scholarly journals Polymorphism, linkage mapping, and association analysis with carcass traits of four porcine candidate genes selected from gene-expression profiles of Czech Large White and Wild Boar muscles

2014 ◽  
Vol 59 (No. 3) ◽  
pp. 116-127
Author(s):  
P. Chalupová ◽  
V. Dvořáková ◽  
A. Knoll ◽  
A. Stratil ◽  
H. Bartenschlager ◽  
...  
Keyword(s):  
Wild Boar ◽  
Association Analysis ◽  
Skeletal Muscles ◽  
Muscle Development ◽  
Expression Profiles ◽  
Carcass Traits ◽  
Muscle Growth ◽  
Gene Expression Profiles ◽  
P Value ◽  
Large White

Genes that are expressed in skeletal muscles may play a role in prenatal muscle development and postnatal muscle growth and can be considered candidates for economically important traits. Four porcine genes that were differentially expressed in skeletal muscles of Czech Large White and Wild Boar (SORT1, EMP3, IL18, and BTG2) were selected to search for polymorphism, linkage assignment, and association analysis with carcass traits. Through comparative sequencing of portions of the genes numerous polymorphisms were revealed (SORT1 &ndash; 21, EMP3 &ndash; 6, IL18 &ndash; 41, BTG2 &ndash; 9). Linkage analysis in a Meishan &times; Pietrain F<sub>2</sub> pedigree showed the positions of the genes relative to other genes and markers on the respective chromosomes &ndash; SORT1 on SSC4, EMP3 on SSC6, IL18 and BTG2 on SSC9. Preliminary association analysis in pig commercial crosses with selected SNPs showed associations with several carcass traits at nominal P value of &lt; 0.05, which may indicate their involvement in muscle growth and fat deposition. The tested polymorphisms may not be causal for the associations, but they may be in linkage disequilibrium with causative mutations. &nbsp;

scholarly journals Aripiprazole as a candidate treatment of COVID-19 identified through genomic analysis

2020 ◽  
Author(s):  
Benedicto Crespo-Facorro ◽  
Miguel Ruiz-Veguilla ◽  
Javier Vazquez-Bourgon ◽  
Ana C. Sanchez-Hidalgo ◽  
Nathalia Garrido-Torres ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Phase 1 ◽  
Gene Expression Profiles ◽  
Genomic Analysis ◽  
Cell Receptor ◽  
Therapeutic Drug ◽  
P Value ◽  
Immunological Parameters ◽  
Altered Expression ◽  
Exact Test

Background: Antipsychotics suppress expression of inflammatory cytokines and inducible inflammatory enzymes. Elopiprazole (a phenylpiperazine antipsychotic drug in phase 1) has been characterized as a therapeutic drug to treat SARS-CoV-2 infection in a repurposing study. We aim to investigate the potential effects of aripiprazole (an FDA approved phenylpiperazine) on COVID19-related immunological parameters. Methods: Differential gene expression profiles of non-COVID versus COVID RNA-Seq samples (CRA002390 project in GSA database) and drug-naive patients with psychosis at baseline and after three months of aripiprazole treatment was identified. An integrative analysis between COVID and aripiprazole immunomodulatory antagonist effects was performed. Findings: 82 out the 377 genes (21.7%) with expression significantly altered by aripiprazole have also their expression altered in COVID-19 patients and in 93.9% of these genes their expression is reverted by aripiprazole. The number of common genes with expression altered in both analyses is significantly higher than expected (Fisher's Exact Test, two tail; P value=3.2e-11). 11 KEGG pathways were significantly enriched with genes with altered expression both in COVID-19 patients and aripiprazole medicated schizophrenia patients (P adj<0.05). The most significant pathways were associated to the immune system such as the inflammatory bowel disease (IBD) (the most significant pathway with a P adj of 0.00021), Th1 and Th2 cell differentiation and B cell receptor signaling pathway, all three related to the defense against infections. Interpretation: This exploratory investigation may provide further support to the notion that protective effect is exerted by phenylpiperazine by modulating the immunological dysregulation associated to COVID-19. Along with many ongoing studies and clinical trials, repurposing available medications could be of use in countering SARS-CoV-2 infection, but require further studies and trials.

scholarly journals Mechanism and Functions of Identified miRNAs in Poultry Skeletal Muscle Development – A Review

