Whole-Genome Sequence of the Metastatic PC3 and LNCaP Human Prostate Cancer Cell Lines

Inge Seim; Penny L Jeffery; Patrick B Thomas; Colleen C Nelson; Lisa K Chopin

doi:10.1534/g3.117.039909

Whole-Genome Sequence of the Metastatic PC3 and LNCaP Human Prostate Cancer Cell Lines

G3 (Bethesda). 2017 Jun 7;7(6):1731-1741. doi: 10.1534/g3.117.039909.

Authors

Inge Seim^{1

2

3}, Penny L Jeffery^{4

2

3}, Patrick B Thomas^{4

2

3}, Colleen C Nelson², Lisa K Chopin^{4

2

3}

Affiliations

¹ Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Brisbane, Queensland 4102, Australia i.seim@qut.edu.au.
² Australian Prostate Cancer Research Centre - Queensland, Princess Alexandra Hospital, Queensland University of Technology, Woolloongabba, Brisbane, Queensland 4102, Australia.
³ Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Brisbane, Queensland 4102, Australia.
⁴ Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Brisbane, Queensland 4102, Australia.

Abstract

The bone metastasis-derived PC3 and the lymph node metastasis-derived LNCaP prostate cancer cell lines are widely studied, having been described in thousands of publications over the last four decades. Here, we report short-read whole-genome sequencing (WGS) and de novo assembly of PC3 (ATCC CRL-1435) and LNCaP (clone FGC; ATCC CRL-1740) at ∼70 × coverage. A known homozygous mutation in TP53 and homozygous loss of PTEN were robustly identified in the PC3 cell line, whereas the LNCaP cell line exhibited a larger number of putative inactivating somatic point and indel mutations (and in particular a loss of stop codon events). This study also provides preliminary evidence that loss of one or both copies of the tumor suppressor Capicua (CIC) contributes to primary tumor relapse and metastatic progression, potentially offering a treatment target for castration-resistant prostate cancer (CRPC). Our work provides a resource for genetic, genomic, and biological studies employing two commonly-used prostate cancer cell lines.

Keywords: Genome Report; WGS; cell line; genomics; human; prostate cancer; sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cell Line, Tumor
Computational Biology / methods
DNA Copy Number Variations
Databases, Nucleic Acid
Genome, Human*
Genome-Wide Association Study*
Genomics / methods
Humans
INDEL Mutation
Male
Neoplasm Metastasis
Polymorphism, Single Nucleotide
Prostatic Neoplasms / genetics*
Prostatic Neoplasms / mortality
Prostatic Neoplasms / pathology
Whole Genome Sequencing*