Journal of Next Generation Sequencing & Applications

ISSN - 2469-9853

+44 1250400002

Abstract

Identification of Mutations, Expression Alterations and Fusion Transcripts by Next Generation RNAseq in Castration-Resistant Prostate Cancer Cell lines with Possible Clinical Relevance

Yuanjun Ma, Yali Miao, Zhuochun Peng, Johanna Sandgren, Teresita Díaz De Ståhl, Lena Lennartsson, Sten Nilsson and Chunde Li

Androgen Deprivation Therapy (ADT) would benefit prostate cancer patients initially but cancer cells can eventually develop castration resistance. In this study, we compared androgen-dependent and androgenindependent cell lines to find potential genes associated with acquired resistance to ADT. Using RNAseq, we found 4397 mutations distributed in 2579 genes, out of which, 1574 mutated genes could also be found in prostate cancer tumor samples collected in Cosmic database (http://cancer.sanger.ac.uk/cosmic). We also discovered 157 and 549 genes which were down and up-regulated respectively in both PC3 and DU145 compared to LNCaP. Network analysis resulted in 3 dominant connection notes: GCR/MCR (NR3C1) and PKA-cat kinase (PRKACB) and PKC family (PRKD1). By ChimeraScan analysis, 48, 117 and 60 chimeric transcripts were discovered in DU145, LNCaP and PC3 respectively. Among them, six predicted fusions expressed specifically in androgen-independent cell lines (DU145 and PC3). Some of these gene mutations and transcription alterations have been reported in tumor samples from prostate cancer patients and may have certain associations with acquired resistance to anti-hormone therapy in prostate cancer. A proportion of mutations are enriched in genes involved in immune response pathways, suggesting new targets to develop effective treatments to overcome castration resistance.

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