title: Identification of tissue-specific cell death using methylation patterns of circulating DNA.
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 type-specific 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, PCR-amplified 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.
authors.affiliation: Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel;
authors.forename: Roni
authors.initials: R
authors.lastname: Lehmann-Werman
authors.affiliation: Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel;
authors.forename: Daniel
authors.initials: D
authors.lastname: Neiman
authors.affiliation: Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel;
authors.forename: Hai
authors.initials: H
authors.lastname: Zemmour
authors.affiliation: Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel;
authors.forename: Joshua
authors.initials: J
authors.lastname: Moss
authors.affiliation: Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel;
authors.forename: Judith
authors.initials: J
authors.lastname: Magenheim
authors.affiliation: Department of Neurology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel;
authors.forename: Adi
authors.initials: A
authors.lastname: Vaknin-Dembinsky
authors.affiliation: Department of Surgical Sciences/Anesthesiology and Intensive Care, Uppsala University Hospital, SE-751 85 Uppsala, Sweden;
authors.forename: Sten
authors.initials: S
authors.lastname: Rubertsson
authors.affiliation: Sahlgrenska University Hospital, S-431 80 Molndal, Sweden;
authors.forename: Bengt
authors.initials: B
authors.lastname: Nellgård
authors.affiliation: Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, S-431 80 Molndal, Sweden;
authors.forename: Kaj
authors.initials: K
authors.lastname: Blennow
authors.affiliation: Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, S-431 80 Molndal, Sweden; Institute of Neurology, University College London, London WC1N 3BG, United Kingdom;
authors.forename: Henrik
authors.initials: H
authors.lastname: Zetterberg
authors.affiliation: Department of Cell and Molecular Biology, Karolinska Institute, Stockholm 171-77, Sweden;
authors.forename: Kirsty
authors.initials: K
authors.lastname: Spalding
authors.affiliation: Division of Endocrinology, University of Florida College of Medicine, Gainesville, FL 32610;
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Haller
authors.affiliation: Division of Endocrinology, University of Florida College of Medicine, Gainesville, FL 32610;
authors.forename: Clive H
authors.initials: CH
authors.lastname: Wasserfall
authors.affiliation: Division of Endocrinology, University of Florida College of Medicine, Gainesville, FL 32610;
authors.forename: Desmond A
authors.initials: DA
authors.lastname: Schatz
authors.affiliation: Benaroya Research Institute, Seattle, WA 98101;
authors.forename: Carla J
authors.initials: CJ
authors.lastname: Greenbaum
authors.affiliation: Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland OR 97239;
authors.forename: Craig
authors.initials: C
authors.lastname: Dorrell
authors.affiliation: Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland OR 97239;
authors.forename: Markus
authors.initials: M
authors.lastname: Grompe
authors.affiliation: Department of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel;
authors.forename: Aviad
authors.initials: A
authors.lastname: Zick
authors.affiliation: Department of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel;
authors.forename: Ayala
authors.initials: A
authors.lastname: Hubert
authors.affiliation: Department of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel;
authors.forename: Myriam
authors.initials: M
authors.lastname: Maoz
authors.affiliation: Department of Surgery, Marburg University, 35037 Marburg, Germany;
authors.forename: Volker
authors.initials: V
authors.lastname: Fendrich
authors.affiliation: Department of Surgery, Marburg University, 35037 Marburg, Germany;
authors.forename: Detlef K
authors.initials: DK
authors.lastname: Bartsch
authors.affiliation: Department of Oncology, Chaim Sheba Medical Center, Tel Hashomer, Israel;
authors.forename: Talia
authors.initials: T
authors.lastname: Golan
authors.affiliation: Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel;
authors.forename: Shmuel A
authors.initials: SA
authors.lastname: Ben Sasson
authors.affiliation: Department of Experimental Surgery, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel;
authors.forename: Gideon
authors.initials: G
authors.lastname: Zamir
authors.affiliation: Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel;
authors.forename: Aharon
authors.initials: A
authors.lastname: Razin
authors.affiliation: Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel;
authors.forename: Howard
authors.initials: H
authors.lastname: Cedar
authors.affiliation: Department of Surgery and the Clinical Islet Transplant Program, University of Alberta, Edmonton, AB T6G 2R3, Canada;
authors.forename: A M James
authors.initials: AM
authors.lastname: Shapiro
authors.affiliation: Endocrinology and Metabolism Service, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel beng@cc.huji.ac.il shemer.ru@mail.huji.ac.il yuvald@ekmd.huji.ac.il.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Glaser
authors.affiliation: Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; beng@cc.huji.ac.il shemer.ru@mail.huji.ac.il yuvald@ekmd.huji.ac.il.
authors.forename: Ruth
authors.initials: R
authors.lastname: Shemer
authors.affiliation: Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel; beng@cc.huji.ac.il shemer.ru@mail.huji.ac.il yuvald@ekmd.huji.ac.il.
authors.forename: Yuval
authors.initials: Y
authors.lastname: Dor
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D002545:Brain Ischemia / Q000235:genetics / Q000473:pathology; D016022:Case-Control Studies; D016923:Cell Death; D002648:Child; D002675:Child, Preschool; D004247:DNA / Q000097:blood* / Q000378:metabolism; D019175:DNA Methylation; D003922:Diabetes Mellitus, Type 1 / Q000235:genetics / Q000473:pathology; D005260:Female; D005819:Genetic Markers; D006801:Humans; D050417:Insulin-Secreting Cells / Q000473:pathology*; D008297:Male; D008875:Middle Aged; D020529:Multiple Sclerosis, Relapsing-Remitting / Q000235:genetics / Q000473:pathology; D009836:Oligodendroglia / Q000473:pathology*; D009928:Organ Specificity; D010190:Pancreatic Neoplasms / Q000235:genetics / Q000473:pathology; D050500:Pancreatitis, Chronic / Q000235:genetics / Q000473:pathology; D011401:Promoter Regions, Genetic; D012680:Sensitivity and Specificity; D055815:Young Adult
chemical_list: D005819:Genetic Markers; D004247:DNA
keywords: circulating DNA; diagnosis; methylation