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Updated: Jan 19, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing
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Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

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Association of copy number alterations with the immune transcriptomic landscape in cancer

Stefan Loipfinger1, Arkajyoti Bhattacharya1, Carlos G Urzúa-Traslaviña1

  • 1Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.

NPJ Systems Biology and Applications
|January 17, 2026
PubMed

Insights

High copy number alteration (CNA) burden in tumors impedes immunotherapy response. This study reveals immune-suppressive transcriptional patterns linked to CNA burden, offering insights to enhance cancer treatment efficacy.

Area of Science:

  • Cancer genomics
  • Immunology
  • Transcriptomics

Background:

  • Tumors with high copy number alteration (CNA) burden often exhibit poor response to immune checkpoint inhibitor therapy.
  • The precise mechanisms by which CNAs influence the anti-cancer immune response remain largely unelucidated.

Purpose of the Study:

  • To elucidate the transcriptional effects of CNAs on the tumor immune microenvironment.
  • To define a comprehensive landscape of immune-related transcriptional patterns associated with CNA burden.
  • To assess the predictive power of these patterns for immunotherapy response.

Main Methods:

  • Applied consensus independent component analysis to a large dataset of 294,159 bulk transcriptomic profiles.
  • Analyzed associations between CNA burden and immune-related gene expression patterns.
  • Validated findings across different data types including bulk, single-cell, and spatial transcriptomics.

Main Results:

  • Identified novel inverse and positive associations between high CNA burden and immune-related transcriptional patterns across diverse cancer types.
  • Demonstrated that higher CNA burden correlates with increased immunosuppression, including the presence of IL-17-producing cells and regulatory T cells.
  • Established the predictive capability of these transcriptional patterns for immunotherapy response and their reproducibility.

Conclusions:

  • High CNA burden is associated with specific immune-suppressive transcriptional signatures.
  • These findings provide a valuable resource for classifying immune-related transcriptional patterns as immune-suppressive or immune-stimulatory.
  • This classification may offer strategies to improve immunotherapy efficacy in tumors characterized by high CNA burden.

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