scholarly journals RNA-Seq Coupling Two Different Methods of Castration Reveals New Insights Into Androgen Deficiency-caused Degereration of Submaxillary Gland in Male Sprague Dawley Rats

2022 ◽  
Author(s):  
Xingfa Han ◽  
Xu Xia ◽  
Yong Zhuo ◽  
Lun Hua ◽  
Guozhi Yu ◽  
...  
Keyword(s):  
Cell Death ◽  
Epithelial Cell ◽  
Submaxillary Gland ◽  
Enrichment Analysis ◽  
Cell Development ◽  
Anatomical Structure ◽  
Functional Enrichment ◽  
Rna Seq ◽  
Sprague Dawley ◽  
Organ Index

Abstract Backgroud: Salivary gland degeneration and dysfunction are common symptoms that occur after sex hormone deprivation, but the underlying mechanisms remain largely unknown. Additionally, immunocastration, which causes drop of sex hormones, has been developed as an alternative to surgical castration, however whether it exerts similar effects as surgical castration on the salivary glands is unknown. Through histological and RNA-seq analysis, we assessed changes in morphology and transcriptome of submaxillary gland (SMG) in response to immunocastration (IM) versus surgical castration (bilateral orchiectomy, ORC). Results: Compared to intact males (EM), ORC caused a dramatical degeneration of SMG in rats, as evidenced by both decreased (P < 0.01) SMG weight and organ index, and by decreased (P < 0.01) quantity of SMG acini and ducts. IM had minimal effects (P > 0.05) on SMG weight and organ index, but it still caused degeneration (P < 0.05) of the acini and ducts. Even though, the quantity of both SMG acini and ducts was much higher (P < 0.001) in IM than in ORC. Functional enrichment analysis of the common regulated genes by ORC/IM revealed disrupted epithelial cell development, angiogenesis, anatomical structure morphogenesis and enhanced cell death are associated with SMG degeneration in deprivation of androgens. Integrated data analysis shown that there existed a selective hyperfunction of SMG ribosome and mitochondrion in ORC but not in IM, which might be associated with more severe degeneration of SMG in ORC than in IM. Conclusions: Our findings suggested that both surgical castration and immunocastration caused SMG degeneration by disrupting epithelial cell development, angiogenesis, anatomical structure morphogenesis and enhancing cell death. But, surgical castration selectively induced hyperfunction of SMG ribosome and mitochondrion, thus causing more severe degeneration of SMG than immunocastration.

Analysis of Expression Profiles of mRNA and lncRNA in Oviduct During Estrus Phase of Sheep (Ovis Aries) with Two Fecundity (FecB Gene) Genotypes

2021 ◽  
Author(s):  
Weihao Chen ◽  
Zhifeng Li ◽  
Wei Sun ◽  
Mingxing Chu
Keyword(s):  
Embryo Development ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Ovis Aries ◽  
Functional Enrichment ◽  
Saga Complex ◽  
Rna Seq ◽  
Estrus Phase

Abstract Background:In sheep, FecB is the essential biomarker of the fertility, previous researches have provided a detailed insight on the regulation involved estrus phase and FecB in the reproductive-related tissues including hypothalamus, pituitary, and ovary. However, as the host of embryo development and connection between the ovary and the uterus, little is known about the interaction between mRNAs and lncRNAs in sheep oviduct. In the present study, RNA-Seq was performed to identify the transcriptomic profiles of mRNAs and lncRNAs in oviduct during estrus phase of sheep with FecBBB/++ genotypes.Results:In total, 21,863 lncRNAs and 43,674 mRNAs were identified, 57 DE lncRNAs and 637 DE mRNAs were revealed in the comparisons between follicular phase and luteal phase, 26 DE lncRNAs and 421 DE lncRNAs were revealed in the comparisons between FecB BB genotype and FecB ++ genotype. Functional enrichment analysis suggested that GO and KEGG terms related to reproduction such as SAGA complex, ATP-binding cassette (ABC), Nestin, and Hippo signalling pathway. DE-interaction network suggested that LNC_018420 maybe the key regulators related to embryo development in sheep oviduct.Conclusion:This was the first study to reveal the transcriptomic profiles of mRNAs and lncRNAs in the oviduct of FecB BB/++ sheep at estrus phase using RNA-Seq. Our findings can provide new understanding on the molecular mechanisms of mRNAs and lncRNAs underlying sheep embryo development and also opening new lines of investigation in sheep reproduction.

