This study proposed to investigate the relationship of PIK3CA somatic mutations, the most common activating mutations in human breast cancer (BC), and the efficacy of neoadjuvant chemotherapy (NCT).Using a novel liquidchip technology, PIK3CA DNA somat ic mutations and HER2, PTEN, EGFR mRNA expression profiles were analyzed in formalin fixed paraffin embedded samples of 93 BC patients treated with epirubicin plus docetaxel NCT.PIK3CA mutations were found in 30 patients (32.3%), in which the point mutations of E542K, E545K, H1047L and H1047R were 4.3, 9.7, 4.3 and 14.0% respectively. The PIK3CA mutations were significantly associated with patients' clinical response; 27 of 30 PIK3CA mutated patients had either a partial or complete response (p=0.002). Multivariate analysis further confirmed that, after adjustments for age, disease stages and NCT cycles, PIK3CA was associated with clinical response (Odds Ration 0.126, 95% CI [0.029, 0.691]). However, there was no significant difference between PIK3CA mutations in pathological complete response (pCR, 7/92) and non-pCR group. Furthermore, no EGFR, KRAS and BRAF mutations were detected in any of the 93 samples.Our data for the first time suggested that PIK3CA mutation status may be a predictor for better understanding clinical response to the combination of epirubicin and docetaxel NCT in patients with BC.

activation of the DNA damage repair (DDR) response, resulting in DNA displacement to the cytosol and cGAS/STING pathway activation. The quality and quantity of tumor antigens is critical for efficient cross-presentation leading to T cell activation. We hypothesized that the transcriptional changes associated with DDR response modulate the expression of immunogenic mutations. This hypothesis is supported by recent findings that an immunogenic mutation expressed in a gene upregulated by RT was the target of CD8 T cells that developed in a non-small cell lung cancer (NSCLC) patient with a complete response to RT and ipilimumab. Materials/Methods: To analyze RT-induced transcriptome changes in NSCLC, we performed RNAseq from 2 untreated and 4 irradiated (8GyX3) patient-derived NSCLC xenografts (PDTX) implanted in NOG mice. DESeq2 was used to determine differentially expressed genes. To assess if immunogenic mutations are commonly encoded by RT-modulated genes, we used previously published data on predicted neoantigens in NSCLC patients. Results: The expression of 1,924 genes was upregulated by RT, while 921 genes were downregulated. In 32 out of 34 NSCLC patients, immunogenic mutations were present in RT-modulated genes. The number of immunogenic mutations predicted to be modulated by RT differed among patients with a median of 14, and range 0 to 79. The degree of modulation of genes encoding immunogenic mutations varied, with increased expression up to w64-folds, and decreased expression up to w128-folds. Considering the baseline expression of genes encoding immunogenic mutations in the unirradiated PDTX, we modeled the pre-and post-RT expression of these genes for each patient. Four major patterns of RT-induced modulation emerged: 1) no change; 2) emergence of a new dominant neoantigen that was not expressed at baseline (i.e., expressed at higher levels than all other immunogenic mutations); 3) increased expression of a dominant neoantigen; 4) decreased expression of a dominant neoantigen. Conclusion: Mutation-associated neoantigens are the targets of T cell responses in NSCLC patients treated with ICB. In most cases, only one or a few of the immunogenic mutations encoded in the cancer exome are recognized by T cells. One limiting factor is the level of expression of the mutated gene product, and competition for presentation by the MHC class I molecules. Our data show that RT modulates the expression of a large number of immunogenic mutations in NSCLC. We are currently testing in a prospective trial if the presence of immunogenic mutations in RT-upregulated genes predicts for RT ability to enhance responses to ICB.