Liquid biopsy epigenomic profiling for cancer subtyping

被引：47

作者：

Baca, Sylvan C. ^{[1
,2
,3
]}

Seo, Ji-Heui ^{[1
,2
]}

Davidsohn, Matthew P. ^{[1
,2
]}

Fortunato, Brad ^{[1
,2
,3
]}

Semaan, Karl ^{[1
,3
]}

Sotudian, Shahabbedin ^{[1
,2
,3
]}

Lakshminarayanan, Gitanjali ^{[1
,2
]}

Diossy, Miklos ^{[4
]}

Qiu, Xintao ^{[1
,2
]}

El Zarif, Talal ^{[1
,2
]}

Savignano, Hunter ^{[1
,2
]}

Canniff, John ^{[1
,2
]}

Madueke, Ikenna ^{[1
,2
]}

Saliby, Renee Maria ^{[1
,2
]}

Zhang, Ziwei ^{[1
,2
,3
]}

Li, Rong ^{[1
,2
]}

Jiang, Yijia ^{[1
,2
]}

Taing, Len ^{[1
,2
]}

Awad, Mark ^{[5
]}

Chau, Cindy H. ^{[6
]}

Decaprio, James A. ^{[1
,7
]}

Figg, William D. ^{[6
]}

Greten, Tim F. ^{[8
]}

Hata, Aaron N. ^{[9
,10
,11
]}

Hodi, F. Stephen ^{[1
]}

Hughes, Melissa E. ^{[1
]}

Ligon, Keith L. ^{[1
,12
]}

Lin, Nancy ^{[1
]}

Ng, Kimmie ^{[1
]}

Oser, Matthew G. ^{[1
]}

Meador, Catherine ^{[9
,10
,11
]}

Parsons, Heather A. ^{[1
]}

Pomerantz, Mark M. ^{[1
,2
]}

Rajan, Arun ^{[13
]}

Ritz, Jerome ^{[1
]}

Thakuria, Manisha ^{[14
,15
]}

Tolaney, Sara M. ^{[1
]}

Wen, Patrick Y. ^{[11
,16
,17
]}

Long, Henry ^{[1
,2
]}

Berchuck, Jacob E. ^{[1
,2
]}

Szallasi, Zoltan ^{[4
,18
,19
,20
]}

Choueiri, Toni K. ^{[1
]}

Freedman, Matthew L. ^{[1
,2
,3
]}

机构：

[1] Dana Farber Canc Inst, Dept Med Oncol, Boston, MA 02215 USA

[2] Dana Farber Canc Inst, Ctr Funct Canc Epigenet, Boston, MA 02215 USA

[3] Eli & Edythe L Broad Inst, Cambridge, MA 02142 USA

[4] Boston Childrens Hosp, Computat Hlth Informat Program, Boston, MA USA

[5] Harvard Med Sch, Dana Farber Canc Inst, Lowe Ctr Thorac Oncol, Boston, MA USA

[6] NIH, NCI, Ctr Canc Res, Mol Pharmacol Sect,Genitourinary Malignancies Bra, Bethesda, MD USA

[7] Harvard Med Sch, Brigham & Womens Hosp, Dept Med, Boston, MA USA

[8] NIH, NCI, Liver Canc Program, Ctr Canc Res, Bethesda, MD USA

[9] Massachusetts Gen Hosp, Canc Ctr, Boston, MA USA

[10] Massachusetts Gen Hosp, Dept Med, Boston, MA USA

[11] Harvard Med Sch, Boston, MA USA

[12] Dana Farber Canc Inst, Dept Pathol, Boston, MA USA

[13] NIH, NCI, Ctr Canc Res, Thorac & Gastrointestinal Malignancies Branch, Bethesda, MD USA

[14] Harvard Med Sch, Brigham & Womens Hosp, Dept Dermatol, Boston, MA USA

[15] Dana Farber Brigham & Womens Canc Ctr, Ctr Cutaneous Oncol, Boston, MA USA

[16] Dana Farber Canc Inst, Ctr Neurooncol, Boston, MA USA

[17] Brigham & Womens Hosp, Dept Neurol, Boston, MA USA

[18] Danish Canc Inst, Copenhagen, Denmark

[19] Semmelweis Univ, Dept Bioinformat, Budapest, Hungary

[20] Semmelweis Univ, Dept Pathol Forens & Insurance Med, Budapest, Hungary

来源：

NATURE MEDICINE | 2023年 / 29卷 / 11期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1038/s41591-023-02605-z

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2737 / 2741

页数：23

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