scholarly journals Identification of associated molecular events in Helicobacter pylori infection and gastric cancer through integrated computational analysis of Microarray and RNA-Seq datasets

2021 ◽  
Author(s):  
Sabaoon Zeb ◽  
Rehan Zafar Paracha ◽  
Maryum Nisar ◽  
Rimsha Khalid ◽  
Zartasha Mustansar ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Helicobacter Pylori ◽  
Cancer Progression ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
World Health ◽  
Separate Analysis ◽  
Rna Seq ◽  
Molecular Events

Abstract According to the World Health Organization, Gastric cancer (GC) is the third leading cause of death worldwide, where, the major precursor of cancer progression is infection with Helicobacter pylori. It has been reported that 50% of the total populace is infected with H.pylori, while in 80% the ulcer emerges in later stages of the infection. Although extensive separate analysis has been performed on H.pylori infection and GC data, however, there is a need to perform comparative analysis to identify the cross-talk between the conditions and to hunt significant molecular events that occurs during H.pylori induced GC. The aim of this multi-population study was to identify common molecular events and potential bio-markers against H.pylori induced GC. We performed microarray and RNA-seq analysis on publicly available H.pylori infection, gastritis, H.pylori induced GC and GC datasets to obtain Differentially Expressed Genes (DEGs). After obtaining the DEGs, integrative analysis, functional enrichment analysis and network biology approaches were utilized to identify common markers and hub genes between various disease conditions. Functional enrichment analysis revealed the DEGs of H.pylori infection, gastritis, H.pylori induced GC and GC were strongly associated with spliceosome, adherens junction, focal adhesion and ribosome. Being one of the common DEG, and highly interactive hub protein in the networks of all the conditions, translationally controlled tumour protein (TPT1) was identified as a significant predictive biomarker for early prognosis and diagnosis of H.pylori induced GC. Therefore, the mechanisms behind TPT1 should be further studied using in vitro cell-based functional assays, to determine its role in the progression of H.pylori induced GC.

scholarly journals Detecting Interactive Gene Groups for Single-Cell RNA-Seq Data Based on Co-Expression Network Analysis and Subgraph Learning

Cells ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1938 ◽  
Author(s):  
Xiucai Ye ◽  
Weihang Zhang ◽  
Yasunori Futamura ◽  
Tetsuya Sakurai
Keyword(s):  
Network Analysis ◽  
Single Cell ◽  
Tumor Heterogeneity ◽  
High Throughput Sequencing ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Cell Subpopulation ◽  
Rna Seq ◽  
Cancer Subtypes ◽  
Learning Framework

High-throughput sequencing technologies have enabled the generation of single-cell RNA-seq (scRNA-seq) data, which explore both genetic heterogeneity and phenotypic variation between cells. Some methods have been proposed to detect the related genes causing cell-to-cell variability for understanding tumor heterogeneity. However, most existing methods detect the related genes separately, without considering gene interactions. In this paper, we proposed a novel learning framework to detect the interactive gene groups for scRNA-seq data based on co-expression network analysis and subgraph learning. We first utilized spectral clustering to identify the subpopulations of cells. For each cell subpopulation, the differentially expressed genes were then selected to construct a gene co-expression network. Finally, the interactive gene groups were detected by learning the dense subgraphs embedded in the gene co-expression networks. We applied the proposed learning framework on a real cancer scRNA-seq dataset to detect interactive gene groups of different cancer subtypes. Systematic gene ontology enrichment analysis was performed to examine the detected genes groups by summarizing the key biological processes and pathways. Our analysis shows that different subtypes exhibit distinct gene co-expression networks and interactive gene groups with different functional enrichment. The interactive genes are expected to yield important references for understanding tumor heterogeneity.

