Abstract

The genomic regulatory programmes that underlie human organogenesis are poorly understood. Pancreas development, in particular, has pivotal implications for pancreatic regeneration, cancer and diabetes. We have now characterized the regulatory landscape of embryonic multipotent progenitor cells that give rise to all pancreatic epithelial lineages. Using human embryonic pancreas and embryonic-stem-cell-derived progenitors we identify stage-specific transcripts and associated enhancers, many of which are co-occupied by transcription factors that are essential for pancreas development. We further show that TEAD1, a Hippo signalling effector, is an integral component of the transcription factor combinatorial code of pancreatic progenitor enhancers. TEAD and its coactivator YAP activate key pancreatic signalling mediators and transcription factors, and regulate the expansion of pancreatic progenitors. This work therefore uncovers a central role for TEAD and YAP as signal-responsive regulators of multipotent pancreatic progenitors, and provides a resource for the study of embryonic development of the human pancreas.

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References

  1. 1.

    et al. An organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro. BMC Syst. Biol. 5, 108 (2011).

  2. 2.

    et al. Transcriptome analysis of early organogenesis in human embryos. Dev. Cell 19, 174–184 (2010).

  3. 3.

    & Pancreas organogenesis: from bud to plexus to gland. Dev. Dynam. 240, 530–565 (2011).

  4. 4.

    & Generation and regeneration of cells of the liver and pancreas. Science 322, 1490–1494 (2008)

  5. 5.

    et al. GATA6 haploinsufficiency causes pancreatic agenesis in humans. Nat. Genet. 44, 20–22 (2012).

  6. 6.

    et al. Pancreas-specific deletion of mouse Gata4 and Gata6 causes pancreatic agenesis. J. Clin. Invest. 122, 3516–3528 (2012).

  7. 7.

    , , , & GATA4 and GATA6 control mouse pancreas organogenesis. J. Clin. Invest. 122, 3504–3515 (2012).

  8. 8.

    et al. PDX-1 is required for pancreatic outgrowth and differentiation of the rostral duodenum. Development 122, 983–995 (1996).

  9. 9.

    , , , & Pancreatic agenesis attributable to a single nucleotide deletion in the human IPF1 gene coding sequence. Nat. Genet. 15, 106–110 (1997).

  10. 10.

    et al. Lack of TCF2/vHNF1 in mice leads to pancreas agenesis. Proc. Natl Acad. Sci. USA 102, 1490–1495 (2005).

  11. 11.

    et al. Transcription factor hepatocyte nuclear factor 6 regulates pancreatic endocrine cell differentiation and controls expression of the proendocrine gene ngn3. Mol. Cell. Biol. 20, 4445–4454 (2000).

  12. 12.

    et al. Dynamic regulation of Pdx1 enhancers by Foxa1 and Foxa2 is essential for pancreas development. Genes Dev. 22, 3435–3448 (2008).

  13. 13.

    et al. Novel SOX9 expression during human pancreas development correlates to abnormalities in Campomelic dysplasia. Mech. Dev. 116, 223–226 (2002).

  14. 14.

    et al. SOX9 is required for maintenance of the pancreatic progenitor cell pool. Proc. Natl Acad. Sci. USA 104, 1865–1870 (2007).

  15. 15.

    et al. The p48 DNA-binding subunit of transcription factor PTF1 is a new exocrine pancreas-specific basic helix-loop-helix protein. EMBO J. 15, 4317–4329 (1996).

  16. 16.

    et al. Development of the human pancreas from foregut to endocrine commitment. Diabetes 62, 3514–3522 (2013).

  17. 17.

    et al. Inhibition of activin/nodal signalling is necessary for pancreatic differentiation of human pluripotent stem cells. Diabetologia 55, 3284–3295 (2012).

  18. 18.

    et al. Dynamic chromatin remodeling mediated by polycomb proteins orchestrates pancreatic differentiation of human embryonic stem cells. Cell Stem Cell 12, 224–237 (2013)

  19. 19.

