46 results on '"Bachmann-Gagescu R"'
Search Results
2. Joubert syndrome: a model for untangling recessive disorders with extreme genetic heterogeneity
- Author
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Bachmann-Gagescu, R, Dempsey, J C, Phelps, I G, OʼRoak, B J, Knutzen, D M, Rue, T C, Ishak, G E, Isabella, C R, Gorden, N, Adkins, J, Boyle, E A, de Lacy, N, OʼDay, D, Alswaid, A, Ramadevi A, Radha, Lingappa, L, Lourenço, C, Martorell, L, Garcia-Cazorla, À, Ozyürek, H, Haliloğlu, G, Tuysuz, B, Topçu, M, Chance, P, Parisi, M A, Glass, I A, Shendure, J, and Doherty, D
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- 2015
- Full Text
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3. A cognitively normal PDH-deficient 18-year-old man carrying the R263G mutation in the PDHA1 gene
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Bachmann-Gagescu, R., Merritt, II, J. Lawrence, and Hahn, S. H.
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- 2009
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4. Dysfunction of the ciliary ARMC9/TOGARAM1 protein module causes Joubert syndrome
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Latour, B.L., Weghe, J.C. Van De, Rusterholz, T.D.S., Letteboer, S.J.F., Gomez, A., Shaheen, R., Gesemann, M., Karamzade, A., Asadollahi, M., Barroso-Gil, M., Chitre, M., Grout, M.E., Reeuwijk, J. van, Beersum, S.E.C. van, Miller, C.V., Dempsey, J.C., Morsy, H., Bamshad, M.J., Nickerson, D.A., Neuhauss, S.C., Boldt, K., Ueffing, M., Keramatipour, M., Sayer, J.A., Alkuraya, F.S., Bachmann-Gagescu, R., Roepman, R., Doherty, D., Latour, B.L., Weghe, J.C. Van De, Rusterholz, T.D.S., Letteboer, S.J.F., Gomez, A., Shaheen, R., Gesemann, M., Karamzade, A., Asadollahi, M., Barroso-Gil, M., Chitre, M., Grout, M.E., Reeuwijk, J. van, Beersum, S.E.C. van, Miller, C.V., Dempsey, J.C., Morsy, H., Bamshad, M.J., Nickerson, D.A., Neuhauss, S.C., Boldt, K., Ueffing, M., Keramatipour, M., Sayer, J.A., Alkuraya, F.S., Bachmann-Gagescu, R., Roepman, R., and Doherty, D.
- Abstract
Contains fulltext : 225431.pdf (Publisher’s version ) (Closed access), Joubert syndrome (JBTS) is a recessive neurodevelopmental ciliopathy characterized by a pathognomonic hindbrain malformation. All known JBTS genes encode proteins involved in the structure or function of primary cilia, ubiquitous antenna-like organelles essential for cellular signal transduction. Here, we used the recently identified JBTS-associated protein armadillo repeat motif-containing 9 (ARMC9) in tandem-affinity purification and yeast 2-hybrid screens to identify a ciliary module whose dysfunction underlies JBTS. In addition to the known JBTS-associated proteins CEP104 and CSPP1, we identified coiled-coil domain containing 66 (CCDC66) and TOG array regulator of axonemal microtubules 1 (TOGARAM1) as ARMC9 interaction partners. We found that TOGARAM1 variants cause JBTS and disrupt TOGARAM1 interaction with ARMC9. Using a combination of protein interaction analyses, characterization of patient-derived fibroblasts, and analysis of CRISPR/Cas9-engineered zebrafish and hTERT-RPE1 cells, we demonstrated that dysfunction of ARMC9 or TOGARAM1 resulted in short cilia with decreased axonemal acetylation and polyglutamylation, but relatively intact transition zone function. Aberrant serum-induced ciliary resorption and cold-induced depolymerization in ARMC9 and TOGARAM1 patient cell lines suggest a role for this new JBTS-associated protein module in ciliary stability.
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- 2020
5. Mutations in ARMC9, which Encodes a Basal Body Protein, Cause Joubert Syndrome in Humans and Ciliopathy Phenotypes in Zebrafish
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Weghe, J.C. Van De, Rusterholz, T.D.S., Latour, B.L., Grout, M.E., Aldinger, K.A., Shaheen, R., Dempsey, J.C., Maddirevula, S., Cheng, Y.H., Phelps, I.G., Gesemann, M., Goel, H., Birk, O.S., Alanzi, T., Rawashdeh, R., Khan, A.O., Bamshad, M.J., Nickerson, D.A., Neuhauss, S.C., Dobyns, W.B., Alkuraya, F.S., Roepman, R., Bachmann-Gagescu, R., Doherty, D., Weghe, J.C. Van De, Rusterholz, T.D.S., Latour, B.L., Grout, M.E., Aldinger, K.A., Shaheen, R., Dempsey, J.C., Maddirevula, S., Cheng, Y.H., Phelps, I.G., Gesemann, M., Goel, H., Birk, O.S., Alanzi, T., Rawashdeh, R., Khan, A.O., Bamshad, M.J., Nickerson, D.A., Neuhauss, S.C., Dobyns, W.B., Alkuraya, F.S., Roepman, R., Bachmann-Gagescu, R., and Doherty, D.
- Abstract
Item does not contain fulltext, Joubert syndrome (JS) is a recessive neurodevelopmental disorder characterized by hypotonia, ataxia, abnormal eye movements, and variable cognitive impairment. It is defined by a distinctive brain malformation known as the "molar tooth sign" on axial MRI. Subsets of affected individuals have malformations such as coloboma, polydactyly, and encephalocele, as well as progressive retinal dystrophy, fibrocystic kidney disease, and liver fibrosis. More than 35 genes have been associated with JS, but in a subset of families the genetic cause remains unknown. All of the gene products localize in and around the primary cilium, making JS a canonical ciliopathy. Ciliopathies are unified by their overlapping clinical features and underlying mechanisms involving ciliary dysfunction. In this work, we identify biallelic rare, predicted-deleterious ARMC9 variants (stop-gain, missense, splice-site, and single-exon deletion) in 11 individuals with JS from 8 families, accounting for approximately 1% of the disorder. The associated phenotypes range from isolated neurological involvement to JS with retinal dystrophy, additional brain abnormalities (e.g., heterotopia, Dandy-Walker malformation), pituitary insufficiency, and/or synpolydactyly. We show that ARMC9 localizes to the basal body of the cilium and is upregulated during ciliogenesis. Typical ciliopathy phenotypes (curved body shape, retinal dystrophy, coloboma, and decreased cilia) in a CRISPR/Cas9-engineered zebrafish mutant model provide additional support for ARMC9 as a ciliopathy-associated gene. Identifying ARMC9 mutations as a cause of JS takes us one step closer to a full genetic understanding of this important disorder and enables future functional work to define the central biological mechanisms underlying JS and other ciliopathies.
- Published
- 2017
6. NINL and DZANK1 Co-function in Vesicle Transport and Are Essential for Photoreceptor Development in Zebrafish
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Dona, M., Bachmann-Gagescu, R., Texier, Y., Toedt, G., Hetterschijt, L., Tonnaer, E.L.G.M., Peters, T.A., Beersum, S.E.C. van, Bergboer, J.G.M., Horn, N., Vrieze, E. de, Slijkerman, R.W.N., Reeuwijk, J. van, Flik, G., Keunen, J.E.E., Ueffing, M., Gibson, T.J., Roepman, R., Boldt, K., Kremer, H., Wijk, E. van, Dona, M., Bachmann-Gagescu, R., Texier, Y., Toedt, G., Hetterschijt, L., Tonnaer, E.L.G.M., Peters, T.A., Beersum, S.E.C. van, Bergboer, J.G.M., Horn, N., Vrieze, E. de, Slijkerman, R.W.N., Reeuwijk, J. van, Flik, G., Keunen, J.E.E., Ueffing, M., Gibson, T.J., Roepman, R., Boldt, K., Kremer, H., and Wijk, E. van
- Abstract
Contains fulltext : 152515.PDF (publisher's version ) (Open Access), Ciliopathies are Mendelian disorders caused by dysfunction of cilia, ubiquitous organelles involved in fluid propulsion (motile cilia) or signal transduction (primary cilia). Retinal dystrophy is a common phenotypic characteristic of ciliopathies since photoreceptor outer segments are specialized primary cilia. These ciliary structures heavily rely on intracellular minus-end directed transport of cargo, mediated at least in part by the cytoplasmic dynein 1 motor complex, for their formation, maintenance and function. Ninein-like protein (NINL) is known to associate with this motor complex and is an important interaction partner of the ciliopathy-associated proteins lebercilin, USH2A and CC2D2A. Here, we scrutinize the function of NINL with combined proteomic and zebrafish in vivo approaches. We identify Double Zinc Ribbon and Ankyrin Repeat domains 1 (DZANK1) as a novel interaction partner of NINL and show that loss of Ninl, Dzank1 or both synergistically leads to dysmorphic photoreceptor outer segments, accumulation of trans-Golgi-derived vesicles and mislocalization of Rhodopsin and Ush2a in zebrafish. In addition, retrograde melanosome transport is severely impaired in zebrafish lacking Ninl or Dzank1. We further demonstrate that NINL and DZANK1 are essential for intracellular dynein-based transport by associating with complementary subunits of the cytoplasmic dynein 1 motor complex, thus shedding light on the structure and stoichiometry of this important motor complex. Altogether, our results support a model in which the NINL-DZANK1 protein module is involved in the proper assembly and folding of the cytoplasmic dynein 1 motor complex in photoreceptor cells, a process essential for outer segment formation and function.
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- 2015
7. The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking
- Author
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Bachmann-Gagescu, R., Dona, M.A., Hetterschijt, L., Tonnaer, E.L.G.M., Peters, T.A., Vrieze, E. de, Mans, D.A., Beersum, S.E.C. van, Phelps, I.G., Arts, H.H., Keunen, J.E.E., Ueffing, M., Roepman, R., Boldt, K., Doherty, D., Moens, C.B., Neuhauss, S.C., Kremer, H., WIjk, E. van, Bachmann-Gagescu, R., Dona, M.A., Hetterschijt, L., Tonnaer, E.L.G.M., Peters, T.A., Vrieze, E. de, Mans, D.A., Beersum, S.E.C. van, Phelps, I.G., Arts, H.H., Keunen, J.E.E., Ueffing, M., Roepman, R., Boldt, K., Doherty, D., Moens, C.B., Neuhauss, S.C., Kremer, H., and WIjk, E. van
- Abstract
Contains fulltext : 152797.PDF (publisher's version ) (Open Access), Ciliopathies are a group of human disorders caused by dysfunction of primary cilia, ubiquitous microtubule-based organelles involved in transduction of extra-cellular signals to the cell. This function requires the concentration of receptors and channels in the ciliary membrane, which is achieved by complex trafficking mechanisms, in part controlled by the small GTPase RAB8, and by sorting at the transition zone located at the entrance of the ciliary compartment. Mutations in the transition zone gene CC2D2A cause the related Joubert and Meckel syndromes, two typical ciliopathies characterized by central nervous system malformations, and result in loss of ciliary localization of multiple proteins in various models. The precise mechanisms by which CC2D2A and other transition zone proteins control protein entrance into the cilium and how they are linked to vesicular trafficking of incoming cargo remain largely unknown. In this work, we identify the centrosomal protein NINL as a physical interaction partner of CC2D2A. NINL partially co-localizes with CC2D2A at the base of cilia and ninl knockdown in zebrafish leads to photoreceptor outer segment loss, mislocalization of opsins and vesicle accumulation, similar to cc2d2a-/- phenotypes. Moreover, partial ninl knockdown in cc2d2a-/- embryos enhances the retinal phenotype of the mutants, indicating a genetic interaction in vivo, for which an illustration is found in patients from a Joubert Syndrome cohort. Similar to zebrafish cc2d2a mutants, ninl morphants display altered Rab8a localization. Further exploration of the NINL-associated interactome identifies MICAL3, a protein known to interact with Rab8 and to play an important role in vesicle docking and fusion. Together, these data support a model where CC2D2A associates with NINL to provide a docking point for cilia-directed cargo vesicles, suggesting a mechanism by which transition zone proteins can control the protein content of the ciliary compartment.