scholarly journals A Novel Three-miRNA Signature Identified Using Bioinformatics Predicts Survival in Esophageal Carcinoma

2020 ◽  
Vol 2020 ◽  
pp. 1-11 ◽  
Author(s):  
KunZhe Wu ◽  
ChunDong Zhang ◽  
Cheng Zhang ◽  
DongQiu Dai
Keyword(s):  
Growth Factor ◽  
Esophageal Carcinoma ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Rna Seq ◽  
Mirna Signature ◽  
Cox Regression Analysis ◽  
Ppi Networks

Objective. We identified differentially expressed microRNAs (DEMs) between esophageal carcinoma (ESCA) tissues and normal esophageal tissues. We then constructed a novel three-miRNA signature to predict the prognosis of ESCA patients using bioinformatics analysis. Materials and Methods. We combined two microarray profiling datasets from the Gene Expression Omnibus (GEO) database and RNA-seq datasets from the Cancer Genome Atlas (TCGA) database to analyze DEMs in ESCA. The clinical data from 168 ESCA patients were selected from the TCGA database to assess the prognostic role of the DEMs. The TargetScan, miRDB, miRWalk, and DIANA websites were used to predict the miRNA target genes. Functional enrichment analysis was conducted using the Database for Annotation, Visualization, and Integrated Discovery (David), and protein-protein interaction (PPI) networks were obtained using the Search Tool for the Retrieval of Interacting Genes database (STRING). Results. With cut-off criteria of P<0.05 and |log2FC| > 1.0, 33 overlapping DEMs, including 27 upregulated and 6 downregulated miRNAs, were identified from GEO microarray datasets and TCGA RNA-seq count datasets. The Kaplan–Meier survival analysis indicated that a three-miRNA signature (miR-1301-3p, miR-431-5p, and miR-769-5p) was significantly associated with the overall survival of ESCA patients. The results of univariate and multivariate Cox regression analysis showed that the three-miRNA signature was a potential prognostic factor in ESCA. Furthermore, the gene functional enrichment analysis revealed that the target genes of the three miRNAs participate in various cancer-related pathways, including viral carcinogenesis, forkhead box O (FoxO), vascular endothelial growth factor (VEGF), human epidermal growth factor receptor 2 (ErbB2), and mammalian target of rapamycin (mTOR) signaling pathways. In the PPI network, three target genes (MAPK1, RB1, and CLTC) with a high degree of connectivity were selected as hub genes. Conclusions. Our results revealed that a three-miRNA signature (miR-1301-3p, miR-431-5p, and miR-769-5p) is a potential novel prognostic biomarker for ESCA.

scholarly journals MiR-103a promotes tumour growth and influences glucose metabolism in hepatocellular carcinoma

2021 ◽  
Vol 12 (6) ◽  
Author(s):  
Yuling Liu ◽  
Yuanzhou Zhang ◽  
Bowen Xiao ◽  
Ning Tang ◽  
Jingying Hu ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cell Death ◽  
Cell Growth ◽  
Glucose Metabolism ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Deep Sequencing Technology ◽  
Subcutaneous Xenograft ◽  
Patient Prognosis

