Liquid biopsy epigenomic profiling for cancer subtyping.

Autor:	Baca SC; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.; Eli and Edythe L. Broad Institute, Cambridge, MA, USA., Seo JH; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA., Davidsohn MP; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA., Fortunato B; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.; Eli and Edythe L. Broad Institute, Cambridge, MA, USA., Semaan K; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Eli and Edythe L. Broad Institute, Cambridge, MA, USA., Sotudian S; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.; Eli and Edythe L. Broad Institute, Cambridge, MA, USA., Lakshminarayanan G; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA., Diossy M; Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA., Qiu X; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA., El Zarif T; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA., Savignano H; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA., Canniff J; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA., Madueke I; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA., Saliby RM; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA., Zhang Z; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.; Eli and Edythe L. Broad Institute, Cambridge, MA, USA., Li R; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA., Jiang Y; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA., Taing L; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA., Awad M; Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA., Chau CH; Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA., DeCaprio JA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA., Figg WD; Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA., Greten TF; Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA., Hata AN; Massachusetts General Hospital Cancer Center, Boston, MA, USA.; Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA., Hodi FS; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA., Hughes ME; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA., Ligon KL; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA., Lin N; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA., Ng K; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA., Oser MG; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA., Meador C; Massachusetts General Hospital Cancer Center, Boston, MA, USA.; Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA., Parsons HA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA., Pomerantz MM; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA., Rajan A; Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA., Ritz J; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA., Thakuria M; Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.; Center for Cutaneous Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA., Tolaney SM; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA., Wen PY; Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA., Long H; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA., Berchuck JE; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA., Szallasi Z; Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA.; Danish Cancer Institute, Copenhagen, Denmark.; Department of Bioinformatics and Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary., Choueiri TK; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA., Freedman ML; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. matthew_freedman@dfci.harvard.edu.; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA. matthew_freedman@dfci.harvard.edu.; Eli and Edythe L. Broad Institute, Cambridge, MA, USA. matthew_freedman@dfci.harvard.edu.
Jazyk:	angličtina
Zdroj:	Nature medicine [Nat Med] 2023 Nov; Vol. 29 (11), pp. 2737-2741. Date of Electronic Publication: 2023 Oct 21.
DOI:	10.1038/s41591-023-02605-z
Abstrakt:	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. (© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.)
Databáze:	MEDLINE
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