    , , & Pancreatic endoderm derived from human embryonic stem cells generates glucose-responsive insulin-secreting cells in vivo. Nature 26, 443–452 (2008)

  20. 20.

    , , , & Small molecules efficiently direct endodermal differentiation of mouse and human embryonic stem cells. Cell Stem Cell 4, 348–358 (2009)

  21. 21.

    et al. Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineage divergence. Genes Dev. 27, 1932–1946 (2013).

  22. 22.

    , , & Planar cell polarity controls pancreatic β cell differentiation and glucose homeostasis. Cell Rep. 2, 1593–1606 (2012).

  23. 23.

    , , & A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279–283 (2011)

  24. 24.

    et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl Acad. Sci. USA 107, 21931–21936 (2010).

  25. 25.

    et al. Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants. Nat. Genet. 46, 136–143 (2014).

  26. 26.

    & On the origin of the β cell. Genes Dev. 22, 1998–2021 (2008).

  27. 27.

    et al. TEAD mediates YAP-dependent gene induction and growth control. Genes Dev. 22, 1962–1971 (2008).

  28. 28.

    , , , & Hippo Signaling Regulates Pancreas Development through Inactivation oelf Yap. Mol. Cell. Biol. 32, 5116–5128 (2012).

  29. 29.

    et al. Genetic and pharmacological disruption of the TEAD-YAP complex suppresses the oncogenic activity of YAP. Genes Dev. 26, 1300–1305 (2012).

  30. 30.

    , , & Role for FGFR2IIIb-mediated signals in controlling pancreatic endocrine progenitor cell proliferation. Proc. Natl Acad. Sci. USA 99, 3884–3889 (2002).

  31. 31.

    et al. Sox9 coordinates a transcriptional network in pancreatic progenitor cells. Proc. Natl Acad. Sci. USA 104, 10500–10505 (2007).

  32. 32.

    et al. Tead proteins activate the Foxa2 enhancer in the node in cooperation with a second factor. Development 132, 4719–4729 (2005).

  33. 33.

    et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307–319 (2013).

  34. 34.

    et al. Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis. Nat. Genet. 46, 61–64 (2014).

  35. 35.

    , , , & Genetics and biology of pancreatic ductal adenocarcinoma. Genes Dev. 20, 1218–1249 (2006).

  36. 36.

    & Pancreatic ductal adenocarcinoma and acinar cells: a matter of differentiation and development? Gut 61, 449–458 (2012).

  37. 37.

    et al. Yap1 activation enables bypass of oncogenic Kras addiction in pancreatic cancer. Cell 158, 185–197 (2014).

  38. 38.

    et al. Downstream of mutant KRAS, the transcription regulator YAP is essential for neoplastic progression to pancreatic ductal adenocarcinoma. Sci. Signal. 7, ra42 (2014).

  39. 39.

    , & The Hippo pathway in organ size control, tissue regeneration and stem cell self-renewal. Nat. Cell Biol. 13, 877–883 (2011)

  40. 40.

    & Hippo signaling regulates differentiation and maintenance in the exocrine pancreas. Gastroenterology 144, 1543–53–1553.e1 (2013).

  41. 41.

    et al. Targeted deletion of a cis-regulatory region reveals differential gene dosage requirements for Pdx1 in foregut organ differentiation and pancreas formation. Genes Dev. 20, 253–266 (2006).

  42. 42.

    , & Regulatory regions driving developmental and tissue-specific expression of the essential pancreatic gene pdx1. Dev. Biol. 238, 185–201 (2001).

  43. 43.

    , , & Computer ranking of the sequence of appearance of 73 features of the brain and related structures in staged human embryos during the sixth week of development. Am. J. Anat. 180, 69–86 (1987).

  44. 44.

    et al. Hnf6 and Tcf2 (MODY5) are linked in a gene network operating in a precursor cell domain of the embryonic pancreas. Hum. Mol. Genet. 12, 3307–3314 (2003).

