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Organogenesis requires the complex interactions of multiple cell lineages that coordinate their expansion, differentiation, and maturation over time. In Chapters 2 and 3, we utilize a combination of single-cell RNA-sequencing, immunofluorescence, in situ hybridization, and genetic lineage tracing, to profile the cell types within the epithelial and mesenchymal compartments of the murine pancreas across developmental time. We find a previously undescribed endocrine progenitor population, as well as an analogous population in both human fetal tissue and human embryonic stem cells differentiating towards a pancreatic beta cell fate. Further, we identify candidate transcriptional regulators along the differentiation trajectory of this population towards the alpha or beta cell lineages. Within the mesenchyme, we identify previously underappreciated cellular heterogeneity and reconstruct potential lineage relationships among the pancreatic mesothelium and mesenchymal cell types. In Chapter 4, we further characterize the pancreatic mesothelium, identifying novel markers and secreted factors expressed within this population. Knockout of the secreted factor specifically expressed by the mesothelium, Fgf9, reveals a hypoplastic pancreas by late gestation. We find a disrupted ratio of epithelial and mesenchymal cells that suggests Fgf9 regulates the epithelial-mesenchymal interactions critical for pancreatic development. In Chapter 5, we extend our single-cell RNA-sequencing approach to adult pancreatic homeostasis and disease, describing multiple subtypes of mesenchymal and mesothelial populations in both conditions. Comparison of diseased and healthy pancreata reveal shifts in mesenchymal cell types, highlighting populations and transcriptional targets that may regulate the development of disease. In summary, this work reveals transcriptional and cellular heterogeneity of the developing, adult, and diseased pancreas, and identifies lineage relationships among novel populations within both the epithelial and mesenchymal compartments.

Sequence variants in cis-acting enhancers are important for polygenic disease, but their role in Mendelian disease is poorly understood. Redundancy between enhancers that regulate the same gene is thought to mitigate the pathogenic impact of enhancer mutations. Recent findings, however, have shown that loss-of-function mutations in a single enhancer near PTF1A cause pancreas agenesis and neonatal diabetes. Using mouse and human genetic models, we show that this enhancer activates an entire PTF1A enhancer cluster in early pancreatic multipotent progenitors. This leading role, therefore, precludes functional redundancy. We further demonstrate that transient expression of PTF1A in multipotent progenitors sets in motion an epigenetic cascade that is required for duct and endocrine differentiation. These findings shed insights into the genome regulatory mechanisms that drive pancreas differentiation. Furthermore, they reveal an enhancer that acts as a regulatory master key and is thus vulnerable to pathogenic loss-of-function mutations. This research was supported by Ministerio de Ciencia e Innovación (BFU2014-54284-R, RTI2018-095666-B-I00), Medical Research Council (MR/L02036X/1), a Wellcome Trust Senior Investigator Award (WT101033), European Research Council Advanced Grant (789055), and CIBERDEM-Instituto de Salud Carlos III. Research in A.S.-P. group was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme Grant Agreement (851647).

