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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).

The Hnf1b-CreERT2 BAC transgenic (Tg(Hnf1b-cre/ERT2)1Jfer) has been used extensively to trace the progeny of pancreatic ducts in developmental, regeneration, or cancer models. Hnf1b-CreERT2 transgenics have been used to show that cells from that form a duct-like plexus in the embryonic pancreas are bipotent duct-endocrine progenitors, whereas adult mouse duct cells are not a common source of β cells in various regenerative settings. The interpretation of such genetic lineage tracing studies is critically dependent on a correct understanding of the cell type specificity of recombinase activity with each reporter system. We have re-examined the performance of Hnf1b-CreERT2 with a Rosa26-RFP reporter transgene. This showed inducible recombination of up to 96% adult duct cells, a much higher efficiency than previously used reporter transgenes. Despite this high duct-cell excision, recombination in α and β cells remained very low, similar to previously used reporters. However, nearly half of somatostatin-expressing δ cells showed reporter activation, which was due to Cre expression in δ cells rather than to duct to δ cell conversions. The high recombination efficiency in duct cells indicates that the Hnf1b-CreERT2 model can be useful for both ductal fate mapping and genetic inactivation studies. The recombination in δ cells does not modify the interpretation of studies that failed to show duct conversions to other cell types, but needs to be considered if this model is used in studies that aim to modify the plasticity of pancreatic duct cells.

Summary Despite the central role of chromosomal context in gene transcription, human noncoding DNA variants are generally studied outside of their genomic location. This limits our understanding of disease-causing regulatory variants. INS promoter mutations cause recessive neonatal diabetes. We show that all INS promoter point mutations in 60 patients disrupt a CC dinucleotide, whereas none affect other elements important for episomal promoter function. To model CC mutations, we humanized an ∼3.1-kb region of the mouse Ins2 gene. This recapitulated developmental chromatin states and cell-specific transcription. A CC mutant allele, however, abrogated active chromatin formation during pancreas development. A search for transcription factors acting through this element revealed that another neonatal diabetes gene product, GLIS3, has a pioneer-like ability to derepress INS chromatin, which is hampered by the CC mutation. Our in vivo analysis, therefore, connects two human genetic defects in an essential mechanism for developmental activation of the INS gene., Graphical abstract, Highlights • Mutations of a CC dinucleotide in the human INS promoter cause neonatal diabetes • We humanized ∼3.1 kb of mouse Ins2 and created a CC mutant version • Humanized Ins2, but not the CC mutant, recapitulates developmental chromatin activation • GLIS3, also mutated in diabetes, activates INS chromatin and requires an intact CC, Mutations in the CC element of the INS promoter or the transcription factor GLIS3 cause neonatal diabetes. Akerman et al. humanize a 3.1-kb region upstream of the mouse Ins2 gene and show that GLIS3 and the CC element form a pioneering mechanism that activates INS chromatin during pancreas development.

