Analysis of renal cancer cell lines from two major resources enables genomics-guided cell line selection Journal Article

Authors: Sinha, R.; Winer, A. G.; Chevinsky, M.; Jakubowski, C.; Chen, Y. B.; Dong, Y. Y.; Tickoo, S. K.; Reuter, V. E.; Russo, P.; Coleman, J. A.; Sander, C.; Hsieh, J. J.; Hakimi, A. A.
Article Title: Analysis of renal cancer cell lines from two major resources enables genomics-guided cell line selection
Abstract: 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.
Keywords: classification; carcinoma; tumor; mutations; gene-expression; metaanalysis; update; drug-sensitivity
Journal Title: Nature Communications
Volume: 8
ISSN: 2041-1723
Publisher: Nature Publishing Group  
Date Published: 2017-05-10
Start Page: 15165
Language: English
ACCESSION: WOS:000400887200001
DOI: 10.1038/ncomms15165
PMCID: PMC5436135
PUBMED: 28489074
Notes: Article -- 15165 -- Source: Wos
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MSK Authors
  1. Jonathan Coleman
    184 Coleman
  2. Paul Russo
    446 Russo
  3. Satish K Tickoo
    369 Tickoo
  4. Yingbei Chen
    221 Chen
  5. Yiyu Dong
    16 Dong
  6. Victor Reuter
    899 Reuter
  7. Rileen Sinha
    19 Sinha
  8. Andrew Gordon Winer
    18 Winer
  9. Abraham Ari Hakimi
    129 Hakimi