NEUROD1 is a transcription factor that helps maintain a mature phenotype of pancreatic β cells. Disruption of Neurod1 during pancreatic development causes severe neonatal diabetes; however, the exact role of NEUROD1 in the differentiation programs of endocrine cells is unknown. Here, we report a crucial role of the NEUROD1 regulatory network in endocrine lineage commitment and differentiation. Mechanistically, transcriptome and chromatin landscape analyses demonstrate that Neurod1 inactivation triggers a downregulation of endocrine differentiation transcription factors and upregulation of non-endocrine genes within the Neurod1-deficient endocrine cell population, disturbing endocrine identity acquisition. Neurod1 deficiency altered the H3K27me3 histone modification pattern in promoter regions of differentially expressed genes, which resulted in gene regulatory network changes in the differentiation pathway of endocrine cells, compromising endocrine cell potential, differentiation, and functional properties.

Diabetes Centre Experimental Medicine Centre Institute for Clinical and Experimental Medicine 14021 Prague Czechia

Laboratory of Gene Expression Institute of Biotechnology CAS 25250 Vestec Czechia

Laboratory of Molecular Pathogenetics Institute of Biotechnology CAS 25250 Vestec Czechia

Zobrazit více v PubMed

Röder PV, Wu B, Liu Y, Han W. Pancreatic regulation of glucose homeostasis. Exp. Mol. Med. 2016;48:e219–e219. PubMed PMC

Perez-Frances M, et al. Adult pancreatic islet endocrine cells emerge as fetal hormone-expressing cells. Cell Rep. 2022;38:110377. PubMed PMC

Pandian GN, Taniguchi J, Sugiyama H. Cellular reprogramming for pancreatic β-cell regeneration: clinical potential of small molecule control. Clin. Transl. Med. 2014;3:6–6. PubMed PMC

Kim H-S, Lee M-K. β-Cell regeneration through the transdifferentiation of pancreatic cells: pancreatic progenitor cells in the pancreas. J. Diabetes Investig. 2016;7:286–296. PubMed PMC

Alvarez Fallas ME, et al. Stem/progenitor cells in normal physiology and disease of the pancreas. Mol. Cell Endocrinol. 2021;538:111459–111459. PubMed PMC

Isaacson A, Spagnoli FM. Pancreatic cell fate specification: insights into developmental mechanisms and their application for lineage reprogramming. Curr. Opin. Genet. Dev. 2021;70:32–39. PubMed

Arda HE, Benitez CM, Kim SK. Gene regulatory networks governing pancreas development. Dev. Cell. 2013;25:5–13. PubMed PMC

Jennings RE, Scharfmann R, Staels W. Transcription factors that shape the mammalian pancreas. Diabetologia. 2020;63:1974–1980. PubMed PMC

Szlachcic WJ, Ziojla N, Kizewska DK, Kempa M, Borowiak M. Endocrine pancreas development and dysfunction through the lens of single-cell RNA-sequencing. Front Cell Dev. Biol. 2021;9:629212. PubMed PMC

Zhou Q, et al. A multipotent progenitor domain guides pancreatic organogenesis. Dev. Cell. 2007;13:103–114. PubMed

Jennings RE, Berry AA, Strutt JP, Gerrard DT, Hanley NA. Human pancreas development. Development. 2015;142:3126–3137. PubMed

Shih HP, et al. A Notch-dependent molecular circuitry initiates pancreatic endocrine and ductal cell differentiation. Development. 2012;139:2488–2499. PubMed PMC

Villasenor A, Chong DC, Cleaver O. Biphasic Ngn3 expression in the developing pancreas. Dev. Dyn. 2008;237:3270–3279. PubMed PMC

Dassaye R, Naidoo S, Cerf ME. Transcription factor regulation of pancreatic organogenesis, differentiation and maturation. Islets. 2016;8:13–34. PubMed PMC

Jennings RE, et al. Development of the human pancreas from foregut to endocrine commitment. Diabetes. 2013;62:3514–3522. PubMed PMC

Herrera PL, et al. Embryogenesis of the murine endocrine pancreas; early expression of pancreatic polypeptide gene. Development. 1991;113:1257–1265. PubMed

Gradwohl G, Dierich A, LeMeur M, Guillemot F. neurogenin3 is required for the development of the four endocrine cell lineages of the pancreas. Proc. Natl Acad. Sci. USA. 2000;97:1607–1611. PubMed PMC

Schreiber V, et al. Extensive NEUROG3 occupancy in the human pancreatic endocrine gene regulatory network. Mol. Metab. 2021;53:101313. PubMed PMC

Kaimala S, Kumar CA, Allouh MZ, Ansari SA, Emerald BS. Epigenetic modifications in pancreas development, diabetes, and therapeutics. Med. Res. Rev. 2022;42:1343–1371. PubMed PMC

