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McNamara ME, Loyfer N, Kiliti AJ, Schmidt MO, Shabi-Porat S, Jain SS, Martinez Roth S, McDeed AP, Shahrour N, Ballew E, Lin YT, Li HH, Deslattes Mays A, Rudra S, Riegel AT, Unger K, Kaplan T, Wellstein A. Circulating cell-free methylated DNA reveals tissue-specific, cellular damage from radiation treatment. JCI Insight 2023; 8:e156529. [PMID: 37318863 PMCID: PMC10443812 DOI: 10.1172/jci.insight.156529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/31/2023] [Indexed: 06/17/2023] Open
Abstract
Radiation therapy is an effective cancer treatment, although damage to healthy tissues is common. Here we analyzed cell-free, methylated DNA released from dying cells into the circulation to evaluate radiation-induced cellular damage in different tissues. To map the circulating DNA fragments to human and mouse tissues, we established sequencing-based, cell-type-specific reference DNA methylation atlases. We found that cell-type-specific DNA blocks were mostly hypomethylated and located within signature genes of cellular identity. Cell-free DNA fragments were captured from serum samples by hybridization to CpG-rich DNA panels and mapped to the DNA methylation atlases. In a mouse model, thoracic radiation-induced tissue damage was reflected by dose-dependent increases in lung endothelial and cardiomyocyte methylated DNA in serum. The analysis of serum samples from patients with breast cancer undergoing radiation treatment revealed distinct dose-dependent and tissue-specific epithelial and endothelial responses to radiation across multiple organs. Strikingly, patients treated for right-sided breast cancers also showed increased hepatocyte and liver endothelial DNA in the circulation, indicating the impact on liver tissues. Thus, changes in cell-free methylated DNA can uncover cell-type-specific effects of radiation and provide a readout of the biologically effective radiation dose received by healthy tissues.
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Affiliation(s)
- Megan E. McNamara
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amber J. Kiliti
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Marcel O. Schmidt
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Sapir Shabi-Porat
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sidharth S. Jain
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Sarah Martinez Roth
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - A. Patrick McDeed
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Nesreen Shahrour
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | | | - Yun-Tien Lin
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Heng-Hong Li
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | | | - Sonali Rudra
- Medstar Georgetown University Hospital, Washington DC, USA
| | - Anna T. Riegel
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Keith Unger
- Medstar Georgetown University Hospital, Washington DC, USA
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anton Wellstein
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
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2
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Peretz A, Loyfer N, Piyanzin S, Ochana BL, Neiman D, Magenheim J, Klochendler A, Drawshy Z, Fox-Fisher I, Fridlich O, Moss J, Cohen D, Zemmour H, Cann G, Bredno J, Venn O, Avni B, Alekberli T, Samet Y, Korach A, Wald O, Yutkin V, Izhar U, Pillar N, Grompe M, Fridlender Z, Rokach A, Planer D, Landesberg G, Glaser B, Shemer R, Kaplan T, Dor Y. The DNA methylome of human vascular endothelium and its use in liquid biopsies. Med 2023; 4:263-281.e4. [PMID: 37060900 DOI: 10.1016/j.medj.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 02/17/2023] [Accepted: 03/17/2023] [Indexed: 04/17/2023]
Abstract
BACKGROUND Vascular endothelial cells (VECs) are an essential component of each tissue, contribute to multiple pathologies, and are targeted by important drugs. Yet, there is a shortage of biomarkers to assess VEC turnover. METHODS To develop DNA methylation-based liquid biopsies for VECs, we determined the methylome of VECs isolated from freshly dissociated human tissues. FINDINGS A comparison with a human cell-type methylome atlas yielded thousands of loci that are uniquely unmethylated in VECs. These sites are typically gene enhancers, often residing adjacent to VEC-specific genes. We also identified hundreds of genomic loci that are differentially methylated in organotypic VECs, indicating that VECs feeding specific organs are distinct cell types with a stable epigenetic identity. We established universal and lung-specific VEC markers and evaluated their presence in circulating cell-free DNA (cfDNA). Nearly 2.5% of cfDNA in the plasma of healthy individuals originates from VECs. Sepsis, graft versus host disease, and cardiac catheterization are associated with elevated levels of VEC-derived cfDNA, indicative of vascular damage. Lung-specific VEC cfDNA is selectively elevated in patients with chronic obstructive pulmonary disease (COPD) or lung cancer, revealing tissue-specific vascular turnover. CONCLUSIONS VEC cfDNA biomarkers inform vascular dynamics in health and disease, potentially contributing to early diagnosis and monitoring of pathologies, and assessment of drug activity. FUNDING This work was supported by the Beutler Research Program, Helmsley Charitable Trust, JDRF, Grail and the DON Foundation (to Y.D.). Y.D holds the Walter & Greta Stiel Chair in heart studies. B.G., R.S., J.M., D.N., T.K., and Y.D. filed patents on cfDNA analysis.
