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

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. Exom...

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Main Authors:	Spans, Lien, Helsen, Christine, Clinckemalie, Liesbeth, Van den Broeck, Thomas, Prekovic, Stefan, Joniau, Steven, Lerut, Evelyne, Claessens, Frank
Format:	Online
Language:	English
Published:	Public Library of Science 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3938550/

id	pubmed-3938550
recordtype	oai_dc
spelling	pubmed-39385502014-03-04 Comparative Genomic and Transcriptomic Analyses of LNCaP and C4-2B Prostate Cancer Cell Lines Spans, Lien Helsen, Christine Clinckemalie, Liesbeth Van den Broeck, Thomas Prekovic, Stefan Joniau, Steven Lerut, Evelyne Claessens, Frank Research Article 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. Public Library of Science 2014-02-28 /pmc/articles/PMC3938550/ /pubmed/24587179 http://dx.doi.org/10.1371/journal.pone.0090002 Text en © 2014 Spans et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Spans, Lien Helsen, Christine Clinckemalie, Liesbeth Van den Broeck, Thomas Prekovic, Stefan Joniau, Steven Lerut, Evelyne Claessens, Frank
spellingShingle	Spans, Lien Helsen, Christine Clinckemalie, Liesbeth Van den Broeck, Thomas Prekovic, Stefan Joniau, Steven Lerut, Evelyne Claessens, Frank Comparative Genomic and Transcriptomic Analyses of LNCaP and C4-2B Prostate Cancer Cell Lines
author_facet	Spans, Lien Helsen, Christine Clinckemalie, Liesbeth Van den Broeck, Thomas Prekovic, Stefan Joniau, Steven Lerut, Evelyne Claessens, Frank
author_sort	Spans, Lien
title	Comparative Genomic and Transcriptomic Analyses of LNCaP and C4-2B Prostate Cancer Cell Lines
title_short	Comparative Genomic and Transcriptomic Analyses of LNCaP and C4-2B Prostate Cancer Cell Lines
title_full	Comparative Genomic and Transcriptomic Analyses of LNCaP and C4-2B Prostate Cancer Cell Lines
title_fullStr	Comparative Genomic and Transcriptomic Analyses of LNCaP and C4-2B Prostate Cancer Cell Lines
title_full_unstemmed	Comparative Genomic and Transcriptomic Analyses of LNCaP and C4-2B Prostate Cancer Cell Lines
title_sort	comparative genomic and transcriptomic analyses of lncap and c4-2b prostate cancer cell lines
description	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.
publisher	Public Library of Science
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3938550/
_version_	1612063159157260288

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

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