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

• Published in: JCI insight Vol. 5; no. 14
• Main Authors: Neiman, Daniel, Gillis, David, Piyanzin, Sheina, Cohen, Daniel, Fridlich, Ori, Moss, Joshua, Zick, Aviad, Oron, Tal, Sundberg, Frida, Forsander, Gun, Skog, Oskar, Korsgren, Olle, Levy-Khademi, Floris, Arbel, Dan, Hashavia, Saar, Shapiro, A.M. James, Speake, Cate, Greenbaum, Carla, Hosford, Jennifer, Posgai, Amanda, Atkinson, Mark A., Glaser, Benjamin, Schatz, Desmond A., Shemer, Ruth, Dor, Yuval
• Format: Journal Article
• Language: English
• Published: United States American Society for Clinical Investigation 23.07.2020
• Subjects: Beta cells; Epigenetics; Molecular diagnosis; Metabolism; Endocrinology
• ISSN: 2379-3708; 2379-3708
• DOI: 10.1172/jci.insight.136579

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.