTSDwEDS (251 genes), and the PTSDwEDS versus the PTSDw/outEDS (1,873 genes) groups. Four candidate networks were identified via the IPA software for analysis. Significantly dysregulated genes across the four candidate networks were associated with sleep and circadian function, metabolism, mitochondrial production and function, ubiquitination, and the glutamate system. Conclusions These results suggest that PTSD with concurrent EDS is associated with gene dysregulation. This dysregulation may present additional biological and health consequences for these military personnel and veterans. Further research, to track these gene changes over time and to determine the cause of the EDS reported, is vital.

Temporal regulation of gene expression is a crucial aspect of metazoan development. In the roundworm Caenorhabditis elegans, the heterochronic pathway controls multiple developmental events in a time-specific manner. The most downstream effector of this pathway, the zinc-finger transcription factor LIN-29, acts in the last larval stage (L4) to regulate elements of the larval-to-adult switch. Here, we explore new LIN-29 targets and their implications for this developmental transition. We used RNA-sequencing to identify genes differentially expressed between animals misexpressing LIN-29 at an early time point and control animals. Among 230 LIN-29-activated genes, we found that genes encoding cuticle collagens were overrepresented. Interestingly, expression of lin-29 and some of these collagens was increased in adults with cuticle damage, suggesting a previously unknown function for LIN-29 in adult cuticle maintenance. On the other hand, genes involved in fat metabolism were enriched among 350 LIN-29-downregulated targets. We used mass spectrometry to assay lipid content in animals overexpressing LIN-29 and observed reduced fatty acid levels. Many LIN-29-repressed genes are normally expressed in the intestine, suggesting cell-nonautonomous regulation. We identified several LIN-29 upregulated genes encoding signaling molecules that may act as mediators in the regulation of intestinally expressed genes encoding fat metabolic enzymes and vitellogenins. Overall, our results support the model of LIN-29 as a major regulator of adult cuticle synthesis and integrity, and as the trigger for metabolic changes that take place at the important transition from rapid growth during larval life to slower growth and offspring production during adulthood.

Military personnel experience posttraumatic stress disorder (PTSD), which is associated with differential DNA methylation across the whole genome. However, the relationship between these DNA methylation patterns and clinically relevant increases in PTSD severity is not yet clearly understood. The purpose of this study was to identify differences in DNA methylation associated with PTSD symptoms and investigate DNA methylation changes related to increases in the severity of PTSD in military personnel. In this pilot study, a cross-sectional comparison was made between military personnel with PTSD (n = 8) and combat-matched controls without PTSD (n = 6). Symptom measures were obtained, and genome-wide DNA methylation was measured using methylated DNA immunoprecipitation (MeDIP-seq) from whole blood samples at baseline and 3 months later. A longitudinal comparison measured DNA methylation changes in military personnel with clinically relevant increases in PTSD symptoms between time points (PTSD onset) and compared methylation patterns to controls with no clinical changes in PTSD. In military personnel with elevated PTSD symptoms 3 months following baseline, 119 genes exhibited reduced methylation and 8 genes exhibited increased methylation. Genes with reduced methylation in the PTSD-onset group relate to the canonical pathways of netrin signaling, Wnt/Ca+ pathway, and axonal guidance signaling. These gene pathways relate to neurological disorders, and the current findings suggest that these epigenetic changes potentially relate to PTSD symptomology. This study provides some novel insights into the role of epigenetic changes in PTSD symptoms and the progression of PTSD symptoms in military personnel.

