Large-Scale Metadata Analysis of Ovary Based Multi-Omics Datasets for Understanding the Genes Regulating Litter Size

Litter Size ◽

Large Scale ◽

Expression Patterns ◽

Genetic Selection ◽

Follicular Development ◽

Oocyte Quality ◽

Metadata Analysis

Abstract Background : Litter size is a very important production index in the livestock industry, which is controlled by various complex physiological processes. To understand and reveal the common gene expression patterns involved in controlling prolificacy, we have performed a large-scale metadata analysis of five genome-wide transcriptome datasets of pig and sheep ovary samples obtained from high and low litter groups, respectively. We analyzed separately each transcriptome dataset using GeneSpring v14.8 software by implementing standard, generic analysis pipelines and further compared the list of most significant and differentially expressed genes obtained from each dataset to identify genes that are found to be common and significant across all the studies. Results : We have observed a total of 62 differentially expressed genes common among more than two gene expression datasets. The KEGG pathway analysis of most significant genes has shown that they are involved in metabolism, the biosynthesis of lipids, cholesterol and steroid hormones, immune system, cell growth and death, cancer-related pathways and signal transduction pathways. Of these 62 genes, we further narrowed the list to the 25 most significant genes by focusing on the ones with fold change >1.5 and p<0.05. These genes are CYP11A1, HSD17B2, STAR, SCARB1, IGSF8, MSMB, SERPINA1 , FAM46C, HEXA, PTTG1, TIMP1, FAM167B, CCNG1, FAXDC2, HMGCS1, L2HGDH, Lipin1, MME, MSMO1, PARM1, PTGFR, SLC22A4, SLC35F5, CCNA2, CENPU, CEP55, RASSF2, and SLC16A3 . Conclusions : Interestingly, comparing the list of genes with the list of genes obtained from our literature search analysis, we found only three genes in common. These genes are HEXA, PTTG1, and TIMP1. Our finding points to the potential of a few genes that may be important for ovarian follicular development and oocyte quality. Future studies revealing the function of these genes will further our understanding of how litter size is controlled in the ovary while also providing insight on genetic selection of high litter gilts.

Transcriptome Analysis of Differentially Expressed mRNA Related to Pigeon Muscle Development

Animals ◽

10.3390/ani11082311 ◽

2021 ◽

Vol 11 (8) ◽

pp. 2311

Author(s):

Hao Ding ◽

Yueyue Lin ◽

Tao Zhang ◽

Lan Chen ◽

Genxi Zhang ◽

...

Keyword(s):

Gene Expression ◽

Skeletal Muscle ◽

Growth And Development ◽

Muscle Development ◽

Expression Patterns ◽

Pathway Enrichment Analysis ◽

Growth Stages ◽

Gene Expression And Regulation

The mechanisms behind the gene expression and regulation that modulate the development and growth of pigeon skeletal muscle remain largely unknown. In this study, we performed gene expression analysis on skeletal muscle samples at different developmental and growth stages using RNA sequencing (RNA−Seq). The differentially expressed genes (DEGs) were identified using edgeR software. Weighted gene co−expression network analysis (WGCNA) was used to identify the gene modules related to the growth and development of pigeon skeletal muscle based on DEGs. A total of 11,311 DEGs were identified. WGCNA aggregated 11,311 DEGs into 12 modules. Black and brown modules were significantly correlated with the 1st and 10th day of skeletal muscle growth, while turquoise and cyan modules were significantly correlated with the 8th and 13th days of skeletal muscle embryonic development. Four mRNA−mRNA regulatory networks corresponding to the four significant modules were constructed and visualised using Cytoscape software. Twenty candidate mRNAs were identified based on their connectivity degrees in the networks, including Abca8b, TCONS−00004461, VWF, OGDH, TGIF1, DKK3, Gfpt1 and RFC5, etc. A KEGG pathway enrichment analysis showed that many pathways were related to the growth and development of pigeon skeletal muscle, including PI3K/AKT/mTOR, AMPK, FAK, and thyroid hormone pathways. Five differentially expressed genes (LAST2, MYPN, DKK3, B4GALT6 and OGDH) in the network were selected, and their expression patterns were quantified by qRT−PCR. The results were consistent with our sequencing results. These findings could enhance our understanding of the gene expression and regulation in the development and growth of pigeon muscle.

