title: An organelle-specific protein landscape identifies novel diseases and molecular mechanisms.
abstract: Cellular organelles provide opportunities to relate biological mechanisms to disease. Here we use affinity proteomics, genetics and cell biology to interrogate cilia: poorly understood organelles, where defects cause genetic diseases. Two hundred and seventeen tagged human ciliary proteins create a final landscape of 1,319 proteins, 4,905 interactions and 52 complexes. Reverse tagging, repetition of purifications and statistical analyses, produce a high-resolution network that reveals organelle-specific interactions and complexes not apparent in larger studies, and links vesicle transport, the cytoskeleton, signalling and ubiquitination to ciliary signalling and proteostasis. We observe sub-complexes in exocyst and intraflagellar transport complexes, which we validate biochemically, and by probing structurally predicted, disruptive, genetic variants from ciliary disease patients. The landscape suggests other genetic diseases could be ciliary including 3M syndrome. We show that 3M genes are involved in ciliogenesis, and that patient fibroblasts lack cilia. Overall, this organelle-specific targeting strategy shows considerable promise for Systems Medicine.
authors.affiliation: Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany.
authors.forename: Karsten
authors.initials: K
authors.lastname: Boldt
authors.affiliation: Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Jeroen
authors.identifier: 0000-0002-0658-4399
authors.initials: J
authors.lastname: van Reeuwijk
authors.affiliation: Biochemie Zentrum Heidelberg (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.|Cell Networks, Bioquant, Ruprecht-Karl University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.
authors.forename: Qianhao
authors.initials: Q
authors.lastname: Lu
authors.affiliation: Institute of Systems and Synthetic Biology, Genopole, CNRS, Université d'Evry, 91030 Evry, France.
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Koutroumpas
authors.affiliation: Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Thanh-Minh T
authors.initials: TM
authors.lastname: Nguyen
authors.affiliation: Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany.|Department of Molecular Epigenetics, Helmholtz Center Munich, Center for Integrated Protein Science, 81377 Munich, Germany.
authors.forename: Yves
authors.initials: Y
authors.lastname: Texier
authors.affiliation: Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Sylvia E C
authors.initials: SE
authors.lastname: van Beersum
authors.affiliation: Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany.
authors.forename: Nicola
authors.initials: N
authors.lastname: Horn
authors.affiliation: Center for Human Disease Modeling, Duke University, Durham, North Carolina 27701, USA.
authors.forename: Jason R
authors.initials: JR
authors.lastname: Willer
authors.affiliation: Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Dorus A
authors.initials: DA
authors.lastname: Mans
authors.affiliation: Department of General Pediatrics, University Children's Hospital Muenster, 48149 Muenster, Germany.
authors.forename: Gerard
authors.initials: G
authors.lastname: Dougherty
authors.affiliation: Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Ideke J C
authors.initials: IJ
authors.lastname: Lamers
authors.affiliation: Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Karlien L M
authors.initials: KL
authors.lastname: Coene
authors.affiliation: Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Heleen H
authors.initials: HH
authors.lastname: Arts
authors.affiliation: Biochemie Zentrum Heidelberg (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.|Cell Networks, Bioquant, Ruprecht-Karl University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Betts
authors.affiliation: Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany.
authors.forename: Tina
authors.initials: T
authors.lastname: Beyer
authors.affiliation: Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Emine
authors.initials: E
authors.lastname: Bolat
authors.affiliation: German Center for Neurodegenerative Diseases (DZNE) within the Helmholz Association, Otfried-Müller Strasse 23, 72076 Tuebingen, Germany.
authors.forename: Christian Johannes
authors.initials: CJ
authors.lastname: Gloeckner
authors.affiliation: Department of Nephrology and Hypertension, Regenerative Medicine Center, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands.
authors.forename: Khatera
authors.initials: K
authors.lastname: Haidari
authors.affiliation: Department of Otorhinolaryngology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Lisette
authors.initials: L
authors.lastname: Hetterschijt
authors.affiliation: Telethon Institute of Genetics and Medicine, TIGEM 80078, Italy.
authors.forename: Daniela
authors.initials: D
authors.lastname: Iaconis
authors.affiliation: Molecular Medicine Unit and Birth Defects Research Centre, UCL Institute of Child Health, London, WC1N 1EH, UK.
authors.forename: Dagan
authors.initials: D
authors.lastname: Jenkins
authors.affiliation: Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany.
authors.forename: Franziska
authors.initials: F
authors.lastname: Klose
authors.affiliation: Cell and Matrix Biology, Inst. of Zoology, Johannes Gutenberg University of Mainz, 55122 Mainz, Germany.
authors.forename: Barbara
authors.initials: B
authors.lastname: Knapp
authors.affiliation: Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Brooke
authors.initials: B
authors.lastname: Latour
authors.affiliation: Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Stef J F
authors.initials: SJ
authors.lastname: Letteboer
authors.affiliation: Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Carlo L
authors.initials: CL
authors.lastname: Marcelis
authors.affiliation: Cambridge Cell Networks Ltd, St John's Innovation Centre, Cowley Road, Cambridge, CB4 0WS, UK.
authors.forename: Dragana
authors.initials: D
authors.lastname: Mitic
authors.affiliation: Telethon Institute of Genetics and Medicine, TIGEM 80078, Italy.|Department of Translational Medicine Federico II University, 80131 Naples, Italy.