Growing evidence in vertebrates predicts that cellular haem levels in animals are maintained not only by a cell’s internal capacity for haem synthesis in a cell-autonomous manner, but also by an inter-organ haem trafficking network through cell-non-autonomous regulation. Using Caenorhabditis elegans, a genetically and optically amenable animal model for visualizing haem-dependent signalling, we show that HRG-7, a protein with homology to aspartic proteases, mediates inter-organ signalling between the intestine and extra-intestinal tissues. Intestinal HRG-7 functions as a secreted signalling factor during haem starvation in extra-intestinal tissues and is regulated through a DBL-1, homologous to BMP5, dependent signal from neurons. Given the evidence that vertebrate homologues exist for each of the components of the HRG-7-mediated signalling pathway, it is conceivable that the cell-non-autonomous signalling framework that we uncovered in C. elegans may have functional relevance for inter-organ regulation of iron and haem metabolism in humans. Sinclair et al. show in Caenorhabditis elegans that intestinal HRG-7 communicates haem status with extra-intestinal tissues. Reciprocally, a DBL-1-dependent signal from neurons regulates both hrg-7 and haem transport.

Posttraumatic stress disorder (PTSD) affects many returning combat veterans, but underlying biological mechanisms remain unclear. In order to compare circulating micro RNA (miRNA) of combat veterans with and without PTSD, peripheral blood from 24 subjects was collected following deployment, and isolated miRNA was sequenced. PTSD was associated with 8 differentially expressed miRNA. Pathway analysis shows that PTSD is related to the axon guidance and Wnt signaling pathways, which work together to support neuronal development through regulation of growth cones. PTSD is associated with miRNAs that regulate biological functions including neuronal activities, suggesting that they play a role in PTSD symptomatology.

Purpose: Nurses investigate reasons for variable patient symptoms and responses to treatments to inform how best to improve outcomes. Genomics has the potential to guide nursing research exploring contributions to individual variability. This article is meant to serve as an introduction to the novel methods available through genomics for addressing this critical issue and includes a review of methodological considerations for selected genomic approaches. Approach: This review presents essential concepts in genetics and genomics that will allow readers to identify upcoming trends in genomics nursing research and improve research practice. It introduces general principles of genomic research and provides an overview of the research process. It also highlights selected nursing studies that serve as clinical examples of the use of genomic technologies. Finally, the authors provide suggestions about how to apply genomic technology in nursing research along with directions for future research. Conclusions: Using genomic approaches in nursing research can advance the understanding of the complex pathophysiology of disease susceptibility and different patient responses to interventions. Nurses should be incorporating genomics into education, clinical practice, and research as the influence of genomics in health-care research and practice continues to grow. Nurses are also well placed to translate genomic discoveries into improved methods for patient assessment and intervention.

Introduction Up to 91% of military personnel and veterans with posttraumatic stress disorder (PTSD) report co-occurring sleep disturbances, including. insomnia and excessive daytime sleepiness (EDS). Sleep disturbances have been shown not only to increase the risk of developing PTSD, but to exacerbate and maintain PTSD symptomology. The aim of this study was to examine gene expression in active duty military personnel and veterans with PTSD, with and without EDS. Participants were categorized into three groups; 1) PTSD with EDS (PTSDwEDS; n=21), 2) PTSD without EDS (PTSDnoEDS; n=25), or 3) Controls (no PTSD and no EDS; n=57). Methods Participants were 79% male, mean age of 37.6years (SD=11.2years). PTSD symptoms were measured using the PTSD checklist for civilians (PCL-C); participants were classified as PTSD-present using DSM-IV-TR criteria of “moderate-to-severe”. Daytime sleepiness was assessed using the Epworth Sleepiness Scale (ESS), high sleepiness was indicated by an ESS score >13. We performed RNA-seq with Illumina’s HiSeq 2500 in paired-end. We conducted quality control using FastQC and aligned to GRCh38 reference genome using STAR (v2.5.3a). Differentially expressed genes identified using DESeq2 (v1.20.0) with False Discovery Rate of 0.10. Finally, Ingenuity Pathway Analysis (IPA) was conducted to identify dysregulated gene networks. Results Between the Controls and PTSDnoEDS groups, two genes were significantly dysregulated. In controls and PTSDwEDS groups, 251 genes were dysregulated. The IPA networks showed that genes associated with inflammation were significantly dysregulated. Finally, between PTSDwEDS and PTSDnoEDS there were 1,873 significantly dysregulated genes. The IPA networks identified dysregulation of genes related to sleep, fatigue, circadian, and mitochondrial function. Conclusion Taken together this data indicates that EDS that is co-morbidly experienced with PTSD is associated with significant gene dysregulation, above and beyond that observed in participants with PTSD without significant EDS and controls. Treating EDS in military personnel and veterans with PTSD is important. Support This work was supported by the Center for Neuroscience and Regenerative Medicine (CNRM)

