Differential expression of microRNAs in bovine papillomavirus type 1 (BPV-1) transformed equine cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Equus caballus Homo sapiens
PROVIDER: GSE73937 | GEO | 2015/10/14
SECONDARY ACCESSION(S): PRJNA298549
REPOSITORIES: GEO
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Project description:Bovine Papillomavirus type 1 (BPV-1) and less commonly BPV-2 are associated with the pathogenesis of common equine skin tumours termed sarcoids. In an attempt to understand the mechanisms by which BPV-1 induces sarcoids, we used gene expression profiling as a screening tool to identify candidates genes implicated in disease pathogenesis. Gene expression profiles of equine fibroblasts transformed by BPV-1 either experimentally or from explanted tumours were compared with control equine fibroblasts to identify genes associated with expression of BPV-1.
2008-07-12 | E-MEXP-1658 | biostudies-arrayexpress
Project description:Purpose: RNA-sequencing (RNA-seq) was used to identify the changes in gene expression profile in horse skin fibroblast cell line expressing one of the BPV genes encoding transforming proteins (BPV-E4 and BPV-E4^E1). The whole transcriptome sequencing allows us to establish the influence of BPV gene transfection on host cells and indicates which virus genes can be responsible for the neoplastic process. It is the first study concerning a cell model of horse skin transfected with BPV genes. Such a model could contribute to a more accurate understanding of changes inside cells during viral infection. Methods: The equine fibroblast cell lines were transfected using the nucleofection method with BPV-E4 and BPV-E4^E1 constructs. RNA was isolated from cell lines directly from culture dishes with PureLink™ RNA mini kit. The quality and quantity of obtained libraries (the TruSeq RNA Kit v2 kit (Illumina, San Diego, CA, USA) ) were assessed using Qubit 2.0 (Qubit™ dsDNA BR AssayKit, Invitrogen, Waltham, MA, USA ) and TapeStation 2200 (D100 screencaps, Agilent). Next, the cDNA libraries were sequenced on NextSeq 500 Illumina platform (Illumina, San Diego, CA, USA) and NextSeq 500/550 High Output KIT v 2.5 (75 cycles) according to protocol. The qPCR validation was used to confirm RNA-seq data. Then, the quality of raw reads was checked with FastQC software followed by removal of adapters and reads of low quality (under phred quality of 20) and reads under length of 36 (Flexbar software). Next, the filtered reads were mapped to EquCab3 genome with STAR software and reads were counted to specific gene thresholds provided in Ensembl gtf file version 100 by htseq-count software. Differential expresion extimation was followed with the use of Deseq2 software. Results: The transcriptome profiling allowed us to perform a comparison of the whole expression profile between the control and both BPV-E4 and BPV-E4^E1 groups. According to the comparison of control and BPV-E4 groups, the 1640 DEGs were identified, of which 624 were up-regulated and 1016 down-regulated in the BPV-E4 group. The highest number of DEGs – 3328 were detected from the control and BPV-E4^E1 comparison. Among them, 1626 genes were up-regulated and 1602 down-regulated in the BPV-E4^E1 group compared to control samples. The most overrepresented Gene Ontology Term between control and BPV-E4 groups were negative regulation of cell proliferation – 34 DEGs (FDR<0.002); positive regulation of cell migration – 24 DEGs (FDR<0.0001); cell adhesion and cell migration; 21 DEGs in both GO terms (FDR<0.003 and 0.0005; respectively). The enrichment analysis performed for differentially expressed genes between control and BPV-E4^E1 samples showed the focal adhesion GO terms were overrepresented by 99 DEGs of which 65 were up-regulated and 34 down-regulated (FDR<0.0001). For cells transfected BPV-E4 and BPV-E4^E1 constructs, the most significant were pathways: of the cell cycle, cytoskeleton, and ECM-matrix remodelling; regulation of actin cytoskeleton; focal adhesion and ECM-receptor interaction. The Pathways in cancer were identified uniquely for cells transfected by BPV-E4 construct, while only for BPV-E4^E1 cells the FoxO, Rap1, and TNF-signaling path-ways and Proteoglycans in cancer. Conclusions: The results obtained showed that both transfection types significantly affected cells transcriptome towards cancer transformation. Nevertheless, cells transfected with BPV-E4^E1 genes seem to be closer to the molecular modification that occurred in vivo in equine sarcoids. The present study showed how equine fibroblast cells could be modified, at the molecular level, in the presence of BPV E4 gene. These findings broaden the knowledge about the possible interaction of BPV viruses on host cells.