Type 1 diabetes (T1D) is an autoimmune disease that results in the destruction of insulin producing pancreatic β-cells. One of the genes associated with T1D is TYK2, which encodes a Janus kinase with critical roles in type-Ι interferon (IFN-Ι) mediated intracellular signalling. To study the role of TYK2 in β-cell development and response to IFNα, we generated TYK2 knockout human iPSCs and directed them into the pancreatic endocrine lineage. Here we show that loss of TYK2 compromises the emergence of endocrine precursors by regulating KRAS expression, while mature stem cell-islets (SC-islets) function is not affected. In the SC-islets, the loss or inhibition of TYK2 prevents IFNα-induced antigen processing and presentation, including MHC Class Ι and Class ΙΙ expression, enhancing their survival against CD8+ T-cell cytotoxicity. These results identify an unsuspected role for TYK2 in β-cell development and support TYK2 inhibition in adult β-cells as a potent therapeutic target to halt T1D progression. We gratefully acknowledge Dr. Fatoumata Samassa for help with cytotoxicity assays. We thank Jarkko Ustinov for the insulin and c-peptide ELISA measurements. S. Eurola, H. Grym, and A. Laitinen are thanked for expert technical support. We thank FIMM Single Cell Analytics unit (supported by HiLIFE and Biocentre Finland) for single cell RNA sequencing services. We want to acknowledge the participants and investigators of the FinnGen study. T.O. acknowledges the funding provided by the Academy of Finland (MetaStem Center of Excellence grant 312437), the Novo Nordisk Foundation and the Sigrid Juselius Foundation. R.M. acknowledges the support of the Agence Nationale de la Recherche (ANR-19-CE15-0014-01) and the Fondation pour la Recherche Medicale (EQU20193007831). C.H. was funded by an Année Recherche fellowship of the Paris Saclay University. F.V. was funded by an international PhD fellowship of the IdEx Université de Paris. R.B.P. acknowledges the funding by Hjelt foundation, Crafoord foundation (2020089) and Swedish Research Council (2021-02623). D.L.E. acknowledges the support of grants from the Welbio-FNRS (Fonds National de la Recherche Scientifique; WELBIO-CR-2019C-04), Belgium; the Innovate2CureType1—Dutch Diabetes Research Foundation (DDRF), Holland; the Juvenile Diabetes Foundation (JDRF; 2-SRA-2019-834-S-B); the NIH (HIRN-CBDS) grant U01 DK127786, USA. D.L.E., T.O., and R.M. acknowledge support from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreements No 115797 (INNODIA) and 945268 (INNODIA HARVEST), supported by the European Union’s Horizon 2020 research and innovation programme. These Joint Undertakings receive support from the Union’s Horizon 2020 research and innovation programme and “EFPIA”, “JDRF” and “The Leona M. and Harry B. Helmsley Charitable Trust”.

Multiple transcription factors have been shown to promote pancreatic β-cell differentiation, yet much less is known about negative regulators. Earlier epigenomic studies suggested that the transcriptional repressor REST could be a suppressor of endocrinogenesis in the embryonic pancreas. However, pancreatic Rest knockout mice failed to show abnormal numbers of endocrine cells, suggesting that REST is not a major regulator of endocrine differentiation. Using a different conditional allele that enables profound REST inactivation, we observed a marked increase in pancreatic endocrine cell formation. REST inhibition also promoted endocrinogenesis in zebrafish and mouse early postnatal ducts and induced β-cell-specific genes in human adult duct-derived organoids. We also defined genomic sites that are bound and repressed by REST in the embryonic pancreas. Our findings show that REST-dependent inhibition ensures a balanced production of endocrine cells from embryonic pancreatic progenitors. This research was supported by Ministerio de Ciencia, Innovación y Universidades (SAF2015-73226-JIN [Agencia Estatal de Investigación {AEI}/European Regional Development Fund, European Union {UE}] and RYC-2017-21950 [AEI/European Social Fund, UE] to M.R., and BFU2014-54284-R and RTI2018-095666-B-I00 to J.F.); the Medical Research Council (MR/L02036X/1), Wellcome Trust (WT101033), and European Research Council Advanced Grant (789055) (to J.F.); the Instituto de Salud Carlos III (CA18/00045 to J.L.M.); and a Spanish Ministry of Science, Innovation, and Universities (MCIU) fellowship (PTA2018-016371-I to M.M.). J.K.-C.'s and F.P.'s research was supported by L'Agence Nationale de la Recherche (ANR) grants, L'Institut Européen de Génomique du Diabète (EGID), ANR-10-LABX-0046, a French state fund managed by ANR under the frame program Investissements d'Avenir (I-SITE ULNE/ANR-16-IDEX-0004 ULNE to F.P.), and the European Consortium for Islet Transplantation funded by the Juvenile Diabetes Research Foundation International. Work in the Centre for Genomic Regulation was supported by the Centres de Recerca de Catalunya (CERCA) Programme, Generalitat de Catalunya, and Centro de Excelencia Severo Ochoa (SEV-2015-0510). Work at Institut d'Investigació Biomèdica de Bellvitge was supported by the CERCA Programme and Generalitat de Catalunya

