Abstract 3874: Genomic mechanisms of resistance to tyrosine kinase inhibitors (TKIs) in HER2+ metastatic breast cancer (HER2+ MBC)
Authors: Parsons Heather A. , Messer Conor , Santos Katheryn , Danysh Brian P. , Hughes Melissa E. , Patel Ashka , Jacobs Raquel A. , Slowik Kara , Hess Julian , Stewart Chip , Schlueter-Kuck Kristy , Rhrissorrakrai Kahn , Utro Filippo , Levovitz Chaya , Wagle Nikhil , Leone Jose Pablo , Freedman Rachel , Parida Laxmi , Krop Ian E. , Getz Gad , Lin Nancy U. 
Published: April 2023

Abstract
Background. Despite substantial progress in the treatment of HER2+ MBC, most patients (pts) still experience disease progression and cancer-related death. HER2-directed TKIs are highly effective therapies for pts with HER2+ MBC; however, an understanding of resistance mechanisms is needed. Pts receiving HER2-directed TKIs with cell-free DNA (cfDNA) sampling across the treatment spectrum present a unique opportunity to examine genomic alterations.
Methods. Pts with biopsy-proven HER2+ MBC were selected from DF/HCC approved protocols for ultra-low pass whole genome sequencing if ≥1 cfDNA and/or tissue sample had been collected prior to and after at least six weeks of TKI treatment. Only pts with ≥ 1 sample with tumor fraction (TFx) ≥ 9.5% and ≥ 1 additional sample with TFx ≥ 4.5% were analyzed. Whole exome sequencing (WES) was performed on 19 tumor biopsies and 64 cfDNA samples from 25 pts. WES samples were analyzed, variants called and annotated, copy number profiles inferred, and TFx estimated. PhylogicNDT was used to detect the phylogenetic architecture, and clones were identified as growing, stable, shrinking, or truncal; mutational signatures were called using SignatureAnalyzer. After filtering likely benign variants, mutations were labeled likely resistance mechanisms if there was known evidence of resistance to anti-HER2 therapy in a human breast cancer cell line, breast cancer mouse models, or in vivo. Findings were correlated with pt clinicopathologic data.
Results. In 4/8 pts with acquired resistance (TKI treatment ≥ 180 days), we identified alterations in previously characterized pathways and genes that could explain treatment resistance (e.g. PIK3CA, ERBB2, FGFR2). Mutations in growing subclones identified potential novel mechanisms of resistance and included inactivating mutations in CDK12, KMT2D, KMT2C, CHEK2, BRCA2, and FAT1 genes. In 7/17 pts with intrinsic resistance, we identified mutations in overlapping pathways and genes such as ERBB2 and PIK3CA, which were present in both growing subclonal and truncal clones. Four pts with hormone receptor positive disease - two of whom had not received prior aromatase inhibitors - had an activating ESR1 hotspot mutation (D538G). This raises the possibility that activating ESR1 mutations may be involved in resistance in these cases. Mutational signature analysis revealed a subset of samples with widespread APOBEC activation (with and without hyper mutation), subclonal HR/MMR-related signature, and capecitabine-related 5FU signature.
Conclusions. Genomic analysis of paired samples from pts with HER2+ MBC identifies candidate resistance mechanisms to anti-HER2 TKIs and clonal evolution over time in the context of heterogeneity in treatment and sample timing. Additional studies will determine the functional role and clinical utility of assessing these alterations to overcome resistance.
Citation Format: Heather A. Parsons, Conor Messer, Katheryn Santos, Brian P. Danysh, Melissa E. Hughes, Ashka Patel, Raquel A. Jacobs, Kara Slowik, Julian Hess, Chip Stewart, Kristy Schlueter-Kuck, Kahn Rhrissorrakrai, Filippo Utro, Chaya Levovitz, Nikhil Wagle, Jose Pablo Leone, Rachel Freedman, Laxmi Parida, Ian E. Krop, Gad Getz, Nancy U. Lin. Genomic mechanisms of resistance to tyrosine kinase inhibitors (TKIs) in HER2+ metastatic breast cancer (HER2+ MBC). [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3874.