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Baca SC, Seo JH, Davidsohn MP, Fortunato B, Semaan K, Sotudian S, Lakshminarayanan G, Diossy M, Qiu X, El Zarif T, Savignano H, Canniff J, Madueke I, Saliby RM, Zhang Z, Li R, Jiang Y, Taing L, Awad M, Chau CH, DeCaprio JA, Figg WD, Greten TF, Hata AN, Hodi FS, Hughes ME, Ligon KL, Lin N, Ng K, Oser MG, Meador C, Parsons HA, Pomerantz MM, Rajan A, Ritz J, Thakuria M, Tolaney SM, Wen PY, Long H, Berchuck JE, Szallasi Z, Choueiri TK, Freedman ML. Liquid biopsy epigenomic profiling for cancer subtyping. Nat Med 2023; 29:2737-2741. [PMID: 37865722 PMCID: PMC10695830 DOI: 10.1038/s41591-023-02605-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/21/2023] [Indexed: 10/23/2023]
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.
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Affiliation(s)
- Sylvan C Baca
- 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
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew P Davidsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brad Fortunato
- 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
| | - Karl Semaan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Shahabbedin Sotudian
- 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
| | - Gitanjali Lakshminarayanan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Miklos Diossy
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Talal El Zarif
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hunter Savignano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John Canniff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ikenna Madueke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Renee Maria Saliby
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ziwei Zhang
- 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
| | - Rong Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yijia Jiang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Len Taing
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Cindy H Chau
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James A DeCaprio
- 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
| | - William D Figg
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tim F Greten
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Aaron N Hata
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Melissa E Hughes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Keith L Ligon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nancy Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Catherine Meador
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Arun Rajan
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Manisha Thakuria
- 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
| | - Sara M Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick Y Wen
- 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
| | - Henry Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob E Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zoltan Szallasi
- 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
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew L Freedman
- 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.
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Yuan H, Suzuki S, Terui H, Hirata-Tsuchiya S, Nemoto E, Yamasaki K, Saito M, Shiba H, Aiba S, Yamada S. Loss of IκBζ Drives Dentin Formation via Altered H3K4me3 Status. J Dent Res 2022; 101:951-961. [PMID: 35193410 DOI: 10.1177/00220345221075968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Enforced enrichment of the active promoter marks trimethylation of histone H3 lysine 4 (H3K4me3) and acetylation of histone H3 lysine 27 (H3K27ac) by inhibiting histone demethylases and deacetylases is positively associated with hard tissue formation through the induction of osteo/odontogenic differentiation. However, the key endogenous epigenetic modulator of odontoblasts to regulate the expression of genes coding dentin extracellular matrix (ECM) proteins has not been identified. We focused on nuclear factor (NF)-κB inhibitor ζ (IκBζ), which was originally identified as the transcriptional regulator of NF-κB and recently regarded as the NF-κB-independent epigenetic modulator, and found that IκBζ null mice exhibit a thicker dentin width and narrower pulp chamber, with aged mice having more marked phenotypes. At 6 mo of age, dentin fluorescent labeling revealed significantly accelerated dentin synthesis in the incisors of IκBζ null mice. In the molars of IκBζ null mice, marked tertiary dentin formation adjacent to the pulp horn was observed. Mechanistically, the expression of COL1A2 and COL1A1 collagen genes increased more in the odontoblast-rich fraction of IκBζ null mice than in wild type in vivo, similar to human odontoblast-like cells transfected with small interfering RNA for IκBζ compared with cells transfected with control siRNA in vitro. Furthermore, the direct binding of IκBζ to the COL1A2 promoter suppressed COL1A2 expression and the local active chromatin status marked by H3K4me3. Based on whole-genome identification of H3K4me3 enrichment, ECM and ECM organization-related gene loci were selectively activated by the knockdown of IκBζ, which consistently resulted in the upregulation of these genes. Collectively, this study suggested that IκBζ is the key negative regulator of dentin formation in odontoblasts by inhibiting dentin ECM- and ECM organization-related gene expression through an altered local chromatin status marked by H3K4me3. Therefore, IκBζ is a potential target for epigenetically improving the clinical outcomes of dentin regeneration therapies such as pulp capping.
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Affiliation(s)
- H Yuan
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - S Suzuki
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - H Terui
- Department of Dermatology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - S Hirata-Tsuchiya
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - E Nemoto
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - K Yamasaki
- Department of Dermatology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - M Saito
- Department of Restorative Dentistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - H Shiba
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - S Aiba
- Department of Dermatology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - S Yamada
- Department of Periodontology and Endodontology, Tohoku University Graduate School of Dentistry, Sendai, Japan
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Piyawajanusorn C, Nguyen LC, Ghislat G, Ballester PJ. A gentle introduction to understanding preclinical data for cancer pharmaco-omic modeling. Brief Bioinform 2021; 22:6343527. [PMID: 34368843 DOI: 10.1093/bib/bbab312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/25/2021] [Accepted: 07/20/2021] [Indexed: 12/16/2022] Open
Abstract
A central goal of precision oncology is to administer an optimal drug treatment to each cancer patient. A common preclinical approach to tackle this problem has been to characterize the tumors of patients at the molecular and drug response levels, and employ the resulting datasets for predictive in silico modeling (mostly using machine learning). Understanding how and why the different variants of these datasets are generated is an important component of this process. This review focuses on providing such introduction aimed at scientists with little previous exposure to this research area.
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Affiliation(s)
- Chayanit Piyawajanusorn
- Cancer Research Center of Marseille, INSERM U1068, F-13009 Marseille, France.,Institut Paoli-Calmettes, F-13009 Marseille, France.,Aix-Marseille Université, F-13284 Marseille, France.,CNRS UMR7258, F-13009 Marseille, France.,Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Linh C Nguyen
- Cancer Research Center of Marseille, INSERM U1068, F-13009 Marseille, France.,Institut Paoli-Calmettes, F-13009 Marseille, France.,Aix-Marseille Université, F-13284 Marseille, France.,CNRS UMR7258, F-13009 Marseille, France.,Department of Life Sciences, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ghita Ghislat
- U1104, CNRS UMR7280, Centre d'Immunologie de Marseille-Luminy, Inserm, Marseille, France
| | - Pedro J Ballester
- Cancer Research Center of Marseille, INSERM U1068, F-13009 Marseille, France.,Institut Paoli-Calmettes, F-13009 Marseille, France.,Aix-Marseille Université, F-13284 Marseille, France.,CNRS UMR7258, F-13009 Marseille, France
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