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

Gabrielle Wheway, Miriam Schmidts, Dorus A. Mans, Katarzyna Szymanska, Thanh-Minh T. Nguyen, Hilary Racher, Ian G. Phelps, Grischa Toedt, Julie Kennedy, Kirsten A. Wunderlich, Nasrin Sorusch, Zakia A. Abdelhamed, Subaashini Natarajan, Warren Herridge, Jeroen van Reeuwijk, Nicola Horn, Karsten Boldt, David A. Parry, Stef J. F. Letteboer, Susanne Roosing & 56 others Matthew Adams, Sandra M. Bell, Jacquelyn Bond, Julie Higgins, Ewan E. Morrison, Darren C. Tomlinson, Gisela G. Slaats, Teunis J. P. van Dam, Lijia Huang, Kristin Kessler, Andreas Giessl, Clare V. Logan, Evan A. Boyle, Jay Shendure, Shamsa Anazi, Mohammed Aldahmesh, Selwa Al Hazzaa, Robert A. Hegele, Carole Ober, Patrick Frosk, Aizeddin A. Mhanni, Bernard N. Chodirker, Albert E. Chudley, Ryan Lamont, Francois P. Bernier, Chandree L. Beaulieu, Paul Gordon, Richard T. Pon, Clem Donahue, A. James Barkovich, Louis Wolf, Carmel Toomes, Christian T. Thiel, Kym M. Boycott, Martin McKibbin, Chris F. Inglehearn, Fiona Stewart, Heymut Omran, Martijn A. Huynen, Panagiotis I. Sergouniotis, Fowzan S. Alkuraya, Jillian S. Parboosingh, A. Micheil Innes, Colin Willoughby, Rachel H. Giles, Andrew R. Webster, Marius Ueffing, Oliver Blacque, Joseph G. Gleeson, Uwe Wolfrum, Philip L. Beales, Toby Gibson, Dan Doherty, Hannah M. Mitchison, Ronald Roepman, Colin A. Johnson

    Research output: Contribution to journalArticle

    76 Citations (Scopus)

    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
    LanguageEnglish
    Pages1074-1087
    JournalNature Cell Biology
    Volume17
    Issue number8
    DOIs
    Publication statusAccepted/In press - 5 Jun 2015

    Fingerprint

    Genomics
    Small Interfering RNA
    Cilia
    Inborn Genetic Diseases
    Genes
    Exome
    Reverse Genetics
    Retinitis Pigmentosa
    RNA Precursors
    Medical Genetics
    Proteasome Endopeptidase Complex
    G-Protein-Coupled Receptors
    Ubiquitin
    Maintenance
    Genome
    Mutation
    Ciliopathies
    Proteins

