scholarly journals Avian Expression Patterns and Genomic Mapping Implicate Leptin in Digestion and TNF Signaling, Suggesting that Their Interacting Adipokine Role is Unique to Mammals

2019 ◽  
Vol 20 (18) ◽  
pp. 4489 ◽  
Author(s):  
Eyal Seroussi ◽  
Martin Knytl ◽  
Frédérique Pitel ◽  
Daniel Elleder ◽  
Vladimir Krylov ◽  
...  
Keyword(s):  
Meta Analysis ◽  
Expression Patterns ◽  
Immune Defense ◽  
Rna Seq ◽  
Appetite Control ◽  
Histocompatibility Complex ◽  
Leptin Expression ◽  
The Brain ◽  
Necrosis Factor ◽  
Receptor Mrnas

In mammals, leptin and tumor-necrosis factor (TNF) are prominent interacting adipokines mediating appetite control and insulin sensitivity. While TNF pleiotropically functions in immune defense and cell survival, leptin is largely confined to signaling energy stores in adipocytes. Knowledge about the function of avian leptin and TNF is limited and they are absent or lowly expressed in adipose, respectively. Employing radiation-hybrid mapping and FISH-TSA, we mapped TNF and its syntenic genes to chicken chromosome 16 within the major histocompatibility complex (MHC) region. This mapping position suggests that avian TNF has a role in regulating immune response. To test its possible interaction with leptin within the immune system and beyond, we compared the transcription patterns of TNF, leptin and their cognate receptors obtained by meta-analysis of GenBank RNA-seq data. While expression of leptin and its receptor (LEPR) were detected in the brain and digestive tract, TNF and its receptor mRNAs were primarily found in viral-infected and LPS-treated leukocytes. We confirmed leptin expression in the duodenum by immunohistochemistry staining. Altogether, we suggest that whereas leptin and TNF interact as adipokines in mammals, in birds, they have distinct roles. Thus, the interaction between leptin and TNF may be unique to mammals.

scholarly journals Meta-Analysis of cortical inhibitory interneurons markers landscape and their performances in scRNA-seq studies.

2021 ◽  
Author(s):  
Lorenzo Martini ◽  
Roberta Bardini ◽  
Stefano Di Carlo
Keyword(s):  
Single Cell ◽  
Meta Analysis ◽  
Cell Types ◽  
Cellular Heterogeneity ◽  
Marker Genes ◽  
Inhibitory Interneurons ◽  
Rna Seq ◽  
Circuit Function ◽  
The Brain

The mammalian cortex contains a great variety of neuronal cells. In particular, GABAergic interneurons, which play a major role in neuronal circuit function, exhibit an extraordinary diversity of cell types. In this regard, single-cell RNA-seq analysis is crucial to study cellular heterogeneity. To identify and analyze rare cell types, it is necessary to reliably label cells through known markers. In this way, all the related studies are dependent on the quality of the employed marker genes. Therefore, in this work, we investigate how a set of chosen inhibitory interneurons markers perform. The gene set consists of both immunohistochemistry-derived genes and single-cell RNA-seq taxonomy ones. We employed various human and mouse datasets of the brain cortex, consequently processed with the Monocle3 pipeline. We defined metrics based on the relations between unsupervised cluster results and the marker expression. Specifically, we calculated the specificity, the fraction of cells expressing, and some metrics derived from decision tree analysis like entropy gain and impurity reduction. The results highlighted the strong reliability of some markers but also the low quality of others. More interestingly, though, a correlation emerges between the general performances of the genes set and the experimental quality of the datasets. Therefore, the proposed method allows evaluating the quality of a dataset in relation to its reliability regarding the inhibitory interneurons cellular heterogeneity study.

scholarly journals Brain and Pituitary Transcriptome Analyses Reveal the Differential Regulation of Reproduction-Related LncRNAs and mRNAs in Cynoglossus semilaevis

2021 ◽  
Vol 12 ◽  
Author(s):  
Yani Dong ◽  
Likang Lyu ◽  
Haishen Wen ◽  
Bao Shi
Keyword(s):  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Interaction ◽  
Cynoglossus Semilaevis ◽  
Rna Seq ◽  
Tongue Sole ◽  
Gene Interaction Networks ◽  
Half Smooth Tongue Sole ◽  
The Brain