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- 2015
8. NINL and DZANK1 Co-function in Vesicle Transport and Are Essential for Photoreceptor Development in Zebrafish
- Author
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Dona, M.A, Bachmann-Gagescu, R., Texier, Y., Toedt, G., Hetterschijt, L., Tonnaer, E.L.G.M., Peters, T.A., Beersum, S.E.C, Bergboer, J.G.M, Horn, N., Vrieze, E de, Slijkerman, R.W.N, Reeuwijk, J, Flik, G., Keunen, J.E., Ueffing, M., Gibson, T.J., Roepman, R, Boldt, K., Kremer, H, WIjk, E, Dona, M.A, Bachmann-Gagescu, R., Texier, Y., Toedt, G., Hetterschijt, L., Tonnaer, E.L.G.M., Peters, T.A., Beersum, S.E.C, Bergboer, J.G.M, Horn, N., Vrieze, E de, Slijkerman, R.W.N, Reeuwijk, J, Flik, G., Keunen, J.E., Ueffing, M., Gibson, T.J., Roepman, R, Boldt, K., Kremer, H, and WIjk, E
- Abstract
Contains fulltext : 151728.pdf (publisher's version ) (Open Access)
- Published
- 2015
9. Genotype-Phenotype correlations in Joubert Syndrome in the Era of Next Generation Sequencing
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Bachmann-Gagescu, R, primary, Dempsey, J, additional, Phelps, IG, additional, Isabella, C, additional, O'Day, D, additional, O'Roak, B, additional, Shendure, J, additional, Glass, I, additional, and Doherty, D, additional
- Published
- 2015
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10. Live imaging of Rab8 trafficking defects in cc2d2a mutant zebrafish
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Bachmann-Gagescu, R, primary, Phelps, IG, additional, Forbes, A, additional, Doherty, D, additional, and Moens, CB, additional
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- 2012
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11. Loss-of-Function Variants in CUL3 Cause a Syndromic Neurodevelopmental Disorder.
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Blackburn PR, Ebstein F, Hsieh TC, Motta M, Radio FC, Herkert JC, Rinne T, Thiffault I, Rapp M, Alders M, Maas S, Gerard B, Smol T, Vincent-Delorme C, Cogné B, Isidor B, Vincent M, Bachmann-Gagescu R, Rauch A, Joset P, Ferrero GB, Ciolfi A, Husson T, Guerrot AM, Bacino C, Macmurdo C, Thompson SS, Rosenfeld JA, Faivre L, Mau-Them FT, Deb W, Vignard V, Agrawal PB, Madden JA, Goldenberg A, Lecoquierre F, Zech M, Prokisch H, Necpál J, Jech R, Winkelmann J, Koprušáková MT, Konstantopoulou V, Younce JR, Shinawi M, Mighton C, Fung C, Morel CF, Lerner-Ellis J, DiTroia S, Barth M, Bonneau D, Krapels I, Stegmann APA, van der Schoot V, Brunet T, Bußmann C, Mignot C, Zampino G, Wortmann SB, Mayr JA, Feichtinger RG, Courtin T, Ravelli C, Keren B, Ziegler A, Hasadsri L, Pichurin PN, Klee EW, Grand K, Sanchez-Lara PA, Krüger E, Bézieau S, Klinkhammer H, Krawitz PM, Eichler EE, Tartaglia M, Küry S, and Wang T
- Abstract
Objective: De novo variants in cullin-3 ubiquitin ligase (CUL3) have been strongly associated with neurodevelopmental disorders (NDDs), but no large case series have been reported so far. Here, we aimed to collect sporadic cases carrying rare variants in CUL3, describe the genotype-phenotype correlation, and investigate the underlying pathogenic mechanism., Methods: Genetic data and detailed clinical records were collected via multicenter collaboration. Dysmorphic facial features were analyzed using GestaltMatcher. Variant effects on CUL3 protein stability were assessed using patient-derived T-cells., Results: We assembled a cohort of 37 individuals with heterozygous CUL3 variants presenting a syndromic NDD characterized by intellectual disability with or without autistic features. Of these, 35 have loss-of-function (LoF) and 2 have missense variants. CUL3 LoF variants in patients may affect protein stability leading to perturbations in protein homeostasis, as evidenced by decreased ubiquitin-protein conjugates in vitro. Notably, we show that 4E-BP1 (EIF4EBP1), a prominent substrate of CUL3, fails to be targeted for proteasomal degradation in patient-derived cells., Interpretation: Our study further refines the clinical and mutational spectrum of CUL3-associated NDDs, expands the spectrum of cullin RING E3 ligase-associated neuropsychiatric disorders, and suggests haploinsufficiency via LoF variants is the predominant pathogenic mechanism. ANN NEUROL 2024., (© 2024 American Neurological Association.)
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- 2024
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12. Nanopore Deep Sequencing as a Tool to Characterize and Quantify Aberrant Splicing Caused by Variants in Inherited Retinal Dystrophy Genes.
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Maggi J, Feil S, Gloggnitzer J, Maggi K, Bachmann-Gagescu R, Gerth-Kahlert C, Koller S, and Berger W
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- Humans, Alternative Splicing genetics, RNA Splicing genetics, Exons genetics, Retinal Dystrophies genetics, Retinal Dystrophies diagnosis, Nanopore Sequencing methods, High-Throughput Nucleotide Sequencing methods
- Abstract
The contribution of splicing variants to molecular diagnostics of inherited diseases is reported to be less than 10%. This figure is likely an underestimation due to several factors including difficulty in predicting the effect of such variants, the need for functional assays, and the inability to detect them (depending on their locations and the sequencing technology used). The aim of this study was to assess the utility of Nanopore sequencing in characterizing and quantifying aberrant splicing events. For this purpose, we selected 19 candidate splicing variants that were identified in patients affected by inherited retinal dystrophies. Several in silico tools were deployed to predict the nature and estimate the magnitude of variant-induced aberrant splicing events. Minigene assay or whole blood-derived cDNA was used to functionally characterize the variants. PCR amplification of minigene-specific cDNA or the target gene in blood cDNA, combined with Nanopore sequencing, was used to identify the resulting transcripts. Thirteen out of nineteen variants caused aberrant splicing events, including cryptic splice site activation, exon skipping, pseudoexon inclusion, or a combination of these. Nanopore sequencing allowed for the identification of full-length transcripts and their precise quantification, which were often in accord with in silico predictions. The method detected reliably low-abundant transcripts, which would not be detected by conventional strategies, such as RT-PCR followed by Sanger sequencing.
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- 2024
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13. Limited Added Diagnostic Value of Whole Genome Sequencing in Genetic Testing of Inherited Retinal Diseases in a Swiss Patient Cohort.
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Maggi J, Koller S, Feil S, Bachmann-Gagescu R, Gerth-Kahlert C, and Berger W
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- Humans, Male, Female, Switzerland, Cohort Studies, Adult, DNA Copy Number Variations, Exome Sequencing methods, Computational Biology methods, Middle Aged, Child, Adolescent, Pedigree, Retinal Diseases genetics, Retinal Diseases diagnosis, Genetic Testing methods, Whole Genome Sequencing methods
- Abstract
The purpose of this study was to assess the added diagnostic value of whole genome sequencing (WGS) for patients with inherited retinal diseases (IRDs) who remained undiagnosed after whole exome sequencing (WES). WGS was performed for index patients in 66 families. The datasets were analyzed according to GATK's guidelines. Additionally, DeepVariant was complemented by GATK's workflow, and a novel structural variant pipeline was developed. Overall, a molecular diagnosis was established in 19/66 (28.8%) index patients. Pathogenic deletions and one deep-intronic variant contributed to the diagnostic yield in 4/19 and 1/19 index patients, respectively. The remaining diagnoses (14/19) were attributed to exonic variants that were missed during WES analysis due to bioinformatic limitations, newly described loci, or unclear pathogenicity. The added diagnostic value of WGS equals 5/66 (9.6%) for our cohort, which is comparable to previous studies. This figure would decrease further to 1/66 (1.5%) with a standardized and reliable copy number variant workflow during WES analysis. Given the higher costs and limited added value, the implementation of WGS as a first-tier assay for inherited eye disorders in a diagnostic laboratory remains untimely. Instead, progress in bioinformatic tools and communication between diagnostic and clinical teams have the potential to ameliorate diagnostic yields.
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- 2024
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14. Challenges for the implementation of next generation sequencing-based expanded carrier screening: Lessons learned from the ciliopathies.
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Vintschger E, Kraemer D, Joset P, Horn AHC, Rauch A, Sticht H, and Bachmann-Gagescu R
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- Humans, Genetic Counseling, Exome Sequencing, Genetic Carrier Screening, High-Throughput Nucleotide Sequencing, Ciliopathies diagnosis, Ciliopathies genetics
- Abstract
Next generation sequencing (NGS) can detect carrier status for rare recessive disorders, informing couples about their reproductive risk. The recent ACMG recommendations support offering NGS-based carrier screening (NGS-CS) in an ethnic and population-neutral manner for all genes that have a carrier frequency >1/200 (based on GnomAD). To evaluate current challenges for NGS-CS, we focused on the ciliopathies, a well-studied group of rare recessive disorders. We analyzed 118 ciliopathy genes by whole exome sequencing in ~400 healthy local individuals and ~1000 individuals from the UK1958-birth cohort. We found 20% of healthy individuals (1% of couples) to be carriers of reportable variants in a ciliopathy gene, while 50% (4% of couples) carry variants of uncertain significance (VUS). This large proportion of VUS is partly explained by the limited utility of the ACMG/AMP variant-interpretation criteria in healthy individuals, where phenotypic match or segregation criteria cannot be used. Most missense variants are thus classified as VUS and not reported, which reduces the negative predictive value of the screening test. We show how gene-specific variation patterns and structural protein information can help prioritize variants most likely to be disease-causing, for (future) functional assays. Even when considering only strictly pathogenic variants, the observed carrier frequency is substantially higher than expected based on estimated disease prevalence, challenging the 1/200 carrier frequency cut-off proposed for choice of genes to screen. Given the challenges linked to variant interpretation in healthy individuals and the uncertainties about true carrier frequencies, genetic counseling must clearly disclose these limitations of NGS-CS., (© 2022. The Author(s).)