Dumasia NP, Pethe PS. Pancreas development and the Polycomb group protein complexes. Mech. Dev. 2020;164:103647. PubMed

Ding Y, et al. JMJD3: a critical epigenetic regulator in stem cell fate. Cell Commun. Signal. 2021;19:72. PubMed PMC

Voigt P, Tee W-W, Reinberg D. A double take on bivalent promoters. Genes Dev. 2013;27:1318–1338. PubMed PMC

Shpargel KB, Starmer J, Yee D, Pohlers M, Magnuson T. KDM6 demethylase independent loss of histone H3 lysine 27 trimethylation during early embryonic development. PLoS Genet. 2014;10:e1004507. PubMed PMC

Harikumar A, Meshorer E. Chromatin remodeling and bivalent histone modifications in embryonic stem cells. EMBO Rep. 2015;16:1609–1619. PubMed PMC

Schwitzgebel VM, et al. Expression of neurogenin3 reveals an islet cell precursor population in the pancreas. Development. 2000;127:3533–3542. PubMed

Huang HP, et al. Regulation of the pancreatic islet-specific gene BETA2 (neuroD) by neurogenin 3. Mol. Cell Biol. 2000;20:3292–3307. PubMed PMC

Jeon J, Correa-Medina M, Ricordi C, Edlund H, Diez JA. Endocrine Cell Clustering During Human Pancreas Development. J. Histochem. Cytochem. 2009;57:811–824. PubMed PMC

Gasa R, et al. Induction of pancreatic islet cell differentiation by the neurogenin-neuroD cascade. Differentiation. 2008;76:381–391. PubMed

Krentz NAJ, et al. Single-cell transcriptome profiling of mouse and hESC-derived pancreatic progenitors. Stem Cell Rep. 2018;11:1551–1564. PubMed PMC

Jensen J, et al. Independent development of pancreatic alpha- and beta-cells from neurogenin3-expressing precursors: a role for the notch pathway in repression of premature differentiation. Diabetes. 2000;49:163–176. PubMed

Yu X-X et al. Dynamics of chromatin marks and the role of JMJD3 during pancreatic endocrine cell fate commitment. Development145 (2018). PubMed

Bankaitis ED, Bechard ME, Wright CVE. Feedback control of growth, differentiation, and morphogenesis of pancreatic endocrine progenitors in an epithelial plexus niche. Genes Dev. 2015;29:2203–2216. PubMed PMC

Matsuda T, et al. Pioneer factor NeuroD1 rearranges transcriptional and epigenetic profiles to execute microglia-neuron conversion. Neuron. 2019;101:472–485.e477. PubMed

Pataskar A, et al. NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program. EMBO J. 2016;35:24–45. PubMed PMC

Akol I, et al. Multimodal epigenetic changes and altered NEUROD1 chromatin binding in the mouse hippocampus underlie FOXG1 syndrome. Proc. Natl Acad. Sci. USA. 2023;120:e2122467120. PubMed PMC

Gao Z, et al. Neurod1 is essential for the survival and maturation of adult-born neurons. Nat. Neurosci. 2009;12:1090–1092. PubMed PMC

Filova I, et al. Early deletion of Neurod1 alters neuronal lineage potential and diminishes neurogenesis in the inner ear. Front Cell Dev. Biol. 2022;10:845461. PubMed PMC

Hevner RF, Hodge RD, Daza RA, Englund C. Transcription factors in glutamatergic neurogenesis: conserved programs in neocortex, cerebellum, and adult hippocampus. Neurosci. Res. 2006;55:223–233. PubMed

Miyata T, Maeda T, Lee JE. NeuroD is required for differentiation of the granule cells in the cerebellum and hippocampus. Genes Dev. 1999;13:1647–1652. PubMed PMC

Gu G, Dubauskaite J, Melton DA. Direct evidence for the pancreatic lineage: NGN3+ cells are islet progenitors and are distinct from duct progenitors. Development. 2002;129:2447–2457. PubMed

Chu K, Nemoz-Gaillard E, Tsai MJ. BETA2 and pancreatic islet development. Recent Prog. Horm. Res. 2001;56:23–46. PubMed

Itkin-Ansari P, et al. NeuroD1 in the endocrine pancreas: localization and dual function as an activator and repressor. Dev. Dyn. 2005;233:946–953. PubMed

Mastracci TL, Anderson KR, Papizan JB, Sussel L. Regulation of Neurod1 contributes to the lineage potential of neurogenin3+ endocrine precursor cells in the pancreas. PLoS Genet. 2013;9:e1003278. PubMed PMC