2019 ◽  
Vol 19 (4) ◽  
pp. 887-904
Author(s):  
Asiamah Amponsah Collins ◽  
Kun Zou ◽  
Zhang Li ◽  
Su Ying
Keyword(s):  
Skeletal Muscle ◽  
Candidate Genes ◽  
Skeletal Muscles ◽  
Muscle Development ◽  
Muscle Growth ◽  
Skeletal Muscle Development ◽  
Single Nucleotide ◽  
Complex Processes ◽  
Muscle Formation ◽  
Gene Regulatory

AbstractDevelopment of the skeletal muscle goes through several complex processes regulated by numerous genetic factors. Although much efforts have been made to understand the mechanisms involved in increased muscle yield, little work is done about the miRNAs and candidate genes that are involved in the skeletal muscle development in poultry. Comprehensive research of candidate genes and single nucleotide related to poultry muscle growth is yet to be experimentally unraveled. However, over a few periods, studies in miRNA have disclosed that they actively participate in muscle formation, differentiation, and determination in poultry. Specifically, miR-1, miR-133, and miR-206 influence tissue development, and they are highly expressed in the skeletal muscles. Candidate genes such as CEBPB, MUSTN1, MSTN, IGF1, FOXO3, mTOR, and NFKB1, have also been identified to express in the poultry skeletal muscles development. However, further researches, analysis, and comprehensive studies should be made on the various miRNAs and gene regulatory factors that influence the skeletal muscle development in poultry. The objective of this review is to summarize recent knowledge in miRNAs and their mode of action as well as transcription and candidate genes identified to regulate poultry skeletal muscle development.

scholarly journals Exploring the Mechanism of Skeletal Muscle in a Tacrolimus-Induced Posttransplantation Diabetes Mellitus Model on Gene Expression Profiles

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Chenlei Zheng ◽  
Cheng Wang ◽  
Tan Zhang ◽  
Ding Li ◽  
Xiao-feng Ni ◽  
...  
Keyword(s):  
Gene Expression ◽  
Diabetes Mellitus ◽  
Skeletal Muscle ◽  
Muscle Development ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Quadriceps Muscle ◽  
Control Group ◽  
Bioinformatics Analyses

Objective. Posttransplantation diabetes mellitus (PTDM) is a known complication of transplantation that affects the prognosis. Tacrolimus (Tac or FK506) is a widely used immunosuppressant that has been reported to be a risk factor for PTDM and to further induce complications in heart and skeletal muscles, but the mechanism is still largely unknown. In our preliminary experiments, we found that after Tac treatment, blood glucose increased, and the weight of skeletal muscle declined. Here, we hypothesize that tacrolimus can induce PTDM and influence the atrophy of skeletal muscle. Methods. We designed preliminary experiments to establish a tacrolimus-induced PTDM model. Gene expression profiles in quadriceps muscle from this rat model were characterized by oligonucleotide microarrays. Then, differences in gene expression profiles in muscle from PTDM rats that received tacrolimus and control subjects were analyzed by using GeneSpring GX 11.0 software (Agilent). Functional annotation and enrichment analysis of differentially expressed genes (DEGs) helped us identify clues for the side effects of tacrolimus. Results. Our experiments found that the quadriceps in tacrolimus-induced PTDM group were smaller than those in the control group. The study identified 275 DEGs that may be responsible for insulin resistance and the progression of PTDM, including 86 upregulated genes and 199 downregulated genes. GO and KEGG functional analysis of the DEGs showed a significant correlation between PTDM and muscle development. PPI network analysis screened eight hub genes and found that they were related to troponin and tropomyosin. Conclusions. This study explored the molecular mechanism of muscle atrophy in a tacrolimus-induced PTDM model by bioinformatics analyses. We identified 275 DEGs and identified significant biomarkers for predicting the development and progression of tacrolimus-induced PTDM.

Identification of synthetic lethal interactions with the BRAF oncogene in colorectal cancer.

2013 ◽  
Vol 31 (4_suppl) ◽  
pp. 403-403
Author(s):  
Loredana Vecchione ◽  
Valentina Gambino ◽  
Giovanni d'Ario ◽  
Sun Tian ◽  
Iris Simon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Gene Expression Signature ◽  
Gene Signature ◽  
Braf V600e ◽  
P Value ◽  
Synthetic Lethal ◽  
Braf Mutant

