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Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis

Nature Genetics volume 46, pages 61–64 (2014)Cite this article

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Abstract

The contribution of cis-regulatory mutations to human disease remains poorly understood. Whole-genome sequencing can identify all noncoding variants, yet the discrimination of causal regulatory mutations represents a formidable challenge. We used epigenomic annotation in human embryonic stem cell (hESC)-derived pancreatic progenitor cells to guide the interpretation of whole-genome sequences from individuals with isolated pancreatic agenesis. This analysis uncovered six different recessive mutations in a previously uncharacterized ∼400-bp sequence located 25 kb downstream of PTF1A (encoding pancreas-specific transcription factor 1a) in ten families with pancreatic agenesis. We show that this region acts as a developmental enhancer of PTF1A and that the mutations abolish enhancer activity. These mutations are the most common cause of isolated pancreatic agenesis. Integrating genome sequencing and epigenomic annotation in a disease-relevant cell type can thus uncover new noncoding elements underlying human development and disease.

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Figure 1: Epigenome annotation of variants from genome sequencing identifies a shared variant in a putative enhancer element.
Figure 2: Families with mutations in the PTF1A enhancer.
Figure 3: Pancreas agenesis–associated mutations disrupt the function of a transcriptional enhancer that is specifically active in pancreatic progenitors.

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Acknowledgements

The authors thank M. Day, A. Damhuis and J. Garcia-Hurtado for technical assistance and R. Tearle (Complete Genomics), J. Tena and J.L. Skarmeta (Centro Andaluz de Biología del Desarrollo) for advice. J.F., S.E. and A.T.H. are supported by Wellcome Trust Senior Investigator awards. M.N.W. is supported by the Wellcome Trust as part of WT Biomedical Informatics Hub funding. E.D.F. is funded by the BOLD grant (European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement FP7-PEOPLE-ITN-2008 (Marie Curie Initial Training Networks, Biology of Liver and Pancreatic Development and Disease)). This work was supported by the National Institute for Health Research Exeter Clinical Research Facility through funding for S.E. and A.T.H. and general infrastructure and by the Ministerio de Economía y Competitividad (SAF2011-27086, PLE2009-0162 to J.F.). The views expressed here are those of the authors and not necessarily those of the National Health Service, the National Institute for Health Research or the Department of Health, UK.

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Author notes

  1. Michael N Weedon, Inês Cebola and Ann-Marie Patch: These authors contributed equally to this work.

  2. Sian Ellard, Jorge Ferrer and Andrew T Hattersley: These authors jointly directed this work.

Authors and Affiliations

  1. Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK

    Michael N Weedon, Ann-Marie Patch, Sarah E Flanagan, Elisa De Franco, Richard Caswell, Charles Shaw-Smith, Hana Lango Allen, Jayne A L Houghton, Anna Murray, Sian Ellard & Andrew T Hattersley

  2. Genomic Regulation of Pancreatic Beta-Cells Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain

    Inês Cebola, Santiago A Rodríguez-Seguí & Jorge Ferrer

  3. Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas, Barcelona, Spain

    Inês Cebola, Santiago A Rodríguez-Seguí & Jorge Ferrer

  4. Department of Medicine, Imperial College, London, UK

    Inês Cebola & Jorge Ferrer

  5. Wellcome Trust–Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory for Regenerative Medicine, Cambridge, UK

    Candy H-H Cho & Ludovic Vallier

  6. Seattle Children's Hospital Research Institute, Seattle, Washington, USA

    Christian L Roth

  7. School of Biomedical Science, Waterloo Campus, King's College London, London, UK

    Rongrong Chen

  8. London Centre for Paediatric Endocrinology and Metabolism, in partnership with the Great Ormond Street Hospital for Children National Health Service Trust, London, UK

    Khalid Hussain

  9. Institute of Child Health, University College London, London, UK

    Khalid Hussain

  10. Diabetes and Nutritional Sciences Division, Diabetes Research Group, School of Medicine, King's College London, London, UK

    Phil Marsh

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  1. Michael N Weedon
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International Pancreatic Agenesis Consortium

Contributions

M.N.W., S.E., J.F. and A.T.H. designed the study. M.N.W., A.-M.P., J.A.L.H. and H.L.A. performed bioinformatic analyses. I.C., S.A.R.-S., C.H.-H.C., A.M., L.V. and J.F. performed functional studies. A.-M.P., J.A.L.H., E.D.F., R. Caswell, S.E.F. and S.E. performed Sanger sequencing or deletion analysis and interpreted the results. S.E.F., C.S.-S., K.H., C.L.R., R. Chen, P.M. and A.T.H. analyzed the clinical data. M.N.W., I.C., A.-M.P., S.E., J.F. and A.T.H. prepared the draft manuscript. All authors contributed to discussion of the results and to manuscript preparation.

Corresponding authors

Correspondence to Jorge Ferrer or Andrew T Hattersley.

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The authors declare no competing financial interests.

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A full list of members and affiliations appears in the Supplementary Note.

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Supplementary Figures 1–8, Supplementary Tables 1–4 and Supplementary Note (PDF 1743 kb)

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Weedon, M., Cebola, I., Patch, AM. et al. Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis. Nat Genet 46, 61–64 (2014). https://doi.org/10.1038/ng.2826

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