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- 2023
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15. Loss-of-function variants in CUL3 cause a syndromic neurodevelopmental disorder.
- Author
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Blackburn PR, Ebstein F, Hsieh TC, Motta M, Radio FC, Herkert JC, Rinne T, Thiffault I, Rapp M, Alders M, Maas S, Gerard B, Smol T, Vincent-Delorme C, Cogné B, Isidor B, Vincent M, Bachmann-Gagescu R, Rauch A, Joset P, Ferrero GB, Ciolfi A, Husson T, Guerrot AM, Bacino C, Macmurdo C, Thompson SS, Rosenfeld JA, Faivre L, Mau-Them FT, Deb W, Vignard V, Agrawal PB, Madden JA, Goldenberg A, Lecoquierre F, Zech M, Prokisch H, Necpál J, Jech R, Winkelmann J, Koprušáková MT, Konstantopoulou V, Younce JR, Shinawi M, Mighton C, Fung C, Morel C, Ellis JL, DiTroia S, Barth M, Bonneau D, Krapels I, Stegmann S, van der Schoot V, Brunet T, Bußmann C, Mignot C, Courtin T, Ravelli C, Keren B, Ziegler A, Hasadsri L, Pichurin PN, Klee EW, Grand K, Sanchez-Lara PA, Krüger E, Bézieau S, Klinkhammer H, Krawitz PM, Eichler EE, Tartaglia M, Küry S, and Wang T
- Abstract
Purpose: De novo variants in CUL3 (Cullin-3 ubiquitin ligase) have been strongly associated with neurodevelopmental disorders (NDDs), but no large case series have been reported so far. Here we aimed to collect sporadic cases carrying rare variants in CUL3, describe the genotype-phenotype correlation, and investigate the underlying pathogenic mechanism., Methods: Genetic data and detailed clinical records were collected via multi-center collaboration. Dysmorphic facial features were analyzed using GestaltMatcher. Variant effects on CUL3 protein stability were assessed using patient-derived T-cells., Results: We assembled a cohort of 35 individuals with heterozygous CUL3 variants presenting a syndromic NDD characterized by intellectual disability with or without autistic features. Of these, 33 have loss-of-function (LoF) and two have missense variants. CUL3 LoF variants in patients may affect protein stability leading to perturbations in protein homeostasis, as evidenced by decreased ubiquitin-protein conjugates in vitro . Specifically, we show that cyclin E1 (CCNE1) and 4E-BP1 (EIF4EBP1), two prominent substrates of CUL3, fail to be targeted for proteasomal degradation in patient-derived cells., Conclusion: Our study further refines the clinical and mutational spectrum of CUL3 -associated NDDs, expands the spectrum of cullin RING E3 ligase-associated neuropsychiatric disorders, and suggests haploinsufficiency via LoF variants is the predominant pathogenic mechanism.
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- 2023
- Full Text
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16. Deleterious, protein-altering variants in the transcriptional coregulator ZMYM3 in 27 individuals with a neurodevelopmental delay phenotype.
- Author
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Hiatt SM, Trajkova S, Sebastiano MR, Partridge EC, Abidi FE, Anderson A, Ansar M, Antonarakis SE, Azadi A, Bachmann-Gagescu R, Bartuli A, Benech C, Berkowitz JL, Betti MJ, Brusco A, Cannon A, Caron G, Chen Y, Cochran ME, Coleman TF, Crenshaw MM, Cuisset L, Curry CJ, Darvish H, Demirdas S, Descartes M, Douglas J, Dyment DA, Elloumi HZ, Ermondi G, Faoucher M, Farrow EG, Felker SA, Fisher H, Hurst ACE, Joset P, Kelly MA, Kmoch S, Leadem BR, Lyons MJ, Macchiaiolo M, Magner M, Mandrile G, Mattioli F, McEown M, Meadows SK, Medne L, Meeks NJL, Montgomery S, Napier MP, Natowicz M, Newberry KM, Niceta M, Noskova L, Nowak CB, Noyes AG, Osmond M, Prijoles EJ, Pugh J, Pullano V, Quélin C, Rahimi-Aliabadi S, Rauch A, Redon S, Reymond A, Schwager CR, Sellars EA, Scheuerle AE, Shukarova-Angelovska E, Skraban C, Stolerman E, Sullivan BR, Tartaglia M, Thiffault I, Uguen K, Umaña LA, van Bever Y, van der Crabben SN, van Slegtenhorst MA, Waisfisz Q, Washington C, Rodan LH, Myers RM, and Cooper GM
- Subjects
- Humans, Male, Female, Phenotype, Gene Expression Regulation, Face, Nuclear Proteins genetics, Histone Demethylases genetics, Neurodevelopmental Disorders genetics, Intellectual Disability genetics, Nervous System Malformations
- Abstract
Neurodevelopmental disorders (NDDs) result from highly penetrant variation in hundreds of different genes, some of which have not yet been identified. Using the MatchMaker Exchange, we assembled a cohort of 27 individuals with rare, protein-altering variation in the transcriptional coregulator ZMYM3, located on the X chromosome. Most (n = 24) individuals were males, 17 of which have a maternally inherited variant; six individuals (4 male, 2 female) harbor de novo variants. Overlapping features included developmental delay, intellectual disability, behavioral abnormalities, and a specific facial gestalt in a subset of males. Variants in almost all individuals (n = 26) are missense, including six that recurrently affect two residues. Four unrelated probands were identified with inherited variation affecting Arg441, a site at which variation has been previously seen in NDD-affected siblings, and two individuals have de novo variation resulting in p.Arg1294Cys (c.3880C>T). All variants affect evolutionarily conserved sites, and most are predicted to damage protein structure or function. ZMYM3 is relatively intolerant to variation in the general population, is widely expressed across human tissues, and encodes a component of the KDM1A-RCOR1 chromatin-modifying complex. ChIP-seq experiments on one variant, p.Arg1274Trp, indicate dramatically reduced genomic occupancy, supporting a hypomorphic effect. While we are unable to perform statistical evaluations to definitively support a causative role for variation in ZMYM3, the totality of the evidence, including 27 affected individuals, recurrent variation at two codons, overlapping phenotypic features, protein-modeling data, evolutionary constraint, and experimentally confirmed functional effects strongly support ZMYM3 as an NDD-associated gene., Competing Interests: Declaration of interests J.L.B., Y.C., B.R.L., M.P.N., A.G.N., and H.Z.E. are employees of GeneDx, LLC. S.E.A. is a cofounder and CEO of MediGenome, the Swiss Institute of Genomic Medicine. All other authors declare no competing interests., (Copyright © 2022 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)
- Published
- 2023
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17. Studying the morphology, composition and function of the photoreceptor primary cilium in zebrafish.
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Masek M, Zang J, Mateos JM, Garbelli M, Ziegler U, Neuhauss SCF, and Bachmann-Gagescu R
- Subjects
- Animals, Humans, Cilia metabolism, Retina, Zebrafish Proteins metabolism, Retinal Cone Photoreceptor Cells metabolism, Zebrafish metabolism, Ciliopathies metabolism
- Abstract
Vision is one of our dominant senses and its loss has a profound impact on the life quality of affected individuals. Highly specialized neurons in the retina called photoreceptors convert photons into neuronal responses. This conversion of photons is mediated by light sensitive opsin proteins, which are found in the outer segments of the photoreceptors. These outer segments are highly specialized primary cilia, explaining why retinal dystrophy is a key feature of ciliopathies, a group of diseases resulting from abnormal and dysfunctional cilia. Therefore, research on ciliopathies often includes the analysis of the retina with special focus on the photoreceptor and its outer segment. In the last decade, the zebrafish has emerged as an excellent model organism to study human diseases, in particular with respect to the retina. The cone-rich retina of zebrafish resembles the fovea of the human macula and thus represents an excellent model to study human retinal diseases. Here we give detailed guidance on how to analyze the morphological and ultra-structural integrity of photoreceptors in the zebrafish using various histological and imaging techniques. We further describe how to conduct functional analysis of the retina by electroretinography and how to prepare isolated outer segment fractions for different -omic approaches. These different methods allow a comprehensive analysis of photoreceptors, helping to enhance our understanding of the molecular and structural basis of ciliary function in health and of the consequences of its dysfunction in disease., (Copyright © 2023 Elsevier Inc. All rights reserved.)
- Published
- 2023
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18. Control of protein and lipid composition of photoreceptor outer segments-Implications for retinal disease.
- Author
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Masek M and Bachmann-Gagescu R
- Subjects
- Humans, Protein Transport, Signal Transduction, Lipids, Cilia metabolism, Retinal Diseases metabolism
- Abstract
Vision is arguably our most important sense, and its loss brings substantial limitations to daily life for affected individuals. Light is perceived in retinal photoreceptors (PRs), which are highly specialized neurons subdivided into several compartments with distinct functions. The outer segments (OSs) of photoreceptors represent highly specialized primary ciliary compartments hosting the phototransduction cascade, which transforms incoming light into a neuronal signal. Retinal disease can result from various pathomechanisms originating in distinct subcompartments of the PR cell, or in the retinal pigment epithelium which supports the PRs. Dysfunction of primary cilia causes human disorders known as "ciliopathies", in which retinal disease is a common feature. This chapter focuses on PR OSs, discussing the mechanisms controlling their complex structure and composition. A sequence of tightly regulated sorting and trafficking events, both upstream of and within this ciliary compartment, ensures the establishment and maintenance of the adequate proteome and lipidome required for signaling in response to light. We discuss in particular our current understanding of the role of ciliopathy proteins involved in multi-protein complexes at the ciliary transition zone (CC2D2A) or BBSome (BBS1) and how their dysfunction causes retinal disease. While the loss of CC2D2A prevents the fusion of vesicles and delivery of the photopigment rhodopsin to the ciliary base, leading to early OS ultrastructural defects, BBS1 deficiency results in precocious accumulation of cholesterol in mutant OSs and decreased visual function preceding morphological changes. These distinct pathomechanisms underscore the central role of ciliary proteins involved in multiple processes controlling OS protein and lipid composition., (Copyright © 2023. Published by Elsevier Inc.)
- Published
- 2023
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19. Insights Gained From Zebrafish Models for the Ciliopathy Joubert Syndrome.
