TY - JOUR
T1 - Analysis of renal cancer cell lines from two major resources enables genomics-guided cell line selection
AU - Sinha, Rileen
AU - Winer, Andrew G.
AU - Chevinsky, Michael
AU - Jakubowski, Christopher
AU - Chen, Ying Bei
AU - Dong, Yiyu
AU - Tickoo, Satish K.
AU - Reuter, Victor E.
AU - Russo, Paul
AU - Coleman, Jonathan A.
AU - Sander, Chris
AU - Hsieh, James J.
AU - Hakimi, A. Ari
N1 - Funding Information:
We acknowledge Ed Reznik for help in figure preparation. This investigation was supported by the NIH/NCI Cancer Center Support Grant P30 CA008748 and the Sidney Kimmel Center for Prostate and Urologic Cancers and MSKCC Center for Translational Cancer Genomic Analysis; U24 CA143840.
Publisher Copyright:
© The Author(s) 2017.
PY - 2017
Y1 - 2017
N2 - The utility of cancer cell lines is affected by the similarity to endogenous tumour cells. Here we compare genomic data from 65 kidney-derived cell lines from the Cancer Cell Line Encyclopedia and the COSMIC Cell Lines Project to three renal cancer subtypes from The Cancer Genome Atlas: clear cell renal cell carcinoma (ccRCC, also known as kidney renal clear cell carcinoma), papillary (pRCC, also known as kidney papillary) and chromophobe (chRCC, also known as kidney chromophobe) renal cell carcinoma. Clustering copy number alterations shows that most cell lines resemble ccRCC, a few (including some often used as models of ccRCC) resemble pRCC, and none resemble chRCC. Human ccRCC tumours clustering with cell lines display clinical and genomic features of more aggressive disease, suggesting that cell lines best represent aggressive tumours. We stratify mutations and copy number alterations for important kidney cancer genes by the consistency between databases, and classify cell lines into established gene expression-based indolent and aggressive subtypes. Our results could aid investigators in analysing appropriate renal cancer cell lines.
AB - The utility of cancer cell lines is affected by the similarity to endogenous tumour cells. Here we compare genomic data from 65 kidney-derived cell lines from the Cancer Cell Line Encyclopedia and the COSMIC Cell Lines Project to three renal cancer subtypes from The Cancer Genome Atlas: clear cell renal cell carcinoma (ccRCC, also known as kidney renal clear cell carcinoma), papillary (pRCC, also known as kidney papillary) and chromophobe (chRCC, also known as kidney chromophobe) renal cell carcinoma. Clustering copy number alterations shows that most cell lines resemble ccRCC, a few (including some often used as models of ccRCC) resemble pRCC, and none resemble chRCC. Human ccRCC tumours clustering with cell lines display clinical and genomic features of more aggressive disease, suggesting that cell lines best represent aggressive tumours. We stratify mutations and copy number alterations for important kidney cancer genes by the consistency between databases, and classify cell lines into established gene expression-based indolent and aggressive subtypes. Our results could aid investigators in analysing appropriate renal cancer cell lines.
UR - http://www.scopus.com/inward/record.url?scp=85037677924&partnerID=8YFLogxK
U2 - 10.1038/ncomms15165
DO - 10.1038/ncomms15165
M3 - Article
C2 - 28489074
AN - SCOPUS:85037677924
SN - 2041-1723
VL - 8
JO - Nature communications
JF - Nature communications
M1 - 15165
ER -