Transcriptomic expression of immunological markers associated with pathological complete response in patients with triple negative breast cancer in NACATRINE trial

The NACATRINE trial aims to evaluate the addition of carboplatin in patients with triple negative breast cancer (TNBC) in the neoadjuvant setting. Obtaining pathological complete response (pCR) is an important prognostic outcome for these patients. Studies have shown that immunological parameters are relevant to the response to neoadjuvant chemotherapy (NAC) in breast cancer. In this study, we performed an analysis of immunological biomarkers based on gene expression to identify markers that can predict pCR in patients with TNBC receiving NAC with anthracycline and taxane-based regimens with or without carboplatin. We evaluated the expression of immune-related genes in TNBC in untreated samples to associate with the outcome of NAC. The RNA was extracted from tissue biopsy and the gene expression was analyzed by nCounter® Breast Cancer™ (34 genes related to the immune system) panel. The data were submitted to a normalization step, to correct the experimental variables among the samples. This step was performed using the package NanoStringNorm, in the statistical-mathematical environment R. The gene counts were normalized by housekeeping. For statistical significance, the T-test was used with p-value <0.05 and fold-change ≥2. For statistical analyses, SPSS software version 23 was used. A total of 66 tissue samples from unique patients were included. We identified ten genes (APOE, CD27, CD8A, CMKLR1, CXCL9, CYBB, GZMA, NKG7, STAT1, TIGIT) that when overexpressed were associated with pCR (FDR adjusted p< 0.05), with sensitivity and specificity values greater than or equal to 70% and 60%, respectively. The univariate logistic regression model demonstrated that the overexpression of the immunological marker CXCL9 was significant (odds ratio [OR] = 5.684, 95% CI = 1.64 - 9.90, p = 0.006) to predict pCR. The CXCL9 gene had 79% sensitivity and 61% specificity with an AUC of 0.7. In conclusion, we describe a set of immunological genes that when overexpressed predict the outcome of neoadjuvant chemotherapy in TNBC. Suggesting that these markers can be used to select patients who would benefit from NAC.