- Author
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Rusterholz TDS, Hofmann C, and Bachmann-Gagescu R
- Abstract
Cilia are quasi-ubiquitous microtubule-based sensory organelles, which play vital roles in signal transduction during development and cell homeostasis. Dysfunction of cilia leads to a group of Mendelian disorders called ciliopathies, divided into different diagnoses according to clinical phenotype constellation and genetic causes. Joubert syndrome (JBTS) is a prototypical ciliopathy defined by a diagnostic cerebellar and brain stem malformation termed the "Molar Tooth Sign" (MTS), in addition to which patients display variable combinations of typical ciliopathy phenotypes such as retinal dystrophy, fibrocystic renal disease, polydactyly or skeletal dystrophy. Like most ciliopathies, JBTS is genetically highly heterogeneous with ∼40 associated genes. Zebrafish are widely used to model ciliopathies given the high conservation of ciliary genes and the variety of specialized cilia types similar to humans. In this review, we compare different existing JBTS zebrafish models with each other and describe their contributions to our understanding of JBTS pathomechanism. We find that retinal dystrophy, which is the most investigated ciliopathy phenotype in zebrafish ciliopathy models, is caused by distinct mechanisms according to the affected gene. Beyond this, differences in phenotypes in other organs observed between different JBTS-mutant models suggest tissue-specific roles for proteins implicated in JBTS. Unfortunately, the lack of systematic assessment of ciliopathy phenotypes in the mutants described in the literature currently limits the conclusions that can be drawn from these comparisons. In the future, the numerous existing JBTS zebrafish models represent a valuable resource that can be leveraged in order to gain further insights into ciliary function, pathomechanisms underlying ciliopathy phenotypes and to develop treatment strategies using small molecules., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Rusterholz, Hofmann and Bachmann-Gagescu.)
- Published
- 2022
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20. Control of meiotic chromosomal bouquet and germ cell morphogenesis by the zygotene cilium.
- Author
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Mytlis A, Kumar V, Qiu T, Deis R, Hart N, Levy K, Masek M, Shawahny A, Ahmad A, Eitan H, Nather F, Adar-Levor S, Birnbaum RY, Elia N, Bachmann-Gagescu R, Roy S, and Elkouby YM
- Subjects
- Animals, Centromere genetics, Centromere physiology, Female, Fertility physiology, Mice, Morphogenesis, Telomere genetics, Telomere physiology, Zebrafish genetics, Zebrafish physiology, Chromosome Pairing genetics, Chromosome Pairing physiology, Cilia physiology, Oocytes growth & development, Oogenesis genetics, Oogenesis physiology, Ovary growth & development
- Abstract
A hallmark of meiosis is chromosomal pairing, which requires telomere tethering and rotation on the nuclear envelope through microtubules, driving chromosome homology searches. Telomere pulling toward the centrosome forms the "zygotene chromosomal bouquet." Here, we identified the "zygotene cilium" in oocytes. This cilium provides a cable system for the bouquet machinery and extends throughout the germline cyst. Using zebrafish mutants and live manipulations, we demonstrate that the cilium anchors the centrosome to counterbalance telomere pulling. The cilium is essential for bouquet and synaptonemal complex formation, oogenesis, ovarian development, and fertility. Thus, a cilium represents a conserved player in zebrafish and mouse meiosis, which sheds light on reproductive aspects in ciliopathies and suggests that cilia can control chromosomal dynamics.
- Published
- 2022
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21. Loss of the Bardet-Biedl protein Bbs1 alters photoreceptor outer segment protein and lipid composition.
- Author
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Masek M, Etard C, Hofmann C, Hülsmeier AJ, Zang J, Takamiya M, Gesemann M, Neuhauss SCF, Hornemann T, Strähle U, and Bachmann-Gagescu R
- Subjects
- Animals, Cilia metabolism, Lipids, Microtubule-Associated Proteins genetics, Microtubule-Associated Proteins metabolism, Zebrafish metabolism, Bardet-Biedl Syndrome genetics
- Abstract
Primary cilia are key sensory organelles whose dysfunction leads to ciliopathy disorders such as Bardet-Biedl syndrome (BBS). Retinal degeneration is common in ciliopathies, since the outer segments (OSs) of photoreceptors are highly specialized primary cilia. BBS1, encoded by the most commonly mutated BBS-associated gene, is part of the BBSome protein complex. Using a bbs1 zebrafish mutant, we show that retinal development and photoreceptor differentiation are unaffected by Bbs1-loss, supported by an initially unaffected transcriptome. Quantitative proteomics and lipidomics on samples enriched for isolated OSs show that Bbs1 is required for BBSome-complex stability and that Bbs1-loss leads to accumulation of membrane-associated proteins in OSs, with enrichment in proteins involved in lipid homeostasis. Disruption of the tightly regulated OS lipid composition with increased OS cholesterol content are paralleled by early functional visual deficits, which precede progressive OS morphological anomalies. Our findings identify a role for Bbs1/BBSome in OS lipid homeostasis, suggesting a pathomechanism underlying retinal degeneration in BBS., (© 2022. The Author(s).)
- Published
- 2022
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22. Genetic compensation for cilia defects in cep290 mutants by upregulation of cilia-associated small GTPases.
- Author
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Cardenas-Rodriguez M, Austin-Tse C, Bergboer JGM, Molinari E, Sugano Y, Bachmann-Gagescu R, Sayer JA, and Drummond IA
- Subjects
- Adaptor Proteins, Signal Transducing, Animals, Humans, Microtubule-Associated Proteins, Mutation genetics, Up-Regulation genetics, Zebrafish genetics, Zebrafish metabolism, Zebrafish Proteins genetics, Zebrafish Proteins metabolism, Antigens, Neoplasm genetics, Cell Cycle Proteins genetics, Cilia genetics, Cilia metabolism, Cytoskeletal Proteins genetics, Monomeric GTP-Binding Proteins
- Abstract
Mutations in CEP290 (also known as NPHP6), a large multidomain coiled coil protein, are associated with multiple cilia-associated syndromes. Over 130 CEP290 mutations have been linked to a wide spectrum of human ciliopathies, raising the question of how mutations in a single gene cause different disease syndromes. In zebrafish, the expressivity of cep290 deficiencies were linked to the type of genetic ablation: acute cep290 morpholino knockdown caused severe cilia-related phenotypes, whereas deficiencies in a CRISPR/Cas9 genetic mutant were restricted to photoreceptor defects. Here, we show that milder phenotypes in genetic mutants were associated with the upregulation of genes encoding the cilia-associated small GTPases arl3, arl13b and unc119b. Upregulation of UNC119b was also observed in urine-derived renal epithelial cells from human Joubert syndrome CEP290 patients. Ectopic expression of arl3, arl13b and unc119b in cep290 morphant zebrafish embryos rescued Kupffer's vesicle cilia and partially rescued photoreceptor outer segment defects. The results suggest that genetic compensation by upregulation of genes involved in a common subcellular process, lipidated protein trafficking to cilia, may be a conserved mechanism contributing to genotype-phenotype variations observed in CEP290 deficiencies. This article has an associated First Person interview with the first author of the paper., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2021. Published by The Company of Biologists Ltd.)
- Published
- 2021
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23. Dysfunction of the ciliary ARMC9/TOGARAM1 protein module causes Joubert syndrome.
- Author
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Latour BL, Van De Weghe JC, Rusterholz TD, Letteboer SJ, Gomez A, Shaheen R, Gesemann M, Karamzade A, Asadollahi M, Barroso-Gil M, Chitre M, Grout ME, van Reeuwijk J, van Beersum SE, Miller CV, Dempsey JC, Morsy H, Bamshad MJ, Nickerson DA, Neuhauss SC, Boldt K, Ueffing M, Keramatipour M, Sayer JA, Alkuraya FS, Bachmann-Gagescu R, Roepman R, and Doherty D
- Subjects
- Acetylation, Animals, CRISPR-Cas Systems, Cerebellum metabolism, Disease Models, Animal, Humans, Peptides genetics, Peptides metabolism, Retina metabolism, Abnormalities, Multiple genetics, Abnormalities, Multiple metabolism, Armadillo Domain Proteins genetics, Armadillo Domain Proteins metabolism, Cerebellum abnormalities, Cilia genetics, Cilia metabolism, Eye Abnormalities genetics, Eye Abnormalities metabolism, Kidney Diseases, Cystic genetics, Kidney Diseases, Cystic metabolism, Retina abnormalities, Zebrafish genetics, Zebrafish metabolism, Zebrafish Proteins genetics, Zebrafish Proteins metabolism
- Abstract
Joubert syndrome (JBTS) is a recessive neurodevelopmental ciliopathy characterized by a pathognomonic hindbrain malformation. All known JBTS genes encode proteins involved in the structure or function of primary cilia, ubiquitous antenna-like organelles essential for cellular signal transduction. Here, we used the recently identified JBTS-associated protein armadillo repeat motif-containing 9 (ARMC9) in tandem-affinity purification and yeast 2-hybrid screens to identify a ciliary module whose dysfunction underlies JBTS. In addition to the known JBTS-associated proteins CEP104 and CSPP1, we identified coiled-coil domain containing 66 (CCDC66) and TOG array regulator of axonemal microtubules 1 (TOGARAM1) as ARMC9 interaction partners. We found that TOGARAM1 variants cause JBTS and disrupt TOGARAM1 interaction with ARMC9. Using a combination of protein interaction analyses, characterization of patient-derived fibroblasts, and analysis of CRISPR/Cas9-engineered zebrafish and hTERT-RPE1 cells, we demonstrated that dysfunction of ARMC9 or TOGARAM1 resulted in short cilia with decreased axonemal acetylation and polyglutamylation, but relatively intact transition zone function. Aberrant serum-induced ciliary resorption and cold-induced depolymerization in ARMC9 and TOGARAM1 patient cell lines suggest a role for this new JBTS-associated protein module in ciliary stability.
- Published
- 2020
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24. Biallelic variants in PSMB1 encoding the proteasome subunit β6 cause impairment of proteasome function, microcephaly, intellectual disability, developmental delay and short stature.
- Author
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Ansar M, Ebstein F, Özkoç H, Paracha SA, Iwaszkiewicz J, Gesemann M, Zoete V, Ranza E, Santoni FA, Sarwar MT, Ahmed J, Krüger E, Bachmann-Gagescu R, and Antonarakis SE
- Subjects
- Alleles, Animals, Child, Consanguinity, Developmental Disabilities complications, Developmental Disabilities genetics, Developmental Disabilities pathology, Dwarfism complications, Female, Homozygote, Humans, Intellectual Disability complications, Intellectual Disability genetics, Intellectual Disability pathology, Male, Microcephaly complications, Microcephaly pathology, Models, Molecular, Pedigree, Phenotype, Zebrafish genetics, Dwarfism genetics, Microcephaly genetics, Proteasome Endopeptidase Complex genetics
- Abstract
The molecular cause of the majority of rare autosomal recessive disorders remains unknown. Consanguinity due to extensive homozygosity unravels many recessive phenotypes and facilitates the detection of novel gene-disease links. Here, we report two siblings with phenotypic signs, including intellectual disability (ID), developmental delay and microcephaly from a Pakistani consanguineous family in which we have identified homozygosity for p(Tyr103His) in the PSMB1 gene (Genbank NM_002793) that segregated with the disease phenotype. PSMB1 encodes a β-type proteasome subunit (i.e. β6). Modeling of the p(Tyr103His) variant indicates that this variant weakens the interactions between PSMB1/β6 and PSMA5/α5 proteasome subunits and thus destabilizes the 20S proteasome complex. Biochemical experiments in human SHSY5Y cells revealed that the p(Tyr103His) variant affects both the processing of PSMB1/β6 and its incorporation into proteasome, thus impairing proteasome activity. CRISPR/Cas9 mutagenesis or morpholino knock-down of the single psmb1 zebrafish orthologue resulted in microcephaly, microphthalmia and reduced brain size. Genetic evidence in the family and functional experiments in human cells and zebrafish indicates that PSMB1/β6 pathogenic variants are the cause of a recessive disease with ID, microcephaly and developmental delay due to abnormal proteasome assembly., (© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)
- Published
- 2020
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25. Healthcare recommendations for Joubert syndrome.
