RNA-Seq analysis to explore the variants in melanoma cells: molecular diagnosis and therapeutics

Shalini kumari, Ruchi Yadav

Amity Institute of Biotechnology, Amity University  Lucknow, Uttar Pradesh, India

ABSTRACT

High throughput sequencing technology that are also called as second generation or Next Generation (NGS) sequencing techniques has enabled researchers to study genome, transcriptome, metabolome of any organism in high throughput manner. RNA seq (Ribonucleic Acid Sequencing) is a NGS technique that is used to sequence total transcripts of cell and to study gene expression. This technique is widely used to identify differentially expressed genes and to identify variants. RNAseq technique has been used to study several diseases like cancers, neurological diseases, bacterial infections diseases and to understand the key mechanism of genes and its functions. Melanoma is a threatening tumor and one of the most successive metastatic diseases. Melanomas ordinarily happen inside the skin yet inside the mouth, digestion tracts or eye. Melanoma carcinoma is also called as cutaneous melanoma or melanoma of the skin. In current research Pair end RNA-seq sequencing data for melanoma cell was retrieved from ENA (European Nucleotide Archive) database with accession no.:SRP252675. RNAseq analysis pipeline of Galaxy online platform was used for the prediction of single nucleotide variations (SNVs). Total three genes are predicted that are expressed in RNAseq samples and involved in the skin cancer these genes are TNFRSF4 (Tumor Necrosis Factor Receptor Superfamily Member 4), TNFRSF18 and AGRN (Agrin). Protein encoded by TNFRSF4 gene is a member of the TNF-receptor superfamily and AGRN gene is associated with Presynaptic Congenital Myasthenic Syndromes. Pathway enrichment of identified genes shows that TNFRSF4 and TNFRSF18 have function in cytokine-cytokine receptor interaction and AGRN in ECM-receptor interaction. These results highlight the importance of TNFRSF4, TNFRSF18 and AGRN in Melanoma condition and can be further used as potential drug targets.

Keywords:

RNAseq, Transcriptome, Melanoma, Differentially Expressed Genes, Galaxy.