Remote immune processes revealed by immune-derived circulating cell-free DNA

  1. Ilana Fox-Fisher
  2. Sheina Piyanzin
  3. Bracha Lea Ochana
  4. Agnes Klochendler
  5. Judith Magenheim
  6. Ayelet Peretz
  7. Netanel Loyfer
  8. Joshua Moss
  9. Daniel Cohen
  10. Yaron Drori
  11. Nehemya Friedman
  12. Michal Mandelboim
  13. Marc E Rothenberg
  14. Julie M Caldwell
  15. Mark Rochman
  16. Arash Jamshidi
  17. Gordon Cann
  18. David Lavi
  19. Tommy Kaplan
  20. Benjamin Glaser
  21. Ruth Shemer
  22. Yuval Dor  Is a corresponding author
  1. The Hebrew University-Hadassah Medical School, Israel
  2. The Hebrew University of Jerusalem, Israel
  3. Chaim Sheba Medical Center, Israel
  4. University of Cincinnati, United States
  5. GRAIL, United States
  6. Hadassah Hebrew University Medical Center, Israel

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.

Data availability

All data generated or analyzed during this study are included in the manuscript and supporting files.The whole-genome bisulfite sequencing data reported in the paper, from 46 samples, is uploaded to GEO as described. The paper also reports data from PCR reactions that were analyzed by massively parallel sequencing. This is a very large set of data that is extremely low in information content and is of little interest to readers or even to people interested in replicating our results or interrogating them further. The key information (methylation status) in each sample is provided in the supplementary information, and we also uploaded the analysis algorithm and some sequence data. The entire set of raw sequencing data is available in the Dor lab to anyone interested.Please contact Prof. Yuval Dor dor@huji.ac.il . All information will be shared. There is no need for any paperwork.Code is uploaded to GitHub as described in the paper.The methylation status of each marker in each sample is provided in Supplementary file 1. This data was used to generate the graphs shown in the paper. Sheets in this file indicate which figure they relate to.

The following data sets were generated

Article and author information

Author details

  1. Ilana Fox-Fisher

    Department of Developmental Biology and Cancer Research, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
    Competing interests
    Ilana Fox-Fisher, has filed patents on cfDNA analysis technology..
  2. Sheina Piyanzin

    Department of Developmental Biology and Cancer Research, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
    Competing interests
    No competing interests declared.
  3. Bracha Lea Ochana

    Department of Developmental Biology and Cancer Research, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
    Competing interests
    No competing interests declared.
  4. Agnes Klochendler

    Department of Developmental Biology and Cancer Research, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
    Competing interests
    No competing interests declared.
  5. Judith Magenheim

    Department of Developmental Biology and Cancer Research, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
    Competing interests
    Judith Magenheim, has filed patents on cfDNA analysis technology..
  6. Ayelet Peretz

    Department of Developmental Biology and Cancer Research, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
    Competing interests
    No competing interests declared.
  7. Netanel Loyfer

    School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
    Competing interests
    No competing interests declared.
  8. Joshua Moss

    Department of Developmental Biology and Cancer Research, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
    Competing interests
    Joshua Moss, has filed patents on cfDNA analysis technology..
  9. Daniel Cohen

    Department of Developmental Biology and Cancer Research, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
    Competing interests
    No competing interests declared.
  10. Yaron Drori

    Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
    Competing interests
    No competing interests declared.
  11. Nehemya Friedman

    Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
    Competing interests
    No competing interests declared.
  12. Michal Mandelboim

    Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
    Competing interests
    No competing interests declared.
  13. Marc E Rothenberg

    Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, United States
    Competing interests
    No competing interests declared.
  14. Julie M Caldwell

    Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, United States
    Competing interests
    No competing interests declared.
  15. Mark Rochman

    Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0818-927X
  16. Arash Jamshidi

    GRAIL, Menlo Park, United States
    Competing interests
    Arash Jamshidi, is an employee of GRAIL..
  17. Gordon Cann

    GRAIL, Menlo Park, United States
    Competing interests
    Gordon Cann, is an employee of GRAIL..
  18. David Lavi

    Department of Hematology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
    Competing interests
    No competing interests declared.
  19. Tommy Kaplan

    School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
    Competing interests
    Tommy Kaplan, has filed patents on cfDNA analysis technology..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1892-5461
  20. Benjamin Glaser

    Endocrinology and Metabolism Service, Hadassah Hebrew University Medical Center, Jerusalem, Israel
    Competing interests
    Benjamin Glaser, has filed patents on cfDNA analysis technology..
  21. Ruth Shemer

    Department of Developmental Biology and Cancer Research, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
    Competing interests
    Ruth Shemer, has filed patents on cfDNA analysis technology..
  22. Yuval Dor

    Department of Developmental Biology and Cancer Research, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
    For correspondence
    yuvald@ekmd.huji.ac.il
    Competing interests
    Yuval Dor, has filed patents on cfDNA analysis technology..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2456-2289

Funding

No external funding was received for this work.

Ethics

Human subjects: This study was conducted according to protocols approved by the Institutional Review Board at each study site (Hadassah Medical Center: HMO-14-0198. A Method to Diagnose Cell Death Based on Methylation Signature of Circulating Cell-Free DNA, Cininnati Children's Hospital: CCHMC IRB protocol 2008-0090: Eosinophils and Inflammation, an Expanded Study), with procedures performed in accordance with the Declaration of Helsinki. Blood and tissue samples were obtained from donors who have provided written informed consent. When using material from deceased organ donor those with legal authority were consented. Subject characteristics are presented in Supplementary File 1.

Reviewing Editor

  1. Iwijn De Vlaminck

Publication history

  1. Received: May 19, 2021
  2. Accepted: November 24, 2021
  3. Accepted Manuscript published: November 29, 2021 (version 1)
  4. Version of Record published: December 7, 2021 (version 2)

Copyright

© 2021, Fox-Fisher et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Ilana Fox-Fisher
  2. Sheina Piyanzin
  3. Bracha Lea Ochana
  4. Agnes Klochendler
  5. Judith Magenheim
  6. Ayelet Peretz
  7. Netanel Loyfer
  8. Joshua Moss
  9. Daniel Cohen
  10. Yaron Drori
  11. Nehemya Friedman
  12. Michal Mandelboim
  13. Marc E Rothenberg
  14. Julie M Caldwell
  15. Mark Rochman
  16. Arash Jamshidi
  17. Gordon Cann
  18. David Lavi
  19. Tommy Kaplan
  20. Benjamin Glaser
  21. Ruth Shemer
  22. Yuval Dor
(2021)
Remote immune processes revealed by immune-derived circulating cell-free DNA
eLife 10:e70520.
https://doi.org/10.7554/eLife.70520

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