HER2+ breast cancer specific hypoxia-associated molecular alterations and vulnerabilities in METABRIC cohort – bioinformatic analysis

Even the best available therapy delivers sub-optimal results in locally advanced/metastatic HER2+ breast cancer (BRCA) patients. Moreover, efficacy of individual anti-HER2 agents is short-lived, especially in recurrence after trastuzumab therapy. Therefore novel therapeutic approaches for HER2+ BRCA are needed. Up to 70% of BRCA cases in recent studies displayed high to intermediate hypoxia scores. The aim of this study was to identify potential hypoxia-associated biomarkers and vulnerabilities in HER2+ BRCA samples of METABRIC data. This study is a part of RSU grant No. 5-1/252/2020 “Hypoxia-associated biomarkers in HER2+ breast cancer cell lines for personalized therapy” METABRIC data was accessed through the European Genome-phenome Archive. Unless specified otherwise, data manipulation was done with R, v.3.4. Data was adjusted for influence of confounding factors with PEER, v.1.2. Only samples that had information on all chosen covariates were kept for adjusting. Samples were scored as corresponding to low, intermediate and high hypoxia with the use of 15-gene hypoxia signature [PMID: 20087356] by unsupervised hierarchical clustering analysis with ‘ward.D’ as method. Differential expression analysis was done using ‘LIMMA’. Gene names were mapped to probes using annotations from ‘illuminaHumanv3.db’ package. 142 samples from METABRIC validation set and 136 samples from discovery set matched at least 2 HER2 overexpression criteria (ERBB2ampl, PAM50, 3gene classifier, HER2expr). 78 genes were significantly (logFC ≥ |1|, adj.p<0.05) associated with hypoxia score. 26 downregulated genes are involved in estrogen-mediated signalling, FOXA1 transcription factor network and nuclear SMAD2/3 signaling, while 52 upregulated genes are associated with glycolysis and gluconeogenesis, vitamin D receptor pathway, beta1 and beta3 integrin cell surface interactions, HIF-1 and HIF-2 signaling pathways. Use of open-access data allowed to identify several potential markers and vulnerabilities in hypoxic HER2+ BRCA, that remain to be experimentally validated in HER2+ BRCA cell lines for development of personalized approach to HER2+ BRCA management.