  45. 45.

    et al. β cell differentiation during early human pancreas development. J. Endocrinol. 181, 11–23 (2004).

  46. 46.

    & A system for ex vivo culturing of embryonic pancreas. J. Vis. Exp. 66, e3979 (2012).

  47. 47.

    et al. A map of open chromatin in human pancreatic islets. Nat. Genet. 42, 255–259 (2010).

  48. 48.

    , , , & Targeted deficiency of the transcriptional activator Hnf1α alters subnuclear positioning of its genomic targets. PLoS Genet. 4, e1000079 (2008).

  49. 49.

    et al. Derepression of Polycomb targets during pancreatic organogenesis allows insulin-producing β-cells to adopt a neural gene activity program. Genome Res. 20, 722–732 (2010).

  50. 50.

    , & TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009).

  51. 51.

    et al. Human β cell transcriptome analysis uncovers lncRNAs that are tissue-specific, dynamically regulated, and abnormally expressed in type 2 diabetes. Cell Metab. 16, 435–448 (2012).

  52. 52.

    , & Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).

  53. 53.

    , , & GREAT improves functional interpretation of cis-regulatory regions. Nature 28, 495–501 (2010).

  54. 54.

    , , & REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE 6, e21800 (2011).

  55. 55.

    , , & Open source clustering software. Bioinformatics 20, 1453–1454 (2004).

  56. 56.

    Java Treeview—extensible visualization of microarray data. Bioinformatics 20, 3246–3248 (2004).

  57. 57.

    et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).

  58. 58.

    , , & Quantifying similarity between motifs. Genome Biol. 8, R24 (2007).

  59. 59.

    Combining probability from independent tests: the weighted Z-method is superior to Fisher’s approach. J. Evol. Biol. 18, 1368–1373 (2005).

  60. 60.

    et al. Fast computation and applications of genome mappability. PLoS ONE 7, e30377 (2012).

  61. 61.

    , , & Primary explant cultures of adult and embryonic pancreas. Methods Mol. Med. 103, 259–271 (2005).

  62. 62.

    et al. Scribble participates in Hippo signaling and is required for normal zebrafish pronephros development. Proc. Natl Acad. Sci. USA 106, 8579–8584 (2009).

  63. 63.

    et al. Two sox9 genes on duplicated zebrafish chromosomes: expression of similar transcription activators in distinct sites. Dev. Biol. 231, 149–163 (2001).

  64. 64.

    , & Early appearance of pancreatic hormone-expressing cells in the zebrafish embryo. Mech. Dev. 87, 217–221 (1999).

  65. 65.

    & Whole-mount in situ hybridizations on zebrafish embryos using a mixture of digoxigenin- and fluorescein-labelled probes. Trends Genet. 10, 73–74 (1994).

  66. 66.

    et al. Zebrafish enhancer detection (ZED) vector: A new tool to facilitate transgenesis and the functional analysis of cis-regulatory regions in zebrafish. Dev. Dynam. 238, 2409–2417 (2009).

  67. 67.

    , & Identification of a functional transposase of the Tol2 element, an Ac-like element from the Japanese medaka fish, and its transposition in the zebrafish germ lineage. Proc. Natl Acad. Sci. USA 97, 11403–11408 (2000).

  68. 68.

    et al. Nkx6.1 and nkx6.2 regulate α- and β-cell formation in zebrafish by acting on pancreatic endocrine progenitor cells. Dev. Biol. 340, 397–407 (2010).