Background Transplantation of pancreatic β cells generated in vitro from pluripotent stem cells (hPSCs) such as embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs) has been proposed as an alternative therapy for diabetes. Though many differentiation protocols have been developed for this purpose, lentivirus-mediated forced expression of transcription factors (TF)—PDX1 and NKX6.1—has been at the forefront for its relatively fast and straightforward approach. However, considering that such cells will be used for therapeutic purposes in the future, it is desirable to develop a procedure that does not leave any footprint on the genome, as any changes of DNAs could potentially be a source of unintended, concerning effects such as tumorigenicity. In this study, we attempted to establish a novel protocol for rapid and footprint-free hESC differentiation into a pancreatic endocrine lineage by using synthetic mRNAs (synRNAs) encoding PDX1 and NKX6.1. We also tested whether siPOU5F1, which reduces the expression of pluripotency gene POU5F1 (also known as OCT4), can enhance differentiation as reported previously for mesoderm and endoderm lineages. Methods synRNA-PDX1 and synRNA-NKX6.1 were synthesized in vitro and were transfected five times to hESCs with a lipofection reagent in a modified differentiation culture condition. siPOU5F1 was included only in the first transfection. Subsequently, cells were seeded onto a low attachment plate and aggregated by an orbital shaker. At day 13, the degree of differentiation was assessed by quantitative RT-PCR (qRT-PCR) and immunohistochemistry for endocrine hormones such as insulin, glucagon, and somatostatin. Results Both PDX1 and NKX6.1 expression were detected in cells co-transfected with synRNA-PDX1 and synRNA-NKX6.1 at day 3. Expression levels of insulin in the transfected cells at day 13 were 450 times and 14 times higher by qRT-PCR compared to the levels at day 0 and in cells cultured without synRNA transfection, respectively. Immunohistochemically, pancreatic endocrine hormones were not detected in cells cultured without synRNA transfection but were highly expressed in cells transfected with synRNA-PDX1, synRNA-NKX6.1, and siPOU5F1 at as early as day 13. Conclusions In this study, we report a novel protocol for rapid and footprint-free differentiation of hESCs to endocrine cells.

The interplay between pancreatic epithelium and the surrounding microenvironment is pivotal for pancreas formation and differentiation as well as adult organ homeostasis. The mesenchyme is the main component of the embryonic pancreatic microenvironment, yet its cellular identity is broadly defined, and whether it comprises functionally distinct cell subsets is not known. Using genetic lineage tracing, transcriptome, and functional studies, we identified mesenchymal populations with different roles during pancreatic development. Moreover, we showed that Pbx transcription factors act within the mouse pancreatic mesenchyme to define a pro-endocrine specialized niche. Pbx directs differentiation of endocrine progenitors into insulin- and glucagon-positive cells through non-cell-autonomous regulation of ECM-integrin interactions and soluble molecules. Next, we measured functional conservation between mouse and human pancreatic mesenchyme by testing identified mesenchymal factors in an iPSC-based differentiation model. Our findings provide insights into how lineage-specific crosstalk between epithelium and neighboring mesenchymal cells underpin the generation of different pancreatic cell types.

