Analysis of the Radiosensitivity Index (RSI) in Paired Pre- and Post-Neoadjuvant Therapy Triple-Negative Breast Cancer.

Abstract

Purpose: The radiosensitivity index (RSI) is a validated gene expression-based biomarker that can predict intrinsic radiosensitivity and has been shown to be associated with local control in triple-negative breast cancer (TNBC) patients treated with upfront surgery. Currently, most patients with TNBC receive neoadjuvant systemic therapy (NAST). Whether the RSI predicts response to NAST and how the RSI and predicted radiosensitivity are altered by exposure to NAST is unknown.

Methods: Total RNA was extracted from pre-treatment core needle biopsy specimens from 197 TNBC patients treated on the *** (***) and *** (***) trials. Total RNA was also extracted from paired post-NAST (residual disease) tumor tissue on 58 patients. A published algorithm using 10 genes was used to compute the RSI for each tumor. Stromal tumor infiltrating lymphocytes (sTILs) were scored on pre-treatment and post-NAST samples by one expert breast pathologist according to international consensus guidelines. CIBERSORTx was used to impute leukocyte fractions in samples using RNA sequencing data.

Results: Cluster analysis of RSI genes in pre-treatment samples revealed immune-depleted (RSI-iD) and immune-enriched (RSI-iE) groups, and this classification was strongly associated with sTIL infiltration (P<0.0001) and likelihood of achieving pathologic complete response (pCR) (P=0.001). RSI showed associations (FDR q<0.01) with M0 and M1 macrophages, CD4+ memory resting, CD4+ memory activated, CD8+, and follicular helper T-cells, activated NK cells, naïve and memory B cells, and resting dendritic cells on CIBERSORTx leukocyte deconvolution. In the entire cohort, NAST-induced change in RSI was variable, but amongst initially RSI-iE tumors that did not achieve pCR, there was a significant decrease in predicted radiosensitivity between paired pre-treatment and post-NAST samples. NAST-induced reduction in sTILs and naïve B cells may be associated with this decrease in radiosensitivity.

Conclusions: Pre-treatment RSI cluster identity is associated with the degree of immune enrichment and response to NAST in TNBC. Initially immune-enriched TNBCs that do not achieve a pathologic complete response to NAST exhibit a decrease in predicted radiosensitivity compared to paired pre-treatment tumors.