Identification of tissue-specific cell death using methylation patterns of circulating DNA

Roni Lehmann-Werman, Daniel Neiman, Hai Zemmour, Joshua Moss, Judith Magenheim, Adi Vaknin-Dembinsky, Sten Rubertsson, Bengt Nellgård, Kaj Blennow, Henrik Zetterberg, Kirsty Spalding, Michael J. Haller, Clive H. Wasserfall, Desmond A. Schatz, Carla J. Greenbaum, Craig Dorrell, Markus Grompe, Aviad Zick, Ayala Hubert, Myriam MaozVolker Fendrich, Detlef K. Bartsch, Talia Golan, Shmuel A.Ben Sasson, Gideon Zamir, Aharon Razin, Howard Cedara, A. M.James Shapiroo, Benjamin Glaser*, Ruth Shemer, Yuval Dor

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

426 Scopus citations

Abstract

Minimally invasive detection of cell death could prove an invaluable resource in many physiologic and pathologic situations. Cell-free circulating DNA (cfDNA) released from dying cells is emerging as a diagnostic tool for monitoring cancer dynamics and graft failure. However, existing methods rely on differences in DNA sequences in source tissues, so that cell death cannot be identified in tissues with a normal genome. We developed a method of detecting tissue-specific cell death in humans based on tissue-specific methylation patterns in cfDNA. We interrogated tissue-specific methylome databases to identify cell typespecific DNA methylation signatures and developed a method to detect these signatures in mixed DNA samples. We isolated cfDNA from plasma or serum of donors, treated the cfDNA with bisulfite, PCRamplified the cfDNA, and sequenced it to quantify cfDNA carrying the methylation markers of the cell type of interest. Pancreatic β-cell DNA was identified in the circulation of patients with recently diagnosed type-1 diabetes and islet-graft recipients; oligodendrocyte DNA was identified in patients with relapsing multiple sclerosis; neuronal/glial DNA was identified in patients after traumatic brain injury or cardiac arrest; and exocrine pancreas DNA was identified in patients with pancreatic cancer or pancreatitis. This proof-of-concept study demonstrates that the tissue origins of cfDNA and thus the rate of death of specific cell types can be determined in humans. The approach can be adapted to identify cfDNA derived from any cell type in the body, offering a minimally invasive window for diagnosing and monitoring a broad spectrum of human pathologies as well as providing a better understanding of normal tissue dynamics.

Original languageAmerican English
Pages (from-to)E1826-E1834
JournalProceedings of the National Academy of Sciences of the United States of America
Volume113
Issue number13
DOIs
StatePublished - 29 Mar 2016

Bibliographical note

Funding Information:
We thank the T1D Exchange Biobank and investigators and staff of T1D Exchange Protocols for subject recruitment, Tomer Nir and Adi Nir for discussions, and Marc Gotkine for critical reading of the manuscript. This work was supported by the T1D Exchange, a program of T1D First; in part by a grant from the American Schools and Hospitals Abroad Program of the US Agency for International Development for upgrading the Hebrew University Medical School Flow Cytometry Laboratory; and by grants from the Juvenile Diabetes Research Foundation (3-SRA-2014-38-Q-R); the Beta-Cell Biology Consortium and the Human Islet Research Network of the National Institutes of Health (DK104216); the Sir Zalman Cowen Universities Fund; a Trilateral German-Israel-Palestine program of the Deutsche Forschungsgemeinschaft; the Soyka Pancreatic Cancer Fund; and the Israeli Centers for Research Excellence Program of The Israel Science Foundation 41.11 (to Y.D.). R.L.-W. was supported by a training grant from Teva Pharmaceutical Industries Ltd. as part of the Israeli National Network of Excellence in Neuroscience. K.B. holds the Torsten Söderberg Professorship in Medicine at the Royal Swedish Academy of Sciences.

Keywords

  • Circulating DNA
  • Diagnosis
  • Methylation

Fingerprint

Dive into the research topics of 'Identification of tissue-specific cell death using methylation patterns of circulating DNA'. Together they form a unique fingerprint.

Cite this