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Bachmann-Gagescu R, Dempsey JC, Bulgheroni S, Chen ML, D'Arrigo S, Glass IA, Heller T, Héon E, Hildebrandt F, Joshi N, Knutzen D, Kroes HY, Mack SH, Nuovo S, Parisi MA, Snow J, Summers AC, Symons JM, Zein WM, Boltshauser E, Sayer JA, Gunay-Aygun M, Valente EM, and Doherty D
- Subjects
- Abnormalities, Multiple genetics, Abnormalities, Multiple pathology, Abnormalities, Multiple therapy, Brain Stem pathology, Cerebellum pathology, Eye Abnormalities genetics, Eye Abnormalities pathology, Eye Abnormalities therapy, Health Planning Guidelines, Humans, Kidney pathology, Kidney Diseases, Cystic genetics, Kidney Diseases, Cystic pathology, Kidney Diseases, Cystic therapy, Liver pathology, Neurodevelopmental Disorders genetics, Neurodevelopmental Disorders pathology, Neurodevelopmental Disorders therapy, Retina pathology, Abnormalities, Multiple epidemiology, Cerebellum abnormalities, Eye Abnormalities epidemiology, Health Personnel, Kidney Diseases, Cystic epidemiology, Neurodevelopmental Disorders epidemiology, Retina abnormalities
- Abstract
Joubert syndrome (JS) is a recessive neurodevelopmental disorder defined by a characteristic cerebellar and brainstem malformation recognizable on axial brain magnetic resonance imaging as the "Molar Tooth Sign". Although defined by the neurological features, JS is associated with clinical features affecting many other organ systems, particularly progressive involvement of the retina, kidney, and liver. JS is a rare condition; therefore, many affected individuals may not have easy access to subspecialty providers familiar with JS (e.g., geneticists, neurologists, developmental pediatricians, ophthalmologists, nephrologists, hepatologists, psychiatrists, therapists, and educators). Expert recommendations can enable practitioners of all types to provide quality care to individuals with JS and know when to refer for subspecialty care. This need will only increase as precision treatments targeting specific genetic causes of JS emerge. The goal of these recommendations is to provide a resource for general practitioners, subspecialists, and families to maximize the health of individuals with JS throughout the lifespan., (© 2019 Wiley Periodicals, Inc.)
- Published
- 2020
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26. Elucidation of the phenotypic spectrum and genetic landscape in primary and secondary microcephaly.
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Boonsawat P, Joset P, Steindl K, Oneda B, Gogoll L, Azzarello-Burri S, Sheth F, Datar C, Verma IC, Puri RD, Zollino M, Bachmann-Gagescu R, Niedrist D, Papik M, Figueiro-Silva J, Masood R, Zweier M, Kraemer D, Lincoln S, Rodan L, Passemard S, Drunat S, Verloes A, Horn AHC, Sticht H, Steinfeld R, Plecko B, Latal B, Jenni O, Asadollahi R, and Rauch A
- Subjects
- Adolescent, Cell Cycle Proteins genetics, Child, Child, Preschool, DEAD-box RNA Helicases genetics, Developmental Disabilities pathology, Exome genetics, Female, Gene Expression Regulation genetics, Humans, Infant, Intellectual Disability pathology, Male, Microcephaly pathology, Mutation, Pedigree, Phenotype, Ubiquitin-Protein Ligases genetics, Exome Sequencing, Wnt Signaling Pathway, Developmental Disabilities genetics, Genetic Predisposition to Disease, Intellectual Disability genetics, Microcephaly genetics
- Abstract
Purpose: Microcephaly is a sign of many genetic conditions but has been rarely systematically evaluated. We therefore comprehensively studied the clinical and genetic landscape of an unselected cohort of patients with microcephaly., Methods: We performed clinical assessment, high-resolution chromosomal microarray analysis, exome sequencing, and functional studies in 62 patients (58% with primary microcephaly [PM], 27% with secondary microcephaly [SM], and 15% of unknown onset)., Results: We found severity of developmental delay/intellectual disability correlating with severity of microcephaly in PM, but not SM. We detected causative variants in 48.4% of patients and found divergent inheritance and variant pattern for PM (mainly recessive and likely gene-disrupting [LGD]) versus SM (all dominant de novo and evenly LGD or missense). While centrosome-related pathways were solely identified in PM, transcriptional regulation was the most frequently affected pathway in both SM and PM. Unexpectedly, we found causative variants in different mitochondria-related genes accounting for ~5% of patients, which emphasizes their role even in syndromic PM. Additionally, we delineated novel candidate genes involved in centrosome-related pathway (SPAG5, TEDC1), Wnt signaling (VPS26A, ZNRF3), and RNA trafficking (DDX1)., Conclusion: Our findings enable improved evaluation and genetic counseling of PM and SM patients and further elucidate microcephaly pathways.
- Published
- 2019
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27. A new mouse model for the neurodevelopmental ciliopathy Joubert syndrome.
- Author
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Bachmann-Gagescu R
- Subjects
- Animals, Cell Cycle Proteins, Cerebellum, Cilia, Hedgehog Proteins, Humans, Mice, Retina, United Kingdom, Abnormalities, Multiple, Ciliopathies, Eye Abnormalities, Kidney Diseases, Cystic
- Abstract
Recent recognition of the key role of primary cilia in orchestrating human development and of the dire consequences of their dysfunction on human health has placed this small organelle in the spotlight. While the causal link between mutations in ciliary genes and central nervous system malformations and dysfunction is well established, the mechanisms by which primary cilia dysfunction acts on development and function of the CNS remain partly unknown. The recent article by Bashford and Subramanian in The Journal of Pathology describes a new mouse model for the neurodevelopmental ciliopathy Joubert syndrome, supporting a role for ciliary-mediated Hedgehog signaling on proliferation, survival, and differentiation of cerebellar granule cell progenitors. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd., (© 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.)
- Published
- 2019
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28. The photoreceptor cilium and its diseases.
- Author
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Bachmann-Gagescu R and Neuhauss SC
- Subjects
- Animals, Cilia genetics, Cilia ultrastructure, Ciliopathies genetics, Gene Expression Regulation, Developmental, Larva genetics, Larva metabolism, Larva ultrastructure, Microscopy, Electron, Transmission, Photoreceptor Cells, Vertebrate ultrastructure, Retinal Degeneration genetics, Zebrafish genetics, Zebrafish growth & development, Zebrafish Proteins genetics, Cilia metabolism, Ciliopathies metabolism, Photoreceptor Cells, Vertebrate metabolism, Retinal Degeneration metabolism, Zebrafish metabolism, Zebrafish Proteins metabolism
- Abstract
Light sensation occurs in photoreceptor outer segments (OS), which derive from highly specialized primary cilia, based on structural and molecular similarities. Ciliary dysfunction causes ciliopathies, in which retinal degeneration is common. The connecting cilium (CC) is the obligate passage for proteins moving between ciliary and cellular compartment, controlling the correct distribution of proteins on either side of its barrier. While new mechanisms for selective entry of ciliary proteins are being elucidated, active transport out of the OS is increasingly studied. We further discuss other recent advances in the field, such as a role for the CC in docking and fusion of incoming transport vesicles, a newly proposed subcompartmentalization into proximal and distal CC, and mechanisms of OS membrane dynamics paralleling ectosome formation in other cilia., (Copyright © 2019 Elsevier Ltd. All rights reserved.)
- Published
- 2019
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29. Deleterious Variation in BRSK2 Associates with a Neurodevelopmental Disorder.
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Hiatt SM, Thompson ML, Prokop JW, Lawlor JMJ, Gray DE, Bebin EM, Rinne T, Kempers M, Pfundt R, van Bon BW, Mignot C, Nava C, Depienne C, Kalsner L, Rauch A, Joset P, Bachmann-Gagescu R, Wentzensen IM, McWalter K, and Cooper GM
- Subjects
- Adolescent, Autistic Disorder genetics, Child, Child Behavior Disorders genetics, Child, Preschool, Exome, Female, Genetic Predisposition to Disease, Genetic Variation, Heterozygote, Humans, Male, Motor Skills Disorders genetics, Mutation, Phenotype, Exome Sequencing, Young Adult, Developmental Disabilities genetics, Gene Deletion, Intellectual Disability genetics, Neurodevelopmental Disorders genetics, Protein Serine-Threonine Kinases genetics
- Abstract
Developmental delay and intellectual disability (DD and ID) are heterogeneous phenotypes that arise in many rare monogenic disorders. Because of this rarity, developing cohorts with enough individuals to robustly identify disease-associated genes is challenging. Social-media platforms that facilitate data sharing among sequencing labs can help to address this challenge. Through one such tool, GeneMatcher, we identified nine DD- and/or ID-affected probands with a rare, heterozygous variant in the gene encoding the serine/threonine-protein kinase BRSK2. All probands have a speech delay, and most present with intellectual disability, motor delay, behavioral issues, and autism. Six of the nine variants are predicted to result in loss of function, and computational modeling predicts that the remaining three missense variants are damaging to BRSK2 structure and function. All nine variants are absent from large variant databases, and BRSK2 is, in general, relatively intolerant to protein-altering variation among humans. In all six probands for whom parents were available, the mutations were found to have arisen de novo. Five of these de novo variants were from cohorts with at least 400 sequenced probands; collectively, the cohorts span 3,429 probands, and the observed rate of de novo variation in these cohorts is significantly higher than the estimated background-mutation rate (p = 2.46 × 10
-6 ). We also find that exome sequencing provides lower coverage and appears less sensitive to rare variation in BRSK2 than does genome sequencing; this fact most likely reduces BRSK2's visibility in many clinical and research sequencing efforts. Altogether, our results implicate damaging variation in BRSK2 as a source of neurodevelopmental disease., (Copyright © 2019 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)- Published
- 2019
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30. Further corroboration of distinct functional features in SCN2A variants causing intellectual disability or epileptic phenotypes.