Introduction Insomnia affects 10–20% of the US population and is associated with negative health and psychosocial sequelae. Despite the public health impact of insomnia little is known about its underlying molecular mechanisms. The purpose of this study is to examine differentially expressed genes in 15 patients with chronic insomnia and age- and sex-matched good sleepers (n=15). Methods We performed total RNA-seq on 30 whole blood samples collected at 09:00 at 150 bp paired-ends on the Illumina NovaSeq-6000 platform. Alignment was performed using the STAR version 2.7.2a software on the human reference genome (GRCh38). Differential gene expression analysis was performed using DESeq2 version 1.24.0. Pathway analysis was performed using IPA, release 2019-08-30. Results An average of 86.7 million paired end reads per sample were sequenced. We found that 289 genes were differentially expressed in insomnia patients with a log fold change (LFC) ±0.50 and had a FDR p-value < 0.05. Top dysregulated genes include CSMD1 (L2FC=-2.78; p=1.35E-06), DUX4L9 (L2FC=3.40; p=2.81E-06) and GRM4 (L2FC=2.45; p=4.50E-05). Among the functionally relevant genes, CSMD encodes a complement control protein that is known to participate in the complement activation and inflammation in the developing central nervous system. UTS2 (L2FC=1.778; p=8.94E-06) is involved in regulation of orexin A and B activity and rapid eye movement during sleep. Ingenuity Pathway Analysis revealed 3 associated networks: Hematological, Hereditary Disorder, Organismal Injury and Abnormalities (score: 46), Developmental, Hereditary Disorder, Metabolic Disease (score: 43), and Cell Cycle, Cell mediated Immune Response, Cellular Development (score: 43). Conclusion Overall, our study revealed dysregulated genes in individuals who suffer from insomnia. Notably, dysregulation of these functionally relevant genes could impair functional brain connectivity and synaptic function. Further investigation of these biological pathways will be useful to elucidate the pathogenesis of insomnia and identify novel biomarkers or drug targets for developing improved diagnostics and therapeutics. Support National Institutes of Nursing Research, Graduate Partnership Program

Temporal regulation of gene expression is a crucial aspect of metazoan development. In the roundworm Caenorhabditis elegans, the heterochronic pathway controls multiple developmental events in a time-specific manner. The most downstream effector of this pathway, the zinc-finger transcription factor LIN-29, acts in the last larval stage (L4) to regulate elements of the larval-to-adult switch. Here, we explore new LIN-29 targets and their implications for this developmental transition. We used RNA-sequencing to identify genes differentially expressed between animals misexpressing LIN-29 at an early time point and control animals. Among 230 LIN-29-activated genes, we found that genes encoding cuticle collagens were overrepresented. Interestingly, expression of lin-29 and some of these collagens was increased in adults with cuticle damage, suggesting a previously unknown function for LIN-29 in adult cuticle maintenance. On the other hand, genes involved in fat metabolism were enriched among 350 LIN-29-downregulated targets. We used mass spectrometry to assay lipid content in animals overexpressing LIN-29 and observed reduced fatty acid levels. Many LIN-29-repressed genes are normally expressed in the intestine, suggesting cell-nonautonomous regulation. We identified several LIN-29 upregulated genes encoding signaling molecules that may act as mediators in the regulation of intestinally expressed genes encoding fat metabolic enzymes and vitellogenins. Overall, our results support the model of LIN-29 as a major regulator of adult cuticle synthesis and integrity, and as the trigger for metabolic changes that take place at the important transition from rapid growth during larval life to slower growth and offspring production during adulthood.