403 Background: Approximately 8-15% of colorectal (CRC) patients carry an activating mutation in BRAF. This CRC subtype is associated with poor outcome and with resistance, both to chemotherapeutic treatments and to tailored drugs. We recently showed that BRAF (V600E) colon cancers (CCs) have a characteristic gene expression signature (1, 2) which is found also in subsets of KRAS mutant and KRAS-BRAF wild type (WT2) tumors. Tumors having this gene signature, referred as “BRAF-like”, have a similar poor prognosis irrespective of the presence of the BRAF (V600E) mutation. By using a shRNA-based genetic screen in BRAF mutant CC cell lines we aimed to identify genes and pathways necessary for survival and growth of BRAFmutant CC. Such studies may reveal additional targets for therapy and potentially provide new biomarkers for patient stratification Methods: We identified 363 genes that are selectively overexpressed in BRAF mutant tumors as compared to WT2 type tumors, based on gene expression profiles of the PETACC3 (1) and Agendia (2) datasets. The TRC human genome-wide shRNA collection (TRC-Hs1.0) was used to generate a 1815 hairpins sub-library targeting those identified genes (BRAF library). BRAF(V600E) CC cell lines were infected with the BRAF library and screened for shRNAs that cause lethality. LIM1215 CC cell line (WT2) was used as a control. Cells stably expressing the shRNA library were cultured for 13 days, after which shRNAs were recovered by PCR. Deep sequencing was applied to determine the specific depletion of shRNA in BRAF(V600E) cells as compared to LIM1215 cells Results: Candidate genes were identified by using following filtering criteria: depletion in BRAF(V600E) cells by at least 50% and depletion in BRAF(V600E) cells 1, 5-fold higher than in control cells with the corresponding p-value to be ≤ 0.1. A total of 34 genes met our criteria of which 6 genes were presented with more than one hairpin and were concordant across the cell lines selected for validation. Conclusions: We identified candidate synthetic lethal genes in BRAF mutant CC cell lines. Functional analysis is ongoing. Data will be presented. References 1. J Clin Oncol 2012 Apr 20;30(12):1288-9 2. Gut (2012). doi:10.1136/gutjnl-2012-302423

scholarly journals Association of predicted deleterious single nucleotide polymorphisms with carcass traits in meat-type chickens

2018 ◽  
Author(s):  
Priscila Anchieta Trevisoli ◽  
Gabriel Costa Monteiro Moreira ◽  
Clarissa Boschiero ◽  
Aline Silva Mello Cesar ◽  
Juliana Petrini ◽  
...  
Keyword(s):  
Carcass Traits ◽  
Muscle Growth ◽  
Substitution Effects ◽  
P Value ◽  
Nucleotide Polymorphisms ◽  
Coding Regions ◽  
Genome Wide ◽  
Allele Substitution ◽  
Steroid Hormone Signaling ◽  
Breast Weight

ABSTRACTIn previous studies, we used genome wide association (GWAS) to identify quantitative trait loci (QTL) associated with weight and yield of abdominal fat, drumstick, thigh and breast traits in chickens. However, this methodology assumes that the studied variants are in linkage disequilibrium with the causal mutation and consequently do not identify it. In an attempt to identify causal mutations in candidate genes for carcass traits in broilers, we selected 20 predicted deleterious SNPs within QTLs for association analysis. Additive, dominance and allele substitution effects were tested. From the 20 SNPs analyzed, we identified six SNPs with significant association (p-value <0.05) with carcass traits, and three are highlighted here. The SNP rs736010549 was associated with drumstick weight and yield with significant additive and dominance effects. The SNP rs739508259 was associated with thigh weight and yield, and with significant additive and allele substitution effects. The SNP rs313532967 was associated with breast weight and yield. The three SNPs that were associated with carcass traits (rs736010549, rs739508259 and rs313532967) are respectively located in the coding regions of the WDR77, VWA8 and BARL genes. These genes are involved in biological processes such as steroid hormone signaling pathway, estrogen binding, and regulation of cell proliferation. Our strategy allowed the identification of putative casual mutations associated with muscle growth.

scholarly journals Analysis of dynamic and widespread lncRNA and miRNA expression in fetal sheep skeletal muscle

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9957
Author(s):  
Chao Yuan ◽  
Ke Zhang ◽  
Yaojing Yue ◽  
Tingting Guo ◽  
Jianbin Liu ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Development ◽  
Expression Profiles ◽  
Muscle Growth ◽  
Skeletal Muscle Development ◽  
Fetal Sheep ◽  
Lncrna Gene ◽  
Skeletal Muscle Growth ◽  
Wide Range ◽  
Non Coding Rnas