- Author
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Begemann A, Acuña MA, Zweier M, Vincent M, Steindl K, Bachmann-Gagescu R, Hackenberg A, Abela L, Plecko B, Kroell-Seger J, Baumer A, Yamakawa K, Inoue Y, Asadollahi R, Sticht H, Zeilhofer HU, and Rauch A
- Subjects
- Adolescent, Child, Epilepsy, Benign Neonatal physiopathology, Epileptic Syndromes physiopathology, Genetic Association Studies, HEK293 Cells, Humans, Intellectual Disability physiopathology, Phenotype, Young Adult, Epilepsy, Benign Neonatal genetics, Epileptic Syndromes genetics, Intellectual Disability genetics, NAV1.2 Voltage-Gated Sodium Channel physiology
- Abstract
Background: Deleterious variants in the voltage-gated sodium channel type 2 (Na
v 1.2) lead to a broad spectrum of phenotypes ranging from benign familial neonatal-infantile epilepsy (BFNIE), severe developmental and epileptic encephalopathy (DEE) and intellectual disability (ID) to autism spectrum disorders (ASD). Yet, the underlying mechanisms are still incompletely understood., Methods: To further elucidate the genotype-phenotype correlation of SCN2A variants we investigated the functional effects of six variants representing the phenotypic spectrum by whole-cell patch-clamp studies in transfected HEK293T cells and in-silico structural modeling., Results: The two variants p.L1342P and p.E1803G detected in patients with early onset epileptic encephalopathy (EE) showed profound and complex changes in channel gating, whereas the BFNIE variant p.L1563V exhibited only a small gain of channel function. The three variants identified in ID patients without seizures, p.R937C, p.L611Vfs*35 and p.W1716*, did not produce measurable currents. Homology modeling of the missense variants predicted structural impairments consistent with the electrophysiological findings., Conclusions: Our findings support the hypothesis that complete loss-of-function variants lead to ID without seizures, small gain-of-function variants cause BFNIE and EE variants exhibit variable but profound Nav 1.2 gating changes. Moreover, structural modeling was able to predict the severity of the variant impact, supporting a potential role of structural modeling as a prognostic tool. Our study on the functional consequences of SCN2A variants causing the distinct phenotypes of EE, BFNIE and ID contributes to the elucidation of mechanisms underlying the broad phenotypic variability reported for SCN2A variants.- Published
- 2019
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31. Publisher Correction: The ciliopathy protein TALPID3/KIAA0586 acts upstream of Rab8 activation in zebrafish photoreceptor outer segment formation and maintenance.
- Author
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Ojeda Naharros I, Cristian FB, Zang J, Gesemann M, Ingham PW, Neuhauss SCF, and Bachmann-Gagescu R
- Abstract
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
- Published
- 2018
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32. The ciliopathy protein TALPID3/KIAA0586 acts upstream of Rab8 activation in zebrafish photoreceptor outer segment formation and maintenance.
- Author
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Ojeda Naharros I, Cristian FB, Zang J, Gesemann M, Ingham PW, Neuhauss SCF, and Bachmann-Gagescu R
- Subjects
- Animals, Cell Survival, Disease Models, Animal, Electroretinography, Mutant Proteins genetics, Opsins metabolism, Zebrafish, Zebrafish Proteins genetics, Ciliopathies pathology, GTP Phosphohydrolases metabolism, Mutant Proteins metabolism, Organelle Biogenesis, Photoreceptor Cells pathology, Retinal Degeneration pathology, Zebrafish Proteins metabolism
- Abstract
Ciliopathies are human disorders caused by dysfunction of primary cilia, ubiquitous microtubule-based organelles involved in signal transduction. Cilia are anchored inside the cell through basal bodies (BBs), modified centrioles also acting as microtubule-organization centers. Photoreceptors (PRs) are sensory neurons, whose primary cilium forms a highly specialized compartment called the outer segment (OS) responsible for sensing incoming light. Thus, ciliopathies often present with retinal degeneration. Mutations in KIAA0586/TALPID3 (TA3) cause Joubert syndrome, in which 30% of affected individuals develop retinal involvement. To elucidate the function of TALPID3 in PRs, we studied talpid3 zebrafish mutants and identified a progressive retinal degeneration phenotype. The majority of PRs lack OS development due to defects in BB positioning and docking at the apical cell surface. Intracellular accumulation of the photopigment opsin leads to PR cell death of moderate severity. Electroretinograms demonstrate severe visual impairement. A small subset of PRs display normally docked BBs and extended OSs through rescue by maternally-deposited Talpid3. While localization of the small GTPase Rab8a, which plays an important role in BB docking, appears unaffected in talpid3-/- PRs, overexpression of constitutively active Rab8a rescues OS formation, indicating that the role of Ta3 in early ciliogenesis lies upstream of Rab8a activation in PRs.
- Published
- 2018
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33. Interpreting the clinical significance of combined variants in multiple recessive disease genes: systematic investigation of Joubert syndrome yields little support for oligogenicity.
- Author
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Phelps IG, Dempsey JC, Grout ME, Isabella CR, Tully HM, Doherty D, and Bachmann-Gagescu R
- Subjects
- Abnormalities, Multiple diagnosis, Abnormalities, Multiple genetics, Alleles, Cerebellum abnormalities, Eye Abnormalities diagnosis, Eye Abnormalities genetics, Genes, Modifier, Humans, Kidney Diseases, Cystic diagnosis, Kidney Diseases, Cystic genetics, Models, Genetic, Multifactorial Inheritance, Mutation, Phenotype, Retina abnormalities, Genes, Recessive, Genetic Association Studies methods, Genetic Diseases, Inborn diagnosis, Genetic Diseases, Inborn genetics, Genetic Predisposition to Disease, Genetic Variation
- Abstract
PurposeNext-generation sequencing (NGS) often identifies multiple rare predicted-deleterious variants (RDVs) in different genes associated with a recessive disorder in a given patient. Such variants have been proposed to contribute to digenicity/oligogenicity or "triallelism" or to act as genetic modifiers.MethodsUsing the recessive ciliopathy Joubert syndrome (JBTS) as a model, we investigated these possibilities systematically, relying on NGS of known JBTS genes in a large JBTS and two control cohorts.Results65% of affected individuals had a recessive genetic cause, while 4.9% were candidates for di-/oligogenicity, harboring heterozygous RDVs in two or more genes, compared with 4.2-8% in controls (P = 0.66-0.21). Based on Exome Aggregation Consortium (ExAC) allele frequencies, the probability of cumulating RDVs in any two JBTS genes is 9.3%. We found no support for triallelism, as no unaffected siblings carried the same biallelic RDVs as their affected relative. Sixty percent of individuals sharing identical causal RDVs displayed phenotypic discordance. Although 38% of affected individuals harbored RDVs in addition to the causal mutations, their presence did not correlate with phenotypic severity.ConclusionOur data offer little support for triallelism or digenicity/oligogenicity as clinically relevant inheritance modes in JBTS. While phenotypic discordance supports the existence of genetic modifiers, identifying clinically relevant modifiers remains challenging.
- Published
- 2018
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34. Loss-of-function of the ciliopathy protein Cc2d2a disorganizes the vesicle fusion machinery at the periciliary membrane and indirectly affects Rab8-trafficking in zebrafish photoreceptors.
- Author
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Ojeda Naharros I, Gesemann M, Mateos JM, Barmettler G, Forbes A, Ziegler U, Neuhauss SCF, and Bachmann-Gagescu R
- Subjects
- Animals, Animals, Genetically Modified, Biological Transport, Cell Movement, Cilia genetics, Cilia metabolism, Humans, Membranes metabolism, Opsins genetics, Opsins metabolism, Photoreceptor Cells, Vertebrate metabolism, Protein Transport, Zebrafish, rab GTP-Binding Proteins genetics, Vesicular Transport Proteins genetics, Vesicular Transport Proteins metabolism, Zebrafish Proteins genetics, Zebrafish Proteins metabolism, rab GTP-Binding Proteins metabolism
- Abstract
Ciliopathies are human disorders caused by dysfunction of primary cilia, ubiquitous organelles involved in transduction of environmental signals such as light sensation in photoreceptors. Concentration of signal detection proteins such as opsins in the ciliary membrane is achieved by RabGTPase-regulated polarized vesicle trafficking and by a selective barrier at the ciliary base, the transition zone (TZ). Dysfunction of the TZ protein CC2D2A causes Joubert/Meckel syndromes in humans and loss of ciliary protein localization in animal models, including opsins in retinal photoreceptors. The link between the TZ and upstream vesicle trafficking has been little explored to date. Moreover, the role of the small GTPase Rab8 in opsin-carrier vesicle (OCV) trafficking has been recently questioned in a mouse model. Using correlative light and electron microscopy and live imaging in zebrafish photoreceptors, we provide the first live characterization of Rab8-mediated trafficking in photoreceptors in vivo. Our results support a possibly redundant role for both Rab8a/b paralogs in OCV trafficking, based on co-localization of Rab8 and opsins in vesicular structures, and joint movement of Rab8-tagged particles with opsin. We further investigate the role of the TZ protein Cc2d2a in Rab8-mediated trafficking using cc2d2a zebrafish mutants and identify a requirement for Cc2d2a in the latest step of OCV trafficking, namely vesicle fusion. Progressive accumulation of opsin-containing vesicles in the apical portion of photoreceptors lacking Cc2d2a is caused by disorganization of the vesicle fusion machinery at the periciliary membrane with mislocalization and loss of the t-SNAREs SNAP25 and Syntaxin3 and of the exocyst component Exoc4. We further observe secondary defects on upstream Rab8-trafficking with cytoplasmic accumulation of Rab8. Taken together, our results support participation of Rab8 in OCV trafficking and identify a novel role for the TZ protein Cc2d2a in fusion of incoming ciliary-directed vesicles, through organization of the vesicle fusion machinery at the periciliary membrane.
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- 2017
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35. Correlative Super-resolution and Electron Microscopy to Resolve Protein Localization in Zebrafish Retina.
- Author
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Mateos JM, Barmettler G, Doehner J, Ojeda Naharros I, Guhl B, Neuhauss SCF, Kaech A, Bachmann-Gagescu R, and Ziegler U
- Subjects
- Animals, Retina pathology, Zebrafish, Microscopy, Electron, Scanning methods, Microscopy, Fluorescence methods, Retina diagnostic imaging
- Abstract
We present a method to investigate the subcellular protein localization in the larval zebrafish retina by combining super-resolution light microscopy and scanning electron microscopy. The sub-diffraction limit resolution capabilities of super-resolution light microscopes allow improving the accuracy of the correlated data. Briefly, 110 nanometer thick cryo-sections are transferred to a silicon wafer and, after immunofluorescence staining, are imaged by super-resolution light microscopy. Subsequently, the sections are preserved in methylcellulose and platinum shadowed prior to imaging in a scanning electron microscope (SEM). The images from these two microscopy modalities are easily merged using tissue landmarks with open source software. Here we describe the adapted method for the larval zebrafish retina. However, this method is also applicable to other types of tissues and organisms. We demonstrate that the complementary information obtained by this correlation is able to resolve the expression of mitochondrial proteins in relation with the membranes and cristae of mitochondria as well as to other compartments of the cell.
- Published
- 2017
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36. Mutations in ARMC9, which Encodes a Basal Body Protein, Cause Joubert Syndrome in Humans and Ciliopathy Phenotypes in Zebrafish.