AbstractHepatocellular carcinoma (HCC) is a common and high-mortality cancer worldwide. Numerous microRNAs have crucial roles in the progression of different cancers. However, identifying the important microRNAs and the target biological function of the microRNA in HCC progression is difficult. In this study, we selected highly expressed microRNAs with different read counts as candidate microRNAs and then tested whether the microRNAs were differentially expressed in HCC tumour tissues, and we found that their expression was related to the HCC prognosis. Then, we investigated the effects of microRNAs on the cell growth and mobility of HCC using a real-time cell analyser (RTCA), colony formation assay and subcutaneous xenograft models. We further used deep-sequencing technology and bioinformatic analyses to evaluate the main functions of the microRNAs. We found that miR-103a was one of the most highly expressed microRNAs in HCC tissues and that it was upregulated in HCC tissue compared with the controls. In addition, high miR-103a expression was associated with poor patient prognosis, and its overexpression promoted HCC cell growth and mobility. A functional enrichment analysis showed that miR-103a mainly promoted glucose metabolism and inhibited cell death. We validated this analysis, and the data showed that miR-103a promoted glucose metabolism-likely function and directly inhibited cell death via ATP11A and EIF5. Therefore, our study revealed that miR-103a may act as a key mediator in HCC progression.

scholarly journals Genome-wide phylogenetic analysis, expression pattern, and transcriptional regulatory network of the pig C/EBP gene family

2020 ◽  
Author(s):  
Chaoxin Zhang ◽  
Tao Wang ◽  
Shengwei Liu ◽  
Bing Zhang ◽  
Xue Li ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Regulatory Network ◽  
Target Genes ◽  
Transcriptional Regulatory Network ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Rna Seq ◽  
Group I

Abstract Background: The vertebrate C/EBP transcription factors regulate many important biological processes, such as cell proliferation, differentiation, signal transduction, inflammation, and energy metabolism. The first C/EBP protein was identified in rat liver nuclei. Development of sequencing technology resulted in identification of the C/EBP genes in various species. In this study, a bioinformatics approach was used to determine the distribution of the members of the C/EBP family in vertebrates. A phylogenetic tree was constructed to analyze the C/EBP genes in vertebrates. Based on RNA-seq data, the expression patterns of pig C/EBP members in various tissues were analyzed. In addition, a gene transcription regulatory network was constructed with pig C/EBP members as the core.Results: We identified a total of 92 C/EBP genes in 17 vertebrate genomes. Phylogenetic analysis showed that all C/EBP TFs were classified into two groups; group I contained C/EBPβ TFs, and group II contained the remaining C/EBP TFs. The C/EBPα, C/EBPβ, C/EBPδ, C/EBPγ, and C/EBPζ genes were expressed ubiquitously with inconsistent expression patterns in various tissues. Moreover, a pig C/EBP regulatory network was constructed, including C/EBP genes, TFs, and miRNAs. A total of 39 FFL motifs were detected in the pig C/EBP regulatory network. Based on the RNA-seq data, gene expression patterns related to this FFL sub-network were analyzed in 27 adult Duroc tissues. Certain FFL motifs may be tissue specific. Functional enrichment analysis indicated that C/EBP and its target genes are involved in many important biological pathways. Conclusions: These results provide valuable information that clarifies the evolutionary relationships of the C/EBP family and contributes to the understanding of the biological function of C/EBP genes.

scholarly journals Dissecting the Transcriptomes of Multiple Metronidazole-Resistant and Sensitive Trichomonas vaginalis Strains Identified Distinct Genes and Pathways Associated with Drug Resistance and Cell Death

Biomedicines ◽  
2021 ◽  
Vol 9 (12) ◽  
pp. 1817
Author(s):  
Po-Jung Huang ◽  
Ching-Yun Huang ◽  
Yu-Xuan Li ◽  
Yi-Chung Liu ◽  
Lichieh-Julie Chu ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Cell Death ◽  
Trichomonas Vaginalis ◽  
Regulatory Networks ◽  
Efflux Pump ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Multidrug Efflux Pump ◽  
Drug Induced ◽  
Transmitted Infection

