Genomic modules and intramodular network concordance in susceptible and resilient male mice across models of stress.
Salvatore G. Caradonna,Tie-Yuan Zhang,Nicholas O’Toole,Mojun Shen,Huzefa Khalil,Nathan R. Einhorn,Xianglan Wen,Carine Parent,Francis S. Lee,Huda Akil,Michael J. Meaney,Bruce S. McEwen,Jordan Marrocco +12 more
TLDR
In this article, the authors investigated the genomic signatures in the ventral hippocampus common to mouse models of stress using RNA-sequencing and found that differentially expressed genes (DEGs) were concordant for gene networks involved in neurotransmission, cytoskeleton function, and vascularization.About:
This article is published in Neuropsychopharmacology.The article was published on 2021-11-30 and is currently open access. It has received 10 citations till now. The article focuses on the topics: Genetic predisposition & Population.read more
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Mineralocorticoid receptor and glucocorticoid receptor work alone and together in cell-type-specific manner: Implications for resilience prediction and targeted therapy
TL;DR: In this article , the authors discuss the cellular, neuroendocrine, and behavioral studies underlying the mineralocorticoid receptor (MR) balance concept, highlight the relevance of hypothalamic-pituitary-adrenal (HPA) -axis patterns and note the limited understanding yet of sexual dimorphism in glucocortication actions, concluding with the prospect that genetically and epigenetically regulated receptor variants dictate cell-type-specific transcriptome signatures of stress-related neuropsychiatric symptoms and selective receptor modulators are becoming available for more targeted treatment.
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Characterizing the behavioral and neuroendocrine features of susceptibility and resilience to social stress
TL;DR: In this paper , behavioral, physiological, and neuroendocrine profiles of mice were analyzed in three separate phases: before, during, and following chronic social defeat stress. And they found that behavioral coping strategies used during the initial social stress encounter better predict which mice will eventually become resilient or susceptible, indicating early differences in coping mechanisms used between the two groups.
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Corticosterone induces discrete epigenetic signatures in the dorsal and ventral hippocampus that depend upon sex and genotype: focus on methylated Nr3c1 gene
Salvatore G. Caradonna,Nathan R. Einhorn,Vikram Saudagar,Huzefa Khalil,Gordon H. Petty,Axel Lihagen,Claire LeFloch,Francis S. Lee,Huda Akil,Alessandro Guidotti,Bruce S. McEwen,Eleonora Gatta,Jordan Marrocco +12 more
TL;DR: In this article , the authors investigated the genomic signatures of oral corticosterone in the dHPC and vHPC of WT and hMet male and female mice, and examined sex and genotype differences in response to oral CORT.
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A genome-wide association study of tinnitus reveals shared genetic links to neuropsychiatric disorders
TL;DR: In this paper , the authors presented a GWAS using the UK Biobank to investigate the genetic processes linked to tinnitus, and they conducted gene-set enrichment analyses.
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An allostatic epigenetic memory on chromatin footprints after double-hit acute stress
TL;DR: This paper investigated the behavioral traits and epigenetic signatures in a double-hit mouse model of acute stress in which heterotypic stressors (acute swim stress and acute restraint stress) were applied within a 7-day interval period.
References
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STAR: ultrafast universal RNA-seq aligner
Alexander Dobin,Carrie A. Davis,Felix Schlesinger,Jorg Drenkow,Chris Zaleski,Sonali Jha,Philippe Batut,Mark Chaisson,Thomas R. Gingeras +8 more
TL;DR: The Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure outperforms other aligners by a factor of >50 in mapping speed.
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limma powers differential expression analyses for RNA-sequencing and microarray studies
Matthew E. Ritchie,Belinda Phipson,Di Wu,Yifang Hu,Charity W. Law,Wei Shi,Gordon K. Smyth,Gordon K. Smyth +7 more
TL;DR: The philosophy and design of the limma package is reviewed, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.
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WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder,Steve Horvath +1 more
TL;DR: The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis that includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software.
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A General Framework for Weighted Gene Co-Expression Network Analysis
Bin Zhang,Steve Horvath +1 more
TL;DR: A general framework for `soft' thresholding that assigns a connection weight to each gene pair is described and several node connectivity measures are introduced and provided empirical evidence that they can be important for predicting the biological significance of a gene.
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MultiQC: summarize analysis results for multiple tools and samples in a single report.
TL;DR: This work presents MultiQC, a tool to create a single report visualising output from multiple tools across many samples, enabling global trends and biases to be quickly identified.