Romer AI, Singer RA, Sui L, Egli D, Sussel L. Murine perinatal β-cell proliferation and the differentiation of human stem cell-derived insulin-expressing cells require NEUROD1. Diabetes. 2019;68:2259–2271. PubMed PMC

Bohuslavova R, et al. NEUROD1 is required for the early α and β endocrine differentiation in the pancreas. Int. J. Mol. Sci. 2021;22:6713. PubMed PMC

Naya FJ, et al. Diabetes, defective pancreatic morphogenesis, and abnormal enteroendocrine differentiation in BETA2/neuroD-deficient mice. Genes Dev. 1997;11:2323–2334. PubMed PMC

Dudek K. D., Osipovich A. B., Cartailler J-P, Gu G. & Magnuson M. A. Insm1, Neurod1, and Pax6 promote murine pancreatic endocrine cell development through overlapping yet distinct RNA transcription and splicing programs. G3 Genes|Genomes|Genetics11 (2021). PubMed PMC

Gu C, et al. Pancreatic beta cells require NeuroD to achieve and maintain functional maturity. Cell Metab. 2010;11:298–310. PubMed PMC

Jia S, et al. Insm1 cooperates with Neurod1 and Foxa2 to maintain mature pancreatic β-cell function. EMBO J. 2015;34:1417–1433. PubMed PMC

Malecki MT, et al. Mutations in NEUROD1 are associated with the development of type 2 diabetes mellitus. Nat. Genet. 1999;23:323–328. PubMed

Rubio-Cabezas O, et al. Homozygous mutations in NEUROD1 are responsible for a novel syndrome of permanent neonatal diabetes and neurological abnormalities. Diabetes. 2010;59:2326–2331. PubMed PMC

Horikawa Y, Enya M. Genetic dissection and clinical features of MODY6 (NEUROD1-MODY) Curr. Diab. Rep. 2019;19:12. PubMed

Docherty HM, et al. Relative contribution of PDX-1, MafA and E47/beta2 to the regulation of the human insulin promoter. Biochem J. 2005;389:813–820. PubMed PMC

Babu DA, Chakrabarti SK, Garmey JC, Mirmira RG. Pdx1 and BETA2/NeuroD1 participate in a transcriptional complex that mediates short-range DNA looping at the insulin gene. J. Biol. Chem. 2008;283:8164–8172. PubMed PMC

Naya FJ, Stellrecht CM, Tsai MJ. Tissue-specific regulation of the insulin gene by a novel basic helix-loop-helix transcription factor. Genes Dev. 1995;9:1009–1019. PubMed

Huang HP, Chu K, Nemoz-Gaillard E, Elberg D, Tsai MJ. Neogenesis of beta-cells in adult BETA2/NeuroD-deficient mice. Mol. Endocrinol. 2002;16:541–551. PubMed

Kaya-Okur HS, et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat. Commun. 2019;10:1930. PubMed PMC

Goebbels S, et al. Cre/loxP-mediated inactivation of the bHLH transcription factor gene NeuroD/BETA2. Genesis. 2005;42:247–252. PubMed

Li HJ, Kapoor A, Giel-Moloney M, Rindi G, Leiter AB. Notch signaling differentially regulates the cell fate of early endocrine precursor cells and their maturing descendants in the mouse pancreas and intestine. Dev. Biol. 2012;371:156–169. PubMed PMC

Madisen L, et al. A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nat. Neurosci. 2010;13:133–140. PubMed PMC

Bohuslavova R, et al. ISL1 controls pancreatic alpha cell fate and beta cell maturation. Cell Biosci. 2023;13:53. PubMed PMC

Qiu WL, et al. Deciphering pancreatic islet β cell and α cell maturation pathways and characteristic features at the single-cell level. Cell Metab. 2017;25:1194–1205.e1194. PubMed

Pauerstein PT, et al. A radial axis defined by semaphorin-to-neuropilin signaling controls pancreatic islet morphogenesis. Development. 2017;144:3744–3754. PubMed PMC

Roscioni SS, Migliorini A, Gegg M, Lickert H. Impact of islet architecture on beta-cell heterogeneity, plasticity and function. Nat. Rev. Endocrinol. 2016;12:695–709. PubMed

Brereton MF, Vergari E, Zhang Q, Clark A. Alpha-, delta- and pp-cells: are they the architectural cornerstones of islet structure and co-ordination? J. Histochem. Cytochem. 2015;63:575–591. PubMed PMC

Migliorini A, Bader E, Lickert H. Islet cell plasticity and regeneration. Mol. Metab. 2014;3:268–274. PubMed PMC

Burlison JS, Long Q, Fujitani Y, Wright CV, Magnuson MA. Pdx-1 and Ptf1a concurrently determine fate specification of pancreatic multipotent progenitor cells. Dev. Biol. 2008;316:74–86. PubMed PMC

