An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes

  • Nat Cell Biol. 2015 Aug;17(8):1074-1087. doi: 10.1038/ncb3201.
Gabrielle Wheway  #  1 ,  Miriam Schmidts  #  2  3  4  5 ,  Dorus A Mans  #  3  4 ,  Katarzyna Szymanska  #  1 ,  Thanh-Minh T Nguyen  #  3  4 ,  Hilary Racher  6 ,  Ian G Phelps  7 ,  Grischa Toedt  8 ,  Julie Kennedy  9 ,  Kirsten A Wunderlich  10 ,  Nasrin Sorusch  10 ,  Zakia A Abdelhamed  1 ,  Subaashini Natarajan  1 ,  Warren Herridge  1 ,  Jeroen van Reeuwijk  3  4 ,  Nicola Horn  11 ,  Karsten Boldt  11 ,  David A Parry  12 ,  Stef J F Letteboer  3  4 ,  Susanne Roosing  13 ,  Matthew Adams  14 ,  Sandra M Bell  14 ,  Jacquelyn Bond  14 ,  Julie Higgins  14 ,  Ewan E Morrison  14 ,  Darren C Tomlinson  14 ,  Gisela G Slaats  15 ,  Teunis J P van Dam  16 ,  Lijia Huang  17 ,  Kristin Kessler  18 ,  Andreas Giessl  19 ,  Clare V Logan  1 ,  Evan A Boyle  20 ,  Jay Shendure  20 ,  Shamsa Anazi  21 ,  Mohammed Aldahmesh  21 ,  Selwa Al Hazzaa  22  23 ,  Robert A Hegele  24 ,  Carole Ober  25 ,  Patrick Frosk  26 ,  Aizeddin A Mhanni  26 ,  Bernard N Chodirker  26 ,  Albert E Chudley  26 ,  Ryan Lamont  6 ,  Francois P Bernier  6 ,  Chandree L Beaulieu  17 ,  Paul Gordon  6 ,  Richard T Pon  6 ,  Clem Donahue  27 ,  A James Barkovich  28 ,  Louis Wolf  29 ,  Carmel Toomes  1 ,  Christian T Thiel  18 ,  Kym M Boycott  17 ,  Martin McKibbin  30 ,  Chris F Inglehearn  1 ,  UK10K Consortium ,  University of Washington Center for Mendelian Genomics ,  Fiona Stewart  31 ,  Heymut Omran  32 ,  Martijn A Huynen  16 ,  Panagiotis I Sergouniotis  33  34 ,  Fowzan S Alkuraya  21  35 ,  Jillian S Parboosingh  6 ,  A Micheil Innes  6 ,  Colin E Willoughby  36 ,  Rachel H Giles  15 ,  Andrew R Webster  33  34 ,  Marius Ueffing  11  37 ,  Oliver Blacque  9 ,  Joseph G Gleeson  13 ,  Uwe Wolfrum  10 ,  Philip L Beales  2 ,  Toby Gibson  8 ,  Dan Doherty  7  38 ,  Hannah M Mitchison  2 ,  Ronald Roepman  3  4 ,  Colin A Johnson  1
Affiliations
  • 1. Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK.
  • 2. Genetics and Genomic Medicine and Birth Defects Research Centre, Institute of Child Health, University College London, London, WC1N 1EH, UK.
  • 3. Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
  • 4. Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
  • 5. Pediatric Genetics Section, Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg 79112, Germany.
  • 6. Department of Medical Genetics and Alberta Children's Hospital Research Institute for Child and Maternal Health, Calgary, T3B 6A8, AB, Canada.
  • 7. Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.
  • 8. Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
  • 9. School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland.
  • 10. Department of Cell and Matrix Biology, Institute of Zoology, Johannes Gutenberg University of Mainz, 55122 Mainz, Germany.
  • 11. Division of Experimental Ophthalmology and Medical Proteome Center, Center of Ophthalmology, University of Tübingen, 72074 Tübingen, Germany.
  • 12. Section of Genetics, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK.
  • 13. Laboratory for Pediatric Brain Disease, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, Box 268, New York, NY 10065, USA.
  • 14. BioScreening Technology Group, Biomedical Health Research Centre, St. James's University Hospital, Leeds, LS9 7TF, UK.
  • 15. Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, 3584 CX, The Netherlands.
  • 16. Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
  • 17. Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, K1H 8L1, ON, Canada.
  • 18. Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany.
  • 19. Animal Physiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany.
  • 20. Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • 21. Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.
  • 22. Department of Ophthalmology, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia.
  • 23. Department of Ophthalmology, College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia.
  • 24. Robarts Research Institute, University of Western Ontario, London, N6G 2V4, ON, Canada.
  • 25. Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
  • 26. Department of Pediatrics and Child Health & Department of Biochemistry and Medical Genetics, Faculty of Medicine, University of Manitoba, Winnipeg, R3E 3P5, MB, Canada.
  • 27. Department of Pediatrics, University of California San Francisco, San Francisco, CA 92093, USA.
  • 28. Department of Radiology, University of California San Francisco, San Francisco, CA 92093, USA.
  • 29. Department of Pathology, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.
  • 30. Department of Ophthalmology, Leeds Teaching Hospitals NHS Trust, St. James's University Hospital, Leeds, LS9 7TF, UK.
  • 31. Department of Medical Genetics, Belfast City Hospital and Queens University, Belfast, BT12 6BA, UK.
  • 32. Department of Pediatrics and Adolescent Medicine, University Hospital Muenster, 48149 Muenster, Germany.
  • 33. Moorfields Eye Hospital NHS Foundation Trust and NIHR Ophthalmology Biomedical Research Centre, London, EC1V 2PD, UK.
  • 34. UCL Institute of Ophthalmology, University College London, London, EC1V 9EL, UK.
  • 35. Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia.
  • 36. Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, Faculty of Health & Life Sciences, University of Liverpool, Liverpool, L69 3BX, UK.
  • 37. Research Unit of Protein Science, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, 85764 Neuherberg, Germany.
  • 38. Divisions of Developmental Medicine and Genetic Medicine, Seattle Children's Research Institute, University of Washington, Seattle, WA 98105, USA.
  • # Contributed equally.
PMID: 26167768 DOI: 10.1038/ncb3201
Abstract

Defects in primary cilium biogenesis underlie the ciliopathies, a growing group of genetic disorders. We describe a whole-genome siRNA-based reverse genetics screen for defects in biogenesis and/or maintenance of the primary cilium, obtaining a global resource. We identify 112 candidate ciliogenesis and ciliopathy genes, including 44 components of the ubiquitin-proteasome system, 12 G-protein-coupled receptors, and 3 pre-mRNA processing factors (PRPF6, PRPF8 and PRPF31) mutated in autosomal dominant retinitis pigmentosa. The PRPFs localize to the connecting cilium, and PRPF8- and PRPF31-mutated cells have ciliary defects. Combining the screen with exome Sequencing data identified recessive mutations in PIBF1, also known as CEP90, and C21orf2, also known as LRRC76, as causes of the ciliopathies Joubert and Jeune syndromes. Biochemical approaches place C21orf2 within key ciliopathy-associated protein modules, offering an explanation for the skeletal and retinal involvement observed in individuals with C21orf2 variants. Our global, unbiased approaches provide insights into ciliogenesis complexity and identify roles for unanticipated pathways in human genetic disease.