Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles.
BACKGROUND
Breast cancer researchers use cell lines to model myriad phenomena ranging from DNA repair to cancer stem cell phenotypes. Though appropriate, and even requisite, for many studies, the suitability of cell lines as tumour models has come into question owing to possibilities of tissue culture artefacts and clonal selection. These issues are compounded by the inability of cancer cells grown in isolation to fully model the in situ tumour environment, which also contains a plethora of non-tumour cell types. It is thus important to understand similarities and differences between cancer cell lines and the tumours that they represent so that the optimal tumour models can be chosen to answer specific research questions.


METHODS
In the present study, we compared the RNA-sequencing transcriptomes of a collection of breast cancer cell lines to transcriptomes obtained from hundreds of tumours using The Cancer Genome Atlas. Tumour purity was accounted for by analysis of stromal and immune scores using the ESTIMATE algorithm so that differences likely resulting from non-tumour cells could be accounted for.


RESULTS
We found the transcriptional characteristics of breast cancer cell lines to mirror those of the tumours. We identified basal and luminal cell lines that are most transcriptionally similar to their respective breast tumours. Our comparison of expression profiles revealed pronounced differences between breast cancer cell lines and tumours, which could largely be attributed to the absence of stromal and immune components in cell culture. A focus on the Wnt pathway revealed the transcriptional downregulation or absence of several secreted Wnt antagonists in culture. Gene set enrichment analysis suggests that cancer cell lines have enhanced proliferation and glycolysis independent of stromal and immune contributions compared with breast cancer cells in situ.


CONCLUSIONS
This study demonstrates that many of the differences between breast cancer cell lines and tumours are due to the absence of stromal and immune components in vitro. Hence, extra precautions should be taken when modelling extracellular proteins in vitro. The specific differences discovered emphasize the importance of choosing an appropriate model for each research question.
Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 114th St and 87th Avenue, Edmonton, AB, T6G 2E1, Canada. kvincent@ualberta.ca.|Department of Anatomy and Cell Biology, Faculty of Medicine and Dentistry, University of Western Ontario, 1151 Richmond Street, London, ON, N6A 3K7, Canada. kvincent@ualberta.ca.
Krista Marie
KM
Vincent
Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 114th St and 87th Avenue, Edmonton, AB, T6G 2E1, Canada. sfindla@uwo.ca.|Department of Anatomy and Cell Biology, Faculty of Medicine and Dentistry, University of Western Ontario, 1151 Richmond Street, London, ON, N6A 3K7, Canada. sfindla@uwo.ca.
Scott D
SD
Findlay
Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 114th St and 87th Avenue, Edmonton, AB, T6G 2E1, Canada. postovit@ualberta.ca.
Lynne Marie
LM
Postovit
D001943:Breast Neoplasms / Q000235:genetics*; D045744:Cell Line, Tumor; D015536:Down-Regulation / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D006801:Humans; D014411:Neoplastic Stem Cells / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
D012333:RNA, Messenger