Long noncoding RNAs (lncRNAs) have been identified to be involved in half-smooth tongue sole (Cynoglossus semilaevis) reproduction. However, studies of their roles in reproduction have focused mainly on the ovary, and their expression patterns and potential roles in the brain and pituitary are unclear. Thus, to explore the mRNAs and lncRNAs that are closely associated with reproduction in the brain and pituitary, we collected tongue sole brain and pituitary tissues at three stages for RNA sequencing (RNA-seq), the 5,135 and 5,630 differentially expressed (DE) mRNAs and 378 and 532 DE lncRNAs were identified in the brain and pituitary, respectively. The RNA-seq results were verified by RT-qPCR. Moreover, enrichment analyses were performed to analyze the functions of DE mRNAs and lncRNAs. Interestingly, their involvement in pathways related to metabolism, signal transduction and endocrine signaling was revealed. LncRNA-target gene interaction networks were constructed based on antisense, cis and trans regulatory mechanisms. Moreover, we constructed competing endogenous RNA (ceRNA) networks. In summary, this study provides mRNA and lncRNA expression profiles in the brain and pituitary to understand the molecular mechanisms regulating tongue sole reproduction.

scholarly journals Mining transcriptomics and clinical data reveals ACE2 expression modulators and identifies cardiomyopathy as a risk factor for mortality in COVID-19 patients

2020 ◽  
Author(s):  
Navchetan Kaur ◽  
Boris Oskotsky ◽  
Atul J. Butte ◽  
Zicheng Hu
Keyword(s):  
Meta Analysis ◽  
Expression Patterns ◽  
Rna Seq ◽  
Experimental Conditions ◽  
Healthy Human ◽  
Angiotensin Converting Enzyme 2 ◽  
Genetic Perturbations ◽  
Drug Treatments ◽  
Multiple Drugs ◽  
Entry Receptor

AbstractAngiotensin-converting enzyme 2 (ACE2) is the cell-entry receptor for SARS-CoV-2. It plays critical roles in both the transmission and the pathogenesis of the coronavirus disease 2019 (COVID-19). Comprehensive profiling of ACE2 expression patterns will help researchers to reveal risk factors of severe COVID-19 illness. While the expression of ACE2 in healthy human tissues has been well characterized, it is not known which diseases and drugs might modulate the ACE2 expression. In this study, we developed GENEVA (GENe Expression Variance Analysis), a semi-automated framework for exploring massive amounts of RNA-seq datasets. We applied GENEVA to 28,6650 publicly available RNA-seq samples to identify any previously studied experimental conditions that could directly or indirectly modulate ACE2 expression. We identified multiple drugs, genetic perturbations, and diseases that modulate the expression of ACE2, including cardiomyopathy, HNF1A overexpression, and drug treatments with RAD140 and Itraconazole. Our unbiased meta-analysis of seven datasets confirms ACE2 up-regulation in all cardiomyopathy categories. Using electronic health records data from 3936 COVID19 patients, we demonstrate that patients with pre-existing cardiomyopathy have an increased mortality risk than age-matched patients with other cardiovascular conditions. GENEVA is applicable to any genes of interest and is freely accessible at http://genevatool.org.

scholarly journals Meta-analysis of RNA-seq studies reveals genes responsible for life stage-dominant functions in Schistosoma mansoni

2018 ◽  
Author(s):  
Zhigang Lu ◽  
Matthew Berriman
Keyword(s):  
Gene Expression ◽  
Schistosoma Mansoni ◽  
Differential Expression ◽  
Meta Analysis ◽  
Life Stage ◽  
Expression Patterns ◽  
Differential Expression Analysis ◽  
Housekeeping Genes ◽  
Life Stages ◽  
Rna Seq

