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Bhatia D, Hinsu A, Panchal K, Sabara P, Jakhesara S, Koringa P. Molecular portrait of squamous cell carcinoma of the bovine horn evaluated by high-throughput targeted exome sequencing: a preliminary report. BMC Vet Res 2020; 16:461. [PMID: 33243240 PMCID: PMC7690171 DOI: 10.1186/s12917-020-02683-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 11/18/2020] [Indexed: 02/04/2023] Open
Abstract
Background Squamous Cell Carcinoma of horn, also known as horn cancer, is a prevailing type of cancer in cattles especially Bos indicus. It is one of the most prevalent disease in Indian bullocks often resulting in death and huge economic losses to farmers. Here, we have reported the use of targeted exome sequencing to identify variants present in horn cancer affected horn mucosa tissue and blood of the same animal to identify some of the prevalent markers of horn cancer. Results We have observed higher number of variants present in tissue as compared to blood as well as among cancer samples compared to samples from normal animals. Eighty six and 1437 cancer-specific variants were identified among the predicted variants in blood and tissue samples, respectively. Total 25 missense variants were observed distributed over 18 genes. KRT8 gene coding for Keratin8, one of the key constituents of horn, displayed 5 missense variants. Additionally, three other genes involved in apoptosis pathway and two genes involved in antigen presentation and processing also contained variants. Conclusions Several genes involved in various apoptotic pathways were found to contain non-synonymous mutations. Keratin8 coding for Keratin, a chief constituent of horn was observed to have the highest number of mutations. In all, we present a preliminary report of mutations observed in horn cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-020-02683-y.
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Affiliation(s)
- Dhruv Bhatia
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H., Anand Agricultural University, Anand, 388001, India
| | - Ankit Hinsu
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H., Anand Agricultural University, Anand, 388001, India
| | - Ketankumar Panchal
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H., Anand Agricultural University, Anand, 388001, India
| | - Pritesh Sabara
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H., Anand Agricultural University, Anand, 388001, India
| | - Subhash Jakhesara
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H., Anand Agricultural University, Anand, 388001, India
| | - Prakash Koringa
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H., Anand Agricultural University, Anand, 388001, India.
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Expression profiling revealed keratins and interleukins as potential biomarkers in squamous cell carcinoma of horn in Indian bullocks ( Bos indicus). 3 Biotech 2020; 10:92. [PMID: 32089987 DOI: 10.1007/s13205-020-2078-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 01/20/2020] [Indexed: 12/11/2022] Open
Abstract
Horn cancer is most prevalent in Bos indicus and poorly defined genetic landscape makes disease diagnosis and treatment difficult. In this study, RNA-Seq and data analysis using CLC Genomics Workbench was employed to identify biomarkers associated with horn cancer. As a result, a total of 149 genes were found significant differentially expressed in horn cancer samples compared to horn normal samples. The study revealed 'keratins' and 'interleukins' as apex groups of significant differentially expressed genes (DEGs). Functional analysis showed that the upregulated keratins support metastasis of tumor via cell proliferation, migration, and affecting cell stability, while downregulated interleukins along with other associated chemokine receptors deprive the immune response to tumor posing clear path for metastasis of horn cancer. Combi-action of both the group facilitates the tumor microenvironment to reproduce tumorigenesis. Analysis of pathways enriched in DEGs and exemplified protein-protein interaction network indicated actual role of DEGs in horn cancer at a fine level. Important effect of deregulated expression of keratin and interleukin genes in horn cancer enrolling their candidacy as potential biomarkers for horn cancer prognosis. This study appraises the possibility to mitigate horn cancer at fine resolution to extract attainable identification of prognostic molecular portraits.
