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5 results on '"Hjeij, Rim"'

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

Author

Sub Bioinformatics, Theoretical Biology and Bioinformatics, van Dam, T.J.P., Kennedy, Julie E., van der Lee, Robin, De Vrieze, Erik, Wunderlich, Kirsten A., Rix, Suzanne, Dougherty, Gerard, Lambacher, Nils J., Li, Chunmei, Jensen, Victor L, Leroux, Michel R., Hjeij, Rim, Horn, Nicola, Texier, Yves, Wissinger, Yasmin, Van Reeuwijk, Jeroen, Wheway, Gabrielle, Knapp, Barbara, Scheel, Jan F., Franco, Brunella, Mans, Dorus A., Van Wijk, Erwin, Kepes, François, Slaats, Gisela G., Toedt, Grischa, Kremer, Hannie, Omran, Heymut, Szymanska, Katarzyna, Koutroumpas, Konstantinos, Ueffing, Marius, 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, Huynen, Martijn H., Sub Bioinformatics, Theoretical Biology and Bioinformatics, van Dam, T.J.P., Kennedy, Julie E., van der Lee, Robin, De Vrieze, Erik, Wunderlich, Kirsten A., Rix, Suzanne, Dougherty, Gerard, Lambacher, Nils J., Li, Chunmei, Jensen, Victor L, Leroux, Michel R., Hjeij, Rim, Horn, Nicola, Texier, Yves, Wissinger, Yasmin, Van Reeuwijk, Jeroen, Wheway, Gabrielle, Knapp, Barbara, Scheel, Jan F., Franco, Brunella, Mans, Dorus A., Van Wijk, Erwin, Kepes, François, Slaats, Gisela G., Toedt, Grischa, Kremer, Hannie, Omran, Heymut, Szymanska, Katarzyna, Koutroumpas, Konstantinos, Ueffing, Marius, 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 H.

Published
2019

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

Author

Regenerative Medicine and Stem Cells, Nefro Vasculaire Geneeskunde, Circulatory Health, 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, Yves, Wissinger, Yasmin, van Reeuwijk, Jeroen, Wheway, Gabrielle, Knapp, Barbara, Scheel, Jan F, Franco, Brunella, Mans, Dorus A, van Wijk, Erwin, Képès, François, Slaats, Gisela G, Toedt, Grischa, Kremer, Hannie, Omran, Heymut, Szymanska, Katarzyna, Koutroumpas, Konstantinos, Ueffing, Marius, 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, Huynen, Martijn A, Regenerative Medicine and Stem Cells, Nefro Vasculaire Geneeskunde, Circulatory Health, 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, Yves, Wissinger, Yasmin, van Reeuwijk, Jeroen, Wheway, Gabrielle, Knapp, Barbara, Scheel, Jan F, Franco, Brunella, Mans, Dorus A, van Wijk, Erwin, Képès, François, Slaats, Gisela G, Toedt, Grischa, Kremer, Hannie, Omran, Heymut, Szymanska, Katarzyna, Koutroumpas, Konstantinos, Ueffing, Marius, 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

Published
2019

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

Author

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, Yves, Wissinger, Yasmin, van Reeuwijk, Jeroen, Wheway, Gabrielle, Knapp, Barbara, Scheel, Jan F., and Franco, Brunella

Subjects
CILIA & ciliary motion, DEVELOPMENTAL biology, CYTOLOGY, GENES, LIFE sciences, OUTLINES
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 . [ABSTRACT FROM AUTHOR]

Published
2019
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4. Homozygous loss-of-function mutations in MNS1 cause laterality defects and likely male infertility.

Author

Ta-Shma, Asaf, Hjeij, Rim, Perles, Zeev, Dougherty, Gerard W., Abu Zahira, Ibrahim, Letteboer, Stef J. F., Antony, Dinu, Darwish, Alaa, Mans, Dorus A., Spittler, Sabrina, Edelbusch, Christine, Cindrić, Sandra, Nöthe-Menchen, Tabea, Olbrich, Heike, Stuhlmann, Friederike, Aprea, Isabella, Pennekamp, Petra, Loges, Niki T., Breuer, Oded, and Shaag, Avraham

Subjects
*GENETIC mutation, *MEIOSIS, *MALE infertility, *CILIA & ciliary motion, *IMMUNOPRECIPITATION
Abstract

The clinical spectrum of ciliopathies affecting motile cilia spans impaired mucociliary clearance in the respiratory system, laterality defects including heart malformations, infertility and hydrocephalus. Using linkage analysis and whole exome sequencing, we identified two recessive loss-of-function MNS1 mutations in five individuals from four consanguineous families: 1) a homozygous nonsense mutation p.Arg242* in four males with laterality defects and infertility and 2) a homozygous nonsense mutation p.Gln203* in one female with laterality defects and recurrent respiratory infections additionally carrying homozygous mutations in DNAH5. Consistent with the laterality defects observed in these individuals, we found Mns1 to be expressed in mouse embryonic ventral node. Immunofluorescence analysis further revealed that MNS1 localizes to the axonemes of respiratory cilia as well as sperm flagella in human. In-depth ultrastructural analyses confirmed a subtle outer dynein arm (ODA) defect in the axonemes of respiratory epithelial cells resembling findings reported in Mns1-deficient mice. Ultrastructural analyses in the female carrying combined mutations in MNS1 and DNAH5 indicated a role for MNS1 in the process of ODA docking (ODA-DC) in the distal respiratory axonemes. Furthermore, co-immunoprecipitation and yeast two hybrid analyses demonstrated that MNS1 dimerizes and interacts with the ODA docking complex component CCDC114. Overall, we demonstrate that MNS1 deficiency in humans causes laterality defects (situs inversus) and likely male infertility and that MNS1 plays a role in the ODA-DC assembly. [ABSTRACT FROM AUTHOR]

Published
2018
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5. 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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