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Single-nucleus RNA-Seq reveals singular gene signatures of human ductal cells during adaptation to insulin resistance
Ercument Dirice, Giorgio Basile, Sevim Kahraman, Danielle Diegisser, Jiang Hu, Rohit N. Kulkarni
Ercument Dirice, Giorgio Basile, Sevim Kahraman, Danielle Diegisser, Jiang Hu, Rohit N. Kulkarni
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Research Article Development Endocrinology

Single-nucleus RNA-Seq reveals singular gene signatures of human ductal cells during adaptation to insulin resistance

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Abstract

Adaptation to increased insulin demand is mediated by β cell proliferation and neogenesis, among other mechanisms. Although it is known that pancreatic β cells can arise from ductal progenitors, these observations have been limited mostly to the neonatal period. We have recently reported that the duct is a source of insulin-secreting cells in adult insulin-resistant states. To further explore the signaling pathways underlying the dynamic β cell reserve during insulin resistance, we undertook human islet and duct transplantations under the kidney capsule of immunodeficient NOD/SCID-γ (NSG) mouse models that were pregnant, were insulin-resistant, or had insulin resistance superimposed upon pregnancy (insulin resistance + pregnancy), followed by single-nucleus RNA-Seq (snRNA-Seq) on snap-frozen graft samples. We observed an upregulation of proliferation markers (e.g., NEAT1) and expression of islet endocrine cell markers (e.g., GCG and PPY), as well as mature β cell markers (e.g., INS), in transplanted human duct grafts in response to high insulin demand. We also noted downregulation of ductal cell identity genes (e.g., KRT19 and ONECUT2) coupled with upregulation of β cell development and insulin signaling pathways. These results indicate that subsets of ductal cells are able to gain β cell identity and reflect a form of compensation during the adaptation to insulin resistance in both physiological and pathological states.

Authors

Ercument Dirice, Giorgio Basile, Sevim Kahraman, Danielle Diegisser, Jiang Hu, Rohit N. Kulkarni

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Figure 5

Ductal cells in models of insulin resistance display regulated pathways and genes similar to T2D human β cells.

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Ductal cells in models of insulin resistance display regulated pathways ...
(A) Selected pathways derived from reanalysis of the publicly available data set (GSE81608) (26) comparing nondiabetic (CTRL) and T2D human β cells. Arrowheads highlight common pathways activated in ductal cells in pregnancy (P NSG-Lox versus NP NSG-Lox), insulin-resistant (NP NSG-LIRKO versus NP NSG-Lox), or combined models (P NSG-LIRKO versus NP NSG-Lox). Red bars indicate upregulated pathways, and blue bars indicate downregulated pathways ordered by –log10 (P value; x axis) (B) Linear regression analysis of expression levels (measured as Z scores) of genes related to the SRP-dependent cotranslational protein pathway (top panels) and the Selenoamino acid metabolism pathway (bottom panels) in T2D versus CTRL human β cells (y axis) and ductal cluster 2 (left panels) or 4 (middle and right panels) in pregnancy (P NSG-Lox versus NP NSG-Lox) or insulin-resistant (NP NSG-LIRKO versus NP NSG-Lox) models. (C) Venn diagrams representing the intersection between the significant differentially expressed genes in T2D versus CTRL human β cells (yellow circles) and the ductal cluster 2 (purple circles, top panels) or 4 (aquamarine circles, bottom panels) in pregnancy (P NSG-Lox versus NP NSG-Lox left panels), insulin-resistant (NP NSG-LIRKO versus NP NSG-Lox, middle panels), or combined (P NSG-LIRKO versus NP NSG-Lox, right panels) models. The upregulated genes are written in red, and the downregulated genes are written in blue.

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