Posttraumatic stress disorder (PTSD) is associated with wide-spread immune dysregulation; however, little is known about the gene expression differences attributed to each PTSD symptom cluster. This is an important consideration when identifying diagnostic and treatment response markers in highly comorbid populations with mental and physical health conditions that share symptoms. To this aim, we utilized a transcriptome-wide analysis of differential gene expression in peripheral blood by comparing military service members: (1) with vs. without PTSD, (2) with high vs. low PTSD cluster symptom severity, and (3) with improved vs. not improved PTSD symptoms following 4 to 8 weeks of evidenced-based sleep treatment. Data were analyzed at a ± 2.0-fold change magnitude with subsequent gene ontology-based pathway analysis. In participants with PTSD (n=39), 89 differentially expressed genes were identified, and 94% were upregulated. In participants with high intrusion symptoms (n=22), 1,040 differentially expressed genes were identified, and 98% were upregulated. No differentially expressed genes were identified for the remaining two PTSD symptom clusters. Ten genes (C5orf24, RBAK, CREBZF, CD69, PMAIP1, AGL, ZNF644, ANKRD13C, ESCO1, and ZCCHC10) were upregulated in participants with PTSD and high intrusion symptoms at baseline and downregulated in participants with improved PTSD symptoms following treatment. Pathway analysis identified upregulated immune response systems and metabolic networks with a NF-kB hub, which were downregulated with symptom reduction. Molecular biomarkers implicated in intrusion symptoms and PTSD symptom improvement may inform the development of therapeutic targets for precise treatment of PTSD.

Primary objective: Excessive accumulation of amyloid beta (Aβ) and tau have been observed in older individuals with chronic neurological symptoms related to a traumatic brain injury (TBI), yet little is known about the possible role of Aβ in younger active duty service members following a TBI. The purpose of the study was to determine if Aβ 40 or 42 related to sustaining a TBI or to chronic neurological symptoms in a young cohort of military personnel. Research design: This was a cross-sectional study of active duty service members who reported sustaining a TBI and provided self-report of neurological and psychological symptoms and provided blood. Methods and procedures: An ultrasensitive single-molecule enzyme-linked immunosorbent assay was used to compare concentrations of Aβ in active duty service members with (TBI+; n = 53) and without (TBI–; n = 18) a history of TBI. Self-report and medical history were used to measure TBI occurrence and approximate the number of total TBIs and the severity of TBIs sustained during deployment. Main outcomes and results: This study reports that TBI is associated with higher concentrations of Aβ40 (F 1,68 = 6.948, p = 0.009) and a lower ratio of Aβ42/Aβ40 (F 1,62 = 5.671, p = 0.020). These differences remained significant after controlling for co-morbid symptoms of post-traumatic stress disorder and depression. Conclusions: These findings suggest that alterations in Aβ relate to TBIs and may contribute to chronic neurological symptoms.

Over four hundred different microRNAs (miRNAs) have been identified in the genome of the model organism the nematode Caenorhabditis elegans. As the germline is dedicated to the preservation of each species, and almost half of all the cells in an adult nematode are germline, it is likely that regulatory miRNAs are important for germline development and maintenance. In C. elegans the miR35 family has strong maternal effects, contributing to normal embryogenesis and to adult fecundity. To determine whether any particular miRNAs are greatly enriched in the C. elegans germline we used RNA-seq to compare the miRNA populations in several germline-defective strains of adult C. elegans worms, including glp-4(germline proliferation-4), glh-1(germline helicase-1) and dcr-1(dicer-1). Statistical analyses of RNA-seq comparisons identified 13 miRNAs that are germline-enriched, including seven members of the well-studied miR35 family that were reduced as much as 1000-fold in TaqMan qRT PCR miRNA assays. Along with the miR35s, six others: miR-56 (a member of the miR51 family),-70, -244, -260 , -788 and -4813, none of which previously considered as such, were also identified by RNA-seq as germline-enriched candidates. We went on to develop a successful miRNA in situ hybridization protocol for C. elegans, revealing miR35s specifically concentrate during oogenesis in the pachytene region of the gonad, and persist throughout early embryogenesis, while in adult animals neither let-7 nor miR-228 has a germline-bias.

