Concurrent mutations associated with trastuzumab-resistance revealed by single cell sequencing

HER2-positive breast cancer patients benefit from HER2-targeted therapies, among which the most commonly used is trastuzumab. However, acquired resistance typically happens within one year. The cellular heterogeneity of it less clear. Here we generated trastuzumab-resistant cells in two cell lines, SK-BR-3 and BT-474. Cells at different time points during induction were examined by exome sequencing to study changes genomic alterations over time. Single cell-targeted was also identify resistance-associated concurrent mutations. We found a rapid increase copy number variation (CNV) regions gradual accumulation single nucleotide variations (SNVs). On pathway level, non-synonymous SNVs for enriched MAPK signaling pathway, while BT-474 they mTOR PI3K-Akt pathways. all three pathways downstream HER2 kinase. Putative trastuzumab-resistance-associated included AIFM1 P548L ERBB2 M833R cells, ADAMTS19 V451L, OR5M9 D230N, COL9A1 R627T, ITGA7 H911Q cells. Single-cell-targeted identified several By validation, that mutations (AIFM1 IL1RAPL2 S546C MFSD11 L242I ANAPC4 E16K cells) led decrease trastuzumab sensitivity. Taken together, our revealed common level trastuzumab-resistance mechanism In addition, identification associated with may be indicative potential targets treatment patients.