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Shil S, Joshi RS, Joshi CG, Patel AK, Shah RK, Patel N, Jakhesara SJ, Kundu S, Reddy B, Koringa PG, Rank DN. Transcriptomic comparison of primary bovine horn core carcinoma culture and parental tissue at early stage. Vet World 2017; 10:38-55. [PMID: 28246447 PMCID: PMC5301178 DOI: 10.14202/vetworld.2017.38-55] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/29/2016] [Indexed: 12/18/2022] Open
Abstract
Aim: Squamous cell carcinoma or SCC of horn in bovines (bovine horn core carcinoma) frequently observed in Bos indicus affecting almost 1% of cattle population. Freshly isolated primary epithelial cells may be closely related to the malignant epithelial cells of the tumor. Comparison of gene expression in between horn’s SCC tissue and its early passage primary culture using next generation sequencing was the aim of this study. Materials and Methods: Whole transcriptome sequencing of horn’s SCC tissue and its early passage cells using Ion Torrent PGM were done. Comparative expression and analysis of different genes and pathways related to cancer and biological processes associated with malignancy, proliferating capacity, differentiation, apoptosis, senescence, adhesion, cohesion, migration, invasion, angiogenesis, and metabolic pathways were identified. Results: Up-regulated genes in SCC of horn’s early passage cells were involved in transporter activity, catalytic activity, nucleic acid binding transcription factor activity, biogenesis, cellular processes, biological regulation and localization and the down-regulated genes mainly were involved in focal adhesion, extracellular matrix receptor interaction and spliceosome activity. Conclusion: The experiment revealed similar transcriptomic nature of horn’s SCC tissue and its early passage cells.
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Affiliation(s)
- Sharadindu Shil
- Veterinary Officer (WBAH & VS), West Bengal Animal Resources Development Department, Bankura - 772 152, West Bengal, India; Department of Animal Genetics & Breeding, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - R S Joshi
- Department of Animal Genetics & Breeding, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - C G Joshi
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - A K Patel
- Hester Biosciences Limited, Ahmedabad, Gujarat, India
| | - Ravi K Shah
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - Namrata Patel
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - Sumana Kundu
- Veterinary Officer, MVC Sarenga, Government of West Bengal, Bankura, West Bengal, India
| | - Bhaskar Reddy
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - P G Koringa
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
| | - D N Rank
- Department of Animal Biotechnology, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India; Department of Animal Genetics & Breeding, College of Veterinary Sciences and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India
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Identification and quantification of novel RNA isoforms in horn cancer of Bos indicus by comprehensive RNA-Seq. 3 Biotech 2016; 6:259. [PMID: 28330331 PMCID: PMC5143338 DOI: 10.1007/s13205-016-0577-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/26/2016] [Indexed: 02/07/2023] Open
Abstract
Horn cancer (HC) is a squamous cell carcinoma of horn, commonly observed in Bos indicus of the Asian countries. To elucidate the complexity of alternative splicing present in the HC, high-throughput sequencing and analysis of HC and matching horn normal (HN) tissue were carried out. A total of 535,067 and 849,077 reads were analysed after stringent quality filtering for HN and HC, respectively. Cufflinks pipeline for transcriptome analysis revealed 4786 novel splice isoforms comprising 2432 exclusively in HC, 2055 exclusively in HN and 298 in both the conditions. Based on pathway clustering and in silico verification, 102 novel splice isoforms were selected and further analysed with respect to change in protein sequence using Blastp. Finally, fourteen novel splicing events supported both by Cufflinks and UCSC genome browser were selected and confirmed expression by RT-qPCR. Future studies targeted at in-depth characterization of these potential candidate splice isoforms might be helpful in the development of relevant biomarkers for early diagnosis of HC. The results reported in this study refine the available information on transcriptome repertoire of bovine species and boost the research in the line of development of relevant biomarkers for early diagnosis of HC.