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Affiliation(s)
- Ayelet Peretz
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sheina Piyanzin
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Bracha Lea Ochana
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Neiman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Judith Magenheim
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Agnes Klochendler
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zeina Drawshy
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilana Fox-Fisher
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ori Fridlich
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Joshua Moss
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Cohen
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hai Zemmour
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gordon Cann
- GRAIL, LLC, a subsidiary of Illumina, LLC, Menlo Park, CA, USA
| | - Joerg Bredno
- GRAIL, LLC, a subsidiary of Illumina, LLC, Menlo Park, CA, USA
| | - Oliver Venn
- GRAIL, LLC, a subsidiary of Illumina, LLC, Menlo Park, CA, USA
| | - Batia Avni
- Department of Bone Marrow Transplantation and Immunotherapy, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tural Alekberli
- Department of Anesthesiology and Critical Care Management, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yaacov Samet
- Department of Vascular Surgery, Shaare Zedek Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amit Korach
- Department of Cardiothoracic Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ori Wald
- Department of Cardiothoracic Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vladimir Yutkin
- Department of Urology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Uzi Izhar
- Department of Cardiothoracic Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nir Pillar
- Department of Pathology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Markus Grompe
- Pape Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Zvi Fridlender
- Institute of Pulmonary Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ariel Rokach
- Pulmonary Institute, Shaare Zedek Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Planer
- Department of Cardiology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Giora Landesberg
- Department of Anesthesiology and Critical Care Management, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Benjamin Glaser
- Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
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3
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Magenheim J, Rokach A, Peretz A, Loyfer N, Cann G, Amini H, Moradi P, Nagaraju S, Sameer W, Cohen A, Fogel O, Kuint R, Abutbul A, Abu Rmeileh A, Karameh M, Cohen Goichman P, Wald O, Korach A, Neiman D, Fox-Fisher I, Moss J, Cohen D, Piyanzin S, Ben Ami R, Quteineh A, Golomb E, Shemer R, Glaser B, Kaplan T, Fridlender Z, Dor Y. Universal lung epithelium DNA methylation markers for detection of lung damage in liquid biopsies. Eur Respir J 2022; 60:13993003.03056-2021. [PMID: 35450968 DOI: 10.1183/13993003.03056-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/15/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND Circulating biomarkers for lung damage are lacking. Lung epithelium-specific DNA methylation patterns can potentially report the presence of lung-derived cell-free DNA (cfDNA) in blood, as an indication of lung cell death. METHODS We sorted human lung alveolar and bronchial epithelial cells from surgical specimens, and obtained their methylomes using whole-genome bisulfite sequencing. We developed a PCR-sequencing assay determining the methylation status of 17 loci with lung-specific methylation patterns, and used it to assess lung-derived cfDNA in the plasma of healthy volunteers and patients with lung disease. RESULTS Loci that are uniquely unmethylated in alveolar or bronchial epithelial cells are enriched for enhancers controlling lung-specific genes. Methylation markers extracted from these methylomes revealed that normal lung cell turnover likely releases cfDNA into the air spaces, rather than to blood. People with advanced lung cancer show a massive elevation of lung cfDNA concentration in blood. Among individuals undergoing bronchoscopy, lung-derived cfDNA is observed in the plasma of those later diagnosed with lung cancer, and to a lesser extent in those diagnosed with other lung diseases. Lung cfDNA is also elevated in patients with acute exacerbation of chronic obstructive pulmonary disease (COPD) compared with patients with stable disease, and is associated with future exacerbation and mortality in these patients. CONCLUSIONS Universal cfDNA methylation markers of normal lung epithelium allow for mutation-independent, sensitive and specific detection of lung-derived cfDNA, reporting on ongoing lung injury. Such markers can find broad utility in the study of normal and pathologic human lung dynamics.