- Author
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Van De Weghe JC, Rusterholz TDS, Latour B, Grout ME, Aldinger KA, Shaheen R, Dempsey JC, Maddirevula S, Cheng YH, Phelps IG, Gesemann M, Goel H, Birk OS, Alanzi T, Rawashdeh R, Khan AO, Bamshad MJ, Nickerson DA, Neuhauss SCF, Dobyns WB, Alkuraya FS, Roepman R, Bachmann-Gagescu R, and Doherty D
- Subjects
- Abnormalities, Multiple pathology, Animals, Armadillo Domain Proteins metabolism, Base Sequence, Brain pathology, Cerebellum pathology, Cilia metabolism, Ciliopathies pathology, Diagnostic Imaging, Exome genetics, Eye Abnormalities pathology, Genetic Predisposition to Disease, Humans, Kidney Diseases, Cystic pathology, Phenotype, Retina pathology, Sequence Analysis, DNA, Up-Regulation genetics, Zebrafish Proteins metabolism, Abnormalities, Multiple genetics, Armadillo Domain Proteins genetics, Basal Bodies metabolism, Cerebellum abnormalities, Ciliopathies genetics, Eye Abnormalities genetics, Kidney Diseases, Cystic genetics, Mutation genetics, Retina abnormalities, Zebrafish genetics, Zebrafish Proteins genetics
- Abstract
Joubert syndrome (JS) is a recessive neurodevelopmental disorder characterized by hypotonia, ataxia, abnormal eye movements, and variable cognitive impairment. It is defined by a distinctive brain malformation known as the "molar tooth sign" on axial MRI. Subsets of affected individuals have malformations such as coloboma, polydactyly, and encephalocele, as well as progressive retinal dystrophy, fibrocystic kidney disease, and liver fibrosis. More than 35 genes have been associated with JS, but in a subset of families the genetic cause remains unknown. All of the gene products localize in and around the primary cilium, making JS a canonical ciliopathy. Ciliopathies are unified by their overlapping clinical features and underlying mechanisms involving ciliary dysfunction. In this work, we identify biallelic rare, predicted-deleterious ARMC9 variants (stop-gain, missense, splice-site, and single-exon deletion) in 11 individuals with JS from 8 families, accounting for approximately 1% of the disorder. The associated phenotypes range from isolated neurological involvement to JS with retinal dystrophy, additional brain abnormalities (e.g., heterotopia, Dandy-Walker malformation), pituitary insufficiency, and/or synpolydactyly. We show that ARMC9 localizes to the basal body of the cilium and is upregulated during ciliogenesis. Typical ciliopathy phenotypes (curved body shape, retinal dystrophy, coloboma, and decreased cilia) in a CRISPR/Cas9-engineered zebrafish mutant model provide additional support for ARMC9 as a ciliopathy-associated gene. Identifying ARMC9 mutations as a cause of JS takes us one step closer to a full genetic understanding of this important disorder and enables future functional work to define the central biological mechanisms underlying JS and other ciliopathies., (Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)
- Published
- 2017
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37. Mortality in Joubert syndrome.
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Dempsey JC, Phelps IG, Bachmann-Gagescu R, Glass IA, Tully HM, and Doherty D
- Subjects
- Abnormalities, Multiple genetics, Abnormalities, Multiple physiopathology, Adolescent, Cerebellum physiopathology, Child, Child, Preschool, Eye Abnormalities complications, Eye Abnormalities genetics, Eye Abnormalities physiopathology, Female, Humans, Kidney Diseases, Cystic complications, Kidney Diseases, Cystic genetics, Kidney Diseases, Cystic physiopathology, Male, Renal Insufficiency complications, Renal Insufficiency genetics, Renal Insufficiency pathology, Retina physiopathology, Rhombencephalon abnormalities, Rhombencephalon physiopathology, Abnormalities, Multiple mortality, Cerebellum abnormalities, Eye Abnormalities mortality, Kidney Diseases, Cystic mortality, Renal Insufficiency mortality, Retina abnormalities
- Abstract
Joubert syndrome (JS) is a rare, recessively inherited neurodevelopmental disorder characterized by a distinctive mid-hindbrain malformation. Little is known about mortality in affected individuals. Identifying the timing and causes of death will allow for development of healthcare guidelines for families and providers and, thus, help to prolong and improve the lives of patients with JS. We evaluated information on 40 deceased individuals with JS to characterize age and cause of death. We compared this population with 525 living individuals with JS to estimate associations between risk of death and extra-neurological features. Genetic causes were examined in both groups. Mean age of death in this cohort was 7.2 years, and the most prevalent causes of death were respiratory failure (35%), particularly in individuals younger than 6 years, and kidney failure (37.5%), which was more common in older individuals. We identified possible associations between risk of death and kidney disease, liver fibrosis, polydactyly, occipital encephalocele, and genetic cause. This work highlights factors (genetic cause, extra-neurological organ involvement, and other malformations) likely to be associated with higher risk of mortality in JS, which should prompt increased monitoring for respiratory issues, kidney disease, and liver fibrosis., (© 2017 Wiley Periodicals, Inc.)
- Published
- 2017
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38. The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking.
- Author
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Bachmann-Gagescu R, Dona M, Hetterschijt L, Tonnaer E, Peters T, de Vrieze E, Mans DA, van Beersum SE, Phelps IG, Arts HH, Keunen JE, Ueffing M, Roepman R, Boldt K, Doherty D, Moens CB, Neuhauss SC, Kremer H, and van Wijk E
- Subjects
- Abnormalities, Multiple genetics, Abnormalities, Multiple metabolism, Abnormalities, Multiple pathology, Animals, Cerebellum metabolism, Cerebellum pathology, Cilia genetics, Cilia metabolism, Cilia pathology, Ciliary Motility Disorders metabolism, Ciliary Motility Disorders pathology, Cytoskeletal Proteins, Encephalocele metabolism, Encephalocele pathology, Eye Abnormalities genetics, Eye Abnormalities metabolism, Eye Abnormalities pathology, Gene Knockdown Techniques, Humans, Kidney Diseases, Cystic genetics, Kidney Diseases, Cystic metabolism, Kidney Diseases, Cystic pathology, Microtubule-Associated Proteins genetics, Mixed Function Oxygenases metabolism, Mutation, Nuclear Proteins genetics, Polycystic Kidney Diseases metabolism, Polycystic Kidney Diseases pathology, Protein Transport genetics, Proteins metabolism, Retina metabolism, Retina pathology, Retinitis Pigmentosa, Signal Transduction, Zebrafish, rab GTP-Binding Proteins metabolism, Cerebellum abnormalities, Ciliary Motility Disorders genetics, Encephalocele genetics, Microtubule-Associated Proteins metabolism, Mixed Function Oxygenases genetics, Nuclear Proteins metabolism, Polycystic Kidney Diseases genetics, Proteins genetics, Retina abnormalities, rab GTP-Binding Proteins genetics
- Abstract
Ciliopathies are a group of human disorders caused by dysfunction of primary cilia, ubiquitous microtubule-based organelles involved in transduction of extra-cellular signals to the cell. This function requires the concentration of receptors and channels in the ciliary membrane, which is achieved by complex trafficking mechanisms, in part controlled by the small GTPase RAB8, and by sorting at the transition zone located at the entrance of the ciliary compartment. Mutations in the transition zone gene CC2D2A cause the related Joubert and Meckel syndromes, two typical ciliopathies characterized by central nervous system malformations, and result in loss of ciliary localization of multiple proteins in various models. The precise mechanisms by which CC2D2A and other transition zone proteins control protein entrance into the cilium and how they are linked to vesicular trafficking of incoming cargo remain largely unknown. In this work, we identify the centrosomal protein NINL as a physical interaction partner of CC2D2A. NINL partially co-localizes with CC2D2A at the base of cilia and ninl knockdown in zebrafish leads to photoreceptor outer segment loss, mislocalization of opsins and vesicle accumulation, similar to cc2d2a-/- phenotypes. Moreover, partial ninl knockdown in cc2d2a-/- embryos enhances the retinal phenotype of the mutants, indicating a genetic interaction in vivo, for which an illustration is found in patients from a Joubert Syndrome cohort. Similar to zebrafish cc2d2a mutants, ninl morphants display altered Rab8a localization. Further exploration of the NINL-associated interactome identifies MICAL3, a protein known to interact with Rab8 and to play an important role in vesicle docking and fusion. Together, these data support a model where CC2D2A associates with NINL to provide a docking point for cilia-directed cargo vesicles, suggesting a mechanism by which transition zone proteins can control the protein content of the ciliary compartment.
- Published
- 2015
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39. NINL and DZANK1 Co-function in Vesicle Transport and Are Essential for Photoreceptor Development in Zebrafish.
- Author
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Dona M, Bachmann-Gagescu R, Texier Y, Toedt G, Hetterschijt L, Tonnaer EL, Peters TA, van Beersum SE, Bergboer JG, Horn N, de Vrieze E, Slijkerman RW, van Reeuwijk J, Flik G, Keunen JE, Ueffing M, Gibson TJ, Roepman R, Boldt K, Kremer H, and van Wijk E
- Subjects
- Animals, Biological Transport genetics, Cilia genetics, HEK293 Cells, Humans, Larva growth & development, Neurogenesis genetics, Proteomics, Signal Transduction, Zebrafish genetics, Zebrafish growth & development, Carrier Proteins genetics, Dyneins genetics, Larva genetics, Microtubule-Associated Proteins genetics, Nuclear Proteins genetics, Photoreceptor Cells, Vertebrate, Retina growth & development, Zebrafish Proteins genetics
- Abstract
Ciliopathies are Mendelian disorders caused by dysfunction of cilia, ubiquitous organelles involved in fluid propulsion (motile cilia) or signal transduction (primary cilia). Retinal dystrophy is a common phenotypic characteristic of ciliopathies since photoreceptor outer segments are specialized primary cilia. These ciliary structures heavily rely on intracellular minus-end directed transport of cargo, mediated at least in part by the cytoplasmic dynein 1 motor complex, for their formation, maintenance and function. Ninein-like protein (NINL) is known to associate with this motor complex and is an important interaction partner of the ciliopathy-associated proteins lebercilin, USH2A and CC2D2A. Here, we scrutinize the function of NINL with combined proteomic and zebrafish in vivo approaches. We identify Double Zinc Ribbon and Ankyrin Repeat domains 1 (DZANK1) as a novel interaction partner of NINL and show that loss of Ninl, Dzank1 or both synergistically leads to dysmorphic photoreceptor outer segments, accumulation of trans-Golgi-derived vesicles and mislocalization of Rhodopsin and Ush2a in zebrafish. In addition, retrograde melanosome transport is severely impaired in zebrafish lacking Ninl or Dzank1. We further demonstrate that NINL and DZANK1 are essential for intracellular dynein-based transport by associating with complementary subunits of the cytoplasmic dynein 1 motor complex, thus shedding light on the structure and stoichiometry of this important motor complex. Altogether, our results support a model in which the NINL-DZANK1 protein module is involved in the proper assembly and folding of the cytoplasmic dynein 1 motor complex in photoreceptor cells, a process essential for outer segment formation and function.
- Published
- 2015
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40. KIAA0586 is Mutated in Joubert Syndrome.
