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

Research output: Contribution to journalArticle

164 Citations (Scopus)

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

Fingerprint

Methylation
Cell Death
DNA
DNA Methylation
Transplants
Exocrine Pancreas
Oligodendroglia
Heart Arrest
Type 1 Diabetes Mellitus
Pancreatic Neoplasms
Neuroglia
Pancreatitis
Multiple Sclerosis
Tissue Donors
Genome
Databases
Pathology
Mortality

Keywords

  • Circulating DNA
  • Diagnosis
  • Methylation

ASJC Scopus subject areas

  • General

Cite this

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

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 113, No. 13, 29.03.2016, p. E1826-E1834.

Research output: Contribution to journalArticle

Lehmann-Werman, R, Neiman, D, Zemmour, H, Moss, J, Magenheim, J, Vaknin-Dembinsky, A, Rubertsson, S, Nellgård, B, Blennow, K, Zetterberg, H, Spalding, K, Haller, MJ, Wasserfall, CH, Schatz, DA, Greenbaum, CJ, Dorrell, C, Grompe, M, Zick, A, Hubert, A, Maoz, M, Fendrich, V, Bartsch, DK, Golan, T, Sasson, SAB, Zamir, G, Razin, A, Cedara, H, Shapiroo, AMJ, Glaser, B, Shemer, R & Dor, Y 2016, 'Identification of tissue-specific cell death using methylation patterns of circulating DNA', Proceedings of the National Academy of Sciences of the United States of America, vol. 113, no. 13, pp. E1826-E1834. https://doi.org/10.1073/pnas.1519286113
Lehmann-Werman, Roni ; Neiman, Daniel ; Zemmour, Hai ; Moss, Joshua ; Magenheim, Judith ; Vaknin-Dembinsky, Adi ; Rubertsson, Sten ; Nellgård, Bengt ; Blennow, Kaj ; Zetterberg, Henrik ; Spalding, Kirsty ; Haller, Michael J. ; Wasserfall, Clive H. ; Schatz, Desmond A. ; Greenbaum, Carla J. ; Dorrell, Craig ; Grompe, Markus ; Zick, Aviad ; Hubert, Ayala ; Maoz, Myriam ; Fendrich, Volker ; Bartsch, Detlef K. ; Golan, Talia ; Sasson, Shmuel A Ben ; Zamir, Gideon ; Razin, Aharon ; Cedara, Howard ; Shapiroo, A. M James ; Glaser, Benjamin ; Shemer, Ruth ; Dor, Yuval. / Identification of tissue-specific cell death using methylation patterns of circulating DNA. In: Proceedings of the National Academy of Sciences of the United States of America. 2016 ; Vol. 113, No. 13. pp. E1826-E1834.
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AU - Lehmann-Werman, Roni

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AU - Zemmour, Hai

AU - Moss, Joshua

AU - Magenheim, Judith

AU - Vaknin-Dembinsky, Adi

AU - Rubertsson, Sten

AU - Nellgård, Bengt

AU - Blennow, Kaj

AU - Zetterberg, Henrik

AU - Spalding, Kirsty

AU - Haller, Michael J.

AU - Wasserfall, Clive H.

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AU - Maoz, Myriam

AU - Fendrich, Volker

AU - Bartsch, Detlef K.

AU - Golan, Talia

AU - Sasson, Shmuel A Ben

AU - Zamir, Gideon

AU - Razin, Aharon

AU - Cedara, Howard

AU - Shapiroo, A. M James

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AU - Dor, Yuval

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N2 - 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.

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