Analysis of Transcriptional Changes in Different Brassica napus Synthetic Allopolyploids

Genes ◽

10.3390/genes12010082 ◽

2021 ◽

Vol 12 (1) ◽

pp. 82

Author(s):

Yunxiao Wei ◽

Guoliang Li ◽

Shujiang Zhang ◽

Shifan Zhang ◽

Hui Zhang ◽

...

Keyword(s):

Gene Expression ◽

Brassica Napus ◽

Expression Patterns ◽

Female Parent ◽

Enrichment Analysis ◽

Transcriptional Changes ◽

Aa Genome ◽

High Degree

Allopolyploidy is an evolutionary and mechanistically intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the gene expression patterns of eight F2 synthetic Brassica napus using RNA sequencing. We found that B. napus allopolyploid formation was accompanied by extensive changes in gene expression. A comparison between F2 and the parent shows a certain proportion of differentially expressed genes (DEG) and activation\silent gene, and the two genomes (female parent (AA)\male parent (CC) genomes) showed significant differences in response to whole-genome duplication (WGD); non-additively expressed genes represented a small portion, while Gene Ontology (GO) enrichment analysis showed that it played an important role in responding to WGD. Besides, genome-wide expression level dominance (ELD) was biased toward the AA genome, and the parental expression pattern of most genes showed a high degree of conservation. Moreover, gene expression showed differences among eight individuals and was consistent with the results of a cluster analysis of traits. Furthermore, the differential expression of waxy synthetic pathways and flowering pathway genes could explain the performance of traits. Collectively, gene expression of the newly formed allopolyploid changed dramatically, and this was different among the selfing offspring, which could be a prominent cause of the trait separation. Our data provide novel insights into the relationship between the expression of differentially expressed genes and trait segregation and provide clues into the evolution of allopolyploids.

Toxoplasma infection alters dopamine-sensitive behaviors and host gene expression patterns associated with neuropsychiatric disease

10.1101/2021.08.16.456298 ◽

2021 ◽

Author(s):

Graham L. Cromar ◽

Jonathan Epp ◽

Ana Popovic ◽

Yusing Gu ◽

Violet Ha ◽

...

Keyword(s):

Gene Expression ◽

Expression Patterns ◽

Neurocognitive Disorders ◽

Gene Expression Patterns ◽

Low Grade ◽

Cocaine Exposure ◽

Multiple Testing Correction ◽

The Impact

ABSTRACTToxoplasma gondii is a single celled parasite thought to infect 1 in 3 worldwide. During chronic infection, T. gondii can migrate to the brain where it promotes low-grade neuroinflammation with the capacity to induce changes in brain morphology and behavior. Consequently, infection with T. gondii has been linked with a number of neurocognitive disorders including schizophrenia (SZ), dementia, and Parkinson’s disease. Beyond neuroinflammation, infection with T. gondii can modulate the production of neurotransmitters, such as dopamine. To further dissect these pathways and examine the impact of altered dopaminergic sensitivity in T. gondii-infected mice on both behavior and gene expression, we developed a novel mouse model, based on stimulant-induced (cocaine) hyperactivity. Employing this model, we found that infection with T. gondii did not alter fear behavior but did impact motor activity and neuropsychiatric-related behaviurs. While both behaviors may help reduce predator avoidance, consistent with previous studies, the latter finding is reminiscent of neurocognitive disorders. Applying RNASeq to two relevant brain regions, striatum and hippocampus, we identified a broad upregulation of immune responses. However, we also noted significant associations with more meaningful neurologically relevant terms were masked due to the sheer number of terms incorporated in multiple testing correction. We therefore performed a more focused analysis using a curated set of neurologically relevant terms revealing significant associations across multiple pathways. We also found that T. gondii and cocaine treatments impacted the expression of similar functional pathways in the hippocampus and striatum although, as indicated by the low overlap among differentially expressed genes, largely via different proteins. Furthermore, while most differentially expressed genes reacted to a single condition and were mostly upregulated, we identified gene expression patterns indicating unexpected interactions between T. gondii infection and cocaine exposure. These include sets of genes which responded to cocaine exposure but not upon cocaine exposure in the context of T. gondii infection, suggestive of a neuroprotective effect advantageous to parasite persistence. Given its ability to uncover such complex relationships, we propose this novel model offers a new perspective to dissect the molecular pathways by which T. gondii infection contributes to neuropsychiatric disorders such as schizophrenia.