    Keywords

    • siRNA
    • cilia
    • ciliopathy
    • retina
    • genetics

    Cite this

    Wheway, G., Schmidts, M., Mans, D. A., Szymanska, K., Nguyen, T-M. T., Racher, H., ... Johnson, C. A. (Accepted/In press). An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes. Nature Cell Biology, 17(8), 1074-1087. https://doi.org/10.1038/ncb3201
    Wheway, Gabrielle ; Schmidts, Miriam ; Mans, Dorus A. ; Szymanska, Katarzyna ; Nguyen, Thanh-Minh T. ; Racher, Hilary ; Phelps, Ian G. ; Toedt, Grischa ; Kennedy, Julie ; Wunderlich, Kirsten A. ; Sorusch, Nasrin ; Abdelhamed, Zakia A. ; Natarajan, Subaashini ; Herridge, Warren ; van Reeuwijk, Jeroen ; Horn, Nicola ; Boldt, Karsten ; Parry, David A. ; Letteboer, Stef J. F. ; Roosing, Susanne ; Adams, Matthew ; Bell, Sandra M. ; Bond, Jacquelyn ; Higgins, Julie ; Morrison, Ewan E. ; Tomlinson, Darren C. ; Slaats, Gisela G. ; van Dam, Teunis J. P. ; Huang, Lijia ; Kessler, Kristin ; Giessl, Andreas ; Logan, Clare V. ; Boyle, Evan A. ; Shendure, Jay ; Anazi, Shamsa ; Aldahmesh, Mohammed ; Al Hazzaa, Selwa ; Hegele, Robert A. ; Ober, Carole ; Frosk, Patrick ; Mhanni, Aizeddin A. ; Chodirker, Bernard N. ; Chudley, Albert E. ; Lamont, Ryan ; Bernier, Francois P. ; Beaulieu, Chandree L. ; Gordon, Paul ; Pon, Richard T. ; Donahue, Clem ; Barkovich, A. James ; Wolf, Louis ; Toomes, Carmel ; Thiel, Christian T. ; Boycott, Kym M. ; McKibbin, Martin ; Inglehearn, Chris F. ; Stewart, Fiona ; Omran, Heymut ; Huynen, Martijn A. ; Sergouniotis, Panagiotis I. ; Alkuraya, Fowzan S. ; Parboosingh, Jillian S. ; Innes, A. Micheil ; Willoughby, Colin ; Giles, Rachel H. ; Webster, Andrew R. ; Ueffing, Marius ; Blacque, Oliver ; Gleeson, Joseph G. ; Wolfrum, Uwe ; Beales, Philip L. ; Gibson, Toby ; Doherty, Dan ; Mitchison, Hannah M. ; Roepman, Ronald ; Johnson, Colin A. / An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes. In: Nature Cell Biology. 2015 ; Vol. 17, No. 8. pp. 1074-1087.
    @article{7e14a8fc2d7f441abf67c97d54325150,
    title = "An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes",
    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",
    keywords = "siRNA, cilia, ciliopathy, retina, genetics",
    author = "Gabrielle Wheway and Miriam Schmidts and Mans, {Dorus A.} and Katarzyna Szymanska and Nguyen, {Thanh-Minh T.} and Hilary Racher and Phelps, {Ian G.} and Grischa Toedt and Julie Kennedy and Wunderlich, {Kirsten A.} and Nasrin Sorusch and Abdelhamed, {Zakia A.} and Subaashini Natarajan and Warren Herridge and {van Reeuwijk}, Jeroen and Nicola Horn and Karsten Boldt and Parry, {David A.} and Letteboer, {Stef J. F.} and Susanne Roosing and Matthew Adams and Bell, {Sandra M.} and Jacquelyn Bond and Julie Higgins and Morrison, {Ewan E.} and Tomlinson, {Darren C.} and Slaats, {Gisela G.} and {van Dam}, {Teunis J. P.} and Lijia Huang and Kristin Kessler and Andreas Giessl and Logan, {Clare V.} and Boyle, {Evan A.} and Jay Shendure and Shamsa Anazi and Mohammed Aldahmesh and {Al Hazzaa}, Selwa and Hegele, {Robert A.} and Carole Ober and Patrick Frosk and Mhanni, {Aizeddin A.} and Chodirker, {Bernard N.} and Chudley, {Albert E.} and Ryan Lamont and Bernier, {Francois P.} and Beaulieu, {Chandree L.} and Paul Gordon and Pon, {Richard T.} and Clem Donahue and Barkovich, {A. James} and Louis Wolf and Carmel Toomes and Thiel, {Christian T.} and Boycott, {Kym M.} and Martin McKibbin and Inglehearn, {Chris F.} and Fiona Stewart and Heymut Omran and Huynen, {Martijn A.} and Sergouniotis, {Panagiotis I.} and Alkuraya, {Fowzan S.} and Parboosingh, {Jillian S.} and Innes, {A. Micheil} and Colin Willoughby and Giles, {Rachel H.} and Webster, {Andrew R.} and Marius Ueffing and Oliver Blacque and Gleeson, {Joseph G.} and Uwe Wolfrum and Beales, {Philip L.} and Toby Gibson and Dan Doherty and Mitchison, {Hannah M.} and Ronald Roepman and Johnson, {Colin A.}",
    year = "2015",
    month = "6",
    day = "5",
    doi = "10.1038/ncb3201",
    language = "English",
    volume = "17",
    pages = "1074--1087",
    journal = "Nature Cell Biology",
    issn = "1465-7392",
    number = "8",

