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Stand-alone transcriptional immune response prediction in primary triple-negative breast cancer

Roostee, Suze LU orcid ; Killander, Fredrika LU ; Saghir, Hani LU ; Nacer, Deborah F LU orcid ; Häkkinen, Jari LU orcid ; Sasiain, Iñaki LU orcid ; Veerla, Srinivas LU orcid ; Vallon-Christersson, Johan LU orcid ; Loman, Niklas LU and Ohlsson, Mattias LU orcid , et al. (2025) In Cancer Research Communications
Abstract

Triple-negative breast cancer (TNBC) accounts for 10-20% of primary breast cancers and often has early relapses and aggressive progression. An activated tumour immune response can be prognostic in treatment-naive and chemotherapy-treated TNBC patients and may be assessed using gene expression data. We derived a stand-alone predictor for a proposed immunomodulatory transcriptional TNBC subtype in a training cohort of 235 patients with primary disease based on random forest modelling of RNA-sequencing data. Validation in independent TNBC cohorts totalling more than 1200 patients demonstrated that the classifier recapitulates the immunomodulatory mRNA subtype classification, is associated with elevated immune expression and diversity of... (More)

Triple-negative breast cancer (TNBC) accounts for 10-20% of primary breast cancers and often has early relapses and aggressive progression. An activated tumour immune response can be prognostic in treatment-naive and chemotherapy-treated TNBC patients and may be assessed using gene expression data. We derived a stand-alone predictor for a proposed immunomodulatory transcriptional TNBC subtype in a training cohort of 235 patients with primary disease based on random forest modelling of RNA-sequencing data. Validation in independent TNBC cohorts totalling more than 1200 patients demonstrated that the classifier recapitulates the immunomodulatory mRNA subtype classification, is associated with elevated immune expression and diversity of T-cell receptor genes, is associated with response to neoadjuvant chemotherapy, and can separate patients into subgroups with better or worse prognosis after adjuvant chemotherapy. The availability of stand-alone classifiers for mRNA-based prediction may further enhance RNA-sequencing's usability in a more routine clinical context and for translational endpoints in clinical trials.

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type
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publication status
epub
subject
in
Cancer Research Communications
external identifiers
  • pmid:41212151
ISSN
2767-9764
DOI
10.1158/2767-9764.CRC-25-0453
language
English
LU publication?
yes
id
558c11cc-9ad4-4c8e-9937-567eb5389418
date added to LUP
2025-11-19 13:38:46
date last changed
2025-11-19 14:48:44
@article{558c11cc-9ad4-4c8e-9937-567eb5389418,
  abstract     = {{<p>Triple-negative breast cancer (TNBC) accounts for 10-20% of primary breast cancers and often has early relapses and aggressive progression. An activated tumour immune response can be prognostic in treatment-naive and chemotherapy-treated TNBC patients and may be assessed using gene expression data. We derived a stand-alone predictor for a proposed immunomodulatory transcriptional TNBC subtype in a training cohort of 235 patients with primary disease based on random forest modelling of RNA-sequencing data. Validation in independent TNBC cohorts totalling more than 1200 patients demonstrated that the classifier recapitulates the immunomodulatory mRNA subtype classification, is associated with elevated immune expression and diversity of T-cell receptor genes, is associated with response to neoadjuvant chemotherapy, and can separate patients into subgroups with better or worse prognosis after adjuvant chemotherapy. The availability of stand-alone classifiers for mRNA-based prediction may further enhance RNA-sequencing's usability in a more routine clinical context and for translational endpoints in clinical trials.</p>}},
  author       = {{Roostee, Suze and Killander, Fredrika and Saghir, Hani and Nacer, Deborah F and Häkkinen, Jari and Sasiain, Iñaki and Veerla, Srinivas and Vallon-Christersson, Johan and Loman, Niklas and Ohlsson, Mattias and Staaf, Johan}},
  issn         = {{2767-9764}},
  language     = {{eng}},
  month        = {{11}},
  series       = {{Cancer Research Communications}},
  title        = {{Stand-alone transcriptional immune response prediction in primary triple-negative breast cancer}},
  url          = {{http://dx.doi.org/10.1158/2767-9764.CRC-25-0453}},
  doi          = {{10.1158/2767-9764.CRC-25-0453}},
  year         = {{2025}},
}