LIM domain–binding 1 maintains the terminally differentiated state of pancreatic β cells
Benjamin N. Ediger, Hee-Woong Lim, Christine Juliana, David N. Groff, LaQueena T. Williams, Giselle Dominguez, Jin-Hua Liu, Brandon L. Taylor, Erik R. Walp, Vasumathi Kameswaran, Juxiang Yang, Chengyang Liu, Chad S. Hunter, Klaus H. Kaestner, Ali Naji, Changhong Li, Maike Sander, Roland Stein, Lori Sussel, Kyoung-Jae Won, Catherine Lee May, Doris A. Stoffers
Benjamin N. Ediger, Hee-Woong Lim, Christine Juliana, David N. Groff, LaQueena T. Williams, Giselle Dominguez, Jin-Hua Liu, Brandon L. Taylor, Erik R. Walp, Vasumathi Kameswaran, Juxiang Yang, Chengyang Liu, Chad S. Hunter, Klaus H. Kaestner, Ali Naji, Changhong Li, Maike Sander, Roland Stein, Lori Sussel, Kyoung-Jae Won, Catherine Lee May, Doris A. Stoffers
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Research Article Genetics

LIM domain–binding 1 maintains the terminally differentiated state of pancreatic β cells

Abstract

The recognition of β cell dedifferentiation in type 2 diabetes raises the translational relevance of mechanisms that direct and maintain β cell identity. LIM domain–binding protein 1 (LDB1) nucleates multimeric transcriptional complexes and establishes promoter-enhancer looping, thereby directing fate assignment and maturation of progenitor populations. Many terminally differentiated endocrine cell types, however, remain enriched for LDB1, but its role is unknown. Here, we have demonstrated a requirement for LDB1 in maintaining the terminally differentiated status of pancreatic β cells. Inducible ablation of LDB1 in mature β cells impaired insulin secretion and glucose homeostasis. Transcriptomic analysis of LDB1-depleted β cells revealed the collapse of the terminally differentiated gene program, indicated by a loss of β cell identity genes and induction of the endocrine progenitor factor neurogenin 3 (NEUROG3). Lineage tracing confirmed that LDB1-depleted, insulin-negative β cells express NEUROG3 but do not adopt alternate endocrine cell fates. In primary mouse islets, LDB1 and its LIM homeodomain–binding partner islet 1 (ISL1) were coenriched at chromatin sites occupied by pancreatic and duodenal homeobox 1 (PDX1), NK6 homeobox 1 (NKX6.1), forkhead box A2 (FOXA2), and NK2 homeobox 2 (NKX2.2) — factors that co-occupy active enhancers in 3D chromatin domains in human islets. Indeed, LDB1 was enriched at active enhancers in human islets. Thus, LDB1 maintains the terminally differentiated state of β cells and is a component of active enhancers in both murine and human islets.

Authors

Benjamin N. Ediger, Hee-Woong Lim, Christine Juliana, David N. Groff, LaQueena T. Williams, Giselle Dominguez, Jin-Hua Liu, Brandon L. Taylor, Erik R. Walp, Vasumathi Kameswaran, Juxiang Yang, Chengyang Liu, Chad S. Hunter, Klaus H. Kaestner, Ali Naji, Changhong Li, Maike Sander, Roland Stein, Lori Sussel, Kyoung-Jae Won, Catherine Lee May, Doris A. Stoffers

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Figure 5

LDB1 and ISL1 are coenriched throughout the β cell genome.

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LDB1 and ISL1 are coenriched throughout the β cell genome. (A) Scatter p...
(A) Scatter plot comparing signal strength in reads per million (RPM) of ISL1 and LDB1 primary islet ChIP-seqs at the combined set of called peaks from both ChIP-seqs. Blue dots represent peaks in the LDB1, ISL1 common set; red-purple dots represent peaks in the ISL1-alone set. log2(ISL1 ChIP-seq RPM/LDB1 ChIP-seq RPM) = 2.0 delineates the 2 sets. (B) De novo motif analysis of the LDB1, ISL1 common peak set. The de novo motif is presented with the percentage of LDB1-ISL1 common peaks containing the motif and the P value. (C) Heatmap of primary mouse islet LDB1, ISL1, PDX1, NKX6.1, FOXA2, NEUROD1, H3K27ac, H3K4me1, H3K4me3, and H3K27me3 ChIP-seq data, Min6 NKX2.2 ChIP-seq data, and evolutionary conservation (phastCon) for the LDB1, ISL1 common and ISL1-alone peak sets. LDB1, ISL1 common peaks are displayed from the highest to lowest average LDB1 and ISL1 ChIP-seq signal. (D) Density of motifs with respect to identified LDB1, ISL1 common peaks. Colors above the plot correspond to the respective curve in the overlay panel. (E) Western blot (WB) of LDB1 and IgG immunoprecipitates using Min6 nuclear lysates (n = 3). The loaded volume is displayed as the percentage of immunoprecipitate volume. See also Supplemental Figures 6 and 7.