Differential CpG methylation atNnatin the early establishment of beta cell heterogeneity
Authors: Yu Vanessa , Yong Fiona , Marta Angellica , Khadayate Sanjay , Osakwe Adrien , Bhattacharya Supriyo , Varghese Sneha S. , Chabosseau Pauline , Tabibi Sayed M. , Chen Keran , Georgiadou Eleni , Parveen Nazia , Suleiman Mara , Stamoulis Zoe , Marselli Lorella , De Luca Carmela , Tesi Marta , Ostinelli Giada , Delgadillo-Silva Luis , Wu Xiwei , Hatanaka Yuki , Montoya Alex , Elliott James , Patel Bhavik , Demchenko Nikita , Whilding Chad , Hajkova Petra , Shliaha Pavel , Kramer Holger , Ali Yusuf , Marchetti Piero , Sladek Robert , Dhawan Sangeeta , Withers Dominic J. , Rutter Guy A. , Millership Steven J. 
Published: February 2023

Aims/hypothesis

Beta cells within the pancreatic islet represent a heterogenous population wherein individual sub-groups of cells make distinct contributions to the overall control of insulin secretion. These include a subpopulation of highly-connected ‘hub’ cells, important for the propagation of intercellular Ca2+waves. Functional subpopulations have also been demonstrated in human beta cells, with an altered subtype distribution apparent in type 2 diabetes. At present, the molecular mechanisms through which beta cell hierarchy is established are poorly understood. Changes at the level of the epigenome provide one such possibility which we explore here by focussing on the imprinted gene neuronatin (Nnat), which is required for normal insulin synthesis and secretion.

Methods

Single cell RNA-seq datasets were examined using Seurat 4.0 and ClusterProfiler running under R. Transgenic mice expressing eGFP under the control of theNnatenhancer/promoter regions were generated for fluorescence-activated cell (FAC) sorting of beta cells and downstream analysis of CpG methylation by bisulphite and RNA sequencing, respectively. Animals deleted for the de novo methyltransferase, DNMT3A from the pancreatic progenitor stage were used to explore control of promoter methylation. Proteomics was performed using affinity purification mass spectrometry and Ca2+dynamics explored by rapid confocal imaging of Cal-520 and Cal-590. Insulin secretion was measured using Homogeneous Time Resolved Fluorescence Imaging.

Results

NnatmRNA was differentially expressed in a discrete beta cell population in a developmental stage- and DNA methylation (DNMT3A)-dependent manner. Thus, pseudo-time analysis of embryonic data sets demonstrated the early establishment ofNnat-positive and negative subpopulations during embryogenesis. NNAT expression is also restricted to a subset of beta cells across the human islet that is maintained throughout adult life. NNAT+beta cells also displayed a discrete transcriptome at adult stages, representing a sub-population specialised for insulin production, reminiscent of recently-described “βHI” cells and were diminished indb/dbmice. ‘Hub’ cells were less abundant in the NNAT+population, consistent with epigenetic control of this functional specialization.

Conclusions/interpretation

These findings demonstrate that differential DNA methylation atNnatrepresents a novel means through which beta cell heterogeneity is established during development. We therefore hypothesise that changes in methylation at this locus may thus contribute to a loss of beta cell hierarchy and connectivity, potentially contributing to defective insulin secretion in some forms of diabetes.

Research in context

What is already known about this subject?

- Neuronatin (Nnat/NNAT) is an imprinted gene in humans and mice and is required for glucose-stimulated insulin secretionin vivo

- Pancreatic beta cells are functionally heterogeneous with specific highly-connected subpopulations known to coordinate islet wide Ca2+dynamics

- Functional subpopulations have been described in human beta cells and their distribution is altered in type 2 diabetes

What is the key question?

- Does NNAT mark a discrete subpopulation of functional beta cells and which epigenetic pathways coordinate its formation and maintenance?

What are the new findings?

- A subpopulation of NNAT+beta cells is established prior to the first week of postnatal life in mice via de novo DNA methylation at theNnatpromoter

- NNAT+beta cells are transcriptionally highly differentiated and appear to be functionally specialised for insulin production, possibly corresponding to recently-described “βHI” and “CD63hi” beta cells. NNAT is expressed in a subset of beta cells across the human islet, and its deficiency in human beta cells diminishes glucose-stimulated insulin secretion

- NNAT+cells are likelier to belong to the population of ‘follower’, rather than ‘hub’ cells, consistent with a role in insulin production rather than glucose detection

How might this impact on clinical practice in the foreseeable future?

- Epigenome-modifying compounds may provide a way of enhancing beta cell function and the ensemble behaviour of the islet to stimulate insulin secretion