American Diabetes Association
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DNA methylation-based assessment of cell composition in human pancreas and islets

Version 2 2024-02-06, 20:09
Version 1 2024-01-24, 18:42
posted on 2024-02-06, 20:09 authored by Zeina Drawshy, Daniel Neiman, Ori Fridlich, Ayelet Peretz, Judith Magenheim, Andrea V Rozo, Nicolai M Doliba, Doris A Stoffers, Klaus H Kaestner, Desmond A Schatz, Clive Wasserfall, Martha Campbell-Thompson, James Shapiro, Tommy Kaplan, Ruth Shemer, Benjamin Glaser, Agnes Klochendler, Yuval Dor

Assessment of pancreas cell type composition is crucial to the understanding of the genesis of diabetes. Current approaches use immunodetection of protein markers, for example insulin as a marker of beta-cells. A major limitation of these methods is that protein content varies in physiological and pathological conditions, complicating the extrapolation to actual cell number. Here we demonstrate the use of cell type-specific DNA methylation markers for determining the fraction of specific cell types in human islet and pancreas specimens. We identified genomic loci that are uniquely demethylated in specific pancreatic cell types and applied targeted PCR to assess the methylation status of these loci in tissue samples, enabling inference of cell type composition. In islet preparations, normalization of insulin secretion to beta-cell DNA revealed similar beta-cell function in pre-T1D, T1D and T2D , which was significantly lower than in non-diabetic donors. In histological pancreas specimens from recent-onset T1D this assay showed beta-cell fraction within the normal range, suggesting a significant contribution of beta-cell dysfunction. In T2D pancreata we observed increased alpha-cell fraction and normal beta-cell fraction. Methylation-based analysis provides an accurate molecular alternative to immune detection of cell types in the human pancreas, with utility in the interpretation of insulin secretion assays and the assessment of pancreas cell composition in health and disease.


Supported by grants from Grail, the Juvenile Diabetes Research Foundation (JDRF), Human Islet Research Network (HIRN), NIDDK, The Alex U Soyka pancreatic cancer fund, The Israel Science Foundation and the DON Foundation (to Y.D.). Y.D holds the Walter and Greta Stiel Chair and Research grant in Heart studies. This manuscript used data acquired from the Human Pancreas Analysis Program (HPAP-RRID:SCR_016202) Database (, a Human Islet Research Network (RRID:SCR_014393) consortium (UC4-DK-112217, U01-DK-123594, UC4-DK-112232, and U01-DK-123716) and the Network for Pancreatic Organ donors with Diabetes (nPOD; RRID:SCR_014641), a collaborative type 1 diabetes research project supported by JDRF (nPOD: 5-SRA-2018-557-Q-R) and The Leona M. & Harry B. Helmsley Charitable Trust (Grant#2018PG-T1D053, G-2108-04793). The content and views expressed are the responsibility of the authors and do not necessarily reflect the official view of nPOD. Organ Procurement Organizations (OPO) partnering with nPOD to provide research resources are listed at