Background: To improve cancer disparities among underrepresented minority (URM) populations, better representation of URM individuals in cancer research is needed. The San Diego State University (SDSU) and University of California San Diego (UCSD) Moores Cancer Center Partnership is addressing cancer disparities through an educational program targeting undergraduate URM students. Aims: To increase the proportion of URM individuals participating in cancer research by providing a range of research education opportunities supported by the Partnership Scholar Program Methods: The Partnership provides a paid intensive summer research internship enriched with year-round activities that include educational sessions, a journal club, mentorship, social activities, and poster sessions and presentations. Program evaluation through follow-up surveys, focus groups and other formal and informal feedback, including advisory and program steering committees are used to improve the program. Long-term follow-up among scholars (minimum of 10 years) provides data to evaluate the program’s long-term impact on scholars’ education and career path. Results: Since 2016, 63 URM undergraduate students participated in the scholar program. At the Year 2 follow-up (2016 cohort; n=12), 50% had completed their GRE and/or applied to graduate school or medical school. Lessons learned during the course of the program led to changes that were implemented to provide a better learning experience and increase overall program satisfaction, which include: 1) Lengthening the recruitment timeline to improve reach of eligible students and to provide more time for scholar selection and onboarding. 2) Improving the recruitment processes by collaborating with organizations serving URM students. 3) Refining the program contracts and onboarding meetings to help clarify expectations for scholars and faculty mentors. 4) Program coordinator skills and responsibilities (e.g., communication with scholars and mentors) are key to scholar satisfaction and retention. The coordinator organizes and communicates program activities, holds one-on-one in-person meetings, and provides ongoing mentorship to increase retention and scholar success in their ongoing academic development. 5) Adjustments to program components, such as scheduling and curricula of the summer education sessions, pairing scholars with clinicians, and the addition of social events were implemented to improve scholars’ learning experience. 6) Efficient tracking of the multitude of evaluation metrics requires a well-mapped and scheduled evaluation plan that includes automated publication notification systems and LinkedIn groups to evaluate scholars’ satisfaction and achievements post-program completion. Conclusions: The Partnership identified best practices and lessons learned for implementing lab-based internship scholar programs in biomedical and public health fields that could be considered in other programs. (U54CA132384 & U54CA132379) Citation Format: Elinor Gaida, Elva M Arredondo, Anthony J Barrios, Sanford I Bernstein, Richard M Cripps, Sheila E Crowe, Jill Dumbauld Nery, Maria Elena Martinez, Bilge Pakiz, Mercedes A Quintana Serrano, Roland Wolkowicz, Hala Madanat. Training the next generation of undergraduate URM cancer scientists: Results and lessons learned from a cancer research Partnership Scholar Program [abstract]. In: Proceedings of the Twelfth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2019 Sep 20-23; San Francisco, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl_2):Abstract nr D037.

Defects in transcriptional regulators of pancreatic exocrine differentiation have been implicated in pancreatic tumorigenesis, but the molecular mechanisms are poorly understood. The locus encoding the transcription factor HNF1A harbors susceptibility variants for pancreatic ductal adenocarcinoma (PDAC), while KDM6A, encoding Lysine‐specific demethylase 6A, carries somatic mutations in PDAC. Here, we show that pancreas‐specific Hnf1a null mutant transcriptomes phenocopy those of Kdm6a mutations, and both defects synergize with Kras G12D to cause PDAC with sarcomatoid features. We combine genetic, epigenomic, and biochemical studies to show that HNF1A recruits KDM6A to genomic binding sites in pancreatic acinar cells. This remodels the acinar enhancer landscape, activates differentiated acinar cell programs, and indirectly suppresses oncogenic and epithelial–mesenchymal transition genes. We also identify a subset of non‐classical PDAC samples that exhibit the HNF1A/KDM6A‐deficient molecular phenotype. These findings provide direct genetic evidence that HNF1A deficiency promotes PDAC. They also connect the tumor‐suppressive role of KDM6A deficiency with a cell‐specific molecular mechanism that underlies PDAC subtype definition., Cooperation between a transcription factor and an epigenetic modifier reveals how defective transcriptional control can contribute to development of pancreatic ductal adenocarcinoma.

Defects in transcriptional regulators of pancreatic exocrine differentiation have been implicated in pancreatic tumorigenesis, but the molecular mechanisms are poorly understood. The locus encoding the transcription factor HNF1A harbors susceptibility variants for pancreatic ductal adenocarcinoma (PDAC), while KDM6A, encoding the histone demethylase UTX, carries somatic mutations in PDAC. Here, we show that pancreas-specific Hnf1a null mutations phenocopy Utx deficient mutations, and both synergize with KrasG12D to cause PDAC with sarcomatoid features. We combine genetic, epigenomic and biochemical studies to show that HNF1A recruits UTX to genomic binding sites in pancreatic acinar cells. This remodels the acinar enhancer landscape, activates a differentiation program, and indirectly suppresses oncogenic and epithelial-mesenchymal transition genes. Finally, we identify a subset of non-classical PDAC samples that exhibit the HNF1A/UTX-deficient molecular phenotype. These findings provide direct genetic evidence that HNF1A-deficiency promotes PDAC. They also connect the tumor suppressive role of UTX deficiency with a cell-specific molecular mechanism that underlies PDAC subtype definition.