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3 results on '"Knapp, Barbara"'

1. CiliaCarta: An integrated and validated compendium of ciliary genes.

Author

van Dam TJP, Kennedy J, van der Lee R, de Vrieze E, Wunderlich KA, Rix S, Dougherty GW, Lambacher NJ, Li C, Jensen VL, Leroux MR, Hjeij R, Horn N, Texier Y, Wissinger Y, van Reeuwijk J, Wheway G, Knapp B, Scheel JF, Franco B, Mans DA, van Wijk E, Képès F, Slaats GG, Toedt G, Kremer H, Omran H, Szymanska K, Koutroumpas K, Ueffing M, Nguyen TT, Letteboer SJF, Oud MM, van Beersum SEC, Schmidts M, Beales PL, Lu Q, Giles RH, Szklarczyk R, Russell RB, Gibson TJ, Johnson CA, Blacque OE, Wolfrum U, Boldt K, Roepman R, Hernandez-Hernandez V, and Huynen MA

Subjects
Animals, Bayes Theorem, Caenorhabditis elegans cytology, Caenorhabditis elegans genetics, Molecular Sequence Annotation, Phenotype, Reproducibility of Results, Sensory Receptor Cells metabolism, Zebrafish genetics, Cilia genetics, Genomics
Abstract

The cilium is an essential organelle at the surface of mammalian cells whose dysfunction causes a wide range of genetic diseases collectively called ciliopathies. The current rate at which new ciliopathy genes are identified suggests that many ciliary components remain undiscovered. We generated and rigorously analyzed genomic, proteomic, transcriptomic and evolutionary data and systematically integrated these using Bayesian statistics into a predictive score for ciliary function. This resulted in 285 candidate ciliary genes. We generated independent experimental evidence of ciliary associations for 24 out of 36 analyzed candidate proteins using multiple cell and animal model systems (mouse, zebrafish and nematode) and techniques. For example, we show that OSCP1, which has previously been implicated in two distinct non-ciliary processes, causes ciliogenic and ciliopathy-associated tissue phenotypes when depleted in zebrafish. The candidate list forms the basis of CiliaCarta, a comprehensive ciliary compendium covering 956 genes. The resource can be used to objectively prioritize candidate genes in whole exome or genome sequencing of ciliopathy patients and can be accessed at http://bioinformatics.bio.uu.nl/john/syscilia/ciliacarta/., Competing Interests: The authors have declared that no competing interests exist.

Published
2019
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2. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms.

Author

Boldt K, van Reeuwijk J, Lu Q, Koutroumpas K, Nguyen TM, Texier Y, van Beersum SE, Horn N, Willer JR, Mans DA, Dougherty G, Lamers IJ, Coene KL, Arts HH, Betts MJ, Beyer T, Bolat E, Gloeckner CJ, Haidari K, Hetterschijt L, Iaconis D, Jenkins D, Klose F, Knapp B, Latour B, Letteboer SJ, Marcelis CL, Mitic D, Morleo M, Oud MM, Riemersma M, Rix S, Terhal PA, Toedt G, van Dam TJ, de Vrieze E, Wissinger Y, Wu KM, Apic G, Beales PL, Blacque OE, Gibson TJ, Huynen MA, Katsanis N, Kremer H, Omran H, van Wijk E, Wolfrum U, Kepes F, Davis EE, Franco B, Giles RH, Ueffing M, Russell RB, and Roepman R

Subjects
Biological Transport physiology, Chromatography, Affinity methods, Ciliopathies pathology, Ciliopathies therapy, DNA Mutational Analysis, Datasets as Topic, Dwarfism pathology, Dwarfism therapy, Fibroblasts, HEK293 Cells, Humans, Mass Spectrometry, Molecular Targeted Therapy methods, Muscle Hypotonia pathology, Muscle Hypotonia therapy, Protein Interaction Mapping methods, Proteins genetics, Proteins isolation & purification, Proteomics methods, Spine pathology, Systems Analysis, Cilia metabolism, Ciliopathies genetics, Dwarfism genetics, Muscle Hypotonia genetics, Protein Interaction Maps, Proteins metabolism, Spine abnormalities
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.

