Abstract

Nephronophthisis-related ciliopathies (NPHP-RC) are recessive disorders that feature dysplasia or degeneration occurring preferentially in the kidney, retina and cerebellum. Here we combined homozygosity mapping with candidate gene analysis by performing 'ciliopathy candidate exome capture' followed by massively parallel sequencing. We identified 12 different truncating mutations of SDCCAG8 (serologically defined colon cancer antigen 8, also known as CCCAP) in 10 families affected by NPHP-RC. We show that SDCCAG8 is localized at both centrioles and interacts directly with OFD1 (oral-facial-digital syndrome 1), which is associated with NPHP-RC. Depletion of sdccag8 causes kidney cysts and a body axis defect in zebrafish and induces cell polarity defects in three-dimensional renal cell cultures. This work identifies loss of SDCCAG8 function as a cause of a retinal-renal ciliopathy and validates exome capture analysis for broadly heterogeneous single-gene disorders.

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Acknowledgements

We thank families and study subjects for their contributions and E. Nigg for the OFD1 antibody. This research was supported by grants from the National Institutes of Health to F.H. (DK1069274, DK1068306, DK064614), to H.K. (EY007961), to D.S.W. (EY13408), to N.K. (HD042601, DK075972, DK072301) and to E.A.P. (EY12910); by grants from the Netherlands Organization for Scientific Research to K.L.M.C. (NWO Toptalent-021.001.014), to R.R. (NWO Vidi-91786396) and to R.H.G. (NWO Vidi-917.66.354); by the WellChild and Wellcome Trust to E.R.M.; by the Avenir-INSERM program, the Agence Nationale pour la Recherche, the Union Nationale pour les Aveugles et Déficients Visuels, RETINA France, Programme Hospitalier de Recherche National 2007 and the Association Bardet-Biedl, France to H.D., C.S. and E.A.P. by the Foundation Fighting Blindness, the Research to Prevent Blindness, the F.M. Kirby Foundation and the Rosanne Silbermann Foundation to E.A.P.; by the Midwest Eye Banks and Transplantation Center and Rare Disease Initiative, University of Michigan to H.K.; by Instituto Gulbenkian de Ciência and EMBO to M.B.D.; by the Deutsche Nierenstiftung, PKD Foundation and DFG (BE 3910/5-1 and SFB/TRR57) to C.B.; by CIHR, FFB-Canada, FRSQ and Reseau Vision to R.K.K.; by the “Else Kröner-Fresenius-Stiftung” (P66/09//A75/09) to H.P.H.N.; and by EU FP7 Consortium “SYSCILIA” to R.H.G., R.R. and N.K. F.H. is an Investigator of the Howard Hughes Medical Institute, a Doris Duke Distinguished Clinical Scientist and a Frederick G. L. Huetwell Professor. D.S.W. is a Jules and Doris Stein RPB professor. N.K. is a George R. Brumley Professor. S.S. is a laureate of the Equipe FRM (Dequation (20071210558)) and the Agence National de la Recherche (R07089KS). We thank the physicians who contributed to this study; A. Toutain, M.-C. Gubler, R. Salomon, M.-A. Macher and M. Fischbach for clinical data; S.J. Allen, A. Saveliev and Y. Liu for technical assistance; K. Tory and C. Becker for linkage analysis and exon sequencing; S. Shi and R. Insolera for shRNA clones; C. Janke for the GT335 antibody; J. Salisbury for the centrin-2 antibody; E. Nigg for the CEP164 antibody; and B. Chang for the CEP290 antibody.

Author information

Author notes

    • Edgar A Otto
    •  & Toby W Hurd

    These authors contributed equally to this work.

Affiliations

  1. Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan, USA.

    • Edgar A Otto
    • , Toby W Hurd
    • , Rannar Airik
    • , Moumita Chaki
    • , Weibin Zhou
    • , Amiya K Ghosh
    • , Heather M McLaughlin
    • , Susanne Held
    • , Jennifer M Kasanuki
    • , Gokul Ramaswami
    • , James MacDonald
    •  & Friedhelm Hildebrandt
  2. Laboratoire de Génétique Médicale EA3949, Equipe AVENIR-Inserm, Faculté de Médecine, Université de Strasbourg, Strasbourg, France.

    • Corinne Stoetzel
    •  & Helene Dollfus
  3. Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, USA.

    • Suresh B Patil
    • , Carlos A Murga-Zamalloa
    •  & Hemant Khanna
  4. HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.

    • Shawn Levy
  5. Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.

    • Jeroen van Reeuwijk
    • , Stef J F Letteboer
    • , Karlien L M Coene
    • , Alejandro Estrada-Cuzcano
    • , Rob W J Collin
    •  & Ronald Roepman
  6. Department of Cell Regulation, Genentech Inc., South San Francisco, California, USA.

    • Liyun Sang
    •  & Peter K Jackson
  7. Department of Medical Oncology, University Medical Center, Utrecht, The Netherlands.

