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      Acute and Chronic Molecular Signatures and Associated Symptoms of Blast Exposure in Military Breachers

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          Abstract

          Injuries from exposure to explosions rose dramatically during the Iraq and Afghanistan wars, which motivated investigations of blast-related neurotrauma and operational breaching. In this study, military “breachers” were exposed to controlled, low-level blast during a 10-day explosive breaching course. Using an omics approach, we assessed epigenetic, transcriptional, and inflammatory profile changes in blood from operational breaching trainees, with varying levels of lifetime blast exposure, along with daily self-reported symptoms (with tinnitus, headaches, and sleep disturbances as the most frequently reported). Although acute exposure to blast did not confer epigenetic changes, specifically in DNA methylation, differentially methylated regions (DMRs) with coordinated gene expression changes associated with lifetime cumulative blast exposures were identified. The accumulative effect of blast showed increased methylation of PAX8 antisense transcript with coordinated repression of gene expression, which has been associated with sleep disturbance. DNA methylation analyses conducted in conjunction with reported symptoms of tinnitus in the low versus high blast incidents groups identified DMRS in KCNE1 and CYP2E1 genes. KCNE1 and CYP2E1 showed the expected inverse correlation between DNA methylation and gene expression, which have been previously implicated in noise-related hearing loss. Although no significant transcriptional changes were observed in samples obtained at the onset of the training course relative to chronic cumulative blast, we identified a large number of transcriptional perturbations acutely pre- versus post-blast exposure. Acutely, 67 robustly differentially expressed genes (fold change ≥1.5), including UFC1 and YOD1 ubiquitin-related proteins, were identified. Inflammatory analyses of cytokines and chemokines revealed dysregulation of MCP-1, GCSF, HGF, MCSF, and RANTES acutely after blast exposure. These data show the importance of an omics approach, revealing that transcriptional and inflammatory biomarkers capture acute low-level blast overpressure exposure, whereas DNA methylation marks encapsulate chronic long-term symptoms.

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          Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values.

          comb-p is a command-line tool and a python library that manipulates BED files of possibly irregularly spaced P-values and (1) calculates auto-correlation, (2) combines adjacent P-values, (3) performs false discovery adjustment, (4) finds regions of enrichment (i.e. series of adjacent low P-values) and (5) assigns significance to those regions. In addition, tools are provided for visualization and assessment. We provide validation and example uses on bisulfite-seq with P-values from Fisher's exact test, tiled methylation probes using a linear model and Dam-ID for chromatin binding using moderated t-statistics. Because the library accepts input in a simple, standardized format and is unaffected by the origin of the P-values, it can be used for a wide variety of applications. comb-p is maintained under the BSD license. The documentation and implementation are available at https://github.com/brentp/combined-pvalues. bpederse@gmail.com
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            High-throughput DNA methylation profiling using universal bead arrays.

            We have developed a high-throughput method for analyzing the methylation status of hundreds of preselected genes simultaneously and have applied it to the discovery of methylation signatures that distinguish normal from cancer tissue samples. Through an adaptation of the GoldenGate genotyping assay implemented on a BeadArray platform, the methylation state of 1536 specific CpG sites in 371 genes (one to nine CpG sites per gene) was measured in a single reaction by multiplexed genotyping of 200 ng of bisulfite-treated genomic DNA. The assay was used to obtain a quantitative measure of the methylation level at each CpG site. After validating the assay in cell lines and normal tissues, we analyzed a panel of lung cancer biopsy samples (N = 22) and identified a panel of methylation markers that distinguished lung adenocarcinomas from normal lung tissues with high specificity. These markers were validated in a second sample set (N = 24). These results demonstrate the effectiveness of the method for reliably profiling many CpG sites in parallel for the discovery of informative methylation markers. The technology should prove useful for DNA methylation analyses in large populations, with potential application to the classification and diagnosis of a broad range of cancers and other diseases.
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              NF-kappaB is a negative regulator of IL-1beta secretion as revealed by genetic and pharmacological inhibition of IKKbeta.

              IKKbeta-dependent NF-kappaB activation plays a key role in innate immunity and inflammation, and inhibition of IKKbeta has been considered as a likely anti-inflammatory therapy. Surprisingly, however, mice with a targeted IKKbeta deletion in myeloid cells are more susceptible to endotoxin-induced shock than control mice. Increased endotoxin susceptibility is associated with elevated plasma IL-1beta as a result of increased pro-IL-1beta processing, which was also seen upon bacterial infection. In macrophages enhanced pro-IL-1beta processing depends on caspase-1, whose activation is inhibited by NF-kappaB-dependent gene products. In neutrophils, however, IL-1beta secretion is caspase-1 independent and depends on serine proteases, whose activity is also inhibited by NF-kappaB gene products. Prolonged pharmacologic inhibition of IKKbeta also augments IL-1beta secretion upon endotoxin challenge. These results unravel an unanticipated role for IKKbeta-dependent NF-kappaB signaling in the negative control of IL-1beta production and highlight potential complications of long-term IKKbeta inhibition.
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                Author and article information

                Journal
                J Neurotrauma
                J. Neurotrauma
                neu
                Journal of Neurotrauma
                Mary Ann Liebert, Inc., publishers (140 Huguenot Street, 3rd FloorNew Rochelle, NY 10801USA )
                0897-7151
                1557-9042
                May 15, 2020
                05 May 2020
                05 May 2020
                : 37
                : 10
                : 1221-1232
                Affiliations
                [ 1 ]Medical Epigenetics, James J. Peters VA Medical Center, Bronx, New York, USA.
                [ 2 ]Neurology Service, James J. Peters VA Medical Center, Bronx, New York, USA.
                [ 3 ]Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
                [ 4 ]Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
                [ 5 ]Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
                [ 6 ]Department of Biostatistics in Psychiatry, Columbia University, New York, New York, USA.
                [ 7 ]Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.
                [ 8 ]Naval Medical Research Center, Silver Spring, Maryland, USA.
                [ 9 ]Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA.
                Author notes
                [*]

                These authors contributed equally.

                [*]Address correspondence to: Fatemeh Haghighi, PhD, Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Room 9-20D, NewYork, NY 10029, USA fatemeh.haghighi@ 123456mssm.edu
                Article
                10.1089/neu.2019.6742
                10.1089/neu.2019.6742
                7232647
                31621494
                95627d58-0340-4ae0-b6ba-18e535f83164
                © Zhaoyu Wang et al., 2020; Published by Mary Ann Liebert, Inc.

                This Open Access article is distributed under the terms of the Creative Commons Attribution Noncommercial License ( http://creativecommons.org/licenses/by-nc/4.0/) which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.

                History
                Page count
                Figures: 5, References: 81, Pages: 12
                Categories
                Original Articles

                blast overpressure,epigenetics,sleep,tinnitus,traumatic brain injury

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