    }

    Wheway, G, Schmidts, M, Mans, DA, Szymanska, K, Nguyen, T-MT, Racher, H, Phelps, IG, Toedt, G, Kennedy, J, Wunderlich, KA, Sorusch, N, Abdelhamed, ZA, Natarajan, S, Herridge, W, van Reeuwijk, J, Horn, N, Boldt, K, Parry, DA, Letteboer, SJF, Roosing, S, Adams, M, Bell, SM, Bond, J, Higgins, J, Morrison, EE, Tomlinson, DC, Slaats, GG, van Dam, TJP, Huang, L, Kessler, K, Giessl, A, Logan, CV, Boyle, EA, Shendure, J, Anazi, S, Aldahmesh, M, Al Hazzaa, S, Hegele, RA, Ober, C, Frosk, P, Mhanni, AA, Chodirker, BN, Chudley, AE, Lamont, R, Bernier, FP, Beaulieu, CL, Gordon, P, Pon, RT, Donahue, C, Barkovich, AJ, Wolf, L, Toomes, C, Thiel, CT, Boycott, KM, McKibbin, M, Inglehearn, CF, Stewart, F, Omran, H, Huynen, MA, Sergouniotis, PI, Alkuraya, FS, Parboosingh, JS, Innes, AM, Willoughby, C, Giles, RH, Webster, AR, Ueffing, M, Blacque, O, Gleeson, JG, Wolfrum, U, Beales, PL, Gibson, T, Doherty, D, Mitchison, HM, Roepman, R & Johnson, CA 2015, 'An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes', Nature Cell Biology, vol. 17, no. 8, pp. 1074-1087. https://doi.org/10.1038/ncb3201

    An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes. / Wheway, Gabrielle; Schmidts, Miriam; Mans, Dorus A.; Szymanska, Katarzyna; Nguyen, Thanh-Minh T.; Racher, Hilary; Phelps, Ian G.; Toedt, Grischa; Kennedy, Julie; Wunderlich, Kirsten A.; Sorusch, Nasrin; Abdelhamed, Zakia A.; Natarajan, Subaashini; Herridge, Warren; van Reeuwijk, Jeroen; Horn, Nicola; Boldt, Karsten; Parry, David A.; Letteboer, Stef J. F.; Roosing, Susanne; Adams, Matthew; Bell, Sandra M.; Bond, Jacquelyn; Higgins, Julie; Morrison, Ewan E.; Tomlinson, Darren C.; Slaats, Gisela G.; van Dam, Teunis J. P.; Huang, Lijia; Kessler, Kristin; Giessl, Andreas; Logan, Clare V.; Boyle, Evan A.; Shendure, Jay; Anazi, Shamsa; Aldahmesh, Mohammed; Al Hazzaa, Selwa; Hegele, Robert A.; Ober, Carole; Frosk, Patrick; Mhanni, Aizeddin A.; Chodirker, Bernard N.; Chudley, Albert E.; Lamont, Ryan; Bernier, Francois P.; Beaulieu, Chandree L.; Gordon, Paul; Pon, Richard T.; Donahue, Clem; Barkovich, A. James; Wolf, Louis; Toomes, Carmel; Thiel, Christian T.; Boycott, Kym M.; McKibbin, Martin; Inglehearn, Chris F.; Stewart, Fiona; Omran, Heymut; Huynen, Martijn A.; Sergouniotis, Panagiotis I.; Alkuraya, Fowzan S.; Parboosingh, Jillian S.; Innes, A. Micheil; Willoughby, Colin; Giles, Rachel H.; Webster, Andrew R.; Ueffing, Marius; Blacque, Oliver; Gleeson, Joseph G.; Wolfrum, Uwe; Beales, Philip L.; Gibson, Toby; Doherty, Dan; Mitchison, Hannah M.; Roepman, Ronald; Johnson, Colin A.