Bastidas-Ponce A, et al. Foxa2 and Pdx1 cooperatively regulate postnatal maturation of pancreatic beta-cells. Mol. Metab. 2017;6:524–534. PubMed PMC

Ahlgren U, Jonsson J, Jonsson L, Simu K, Edlund H. beta-cell-specific inactivation of the mouse Ipf1/Pdx1 gene results in loss of the beta-cell phenotype and maturity onset diabetes. Genes Dev. 1998;12:1763–1768. PubMed PMC

Duvillie B, et al. Phenotypic alterations in insulin-deficient mutant mice. Proc. Natl Acad. Sci. USA. 1997;94:5137–5140. PubMed PMC

Raudvere U, et al. g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update) Nucleic Acids Res. 2019;47:W191–W198. PubMed PMC

Liew CW, et al. Insulin regulates carboxypeptidase E by modulating translation initiation scaffolding protein eIF4G1 in pancreatic β cells. Proc. Natl Acad. Sci. USA. 2014;111:E2319–E2328. PubMed PMC

Kohara K, et al. Suppression of free fatty acid receptor 1 expression in pancreatic β-cells in obese type 2 diabetic db/db mice: a potential role of pancreatic and duodenal homeobox factor 1. Endocr. J. 2019;66:43–50. PubMed

Millership SJ, et al. Neuronatin regulates pancreatic β cell insulin content and secretion. J. Clin. Invest. 2018;128:3369–3381. PubMed PMC

Farber CR, et al. Overexpression of Scg5 increases enzymatic activity of PCSK2 and is inversely correlated with body weight in congenic mice. BMC Genet. 2008;9:34. PubMed PMC

Jonsson A, et al. Effect of a common variant of the PCSK2 gene on reduced insulin secretion. Diabetologia. 2012;55:3245–3251. PubMed

Choi S, Korstanje R. Proprotein convertases in high-density lipoprotein metabolism. Biomark. Res. 2013;1:27. PubMed PMC

Manialawy Y, Khan SR, Bhattacharjee A, Wheeler MB. The magnesium transporter NIPAL1 is a pancreatic islet–expressed protein that conditionally impacts insulin secretion. J. Biol. Chem. 2020;295:9879–9892. PubMed PMC

Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic. Acids Res. 2010;38:D355–D360. PubMed PMC

Zhang C, et al. MafA is a key regulator of glucose-stimulated insulin secretion. Mol. Cell. Biol. 2005;25:4969–4976. PubMed PMC

Schulla V, et al. Impaired insulin secretion and glucose tolerance in beta cell-selective Ca(v)1.2 Ca2+ channel null mice. EMBO J. 2003;22:3844–3854. PubMed PMC

Sadagurski M, Dong XC, Myers MG, Jr., White MF. Irs2 and Irs4 synergize in non-LepRb neurons to control energy balance and glucose homeostasis. Mol. Metab. 2013;3:55–63. PubMed PMC

Sugawara K, Shibasaki T, Takahashi H, Seino S. Structure and functional roles of Epac2 (Rapgef4) Gene. 2016;575:577–583. PubMed PMC

Tengholm A, Gylfe E. cAMP signalling in insulin and glucagon secretion. Diabetes Obes. Metab. 2017;19:42–53. PubMed

Prentki M, Matschinsky Franz M, Madiraju SRM. Metabolic signaling in fuel-induced insulin secretion. Cell Metab. 2013;18:162–185. PubMed

Yavari A, et al. Chronic activation of γ2 AMPK induces obesity and reduces β cell function. Cell Metab. 2016;23:821–836. PubMed PMC

Loh K, et al. Inhibition of adenosine monophosphate-activated protein kinase-3-hydroxy-3-methylglutaryl coenzyme a reductase signaling leads to hypercholesterolemia and promotes hepatic steatosis and insulin resistance. Hepatol. Commun. 2019;3:84–98. PubMed PMC

Joshi T, et al. Targeting AMPK signaling pathway by natural products for treatment of diabetes mellitus and its complications. J. Cell Physiol. 2019;234:17212–17231. PubMed

Machida Y, et al. Pancreatic islet neuropeptide Y overexpression has minimal effect on islet morphology and β-cell adaptation to high-fat diet. Endocrinology. 2014;155:4634–4640. PubMed PMC

Mihaylova MM, Shaw RJ. The AMPK signalling pathway coordinates cell growth, autophagy and metabolism. Nat. Cell Biol. 2011;13:1016–1023. PubMed PMC

Lodh S. Primary Cilium, An Unsung Hero in Maintaining Functional β-cell Population. Yale J. Biol. Med. 2019;92:471–480. PubMed PMC

