Autosomal recessive polycystic kidney disease (ARPKD), usually considered to be a genetically homogeneous disease caused by mutations in PKHD1, has been associated with ciliary dysfunction. Here, we describe mutations in DZIP1L, which encodes DAZ interacting protein 1-like, in patients with ARPKD. We further validated these findings through loss-of-function studies in mice and zebrafish. DZIP1L localizes to centrioles and to the distal ends of basal bodies, and interacts with septin2, a protein implicated in maintenance of the periciliary diffusion barrier at the ciliary transition zone. In agreement with a defect in the diffusion barrier, we found that the ciliary-membrane translocation of the PKD proteins polycystin-1 and polycystin-2 is compromised in DZIP1L-mutant cells. Together, these data provide what is, to our knowledge, the first conclusive evidence that ARPKD is not a homogeneous disorder and further establish DZIP1L as a second gene involved in ARPKD pathogenesis.

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  1. 1.

    et al. Consensus expert recommendations for the diagnosis and management of autosomal recessive polycystic kidney disease: report of an international conference. J. Pediatr. 165, 611–617 (2014).

  2. 2.

    et al. Clinical consequences of PKHD1 mutations in 164 patients with autosomal-recessive polycystic kidney disease (ARPKD). Kidney Int. 67, 829–848 (2005).

  3. 3.

    & Ciliopathies: from rare inherited cystic kidney diseases to basic cellular function. Mol Cell Pediatr 2, 8 (2015).

  4. 4.

    et al. A transition zone complex regulates mammalian ciliogenesis and ciliary membrane composition. Nat. Genet. 43, 776–784 (2011).

  5. 5.

    et al. Formation of the transition zone by Mks5/Rpgrip1L establishes a ciliary zone of exclusion (CIZE) that compartmentalises ciliary signalling proteins and controls PIP2 ciliary abundance. EMBO J. 34, 2537–2556 (2015).

  6. 6.

    , & The base of the cilium: roles for transition fibres and the transition zone in ciliary formation, maintenance and compartmentalization. EMBO Rep. 13, 608–618 (2012).

  7. 7.

    Autosomal recessive polycystic kidney disease: the prototype of the hepato-renal fibrocystic diseases. J. Pediatr. Genet. 3, 89–101 (2014).

  8. 8.

    , , , & The autosomal recessive polycystic kidney disease protein is localized to primary cilia, with concentration in the basal body area. J. Am. Soc. Nephrol. 15, 592–602 (2004).

  9. 9.

    et al. PKHD1 protein encoded by the gene for autosomal recessive polycystic kidney disease associates with basal bodies and primary cilia in renal epithelial cells. Proc. Natl. Acad. Sci. USA 101, 2311–2316 (2004).

  10. 10.

    et al. Kinesin-2 mediates physical and functional interactions between polycystin-2 and fibrocystin. Hum. Mol. Genet. 15, 3280–3292 (2006).

  11. 11.

    et al. Fibrocystin/polyductin, found in the same protein complex with polycystin-2, regulates calcium responses in kidney epithelia. Mol. Cell. Biol. 27, 3241–3252 (2007).

  12. 12.

    et al. Fibrocystin/polyductin modulates renal tubular formation by regulating polycystin-2 expression and function. J. Am. Soc. Nephrol. 19, 455–468 (2008).

  13. 13.

    , , , & Primary cilia are specialized calcium signalling organelles. Nature 504, 311–314 (2013).

  14. 14.

    , , & Direct recording and molecular identification of the calcium channel of primary cilia. Nature 504, 315–318 (2013).

  15. 15.

    et al. Primary cilia are not calcium-responsive mechanosensors. Nature 531, 656–660 (2016).

  16. 16.

    et al. An efficient and comprehensive strategy for genetic diagnostics of polycystic kidney disease. PLoS One 10, e0116680 (2015).

  17. 17.

    et al. The Zn finger protein Iguana impacts Hedgehog signaling by promoting ciliogenesis. Dev. Biol. 337, 148–156 (2010).

  18. 18.

    et al. The iguana/DZIP1 protein is a novel component of the ciliogenic pathway essential for axonemal biogenesis. Dev. Dyn. 239, 527–534 (2010).

  19. 19.

    et al. iguana encodes a novel zinc-finger protein with coiled-coil domains essential for Hedgehog signal transduction in the zebrafish embryo. Genes Dev. 18, 1565–1576 (2004).

  20. 20.

    et al. The zebrafish iguana locus encodes Dzip1, a novel zinc-finger protein required for proper regulation of Hedgehog signaling. Development 131, 2521–2532 (2004).

  21. 21.

    , , & Gli2a protein localization reveals a role for Iguana/DZIP1 in primary ciliogenesis and a dependence of Hedgehog signal transduction on primary cilia in the zebrafish. BMC Biol. 8, 65 (2010).