Published
2016
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3. CiliaCarta: An integrated and validated compendium of ciliary genes

Author

Gerard W. Dougherty, Victor L. Jensen, Jan Frederik Scheel, Katarzyna Szymanska, Uwe Wolfrum, Radek Szklarczyk, Miriam Schmidts, Julie Kennedy, Erwin van Wijk, Brunella Franco, Toby J. Gibson, Machteld M. Oud, Chunmei Li, Nils J. Lambacher, Erik de Vrieze, Grischa Toedt, Teunis J. P. van Dam, Karsten Boldt, Heymut Omran, Yves Texier, Rachel H. Giles, Ronald Roepman, Kirsten A. Wunderlich, Sylvia E. C. van Beersum, Oliver E. Blacque, Thanh-Minh T. Nguyen, Konstantinos Koutroumpas, Hannie Kremer, Nicola Horn, Martijn A. Huynen, Michel R. Leroux, Gabrielle Wheway, Rim Hjeij, Philip L. Beales, Gisela G. Slaats, Robert B. Russell, Robin van der Lee, François Képès, Yasmin Wissinger, Barbara Knapp, Dorus A. Mans, Suzanne Rix, Marius Ueffing, Colin A. Johnson, Stef J.F. Letteboer, Victor Hernandez-Hernandez, Qianhao Lu, Jeroen van Reeuwijk, Sub Bioinformatics, Theoretical Biology and Bioinformatics, MUMC+: DA KG Lab Centraal Lab (9), Klinische Genetica, RS: GROW - R4 - Reproductive and Perinatal Medicine, van Dam, Teunis J P, Kennedy, Julie, van der Lee, Robin, de Vrieze, Erik, Wunderlich, Kirsten A, Rix, Suzanne, Dougherty, Gerard W, Lambacher, Nils J, Li, Chunmei, Jensen, Victor L, Leroux, Michel R, Hjeij, Rim, Horn, Nicola, Texier, Yve, Wissinger, Yasmin, van Reeuwijk, Jeroen, Wheway, Gabrielle, Knapp, Barbara, Scheel, Jan F, Franco, Brunella, Mans, Dorus A, van Wijk, Erwin, Képès, Françoi, Slaats, Gisela G, Toedt, Grischa, Kremer, Hannie, Omran, Heymut, Szymanska, Katarzyna, Koutroumpas, Konstantino, Ueffing, Mariu, Nguyen, Thanh-Minh T, Letteboer, Stef J F, Oud, Machteld M, van Beersum, Sylvia E C, Schmidts, Miriam, Beales, Philip L, Lu, Qianhao, Giles, Rachel H, Szklarczyk, Radek, Russell, Robert B, Gibson, Toby J, Johnson, Colin A, Blacque, Oliver E, Wolfrum, Uwe, Boldt, Karsten, Roepman, Ronald, Hernandez-Hernandez, Victor, and Huynen, Martijn A

