DNA Methylation–Based Assessment of Cell Composition in Human Pancreas and Islets

Author:

Drawshy Zeina1ORCID,Neiman Daniel1,Fridlich Ori1,Peretz Ayelet1,Magenheim Judith1,Rozo Andrea V.23,Doliba Nicolai M.23,Stoffers Doris A.23,Kaestner Klaus H.23,Schatz Desmond A.4,Wasserfall Clive5,Campbell-Thompson Martha5,Shapiro James6,Kaplan Tommy17,Shemer Ruth1,Glaser Benjamin1ORCID,Klochendler Agnes1,Dor Yuval1ORCID

Affiliation:

1. 1Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada (IMRIC), Hebrew University-Hadassah Medical School, Jerusalem, Israel

2. 2Human Pancreas Analysis Program, University of Pennsylvania, Philadelphia, PA

3. 3Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA

4. 4Department of Pediatrics, University of Florida, Gainesville, FL

5. 5Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL

6. 6Surgery Department, Faculty of Medicine and Dentistry, Li Ka Shing Centre for Research, Edmonton, Alberta, Canada

7. 7School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel

Abstract

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 β-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 β-cell DNA revealed similar β-cell function in pre–type 1 diabetes (T1D), T1D, and type 2 diabetes (T2D), which was significantly lower than in donors without diabetes. In histological pancreas specimens from recent-onset T1D, this assay showed β-cell fraction within the normal range, suggesting a significant contribution of β-cell dysfunction. In T2D pancreata, we observed increased α-cell fraction and normal β-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. Article Highlights

Funder

Division of Diabetes, Endocrinology, and Metabolic Diseases

Juvenile Diabetes Research Foundation United States of America

Publisher

American Diabetes Association

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