Transcriptome analysis of equine sarcoids
Ontology highlight
ABSTRACT:
ORGANISM(S): Equus caballus
PROVIDER: GSE83430 | GEO | 2016/06/18
SECONDARY ACCESSION(S): PRJNA326059
REPOSITORIES: GEO
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Project description:The aim of this study was to identify changes in transcriptome of horse sarcoids - a locally invasive skin tumors of equids, which are considered to be the most common equine skin neoplasm. The global expression of genes was investigated in 12 tumour samples and in 12 of healthy skin samples.
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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.
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Project description:DNA methylation is a key mechanism in transcription regulation, and aberrant methylation is a common and important mechanism in tumor initiation, maintenance, and progression. To find genes that are aberrantly regulated by altered methylation in horse sarcoids, we used reduced representation bisulfite sequencing (RRBS) accompanied by RNA sequencing (RNA-Seq) for methylome (whole genome DNA methylation sequencing) and transcriptome profiling, respectively. We found that the DNA methylation level was generally lower in lesion samples than in controls. In the analyzed samples, a total of 14,692 differentially methylated sites (DMSs) in the context of CpG (where cytosine and guanine are separated by a phosphate), and 11,712 differentially expressed genes (DEGs) were identified. The integration of the methylome and transcriptome data suggests that aberrant DNA methylation may be involved in the deregulation of expression of the 493 genes in equine sarcoid. Furthermore, enrichment analysis of the genes demonstrated the activation of multiple molecular pathways related to extracellular matrix (ECM), oxidative phosphorylation (OXPHOS), immune response, and disease processes that can be related to tumor progression. The results provide further insight into the epigenetic alterations in equine sarcoids and provide a valuable resource for follow-up studies to identify biomarkers for predicting susceptibility to this common condition in horses.
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Project description:The proteomic analysis of serum sample was performed to identify and quantify the expression of proteins between normal and Equine melanocytic neoplasm (EMN) gray horse.
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Project description:We report the application of next-generation sequencing for high-throughput profiling of microRNA expression characterictic for horse sarcoid, which is a skin tumor. With the use of HiScanSQ system (Illumina), we obtained over 124 million sequence reads from microRNA libraries. As a result, we identified over 200 known, as well as around 500 potentially novel, miRNA sequences. The analysis of differential expression of the identified miRNAs revealed that over 100 miRNAs were up- or downregulated in the sarcoid tissue in comparison to the control. The analysis of pathways showed e.g. pathways in cancer, viral carcinogenesis or transcriptional misregulation in cancer. Furthermore, microRNAs associated with carcinogenesis in humans were identified, such as: miR-10a, miR-21, miR-200 family. Concluding, our results suggest that microRNAs are largely involved in the neoplastic transformation of horse sarcoids.
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Project description:Horse-specific genes are not readily identified from available equine EST/cDNA resources due to relatively limited coverage. In addition, equine gene sets predicted in silico by Ensembl and NCBI will not identify horse specific genes since they rely on homology-based projection of gene structure annotation from other species. In this study, RNA-seq of 8 equine RNA samples representing 6 distinct tissues was performed and used to improve and refine equine gene structure annotation. The samples and RNA were collected as part of the related study E-GEOD-21925 and are described in Coleman et al 2010. Anim Genet 41 Suppl 2: 121-30 (PMID: 21070285). The RNA from these samples was re-sequenced in this experiment. The tissues were i). the articular cartilage and synovial membrane samples from a 3-year-old male pony. The left carpal joints received four LPS injections (0.5 ng) over 8 days, while the right carpal joints received control injections of PBS. ii) A cerebellum sample was collected from a 2-year-old female thoroughbred. iii) A testis sample from a 4-year-old thoroughbred. iv) A placental villous sample collected immediately post-partum from a full-term female thoroughbred foal. v) A whole embryo sample was obtained from a 34-day-old male thoroughbred conceptus. The embryo, cerebellum, testis and placental samples were of apparent normal gross morphology.
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Project description:A tissue survey of gene expression was conducted using microarray-based transcriptional profiling to compare equine articular cartilage to 10 other normal adult horse tissues. The ten comparative tissues were bladder, cerebellum, kidney, liver, lung, lymph node, muscle, placental villous, spleen, and testis.
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Project description:The aim of the project was to identify sites undergoing changes in methylation level in cancer cells of equine sarcoid. The comparative analysis of DNA methylation patterns of the genome fraction rich in CpG dinucleotides was investigated using Reduced Representation Bisulfite Sequencing (RRBS) technique. In this study, for the first time we report the genome-wide DNA methylation profile of skin tumour in horses and describe differentially methylated genomic regions with respect to healthy skin.
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Project description:Sequencing of equine mRNA (RNA-seq) identified 428 putative transcripts which do not map to any previously annotated or predicted horse genes. Most of these encode the equine homologs of known protein-coding genes described in other species, yet the potential exists to identify novel and perhaps equine-specific gene structures. A set of 36 transcripts were prioritized for further study by filtering for levels of expression (depth of RNA-seq read coverage), distance from annotated features in the equine genome, the number of putative exons, and patterns of gene expression between tissues. From these, four were selected for further investigation based on predicted open reading frames of greater than or equal to 50 amino acids and lack of detectable homology to known genes across species. Sanger sequencing of RT-PCR amplicons from additional equine samples confirmed expression and structural annotation of each transcript. Functional predictions were made by conserved domain searches. A single transcript, expressed in the cerebellum, contains a putative kruppel-associated box (KRAB) domain, suggesting a potential function associated with zinc finger proteins and transcriptional regulation. Overall levels of conserved synteny and sequence conservation across a 1MB region surrounding each transcript were approximately 73% compared to the human, canine, and bovine genomes; however, the four loci display some areas of low conservation and sequence inversion in regions that immediately flank these previously unannotated equine transcripts. Taken together, the evidence suggests that these four transcripts are likely to be equine-specific.
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Project description:The horse, like a majority of animal species, has a limited amount of species-specific expressed sequence data available in public databases. As a result, structural models for a majority of genes defined in the equine genome are predictions based on ab initio sequence analysis or the projection of gene structures from other mammalian species. The current study used Illumina-based sequencing of messenger RNA (RNA-seq) to help refine structural annotation of equine protein-coding genes and for a preliminary assessment of gene expression patterns. Sequencing of mRNA from eight equine tissues generated 293,758,105 thirty five-base sequence tags, equaling 10.28 giga-basepairs of total sequence data. The tag alignments represent approximately 208X coverage of the equine mRNA transcriptome and confirmed transcriptional activity for roughly 90% of the protein-coding gene structures predicted by Ensembl and NCBI. Tag coverage was sufficient to define structural annotation for 11,356 genes, while also identifying an additional 456 transcripts with exon/intron features that are not listed by either Ensembl or NCBI. Genomic locus data and intervals for the protein-coding genes predicted by the Ensembl and NCBI annotation pipelines were combined with 75,116 RNA-seq derived transcriptional units to generate a consensus equine protein-coding gene set of 20,302 defined loci. Gene ontology annotation was used to compare the functional and structural categories of genes expressed in either a tissue-restricted pattern or broadly across all tissue samples. Examination of 8 equine RNA samples representing 6 distinct tissues
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