Human Pancreatic α-Cell Heterogeneity and Trajectory Inference Analysis Using Integrated Single Cell- and Single Nucleus-RNA Sequencing Platforms

ABSTRACT Prior studies have shown that pancreatic α-cells can transdifferentiate into β-cells, and that β-cells de-differentiate and are prone to acquire an α-cell phenotype in type 2 diabetes (T2D). However, the specific human α-cell and β-cell subtypes that are involved in α-to-β-cell and β-to-α-cell transitions are unknown. Here, we have integrated single cell RNA sequencing (scRNA-seq) and single nucleus RNA-seq (snRNA-seq) of isolated human islets and human islet grafts and provide additional insight into α-β cell fate switching. Using this approach, we make seven novel observations. 1) There are five differentGCG-expressing human α-cell subclusters [α1, α2, α-β-transition 1 (AB-Tr1), α-β-transition 2 (AB-Tr2), and α-β (AB) cluster] with different transcriptome profiles in human islets from non-diabetic donors. 2) The AB subcluster displays multihormonal gene expression, inferred mostly from snRNA-seq data suggesting identification by pre-mRNA expression. 3) The α1, α2, AB-Tr1, and AB-Tr2 subclusters are enriched in genes specific for α-cell function while AB cells are enriched in genes related to pancreatic progenitor and β-cell pathways; 4) Trajectory inference analysis of extracted α- and β-cell clusters and RNA velocity/PAGA analysis suggests a bifurcate transition potential for AB towards both α- and β-cells. 5) Gene commonality analysis identifiesZNF385D, TRPM3, CASR, MEG3andHDAC9as signature for trajectories moving towards β-cells andSMOC1, PLCE1, PAPPA2, ZNF331, ALDH1A1, SLC30A8, BTG2, TM4SF4, NR4A1andPSCK2as signature for trajectories moving towards α-cells. 6) Remarkably, in contrast to the eventsin vitro, the AB subcluster is not identifiedin vivoin human islet grafts and trajectory inference analysis suggests only unidirectional transition from α-to-β-cellsin vivo. 7) Analysis of scRNA-seq datasets from adult human T2D donor islets reveals a clear unidirectional transition from β-to-α-cells compatible with dedifferentiation or conversion into α-cells. Collectively, these studies show that snRNA-seq and scRNA-seq can be leveraged to identify transitions in the transcriptional status among human islet endocrine cell subpopulationsin vitro,in vivo, in non-diabetes and in T2D. They reveal the potential gene signatures for common trajectories involved in interconversion between α- and β-cells and highlight the utility and power of studying single nuclear transcriptomes of human isletsin vivo. Most importantly, they illustrate the importance of studying human islets in their naturalin vivosetting..

Medienart:	Preprint

Erscheinungsjahr:	2023
Erschienen:	2023

Enthalten in:	bioRxiv.org - (2023) vom: 22. Nov. Zur Gesamtaufnahme - year:2023

Sprache:	Englisch

Beteiligte Personen:	Kang, Randy B. [VerfasserIn] Lee, Jungeun [VerfasserIn] Varela, Miguel [VerfasserIn] Li, Yansui [VerfasserIn] Rosselot, Carolina [VerfasserIn] Zhang, Tuo [VerfasserIn] Karakose, Esra [VerfasserIn] Stewart, Andrew F. [VerfasserIn] Scott, Donald K. [VerfasserIn] Garcia-Ocana, Adolfo [VerfasserIn] Lu, Geming [VerfasserIn]

Links:	Volltext [kostenfrei]

Themen:	570 Biology

doi:	10.1101/2023.11.19.567715

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PPN (Katalog-ID):	XBI041601742