Summary Generating an unlimited source of human insulin-producing cells is a prerequisite to advance β cell replacement therapy for diabetes. Here, we describe a 3D culture system that supports the expansion of adult human pancreatic tissue and the generation of a cell subpopulation with progenitor characteristics. These cells display high aldehyde dehydrogenase activity (ALDHhi), express pancreatic progenitors markers (PDX1, PTF1A, CPA1, and MYC), and can form new organoids in contrast to ALDHlo cells. Interestingly, gene expression profiling revealed that ALDHhi cells are closer to human fetal pancreatic tissue compared with adult pancreatic tissue. Endocrine lineage markers were detected upon in vitro differentiation. Engrafted organoids differentiated toward insulin-positive (INS+) cells, and circulating human C-peptide was detected upon glucose challenge 1 month after transplantation. Engrafted ALDHhi cells formed INS+ cells. We conclude that adult human pancreatic tissue has potential for expansion into 3D structures harboring progenitor cells with endocrine differentiation potential., Highlights • A 3D culture system can support the expansion of adult human pancreatic tissue • An ALDHhi cell subpopulation is identified in these organoids • ALDHhi cells, and not ALDHlo cells, are capable of forming new organoids • ALDHhi cells show endocrine differentiation potential, In the context of β cell replacement therapy for diabetes, de Koning and colleagues describe a 3D culture platform that supports ex vivo expansion of human pancreatic tissue as organoids. These organoids harbor a subpopulation of ALDHhi cells that display proliferative capacity and can differentiate to an endocrine fate.

Summary The proneural transcription factor Neurogenin3 (Ngn3) plays a critical role in pancreatic endocrine cell differentiation, although regulation of Ngn3 protein is largely unexplored. Here we demonstrate that Ngn3 protein undergoes cyclin-dependent kinase (Cdk)-mediated phosphorylation on multiple serine-proline sites. Replacing wild-type protein with a phosphomutant form of Ngn3 increases α cell generation, the earliest endocrine cell type to be formed in the developing pancreas. Moreover, un(der)phosphorylated Ngn3 maintains insulin expression in adult β cells in the presence of elevated c-Myc and enhances endocrine specification during ductal reprogramming. Mechanistically, preventing multi-site phosphorylation enhances both Ngn3 stability and DNA binding, promoting the increased expression of target genes that drive differentiation. Therefore, multi-site phosphorylation of Ngn3 controls its ability to promote pancreatic endocrine differentiation and to maintain β cell function in the presence of pro-proliferation cues and could be manipulated to promote and maintain endocrine differentiation in vitro and in vivo., Graphical Abstract, Highlights • Ngn3 can be phosphorylated on multiple serine-proline sites • Un(der)phosphorylated Ngn3 is more stable and active than wild-type Ngn3 • Ngn3 phosphorylation regulates pancreatic endocrine cell generation in vivo • Un(der)phosphorylated Ngn3 promotes endocrine cell reprogramming in organoids, Azzarelli et al. show that multi-site phosphorylation of Neurogenin3 regulates pancreatic endocrine differentiation during development, and maintenance of adult β cell function in the presence of pathological pro-proliferative cues. The results suggest that dephosphorylation of Neurogenin3 may improve β cell generation in vitro and help maintain islet function in disease.

The proneural transcription factor Neurogenin3 (Ngn3) plays a critical role in pancreatic endocrine cell differentiation, although regulation of Ngn3 protein is largely unexplored. Here we demonstrate that Ngn3 protein undergoes cyclin-dependent kinase (Cdk)-mediated phosphorylation on multiple serine-proline sites. Replacing wild-type protein with a phosphomutant form of Ngn3 increases a cell generation, the earliest endocrine cell type to be formed in the developing pancreas. Moreover, un(der)phosphorylated Ngn3 maintains insulin expression in adult beta cells in the presence of elevated c-Myc and enhances endocrine specification during ductal reprogramming. Mechanistically, preventing multi-site phosphorylation enhances both Ngn3 stability and DNA binding, promoting the increased expression of target genes that drive differentiation. Therefore, multi-site phosphorylation of Ngn3 controls its ability to promote pancreatic endocrine differentiation and to maintain beta cell function in the presence of pro-proliferation cues and could be manipulated to promote and maintain endocrine differentiation in vitro and in vivo.