  22. 22.

    , , & Centrosomal protein DZIP1 regulates Hedgehog signaling by promoting cytoplasmic retention of transcription factor GLI3 and affecting ciliogenesis. J. Biol. Chem. 288, 29518–29529 (2013).

  23. 23.

    et al. A recessive screen for genes regulating hematopoietic stem cells. Blood 116, 5849–5858 (2010).

  24. 24.

    & Cilia and Hedgehog responsiveness in the mouse. Proc. Natl. Acad. Sci. USA 102, 11325–11330 (2005).

  25. 25.

    , , , & Shh and Gli3 are dispensable for limb skeleton formation but regulate digit number and identity. Nature 418, 979–983 (2002).

  26. 26.

    , & The Wilms tumor genes wt1a and wt1b control different steps during formation of the zebrafish pronephros. Dev. Biol. 309, 87–96 (2007).

  27. 27.

    & Regulating the transition from centriole to basal body. J. Cell Biol. 193, 435–444 (2011).

  28. 28.

    et al. A septin diffusion barrier at the base of the primary cilium maintains ciliary membrane protein distribution. Science 329, 436–439 (2010).

  29. 29.

    et al. A ciliopathy complex at the transition zone protects the cilia as a privileged membrane domain. Nat. Cell Biol. 14, 61–72 (2011).

  30. 30.

    et al. Polycystin-1 expression in PKD1, early-onset PKD1, and TSC2/PKD1 cystic tissue. Kidney Int. 56, 1324–1333 (1999).

  31. 31.

    et al. Spectrum of mutations in the gene for autosomal recessive polycystic kidney disease (ARPKD/PKHD1). J. Am. Soc. Nephrol. 14, 76–89 (2003).

  32. 32.

    et al. PKHD1 mutations in autosomal recessive polycystic kidney disease (ARPKD). Hum. Mutat. 23, 453–463 (2004).

  33. 33.

    et al. Correlation of kidney function, volume and imaging findings, and PKHD1 mutations in 73 patients with autosomal recessive polycystic kidney disease. Clin. J. Am. Soc. Nephrol. 5, 972–984 (2010).

  34. 34.

    , , , & Proximal tubular cysts in fetal human autosomal recessive polycystic kidney disease. J. Am. Soc. Nephrol. 11, 760–763 (2000).

  35. 35.

    , , , & Kidney cysts, pancreatic cysts, and biliary disease in a mouse model of autosomal recessive polycystic kidney disease. Pediatr. Nephrol. 23, 733–741 (2008).

  36. 36.

    et al. Epitope-tagged Pkhd1 tracks the processing, secretion, and localization of fibrocystin. J. Am. Soc. Nephrol. 22, 2266–2277 (2011).

  37. 37.

    et al. A mouse model of autosomal recessive polycystic kidney disease with biliary duct and proximal tubule dilatation. Kidney Int. 72, 328–336 (2007).

  38. 38.

    & The ciliopathies: a transitional model into systems biology of human genetic disease. Curr. Opin. Genet. Dev. 22, 290–303 (2012).

  39. 39.

    et al. Cardiovascular, skeletal, and renal defects in mice with a targeted disruption of the Pkd1 gene. Proc. Natl. Acad. Sci. USA 98, 12174–12179 (2001).

  40. 40.

    et al. Growth of cranial synchondroses and sutures requires polycystin-1. Dev. Biol. 321, 407–419 (2008).

  41. 41.

    et al. Genetic compensation induced by deleterious mutations but not gene knockdowns. Nature 524, 230–233 (2015).

  42. 42.

    , , & Morpholinos: antisense and Sensibility. Dev. Cell 35, 145–149 (2015).

  43. 43.

    et al. GSK3β-Dzip1-Rab8 cascade regulates ciliogenesis after mitosis. PLoS Biol. 13, e1002129 (2015).

  44. 44.

    , & Proteomic analysis of isolated ciliary transition zones reveals the presence of ESCRT proteins. Curr. Biol. 25, 379–384 (2015).

  45. 45.

    et al. The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery. Nat. Genet. 48, 648–656 (2016).

  46. 46.

    , , , & Loss of cilia suppresses cyst growth in genetic models of autosomal dominant polycystic kidney disease. Nat. Genet. 45, 1004–1012 (2013).

  47. 47.

    et al. Mutations in nuclear pore genes NUP93, NUP205 and XPO5 cause steroid-resistant nephrotic syndrome. Nat. Genet. 48, 457–465 (2016).

  48. 48.

    et al. FAN1 mutations cause karyomegalic interstitial nephritis, linking chronic kidney failure to defective DNA damage repair. Nat. Genet. 44, 910–915 (2012).