AbstractBackgroundSince the genome of the parasitic flatworm Schistosoma mansoni was sequenced in 2009, various RNA-seq studies have been conducted to investigate differential gene expression between certain life stages. Based on these studies, the overview of gene expression in all life stages can improve our understanding of S. mansoni genome biology.Methodspublicly available RNA-seq data covering all life stages and gonads were mapped to the latest S. mansoni genome. Read counts were normalised across all samples and differential expression analysis was preformed using the generalized linear model (GLM) approach.Resultswe revealed for the first time the dissimilarities among all life stages. Genes that are abundantly-expressed in all life stages, as well as those preferentially-expressed in certain stage(s), were determined. The latter reveals genes responsible for stage-dominant functions of the parasite, which can be a guidance for the investigation and annotation of gene functions. In addition, distinct differential expression patterns were observed between adjacent life stages, which not only correlate well with original individual studies, but also provide additional information on changes in gene expression during parasite transitions. Furthermore, thirteen novel housekeeping genes across all life stages were identified, which is valuable for quantitative studies (e.g., qPCR).Conclusionsthe metaanalysis provides valuable information on the expression and potential functions of S. mansoni genes across all life stages, and can facilitate basic as well as applied research for the community.

scholarly journals Oxytocin gene networks in the human brain: A gene expression and large-scale fMRI meta-analysis study

2017 ◽  
Author(s):  
Daniel S. Quintana ◽  
Jaroslav Rokicki ◽  
Dennis van der Meer ◽  
Dag Alnæs ◽  
Tobias Kaufmann ◽  
...  
Keyword(s):  
Gene Expression ◽  
Social Behavior ◽  
Human Brain ◽  
Signaling Pathway ◽  
Large Scale ◽  
Meta Analysis ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Gene Pathway ◽  
The Brain

AbstractOxytocin is a neuropeptide involved in animal and human reproductive and social behavior, with implications for a range of psychiatric disorders. However, the therapeutic potential of oxytocin in mental health care suggested by animal research has not been successfully translated into clinical practice. This may be partly due to a poor understanding of the expression and distribution of the oxytocin signaling pathway in the human brain, and its complex interactions with other biological systems. Among the genes involved in the oxytocin signaling pathway, three genes have been frequently implicated in human social behavior: OXT (structural gene for oxytocin), OXTR (oxytocin receptor), and CD38 (central oxytocin secretion). We characterized the distribution of OXT, OXTR, and CD38 mRNA across the brain, identified putative gene pathway interactions by comparing gene expression patterns across 20737 genes, and assessed associations between gene expression patterns and mental states via large-scale fMRI metaanalysis. In line with the animal literature, expression of the three selected oxytocin pathway genes was increased in central, temporal, and olfactory regions. Across the brain, there was high co-expression with several dopaminergic and muscarinic acetylcholine genes, reflecting an anatomical basis for critical gene pathway interactions. Finally, fMRI meta-analysis revealed that the oxytocin pathway gene maps correspond with motivation and emotion processing.

scholarly journals Aberrant Expression of Collagen Gene Family in the Brain Regions of Male Mice with Behavioral Psychopathologies Induced by Chronic Agonistic Interactions

2019 ◽  
Vol 2019 ◽  
pp. 1-13 ◽  
Author(s):  
Dmitry A. Smagin ◽  
Anna G. Galyamina ◽  
Irina L. Kovalenko ◽  
Vladimir N. Babenko ◽  
Natalia N. Kudryavtseva
Keyword(s):  
Expression Patterns ◽  
Brain Regions ◽  
Research Data ◽  
Collagen Gene ◽  
Rna Seq ◽  
Agonistic Interactions ◽  
Aberrant Expression ◽  
Genes Encoding ◽  
Collagen Genes ◽  
The Brain

Chronic agonistic interactions promote the development of experimental psychopathologies in animals: a depression-like state in chronically defeated mice and the pathology of aggressive behavior in the mice with repeated wins. The abundant research data indicate that such psychopathological states are associated with significant molecular and cellular changes in the brain. This paper aims to study the influence of a 20-day period of agonistic interactions on the expression patterns of collagen family genes encoding the proteins which are basic components of extracellular matrix (ECM) in different brain regions of mice using the RNA-Seq database. Most of differentially expressed collagen genes were shown to be upregulated in the hypothalamus and striatum of chronically aggressive and defeated mice and in the hippocampus of defeated mice, whereas downregulation of collagen genes was demonstrated in the ventral tegmental areas in both experimental groups. Aberrant expression of collagen genes induced by chronic agonistic interactions may be indicative of specific ECM defects in the brain regions of mice with alternative social experience. This is the first study demonstrating remodeling of ECM under the development of experimental disorders.

scholarly journals Predominance of Interferon-Related Responses in the Brain during Murine Malaria, as Identified by Microarray Analysis