During pancreatic development insulin(+) cells co-express the transcription factors MafB and Pax6, and transition from a MafA(-) to MafA(+) state. To examine the role of Pax6 and MafB in the development of beta-cells, we analyzed embryonic pancreata from Pax6- and MafB-deficient mice. Pax6 deficiency, as manifest in the Pax6(Sey-Neu) allele, reduced not only the number of cells expressing insulin or glucagon, but also the number of MafB, PDX-1 and MafA expressing cells. We show that MafB can directly activate expression of insulin and glucagon, and a MafB protein engineered to contain N248S mutation in the MafB (kr(ENU)) results in significantly reduced activation. Furthermore, pancreata from MafB deficient (kr(ENU)/kr(ENU)) mice exhibited reduced number of cells expressing insulin, glucagon, PDX-1 and MafA, with only a minor reduction in MafB expressing cells. MafB deficiency does not affect endocrine specification but does affect the lineage commitment of the endocrine cells and their maturation. Similar to Pax6 deficient mice, MafB deficient mice showed reductions both in insulin and glucagon expressing cells and in the ability of MafB and PDX-1 expressing cells to activate expression of these hormones. However, MafB deficient mice exhibited no effect on Pax6 expression. These results suggest that MafB may function as a downstream mediator of Pax6 in regulating the specification of insulin and glucagon expressing cells. Interestingly, the remaining insulin(+) cells in these knockouts preferentially express Hb9, suggesting the existence of an alternate pathway for the generation of insulin expressing cells, even in the absence of Pax6 and MafB function. Thus, Pax6 acts upstream of MafB, which in turn may trigger the expression of insulin and regulate the PDX-1 and MafA expression required for beta-cell maturation.

The Onecut (OC) transcription factor HNF-6 (OC-1) is required during embryogenesis for pancreatic specification, morphogenesis and endocrine differentiation. In mammals, HNF-6 has two paralogs, OC-2 and OC-3, which share DNA-binding and transcriptional activation properties and have expression patterns that overlap with that of HNF-6. This suggested that OC-2 and OC-3 play redundant roles with HNF-6 in pancreas development. Here, we have addressed this hypothesis by analyzing the phenotype of mice knockout for the Onecut factors. We found that neither OC-2 nor OC-3 is required for pancreas specification. However, OC-2 plays partially redundant roles with HNF-6 in pancreas morphogenesis and in the differentiation of endocrine precursors. As similar molecular events drive endocrine differentiation in the pancreas and gastrointestinal tract, we also investigated if Onecut factors are involved in enteroendocrine differentiation. OC-2 and OC-3 were found to delineate specific antero-posterior regions of the gut around embryonic day 12.5. Later on, OC2 was expressed in several gut cell types, whereas OC-3 behaved as a specific marker of the enteroendocrine lineage. However, OC-2 and OC-3, alone or in combination, were dispensable for gut development and enteroendocrine differentiation. In conclusion, our data reveal partially redundant roles for HNF-6 and OC-2 in developing pancreas and identify new markers for antero-posterior patterning of the gut and for enteroendocrine differentiation.

Studies show that Menin, a tumour suppressor encoded by the multiple endocrine neoplasia type 1 (Men1) gene, is required during murine pancreatic development. In humans, mutation results in the MEN1 tumourigenic syndrome; however, knowledge of menin in human pancreatic development is limited. This study examined the expression pattern and functional role of menin during human fetal islet development. Immunostaining revealed the presence of nuclear menin within pancreatic cells from the 1st through 2nd trimester co-localizing with various developmental factors. Knockdown of MEN1 in human fetal islet-epithelial cells significantly increased apoptosis, reduced proliferation, and decreased SOX9, NKX2.2, and NKX6.1 mRNA levels (transcription factors required in maintenance of the progenitor pool and endocrine differentiation). Overexpression of MEN1 confirmed these results suggesting that menin promotes cell survival and proliferation, maintains the islet progenitor pool, and regulates islet differentiation in the human fetal pancreas: a different function compared to its anti-tumourigenic role during adulthood.