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Affiliation(s)
- Judith Magenheim
- Dept. of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel.,Equal contributors
| | - Ariel Rokach
- Pulmonary Institute, Shaare Zedek Medical Center, Jerusalem and the Faculty of Medicine, Hebrew University of Jerusalem, Israel.,Equal contributors
| | - Ayelet Peretz
- Dept. of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
| | - Gordon Cann
- GRAIL LLC, Menlo Park, California, United States of America
| | - Hamed Amini
- GRAIL LLC, Menlo Park, California, United States of America
| | - Patriss Moradi
- GRAIL LLC, Menlo Park, California, United States of America
| | | | - Wafa Sameer
- Institute of Pulmonary Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Asaf Cohen
- Pulmonary Institute, Shaare Zedek Medical Center, Jerusalem and the Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Ophir Fogel
- Pulmonary Institute, Shaare Zedek Medical Center, Jerusalem and the Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Rottem Kuint
- Institute of Pulmonary Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Avraham Abutbul
- Institute of Pulmonary Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Aiman Abu Rmeileh
- Institute of Pulmonary Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Mutaz Karameh
- Institute of Pulmonary Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Polina Cohen Goichman
- Institute of Pulmonary Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Ori Wald
- Dept. of Cardiothoracic Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Amit Korach
- Dept. of Cardiothoracic Surgery, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Daniel Neiman
- Dept. of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Ilana Fox-Fisher
- Dept. of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Joshua Moss
- Dept. of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Daniel Cohen
- Dept. of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Sheina Piyanzin
- Dept. of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Roni Ben Ami
- Dept. of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Ahmad Quteineh
- The Institute of Pediatric Gastroenterology and Nutrition, Shaare Zedek Medical Center, Israel
| | - Eliahu Golomb
- Dept. of Pathology, Shaare Zedek Medical Center, Hebrew University of Jerusalem, Israel
| | - Ruth Shemer
- Dept. of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Benjamin Glaser
- Dept. of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Tommy Kaplan
- Dept. of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel.,School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
| | - Zvi Fridlender
- Institute of Pulmonary Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Yuval Dor
- Dept. of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
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4
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Lubotzky A, Zemmour H, Neiman D, Gotkine M, Loyfer N, Piyanzin S, Ochana BL, Lehmann-Werman R, Cohen D, Moss J, Magenheim J, Loftus MF, Brais L, Ng K, Mostoslavsky R, Wolpin BM, Zick A, Maoz M, Grinshpun A, Kustanovich A, Makranz C, Cohen JE, Peretz T, Hubert A, Temper M, Salah A, Avniel-Polak S, Grozinsky-Glasberg S, Spalding KL, Rokach A, Kaplan T, Glaser B, Shemer R, Dor Y. Liquid biopsy reveals collateral tissue damage in cancer. JCI Insight 2022; 7:153559. [PMID: 35076021 PMCID: PMC8855834 DOI: 10.1172/jci.insight.153559] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/03/2021] [Indexed: 11/28/2022] Open
Abstract
Cancer inflicts damage to surrounding normal tissues, which can culminate in fatal organ failure. Here, we demonstrate that cell death in organs affected by cancer can be detected by tissue-specific methylation patterns of circulating cell-free DNA (cfDNA). We detected elevated levels of hepatocyte-derived cfDNA in the plasma of patients with liver metastases originating from different primary tumors, compared with cancer patients without liver metastases. In addition, patients with localized pancreatic or colon cancer showed elevated hepatocyte cfDNA, suggesting liver damage inflicted by micrometastatic disease, by primary pancreatic tumor pressing the bile duct, or by a systemic response to the primary tumor. We also identified elevated neuron-, oligodendrocyte-, and astrocyte-derived cfDNA in a subpopulation of patients with brain metastases compared with cancer patients without brain metastasis. Cell type–specific cfDNA methylation markers enable the identification of collateral tissue damage in cancer, revealing the presence of metastases in specific locations and potentially assisting in early cancer detection.