Seymour PA, et al. SOX9 is required for maintenance of the pancreatic progenitor cell pool. Proc. Natl Acad. Sci. USA. 2007;104:1865–1870. PubMed PMC

Yu J, et al. WLS retrograde transport to the endoplasmic reticulum during Wnt secretion. Dev. Cell. 2014;29:277–291. PubMed

Baumgartner BK, Cash G, Hansen H, Ostler S, Murtaugh LC. Distinct requirements for beta-catenin in pancreatic epithelial growth and patterning. Dev. Biol. 2014;391:89–98. PubMed PMC

Yebra M, et al. Endothelium-derived Netrin-4 supports pancreatic epithelial cell adhesion and differentiation through integrins α2β1 and α3β1. PLoS ONE. 2011;6:e22750. PubMed PMC

Kojima T, et al. Tight junctions in human pancreatic duct epithelial cells. Tissue Barriers. 2013;1:e24894. PubMed PMC

Suwa H, et al. Overexpression of the rhoC gene correlates with progression of ductal adenocarcinoma of the pancreas. Br. J. Cancer. 1998;77:147–152. PubMed PMC

Bydoun M, et al. S100A10, a novel biomarker in pancreatic ductal adenocarcinoma. Mol. Oncol. 2018;12:1895–1916. PubMed PMC

Esposito I, et al. Tumor-suppressor function of SPARC-like protein 1/Hevin in pancreatic cancer. Neoplasia. 2007;9:8–17. PubMed PMC

Guerriero, I. et al. Exploring the molecular crosstalk between pancreatic bud and mesenchyme in embryogenesis: novel signals involved. Int. J. Mol. Sci.20 (2019). PubMed PMC

Willmann SJ, et al. The global gene expression profile of the secondary transition during pancreatic development. Mech. Dev. 2016;139:51–64. PubMed

Ogaki S, Harada S, Shiraki N, Kume K, Kume S. An expression profile analysis of ES cell-derived definitive endodermal cells and Pdx1-expressing cells. BMC Dev. Biol. 2011;11:13. PubMed PMC

Sjödin A, Dahl U, Semb H. Mouse R-cadherin: expression during the organogenesis of pancreas and gastrointestinal tract. Exp. Cell Res. 1995;221:413–425. PubMed

Nagaraj V, et al. Complement inhibitor CD55 governs the integrity of membrane rafts in pancreatic beta cells, but plays no role in insulin secretion. Biochem. Biophys. Res. Commun. 2015;460:518–524. PubMed

Zbinden A, et al. Nidogen-1 mitigates ischemia and promotes tissue survival and regeneration. Adv. Sci. 2021;8:2002500. PubMed PMC

Zhang Q, et al. CD8+ effector T cell migration to pancreatic islet grafts is dependent on cognate antigen presentation by donor graft cells. J. Immunol. 2016;197:1471–1476. PubMed PMC

Warner SL, et al. Validation of TPX2 as a potential therapeutic target in pancreatic cancer cells. Clin. Cancer Res. 2009;15:6519–6528. PubMed PMC

Lee S-H, et al. The Id3/E47 axis mediates cell-cycle control in human pancreatic ducts and adenocarcinoma. Mol. Cancer Res. 2011;9:782–790. PubMed PMC

Pei YF, Yin XM, Liu XQ. TOP2A induces malignant character of pancreatic cancer through activating β-catenin signaling pathway. Biochim. Biophys. Acta Mol. Basis Dis. 2018;1864:197–207. PubMed

Hocevar BA. Loss of disabled-2 expression in pancreatic cancer progression. Sci. Rep. 2019;9:7532. PubMed PMC

Backx E, et al. MECOM permits pancreatic acinar cell dedifferentiation avoiding cell death under stress conditions. Cell Death Differ. 2021;28:2601–2615. PubMed PMC

He LH, et al. Neuropilin1 silencing impairs the proliferation and migration of cells in pancreatic cancer. J. Clin. Lab Anal. 2020;34:e23394. PubMed PMC

Yang HY, et al. Gelsolin impairs barrier function in pancreatic ductal epithelial cells by actin filament depolymerization in hypertriglyceridemia-induced pancreatitis in vitro. Exp. Ther. Med. 2022;23:290. PubMed PMC

Yu X-X, et al. Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution. EMBO J. 2019;38:e100164. PubMed PMC

Memon B, Abdelalim EM. ACE2 function in the pancreatic islet: Implications for relationship between SARS-CoV-2 and diabetes. Acta Physiol. (Oxf.) 2021;233:e13733. PubMed PMC

Favre GA, Esnault VLM, Obberghen EV. Modulation of glucose metabolism by the renin-angiotensin-aldosterone system. Am. J. Physiol.—Endocrinol. Metab. 2015;308:E435–E449. PubMed