The sheep is an economically important animal, and there is currently a major focus on improving its meat quality through breeding. There are variations in the growth regulation mechanisms of different sheep breeds, making fundamental research on skeletal muscle growth essential in understanding the regulation of (thus far) unknown genes. Skeletal muscle development is a complex biological process regulated by numerous genes and non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). In this study, we used deep sequencing data from sheep longissimus dorsi (LD) muscles sampled at day 60, 90, and 120 of gestation, as well as at day 0 and 360 following birth, to identify and examine the lncRNA and miRNA temporal expression profiles that regulate sheep skeletal myogenesis. We stained LD muscles using histological sections to analyse the area and circumference of muscle fibers from the embryonic to postnatal development stages. Our results showed that embryonic skeletal muscle growth can be characterized by time. We obtained a total of 694 different lncRNAs and compared the differential expression between the E60 vs. E90, E90 vs. E120, E120 vs. D0, and D0 vs. D360 lncRNA and gene samples. Of the total 701 known sheep miRNAs we detected, the following showed a wide range of expression during the embryonic stage: miR-2387, miR-105, miR-767, miR-432, and miR-433. We propose that the detected lncRNA expression was time-specific during the gestational and postnatal stages. GO and KEGG analyses of the genes targeted by different miRNAs and lncRNAs revealed that these significantly enriched processes and pathways were consistent with skeletal muscle development over time across all sampled stages. We found four visual lncRNA–gene regulatory networks that can be used to explore the function of lncRNAs in sheep and may be valuable in helping improve muscle growth. This study also describes the function of several lncRNAs that interact with miRNAs to regulate myogenic differentiation.

scholarly journals circTAF8 Regulates Myoblast Development and Associated Carcass Traits in Chicken

2022 ◽  
Vol 12 ◽  
Author(s):  
Kan Li ◽  
Weichen Huang ◽  
Zhijun Wang ◽  
Yangfeng Chen ◽  
Danfeng Cai ◽  
...  
Keyword(s):  
Association Analysis ◽  
Muscle Development ◽  
Carcass Traits ◽  
Live Weight ◽  
Circular Rnas ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Muscle Weight ◽  
Primary Myoblasts ◽  
Leg Muscle

Recent studies have shown that circular RNAs (circRNAs) play important roles in skeletal muscle development. CircRNA biogenesis is dependent on the genetic context. Single-nucleotide polymorphisms in the introns flanking circRNAs may be intermediate-inducible factors between circRNA expression and phenotypic traits. Our previous study showed that circTAF8 is an abundantly and differentially expressed circRNA in leg muscle during chicken embryonic development. Here, we aimed to investigate circTAF8 function in muscle development and the association of the SNPs in the circTAF8 flanking introns with carcass traits. In this study, we observed that overexpression of circTAF8 could promote the proliferation of chicken primary myoblasts and inhibit their differentiation. In addition, the SNPs in the introns flanking the circTAF8 locus and those associated with chicken carcass traits were analyzed in 335 partridge chickens. A total of eight SNPs were found associated with carcass traits such as leg muscle weight, live weight, and half and full-bore weight. The association analysis results of haplotype combinations were consistent with the association analysis of a single SNP. These results suggest that circTAF8 plays a regulatory role in muscle development. These identified SNPs were found correlated with traits to muscle development and carcass muscle weight in chickens.

scholarly journals Whole Transcription Profile of Responders to Anti-TNF Drugs in Pediatric Inflammatory Bowel Disease

Pharmaceutics ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 77
Author(s):  
Sara Salvador-Martín ◽  
Bartosz Kaczmarczyk ◽  
Rebeca Álvarez ◽  
Víctor Manuel Navas-López ◽  
Carmen Gallego-Fernández ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Bowel Disease ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Early Response ◽  
P Value ◽  
Pediatric Inflammatory Bowel Disease ◽  
Study Population ◽  
Inflammatory Bowel ◽  
Necrosis Factor

Background: Up to 30% of patients with pediatric inflammatory bowel disease (IBD) do not respond to anti-Tumor Necrosis Factor (anti-TNF) therapy. The aim of this study was to identify pharmacogenomic markers that predict early response to anti-TNF drugs in pediatric patients with IBD. Methods: An observational, longitudinal, prospective cohort study was conducted. The study population comprised 38 patients with IBD aged < 18 years who started treatment with infliximab or adalimumab (29 responders and nine non-responders). Whole gene expression profiles from total RNA isolated from whole blood samples of six responders and six non-responders taken before administration of the biologic and after two weeks of therapy were analyzed using next-generation RNA sequencing. The expression of six selected genes was measured for purposes of validation in all of the 38 patients recruited using qPCR. Results: Genes were differentially expressed in non-responders and responders (32 before initiation of treatment and 44 after two weeks, Log2FC (Fold change) >0.6 or <−0.6 and p value < 0.05). After validation, FCGR1A, FCGR1B, and GBP1 were overexpressed in non-responders two weeks after initiation of anti-TNF treatment (Log2FC 1.05, 1.21, and 1.08, respectively, p value < 0.05). Conclusion: Expression of the FCGR1A, FCGR1B, and GBP1 genes is a pharmacogenomic biomarker of early response to anti-TNF agents in pediatric IBD.