El pàncrees és una glàndula secretora formada per teixit exocrí i endocrí. El compartiment endocrí està format per les cèl•lules alpha (productores de glucagó), les cèl•lules beta (productores d'insulina), les cèl•lules delta (somatostatina), les cèl•lules PP (polipèptid pancreàtic) i les cèl•lules epsilon (grelina). La Diabetis Mellitus és un grup de malalties metabòliques que es caracteritzen per mantenir nivells elevats de glucosa en sang com a resultat de la incapacitat de produir o utilitzar la insulina. Les cèl•lules productores d'insulina són les cèl•lules beta del pàncrees. Actualment, el tractament de la diabetis es basa en injeccions periòdiques d'insulina. Per solucionar i millorar la vida d'aquests pacients hi ha molts grups que treballen per trobar noves fonts de cèl•lules productores d'insulina que recuperin la massa de cèl•lules beta perdudes durant la diabetis. Per a això, és necessari conèixer detalladament els passos que se succeeixen per generar una cèl•lula productora d'insulina a partir d'una cèl•lula indiferenciada. Durant la organogènesi pancreàtica s'activen un conjunt de factors de transcripció que són essencials per a la correcta formació de l'òrgan, entre ells el factor proendocrí Neurogenina3 (Neurog3), així com també un seguit de senyals extrínsecs (vies de senyalització) que participen en aquest procés. Neurogenina3 és un factor de transcripció de la família bHLH que exerceix un paper essencial en la diferenciació endocrino-pancreàtica, ja que en la seva absència no hi ha formació de les cèl•lules endocrines del pàncrees. En el primer objectiu d'aquesta tesi hem identificat possibles noves dianes de Neurog3, mitjançant l'ús d'un model de diferenciació endocrina in vitro de cèl•lules ductals pancreàtiques, en el qual la sobreexpresió de Neurog3 indueix l'activació del programa transcripcional endocrino-pancreàtic. Mitjançant l'estudi de canvis globals en el perfil d'expressió gènica d'aquestes cèl•lules hem identificat un conjunt de gens relacionats amb la via de senyalització Wingless (Wnt) com a dianes potencials de Neurog3 in vitro. Entre aquests gens, hem centrat els nostres estudis en l'anàlisi del gen que codifica pel lligand de la via Wnt, Wnt9a. El segon objectiu d'aquesta tesi se centra a estudiar la possible participació del lligand Wnt9a en el procés de diferenciació endocrina del pàncrees. Així, vam demostrar per primera vegada la presència en pàncrees embrionari de ratolí del mRNA de Wnt9a, així com la regulació gènica d'aquest lligand per part de factors de transcripció que participen al programa de diferenciació endocrina. Estudiem també el paper de Wnt9a dins de la cascada endocrino-pancreàtica, demostrant un paper regulador de Wnt9a sobre els efectes promoguts per Neurog3 en alguns dels gens endocrins estudiats. Aquests resultats ens han portat al tercer objectiu d'aquesta tesi: caracterització de la diferenciació endocrino-pancreàtica en el model murí gen-anul•lat per Wnt9a. A estadi e18.5 (just abans del naixement) observem un augment generalitzat de les cèl•lules productores d'hormones del compartiment endocrí (cèl•lules β insulina-positives, cèl•lules α glucagó-positives i cèl•lules δ somatostatina-positives) en relació a l'àrea pancreàtica total, que correlaciona amb una major taxa de proliferació d'aquestes. L'anàlisi de l'expressió gènica realitzat a estadi e15.5 (moment de màxima expansió endocrina) no mostra diferències en els nivells del mRNA de Neurog3, indicant que l'augment en el compartiment endocrí observat a e18.5 no es deu a una major especificació endocrina. No obstant això, l'estudi de diferents factors integrants del programa transcripcional endocrí mostra un augment en l'expressió de Pdx1 en els animals deficients que podria explicar l'augment en cèl•lules beta observat a e18.5. Per tant, en aquesta tesi definim per primera vegada la relació directa entre factors de transcripció bHLH i components de la via Wnt en pàncrees, així com identifiquem la presència del mRNA de Wnt9a en pàncrees embrionari de ratolí i en illots adults. Demostrem la regulació gènica de Wnt9a per part de factors de la cascada de transcripció endocrina, així com la regulació d'aquests per part de Wnt9a sota l'acció de Neurog3. Identifiquem, mitjançant l'estudi del model animal gen anul•lat per Wnt9a, un augment del compartiment endocrí abans del naixement, a causa d'una major taxa de proliferació, en absència de Wnt9a. Per tant, el conjunt d'aquests resultats indicaria que la via de senyalització Wnt juga un paper important durant el procés de diferenciació endocrina del pàncrees, suggerint una connexió entre el programa transcripcional endocrí i la via de senyalització intracel•lular Wnt., The pancreas is a gland consisting of secretory exocrine and endocrine tissue. The endocrine compartment is formed by the alpha cells (glucagon producing), the beta cells (insulin producing), delta cells (somatostatin), PP (pancreatic polypeptide) cells and epsilon cells (ghrelin). Diabetes Mellitus is a group of metabolic diseases characterized by maintaining high levels of blood glucose resulting from the inability to produce or use insulin. Currently, the treatment for diabetes is based on regular injections of insulin. There are many groups working on finding new sources of insulin-producing cells to recover beta cells mass lost during diabetes development. For this reason, it’s necessary to detail the molecular steps that occur from an undifferentiated cell to an insulin-producing cell. During pancreatic organogenesis, a set of transcription factors that are essential for proper formation of the organ are activated, including the proendocrine factor Neurogenin3 (Neurog3), as well as a number of extrinsic signals (signalling pathways). Neurogenin3 is a transcription factor that belongs to bHLH transcription factors family. It plays an essential role in pancreatic-endocrine differentiation, since in its absence there is no formation of endocrine cells. In the first objective of this thesis we have identified potential new targets for Neurog3, using an in vitro model of endocrine differentiation process, pancreatic ductal cells (mPAC), in which adenoviral overexpression of Neurog3 induces the activation of the transcriptional differentiation program. Using whole genomic profile study, we identified a set of genes related to signalling Wingless (Wnt) pathway as potential targets of Neurog3 in vitro. Among these genes, we focused our studies on the analysis of the gene encoding the ligand of the Wnt pathway, Wingless- type MMTV integration site 9A (Wnt9a). The second objective of this thesis focuses on the study of the possible role of Wnt9a during endocrine differentiation. Thus, we demonstrate for the first time, the presence of Wnt9a mRNA in mouse embryonic pancreas, as well as its regulation by transcription factors involved in endocrine differentiation program. We studied the role of Wnt9a within the endocrine differentiation cascade, demonstrating a regulatory role of Wnt9a on some Neurog3 activated genes. Finally, we did the characterization of the endocrine differentiation process in the Wnt9a knock out animal mouse model. At embryonic stage (e) 18.5 (just before birth), we observed a general increase in the major hormone-producing cells of the endocrine compartment (β cell insulin-positive, α cells glucagon-positive cells and δ somatostatin- positive) in relation to the total pancreatic area, which correlated with a high rate of proliferation. The analysis of gene expression performed at (e) 15.5 (time of maximum endocrine expansion) shows no difference in levels of Neurog3 mRNA, indicating that the increase in the endocrine compartment observed at (e) 18.5 is not due to a greater endocrine specification. However, the study of transcriptional endocrine factors shows an increase in the expression of Pdx1 gene in the deficient Wnt9a animals; this could explain the increase in beta cells observed at (e) 18.5. Therefore, this thesis define for the first time the direct relationship between bHLH transcription factors and components of the Wnt pathway in the pancreas, as well as the identification of Wnt9a mRNA in embryonic mouse pancreas and in adult islets. We demonstrate the regulation of Wnt9a by transcription factors of the endocrine cascade and the regulation of some of them by Wnt9a. We have identified an increase of the endocrine compartment, just before birth, in Wnt9a deficient animals, probably due to a higher rate of proliferation in the absence of Wnt9a. Hence, all these results indicate that Wnt signalling pathway plays an important role during pancreatic endocrine differentiation, suggesting a connection between the endocrine transcriptional program and Wnt signalling.

