Oncotarget

Research Papers:

Methylation of RAD51B, XRCC3 and other homologous recombination genes is associated with expression of immune checkpoints and an inflammatory signature in squamous cell carcinoma of the head and neck, lung and cervix

Damian T. Rieke _, Sebastian Ochsenreither, Konrad Klinghammer, Tanguy Y. Seiwert, Frederick Klauschen, Inge Tinhofer and Ulrich Keilholz

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Oncotarget. 2016; 7:75379-75393. https://doi.org/10.18632/oncotarget.12211

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Abstract

Damian T. Rieke1, Sebastian Ochsenreither1,2, Konrad Klinghammer2, Tanguy Y. Seiwert3, Frederick Klauschen4, Inge Tinhofer5,6, Ulrich Keilholz1,2

1Charité Comprehensive Cancer Center, Charité – Universitätsmedizin Berlin, Berlin, Germany

2Department of Hematology and Medical Oncology, Campus Benjamin Franklin, Charité – Universitätsmedizin Berlin, Berlin, Germany

3Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA

4Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany

5Department of Radiooncology and Radiotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany

6German Cancer Research Center Heidelberg (DKFZ)/German Cancer Consortium (DKTK) partner site Berlin, Berlin, Germany

Correspondence to:

Damian T. Rieke, email: damian.rieke@charite.de

Keywords: HRD, DNA repair, immune checkpoints, inflamed gene expression signature, immune therapy

Received: July 13, 2016    Accepted: September 07, 2016    Published: September 23, 2016

ABSTRACT

Immune checkpoints are emerging treatment targets, but mechanisms underlying checkpoint expression are poorly understood. Since alterations in DNA repair genes have been connected to the efficacy of checkpoint inhibitors, we investigated associations between methylation of DNA repair genes and CTLA4 and CD274 (PD-L1) expression.

A list of DNA repair genes (179 genes) was selected from the literature, methylation status and expression of inflammation-associated genes (The Cancer Genome Atlas data) was correlated in head and neck squamous cell carcinoma (HNSCC), cervical and lung squamous cell carcinoma.

A significant positive correlation of the methylation status of 15, 3 and 2 genes with checkpoint expression was identified, respectively. RAD51B methylation was identified in all cancer subtypes. In HNSCC and cervical cancer, there was significant enrichment for homologous recombination genes. Methylation of the candidate genes was also associated with expression of other checkpoints, ligands, MHC- and T-cell associated genes as well as an interferon-inflammatory immune gene signature, predictive for the efficacy of PD-1 inhibition in HNSCC.

Homologous recombination deficiency might therefore be mediated by DNA repair gene hypermethylation and linked to an immune-evasive phenotype in SCC. The methylation status of these genes could represent a new predictive biomarker for immune checkpoint inhibition.


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