Comparative Genomic and Transcriptomic Analyses of LNCaP and C4-2B Prostate Cancer Cell Lines

Lien Spans,Thomas Van Den Broeck,Liesbeth Clinckemalie,Frank Claessens,Evelyne Lerut,Steven Joniau,Christine Helsen,Stefan Prekovic,Irina U Agoulnik

doi:10.1371/journal.pone.0090002

Abstract

The LNCaP and C4-2B cell lines form an excellent preclinical model to study the development of metastatic castration-resistant prostate cancer, since C4-2B cells were derived from a bone metastasis that grew in nude mice after inoculation with the LNCaP-derived, castration-resistant C4-2 cells. Exome sequencing detected 2188 and 3840 mutations in LNCaP and C4-2B cells, respectively, of which 1784 were found in both cell lines. Surprisingly, the parental LNCaP cells have over 400 mutations that were not found in the C4-2B genome. More than half of the mutations found in the exomes were confirmed by analyzing the RNA-seq data, and we observed that the expressed genes are more prone to mutations than non-expressed genes. The transcriptomes also revealed that 457 genes show increased expression and 246 genes show decreased expression in C4-2B compared to LNCaP cells. By combining the list of C4-2B-specific mutations with the list of differentially expressed genes, we detected important changes in the focal adhesion and ECM-receptor interaction pathways. Integration of these pathways converges on the myosin light chain kinase gene (MLCK) which might contribute to the metastatic potential of C4-2B cells. In conclusion, we provide extensive databases for mutated genes and differentially expressed genes in the LNCaP and C4-2B prostate cancer cell lines. These can be useful for other researchers using these cell models.

Highlights

Prostate cancer (PCa) is the most frequently diagnosed cancer and third leading cause of death amongst men in Europe [1]
We performed a whole-exome re-sequencing study for both LNCaP and C4-2B cells using 100 base pair, paired-end reads on the Illumina platform. This generated 49 and 80 million reads for LNCaP and C4-2B respectively (Table S1); for LNCaP cells, 74% of the exome was covered at least 20x, versus 88% for C4-2B cells
Strand bias was eliminated manually (Table S2). This resulted in lists of 2188 and 3840 non-synonymous point mutations in LNCaP and C4-2B cells, respectively (Table S3–4)

Summary

Introduction

Prostate cancer (PCa) is the most frequently diagnosed cancer and third leading cause of death amongst men in Europe [1]. A majority of men is diagnosed with localized, low-risk PCa and would never die because of their cancer when left untreated [2]. Patients with high-risk and especially metastatic disease have a much higher risk of dying from PCa with reported PCa-specific mortality rates up to 28.8% for high-risk disease and 66.1% for metastatic disease at 10-years follow-up [3]. One of the best studied PCa cell lines undoubtedly is the LNCaP cell line. This cell line was derived from a needle biopsy taken from the left supraclavicular lymph node of a 50-year old Caucasian male [8]

Objectives

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Results

Conclusion