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

  • Nat Commun. 2017 May 10:8:15165. doi: 10.1038/ncomms15165.
Rileen Sinha  1  2 ,  Andrew G Winer  3 ,  Michael Chevinsky  3 ,  Christopher Jakubowski  3 ,  Ying-Bei Chen  4 ,  Yiyu Dong  5 ,  Satish K Tickoo  4 ,  Victor E Reuter  4 ,  Paul Russo  3 ,  Jonathan A Coleman  3 ,  Chris Sander  6 ,  James J Hsieh  7 ,  A Ari Hakimi  1  3
Affiliations
  • 1. Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, 417 E 68th St, New York, New York 10065, USA.
  • 2. Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, New York 10029, USA.
  • 3. Urology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, 417 E 68th St, New York, New York 10065, USA.
  • 4. Department of Pathology, Memorial Sloan-Kettering Cancer Center, 417 E 68th St, New York, New York 10065, USA.
  • 5. Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, 417 E 68th St, New York, New York 10065, USA.
  • 6. cBio Center, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Compbio Collaboratory, Department of Cell Biology, Harvard Medical School, 450 Brookline Avenue, Boston, Massachusetts 02215-5450, USA.
  • 7. Molecular Oncology, Department of Medicine, Siteman Cancer Center, Washington University, St. Louis, Missouri 63110, USA.
PMID: 28489074 DOI: 10.1038/ncomms15165
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.