Identification and quantification of novel RNA isoforms in horn cancer of Bos indicus by comprehensive RNA-Seq

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.Electronic supplementary materialThe online version of this article (doi:10.1007/s13205-016-0577-5) contains supplementary material, which is available to authorized users.

Transcriptome analysis alk-SMase knockout mice reveals the effect of alkaline sphingomyelinase on liver

“…Bowtie2 [ 19 ] and Tophat 2.0.6 [ 30 ] was chose to mapping the reads to the mouse reference genome (mm10) from UCSC database，resulting in alignment rate of 96.83%–97.63%. The accepted_hits.bam files were generated by the tophat mapping, which were used to assembled into transcripts using Cufflinks (Version 2.2.1) [ 18 ]. After the alignment, we used ANNOVAR to annotate the position on the reads alignment.…”

Molecular portrait of squamous cell carcinoma of the bovine horn evaluated by high-throughput targeted exome sequencing: a preliminary report

“…It is a type of SCC with poorly defined genetic landscape, which arise from pseudo stratified columnar epithelium of the horn core mucosa, reported only in Bos indicus . Horn Cancer often results in death of an animal in the event of metastasis [ 5 ]. In India, horn cancer affects approximately 1% of the cattle population and accounts for 83.34% of total tumours reported [ 6 ].…”

“…Here, we employed high throughput targeted exome sequencing using Illumina MiSeq for identification of mutations associated with squamous cell carcinoma of horn in Kankrej ( Bos indicus ) bullock. Previous studies on horn cancer have identified various SNPs and differential expression of genes using RNAseq or transcriptome sequencing [ 5 , 7 , 8 , 10 – 14 ]. As per our knowledge, this is the first study of exome sequencing in bovine horn cancer (as well as other types of cancers in bovines).…”