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

Marcel Smid, F. Germán Rodríguez-González, Anieta M. Sieuwerts, Roberto Salgado, Wendy J C Prager-Van Der Smissen, Michelle Van Der Vlugt-Daane, Anne Van Galen, Serena Nik-Zainal, Johan Staaf, Arie B. Brinkman, Marc J. Van De Vijver, Andrea Richardson, Aquila Fatima, Kim Berentsen, Adam Butler, Sancha Martin, Helen R. Davies, Reno Debets, Marion E Meijer Van Gelder, Carolien H M Van Deurzen & 27 others Gaëtan Macgrogan, Gert G G M Van Den Eynden, Colin Purdie, Alastair M. Thompson, Carlos Caldas, Paul N. Span, Peter T. Simpson, Sunil R. Lakhani, Steven Van Laere, Christine Desmedt, Markus Ringnér, Stefania Tommasi, Jorunn Eyford, Annegien Broeks, Anne Vincent-Salomon, P. Andrew Futreal, Stian Knappskog, Tari King, Gilles Thomas, Alain Viari, Anita Langerød, Anne Lise Børresen-Dale, Ewan Birney, Hendrik G. Stunnenberg, Mike Stratton, John A. Foekens, John W M Martens

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number12910
JournalNature Communications
Volume7
DOIs
StatePublished - Sep 26 2016
Externally publishedYes

Fingerprint

genome
infiltration
Transcriptome
Infiltration
breast
Substitution reactions
Genes
gene expression
cancer
signatures
Genome
substitutes
Breast Neoplasms
Aberrations
Tumor-Infiltrating Lymphocytes
Gene Expression
Gene expression
cdc Genes
aberration
cells

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Smid, M., Rodríguez-González, F. G., Sieuwerts, A. M., Salgado, R., Prager-Van Der Smissen, W. J. C., Vlugt-Daane, M. V. D., ... Martens, J. W. M. (2016). Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration. Nature Communications, 7, [12910]. https://doi.org/10.1038/ncomms12910

Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration. / Smid, Marcel; Rodríguez-González, F. Germán; Sieuwerts, Anieta M.; Salgado, Roberto; Prager-Van Der Smissen, Wendy J C; Vlugt-Daane, Michelle Van Der; Van Galen, Anne; Nik-Zainal, Serena; Staaf, Johan; Brinkman, Arie B.; Van De Vijver, Marc J.; Richardson, Andrea; Fatima, Aquila; Berentsen, Kim; Butler, Adam; Martin, Sancha; Davies, Helen R.; Debets, Reno; Gelder, Marion E Meijer Van; Van Deurzen, Carolien H M; Macgrogan, Gaëtan; 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; Ringnér, Markus; Tommasi, Stefania; Eyford, Jorunn; Broeks, Annegien; Vincent-Salomon, Anne; Futreal, P. Andrew; Knappskog, Stian; King, Tari; Thomas, Gilles; Viari, Alain; Langerød, Anita; Børresen-Dale, Anne Lise; Birney, Ewan; Stunnenberg, Hendrik G.; Stratton, Mike; Foekens, John A.; Martens, John W M.

In: Nature Communications, Vol. 7, 12910, 26.09.2016.

Research output: Contribution to journalArticle

Smid, M, Rodríguez-González, FG, Sieuwerts, AM, Salgado, R, Prager-Van Der Smissen, WJC, Vlugt-Daane, MVD, Van Galen, A, Nik-Zainal, S, Staaf, J, Brinkman, AB, Van De Vijver, MJ, Richardson, A, Fatima, A, Berentsen, K, Butler, A, Martin, S, Davies, HR, Debets, R, Gelder, MEMV, Van Deurzen, CHM, Macgrogan, G, Van Den Eynden, GGGM, Purdie, C, Thompson, AM, Caldas, C, Span, PN, Simpson, PT, Lakhani, SR, Van Laere, S, Desmedt, C, Ringnér, M, Tommasi, S, Eyford, J, Broeks, A, Vincent-Salomon, A, Futreal, PA, Knappskog, S, King, T, Thomas, G, Viari, A, Langerød, A, Børresen-Dale, AL, Birney, E, Stunnenberg, HG, Stratton, M, Foekens, JA & Martens, JWM 2016, 'Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration', Nature Communications, vol. 7, 12910. https://doi.org/10.1038/ncomms12910
Smid M, Rodríguez-González FG, Sieuwerts AM, Salgado R, Prager-Van Der Smissen WJC, Vlugt-Daane MVD et al. Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration. Nature Communications. 2016 Sep 26;7. 12910. https://doi.org/10.1038/ncomms12910
Smid, Marcel ; Rodríguez-González, F. Germán ; Sieuwerts, Anieta M. ; Salgado, Roberto ; Prager-Van Der Smissen, Wendy J C ; Vlugt-Daane, Michelle Van Der ; Van Galen, Anne ; Nik-Zainal, Serena ; Staaf, Johan ; Brinkman, Arie B. ; Van De Vijver, Marc J. ; Richardson, Andrea ; Fatima, Aquila ; Berentsen, Kim ; Butler, Adam ; Martin, Sancha ; Davies, Helen R. ; Debets, Reno ; Gelder, Marion E Meijer Van ; Van Deurzen, Carolien H M ; Macgrogan, Gaëtan ; 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 ; Ringnér, Markus ; Tommasi, Stefania ; Eyford, Jorunn ; Broeks, Annegien ; Vincent-Salomon, Anne ; Futreal, P. Andrew ; Knappskog, Stian ; King, Tari ; Thomas, Gilles ; Viari, Alain ; Langerød, Anita ; Børresen-Dale, Anne Lise ; Birney, Ewan ; Stunnenberg, Hendrik G. ; Stratton, Mike ; Foekens, John A. ; Martens, John W M. / Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration. In: Nature Communications. 2016 ; Vol. 7.
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