  49. 49.

    et al. ANKS6 is a central component of a nephronophthisis module linking NEK8 to INVS and NPHP3. Nat. Genet. 45, 951–956 (2013).

  50. 50.

    et al. Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models. Open Biol. 2, 120061 (2012).

  51. 51.

    , & Patched1 regulates hedgehog signaling at the primary cilium. Science 317, 372–376 (2007).

  52. 52.

    et al. Inactivation of Patched1 in the mouse limb has novel inhibitory effects on the chondrogenic program. J. Biol. Chem. 285, 27967–27981 (2010).

  53. 53.

    et al. Genomic screen for genes involved in mammalian craniofacial development. Genesis 35, 73–87 (2003).

  54. 54.

    et al. Patched 1 is a crucial determinant of asymmetry and digit number in the vertebrate limb. Development 136, 3515–3524 (2009).

  55. 55.

    et al. Mutations in mouse Ift144 model the craniofacial, limb and rib defects in skeletal ciliopathies. Hum. Mol. Genet. 21, 1808–1823 (2012).

  56. 56.

    & Quantitative studies of the growth of mouse embryo cells in culture and their development into established lines. J. Cell Biol. 17, 299–313 (1963).

  57. 57.

    et al. Cyst formation and activation of the extracellular regulated kinase pathway after kidney specific inactivation of Pkd1. Hum. Mol. Genet. 17, 1505–1516 (2008).

  58. 58.

    et al. Polycystin-1 distribution is modulated by polycystin-2 expression in mammalian cells. J. Biol. Chem. 278, 36786–36793 (2003).

  59. 59.

    et al. Somatic inactivation of Pkd2 results in polycystic kidney disease. Cell 93, 177–188 (1998).

  60. 60.

    , & Superresolution microscopy of the nuclear envelope and associated proteins. Methods Mol. Biol. 1411, 83–97 (2016).

  61. 61.

    et al. Patched1 is required in neural crest cells for the prevention of orofacial clefts. Hum. Mol. Genet. 22, 5026–5035 (2013).

  62. 62.

    , , , & Stages of embryonic development of the zebrafish. Dev. Dyn. 203, 253–310 (1995).

  63. 63.

    , , , & CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res. 42, W401–W407 (2014).

  64. 64.

    , , & Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Rep. 4, 220–228 (2013).

  65. 65.

    , , & A PCR based protocol for detecting indel mutations induced by TALENs and CRISPR/Cas9 in zebrafish. PLoS One 9, e98282 (2014).

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The authors thank the patients and their families for their cooperation and interest in the study; M.T. Toh and Y.T. Koh for technical assistance; W.I. Goh of the Institute of Medical Biology's Microscopy Unit for assistance with super-resolution microscopy; J. Lefevre and N. Hamilton for advice on statistical analyses; and C. Cortés, M. Pitt, F. Olsson, L. Zhao, L. Wilkinson and P. Karaith Oliva for assistance, insightful discussion and advice. The authors also thank C. Has (University Medical Center Freiburg) for kindly providing control fibroblasts; S. Somlo, M. Ma and K. Dong (Yale University) for Pkd1- and Pkd2-mutant cells; L. Lei (Nanyang Technological University) for the RPE-1 cell line stably expressing Arl13b–GFP; L. Pelletier (Lunenfeld-Tanenbaum Research Institute) for basal-body and transition-zone-protein cDNA clones; and R. Witzgall (Institute for Molecular and Cellular Anatomy, University of Regensburg), G. Wu (Center of Translational Cancer Research and Therapy, Beijing) and R. Rohatgi (Stanford University) for antibodies. We also thank the staff of the University of Queensland (UQ) QBP animal house for assistance with mouse husbandry and the Australian Phenomics Facility for maintaining mice throughout the screen. Confocal microscopy at UQ was carried out at the Institute for Molecular Bioscience Dynamic Imaging Facility for Cancer Biology, which is funded through the generous support of the Australian Cancer Research Foundation. We also acknowledge the Australian Microscopy & Microanalysis Facility (AMMRF) at the Centre for Microscopy and Microanalysis at UQ. M.H., S.N., V.F. and C.B. are supported as employees of Bioscientia/Sonic Healthcare; C.W. was supported as a recipient of a University of Queensland Vice-Chancellor's Senior Research Fellowship; and S.R. is supported as a Senior Principal Investigator at the Institute of Molecular and Cell Biology, Singapore. M.H.L. is supported as a Senior Principal Research Fellow of the Australian National Health and Medical Research Council (NHMRC). F.H. is supported as the Warren E. Grupe Professor. This work was supported by grants from the German Research Fund (DFG) to K.Z. and C.B., the DFG Collaborative Research Centre (SFB) KIDGEM 1140 and the Federal Ministry of Education and Research (BMBF, 01GM1515C) to C.B., the Australian NHMRC (APP1045464) to C.W., the National Institutes of Health NIH (DK068306) to F.H. and the Agency for Science, Technology and Research (A*STAR) of Singapore to W.H. and S.R. This paper is dedicated to the memory of Markus Nauck, who recently passed away.