scholarly journals Gene expression profiling of skeletal muscles

2021 ◽  
Author(s):  
Sarah I. Alto ◽  
Chih-Ning Chang ◽  
Kevin Brown ◽  
Chrissa Kioussi ◽  
Theresa M. Filtz
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Differentially Expressed Genes ◽  
Tibialis Anterior ◽  
Skeletal Muscles ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Analysis Tool

AbstractSoleus and tibialis anterior are two well-characterized skeletal muscles commonly utilized in skeletal muscle-related studies. Next-generation sequencing provides an opportunity for an in-depth biocomputational analysis to identify the gene expression patterns between soleus and tibialis anterior and analyze those genes’ functions based on past literature. This study acquired the gene expression profiles from soleus and tibialis anterior murine skeletal muscle biopsies via RNA-sequencing. Read counts were processed through edgeR’s differential gene expression analysis. Differentially expressed genes were filtered down using a false discovery rate less than 0.05c, a fold-change value larger than twenty, and an association with overrepresented pathways based on the Reactome pathway over-representation analysis tool. Most of the differentially expressed genes associated with soleus encoded for components of lipid metabolism and unique contractile elements. Differentially expressed genes associated with tibialis anterior encoded mostly for glucose and glycogen metabolic pathways’ regulatory enzymes and calcium-sensitive contractile components. These gene expression distinctions partly explain the genetic basis for muscle specialization and may help to explain skeletal muscle susceptibility to disease and drugs and refine tissue engineering approaches.

scholarly journals Age-associated different transcriptome profiling in zebrafish and rat: insight into diversity of vertebrate aging

2018 ◽  
Author(s):  
Yusuke Kijima ◽  
Wang Wantong ◽  
Yoji Igarashi ◽  
Kazutoshi Yoshitake ◽  
Shuichi Asakawa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Muscle Development ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Model Organisms ◽  
Human Beings ◽  
Rna Seq ◽  
Down Regulation ◽  
Circadian Genes ◽  
Age Related

AbstractBackgroundAging and death are inevitable for most species and are of intense interest for human beings. Most mammals, including humans, show obvious aging phenotypes, for example, loss of tissue plasticity and sarcopenia. In this regard, fish provide attractive models because of their unique aging characteristics. First, the lifespan of fish is highly varied and some long-lived fish can live for over 200 years. Second, some fish show anti-aging features and indeterminate growth throughout their life. Because these characteristics are not found in mammalian model organisms, exploring mechanisms of senescence in fish is expected to provide new insights into vertebrate aging. Therefore, we conducted transcriptome analysis for brain, gill, heart, liver and muscle from 2-month-, 7-month-, 16month- and 39-month-old zebrafish. In addition, we downloaded RNA-seq data for sequential age related gene expression in brain, heart, liver and muscle of rat (1). These RNA-seq data from two species were compared, and common and species-specific features of senescence were analyzed.ResultsScreening of differentially expressed genes (DEGs) in all zebrafish tissues examined revealed up-regulation of circadian genes and down-regulation of hmgb3a. Comparative analysis of DEG profiles associated with aging between zebrafish and rat showed both conserved and clearly different aging phenomena. Furthermore, up-regulation of circadian genes with aging and down-regulation of collagen genes were observed in both species. On the other hand, in zebrafish, up-regulation of autophagy related genes in muscle and atf3 in various tissues suggested fish-specific anti- aging characteristics. Consistent with our knowledge of mammalian aging, a tissue deterioration-related DEG profile was observed in rat. We also detected aging-associated down-regulation of muscle development and ATP metabolism-related genes in zebrafish gill. Correspondingly, hypoxia-related genes were systemically up-regulated in aged zebrafish, suggesting age-related hypoxia as a senescence modulator in fish.ConclusionsOur results indicate both common and different aging profiles between fish and mammals. Gene expression profiles specific to fish will provide new insight for future translational research.

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