Liquid biopsy epigenomic profiling for cancer subtyping
Abstract
Although circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypes and their dynamic changes during the course of disease. To address these limitations, we developed a method for comprehensive epigenomic profiling of cancer from 1 ml of patient plasma. Using an immunoprecipitation-based approach targeting histone modifications and DNA methylation, we measured 1,268 epigenomic profiles in plasma from 433 individuals with one of 15 cancers. Our assay provided a robust proxy for transcriptional activity, allowing us to infer the expression levels of diagnostic markers and drug targets, measure the activity of therapeutically targetable transcription factors and detect epigenetic mechanisms of resistance. This proof-of-concept study in advanced cancers shows how plasma epigenomic profiling has the potential to unlock clinically actionable information that is currently accessible only via direct tissue sampling.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Oct 21, 2023
- Source ID
- 10.1038/s41591-023-02605-z
Entities
People
- Aaron N Hata
- Arun Rajan
- Brad Fortunato
- Catherine Meador
- Cindy H. Chau
- F Stephen Hodi
- Gitanjali Lakshminarayanan
- Heather Parsons
- Henry W Long
- Hunter Savignano
- Ikenna Madueke
- Jacob E Berchuck
- James A DeCaprio
- Jerome Ritz
- Ji-Heui Seo
- John Canniff
- Karl Semaan
- Keith L Ligon
- Kimmie Ng
- Len Taing
- Manisha Thakuria
- Mark Awad
- Mark M. Pomerantz
- Matthew G. Oser
- Matthew L Freedman
- Matthew P. Davidsohn
- Melissa E. Hughes
- Miklos Diossy
- Nancy U Lin
- Patrick Y. Wen
- Renée Maria Saliby
- Rong Li
- Sara M Tolaney
- Shahabeddin Sotudian
- Sylvan C. Baca
- Talal El Zarif
- Tim F Greten
- Toni K Choueiri
- William Douglas Figg, Sr.
- Xintao Qiu
- Yijia Jiang
- Ziwei Zhang
- Zoltán Szállási
Organizations
- National Cancer Institute
- United States Department of Defense