Luther JM. Effects of aldosterone on insulin sensitivity and secretion. Steroids. 2014;91:54–60. PubMed PMC

Ceasrine, A. M., Lin, E. E., Lumelsky, D. N., Iyer, R. & Kuruvilla R. Adrb2 controls glucose homeostasis by developmental regulation of pancreatic islet vasculature. Elife7 (2018). PubMed PMC

Yao LJ, et al. Novel role for SGK3 in glucose homeostasis revealed in SGK3/Akt2 double-null mice. Mol. Endocrinol. 2011;25:2106–2118. PubMed PMC

Sherman BT, et al. DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update) Nucleic Acids Res. 2022;50:W216–W221. PubMed PMC

Mellitzer G, et al. IA1 is NGN3-dependent and essential for differentiation of the endocrine pancreas. EMBO J. 2006;25:1344–1352. PubMed PMC

Gierl MS, Karoulias N, Wende H, Strehle M, Birchmeier C. The zinc-finger factor Insm1 (IA-1) is essential for the development of pancreatic beta cells and intestinal endocrine cells. Genes Dev. 2006;20:2465–2478. PubMed PMC

Ahlgren U, Pfaff SL, Jessell TM, Edlund T, Edlund H. Independent requirement for ISL1 in formation of pancreatic mesenchyme and islet cells. Nature. 1997;385:257–260. PubMed

Matsuoka TA, et al. The MafA transcription factor appears to be responsible for tissue-specific expression of insulin. Proc. Natl Acad. Sci. USA. 2004;101:2930–2933. PubMed PMC

Scavuzzo MA, et al. Endocrine lineage biases arise in temporally distinct endocrine progenitors during pancreatic morphogenesis. Nat. Commun. 2018;9:3356. PubMed PMC

Wang Y, Sun L, Luo Y, He S. Knockdown of KDM1B inhibits cell proliferation and induces apoptosis of pancreatic cancer cells. Pathol. Res. Pr. 2019;215:1054–1060. PubMed

Duvall E, et al. Single-cell transcriptome and accessible chromatin dynamics during endocrine pancreas development. Proc. Natl Acad. Sci. 2022;119:e2201267119. PubMed PMC

Henry C, Close AF, Buteau J. A critical role for the neural zinc factor ST18 in pancreatic β-cell apoptosis. J. Biol. Chem. 2014;289:8413–8419. PubMed PMC

Yang YH, Manning Fox JE, Zhang KL, MacDonald PE, Johnson JD. Intraislet SLIT-ROBO signaling is required for beta-cell survival and potentiates insulin secretion. Proc. Natl Acad. Sci. USA. 2013;110:16480–16485. PubMed PMC

Wei D, et al. KLF4 is essential for induction of cellular identity change and acinar-to-ductal reprogramming during early pancreatic carcinogenesis. Cancer Cell. 2016;29:324–338. PubMed PMC

Zhang C, Guo Z-M. Multiple functions of Maf in the regulation of cellular development and differentiation. Diabetes/Metab. Res. Rev. 2015;31:773–778. PubMed PMC

Huang W, Lu N, Eberspaecher H, de Crombrugghe B. A new long form of c-Maf cooperates with Sox9 to activate the type II collagen gene*. J. Biol. Chem. 2002;277:50668–50675. PubMed

Rossetti S, Hoogeveen AT, Sacchi N. The MTG proteins: chromatin repression players with a passion for networking. Genomics. 2004;84:1–9. PubMed

Suk F-M, et al. ZFP36L1 and ZFP36L2 inhibit cell proliferation in a cyclin D-dependent and p53-independent manner. Sci. Rep. 2018;8:2742. PubMed PMC

Dong H, et al. Regulator of G protein signaling 2 is a key regulator of pancreatic β-cell mass and function. Cell Death Dis. 2017;8:e2821. PubMed PMC

Baron M, et al. A single-cell transcriptomic map of the human and mouse pancreas reveals inter- and intra-cell population structure. Cell Syst. 2016;3:346–360.e344. PubMed PMC

van Gurp, L. et al. A transcriptomic roadmap to alpha- and beta-cell differentiation in the embryonic pancreas. Development146 (2019). PubMed

Chu K, Tsai MJ. Neuronatin, a downstream target of BETA2/NeuroD1 in the pancreas, is involved in glucose-mediated insulin secretion. Diabetes. 2005;54:1064–1073. PubMed PMC

Heinz S, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell. 2010;38:576–589. PubMed PMC

Fujikura J, et al. Rbp-j regulates expansion of pancreatic epithelial cells and their differentiation into exocrine cells during mouse development. Dev. Dyn. 2007;236:2779–2791. PubMed