Identification and Characterization of Key Differentially Expressed Genes Associated With Metronomic Dosing of Topotecan in Human Prostate Cancer

Frontiers in Pharmacology ◽

10.3389/fphar.2021.736951 ◽

2021 ◽

Vol 12 ◽

Author(s):

Taraswi Mitra Ghosh ◽

Jason White ◽

Joshua Davis ◽

Suman Mazumder ◽

Teeratas Kansom ◽

...

Keyword(s):

Gene Expression ◽

Prostate Cancer ◽

Cell Lines ◽

Expression Patterns ◽

Molecular Networks ◽

Human Prostate ◽

Mouse Tumor ◽

Human Prostate Cancer

Repetitive, low-dose (metronomic; METRO) drug administration of some anticancer agents can overcome drug resistance and increase drug efficacy in many cancers, but the mechanisms are not understood fully. Previously, we showed that METRO dosing of topotecan (TOPO) is more effective than conventional (CONV) dosing in aggressive human prostate cancer (PCa) cell lines and in mouse tumor xenograft models. To gain mechanistic insights into METRO-TOPO activity, in this study we determined the effect of METRO- and CONV-TOPO treatment in a panel of human PCa cell lines representing castration-sensitive/resistant, androgen receptor (+/−), and those of different ethnicity on cell growth and gene expression. Differentially expressed genes (DEGs) were identified for METRO-TOPO therapy and compared to a PCa patient cohort and The Cancer Genome Atlas (TCGA) database. The top five DEGs were SERPINB5, CDKN1A, TNF, FOS, and ANGPT1. Ingenuity Pathway Analysis predicted several upstream regulators and identified top molecular networks associated with METRO dosing, including tumor suppression, anti-proliferation, angiogenesis, invasion, metastasis, and inflammation. Further, the top DEGs were associated with increase survival of PCa patients (TCGA database), as well as ethnic differences in gene expression patterns in patients and cell lines representing African Americans (AA) and European Americans (EA). Thus, we have identified candidate pharmacogenomic biomarkers and novel pathways associated with METRO-TOPO therapy that will serve as a foundation for further investigation and validation of METRO-TOPO as a novel treatment option for prostate cancers.

Diabetes-specific modulation of peripheral blood gene expression signatures in colorectal cancer

Current Molecular Medicine ◽

10.2174/1566524020666200504084626 ◽

2020 ◽

Vol 20 ◽

Author(s):

Zsuzsanna Molnár ◽

Zsófia Bánlaki ◽

Anikó Somogyi ◽

Zoltán Herold ◽

Magdolna Herold ◽

...

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Peripheral Blood ◽

Expression Patterns ◽

Enrichment Analysis ◽

Colorectal Carcinogenesis ◽

Blood Leukocytes ◽

Significant Expression

Background: Type 2 diabetes (T2DM) and colorectal cancer (CRC) are both known to modulate gene expression patterns in peripheral blood leukocytes (PBLs). Objective : As T2DM has been shown to increase the incidence of CRC, we were prompted to check whether diabetes affects mRNA signatures in PBLs isolated from CRC patients. Methods : 22 patients were recruited to the study and classified into four cohorts (healthy controls; T2DM; CRC; CRC and T2DM). Relative expression levels of 573 cell signaling gene transcripts were determined by reverse transcription real-time PCR assays run on low-density OpenArray platforms. Enrichment analysis was performed with the g:GOSt profiling tool to order differentially expressed genes into functional pathways. Results : 49 genes were found to be significantly up- or downregulated in tumorous diabetic individuals as compared to tumor-free diabetic controls, while 11 transcripts were differentially regulated in patients with CRC versus healthy, tumor-free and non-diabetic controls. Importantly, these gene sets were completely distinct, implying that diabetes exerts profound influence on the transcription of signaling genes in CRC. The top 5 genes showing most significant expression differences in both contexts were PCK2, MAPK9, CCND1, HMBS, TLR3 (p≤ 0.0040) and CREBBP, PPIA, NFKBIL1, MDM2 and SELPLG (p0.0121), respectively. Functional analysis revealed that most significantly affected pathways were cytokine, interleukin and PI3K/Akt/mTOR signaling cascades as well as mitotic regulation. Conclusions : We propose that differentially expressed genes listed above might be potential biomarkers of CRC and should be studied further on larger patient groups. Diabetes might promote colorectal carcinogenesis by impairing signaling pathways in PBLs.

