Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration

Smid, Marcel, Rodriguez-Gonzalez, F. German, Sieuwerts, Anieta M., Salgado, Roberto, Prager-Van Der Smissen, Wendy J. C., van der Vlugt-Daane, Michelle, Van Galen, Anne, Nik-Zainal, Serena, Staaf, Johan, Brinkman, Arie B., Van De Vijver, Marc J., Richardson, Andrea L., Fatima, Aquila, Berentsen, Kim, Butler, Adam, Martin, Sancha, Davies, Helen R., Debets, Reno, Meijer-Van Gelder, Marion E., Van Deurzen, Carolien H. M., Macgrogan, Gaeetan, Van Den Eynden, Gert G. G. M., Purdie, Colin, Thompson, Alastair M., Caldas, Carlos, Span, Paul N., Simpson, Peter T., Lakhani, Sunil R., Van Laere, Steven, Desmedt, Christine, Ringner, Markus, Tommasi, Stefania, Eyford, Jorunn, Broeks, Annegien, Vincent-Salomon, Anne, Futreal, P. Andrew, Knappskog, Stian, King, Tari, Thomas, Gilles, Viari, Alain, Langerod, Anita, Borresen-Dale, Anne-Lise, Birney, Ewan, Stunnenberg, Hendrik G., Stratton, Mike, Foekens, John A. and Martens, John W. M. (2016) Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration. Nature Communications, 7 12910.1-12910.9. doi:10.1038/ncomms12910


Author Smid, Marcel
Rodriguez-Gonzalez, F. German
Sieuwerts, Anieta M.
Salgado, Roberto
Prager-Van Der Smissen, Wendy J. C.
van der Vlugt-Daane, Michelle
Van Galen, Anne
Nik-Zainal, Serena
Staaf, Johan
Brinkman, Arie B.
Van De Vijver, Marc J.
Richardson, Andrea L.
Fatima, Aquila
Berentsen, Kim
Butler, Adam
Martin, Sancha
Davies, Helen R.
Debets, Reno
Meijer-Van Gelder, Marion E.
Van Deurzen, Carolien H. M.
Macgrogan, Gaeetan
Van Den Eynden, Gert G. G. M.
Purdie, Colin
Thompson, Alastair M.
Caldas, Carlos
Span, Paul N.
Simpson, Peter T.
Lakhani, Sunil R.
Van Laere, Steven
Desmedt, Christine
Ringner, Markus
Tommasi, Stefania
Eyford, Jorunn
Broeks, Annegien
Vincent-Salomon, Anne
Futreal, P. Andrew
Knappskog, Stian
King, Tari
Thomas, Gilles
Viari, Alain
Langerod, Anita
Borresen-Dale, Anne-Lise
Birney, Ewan
Stunnenberg, Hendrik G.
Stratton, Mike
Foekens, John A.
Martens, John W. M.
Title Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration
Journal name Nature Communications   Check publisher's open access policy
ISSN 2041-1723
Publication date 2016-09-26
Year available 2016
Sub-type Article (original research)
DOI 10.1038/ncomms12910
Open Access Status DOI
Volume 7
Start page 12910.1
End page 12910.9
Total pages 9
Place of publication London, United Kingdom
Publisher Nature Publishing Group
Collection year 2017
Language eng
Formatted abstract
A recent comprehensive whole genome analysis of a large breast cancer cohort was used to link known and novel drivers and substitution signatures to the transcriptome of 266 cases. Here, we validate that subtype-specific aberrations show concordant expression changes for, for example, TP53, PIK3CA, PTEN, CCND1 and CDH1. We find that CCND3 expression levels do not correlate with amplification, while increased GATA3 expression in mutant GATA3 cancers suggests GATA3 is an oncogene. In luminal cases the total number of substitutions, irrespective of type, associates with cell cycle gene expression and adverse outcome, whereas the number of mutations of signatures 3 and 13 associates with immune-response specific gene expression, increased numbers of tumour-infiltrating lymphocytes and better outcome. Thus, while earlier reports imply that the sheer number of somatic aberrations could trigger an immune-response, our data suggests that substitutions of a particular type are more effective in doing so than others.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

 
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