Fujikura J, et al. Notch/Rbp-j signaling prevents premature endocrine and ductal cell differentiation in the pancreas. Cell Metab. 2006;3:59–65. PubMed

Swift GH, et al. An endocrine-exocrine switch in the activity of the pancreatic homeodomain protein PDX1 through formation of a trimeric complex with PBX1b and MRG1 (MEIS2) Mol. Cell Biol. 1998;18:5109–5120. PubMed PMC

Scavuzzo MA, et al. Pancreatic cell fate determination relies on notch ligand trafficking by NFIA. Cell Rep. 2018;25:3811–3827.e3817. PubMed

Santangelo L, et al. The stable repression of mesenchymal program is required for hepatocyte identity: a novel role for hepatocyte nuclear factor 4alpha. Hepatology. 2011;53:2063–2074. PubMed PMC

Saha SK, et al. Mutant IDH inhibits HNF-4alpha to block hepatocyte differentiation and promote biliary cancer. Nature. 2014;513:110–114. PubMed PMC

Stoffel M, Duncan SA. The maturity-onset diabetes of the young (MODY1) transcription factor HNF4alpha regulates expression of genes required for glucose transport and metabolism. Proc. Natl Acad. Sci. USA. 1997;94:13209–13214. PubMed PMC

Wang H, Maechler P, Antinozzi PA, Hagenfeldt KA, Wollheim CB. Hepatocyte nuclear factor 4alpha regulates the expression of pancreatic beta-cell genes implicated in glucose metabolism and nutrient-induced insulin secretion. J. Biol. Chem. 2000;275:35953–35959. PubMed

Ng NHJ, et al. HNF4A haploinsufficiency in MODY1 abrogates liver and pancreas differentiation from patient-derived induced pluripotent stem cells. iScience. 2019;16:192–205. PubMed PMC

Eto K, Kaur V, Thomas MK. Regulation of pancreas duodenum homeobox-1 expression by early growth response-1*. J. Biol. Chem. 2007;282:5973–5983. PubMed

Leu SY, et al. Loss of EGR-1 uncouples compensatory responses of pancreatic β cells. Theranostics. 2020;10:4233–4249. PubMed PMC

Seymour PA, et al. Jag1 modulates an oscillatory Dll1-Notch-Hes1 signaling module to coordinate growth and fate of pancreatic progenitors. Dev. Cell. 2020;52:731–747.e738. PubMed

Shi X, et al. Nr2e1 deficiency augments palmitate-induced oxidative stress in beta cells. Oxid. Med. Cell Longev. 2016;2016:9648769. PubMed PMC

Kundu S, et al. Polycomb repressive complex 1 generates discrete compacted domains that change during differentiation. Mol. Cell. 2017;65:432–446.e435. PubMed PMC

Bernstein BE, et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006;125:315–326. PubMed

Gribben C, et al. Ductal Ngn3-expressing progenitors contribute to adult beta cell neogenesis in the pancreas. Cell Stem Cell. 2021;28:2000–2008.e2004. PubMed PMC

Blum B, et al. Functional beta-cell maturation is marked by an increased glucose threshold and by expression of urocortin 3. Nat. Biotechnol. 2012;30:261–264. PubMed PMC

Sachs S, et al. Targeted pharmacological therapy restores beta-cell function for diabetes remission. Nat. Metab. 2020;2:192–209. PubMed

Artner I, et al. MafB: an activator of the glucagon gene expressed in developing islet alpha- and beta-cells. Diabetes. 2006;55:297–304. PubMed

Artner I, et al. MafB is required for islet beta cell maturation. Proc. Natl Acad. Sci. USA. 2007;104:3853–3858. PubMed PMC

Camunas-Soler J, et al. Patch-seq links single-cell transcriptomes to human islet dysfunction in diabetes. Cell Metab. 2020;31:1017–1031.e1014. PubMed PMC

Yoshihara E, et al. Immune-evasive human islet-like organoids ameliorate diabetes. Nature. 2020;586:606–611. PubMed PMC

Zhang H, et al. The LIM-homeodomain protein ISL1 activates insulin gene promoter directly through synergy with BETA2. J. Mol. Biol. 2009;392:566–577. PubMed

Taylor BL, Liu FF, Sander M. Nkx6.1 is essential for maintaining the functional state of pancreatic beta cells. Cell Rep. 2013;4:1262–1275. PubMed PMC

Ediger BN, et al. Islet-1 Is essential for pancreatic beta-cell function. Diabetes. 2014;63:4206–4217. PubMed PMC

Wang Z, York NW, Nichols CG, Remedi MS. Pancreatic beta cell dedifferentiation in diabetes and redifferentiation following insulin therapy. Cell Metab. 2014;19:872–882. PubMed PMC