Bioinformatics Study on the Response of Human Endothelial Cells to Different Strains of Staphylococcus Aureus

10.21203/rs.3.rs-100257/v1 ◽

2020 ◽

Author(s):

Tian-ao Xie ◽

Ke-ying Fang ◽

Wen-chao Cao ◽

Jie Lv ◽

Jia-xin Chen ◽

...

Keyword(s):

Gene Expression ◽

Staphylococcus Aureus ◽

Endothelial Cells ◽

Expression Patterns ◽

Specific Gene ◽

Human Endothelial Cells ◽

Different Strains ◽

Differential Genes

Abstract BackgroundStaphylococcus aureus-induced bacteremia has an impact on human health due to its high mortality rate of 20–30%. To better study the invasion process of staphylococcus aureus, we conducted a study in human endothelial cells to try to find a link between the infection process and bacteremia at the molecular level.MethodsIn this study, the datasets GSE13736, GSE82036 were analyzed using R software to identify differentially expressed genes. Only the infection samples of four different strains had differential gene expression compared to the control samples. Then the GO analysis and KEGG analysis were conducted to construct a protein-protein interaction (PPI) network which shows the interaction and influence relationship between these differential genes. Finally, the central gene of the selected CytoHubba plug-in was verified using GraphPad Prism 8.ResultsThere were 421 differential genes in the Strain 6850, including 64 up-regulated and 357 down-regulated; There were 319 differential genes in the Strain 8325-4, including 14 up-regulated and 305 down-regulated. There were 90 differential genes in the Strain K70058396, including 12 up-regulated and 78 down-regulated. There were 876 differential genes in the Strain K1801/10, accompanied by 261 up-regulated and 615 down-regulated. An analysis of GO and KEGG revealed that these differentially expressed genes were significantly enriched in pathways associated with immune response and cytokines; Verification of the hub gene can provide a molecular basis for studying the relationship between invasive endothelial infection and bacteremia.ConclusionsWe found specific gene expression patterns in endothelial cells in response to infection with Strain K70058396, and these central genes and their expression products (RSAD2, DDX58, IFITT3, and IFIH1) play a key role in this process of infection.

Transcriptomic analysis reveals distinct resistant response by physcion and chrysophanol against cucumber powdery mildew

PeerJ ◽

10.7717/peerj.1991 ◽

2016 ◽

Vol 4 ◽

pp. e1991 ◽

Cited By ~ 9

Author(s):

Yanping Li ◽

Shilin Tian ◽

Xiaojun Yang ◽

Xin Wang ◽

Yuhai Guo ◽

...

Keyword(s):

Gene Expression ◽

Disease Resistance ◽

Powdery Mildew ◽

Expression Patterns ◽

Defense Responses ◽

Rna Seq ◽

Sequencing Data ◽

Transcriptional Change

Physcion and chrysophanol induce defense responses against powdery mildew in cucumbers. The combination of these two compounds has synergistic interaction against the disease. We performed RNA-seq on cucumber leaf samples treated with physcion and chrysophanol alone and with their combination. We generated 17.6 Gb of high-quality sequencing data (∼2 Gb per sample) and catalogued the expressions profiles of 12,293 annotated cucumber genes in each sample. We identified numerous differentially expressed genes that exhibited distinct expression patterns among the three treatments. The gene expression patterns of the Chr and Phy treatments were more similar to each other than to the Phy × Chr treatment. The Phy × Chr treatment induced the highest number of differentially expressed genes. This dramatic transcriptional change after Phy × Chr treatment leaves reflects that physcion combined with chrysophanol treatment was most closely associated with induction of disease resistance. The analysis showed that the combination treatment caused expression changes of numerous defense-related genes. These genes have known or potential roles in structural, chemical and signaling defense responses and were enriched in functional gene categories potentially responsible for cucumber resistance. These results clearly demonstrated that disease resistance in cucumber leaves was significantly influenced by the combined physcion and chrysophanol treatment. Thus, physcion and chrysophanol are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to the defense response.