2022-01-21 | GSE193906 | GEO
Project description:In human cancer cells, BAG3 protein is known to sustain cell survival. Here, for the first time, we demonstrate the expression of BAG3 protein both in equine sarcoids in vivo and in EqS04b cells, a sarcoid-derived fully transformed cell line harbouring bovine papilloma virus (BPV)-1 genome. Evidence of a possible involvement of BAG3 in equine sarcoid carcinogenesis was obtained by immunohistochemistry analysis of tumour samples. We found that most tumour samples stained positive for BAG3, even though to a different grade, while normal dermal fibroblasts from healthy horses displayed very weak staining pattern for BAG3 expression. By siRNA technology, we demonstrate in EqS04b the role of BAG3 in counteracting basal as well as chemical-triggered pro-death signals. BAG3 down-modulation was indeed shown to promote cell death and cell cycle arrest in G0/G1. In addition, we found that BAG3 silencing sensitized EqS04b cells to phenethylisothiocyanate (PEITC), a promising cancer chemopreventive/chemotherapeutic agent present in edible cruciferous vegetables. Notably, such a pro-survival role of BAG3 was less marked in E. Derm cells, an equine BPV-negative fibroblast cell line taken as a normal counterpart. Altogether our findings might suggest a mutual cooperation between BAG3 and viral oncoproteins to sustain cell survival.
| S-EPMC3729419 | biostudies-literature
Project description:Equine sarcoids (EqS) are fibroblast-derived skin tumors associated with bovine papillomavirus 1 and 2 (BPV-1 and -2). Based on Southern blotting, the BPV-1 genome was not found to be integrated in the host cell genome, suggesting that EqS pathogenesis does not result from insertional mutagenesis. Hence, CRISPR/Cas9 implies an interesting tool for selectively targeting BPV-1 episomes or genetically anchored suspected host factors. To address this in a proof-of-concept study, we confirmed the exclusive episomal persistence of BPV-1 in EqS using targeted locus amplification (TLA). To investigate the CRISPR/Cas9-mediated editing of BPV-1 episomes, primary equine fibroblast cultures were established and characterized. In the EqS fibroblast cultures, CRISPR-mediated targeting of the episomal E5 and E6 oncogenes as well as the BPV-1 long control region was successful and resulted in a pronounced reduction of the BPV-1 load. Moreover, the deletion of the equine Vimentin (VIM), which is highly expressed in EqS, considerably decreased the number of BPV-1 episomes. Our results suggest CRISPR/Cas9-based gene targeting may serve as a tool to help further unravel the biology of EqS pathogenesis.
| S-EPMC10536948 | biostudies-literature
Project description:Bovine papillomavirus (BPV) is the causative agent of papillomatosis in cattle. The disease causes cutaneous and mucosal lesions that can be minimized or lead to the appearance of malignant tumors. This study aims to identify possible molecular mechanisms that are behind the pathological processes associated with bovine papillomatosis through the identification of genes related to the development of the lesions. For this, next-generation RNA sequencing was used to assess differentially expressed genes in infected by BPV and non-infected bovines. Three animals with papillomatosis lesion and three without papillomatosis lesion were studied. The Galaxy platform was used to analyze the data generated by the sequencing. The Illumina output files were converted to FASTQ format. Quality evaluation was performed using FastQC and the sequence quality cut was performed using Trimmomatic. TopHat and Bowtie were used to map and align the reads with the reference genome. The abundance of the expressed genes was verified using Cuffilinks. Cuffdiff was used for differential expression analysis. Functional annotation of the differentially expressed genes was performed using Gene Ontology (GO) databases. RNA-sequencing generated a total of 121,722,238 of reads. In the gene expression analysis, a total of 13,421 genes expressed were identified and of these 1343 were differentially expressed. The functional annotation of differentially significant genes showed that many genes presented functions or they were related to metabolic pathways associated with the progression of papillomatosis lesions and cancer development in cattle. Although more studies are needed, this is the first study that focused on a large-scale evaluation of gene expression associated with the BPV infection, which is important to identify possible mechanisms regulated by the host genes that are necessary the development of the lesion
2018-12-04 | GSE122853 | GEO
Project description:To find out differentially expressed mRNAs in MDBK cells expressing BPV-13 E5
2019-07-02 | GSE133613 | GEO
Project description:To find out differentially expressed miRNAs in MDBK cells expressing BPV-13 E5
2019-07-02 | GSE133610 | GEO
Project description:To find out differentially expressed mRNAs in NIH/3T3 cells overexpressing BPV-13 E6
2019-04-11 | GSE129593 | GEO
Project description:To find out differentially expressed miRNAs in NIH/3T3 cells overexpressing BPV-13 E6
2019-04-11 | GSE129592 | GEO
Project description:Biospecimen Pre-analytical Variables (BPV)
| PRJNA932917 | ENA