Talchai C, Xuan S, Lin HV, Sussel L, Accili D. Pancreatic beta cell dedifferentiation as a mechanism of diabetic beta cell failure. Cell. 2012;150:1223–1234. PubMed PMC

Hoffman BG, Zavaglia B, Beach M, Helgason CD. Expression of Groucho/TLE proteins during pancreas development. BMC Dev. Biol. 2008;8:81. PubMed PMC

D’Avino PP. Citron kinase—renaissance of a neglected mitotic kinase. J. Cell Sci. 2017;130:1701–1708. PubMed

Messina G, et al. Nfix regulates fetal-specific transcription in developing skeletal muscle. Cell. 2010;140:554–566. PubMed

Fraser J, et al. Common regulatory targets of NFIA, NFIX and NFIB during postnatal cerebellar development. Cerebellum. 2020;19:89–101. PubMed PMC

Ribeiro, V. et al. NFIXing cancer: the role of NFIX in oxidative stress response and cell fate. Int. J. Mol. Sci.24 (2023). PubMed PMC

McCloskey AG, Miskelly MG, Flatt PR, McKillop AM. Pharmacological potential of novel agonists for FFAR4 on islet and enteroendocrine cell function and glucose homeostasis. Eur. J. Pharm. Sci. 2020;142:105104. PubMed

Dror E, et al. Epigenetic dosage identifies two major and functionally distinct beta cell subtypes. Cell Metab. 2023;35:821–836.e827. PubMed PMC

Lynn FC, et al. Sox9 coordinates a transcriptional network in pancreatic progenitor cells. Proc. Natl Acad. Sci. USA. 2007;104:10500–10505. PubMed PMC

Cerychova R, et al. Adverse effects of Hif1a mutation and maternal diabetes on the offspring heart. Cardiovasc. Diabetol. 2018;17:68. PubMed PMC

Ye J, et al. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinform. 2012;13:134. PubMed PMC

Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods. 2012;9:671–675. PubMed PMC

Filova I, et al. ISL1 is necessary for auditory neuron development and contributes toward tonotopic organization. Proc. Natl Acad. Sci. USA. 2022;119:e2207433119. PubMed PMC

Sugiyama T, Rodriguez RT, McLean GW, Kim SK. Conserved markers of fetal pancreatic epithelium permit prospective isolation of islet progenitor cells by FACS. Proc. Natl Acad. Sci. USA. 2007;104:175–180. PubMed PMC

Dobin A, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21. PubMed PMC

Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:3.

Kopylova E, Noe L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012;28:3211–3217. PubMed

Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. PubMed PMC

Blake JA, et al. Mouse Genome Database (MGD): knowledgebase for mouse-human comparative biology. Nucleic Acids Res. 2021;49:D981–d987. PubMed PMC

Smith CL, Eppig JT. The mammalian phenotype ontology: enabling robust annotation and comparative analysis. Wiley Interdiscip. Rev. Syst. Biol. Med. 2009;1:390–399. PubMed PMC

Hayamizu TF, Baldock RA, Ringwald M. Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data. Mamm. Genome. 2015;26:422–430. PubMed PMC

Newman AM, et al. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nat. Biotechnol. 2019;37:773–782. PubMed PMC

Kaya-Okur HS, Janssens DH, Henikoff JG, Ahmad K, Henikoff S. Efficient low-cost chromatin profiling with CUT&Tag. Nat. Protoc. 2020;15:3264–3283. PubMed PMC

Zheng, Y., Ahmad, K. & Henikoff, S. CUT&Tag Data Processing and Analysis Tutorial https://yezhengstat.github.io/CUTTag_tutorial/index.html (2020).

Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat. Methods. 2012;9:357–359. PubMed PMC

Meers MP, Tenenbaum D, Henikoff S. Peak calling by sparse enrichment analysis for CUT&RUN chromatin profiling. Epigenetics Chromatin. 2019;12:42. PubMed PMC

Yu G, Wang LG, He QY. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics. 2015;31:2382–2383. PubMed

Robinson JT, et al. Integrative genomics viewer. Nat. Biotechnol. 2011;29:24–26. PubMed PMC

Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010;26:2204–2207. PubMed PMC

Kent WJ, et al. The Human Genome Browser at UCSC. Genome Res. 2002;12:996–1006. PubMed PMC

Hao Y, et al. Integrated analysis of multimodal single-cell data. Cell. 2021;184:3573–3587.e3529. PubMed PMC

Lun ATL, et al. EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data. Genome Biol. 2019;20:63. PubMed PMC

McGinnis CS, Murrow LM, Gartner ZJ. DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. Cell Syst. 2019;8:329–337.e324. PubMed PMC

NEUROD1: transcriptional and epigenetic regulator of human and mouse neuronal and endocrine cell lineage programs