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Affiliation(s)
- Asael Lubotzky
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- Neuropediatric Unit, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Hai Zemmour
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Daniel Neiman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Marc Gotkine
- Department of Neurology, The Agnes-Ginges Center for Neurogenetics, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
| | - Sheina Piyanzin
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Bracha-Lea Ochana
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Roni Lehmann-Werman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Daniel Cohen
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Joshua Moss
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Judith Magenheim
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Maureen F. Loftus
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Lauren Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Raul Mostoslavsky
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Brian M. Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Aviad Zick
- Sharett Institute of Oncology, Hadassah Medical Center and the Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Myriam Maoz
- Sharett Institute of Oncology, Hadassah Medical Center and the Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Albert Grinshpun
- Sharett Institute of Oncology, Hadassah Medical Center and the Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anatoli Kustanovich
- Sharett Institute of Oncology, Hadassah Medical Center and the Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Chen Makranz
- Department of Neurology and Oncology, Gaffin Center for Neuro-Oncology, Sharett Institute of Oncology, and
| | - Jonathan E. Cohen
- Sharett Institute of Oncology, Hadassah Medical Center and the Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tamar Peretz
- Sharett Institute of Oncology, Hadassah Medical Center and the Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ayala Hubert
- Sharett Institute of Oncology, Hadassah Medical Center and the Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mark Temper
- Sharett Institute of Oncology, Hadassah Medical Center and the Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Azzam Salah
- Sharett Institute of Oncology, Hadassah Medical Center and the Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shani Avniel-Polak
- Department of Endocrinology and Metabolism Service, Hadassah Medical Organization and The Faculty of Medicine, The Hebrew University of Jerusalem, Israel
| | - Simona Grozinsky-Glasberg
- Department of Endocrinology and Metabolism Service, Hadassah Medical Organization and The Faculty of Medicine, The Hebrew University of Jerusalem, Israel
| | - Kirsty L. Spalding
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ariel Rokach
- Pulmonary Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Tommy Kaplan
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
| | - Benjamin Glaser
- Department of Endocrinology and Metabolism Service, Hadassah Medical Organization and The Faculty of Medicine, The Hebrew University of Jerusalem, Israel
| | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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5
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Fox-Fisher I, Piyanzin S, Ochana BL, Klochendler A, Magenheim J, Peretz A, Loyfer N, Moss J, Cohen D, Drori Y, Friedman N, Mandelboim M, Rothenberg ME, Caldwell JM, Rochman M, Jamshidi A, Cann G, Lavi D, Kaplan T, Glaser B, Shemer R, Dor Y. Remote immune processes revealed by immune-derived circulating cell-free DNA. eLife 2021; 10:70520. [PMID: 34842142 PMCID: PMC8651286 DOI: 10.7554/elife.70520] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 11/24/2021] [Indexed: 01/08/2023] Open
Abstract
Blood cell counts often fail to report on immune processes occurring in remote tissues. Here, we use immune cell type-specific methylation patterns in circulating cell-free DNA (cfDNA) for studying human immune cell dynamics. We characterized cfDNA released from specific immune cell types in healthy individuals (N = 242), cross sectionally and longitudinally. Immune cfDNA levels had no individual steady state as opposed to blood cell counts, suggesting that cfDNA concentration reflects adjustment of cell survival to maintain homeostatic cell numbers. We also observed selective elevation of immune-derived cfDNA upon perturbations of immune homeostasis. Following influenza vaccination (N = 92), B-cell-derived cfDNA levels increased prior to elevated B-cell counts and predicted efficacy of antibody production. Patients with eosinophilic esophagitis (N = 21) and B-cell lymphoma (N = 27) showed selective elevation of eosinophil and B-cell cfDNA, respectively, which were undetectable by cell counts in blood. Immune-derived cfDNA provides a novel biomarker for monitoring immune responses to physiological and pathological processes that are not accessible using conventional methods.