authors.forename: Manuela
authors.initials: M
authors.lastname: Morleo
authors.affiliation: Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Machteld M
authors.initials: MM
authors.lastname: Oud
authors.affiliation: Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Moniek
authors.initials: M
authors.lastname: Riemersma
authors.affiliation: Molecular Medicine Unit and Birth Defects Research Centre, UCL Institute of Child Health, London, WC1N 1EH, UK.
authors.forename: Susan
authors.initials: S
authors.lastname: Rix
authors.affiliation: Department of Genetics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands.
authors.forename: Paulien A
authors.initials: PA
authors.lastname: Terhal
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Grischa
authors.initials: G
authors.lastname: Toedt
authors.affiliation: Centre for Molecular and Biomolecular Informatics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands.
authors.forename: Teunis J P
authors.initials: TJ
authors.lastname: van Dam
authors.affiliation: Department of Otorhinolaryngology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Erik
authors.initials: E
authors.lastname: de Vrieze
authors.affiliation: Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany.
authors.forename: Yasmin
authors.initials: Y
authors.lastname: Wissinger
authors.affiliation: Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Ka Man
authors.initials: KM
authors.lastname: Wu
authors.affiliation: Cambridge Cell Networks Ltd, St John's Innovation Centre, Cowley Road, Cambridge, CB4 0WS, UK.
authors.forename: Gordana
authors.initials: G
authors.lastname: Apic
authors.affiliation: Molecular Medicine Unit and Birth Defects Research Centre, UCL Institute of Child Health, London, WC1N 1EH, UK.
authors.forename: Philip L
authors.initials: PL
authors.lastname: Beales
authors.affiliation: School of Biomolecular &Biomed Science, Conway Institute, University College Dublin, Dublin 4, Ireland.
authors.forename: Oliver E
authors.initials: OE
authors.lastname: Blacque
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Toby J
authors.initials: TJ
authors.lastname: Gibson
authors.affiliation: Centre for Molecular and Biomolecular Informatics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands.
authors.forename: Martijn A
authors.initials: MA
authors.lastname: Huynen
authors.affiliation: Center for Human Disease Modeling, Duke University, Durham, North Carolina 27701, USA.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Katsanis
authors.affiliation: Department of Otorhinolaryngology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Hannie
authors.initials: H
authors.lastname: Kremer
authors.affiliation: Department of General Pediatrics, University Children's Hospital Muenster, 48149 Muenster, Germany.
authors.forename: Heymut
authors.initials: H
authors.lastname: Omran
authors.affiliation: Department of Otorhinolaryngology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Erwin
authors.initials: E
authors.lastname: van Wijk
authors.affiliation: Cell and Matrix Biology, Inst. of Zoology, Johannes Gutenberg University of Mainz, 55122 Mainz, Germany.
authors.forename: Uwe
authors.initials: U
authors.lastname: Wolfrum
authors.affiliation: Institute of Systems and Synthetic Biology, Genopole, CNRS, Université d'Evry, 91030 Evry, France.
authors.forename: François
authors.initials: F
authors.lastname: Kepes
authors.affiliation: Center for Human Disease Modeling, Duke University, Durham, North Carolina 27701, USA.
authors.forename: Erica E
authors.initials: EE
authors.lastname: Davis
authors.affiliation: Telethon Institute of Genetics and Medicine, TIGEM 80078, Italy.|Department of Translational Medicine Federico II University, 80131 Naples, Italy.
authors.forename: Brunella
authors.initials: B
authors.lastname: Franco
authors.affiliation: Department of Nephrology and Hypertension, Regenerative Medicine Center, University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands.
authors.forename: Rachel H
authors.identifier: 0000-0001-9133-2008
authors.initials: RH
authors.lastname: Giles
authors.affiliation: Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 72074 Tuebingen, Germany.
authors.forename: Marius
authors.initials: M
authors.lastname: Ueffing
authors.affiliation: Biochemie Zentrum Heidelberg (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.|Cell Networks, Bioquant, Ruprecht-Karl University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.
authors.forename: Robert B
authors.identifier: 0000-0002-1905-4717
authors.initials: RB
authors.lastname: Russell
authors.affiliation: Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands.
authors.forename: Ronald
authors.initials: R
authors.lastname: Roepman
mesh_terms: D001692:Biological Transport / Q000502:physiology; D002846:Chromatography, Affinity / Q000379:methods; D002923:Cilia / Q000378:metabolism*; D000072661:Ciliopathies / Q000235:genetics* / Q000473:pathology / Q000628:therapy; D004252:DNA Mutational Analysis; D066264:Datasets as Topic; D004392:Dwarfism / Q000235:genetics* / Q000473:pathology / Q000628:therapy; D005347:Fibroblasts; D057809:HEK293 Cells; D006801:Humans; D013058:Mass Spectrometry; D058990:Molecular Targeted Therapy / Q000379:methods; D009123:Muscle Hypotonia / Q000235:genetics* / Q000473:pathology / Q000628:therapy; D025941:Protein Interaction Mapping / Q000379:methods; D060066:Protein Interaction Maps; D011506:Proteins / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D040901:Proteomics / Q000379:methods; D013131:Spine / Q000002:abnormalities* / Q000473:pathology; D013597:Systems Analysis
chemical_list: D011506:Proteins