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 6

LDB1-mediated complexes occupy active enhancers in murine and human islets.

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LDB1-mediated complexes occupy active enhancers in murine and human isle...
(A–H) Co-IF for Insulin, LDB1, and ISL1 using human pancreatic sections. n = 1 nondiabetic donor; n = 1 type 2 diabetic donor (T2D). All images were captured at ×20 zoom. (I) Murine Slc2a2 downstream locus and ChIP-qPCR at the human SLC2A2 C3-2 locus. (J) Murine Zmiz1 locus and ChIP-qPCR at the human ZMIZ1 locus. (K) Murine Ucn3 locus and ChIP-qPCR at the human UCN3 locus. (I–K) IGV windows of murine loci. LDB1 and ISL1 ChIP-seqs labeled in blue. LDB1-ISL1 common peaks are indicated by blue line segments. PDX1, NKX6.1, FOXA2, NKX2.2, and NEUROD1 ChIP-seqs are labeled in gray. Human islet regulome active enhancers: human liftOvers (indicated by red line segments); human SNP liftOvers (indicated by orange line segments). FG, fasting glycemia associated and T2D, type 2 diabetes associated. H3K27ac and H3K4me1 ChIP-seqs are labeled in green; H3K27me3 ChIP-seq is labeled in red; PhastCon (evolutionary conservation) is labeled in black. Published cis-elements are indicated in red text. Nondiabetic donor ChIPs are indicated by blue and white squares: LDB1 IP = blue squares (n = 10); normal goat IgG IP = white squares (n = 8). Type 2 diabetic donor ChIPs are indicated by red and white triangles: LDB1 IP = red triangles (n = 6); normal goat IgG IP = white triangles (n = 5). Pooled data represent the mean ± SEM. #P < 0.05 by 1-way ANOVA with Holm-Sidak correction for the following post-hoc comparisons: nondiabetic LDB1 versus nondiabetic normal goat IgG; nondiabetic LDB1 versus type 2 diabetic LDB1; type 2 diabetic LDB1 versus type 2 diabetic normal goat IgG; and nondiabetic normal goat IgG versus type 2 diabetic normal goat IgG. Absent statistical annotation indicates comparisons were not significant. See also Supplemental Figures 8–10 and Supplemental Tables 1–4. chr, chromosome.