Session Item

Transforming growth factor β (TGFβ) enforces effective DNA repair by promoting homologous recombination and suppressing the use of less efficient alternative end-joining (alt-EJ). We previously translated this mechanistic relationship into gene expression signatures of chronic TGFβ signaling and alt-EJ DNA repair to establish a score, βAlt, that predicts patient outcomes in response to genotoxic cancer therapy with radiation or platinum chemotherapy (doi: 10.1126/scitranslmed.abc4465). Here we sought to verify this biology in live human tumors and to further refine the βAlt biomarker to improve its predictive capacity. 

Explants of head and neck squamous cell carcinoma (HNSC) tumors and patient-derived xenographs were immunostained to measure TGFβ signaling, indicated by SMAD2 phosphorylation, and unrepaired DNA damage, indicated by persistent 53BP1 foci at 5 hours after 5 Gy irradiation. Each signature gene was then weighted by its association with percent pSMAD2 and 53BP1 positive cells, as well as by its centrality degree within their respective gene coexpression network. These results were used to define a modified score, βAlt_w, based on the sum of gene expression levels multiplied by their estimated weights. The βAlt_w score was compared to the original βAlt biomarker for association with patients’ response to genotoxic therapies and validated in independent datasets.  

Most TGFβ genes were positively correlated with the frequency of pSMAD2 positive cells (37/50) and negatively correlated with 53BP1 positive cells (36/50), whereas most alt-EJ genes were positively correlated with residual DNA damage marked by 53BP1 (30/36) and negatively correlated with pSMAD2 (31/36), supporting that the signatures accurately report TGFβ signaling competency and inefficient DNA repair, respectively. As expected, βAlt_w was correlated with the surviving fraction after exposure to 2 Gy of NCI-60 pancancer cell lines (Spearman correlation coefficient = -0.36, P = 0.005). βAlt_w predicted overall survival in TCGA pancancer patients whose standard of care includes radiotherapy and/or genotoxic chemotherapy based on their cancer type and stage (P<0.001; Figure 1); its performance was significantly superior to the original βAlt (P < 0.001; Figure 1). The association between the βAlt_w and survival was significant in three HNSC and ovarian cancer patients data sets: HNSC GSE41613 (P = 0.015; Figure 2B), HNSC TCGA (P = 0.019; Figure 2A), and ovarian cancer GSE41613 (P = 0.036; Figure 2C,D). 

The integration of biological response and signature expression validates TGFβ competency as a key mediator of DNA repair. If prospectively validated, βAlt_w could be a useful biomarker to assist in clinical decision-making to personalize treatment.