Purpose of study: Female breast cancer is the second leading cause of cancer death in U.S. women, and the incidence of new breast cancer cases continues to increase. Despite slightly lower breast cancer incidence rates among African American (AA) compared to European American (EA) women in the U.S., AA women experience significantly higher breast cancer mortality. To better understand the extent to which environmental and genetic factors might help explain higher mortality rates among AA women, we examined the association between a measure of exposure to chemical pollutants and genomic profiling with breast cancer mortality among women with breast cancer in North Carolina. Procedures: Using a molecular epidemiologic approach, we examined the association of county hog concentration (a marker of environmental exposure to chemical pollutants) and genomic variations identified via targeted exome sequencing with age-adjusted breast cancer mortality rates among 146 women in North Carolina, stratified by race (AA vs. EA). The odds of breast cancer-specific mortality were estimated as a function of county hog concentration quintiles. Results: Overall, breast cancer mortality among AA women was higher than among EA women (OR=1.4, p Conclusions: Our findings suggest that living in a county with a high concentration of hogs may increase breast cancer mortality risk among AA women, and the high frequency of CNVs varies by race; both CNV and county hog concentration may contribute to racial disparities in breast cancer mortality among AA and EA women in North Carolina. Citation Format: Jung S. Byun, Sean Lee, Sijung Yun, Eliseo J. Perez-Stable, Anna M. Napoles, Paul Strickland, Kevin L. Gardner. Race, copy number variation, and local hog concentration in breast cancer mortality [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1183.

Nutrient-driven O-GlcNAcylation has been linked to epigenetic regulation of gene expression in metazoans. In C. elegans, O-GlcNAc marks the promoters of over 800 developmental, metabolic, and stress-related genes; these O-GlcNAc marked genes show a strong 5′, promoter-proximal bias in the distribution of RNA Polymerase II (Pol II). In response to starvation or feeding, the steady state distribution of O-GlcNAc at promoters remain nearly constant presumably due to dynamic cycling mediated by the transferase OGT-1 and the O-GlcNAcase OGA-1. However, in viable mutants lacking either of these enzymes of O-GlcNAc metabolism, the nutrient-responsive GlcNAcylation of promoters is dramatically altered. Blocked O-GlcNAc cycling leads to a striking nutrient-dependent accumulation of O-GlcNAc on RNA Pol II. O-GlcNAc cycling mutants also show an exaggerated, nutrient-responsive redistribution of promoter-proximal RNA Pol II isoforms and extensive transcriptional deregulation. Our findings suggest a complex interplay between the O-GlcNAc modification at promoters, the kinase-dependent “CTD-code,” and co-factors regulating RNA Pol II dynamics. Nutrient-responsive O-GlcNAc cycling may buffer the transcriptional apparatus from dramatic swings in nutrient availability by modulating promoter activity to meet metabolic and developmental needs.

Nutrient-driven

Supplemental Material, Cho_17010005_toSage_suppl_(1)(1) for Altered DNA Methylation Patterns Associated With Clinically Relevant Increases in PTSD Symptoms and PTSD Symptom Profiles in Military Personnel by Christiana Martin, Young-Eun Cho, Hyungsuk Kim, Sijung Yun, Rebekah Kanefsky, Hyunhwa Lee, Vincent Mysliwiec, Ann Cashion, and Jessica Gill in Biological Research For Nursing