Author information

Author notes

    • Vicki Metzis
    • , Shubha Vij
    • , Melissa H Little
    •  & Peter Papathanasiou

    Present addresses: Francis Crick Institute, London, UK (V.M.), Temasek Life Sciences Laboratory Limited, National University of Singapore, Singapore (S.V.), Murdoch Children's Research Institute and Department of Pediatrics, University of Melbourne, Melbourne, Victoria, Australia (M.H.L.) and Department of Materials, Imperial College London, London, UK (P.P.).

    • Hao Lu
    • , Maria C Rondón Galeano
    •  & Elisabeth Ott

    These authors contributed equally to this work.

    • Carol Wicking
    •  & Carsten Bergmann

    These authors jointly directed this work.


  1. Institute of Molecular and Cell Biology, Singapore.

    • Hao Lu
    • , P Jaya Kausalya
    • , Shang Yew Tay
    • , Shubha Vij
    • , Walter Hunziker
    •  & Sudipto Roy
  2. Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.

    • Maria C Rondón Galeano
    • , Geraldine Kaeslin
    • , Vicki Metzis
    • , Andrew D Courtney
    • , Melissa H Little
    • , Andrew C Perkins
    •  & Carol Wicking
  3. Department of Medicine IV, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.

    • Elisabeth Ott
    • , Carina Kramer
    • , Daniel Epting
    •  & Carsten Bergmann
  4. Institute of Human Genetics, RWTH Aachen University, Aachen, Germany.

    • Nadina Ortiz-Brüchle
    • , Nadescha Hilger
    • , Klaus Zerres
    •  & Carsten Bergmann
  5. Center for Human Genetics, Bioscientia, Ingelheim, Germany.

    • Milan Hiersche
    • , Steffen Neuber
    • , Valeska Frank
    •  & Carsten Bergmann
  6. John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory, Australia.

    • Robert Tunningley
    • , Belinda Whittle
    •  & Peter Papathanasiou
  7. Division of Pediatric Nephrology, University Children's Hospital Center for Child and Adolescent Medicine, Heidelberg University Hospital, Heidelberg, Germany.

    • Elke Wühl
  8. Department of Pediatric Nephrology, University Children's Hospital Essen, Essen, Germany.

    • Udo Vester
  9. Institute of Pathology, MHH University Medical School Hannover, Hannover, Germany.

    • Björn Hartleben
  10. Mater Research Institute, Faculty of Medicine and Biomedical Sciences, The University of Queensland, Woolloongabba, Queensland, Australia.

    • Andrew C Perkins
  11. Institute of Medical Biology, A*STAR, Singapore.

    • Graham D Wright
  12. Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.

    • Walter Hunziker
  13. Singapore Eye Research Institute, Singapore.

    • Walter Hunziker
  14. Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.

    • Heon Yung Gee
    •  & Friedhelm Hildebrandt
  15. Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea.

    • Heon Yung Gee
  16. Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan, USA.

    • Edgar A Otto
  17. Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.

    • Sudipto Roy
  18. Department of Biological Sciences, National University of Singapore, Singapore.

    • Sudipto Roy


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H.L., P.J.K., S.Y.T., S.V. and S.R. performed the zebrafish mutant and morphant analyses, protein interaction studies, localization experiments with human fibroblasts and validation of antibodies to PCs. W.H. supervised the protein interaction studies. E.O., C.K. and D.E. performed the zebrafish morpholino analyses. M.C.R.G., G.K., V.M. and A.D.C. performed the mouse analyses, and M.C.R.G. and G.K. performed the localization experiments with mouse cells. R.T., P.P. and A.C.P. performed the screen that identified the mouse mutant, and B.W. was involved in mapping and identifying the mouse mutation. G.D.W. performed the super-resolution microscopy experiments. M.H.L. assisted with design and analysis of mouse kidney experiments. N.O.-B., N.H., V.F. and S.N. performed the human mutation analysis. S.N., V.F., M.H., H.Y.G., E.A.O., F.H. and C.B. carried out the WES data processing and analyses. S.N., V.F., E.W., U.V., H.Y.G., K.Z., F.H. and C.B. recruited and clinically characterized the study subjects and collected samples. B.H. performed histologic evaluation of the data. S.R., C.W. and C.B. conceived the project, designed and supervised the experiments, analyzed and interpreted the data and wrote the manuscript. All authors reviewed the final manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Sudipto Roy or Carol Wicking or Carsten Bergmann.

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    DZIP1L Y2H screen.

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