Summary Several distinct differentiation protocols for deriving pancreatic progenitors (PPs) from human pluripotent stem cells have been described, but it remains to be shown how similar the PPs are across protocols and how well they resemble their in vivo counterparts. Here, we evaluated three differentiation protocols, performed RNA and assay for transposase-accessible chromatin using sequencing on isolated PPs derived with these, and compared them with fetal human pancreas populations. This enabled us to define a shared transcriptional and epigenomic signature of the PPs, including several genes not previously implicated in pancreas development. Furthermore, we identified a significant and previously unappreciated cross-protocol variation of the PPs through multi-omics analysis and demonstrate how such information can be applied to refine differentiation protocols for derivation of insulin-producing beta-like cells. Together, our study highlights the importance of a detailed characterization of defined cell populations derived from distinct differentiation protocols and provides a valuable resource for exploring human pancreatic development., Highlights • Systematic comparison of three protocols for hPSC-pancreatic progenitor differentiation • Individual hPSC lines differentiate preferentially with different protocols • Shared transcriptomic and epigenomic signatures of hPSC-pancreatic progenitors • Molecular characterization of hPSC-pancreatic progenitors guides protocol refinement, Wesolowska-Andersen and colleagues present a comprehensive molecular and functional analysis of human PSC-derived pancreatic progenitors derived using three differentiation protocols. They define their shared transcriptomic and epigenomic signatures but also highlight significant differences between protocols, which are then used to guide protocol modifications to enhance further differentiation toward endocrine lineage.

