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.
Original language | English (US) |
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Article number | 11491 |
Journal | Nature communications |
Volume | 7 |
DOIs | |
State | Published - May 13 2016 |
Funding
We thank the patient and parents for participation in research. We thank Gisela Slaats for technical assistance, the Syscilia consortium members for helpful scientific discussions, Colin Johnson for access to the siRNA datasets, and the Cell Microscopy Center Utrecht for Imaging assistance. The research leading to these results has received funding from the European Community's Seventh Framework Programme FP7/2009 under grant agreement no: 241955, SYSCILIA (to G.A., P.L.B, O.E.B., T.J.G., M.A.H., N.K., H.K., H.O., U.W., F.K., B.F., R.H.G., M.U., R.B.R. and R.R.), FP7 grant agreement no. 278568, PRIMES (to M.U and K.B.); the Dutch Kidney Foundation 'Kouncil' (CP11.18 to H.H.A., P.L.B., R.H.G. and R.R.); the Netherlands Organisation for Scientific Research (Veni- 016.136.091 to E.v.W., Veni-91613008 to H.H.A., and Vici-865.12.005 to R.R.); the Foundation Fighting Blindness (grant C-CMM-0811-0546-RAD02 to R.R., and grant C-CMM-0811-0547-RAD03 to H.K. and E.v.W.); NIH grants DK075972 and HD042601 (N.K.); DK072301 (N.K. and E.E.D); and EY021872 (E.E.D). H.K. and E.v.W. acknowledge 'Stichting Nederlands Oogheelkundig Onderzoek', 'Stichting Blindenhulp', 'Stichting Researchfonds Nijmegen', 'Landelijke Stichting voor Blinden en Slechtzienden', and the Netherlands Organisation for Health Research and Development (ZonMW E-rare grant 40-42900-98-1006). M.B., Q.L. and R.B.R. are supported by the Excellence Initiative Cell Networks, Germany Science Ministry. N.K. is a distinguished Jean and George Brumley Professor. B.F. acknowledges support from the Telethon Foundation (TGM11CB3). M.U. was supported by the Tistou & Charlotte Kerstan Stiftung.
ASJC Scopus subject areas
- General Chemistry
- General Biochemistry, Genetics and Molecular Biology
- General Physics and Astronomy