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Mutations in PNKP cause microcephaly, seizures and defects in DNA repair

Nature Genetics volume 42, pages 245–249 (2010)Cite this article

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Abstract

Maintenance of DNA integrity is crucial for all cell types, but neurons are particularly sensitive to mutations in DNA repair genes, which lead to both abnormal development and neurodegeneration1. We describe a previously unknown autosomal recessive disease characterized by microcephaly, early-onset, intractable seizures and developmental delay (denoted MCSZ). Using genome-wide linkage analysis in consanguineous families, we mapped the disease locus to chromosome 19q13.33 and identified multiple mutations in PNKP (polynucleotide kinase 3′-phosphatase) that result in severe neurological disease; in contrast, a splicing mutation is associated with more moderate symptoms. Unexpectedly, although the cells of individuals carrying this mutation are sensitive to radiation and other DNA-damaging agents, no such individual has yet developed cancer or immunodeficiency. Unlike other DNA repair defects that affect humans, PNKP mutations universally cause severe seizures. The neurological abnormalities in individuals with MCSZ may reflect a role for PNKP in several DNA repair pathways.

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Figure 1: Pedigrees of MCSZ families.
Figure 2: Brain MRIs of individuals with MCSZ.
Figure 3: PNKP mutations in individuals with MCSZ.
Figure 4: Lymphocytes from individuals with MCSZ show abnormal DNA repair.
Figure 5: PNKP in situ hybridization.

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Acknowledgements

J.S. was supported by the Victoria and Stuart Quan Fellowship. Research was supported by grants from the US National Institute of Neurological Disorders and Stroke to E.C.G. (5K08NS059673-02) and to C.A.W. (NSR01-35129), the Fogarty International Center (R21 NS061772), the Manton Center for Orphan Disease Research, the Simons Foundation and by Dubai Harvard Foundation for Medical Research. E.C.G. was also supported by a K12 Child Health Research Center award to Children's Hospital Boston (1 K12 HD052896-01A1) and a Research in Training Award from the Child Neurology Foundation. J.J.R. and K.W.C. are supported by the UK Medical Research Council (G0600776 & G0400959). C.A.W. is an Investigator of the Howard Hughes Medical Institute. We thank S. Lindsay and S. Lisgo from the Medical Research Council–Wellcome Trust Human Developmental Biology Resource (HDBR), Institute of Human Genetics, International Centre for Life, Newcastle upon Tyne, UK, for performing human in situ hybridizations. We are grateful for genotyping services provided by the Center for Inherited Disease Research (CIDR). CIDR is fully funded through a federal contract from the US National Institutes of Health to The Johns Hopkins University, contract number HHSN268200782096C and NIH N01-HG-65403. Genotyping at Children's Hospital Boston is supported by the Intellectual and Developmental Disabilities Research Centers (CHB MRDDRC, P30 HD18655).

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Author notes

  1. Mary Haddadin

    Present address: Present address: Quest Diagnostics, Nichols Institute, San Juan Capistrano, California, USA.,

  2. Jun Shen and Edward C Gilmore: These authors contributed equally to the work.

Authors and Affiliations

  1. Department of Neurology, Howard Hughes Medical Institute, Beth Israel Deaconess Medical Center and Program in Neuroscience, Harvard Medical School, Boston, Massachusetts, USA

    Jun Shen, Christine A Marshall, Adria Bodell, Brenda Barry, Kathryn Allen, Vijay S Ganesh, Bernard S Chang & Christopher A Walsh

  2. Division of Genetics and The Manton Center for Orphan Disease Research, Department of Medicine, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA

    Edward C Gilmore, Danielle Gleason, R Sean Hill & Christopher A Walsh

  3. Division of Child Neurology, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA

    Edward C Gilmore

  4. Department of Pathology, Cytogenetics Laboratory, Al-Bashir Hospital, Ministry of Health, Amman, Jordan

    Mary Haddadin

  5. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, UK.,

    John J Reynolds & Keith W Caldecott

  6. Department of Pediatrics, Genetics & Endocrinology, King Fahad National Guard Hospital, King Abdul Aziz Medical City, Saudi Arabia

    Wafaa Eyaid

  7. Department of Medical Genetics, Kaiser-Permanente Point West Medical Offices, Sacramento, California, USA

    Arthur Grix

  8. Department of Pediatrics, Hacettepe University, Medical Faculty, Ihsan Dogramaci Children's Hospital, Section of Pediatric Neurology, Ankara, Turkey

    Meral Topcu

  9. Department of Radiology, Department of Neurology and Department of Pediatrics, University of California at San Francisco, San Francisco, California, USA

    A James Barkovich

  10. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA

    Christopher A Walsh

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Contributions

J.S. helped to characterize MCSZ syndrome, identified the MCSZ locus and calculated lod scores, sequenced genes in the MCSZ locus to identify PNKP mutations and wrote the manuscript; E.C.G. helped to characterize MCSZ syndrome, identified the moderately affected MCSZ family, performed RT-PCR on moderately affected family samples, performed comet assays, organized and analyzed Sequenom experiments, did analysis of PNKP mutation, performed mouse RNAi experiments, helped perform mouse in situ hybridizations and wrote the manuscript; C.A.M. sequenced genes in the MCSZ locus to identify PNKP mutations and helped perform human in situ hybridizations; M.H. identified affected patients and provided clinical information; J.J.R. performed PNKP protein blots and confirmatory comet assays; W.E. identified affected patients and provided clinical information; A.B. organized clinical information and patient samples; B.B. organized clinical information and patient samples; D.G. organized patient samples and helped perform Sequenom experiments; K.A. organized patient samples and helped perform sequencing experiments; V.S.G. helped analyze Sequenom experiments; B.S.C. helped organize clinical information to identify MCSZ syndrome; A.G. identified affected patients and provided clinical information; R.S.H. helped organize genetic data and calculate lod scores; M.T. identified affected patients and provided clinical information; K.W.C. advised on comet assays, supervised PNKP protein blotting and edited the manuscript; A.J.B. characterized MRIs for patient classification; C.A.W. directed the overall research and wrote the manuscript.

The genetic study was approved by Beth Israel Deaconess Medical Center and Children's Hospital Boston Institutional Review Boards. Appropriate informed consent was obtained from all involved human subjects. All animal work was approved by Harvard Medical School, Beth Israel Deaconess Medical Center and Children's Hospital Boston Institutional Animal Care and Use Committees.

Corresponding author

Correspondence to Christopher A Walsh.

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The authors declare no competing financial interests.

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Shen, J., Gilmore, E., Marshall, C. et al. Mutations in PNKP cause microcephaly, seizures and defects in DNA repair. Nat Genet 42, 245–249 (2010). https://doi.org/10.1038/ng.526

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