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Chromosome 9p copy number gains involving PD-L1 are associated with a specific proliferation and immune-modulating

Jan Budczies1,2, Carsten Denkert3,4, Balázs Győrffy5,6

  • 1Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany. jan.budczies@charite.de.

BMC Medical Genomics
|December 8, 2017
PubMed
Abstract

Insights

Copy number gains in chromosome 9p, including PD-L1, are linked to immune escape and proliferation in various cancers. This study identifies key genes and pathways for potential new cancer immunotherapies.

Area of Science:

  • Oncology
  • Genomics
  • Immunology

Background:

  • Immune checkpoint inhibition (PD-L1/PD-1 axis) is a key cancer immunotherapy strategy.
  • Biomarkers are needed to identify patient subpopulations who benefit from immunotherapy.
  • Recurrent copy number gains (CNG) on chromosome 9p, involving PD-L1, are observed in multiple cancer types.

Purpose of the Study:

  • To investigate global mRNA expression changes associated with chromosome 9p gains using functional genomics.
  • To identify genes and biological pathways affected by chromosome 9p gains across diverse cancers.

Main Methods:

  • Applied functional genomics to analyze mRNA expression data.
  • Utilized The Cancer Genome Atlas (TCGA) dataset.
  • Identified 75 genes significantly up-regulated in tumors with chromosome 9p gains.

Main Results:

  • Identified gene sets enriched for chromosome 9p, particularly 9p24.
  • Discovered enrichment of cell cycle regulation (22 genes) and immune system modulation (16 genes) expression programs.
  • Found key immunoregulatory genes (e.g., CCL4, CXCL10, IFN-G, IDO1) and proliferation-related kinases (e.g., PLK1, TTK) as potential drug targets.

Conclusions:

  • Chromosome 9p gains contribute to immune escape and proliferation in cancers with PD-L1 CNG.
  • Identified novel therapeutic vulnerabilities for exploiting these mechanisms.
  • Highlights the potential of targeting identified genes for cancer treatment.
Keywords:
CancerChromosome 9p gainDNA copy number alterationsImmunotherapyPD-L1

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