Abstract PS06-07: Liquid biopsy determination of HER2 status in breast cancer: results from a novel epigenomic platform
Authors: Parsons Heather , Baca Sylvan , D'Ippolito Anthony , Jeong Hyun-Hwan , Smith Kalie , Tarantino Paolo , Hughes Melissa , Sendrick Kerry , Painter Corrie , Seo Ji-Heui , Grant Elizabeth , Guess Jamey , Davidsohn Matthew , Lakshminarayanan Gitanjali , Strauss Sarah , Savignano Hunter , Canniff John , Fortunato Brad , Eaton Matthew , Choueiri Toni , Tolaney Sara , Freedman Matthew , Lin Nancy 
Published: May 2024

Abstract
Background:
Tumor HER2 status remains a critical predictive biomarker for patients with breast cancer given the availability of highly effective anti-HER2 therapies. However, determination of HER2 status relies on a complex, tissue-dependent algorithm optimized for extremes of the phenotype – HER2+ vs HER2- status. Given the challenges in reliably obtaining informative tissue biopsies as disease progresses, the new therapeutic relevance of HER2-low breast cancer (IHC 1+ and FISH-negative IHC 2+), and the undependability of biomarkers in this range, better approaches are needed. Epigenomic signatures detectable in cell-free tumor DNA (cfDNA) may provide a minimally invasive, reliable determination of HER2 status. Here, we present a multimodal epigenomic liquid biopsy platform that could offer a minimally invasive alternative to tissue-based determination of transcriptionally regulated targets such as HER2.
Methods:
We identified patients with metastatic breast cancer (n=20) that were HER2-positive with IHC 3+ (n=6) or HER2-negative with IHC 0 (n=14) based on ASCO/CAP guidelines who underwent research biopsies at the Dana-Farber Cancer Institute from 2012-2023. Study participants had undergone concurrent blood sampling collected in Streck Tubes, processed as plasma, and stored at -80ºC. We applied a novel, multimodal epigenomic assay to profile tumor-derived gene regulatory programs from 1mL plasma. This genome-wide approach analyzed histone modifications associated with active gene promoters and enhancers, and DNA methylation. Classifier feature selection was derived from epigenomically profiled breast cancer cell lines. Final classifier performance was cross validated using a standard Leave one Out (LoO) scheme.
Results:
Our cross-validated classifier yielded an area under the ROC curve (AUC) of 0.91 in the 20 samples tested. When including only samples with detectable ctDNA as assessed by low pass whole genome sequencing (ichorCNA algorithm) (N=13), our classifier had an AUC of 0.98. Using regularized regression approach, we identified 33 loci with the highest predictive value; 8 loci were within the ERBB2 amplicon on chromosome 17, while the remaining 25 loci were in other genomic regions. We will present results from this and an expanded cohort, including participants with HER2 IHC 1+ and 2+ disease.
Conclusions:
We present a novel, minimally invasive HER2 classifier leveraging epigenomic information from cell-free tumor DNA from 1 mL plasma. If this approach remains robust in accurately classifying additional HER2 states, it could address the limitations of current tissue-based testing. Integration of this epigenomic platform in prospective interventional studies could support the development of novel and improved predictive classifiers for response to HER2-directed therapy.
Citation Format: Heather Parsons, Sylvan Baca, Anthony D'Ippolito, Hyun-Hwan Jeong, Kalie Smith, Paolo Tarantino, Melissa Hughes, Kerry Sendrick, Corrie Painter, Ji-Heui Seo, Elizabeth Grant, Jamey Guess, Matthew Davidsohn, Gitanjali Lakshminarayanan, Sarah Strauss, Hunter Savignano, John Canniff, Brad Fortunato, Matthew Eaton, Toni Choueiri, Sara Tolaney, Matthew Freedman, Nancy Lin. Liquid biopsy determination of HER2 status in breast cancer: results from a novel epigenomic platform [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PS06-07.