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Affiliation(s)
- Ilana Fox-Fisher
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Sheina Piyanzin
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Bracha Lea Ochana
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Agnes Klochendler
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Judith Magenheim
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ayelet Peretz
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Joshua Moss
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Daniel Cohen
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yaron Drori
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel, and Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Nehemya Friedman
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel, and Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Michal Mandelboim
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel, and Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, United States
| | - Julie M Caldwell
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, United States
| | - Mark Rochman
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, United States
| | | | | | - David Lavi
- Department of Hematology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Developmental Biology and Cancer Research, The Institute for Medical Research, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Benjamin Glaser
- Endocrinology and Metabolism Service, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research, Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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6
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Barefoot ME, Loyfer N, Kiliti AJ, McDeed AP, Kaplan T, Wellstein A. Detection of Cell Types Contributing to Cancer From Circulating, Cell-Free Methylated DNA. Front Genet 2021; 12:671057. [PMID: 34386036 PMCID: PMC8353442 DOI: 10.3389/fgene.2021.671057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/17/2021] [Indexed: 12/24/2022] Open
Abstract
Detection of cellular changes in tissue biopsies has been the basis for cancer diagnostics. However, tissue biopsies are invasive and limited by inaccuracies due to sampling locations, restricted sampling frequency, and poor representation of tissue heterogeneity. Liquid biopsies are emerging as a complementary approach to traditional tissue biopsies to detect dynamic changes in specific cell populations. Cell-free DNA (cfDNA) fragments released into the circulation from dying cells can be traced back to the tissues and cell types they originated from using DNA methylation, an epigenetic regulatory mechanism that is highly cell-type specific. Decoding changes in the cellular origins of cfDNA over time can reveal altered host tissue homeostasis due to local cancer invasion and metastatic spread to distant organs as well as treatment responses. In addition to host-derived cfDNA, changes in cancer cells can be detected from cell-free, circulating tumor DNA (ctDNA) by monitoring DNA mutations carried by cancer cells. Here, we will discuss computational approaches to identify and validate robust biomarkers of changed tissue homeostasis using cell-free, methylated DNA in the circulation. We highlight studies performing genome-wide profiling of cfDNA methylation and those that combine genetic and epigenetic markers to further identify cell-type specific signatures. Finally, we discuss opportunities and current limitations of these approaches for implementation in clinical oncology.
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Affiliation(s)
- Megan E. Barefoot
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amber J. Kiliti
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, United States
| | - A. Patrick McDeed
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Washington, DC, United States
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anton Wellstein
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
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7
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Brill-Karniely Y, Dror D, Duanis-Assaf T, Goldstein Y, Schwob O, Millo T, Orehov N, Stern T, Jaber M, Loyfer N, Vosk-Artzi M, Benyamini H, Bielenberg D, Kaplan T, Buganim Y, Reches M, Benny O. Triangular correlation (TrC) between cancer aggressiveness, cell uptake capability, and cell deformability. Sci Adv 2020; 6:eaax2861. [PMID: 31998832 PMCID: PMC6962040 DOI: 10.1126/sciadv.aax2861] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 11/18/2019] [Indexed: 05/14/2023]
Abstract
The malignancy potential is correlated with the mechanical deformability of the cancer cells. However, mechanical tests for clinical applications are limited. We present here a Triangular Correlation (TrC) between cell deformability, phagocytic capacity, and cancer aggressiveness, suggesting that phagocytic measurements can be a mechanical surrogate marker of malignancy. The TrC was proved in human prostate cancer cells with different malignancy potential, and in human bladder cancer and melanoma cells that were sorted into subpopulations based solely on their phagocytic capacity. The more phagocytic subpopulations showed elevated aggressiveness ex vivo and in vivo. The uptake potential was preserved, and differences in gene expression and in epigenetic signature were detected. In all cases, enhanced phagocytic and aggressiveness phenotypes were correlated with greater cell deformability and predicted by a computational model. Our multidisciplinary study provides the proof of concept that phagocytic measurements can be applied for cancer diagnostics and precision medicine.
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Affiliation(s)
- Yifat Brill-Karniely
- Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
- Corresponding author. (O.B.); (Y.B.-K.)
| | - Dvir Dror
- Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Tal Duanis-Assaf
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Yoel Goldstein
- Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Ouri Schwob
- Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Talya Millo
- Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Natalie Orehov
- Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Tal Stern
- Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Mohammad Jaber
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University–Hadassah Medical School, Jerusalem 91120, Israel
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Margarita Vosk-Artzi
- Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Hadar Benyamini
- Info-CORE, Bioinformatics Unit of the I-CORE at the Hebrew University and Hadassah Medical Center, Jerusalem 9112001, Israel
| | - Diane Bielenberg
- Department of Surgery, Harvard Medical School, Vascular Biology Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University–Hadassah Medical School, Jerusalem 91120, Israel
| | - Meital Reches
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ofra Benny
- Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
- Corresponding author. (O.B.); (Y.B.-K.)
