title: Identification of novel transcripts deregulated in buccal cancer by RNA-seq.
abstract: The differential transcriptome analysis provides better understanding of molecular pathways leading to cancer, which in turn allows designing the effective strategies for diagnosis, therapeutic intervention and prediction of therapeutic outcome. This study describes the transcriptome analysis of buccal cancer and normal tissue by CLC Genomics Workbench from the data generated by Roche's 454 sequencing platform, which identified total of 1797 and 2655 genes uniquely expressed in normal and cancer tissues, respectively with 2466 genes expressed in both tissues. Among the genes expressed in both tissues, 1842 were up-regulated whereas 624 were down-regulated in cancer tissue. Besides transcripts known to be involved in cancer, this study led to the identification of novel transcripts, with significantly altered expression in buccal cancer tissue, providing potential targets for diagnosis and cancer therapeutics. The functional categorization by the KEGG pathway and gene ontology analysis revealed enrichment of differentially expressed transcripts to various pathways leading to cancer, including the p53 signaling pathway. Moreover, the gene ontology analysis unfolded suppression of transcripts involved in actin mediated cell contraction process. The down-regulation of four of these transcripts MYL1, ACTA1, TCAP and DESMIN in buccal cancer were further supported by quantitative PCR signifying its possible implication in the cancer progression.
authors: Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand-388 001, Gujarat, India.
authors: Manisha R
authors: MR
authors: Sajnani
authors: Amrutlal K
authors: AK
authors: Patel
authors: Vaibhav D
authors: VD
authors: Bhatt
authors: Ajai K
authors: AK
authors: Tripathi
authors: Viral B
authors: VB
authors: Ahir
authors: Vangipuram
authors: V
authors: Shankar
authors: Siddharth
authors: S
authors: Shah
authors: Tejas M
authors: TM
authors: Shah
authors: Prakash G
authors: PG
authors: Koringa
authors: Subhash J
authors: SJ
authors: Jakhesara
authors: Chaitanya G
authors: CG
authors: Joshi
mesh_terms: D001483:Base Sequence; D002294:Carcinoma, Squamous Cell / Q000235:genetics*; D017931:DNA Primers / Q000235:genetics; D015536:Down-Regulation; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009061:Mouth Mucosa; D009062:Mouth Neoplasms / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D012334:RNA, Neoplasm / Q000235:genetics*; D017423:Sequence Analysis, RNA; D015854:Up-Regulation
chemical_list: D017931:DNA Primers; D012333:RNA, Messenger; D012334:RNA, Neoplasm