Evaluating cell lines as tumour models by comparison of genomic profiles

By Silvia Domcke, Rileen Sinha, D. Levine, Christopher Sander, Nikolaus Schultz. Nature Communications, 2013

1,358 citations recorded by the source corpus.

Cancer cell lines are frequently used as in vitro tumour models. Recent molecular profiles of hundreds of cell lines from The Cancer Cell Line Encyclopedia and thousands of tumour samples from the Cancer Genome Atlas now allow a systematic genomic comparison of cell lines and tumours. Here we analyse a panel of 47 ovarian cancer cell lines and identify those that have the highest genetic similarity to ovarian tumours. Our comparison of copy-number changes, mutations and mRNA expression profiles reveals pronounced differences in molecular profiles between commonly used ovarian cancer cell lines and high-grade serous ovarian cancer tumour samples. We identify several rarely used cell lines that more closely resemble cognate tumour profiles than commonly used cell lines, and we propose these lines as the most suitable models of ovarian cancer. Our results indicate that the gap between cell lines and tumours can be bridged by genomically informed choices of cell line models for all tumour types. Cell lines are widely used in cancer research to study tumour biology. Here Domcke et al.compare genomic data from ovarian cancer cell lines with those from clinical ovarian tumour samples and identify cell lines that most closely resemble the genomic features of high-grade serous ovarian cancer.

Subfields: Cancer Research, Pathology and Forensic Medicine, Reproductive Medicine

View Paper: https://www.semanticscholar.org/paper/2c2d806920f97804099b7c9be81100727c500a4f

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In Cancer Research

In Pathology and Forensic Medicine

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Citations in the corpus

Cholangiocarcinoma 2020: the next horizon in mechanisms and management (2020, positive): “In vitro cell lines, mainly derived from human CCA specimens, have been used widely as a tool to study this disease 76,233–235 .”
A survey of current trends in computational drug repositioning (2016, background): “Half of the hepatocelluar carcinoma (HCC) cell lines are not significantly correlated to the HCC tumors from TCGA, while a few rarely used ovarian cancer cell lines more closely resemble ovarian tumor profiles than common used cell lines [87].”
Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses (2015, neutral): “Domcke et al., 2013).”
Loss of BRCA1 in the cells of origin of ovarian cancer induces glycolysis: A window of opportunity for ovarian cancer chemoprevention (2017, background): “Three cell lines that represent high-grade serous ovarian cancer (TYK-nu, SNU119, and Kuramochi) were selected: all have wild-type BRCA1 (26).”
Concise Polygenic Models for Cancer-Specific Identification of Drug-Sensitive Tumors from Their Multi-Omics Profiles (2020, background): “Despite these issues, several cell lines have proven to be relevant by retaining sufficient correlation to primary tumors [55,57,58].”
In Vitro Tumor Models: Advantages, Disadvantages, Variables, and Selecting the Right Platform (2016, methodology): “…Cell Line Encyclopedia (Barretina et al., 2012), and these profiles can be compared to the profiles of a large number of human tumors, compiled as part of the Cancer Genome Atlas Research Network (Holliday and Speirs, 2011; Cancer Genome Atlas Research Network et al., 2013; Domcke et al., 2013).”