Poor prognosis breast cancers are treated with cytotoxic chemotherapy, but often without any guidance from therapy predictive markers since universally-accepted markers are not currently available. Treatment failure, in the form of recurrences, is relatively common. We aimed to identify chemotherapy predictive markers and resistance pathways in breast cancer. Our hypothesis was that tumour cells remaining after neoadjuvant chemotherapy (NAC) contain somatic variants causing therapy resistance, while variants present pre-NAC but lost post-NAC cause sensitivity. Whole exome sequencing was performed on matched pre- and post-NAC cancer cells, which were isolated by laser microdissection, from 6 cancer cases, and somatic variants selected for or against by NAC were identified. Somatic variant diversity was significantly reduced after therapy (p<0.05). MUC17 variants were identified in 3 tumours and were selected against by NAC in each case, while PCNX1 variants were identified in 2 tumours and were selected for in both cases, implicating the function of these genes in defining chemoresponse. In vitro knock-down of MUC17 or PCNX1 was associated with significantly increased or decreased chemotherapy sensitivity respectively (p<0.05), further supporting their roles in chemotherapy response. Expression was tested for predictive value in two independent cohorts of chemotherapy-treated breast cancers (n=53, n=303). Kaplan-Meier analyses revealed that low MUC17 expression was significantly associated with longer survival after chemotherapy, while low PCNX1 was significantly associated with reduced survival. We concluded that therapy-driven selection of somatic variants allows identification of chemotherapy response genes. With respect to MUC17 and PCNX1, therapy-driven selection acting on somatic variants, in vitro knock-down data concerning drug sensitivity, and survival analysis of expression levels in patient cohorts all define the genes as mediators of and predictive markers for chemotherapy response in breast cancer.
CORE (COnnecting REpositories)
CORE (COnnecting REpositories)