Subjects
Proteomics, Sensory Receptors, Nematoda, Social Sciences, Ciliopathies, Biochemistry, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], Transcriptome, 0302 clinical medicine, Animal Cells, Psychology, RETINAL PHOTORECEPTOR CELLS, Exome, Neurons, 0303 health sciences, 030302 biochemistry & molecular biology, Eukaryota, Genomics, PRIMARY CILIUM, thecilium, 3. Good health, Nucleic acids, Genetic interference, Osteichthyes, Medicine, Epigenetics, Cellular Structures and Organelles, Cellular Types, proteomic databases, Sensory Receptor Cells, Science, education, Ciliary genes, LEBER CONGENITAL AMAUROSIS, 03 medical and health sciences, Genetics, Cilia, Caenorhabditis elegans, IDENTIFICATION, MUTATIONS, Embryos, cilia, Organisms, Biology and Life Sciences, Bayes Theorem, Molecular Sequence Annotation, medicine.disease, Invertebrates, Fish, ciliary proteome, Animal Studies, Caenorhabditis, Gene expression, embryos, 030217 neurology & neurosurgery, Developmental Biology, Neuroscience, Photoreceptors, Candidate gene, Embryology, Oligonucleotides, Morpholino, Database and Informatics Methods, RNA interference, Bayesian classifier, TRANSITION ZONE, Zebrafish, Antisense Oligonucleotides, Multidisciplinary, Spectrometric Identification of Proteins, Proteomic Databases, Nucleotides, Cilium, Stable Isotope Labeling by Amino Acids in Cell Culture, photoreceptors, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], Animal Models, Phenotype, INTRAFLAGELLAR TRANSPORT, DIFFERENTIATION, Experimental Organism Systems, Caenorhabditis Elegans, Vertebrates, Sensory Perception, Research Article, Signal Transduction, EXPRESSION, Stable isotope labeling by amino acids in cell culture, Computational biology, Biology, Research and Analysis Methods, SOLUTE-CARRIER-PROTEIN, Model Organisms, medicine, Animals, data integration, 030304 developmental biology, Afferent Neurons, Reproducibility of Results, Cell Biology, zebrafish, biology.organism_classification, Ciliopathy, Renal disorders Radboud Institute for Molecular Life Sciences [Radboudumc 11], Biological Databases, Cellular Neuroscience, RNA, OSCP1, CiliaCarta
Abstract

The cilium is an essential organelle at the surface of mammalian cells whose dysfunction causes a wide range of genetic diseases collectively called ciliopathies. The current rate at which new ciliopathy genes are identified suggests that many ciliary components remain undiscovered. We generated and rigorously analyzed genomic, proteomic, transcriptomic and evolutionary data and systematically integrated these using Bayesian statistics into a predictive score for ciliary function. This resulted in 285 candidate ciliary genes. We generated independent experimental evidence of ciliary associations for 24 out of 36 analyzed candidate proteins using multiple cell and animal model systems (mouse, zebrafish and nematode) and techniques. For example, we show that OSCP1, which has previously been implicated in two distinct non-ciliary processes, causes ciliogenic and ciliopathy-associated tissue phenotypes when depleted in zebrafish. The candidate list forms the basis of CiliaCarta, a comprehensive ciliary compendium covering 956 genes. The resource can be used to objectively prioritize candidate genes in whole exome or genome sequencing of ciliopathy patients and can be accessed at http://bioinformatics.bio.uu.nl/john/syscilia/ciliacarta/. This work was supported by the European Community’s Seventh Framework Programme [241955, 278568 to MU and KB, 602273 to RS]; the Virgo consortium, funded by the Dutch government [FES0908 to TvD, RvdL and MAH]; the Netherlands Genomics Initiative [050-060-452 to TvD, RvdL and MAH]; the Canadian Institutes of Health Research [MOP-142243, MOP-82870 and PJT-156042 to MRL]; Michael Smith Foundation for Health Research to MRL and VLJ; Kidney Research Scientist Core Education and National Training fellowship to VLJ; The Foundation Fighting Blindness [PPA-0717-0719-RAD to UW, RR, and MU]; the Dutch Kidney Foundation “KOUNCIL” consortium [CP11.18 to RHG, PLB and RR]; The Deutsche Forschungsgemeinschaft [Excellence grant CellNetworks to RBR and QL, CRC1140 “Kidney Disease – From Genes to Mechanisms” to MS, collaborative research center grant SFB-1411 KIDGEM to MS]; Metakids Foundation to RS; the National Institute for Health Research to PLB and VH-H. PLB is an NIHR Senior Investigator; Radboudumc Hypatia Tenure Track Fellowship, Radboud Universiteit excellence fellowship, ERC starting grant TREATCilia, grant agreement no. 716344 to MS; and the Netherlands Organization for Scientific Research [NWO Vici-865.12.005 to RR].

Published
2019

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