Major insulin gene transcription factors, such as PDX-1 or NeuroD1, have equally important roles in pancreatic development and the differentiation of pancreatic endocrine cells. Previously, we identified and cloned another critical insulin gene transcription factor MafA (RIPE3b1) and reported that other Maf factors were expressed in pancreatic endocrine cells. Maf factors are important regulators of cellular differentiation; to understand their role in differentiation of pancreatic endocrine cells, we analyzed the expression pattern of large-Maf factors in the pancreas of embryonic and adult mice. Ectopically expressed large-Maf factors, MafA, MafB, or cMaf, induced expression from insulin and glucagon reporter constructs, demonstrating a redundancy in their function. Yet in adult pancreas, cMaf was expressed in both alpha- and beta-cells, and MafA and MafB showed selective expression in the beta- and alpha-cells, respectively. Interestingly, during embryonic development, a significant proportion of MafB-expressing cells also expressed insulin. In embryos, MafB is expressed before MafA, and our results suggest that the differentiation of beta-cells proceeds through a MafB+ MafA- Ins+ intermediate cell to MafB- MafA+ Ins+ cells. Furthermore, the MafB to MafA transition follows induction of PDX-1 expression (Pdx-1(high)) in MafB+ Ins+ cells. We suggest that MafB may have a dual role in regulating embryonic differentiation of both beta- and alpha-cells while MafA may regulate replication/survival and function of beta-cells after birth. Thus, this redundancy in the function and expression of the large-Maf factors may explain the normal islet morphology observed in the MafA knockout mice at birth.

The proneural transcription factor Neurogenin3 (Ngn3) plays a critical role in pancreatic endocrine cell differentiation, although regulation of Ngn3 protein is largely unexplored. Here we demonstrate that Ngn3 protein undergoes cyclin-dependent kinase (Cdk)-mediated phosphorylation on multiple serine-proline sites. Replacing wild-type protein with a phosphomutant form of Ngn3 increases α cell generation, the earliest endocrine cell type to be formed in the developing pancreas. Moreover, un(der)phosphorylated Ngn3 maintains insulin expression in adult β cells in the presence of elevated c-Myc and enhances endocrine specification during ductal reprogramming. Mechanistically, preventing multi-site phosphorylation enhances both Ngn3 stability and DNA binding, promoting the increased expression of target genes that drive differentiation. Therefore, multi-site phosphorylation of Ngn3 controls its ability to promote pancreatic endocrine differentiation and to maintain β cell function in the presence of pro-proliferation cues and could be manipulated to promote and maintain endocrine differentiation in vitro and in vivo.