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Acknowledgements

The research was supported by the National Institute for Health Research (NIHR) Imperial Biomedical Research Centre. Work was funded by grants from the Ministerio de Economía y Competitividad (CB07/08/0021, SAF2011-27086, PLE2009-0162 to J.F., BFU2013-41322-P to J.L.G-S.), the Andalusian Government (BIO-396 to J.L.G-S.), the Wellcome Trust (WT088566 and WT097820 to N.A.H., WT101033 to J.F.), the Manchester Biomedical Research Centre, ERC advanced starting grant IMDs (C.H-H.C. and L.V.) and the Cambridge Hospitals National Institute for Health Research Biomedical Research Centre (L.V.). R.E.J. is a Medical Research Council clinical training fellow. The authors are grateful to C. Wright (Vanderbilt University) for zebrafish Pdx1 antiserum, J. Postlethwait (Purdue University) for a Sox9b clone, H. Sasaki (Kumamoto University) for a TEAD–EnR clone, C. Vinod and L. Abi for research nurse assistance, and clinical colleagues at Central Manchester University Hospitals NHS Foundation Trust. The authors thank J. Garcia-Hurtado for technical assistance (IDIBAPS).

Author information

Author notes

    • Inês Cebola
    • , Santiago A. Rodríguez-Seguí
    • , Candy H-H. Cho
    • , José Bessa
    •  & Meritxell Rovira

    These authors contributed equally to this work.

    • Candy H-H. Cho
    •  & Lorenzo Pasquali

    Present addresses: Genomics Research Center, Academia Sinica, Taipei 115, Taiwan (C.H-H.C.); Division of Endocrinology, Germans Trias i Pujol University Hospital and Research Institute and Josep Carreras Leukaemia Research Institute, 08916 Badalona, Spain (L.P.).

Affiliations

  1. Department of Medicine, Imperial College London, London W12 0NN, UK

    • Inês Cebola
    • , Joan Ponsa-Cobas
    • , Ignasi Morán
    •  & Jorge Ferrer
  2. Genomic Programming of Beta-cells Laboratory, Institut d’Investigacions August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain

    • Santiago A. Rodríguez-Seguí
    • , Meritxell Rovira
    • , Miguel Angel Maestro
    • , Lorenzo Pasquali
    • , Natalia Castro
    •  & Jorge Ferrer
  3. CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), 08036 Barcelona, Spain

    • Santiago A. Rodríguez-Seguí
    • , Meritxell Rovira
    • , Miguel Angel Maestro
    • , Lorenzo Pasquali
    • , Natalia Castro
    •  & Jorge Ferrer
  4. Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular y Celular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina

    • Santiago A. Rodríguez-Seguí
  5. Wellcome Trust and MRC Stem Cells Centre, Anne McLaren Laboratory for Regenerative Medicine, Department of Surgery and Wellcome Trust—Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK

    • Candy H-H. Cho
    •  & Ludovic Vallier
  6. Instituto de Biologia Molecular e Celular (IBMC), 4150-180 Porto, Portugal

    • José Bessa
  7. Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal

    • José Bessa
  8. Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013 Sevilla, Spain

    • Mario Luengo
    •  & Jose Luis Gomez-Skarmeta
  9. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK

    • Mariya Chhatriwala
    •  & Ludovic Vallier
  10. Centre for Endocrinology and Diabetes, Institute of Human Development, Faculty of Medical & Human Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, UK

    • Andrew Berry
    • , Rachel E. Jennings
    •  & Neil A. Hanley
  11. Endocrinology Department, Central Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WU, UK

    • Neil A. Hanley

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Contributions

J.F. coordinated the overall project and supervised epigenomic analysis and mouse studies, N.A.H. supervised human embryo characterization, L.V. supervised hESC differentiation studies and J.L.G-S. supervised zebrafish studies. I.C., S.A.R-S., C.H-H.C., J.B., M.R., M.L., M.C., A.B., M.A.M. and R.E.J. designed, carried out and analysed experiments. N.C. carried out experiments. I.C., S.A.R-S., J.P-C., L.P. and I.M. carried out computational analysis. I.C., S.A.R-S. and J.F. wrote the manuscript with contributions from C.H-H.C., J.B., M.R., M.L., J.P-C., N.A.H., J.L.G-S. and L.V.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Neil A. Hanley or Jose Luis Gomez-Skarmeta or Ludovic Vallier or Jorge Ferrer.

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https://doi.org/10.1038/ncb3160

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