Trichomonas vaginalis is the causative agent of trichomoniasis, the most prevalent non-viral sexually transmitted infection worldwide. Metronidazole (MTZ) is the mainstay of anti-trichomonal chemotherapy; however, drug resistance has become an increasingly worrying issue. Additionally, the molecular events of MTZ-induced cell death in T. vaginalis remain elusive. To gain insight into the differential expression of genes related to MTZ resistance and cell death, we conducted RNA-sequencing of three paired MTZ-resistant (MTZ-R) and MTZ-sensitive (MTZ-S) T. vaginalis strains treated with or without MTZ. Comparative transcriptomes analysis identified that several putative drug-resistant genes were exclusively upregulated in different MTZ-R strains, such as ATP-binding cassette (ABC) transporters and multidrug resistance pumps. Additionally, several shared upregulated genes among all the MTZ-R transcriptomes were not previously identified in T. vaginalis, such as 5′-nucleotidase surE and Na+-driven multidrug efflux pump, which are a potential stress response protein and a multidrug and toxic compound extrusion (MATE)-like protein, respectively. Functional enrichment analysis revealed that purine and pyrimidine metabolisms were suppressed in MTZ-S parasites upon drug treatment, whereas the endoplasmic reticulum-associated degradation (ERAD) pathway, proteasome, and ubiquitin-mediated proteolysis were strikingly activated, highlighting the novel pathways responsible for drug-induced stress. Our work presents the most detailed analysis of the transcriptional changes and the regulatory networks associated with MTZ resistance and MTZ-induced signaling, providing insights into MTZ resistance and cell death mechanisms in trichomonads.

scholarly journals Integrated Analysis of lncRNA and mRNA Reveals Novel Insights into Wool Bending in Zhongwei Goat

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3326
Author(s):  
Xiaobo Li ◽  
Zhanfa Liu ◽  
Shaohui Ye ◽  
Yue Liu ◽  
Qian Chen ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Target Genes ◽  
Economic Value ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Hair Follicles ◽  
Functional Enrichment ◽  
Integrated Analysis ◽  
Rna Seq ◽  
Camp Signaling Pathway

Chinese Zhongwei goat is a rare and precious fur breed as its lamb fur is a well-known fur product. Wool bending of lamb fur of the Zhongwei goat is its most striking feature. However, the curvature of the wool decreases gradually with growth, which significantly affects its quality and economic value. The mechanism regulating the phenotypic changes of hair bending is still unclear. In the present study, the skin tissues of Zhongwei goats at 45 days (curving wool) and 108 days (slight-curving wool) after birth were taken as the research objects, and the expression profiling of long non-coding RNAs (lncRNAs) and mRNAs were analyzed based on the Ribo Zero RNA sequencing (RNA-seq) method. In total, 46,013 mRNAs and 13,549 lncRNAs were identified, of which 352 were differentially expressed mRNAs and 60 were. lncRNAs. Functional enrichment analysis of the target genes of lncRNAs were mainly enriched in PI3K-Akt, Arachidonic acid metabolic, cAMP, Wnt, and other signaling pathways. The qRT-PCR results of eight selected lncRNAs and target genes were consistent with the sequencing result, which indicated our data were reliable. Through the analysis of the weighted gene co-expression network, 13 co-expression modules were identified. The turquoise module contained a large number of differential expressed lncRNAs, which were mainly enriched in the PI3K-Akt signaling pathway and cAMP signaling pathway. The predicted LOC102172600 and LOC102191729 might affect the development of hair follicles and the curvature of wool by regulating the target genes. Our study provides novel insights into the potential roles of lncRNAs in the regulation of wool bending. In addition, the study offers a theoretical basis for further study of goat wool growth, so as to be a guidance and reference for breeding and improvement in the future.

scholarly journals Comprehensive RNA-Seq Profiling Reveals Temporal and Tissue-Specific Changes in Gene Expression in Sprague–Dawley Rats as Response to Heat Stress Challenges

2021 ◽  
Vol 12 ◽  
Author(s):  
Jinhuan Dou ◽  
Angela Cánovas ◽  
Luiz F. Brito ◽  
Ying Yu ◽  
Flavio S. Schenkel ◽  
...  
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
Metabolic Pathways ◽  
Adrenal Glands ◽  
Functional Enrichment ◽  
Rna Seq ◽  
Sprague Dawley ◽  
Mammal Species ◽  
Heat Stress Response ◽  
Sprague Dawley Rats