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8
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Moss J, Magenheim J, Neiman D, Zemmour H, Loyfer N, Korach A, Samet Y, Maoz M, Druid H, Arner P, Fu KY, Kiss E, Spalding KL, Landesberg G, Zick A, Grinshpun A, Shapiro AMJ, Grompe M, Wittenberg AD, Glaser B, Shemer R, Kaplan T, Dor Y. Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease. Nat Commun 2018; 9:5068. [PMID: 30498206 PMCID: PMC6265251 DOI: 10.1038/s41467-018-07466-6] [Citation(s) in RCA: 475] [Impact Index Per Article: 79.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/05/2018] [Indexed: 01/12/2023] Open
Abstract
Methylation patterns of circulating cell-free DNA (cfDNA) contain rich information about recent cell death events in the body. Here, we present an approach for unbiased determination of the tissue origins of cfDNA, using a reference methylation atlas of 25 human tissues and cell types. The method is validated using in silico simulations as well as in vitro mixes of DNA from different tissue sources at known proportions. We show that plasma cfDNA of healthy donors originates from white blood cells (55%), erythrocyte progenitors (30%), vascular endothelial cells (10%) and hepatocytes (1%). Deconvolution of cfDNA from patients reveals tissue contributions that agree with clinical findings in sepsis, islet transplantation, cancer of the colon, lung, breast and prostate, and cancer of unknown primary. We propose a procedure which can be easily adapted to study the cellular contributors to cfDNA in many settings, opening a broad window into healthy and pathologic human tissue dynamics. The methylation status of circulating cell-free DNA (cfDNA) can be informative about recent cell death events. Here the authors present an approach to determine the tissue origins of cfDNA, using a reference methylation atlas of 25 human tissues and cell types, and find that cfDNA from patients reveals tissue contributions that agree with clinical findings.
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Affiliation(s)
- Joshua Moss
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel.,School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Judith Magenheim
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Daniel Neiman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Hai Zemmour
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Amit Korach
- Department of Cardio-Thoracic Surgery, Hadassah-Hebrew University Medical Center, Jerusalem, 9112001, Israel
| | - Yaacov Samet
- Department of Vascular Surgery, Hadassah-Hebrew University Medical Center, Jerusalem, 9112001, Israel
| | - Myriam Maoz
- Department of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, 9112001, Israel
| | - Henrik Druid
- Department of Oncology-Pathology, Karolinska Institutet, SE17177, Stockholm, Sweden.,Dept of Forensic Medicine, The National Board of Forensic Medicine, SE11120, Stockholm, Sweden
| | - Peter Arner
- Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE17176, Stockholm, Sweden
| | - Keng-Yeh Fu
- Department of Cell and Molecular Biology, Karolinska Institutet, SE17177, Stockholm, Sweden
| | - Endre Kiss
- Department of Cell and Molecular Biology, Karolinska Institutet, SE17177, Stockholm, Sweden
| | - Kirsty L Spalding
- Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE17176, Stockholm, Sweden.,Department of Cell and Molecular Biology, Karolinska Institutet, SE17177, Stockholm, Sweden
| | - Giora Landesberg
- Dept of Anesthesiology and Critical Care Medicine, Hadassah-Hebrew University Medical Center, 9112001, Jerusalem, Israel
| | - Aviad Zick
- Department of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, 9112001, Israel
| | - Albert Grinshpun
- Department of Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, 9112001, Israel
| | - A M James Shapiro
- Department of Surgery and the Clinical Islet Transplant Program, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - Markus Grompe
- Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Avigail Dreazan Wittenberg
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Benjamin Glaser
- Dept of Endocrinology and Metabolism Service, Hadassah-Hebrew University Medical Center, 9112001, Jerusalem, Israel
| | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel.
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel.
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