Chronic alcohol exposure alters transcription broadly in a key integrative brain nucleus for homeostasis: the nucleus tractus solitarius

Physiological Genomics ◽

10.1152/physiolgenomics.00184.2005 ◽

2006 ◽

Vol 24 (1) ◽

pp. 45-58 ◽

Cited By ~ 19

Author(s):

Maria Yolanda Covarrubias ◽

Rishi L. Khan ◽

Rajanikanth Vadigepalli ◽

Jan B. Hoek ◽

James S. Schwaber

Keyword(s):

Gene Expression ◽

Signaling Pathways ◽

Nucleus Tractus Solitarius ◽

Expression Patterns ◽

Alcohol Exposure ◽

Chronic Alcohol ◽

Brain Nucleus ◽

Chronic Alcohol Exposure

Chronic exposure to alcohol modifies physiological processes in the brain, and the severe symptoms resulting from sudden removal of alcohol from the diet indicate that these modifications are functionally important. We investigated the gene expression patterns in response to chronic alcohol exposure (21–28 wk) in the rat nucleus tractus solitarius (NTS), a brain nucleus with a key integrative role in homeostasis and cardiorespiratory function. Using methods and an experimental design optimized for detecting transcriptional changes less than twofold, we found 575 differentially expressed genes. We tested these genes for significant associations with physiological functions and signaling pathways using Gene Ontology terms and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, respectively. Chronic alcohol exposure resulted in significant NTS gene regulation related to the general processes of synaptic transmission, intracellular signaling, and cation transport as well as specific neuronal functions including plasticity and seizure behavior that could be related to alcohol withdrawal symptoms. The differentially expressed genes were also significantly enriched for enzymes of lipid metabolism, glucose metabolism, oxidative phosphorylation, MAP kinase signaling, and calcium signaling pathways from KEGG. Intriguingly, many of the genes we found to be differentially expressed in the NTS are known to be involved in alcohol-induced oxidative stress and/or cell death. The study provides evidence of very extensive alterations of physiological gene expression in the NTS in the adapted state to chronic alcohol exposure.

Gene expression profiling of skeletal muscles

10.1101/2021.02.17.431599 ◽

2021 ◽

Author(s):

Sarah I. Alto ◽

Chih-Ning Chang ◽

Kevin Brown ◽

Chrissa Kioussi ◽

Theresa M. Filtz

Keyword(s):

Gene Expression ◽

Skeletal Muscle ◽

Tibialis Anterior ◽

Skeletal Muscles ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

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.

Weighted gene co-expression network analysis to identify key modules and hub genes associated with paucigranulocytic asthma

BMC Pulmonary Medicine ◽

10.1186/s12890-021-01711-3 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Min Li ◽

Wenye Zhu ◽

Chu Wang ◽

Yuanyuan Zheng ◽

Shibo Sun ◽

...

Keyword(s):

Gene Expression ◽

Network Analysis ◽

Immune Status ◽

Expression Patterns ◽

Gene Expression Pattern ◽

Gene Set Enrichment Analysis ◽

Functional Enrichment ◽

Hub Genes

Abstract Background Asthma is a heterogeneous disease that can be divided into four inflammatory phenotypes: eosinophilic asthma (EA), neutrophilic asthma (NA), mixed granulocytic asthma (MGA), and paucigranulocytic asthma (PGA). While research has mainly focused on EA and NA, the understanding of PGA is limited. In this study, we aimed to identify underlying mechanisms and hub genes of PGA. Methods Based on the dataset from Gene Expression Omnibus(GEO), weighted gene coexpression network analysis (WGCNA), differentially expressed genes (DEGs) analysis and protein–protein interaction (PPI) network analysis were conducted to construct a gene network and to identify key gene modules and hub genes. Functional enrichment analyses were performed to investigate the biological process, pathways and immune status of PGA. The hub genes were validated in a separate dataset. Results Compared to non-PGA, PGA had a different gene expression pattern, in which 449 genes were differentially expressed. One gene module significantly associated with PGA was identified. Intersection between the differentially expressed genes (DEGs) and the genes from the module that were most relevant to PGA were mainly enriched in inflammation and immune response regulation. The single sample Gene Set Enrichment Analysis (ssGSEA) suggested a decreased immune infiltration and function in PGA. Finally six hub genes of PGA were identified, including ADCY2, CXCL1, FPRL1, GPR109B, GPR109A and ADCY3, which were validated in a separate dataset of GSE137268. Conclusions Our study characterized distinct gene expression patterns, biological processes and immune status of PGA and identified hub genes, which may improve the understanding of underlying mechanism and provide potential therapeutic targets for PGA.