Background Epigenetics, such as DNA methylation, has been hypothesized as one possible mechanism to explain the association between adverse childhood experiences and later health problems. The goal of this study was to identify genome-wide DNA methylation markers from peripheral blood associated with child abuse history among 6 African American adult females with Fibromyalgia Syndrome (FMS) using Methylated DNA Immuno-Precipitation sequencing (MeDIP-Seq). Methods Data were from a fibromyalgia, natural history study approved by the MedStar Health IRB. FMS was diagnosed using the 1990 or the 2010 American College of Rheumatology criteria and the Widespread Pain Index. Pain, fatigue, anxiety, depression, and cognitive function were assessed. A detailed abuse history was obtained, including age at the time and type of abuse (i.e., emotional, physical, or rape). A total of 6 FMS African American females, including 4 with any abuse before age 18 (Abused FMS female; AbFF) and 2 without (Non-abused FMS female; NFF), were selected in this study. Using peripheral blood collected from the subjects’ genomic DNA was extracted. DNA fragments containing methylated CpG were enriched and sequenced in the HiSeq-2500 system using MeDIP-Seq. Reads were aligned to the reference human genome of hg38. Generated sam files were sorted according to chromosomal position. Peaks were called using MACS version 2.1.1.20160309, to identify methylated DNA regions. DiffBind software package was used to perform clustering, Principal Component Analysis (PCA), and differential peak interval analysis with False Discovery Rate (FDR) of 0.05 cutoff. Results All of the 6 subjects with FMS met both the 1990 and 2010 criteria, except 1 NFF who only met the 1990 criteria. Age ranged from 45 to 56 years (mean=53.5, SD=4.23). The majority (66.7%) did not have a college education, unemployed, or divorced or widowed. Among the 4 AFFs, 1 reported rape + physical abuse, 2 reported rape only, and 1 reported emotional abuse. No significant differences were found in clinical symptoms or characteristics between AbFFs and NFFs. The number of methylated intervals per each subject ranged from 234,842 to 454,508. With the union of all these intervals, we obtained 412,226 methylated intervals, overall. Both of clustering analysis and PCA clearly separated AbFFs and NFFs. The differential analysis with FDR of 0.05 identified 15 intervals hypermethylated for AFPs and another 15 intervals hypermethylated for NFPs. After excluding ambiguous regions to interpret (e.g., repetitive DNA regions such as ribosomal repeating regions, the human alpha satellite repeat region) we identified DAP3 and mir2110 hypermethylated for AbFFs compared to NFFs. Discussion This study suggests hypermethylation in DAP3 and mir2110 could be used as candidates for novel biomarkers associated with child abuse history in African American females with fibromyalgia. Epigenetic inactivation patterns, especially one in DAP3, are found in numerous tumor cells and negatively affect cancer prognosis. Reduced DAP3 expression affects its normal regulation of cell respiration and apoptosis induced by oxidative stress, which is important of cell death pathways related to the ischemia-reperfusion injury. Further study is required to confirm this finding with more clinical samples.

Objective:To explore gene expression after moderate blast exposure (vs baseline) and proteomic changes after moderate- (vs low-) blast exposure.Methods:Military personnel (N = 69) donated blood for quantification of protein level, and peak pressure exposures were detected by helmet sensors before and during a blast training program (10 days total). On day 7, some participants (n = 29) sustained a moderate blast (mean peak pressure = 7.9 psi) and were matched to participants with no/low-blast exposure during the training (n = 40). PAXgene tubes were collected from one training site at baseline and day 10; RNA-sequencing day 10 expression was compared with each participant's own baseline samples to identify genes and pathways differentially expressed in moderate blast-exposed participants. Changes in amyloid precursor protein (APP) from baseline to the day of blast and following 2 days were evaluated. Symptoms were assessed using a self-reported form.Results:We identified 1,803 differentially expressed genes after moderate blast exposure; the most altered network was APP. Significantly reduced levels of peripheral APP were detected the day after the moderate blast exposure and the following day. Protein concentrations correlated with the magnitude of the moderate blast exposure on days 8 and 9. APP concentrations returned to baseline levels 3 days following the blast, likely due to increases in the genetic expression of APP. Onset of concentration problems and headaches occurred after moderate blast.Conclusions:Moderate blast exposure results in a signature biological profile that includes acute APP reductions, followed by genetic expression increases and normalization of APP levels; these changes likely influence neuronal recovery.