Insights into islet development and biology through characterization of a human iPSC-derived endocrine pancreas model

Abstract

Directed differentiation of stem cells offers a scalable solution to the need for human cell models recapitulating islet biology and T2D pathogenesis. We profiled mRNA expression at 6 stages of an induced pluripotent stem cell (iPSC) model of endocrine pancreas development from 2 donors, and characterized the distinct transcriptomic profiles associated with each stage. Established regulators of endodermal lineage commitment, such as SOX17 (log2 fold change [FC] compared to iPSCs = 14.2, p-value = 4.9 × 10(-5)) and the pancreatic agenesis gene GATA6 (log2 FC = 12.1, p-value = 8.6 × 10(-5)), showed transcriptional variation consistent with their known developmental roles. However, these analyses highlighted many other genes with stage-specific expression patterns, some of which may be novel drivers or markers of islet development. For example, the leptin receptor gene, LEPR, was most highly expressed in published data from in vivo-matured cells compared to our endocrine pancreas-like cells (log2 FC = 5.5, p-value = 2.0 × 10(-12)), suggesting a role for the leptin pathway in the maturation process. Endocrine pancreas-like cells showed significant stage-selective expression of adult islet genes, including INS, ABCC8, and GLP1R, and enrichment of relevant GO-terms (e.g. "insulin secretion"; odds ratio = 4.2, p-value = 1.9 × 10(-3)): however, principal component analysis indicated that in vitro-differentiated cells were more immature than adult islets. Integration of the stage-specific expression information with genetic data from T2D genome-wide association studies revealed that 46 of 82 T2D-associated loci harbor genes present in at least one developmental stage, facilitating refinement of potential effector transcripts. Together, these data show that expression profiling in an iPSC islet development model can further understanding of islet biology and T2D pathogenesis.

Keywords: diabetes; differentiation; endocrine pancreas; pluripotent stem cells; transcriptional profiling.

Figure 1.

Characterizing the transcriptome of an iPSC-derived endocrine pancreas-like cell model. (A) Expression pattern of 6 differentiation stage marker genes for 2 independent iPSC lines (green = donor 1; pink = donor 2). (B) Heatmap showing the Euclidean distances between the samples as calculated from voom-transformed expression values. (C) FACS plots showing c-Peptide/NKX6.1 (and relevant isotype controls) expression in the EN-stage of both iPSC lines. iPSC = induced pluripotent stem cells; DE = definitive endoderm; GT = primitive gut tube; PF = posterior foregut; PE = pancreatic endoderm; EN = endocrine pancreas-like cells; TPM = transcripts per kilobase million.

Figure 2.

Transcriptomic comparison of in vitro-differentiated versus in vivo-matured human embryonic stem cells and primary human adult islets. (A) Heatmap showing the Euclidean distances between samples generated in this study and similar in vitro-differentiated and in vivo-matured human embryonic stem cells as calculated from the voom-transformed expression values. (B) Plot of the first 2 principal components derived from the normalized expression profiles of iPSC in vitro-differentiated and hESC in vivo-matured cells, as well as adult islets and FACS-enriched β-cell fractions. ES = embryonic stem cells; iPSC = induced pluripotent stem cells; DE = definitive endoderm; GT = primitive gut tube; PF = posterior foregut; PE = pancreatic endoderm; EN = endocrine pancreas-like cells.