    In: Nature Cell Biology, Vol. 17, No. 8, 05.06.2015, p. 1074-1087.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes

    AU - Wheway, Gabrielle

    AU - Schmidts, Miriam

    AU - Mans, Dorus A.

    AU - Szymanska, Katarzyna

    AU - Nguyen, Thanh-Minh T.

    AU - Racher, Hilary

    AU - Phelps, Ian G.

    AU - Toedt, Grischa

    AU - Kennedy, Julie

    AU - Wunderlich, Kirsten A.

    AU - Sorusch, Nasrin

    AU - Abdelhamed, Zakia A.

    AU - Natarajan, Subaashini

    AU - Herridge, Warren

    AU - van Reeuwijk, Jeroen

    AU - Horn, Nicola

    AU - Boldt, Karsten

    AU - Parry, David A.

    AU - Letteboer, Stef J. F.

    AU - Roosing, Susanne

    AU - Adams, Matthew

    AU - Bell, Sandra M.

    AU - Bond, Jacquelyn

    AU - Higgins, Julie

    AU - Morrison, Ewan E.

    AU - Tomlinson, Darren C.

    AU - Slaats, Gisela G.

    AU - van Dam, Teunis J. P.

    AU - Huang, Lijia

    AU - Kessler, Kristin

    AU - Giessl, Andreas

    AU - Logan, Clare V.

    AU - Boyle, Evan A.

    AU - Shendure, Jay

    AU - Anazi, Shamsa

    AU - Aldahmesh, Mohammed

    AU - Al Hazzaa, Selwa

    AU - Hegele, Robert A.

    AU - Ober, Carole

    AU - Frosk, Patrick

    AU - Mhanni, Aizeddin A.

    AU - Chodirker, Bernard N.

    AU - Chudley, Albert E.

    AU - Lamont, Ryan

    AU - Bernier, Francois P.

    AU - Beaulieu, Chandree L.

    AU - Gordon, Paul

    AU - Pon, Richard T.

    AU - Donahue, Clem

    AU - Barkovich, A. James

    AU - Wolf, Louis

    AU - Toomes, Carmel

    AU - Thiel, Christian T.

    AU - Boycott, Kym M.

    AU - McKibbin, Martin

    AU - Inglehearn, Chris F.

    AU - Stewart, Fiona

    AU - Omran, Heymut

    AU - Huynen, Martijn A.

    AU - Sergouniotis, Panagiotis I.

    AU - Alkuraya, Fowzan S.

    AU - Parboosingh, Jillian S.

    AU - Innes, A. Micheil

    AU - Willoughby, Colin

    AU - Giles, Rachel H.

    AU - Webster, Andrew R.

    AU - Ueffing, Marius

    AU - Blacque, Oliver

    AU - Gleeson, Joseph G.

    AU - Wolfrum, Uwe

    AU - Beales, Philip L.

    AU - Gibson, Toby

    AU - Doherty, Dan

    AU - Mitchison, Hannah M.

    AU - Roepman, Ronald

    AU - Johnson, Colin A.

    PY - 2015/6/5

    Y1 - 2015/6/5

    N2 - 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

    AB - 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

    KW - siRNA

    KW - cilia

    KW - ciliopathy

    KW - retina

    KW - genetics

    U2 - 10.1038/ncb3201

    DO - 10.1038/ncb3201

    M3 - Article

    VL - 17

    SP - 1074

    EP - 1087

    JO - Nature Cell Biology

    T2 - Nature Cell Biology

    JF - Nature Cell Biology

    SN - 1465-7392

    IS - 8

    ER -