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Transcriptome analysis of tongue cancer based on high?throughput sequencing.

ABSTRACT: Tongue cancer is one of the most common types of cancer, but its molecular etiology and pathogenesis remain unclear. The aim of the present study was to elucidate the pathogenesis of tongue cancer and investigate novel potential diagnostic and therapeutic targets. Four matched pairs of tongue cancer and paracancerous tissues were collected for RNA sequencing (RNA?Seq), and the differentially expressed genes were analyzed. The RNA?Seq data of tongue cancer tissues were further analyzed using bioinformatics and reverse transcription?quantitative PCR analysis. The sequenced reads were quantified and qualified in accordance with the analysis demands. The transcriptomes of the tongue cancer tissues and paired paracancerous tissues were analyzed, and 1,700 upregulated and 2,249 downregulated genes were identified. Gene Ontology analysis uncovered a significant enrichment in the terms associated with extracellular matrix (ECM) organization, cell adhesion and collagen catabolic processes. Kyoto Encyclopedia of Genes and Genomes analysis demonstrated that these differentially expressed genes were mainly enriched in the focal adhesion pathway, ECM?receptor interaction pathway, phosphoinositide 3?kinase (PI3K)?Akt pathway, and cell adhesion molecules. Comprehensive analyses of the gene tree and pathway network revealed that the majority of cell cycle genes were upregulated, while the majority of the genes associated with intracellular response, cell adhesion and cell differentiation were downregulated. The ECM?receptor interaction, focal adhesion kinase (FAK) and PI3K?Akt pathways were closely associated with one another and held key positions in differential signaling pathways. The ECM?receptor, FAK and PI3K?Akt signaling pathways were found to synergistically promote tongue cancer occurrence and progression, and may serve as potential diagnostic and therapeutic targets for this type of cancer.

SUBMITTER: Tang M

PROVIDER: S-EPMC7160550 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Transcriptome analysis of tongue cancer based on high‑throughput sequencing.

Tang Mingming M Dai Wencheng W Wu Hao H Xu Xinjiang X Jiang Bin B Wei Yingze Y Qian Hongyan H Han Liang L

Oncology reports 20200323 6

Tongue cancer is one of the most common types of cancer, but its molecular etiology and pathogenesis remain unclear. The aim of the present study was to elucidate the pathogenesis of tongue cancer and investigate novel potential diagnostic and therapeutic targets. Four matched pairs of tongue cancer and paracancerous tissues were collected for RNA sequencing (RNA‑Seq), and the differentially expressed genes were analyzed. The RNA‑Seq data of tongue cancer tissues were further analyzed using bioi ...[more]

PMID: 32236620

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Project description:BACKGROUND: The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources. RESULTS: In this study, we analysed the transcriptome of four tropical tree species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Virola michelii) with contrasting ecological features, belonging to four widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae and Myristicaceae). We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454 pyrosequencing. We have developed an R and bioperl-based bioinformatic procedure for de novo assembly, gene functional annotation and marker discovery. Mismatch identification takes into account single-base quality values as well as the likelihood of false variants as a function of contig depth and number of sequenced chromosomes. Between 17103 (for Symphonia globulifera) and 23390 (for Eperua falcata) contigs were assembled. Organs varied in the numbers of unigenes they apparently express, with higher number in roots. Patterns of gene expression were similar across species, with metabolism of aromatic compounds standing out as an overrepresented gene function. Transcripts corresponding to several gene functions were found to be over- or underrepresented in each organ. We identified between 4434 (for Symphonia globulifera) and 9076 (for Virola surinamensis) well-supported mismatches. The resulting overall mismatch density was comprised between 0.89 (S. globulifera) and 1.05 (V. surinamensis) mismatches/100 bp in variation-containing contigs. CONCLUSION: The relative representation of gene functions in the four transcriptomes suggests that secondary metabolism may be particularly important in tropical trees. The differential representation of transcripts among tissues suggests differential gene expression, which opens the way to functional studies in these non-model, ecologically important species. We found substantial amounts of mismatches in the four species. These newly identified putative variants are a first step towards acquiring much needed genomic resources for tropical tree species.

Dataset Information

Transcriptome analysis of tongue cancer based on high?throughput sequencing.

Publications

Transcriptome analysis of tongue cancer based on high‑throughput sequencing.

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