Dataset Information

Differential CpG methylation at Nnat in the early establishment of beta cell heterogeneity

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive HF-X, Q Exactive

ORGANISM(S): Rattus Norvegicus (rat) Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Type B Pancreatic Cell

DISEASE(S): Type 2 Diabetes Mellitus

SUBMITTER: Alex Montoya

LAB HEAD: Dr Pavel Shliaha

PROVIDER: PXD048465 | Pride | 2024-03-22

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Mmusculus_UP000000589_10090_20220322.fasta	Fasta
	Rnorvegicus_UP000002494_10116_20220531.fasta	Fasta
	Swissprot_human_20180104.fasta	Fasta
	b010p040_M1_TR01.raw	Raw
	b010p040_M1_TR02.raw	Raw

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Publications

Differential CpG methylation at <i>Nnat</i> in the early establishment of beta cell heterogeneity.

Yu Vanessa V Yong Fiona F Marta Angellica A Khadayate Sanjay S Osakwe Adrien A Bhattacharya Supriyo S Varghese Sneha S SS Chabosseau Pauline P Tabibi Sayed M SM Chen Keran K Georgiadou Eleni E Parveen Nazia N Suleiman Mara M Stamoulis Zoe Z Marselli Lorella L De Luca Carmela C Tesi Marta M Ostinelli Giada G Delgadillo-Silva Luis L Wu Xiwei X Hatanaka Yuki Y Montoya Alex A Elliott James J Patel Bhavik B Demchenko Nikita N Whilding Chad C Hajkova Petra P Shliaha Pavel P Kramer Holger H Ali Yusuf Y Marchetti Piero P Sladek Robert R Dhawan Sangeeta S Withers Dominic J DJ Rutter Guy A GA Millership Steven J SJ

bioRxiv : the preprint server for biology 20231130

<h4>Aims/hypothesis</h4>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 Ca<sup>2+</sup> waves. Functional subpopulations have also been demonstrated in human beta cells, with an altered subtype distribution apparent in type 2 diabetes. At present, the ...[more]

PMID: 38076935

Similar Datasets

Project description: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 the Nnat enhancer/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: Nnat mRNA 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 of Nnat-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 “bHI” cells and were diminished in db/db mice. ‘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 at Nnat represents 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.