Multiplexing DNA methylation markers to detect circulating cell-free DNA derived from human pancreatic β cells

Daniel Neiman, David Gillis, Sheina Piyanzin, Daniel Cohen, Ori Fridlich, Joshua Moss, Aviad Zick, Tal Oron, Frida Sundberg, Gun Forsander, Oskar Skog, Olle Korsgren, Floris Levy-Khademi, Dan Arbel, Saar Hashavya, A. M. James Shapiro, Cate Speake, Carla Greenbaum, Jennifer Hosford, Amanda PosgaiMark A. Atkinson, Benjamin Glaser, Desmond A. Schatz*, Ruth Shemer*, Yuval Dor*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

26 Scopus citations


It has been proposed that unmethylated insulin promoter fragments in plasma derive exclusively from β cells, reflect their recent demise, and can be used to assess β cell damage in type 1 diabetes. Herein we describe an ultrasensitive assay for detection of a β cell–specific DNA methylation signature, by simultaneous assessment of 6 DNA methylation markers, that identifies β cell DNA in mixtures containing as little as 0.03% β cell DNA (less than 1 β cell genome equivalent). Based on this assay, plasma from nondiabetic individuals (N = 218, aged 4–78 years) contained on average only 1 β cell genome equivalent/mL. As expected, cell-free DNA (cfDNA) from β cells was significantly elevated in islet transplant recipients shortly after transplantation. We also detected β cell cfDNA in a patient with KATP congenital hyperinsulinism, in which substantial β cell turnover is thought to occur. Strikingly, in contrast to previous reports, we observed no elevation of β cell–derived cfDNA in autoantibody-positive subjects at risk for type 1 diabetes (N = 32), individuals with recent-onset type 1 diabetes (<4 months, N = 92), or those with long-standing disease (>4 months, N = 38). We discuss the utility of sensitive β cell cfDNA analysis and potential explanations for the lack of a β cell cfDNA signal in type 1 diabetes.

Original languageAmerican English
Article numbere136579
JournalJCI insight
Issue number14
StatePublished - 23 Jun 2020

Bibliographical note

Funding Information:
We thank Markus Grompe for providing protocols and antibodies for sorting human acinar cells and Ilana Koren for provision of blood samples. This work was supported by grants from Human Islet Research Network (HIRN UC4DK116274 to RS, CB, YD, and DAS and UC4DK104216 to RS, YD, and DAS), JDRF (3-SRA-2014-38 and 1-SRA-2019-705), Ernest and Bonnie Beutler Research Program of Excellence in Genomic Medicine, The Alex U. Soyka pancreatic cancer fund, The Israel Science Foundation, the Waldholtz/Pakula family, the Robert M. and Marilyn Sternberg Family Charitable Foundation (to YD), the NIH (P01 AI42288 and DK108132 to MAA), and The Swedish Child Diabetes Foundation (Barndi-abetesfonden) and the Swedish national strategic research initiative EXODIAB (Excellence of Diabetes Research in Sweden) (to OK). Samples from antibody-positive individuals were obtained through a Diabetes TrialNet ancillary study. We acknowledge the support of the Type 1 Diabetes TrialNet Study Group, which identified study participants and provided samples and follow-up data for this study. The Type 1 Diabetes TrialNet Study Group is a clinical trials network funded by the NIH through the National Institute of Diabetes and Digestive and Kidney Diseases, the National Institute of Allergy and Infectious Diseases, and the Eunice Kennedy Shriver National Institute of Child Health and Human Development, through cooperative agreements U01 DK061010, U01 DK061034, U01 DK061042, U01 DK061058, U01 DK085465, U01 DK085453, U01 DK085461, U01 DK085466, U01 DK085499, U01 DK085504, U01 DK085509, U01 DK103180, U01 DK103153, U01 DK085476, U01 DK103266, U01 DK103282, U01 DK106984, U01 DK106994, U01 DK107013, U01 DK107014, UC4 DK106993, and the JDRF. YD holds the Walter and Greta Stiel Chair and Research Grant in Heart Studies.

Publisher Copyright:
Copyright: © 2020, American Society for Clinical Investigation.


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