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Analysis of differential gene expression and novel transcript units of ovine muscle transcriptomes. PLoS One 2014; 9:e89817. [PMID: 24587058 PMCID: PMC3935930 DOI: 10.1371/journal.pone.0089817] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 01/27/2014] [Indexed: 12/01/2022] Open
Abstract
In this study, we characterized differentially expressed genes (DEGs) between the muscle transcriptomes of Small-tailed Han sheep and Dorper sheep and predicted novel transcript units using high-throughput RNA sequencing technology. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that 1,300 DEGs were involved in cellular processes, metabolic pathways, and the actin cytoskeleton pathway. Importantly, we identified 34 DEGs related to muscle cell development and differentiation. Additionally, we were able to optimize the gene structure and predict the untranslated regions (UTRs) for some of the DEGs. Among the 123,678 novel predicted transcript units (TUs), 15,015 units were predicted protein sequences. The reliability of the sequencing data was verified through qRT-PCR analysis of 12 genes. These results will provide useful information for functional genetic research in the future.
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Koringa PG, Jakhesara SJ, Bhatt VD, Meshram CP, Patel AK, Fefar DT, Joshi CG. Comprehensive transcriptome profiling of squamous cell carcinoma of horn in Bos indicus. Vet Comp Oncol 2013; 14:122-36. [PMID: 24314272 DOI: 10.1111/vco.12079] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 09/25/2013] [Accepted: 10/31/2013] [Indexed: 01/05/2023]
Abstract
Squamous cell carcinoma (SCC) of horn is frequently observed in Bos indicus affecting 1% of cattle population and accounting 83.34% of total tumours found. The transcriptome profile of horn cancer (HC) tissue and the matched normal (HN) tissue were analysed by RNA-seq using Roche 454 sequencing. A total of 1 504 900 reads comprising of 612 MB data were used to identify differentially expressed genes using CLC Genomic Workbench. These include up-regulation of KRT6A, KRT6B, KRT6C, KRT14, SFN, KRT84, PI3, COL17A1, ANLN, SERPINB5 and down-regulation of BOLA, SCGB1A1, CXCL17, KRT19, BPIFB1, NR4A1 and TFF3 in HC, which are involved in regulation of gene transcription, cell proliferation, apoptosis, cell survival and metabolic pathways. The qPCR analysis of several targets suggested concordance of gene expression profile with RNA-seq analysis. The present findings would provide basis for further screening of genes and identification of markers for early diagnosis and therapeutic intervention of HC.
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Affiliation(s)
- P G Koringa
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, 388001, Gujarat, India
| | - S J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, 388001, Gujarat, India
| | - V D Bhatt
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, 388001, Gujarat, India
| | - C P Meshram
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, 388001, Gujarat, India
| | - A K Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, 388001, Gujarat, India
| | - D T Fefar
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, 388001, Gujarat, India
| | - C G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, 388001, Gujarat, India
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Jakhesara SJ, Koringa PG, Joshi CG. Identification of novel exons and transcripts by comprehensive RNA-Seq of horn cancer transcriptome in Bos indicus. J Biotechnol 2013; 165:37-44. [DOI: 10.1016/j.jbiotec.2013.02.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 02/25/2013] [Accepted: 02/25/2013] [Indexed: 10/27/2022]
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Identification of novel splice variants in horn cancer by RNA-Seq analysis in Zebu cattle. Genomics 2012; 101:57-63. [PMID: 23063905 DOI: 10.1016/j.ygeno.2012.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 08/11/2012] [Accepted: 10/03/2012] [Indexed: 10/27/2022]
Abstract
Horn cancer accounts for nearly 83% of total tumors found in Indian Zebu cattle, which results in chronic suffering and causes heavy economic losses. Alternative splicing has been frequently implicated in the various types of cancer progression. Utilizing the transcriptome sequence generated by next generation sequencing, we analyzed the transcript data for the presence of alternative splicing using BLAT program and identified 27 alternatively spliced genes, of which 12 spliced variants appeared to be the novel spliced candidates. Protein prediction of these novel spliced variants revealed that splice variation has caused either truncation of protein, insertion/deletion of stretch of amino acids or formation of unique carboxy terminus. The RT-PCR analysis confirmed the expression of 8 of the 12 novel spliced variants observed by transcriptome sequencing. Additionally, altered splicing/expression of these novel candidates between cancer and normal tissues revealed by qPCR suggests their potential involvement in the development of horn cancer.
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