Abstract 963: Comprehensive epigenomic profiling from plasma to inform therapy selection: A proof-of-concept study in cancer
Authors: Clark Travis , Seo Ji-Heui , D'Ippolito Anthony , Gorthi Aparna , Beagan Jonathan , Guess Jamey , Donahue Amy , Greene Mandy , Lau Alyssa , Ramirez Fernando , Cibulskis Kristian , Jeong Hyun-Hwan , Davidsohn Matthew , Lakshminarayanam Gitanjali , Coyne Michael , Tran Baovy , Tamakloe Tyrone , Sawaengsri Hathairat , Eid Marc , Semaan Karl , Fortunato Brad , Painter Corrie A. , Chmielecki Juliann , Choueiri Toni K. , Barrett J Carl , Otto Geoff , Freedman Matthew L. , Eaton Matthew L. , Baca Sylvan C. 
Published: March 2024

Abstract
BACKGROUND: Analysis of genomic alterations in circulating tumor DNA is gaining traction in clinical oncology and can provide insights into tumor biology without the need for invasive tissue sampling. In addition to genetic alterations, epigenomic reprogramming leads to transcriptional dysregulation and drives cancer phenotypes including molecular subtypes, histologic subtypes, and mechanisms resistance. As current liquid biopsy assays fail to effectively capture transcriptional biology, new approaches are needed to examine the transcriptional status of therapeutic gene targets and pathways including those relevant to rapidly emerging classes such as antibody-drug conjugates (ADC) and radio-conjugates.
METHODS: We developed a novel multimodal assay that reveals genome-wide transcriptional activity of promoters, enhancers from chromatin and surveys the DNA methylome using 1ml of patient plasma. We applied this assay to patient plasma samples from across 15 tumor types generating 7000 genome-wide transcriptional profiles.
RESULTS: We confirmed a significant correlation between epigenomic signals of transcriptional activation and gene expression from RNA-seq (Promoter vs RNA-seq: ⍴ =0.95, p&lt;0.05; DNA methylation vs RNA-seq: ⍴=-0.16, p&lt;0.05). We identified transcriptional activation in cancer patient plasma of well-established cancer-associated biomarkers (e.g. MET, DLL3, PSMA) in a tumor-specific manner. Epigenomic profiling simultaneously inferred the expression of multiple pertinent ADC targets currently under investigation (MET, HER2, HER3, TROP2, B7H4 in breast cancer), and SLFN11, a known biomarker for sensitivity to these agents. Unlike targeted panels, the platform assesses transcriptional regulation genome-wide, enabling the assessment of transcriptional activity of select genes as well as related pathways. For example, a multimodal classifier robustly predicted HER2 status across metastatic breast cancer plasma samples based on features both within the HER2 amplicon as well as HER2-distal genes that are activated in HER2+ cancers (AUC = 0.93, 0.84-1.0 95% CI). The multimodal classifier out-performed individual analyte-based classifiers (AUCPromoter+Enhancer = 0.85, 0.72-0.98 95% CI; AUCDNA-methylation = 0.69, 0.48-0.90 95% CI). Epigenomic signatures were also used to delineate multiple mechanisms of resistance to androgen receptor signaling inhibition in prostate cancer, including reactivation of the androgen receptor, glucocorticoid signaling bypass, and histological transformation to a neuroendocrine subtype.
CONCLUSION: This comprehensive epigenomic liquid biopsy assay provides a platform for simultaneous genome-wide transcriptional assessment of disease and therapy relevant genes and pathways, representing a paradigm shift in our ability to longitudinally monitor cancer in individual patients.
Citation Format: Travis Clark, Ji-Heui Seo, Anthony D'Ippolito, Aparna Gorthi, Jonathan Beagan, Jamey Guess, Amy Donahue, Mandy Greene, Alyssa Lau, Fernando Ramirez, Kristian Cibulskis, Hyun-Hwan Jeong, Matthew Davidsohn, Gitanjali Lakshminarayanam, Michael Coyne, Baovy Tran, Tyrone Tamakloe, Hathairat Sawaengsri, Marc Eid, Karl Semaan, Brad Fortunato, Corrie A. Painter, Juliann Chmielecki, Toni K. Choueiri, J Carl Barrett, Geoff Otto, Matthew L. Freedman, Matthew L. Eaton, Sylvan C. Baca. Comprehensive epigenomic profiling from plasma to inform therapy selection: A proof-of-concept study in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 963.