Validation of Anticorrelated TGFb Signaling and Alternative End-Joining DNA Repair Signatures that Predict Response to Genotoxic Cancer Therapy

Abstract

Purpose: Loss of TGFb signaling increases error-prone alternative end-joining (alt-EJ) DNA repair. We previously translated this mechanistic relationship as TGFb and alt-EJ gene expression signatures, which we showed are anticorrelated across cancer types. A score representing anticorrelation, bAlt, predicts patient outcome in response to genotoxic therapy. Here we sought to verify this biology in live specimens and additional datasets. Experimental Design: Human head and neck squamous carcinoma (HNSC) explants were treated in vitro to test whether the signatures report TGFb signaling, indicated by SMAD2 phosphor-ylation, and unrepaired DNA damage, indicated by persistent 53BP1 foci after irradiation or olaparib. A custom NanoString assay was implemented to analyze the signatures’ expression in explants. Each signature gene was then weighted by its association with functional responses to define a modified score, bAltw, that was retested for association with response to genotoxic therapies in independent datasets. Results: Most genes in each signature were positively correlated with the expected biological response in tumor explants. Anticorrelation of TGFb and alt-EJ signatures measured by NanoString was confirmed in explants. bAltw was significantly (P < 0.001) better than bAlt in predicting overall survival in response to genotoxic therapy in The Cancer Genome Atlas (TCGA) pancancer patients and in independent HNSC and ovarian cancer patient datasets. Conclusions: Association of the TGFb and alt-EJ signatures with their biological response validates TGFb competency as a key mediator of DNA repair that can be readily assayed by gene expression. The predictive value of bAltw supports its development to assist in clinical decision making.