Journal Article

An organelle-specific protein landscape identifies novel diseases and molecular mechanisms

Lamers, Ideke J. C., Dougherty, Gerard, van Reeuwijk, Jeroen, Blacque, Oliver E., Ueffing, Marius, Katsanis, Nicholas, Toedt, Grischa, Apic, Gordana, Klose, Franziska, Rix, Susan, Horn, Nicola, Huynen, Martijn A., Wu, Ka Man, de Vrieze, Erik, Betts, Matthew J., Morleo, Manuela, Marcelis, Carlo L., Wissinger, Yasmin, Beales, Philip L., Knapp, Barbara, Texier, Yves, Terhal, Paulien A., Franco, Brunella, Kepes, François, van Beersum, Sylvia E. C., Willer, Jason R., Mitic, Dragana, Giles, Rachel H., Coene, Karlien L. M., van Wijk, Erwin, Russell, Robert B., Bolat, Emine, Jenkins, Dagan, Latour, Brooke, Oud, Machteld M., Gloeckner, Christian Johannes, Wolfrum, Uwe, Arts, Heleen H., Gibson, Toby J., Riemersma, Moniek, Kremer, Hannie, Iaconis, Daniela, Hetterschijt, Lisette, Mans, Dorus A., Omran, Heymut, Davis, Erica E., Boldt, Karsten, van Dam, Teunis J. P., Letteboer, Stef J. F., Koutroumpas, Konstantinos, Lu, Qianhao, Beyer, Tina, Haidari, Khatera, Nguyen, Thanh-Minh T., Roepman, Ronald

2016

Overview

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. Mutations in proteins that localize to primary cilia cause devastating diseases, yet the primary cilium is a poorly understood organelle. Here the authors use interaction proteomics to identify a network of human ciliary proteins that provides new insights into several biological processes and diseases.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 13/106 / 13/109 / 13/51 / 631/1647/48 / 631/337/475 / 631/80/642 / 692/308 / 82/58 / 82/80 / 82/83 / Biological Transport - physiology / Biology / Chromatography, Affinity - methods / Cilia - metabolism / Ciliopathies - genetics / Ciliopathies - pathology / Ciliopathies - therapy / Datasets as Topic / DNA Mutational Analysis / Dwarfism - genetics / Dwarfism - pathology / Dwarfism - therapy / Fibroblasts / Genetic disorders / Genetic variance / Genetics / HEK293 Cells / Humanities and Social Sciences / Humans / Kidney diseases / Life sciences / Mass Spectrometry / Medicine / Molecular Targeted Therapy - methods / multidisciplinary / Muscle Hypotonia - genetics / Muscle Hypotonia - pathology / Muscle Hypotonia - therapy / Mutation / Otolaryngology / Protein Interaction Mapping - methods / Protein Interaction Maps / Proteins / Proteins - genetics / Proteins - isolation & purification / Proteins - metabolism / Proteomics / Proteomics - methods / Rare diseases / Science / Science (multidisciplinary) / Spine - abnormalities / Spine - pathology / Statistical analysis / Systems Analysis