Understanding heat stress physiology and identifying reliable biomarkers are paramount for developing effective management and mitigation strategies. However, little is known about the molecular mechanisms underlying thermal tolerance in animals. In an experimental model of Sprague–Dawley rats subjected to temperatures of 22 ± 1°C (control group; CT) and 42°C for 30 min (H30), 60 min (H60), and 120 min (H120), RNA-sequencing (RNA-Seq) assays were performed for blood (CT and H120), liver (CT, H30, H60, and H120), and adrenal glands (CT, H30, H60, and H120). A total of 53, 1,310, and 1,501 differentially expressed genes (DEGs) were significantly identified in the blood (P &lt; 0.05 and |fold change (FC)| &gt;2), liver (P &lt; 0.01, false discovery rate (FDR)–adjusted P = 0.05 and |FC| &gt;2) and adrenal glands (P &lt; 0.01, FDR-adjusted P = 0.05 and |FC| &gt;2), respectively. Of these, four DEGs, namely Junb, P4ha1, Chordc1, and RT1-Bb, were shared among the three tissues in CT vs. H120 comparison. Functional enrichment analyses of the DEGs identified in the blood (CT vs. H120) revealed 12 biological processes (BPs) and 25 metabolic pathways significantly enriched (FDR = 0.05). In the liver, 133 BPs and three metabolic pathways were significantly detected by comparing CT vs. H30, H60, and H120. Furthermore, 237 BPs were significantly (FDR = 0.05) enriched in the adrenal glands, and no shared metabolic pathways were detected among the different heat-stressed groups of rats. Five and four expression patterns (P &lt; 0.05) were uncovered by 73 and 91 shared DEGs in the liver and adrenal glands, respectively, over the different comparisons. Among these, 69 and 73 genes, respectively, were proposed as candidates for regulating heat stress response in rats. Finally, together with genome-wide association study (GWAS) results in cattle and phenome-wide association studies (PheWAS) analysis in humans, five genes (Slco1b2, Clu, Arntl, Fads1, and Npas2) were considered as being associated with heat stress response across mammal species. The datasets and findings of this study will contribute to a better understanding of heat stress response in mammals and to the development of effective approaches to mitigate heat stress response in livestock through breeding.

scholarly journals Gestational vinclozolin exposure suppresses fetal Leydig cell development in rats

2020 ◽  
Author(s):  
Keyang Wu ◽  
Yang Li ◽  
Peipei Pan ◽  
Zengqiang Li ◽  
Yige Yu ◽  
...  
Keyword(s):  
Leydig Cell ◽  
Endocrine Disruptor ◽  
Serum Testosterone ◽  
Cell Number ◽  
Cell Development ◽  
Rna Seq ◽  
Sprague Dawley ◽  
Oral Gavage ◽  
Anogenital Distance ◽  
Sprague Dawley Rats

Abstract Background: Vinclozolin is not only a common dicarboximide fungicide used to protect crops against diseases but also an endocrine disruptor. This study aimed to investigate the effects of gestational vinclozolin exposure on the development of rat fetal Leydig cells.Methods: Female pregnant Sprague-Dawley rats were exposed to vinclozolin (0, 25, 50, and 100 mg/kg body weight/day) by oral gavage from gestational day 14 to 21.Results: Vinclozolin dose-dependently depressed serum testosterone levels at doses of 50 and 100 mg/kg and anogenital distance at 100 mg/kg. RNA-seq, qPCR, and Western blot showed that vinclozolin down-regulated the expression of Nr5a1 , Sox9 , Lhcgr , Cyp11a1 , Hsd3b1 , Hsd17b3 , Amh , Pdgfa , and Dhh and their encoded proteins. Vinclozolin depressed NR2F2-positive stem Leydig cell number at a dose of 100 mg/kg and also enhanced autophagy in the testis.Conclusion: Vinclozolin disrupts fetal Leydig cell development via several pathways.

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