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Predictive Immune Modeling of Solid Tumors
Published on: February 25, 2020
EZH2-Associated Hypermethylated Gene Signature Predicts Immunotherapy Response and Implicates DUSP5 in Tumor-Immune
Mingzhan Xue1, Sujitha Jeya1, Reem Elasad1
1Translational Oncology Research Centre, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar.
Abstract:
Background/Objectives: Triple-negative breast cancer (TNBC) is a candidate for immune checkpoint blockade; however, current biomarkers remain insufficient to predict therapeutic response or capture tumor-intrinsic mechanisms. Enhancer of Zeste Homolog 2 (EZH2)-mediated epigenetic repression has been implicated in immune evasion, yet the contribution of EZH2-repressed genes to anti-tumor immunity and clinical outcomes in TNBC remains unclear. We aimed to identify EZH2-associated epigenetically repressed genes in TNBC and evaluate their relevance as tumor-intrinsic regulators and potential predictors of immunotherapy outcome. Methods: We performed integrative in silico analyses of The Cancer Genome Atlas (TCGA) breast cancer cohorts to identify EZH2-associated hypermethylated genes in TNBC. A composite 30-gene signature (30GS) was defined based on transcriptional repression and promoter hypermethylation. Associations with clinical outcomes, tumor- and immune-related programs, and therapeutic response were evaluated, with validation in the I-SPY2 cohort and an independent TNBC patient cohort. Results: The 30GS was significantly reduced in TNBC and basal-like tumors and associated with improved clinical outcomes and enrichment of tumor- and immune-related signatures. In the I-SPY2 cohort, the 30GS predicted pathological complete response in patients receiving chemo-immunotherapy (AUC = 0.7377, p = 0.0007). Gene-level analysis identified Dual Specificity Phosphatase 5 (DUSP5) as the gene most consistently associated with immune-related parameters. In an independent TNBC cohort, DUSP5-high tumors demonstrated transcriptional programs enriched for inflammatory, immune-related, and signaling pathways within the NanoString Breast Cancer 360 panel. Conclusions: This study defines an EZH2-associated epigenetic program linked to tumor-intrinsic immune programs in TNBC and identifies DUSP5 as a candidate gene associated with immune-related transcriptional states.
Insights
This study identifies an epigenetic signature in triple-negative breast cancer (TNBC) linked to immune evasion. The Dual Specificity Phosphatase 5 (DUSP5) gene may predict immunotherapy response in TNBC patients.
Area of Science:
- Oncology
- Epigenetics
- Immunotherapy
Background:
- Triple-negative breast cancer (TNBC) is a target for immune checkpoint blockade, but biomarkers for treatment response are lacking.
- Enhancer of Zeste Homolog 2 (EZH2)-mediated repression contributes to immune evasion, but its role in TNBC immunity and outcomes is unclear.
Purpose of the Study:
- Identify EZH2-repressed genes in TNBC.
- Evaluate their role in anti-tumor immunity and as predictors of immunotherapy response.
Main Methods:
- In silico analysis of TCGA breast cancer cohorts to find EZH2-associated hypermethylated genes.
- Defined a 30-gene signature (30GS) based on repression and hypermethylation.
- Validated associations with outcomes and immunotherapy response in I-SPY2 and independent TNBC cohorts.
Main Results:
- The 30GS was reduced in TNBC and associated with better outcomes and immune signatures.
- The 30GS predicted pathological complete response to chemo-immunotherapy in the I-SPY2 cohort (AUC=0.7377).
- Dual Specificity Phosphatase 5 (DUSP5) was strongly linked to immune parameters; high DUSP5 correlated with immune-related pathways in TNBC.
Conclusions:
- An EZH2-associated epigenetic program influences tumor-intrinsic immunity in TNBC.
- DUSP5 is a potential biomarker for immune-related transcriptional states and immunotherapy response in TNBC.
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