2008 ◽  
Vol 76 (5) ◽  
pp. 1812-1824 ◽  
Author(s):  
Jenny Miu ◽  
Nicholas H. Hunt ◽  
Helen J. Ball
Keyword(s):  
Microarray Analysis ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Interferon Signaling ◽  
Temporal Expression ◽  
Histocompatibility Complex ◽  
Number Of Genes ◽  
Cellular Source ◽  
Interferon Responses ◽  
The Brain

ABSTRACT Cerebral malaria (CM) can be a fatal manifestation of Plasmodium falciparum infection. We examined global gene expression patterns during fatal murine CM (FMCM) and noncerebral malaria (NCM) by microarray analysis. There was differential expression of a number of genes, including some not yet characterized in the pathogenesis of FMCM. Some gene induction was observed during Plasmodium berghei infection regardless of the development of CM, and there was a predominance of genes linked to interferon responses, even in NCM. However, upon real-time PCR validation and quantitation, these genes were much more highly expressed in FMCM than in NCM. The observed changes included genes belonging to pathways such as interferon signaling, major histocompatibility complex processing and presentation, apoptosis, and immunomodulatory and antimicrobial processes. We further characterized differentially expressed genes by examining the cellular source of their expression as well as their temporal expression patterns during the course of malaria infection. These data identify a number of novel genes that represent interesting candidates for further investigation in FMCM.

Morphological Changes in the Brain of Acutely Ill and Weight-Recovered Patients with Anorexia Nervosa

2014 ◽  
Vol 42 (1) ◽  
pp. 7-18 ◽  
Author(s):  
Jochen Seitz ◽  
Katharina Bühren ◽  
Georg G. von Polier ◽  
Nicole Heussen ◽  
Beate Herpertz-Dahlmann ◽  
...  
Keyword(s):  
Anorexia Nervosa ◽  
Cognitive Deficits ◽  
Time Course ◽  
Morphological Changes ◽  
Meta Analysis ◽  
Short Term ◽  
Clinical Prognosis ◽  
Qualitative Review ◽  
Brain Changes ◽  
The Brain

Objective: Acute anorexia nervosa (AN) leads to reduced gray (GM) and white matter (WM) volume in the brain, which however improves again upon restoration of weight. Yet little is known about the extent and clinical correlates of these brain changes, nor do we know much about the time-course and completeness of their recovery. Methods: We conducted a meta-analysis and a qualitative review of all magnetic resonance imaging studies involving volume analyses of the brain in both acute and recovered AN. Results: We identified structural neuroimaging studies with a total of 214 acute AN patients and 177 weight-recovered AN patients. In acute AN, GM was reduced by 5.6% and WM by 3.8% compared to healthy controls (HC). Short-term weight recovery 2–5 months after admission resulted in restitution of about half of the GM aberrations and almost full WM recovery. After 2–8 years of remission GM and WM were nearly normalized, and differences to HC (GM: –1.0%, WM: –0.7%) were no longer significant, although small residual changes could not be ruled out. In the qualitative review some studies found GM volume loss to be associated with cognitive deficits and clinical prognosis. Conclusions: GM and WM were strongly reduced in acute AN. The completeness of brain volume rehabilitation remained equivocal.

The Auditory Brainstem Implant

2019 ◽  
pp. 758-770
Author(s):  
Robert V. Shannon
Keyword(s):  
Surgical Technique ◽  
Cochlear Nucleus ◽  
Meta Analysis ◽  
Auditory Brainstem ◽  
Auditory Information ◽  
Speech Understanding ◽  
Auditory Neurons ◽  
Auditory Brainstem Implant ◽  
The Brain ◽  
Implanted Device

The auditory brainstem implant (ABI) is a surgically implanted device to electrically stimulate auditory neurons in the cochlear nucleus complex of the brainstem in humans to restore hearing sensations. The ABI is similar in function to a cochlear implant, but overall outcomes are poorer. However, recent applications of the ABI to new patient populations and improvements in surgical technique have led to significant improvements in outcomes. While the ABI provides hearing benefits to patients, the outcomes challenge our understanding of how the brain processes neural patterns of auditory information. The neural pattern of activation produced by an ABI is highly unnatural, yet some patients achieve high levels of speech understanding. Based on a meta-analysis of ABI surgeries and outcomes, a theory is proposed of a specialized sub-system of the cochlear nucleus that is critical for speech understanding.

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