    • Rachel H Giles
  8. F.M. Kirby Center for Molecular Ophthalmology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.

    • Qin Liu
    •  & Eric A Pierce
  9. Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA.

    • Heather M McLaughlin
    •  & Friedhelm Hildebrandt
  10. McGill Ocular Genetics Laboratory, Montreal Children's Hospital, McGill University Health Centre, Montreal, Canada.

    • Jinny Conte
    • , Irma Lopez
    •  & Robert K Koenekoop
  11. University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA.

    • Joseph Washburn
  12. Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA.

    • Jinghua Hu
  13. Department of Cell and Developmental Biology, University of Michigan, Michigan, USA.

    • Yukiko Yamashita
  14. Department of Medical and Molecular Genetics, School of Clinical and Experimental Medicine and Centre for Rare Diseases and Personalised Medicine, University of Birmingham, Institute of Biomedical Research, Edgbaston, Birmingham, UK.

    • Eamonn R Maher
  15. UAB Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, Alabama, USA.

    • Lisa M Guay-Woodford
  16. Department of Nephrology and General Medicine, University Medical Center, Albert-Ludwigs-University, Freiburg, Germany.

    • Hartmut P H Neumann
  17. Department of Nephrology, III. Medical Clinic, University Hospital, Frankfurt, Germany.

    • Nicholas Obermüller
  18. Department of Human Genetics, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, Aachen, Germany.

    • Carsten Bergmann
  19. Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, USA.

    • Xiaoshu Bei
    •  & Nicholas Katsanis
  20. Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, USA.

    • Xiaoshu Bei
    •  & Nicholas Katsanis
  21. Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA.

    • Xiaoshu Bei
    •  & Nicholas Katsanis
  22. Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, USA.

    • Richard A Lewis
  23. Jules Stein Eye Institute, UCLA School of Medicine, Los Angeles, California, USA.

    • Vanda Lopes
    •  & David S Williams
  24. Department of Biological Chemistry and DNA Sequencing Core, University of Michigan, Ann Arbor, Michigan, USA.

    • Robert H Lyons
  25. Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

    • Chi V Dang
  26. Instituto Gulbenkian de Ciência, Oeiras, Portugal.

    • Daniela A Brito
    •  & Mónica Bettencourt Dias
  27. Roche NimbleGen, Inc., Madison, Wisconsin, USA.

    • Xinmin Zhang
  28. Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.

    • James D Cavalcoli
  29. Cologne Center for Genomics, University of Cologne, Cologne, Germany.

    • Gudrun Nürnberg
    •  & Peter Nürnberg
  30. Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.

    • Gudrun Nürnberg
    •  & Peter Nürnberg
  31. Cologne Excellence Cluster on Cellular Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany.

    • Gudrun Nürnberg
    •  & Peter Nürnberg
  32. Department of Genetics, Hôpital Necker-Enfants Malades, Assistance Publique–Hôpitaux de Paris, Paris, France.

    • Corinne Antignac
    •  & Sophie Saunier
  33. INSERM U-983, Hôpital Necker-Enfants Malades, Université Paris Descartes, Paris, France.

    • Corinne Antignac
  34. Institute for Genetic and Metabolic Disease, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.

    • Ronald Roepman
  35. Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO) et Service de Génétique Médicale, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.

    • Helene Dollfus
  36. Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.

    • Friedhelm Hildebrandt

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Contributions

E.A.O., H.M.M., S.H., J.M.K. and G.R. generated total genome linkage, exon capture and gene identification data. T.W.H. generated antibody characterization, immunoprecipitation and cell cycle expression data. R.A., M.C., H.K., A.K.G., S.B.P., C.A.M.-Z., J.H., Y.Y. and C.V.D. performed immunofluorescence and subcellular localization studies by confocal microscopy. W.Z. performed zebrafish experiments. J.v.R., S.J.F.L. and R.R. contributed the OFD1 work. L.S., R.H.G. and P.K.J. generated spheroid assay and protein expression data. Q.L. and E.A.P. performed retinal electroporation studies. C.A., S.S., E.R.M., L.M.G.-W., H.P.H.N., N.O. and C.B. recruited patients and gathered detailed clinical information for the study. N.K., X.B., R.A.L., R.K.K., J.C., I.L., K.L.M.C., A.E.-C. and R.W.J.C. performed mutation analysis. D.A.B., M.B.D., Q.L., E.A.P., V.L. and D.S.W. performed high-resolution confocal microscopy and EM studies. S.L., R.H.L. and X.Z. performed large-scale sequencing or exon capture. G.N., P.N., F.H., J.D.C., J.W. and J.M. did linkage calculations. H.D. and C.S. independently mapped and identified SDCCAG8 in families FII.22 and FI.2. F.H. conceived and directed the project and wrote the paper with contributions from R.R., M.B.D. and H.D.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Friedhelm Hildebrandt.

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DOI

https://doi.org/10.1038/ng.662

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