A comprehensive transcriptional portrait of human cancer cell lines - PubMed (original) (raw)

doi: 10.1038/nbt.3080. Epub 2014 Dec 8.

Steffen Durinck 2, Eric W Stawiski 2, Peter M Haverty 1, Zhaoshi Jiang 1, Hanbin Liu 1, Jeremiah Degenhardt 1, Oleg Mayba 1, Florian Gnad 1, Jinfeng Liu 1, Gregoire Pau 1, Jens Reeder 1, Yi Cao 3, Kiran Mukhyala 1, Suresh K Selvaraj 4, Mamie Yu 4, Gregory J Zynda 1, Matthew J Brauer 1, Thomas D Wu 1, Robert C Gentleman 1, Gerard Manning 1, Robert L Yauch 4, Richard Bourgon 1, David Stokoe 4, Zora Modrusan 5, Richard M Neve 4, Frederic J de Sauvage 5, Jeffrey Settleman 4, Somasekar Seshagiri 5, Zemin Zhang 1

Affiliations

• PMID: 25485619
• DOI: 10.1038/nbt.3080

A comprehensive transcriptional portrait of human cancer cell lines

Christiaan Klijn et al. Nat Biotechnol. 2015 Mar.

Abstract

Tumor-derived cell lines have served as vital models to advance our understanding of oncogene function and therapeutic responses. Although substantial effort has been made to define the genomic constitution of cancer cell line panels, the transcriptome remains understudied. Here we describe RNA sequencing and single-nucleotide polymorphism (SNP) array analysis of 675 human cancer cell lines. We report comprehensive analyses of transcriptome features including gene expression, mutations, gene fusions and expression of non-human sequences. Of the 2,200 gene fusions catalogued, 1,435 consist of genes not previously found in fusions, providing many leads for further investigation. We combine multiple genome and transcriptome features in a pathway-based approach to enhance prediction of response to targeted therapeutics. Our results provide a valuable resource for studies that use cancer cell lines.

PubMed Disclaimer

Similar articles

• Cross-cancer profiling of molecular alterations within the human autophagy interaction network.
  Lebovitz CB, Robertson AG, Goya R, Jones SJ, Morin RD, Marra MA, Gorski SM. Lebovitz CB, et al. Autophagy. 2015;11(9):1668-87. doi: 10.1080/15548627.2015.1067362. Autophagy. 2015. PMID: 26208877 Free PMC article.
• The landscape of antisense gene expression in human cancers.
  Balbin OA, Malik R, Dhanasekaran SM, Prensner JR, Cao X, Wu YM, Robinson D, Wang R, Chen G, Beer DG, Nesvizhskii AI, Chinnaiyan AM. Balbin OA, et al. Genome Res. 2015 Jul;25(7):1068-79. doi: 10.1101/gr.180596.114. Epub 2015 Jun 10. Genome Res. 2015. PMID: 26063736 Free PMC article.
• Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing.
  Patil V, Pal J, Somasundaram K. Patil V, et al. Oncotarget. 2015 Dec 22;6(41):43452-71. doi: 10.18632/oncotarget.6171. Oncotarget. 2015. PMID: 26496030 Free PMC article.
• The emerging complexity of gene fusions in cancer.
  Mertens F, Johansson B, Fioretos T, Mitelman F. Mertens F, et al. Nat Rev Cancer. 2015 Jun;15(6):371-81. doi: 10.1038/nrc3947. Nat Rev Cancer. 2015. PMID: 25998716 Review.
• Deep sequencing in cancer research.
  Yoshida K, Sanada M, Ogawa S. Yoshida K, et al. Jpn J Clin Oncol. 2013 Feb;43(2):110-5. doi: 10.1093/jjco/hys206. Epub 2012 Dec 5. Jpn J Clin Oncol. 2013. PMID: 23225907 Review.

Cited by

• Computational models for predicting drug responses in cancer research.
  Azuaje F. Azuaje F. Brief Bioinform. 2017 Sep 1;18(5):820-829. doi: 10.1093/bib/bbw065. Brief Bioinform. 2017. PMID: 27444372 Free PMC article. Review.
• An Oncogenic NTRK Fusion in a Patient with Soft-Tissue Sarcoma with Response to the Tropomyosin-Related Kinase Inhibitor LOXO-101.
  Doebele RC, Davis LE, Vaishnavi A, Le AT, Estrada-Bernal A, Keysar S, Jimeno A, Varella-Garcia M, Aisner DL, Li Y, Stephens PJ, Morosini D, Tuch BB, Fernandes M, Nanda N, Low JA. Doebele RC, et al. Cancer Discov. 2015 Oct;5(10):1049-57. doi: 10.1158/2159-8290.CD-15-0443. Epub 2015 Jul 27. Cancer Discov. 2015. PMID: 26216294 Free PMC article. Clinical Trial.
• Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor.
  Jaiswal A, Gautam P, Pietilä EA, Timonen S, Nordström N, Akimov Y, Sipari N, Tanoli Z, Fleischer T, Lehti K, Wennerberg K, Aittokallio T. Jaiswal A, et al. Mol Syst Biol. 2021 Mar;17(3):e9526. doi: 10.15252/msb.20209526. Mol Syst Biol. 2021. PMID: 33750001 Free PMC article.
• A Six-Stage Workflow for Robust Application of Systems Pharmacology.
  Gadkar K, Kirouac DC, Mager DE, van der Graaf PH, Ramanujan S. Gadkar K, et al. CPT Pharmacometrics Syst Pharmacol. 2016 May;5(5):235-49. doi: 10.1002/psp4.12071. Epub 2016 Apr 16. CPT Pharmacometrics Syst Pharmacol. 2016. PMID: 27299936 Free PMC article.
• Evolutionary and cellular analysis of the 'dark' pseudokinase PSKH2.
  Byrne DP, Shrestha S, Daly LA, Marensi V, Ramakrishnan K, Eyers CE, Kannan N, Eyers PA. Byrne DP, et al. Biochem J. 2023 Jan 31;480(2):141-160. doi: 10.1042/BCJ20220474. Biochem J. 2023. PMID: 36520605 Free PMC article.

References

1. 1. Stem Cells. 2013 Dec;31(12):2827-32 - PubMed
2. 1. Cell. 2013 Mar 28;153(1):17-37 - PubMed
3. 1. Nature. 2013 Jan 10;493(7431):216-20 - PubMed
4. 1. J Virol. 2012 Mar;86(6):2970-7 - PubMed
5. 1. Cancer Res. 2012 Jan 1;72(1):210-9 - PubMed

MeSH terms

LinkOut - more resources

• Full Text Sources

  • Nature Publishing Group

• Other Literature Sources

  • The Lens - Patent Citations Database
  • scite Smart Citations

• Research Materials

  • Cellosaurus - a cell line knowledge resource