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

Area of Science:

• Oncology
• Genomics
• Molecular Biology

Background:

• HER2-positive breast cancer is treated with HER2-targeted therapies like trastuzumab.
• Acquired resistance to trastuzumab develops rapidly, often within a year.
• The cellular and genomic heterogeneity underlying trastuzumab resistance remains unclear.

Purpose of the Study:

• To investigate the genomic alterations and cellular heterogeneity associated with acquired trastuzumab resistance in HER2-positive breast cancer.
• To identify specific mutations and pathways involved in the development of trastuzumab resistance.

Main Methods:

• Generated trastuzumab-resistant cell lines from SK-BR-3 and BT-474 HER2-positive breast cancer cell lines.
• Utilized exome sequencing to track genomic changes during resistance induction.
• Employed single-cell-targeted sequencing to identify concurrent mutations linked to resistance.

Main Results:

• Observed rapid increases in copy number variations (CNVs) and gradual accumulation of single nucleotide variations (SNVs).
• Identified pathway enrichment in MAPK, mTOR, and PI3K-Akt signaling pathways, all downstream of HER2.
• Validated specific concurrent mutations (e.g., AIFM1 P548L, MFSD11 L242I) that decrease trastuzumab sensitivity.

Conclusions:

• Established a common pathway-level resistance mechanism to trastuzumab in HER2-positive breast cancer.
• Highlighted the significance of concurrent SNVs as potential therapeutic targets for trastuzumab-resistant breast cancer.