- Author
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Bachmann-Gagescu R, Phelps IG, Dempsey JC, Sharma VA, Ishak GE, Boyle EA, Wilson M, Marques Lourenço C, Arslan M, Shendure J, and Doherty D
- Subjects
- Abnormalities, Multiple diagnosis, Abnormalities, Multiple genetics, Adolescent, Adult, Alternative Splicing, Brain pathology, Child, Child, Preschool, DNA Mutational Analysis, Eye Abnormalities diagnosis, Eye Abnormalities genetics, Gene Order, Genetic Association Studies, Humans, Kidney Diseases, Cystic diagnosis, Kidney Diseases, Cystic genetics, Magnetic Resonance Imaging, Phenotype, Young Adult, Cell Cycle Proteins genetics, Cerebellum abnormalities, Mutation, Retina abnormalities
- Abstract
Joubert syndrome (JS) is a recessive neurodevelopmental disorder characterized by a distinctive mid-hindbrain malformation. JS is part of a group of disorders called ciliopathies based on their overlapping phenotypes and common underlying pathophysiology linked to primary cilium dysfunction. Biallelic mutations in one of 28 genes, all encoding proteins localizing to the primary cilium or basal body, can cause JS. Despite this large number of genes, the genetic cause can currently be determined in about 62% of individuals with JS. To identify novel JS genes, we performed whole exome sequencing on 35 individuals with JS and found biallelic rare deleterious variants (RDVs) in KIAA0586, encoding a centrosomal protein required for ciliogenesis, in one individual. Targeted next-generation sequencing in a large JS cohort identified biallelic RDVs in eight additional families for an estimated prevalence of 2.5% (9/366 JS families). All affected individuals displayed JS phenotypes toward the mild end of the spectrum., (© 2015 WILEY PERIODICALS, INC.)
- Published
- 2015
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41. [Genetic complexity of ciliopathies and novel genes identification].
- Author
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Bachmann-Gagescu R
- Subjects
- Abnormalities, Multiple, Animals, Cell Polarity, Cerebellar Diseases genetics, Cerebellar Diseases pathology, Cerebellum abnormalities, Chromosome Mapping, Cilia chemistry, Cilia physiology, Cilia ultrastructure, Ciliary Motility Disorders classification, Disease Models, Animal, Eye Abnormalities genetics, Eye Abnormalities pathology, Forecasting, Genes, Recessive, Genetic Diseases, Inborn pathology, Humans, Kidney Diseases, Cystic genetics, Kidney Diseases, Cystic pathology, Membrane Proteins deficiency, Membrane Proteins genetics, Membrane Proteins physiology, Microtubule Proteins deficiency, Microtubule Proteins genetics, Microtubule Proteins physiology, Molecular Motor Proteins deficiency, Molecular Motor Proteins genetics, Molecular Motor Proteins physiology, Phenotype, Polymorphism, Single Nucleotide, Proteomics, Retina abnormalities, Retina pathology, Sequence Analysis, DNA methods, Syndrome, Systems Biology methods, Ciliary Motility Disorders genetics, Genetic Association Studies, Genetic Diseases, Inborn genetics, Genetic Heterogeneity
- Abstract
Ciliopathies are a large group of human disorders caused by dysfunction of primary or motile cilia and unified by their overlapping clinical features (brain malformations, retinal dystrophy, cystic kidney disease, liver fibrosis and skeletal abnormalities). Ciliopathies are mendelian disorders with prominent genetic heterogeneity and marked allelism between different clinical entities, which are in part explained by the recently identified functional modules and multi-protein complexes formed by ciliopathy-associated gene products. The current review provides an updated snapshot of this complex evolving field, highlighting the key phenotypic features and causative genes for commonly-studied ciliopathies and summarizing our emerging understanding of the correlations between the functions of subgroups of genes and clinical sub-types of ciliopathies. Using the example of Joubert syndrome, a ciliopathy characterized by a distinctive hindbrain malformation and caused by mutations in more than 20 different genes, this work also reviews the principal methods used for new gene identification, including candidate gene approaches, homozygosity mapping as well as high throughput next-generation and exome sequencing., (© 2014 médecine/sciences – Inserm.)
- Published
- 2014
- Full Text
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42. Mutations in CSPP1 cause primary cilia abnormalities and Joubert syndrome with or without Jeune asphyxiating thoracic dystrophy.
- Author
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Tuz K, Bachmann-Gagescu R, O'Day DR, Hua K, Isabella CR, Phelps IG, Stolarski AE, O'Roak BJ, Dempsey JC, Lourenco C, Alswaid A, Bönnemann CG, Medne L, Nampoothiri S, Stark Z, Leventer RJ, Topçu M, Cansu A, Jagadeesh S, Done S, Ishak GE, Glass IA, Shendure J, Neuhauss SC, Haldeman-Englert CR, Doherty D, and Ferland RJ
- Subjects
- Abnormalities, Multiple, Adolescent, Animals, Cerebellum abnormalities, Child, Child, Preschool, Cilia pathology, Exons, Female, Fibroblasts cytology, Fibroblasts metabolism, Gene Knockdown Techniques, Humans, Infant, Male, Phenotype, Sequence Analysis, DNA, Young Adult, Zebrafish genetics, Cell Cycle Proteins genetics, Cerebellar Diseases genetics, Cilia genetics, Ellis-Van Creveld Syndrome genetics, Eye Abnormalities genetics, Kidney Diseases, Cystic genetics, Microtubule-Associated Proteins genetics, Mutation, Retina abnormalities
- Abstract
Joubert syndrome (JBTS) is a recessive ciliopathy in which a subset of affected individuals also have the skeletal dysplasia Jeune asphyxiating thoracic dystrophy (JATD). Here, we have identified biallelic truncating CSPP1 (centrosome and spindle pole associated protein 1) mutations in 19 JBTS-affected individuals, four of whom also have features of JATD. CSPP1 mutations explain ∼5% of JBTS in our cohort, and despite truncating mutations in all affected individuals, the range of phenotypic severity is broad. Morpholino knockdown of cspp1 in zebrafish caused phenotypes reported in other zebrafish models of JBTS (curved body shape, pronephric cysts, and cerebellar abnormalities) and reduced ciliary localization of Arl13b, further supporting loss of CSPP1 function as a cause of JBTS. Fibroblasts from affected individuals with CSPP1 mutations showed reduced numbers of primary cilia and/or short primary cilia, as well as reduced axonemal localization of ciliary proteins ARL13B and adenylyl cyclase III. In summary, CSPP1 mutations are a major cause of the Joubert-Jeune phenotype in humans; however, the mechanism by which these mutations lead to both JBTS and JATD remains unknown., (Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)
- Published
- 2014
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43. Genotype-phenotype correlation in CC2D2A-related Joubert syndrome reveals an association with ventriculomegaly and seizures.
- Author
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Bachmann-Gagescu R, Ishak GE, Dempsey JC, Adkins J, O'Day D, Phelps IG, Gunay-Aygun M, Kline AD, Szczaluba K, Martorell L, Alswaid A, Alrasheed S, Pai S, Izatt L, Ronan A, Parisi MA, Mefford H, Glass I, and Doherty D
- Subjects
- Abnormalities, Multiple, Adolescent, Adult, Alleles, Cerebellar Diseases diagnosis, Cerebellar Diseases epidemiology, Cerebellum abnormalities, Child, Child, Preschool, Cytoskeletal Proteins, Eye Abnormalities diagnosis, Eye Abnormalities epidemiology, Genotype, Humans, Hydrocephalus diagnosis, Infant, Kidney Diseases, Cystic diagnosis, Kidney Diseases, Cystic epidemiology, Magnetic Resonance Imaging, Neuroimaging, Phenotype, Prevalence, Retina abnormalities, Young Adult, Cerebellar Diseases genetics, Eye Abnormalities genetics, Genetic Association Studies, Hydrocephalus genetics, Kidney Diseases, Cystic genetics, Proteins genetics, Seizures genetics
- Abstract
Background: Joubert syndrome (JS) is a ciliopathy characterised by a distinctive brain malformation (the 'molar tooth sign'), developmental delay, abnormal eye movements and abnormal breathing pattern. Retinal dystrophy, cystic kidney disease, liver fibrosis and polydactyly are variably present, resulting in significant phenotypic heterogeneity and overlap with other ciliopathies. JS is also genetically heterogeneous, resulting from mutations in 13 genes. These factors render clinical/molecular diagnosis and management challenging. CC2D2A mutations are a relatively common cause of JS and also cause Meckel syndrome. The clinical consequences of CC2D2A mutations in patients with JS have been incompletely reported., Methods: Subjects with JS from 209 families were evaluated to identify mutations in CC2D2A. Clinical and imaging features in subjects with CC2D2A mutations were compared with those in subjects without CC2D2A mutations and reports in the literature., Results: 10 novel CC2D2A mutations in 20 subjects were identified; a summary is provided of all published CC2D2A mutations. Subjects with CC2D2A-related JS were more likely to have ventriculomegaly (p<0.0001) and seizures (p=0.024) than subjects without CC2D2A mutations. No mutation-specific genotype-phenotype correlations could be identified, but the findings confirm the observation that mutations that cause CC2D2A-related JS are predicted to be less deleterious than mutations that cause CC2D2A-related Meckel syndrome. Missense variants in the coiled-coil and C2 domains, as well as the C-terminal region, identify these regions as important for the biological mechanisms underlying JS., Conclusions: CC2D2A testing should be prioritised in patients with JS and ventriculomegaly and/or seizures. Patients with CC2D2A-related JS should be monitored for hydrocephalus and seizures.
- Published
- 2012
- Full Text
- View/download PDF
44. The ciliopathy gene cc2d2a controls zebrafish photoreceptor outer segment development through a role in Rab8-dependent vesicle trafficking.
- Author
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Bachmann-Gagescu R, Phelps IG, Stearns G, Link BA, Brockerhoff SE, Moens CB, and Doherty D
- Subjects
- Animals, Animals, Genetically Modified, Cilia metabolism, Female, Gene Knockout Techniques, HEK293 Cells, Humans, Male, Membrane Proteins metabolism, Protein Binding, Protein Transport, Transport Vesicles ultrastructure, Vesicular Transport Proteins metabolism, Vision, Ocular genetics, Zebrafish embryology, Zebrafish growth & development, Zebrafish Proteins genetics, Zebrafish Proteins metabolism, rab GTP-Binding Proteins metabolism, Cilia genetics, Retinal Photoreceptor Cell Outer Segment metabolism, Transport Vesicles metabolism, Vesicular Transport Proteins genetics, Vesicular Transport Proteins physiology, Zebrafish genetics, Zebrafish Proteins physiology, rab GTP-Binding Proteins genetics
- Abstract
Ciliopathies are a genetically and phenotypically heterogeneous group of human developmental disorders whose root cause is the absence or dysfunction of primary cilia. Joubert syndrome is characterized by a distinctive hindbrain malformation variably associated with retinal dystrophy and cystic kidney disease. Mutations in CC2D2A are found in ∼10% of patients with Joubert syndrome. Here we describe the retinal phenotype of cc2d2a mutant zebrafish consisting of disorganized rod and cone photoreceptor outer segments resulting in abnormal visual function as measured by electroretinogram. Our analysis reveals trafficking defects in mutant photoreceptors affecting transmembrane outer segment proteins (opsins) and striking accumulation of vesicles, suggesting a role for Cc2d2a in vesicle trafficking and fusion. This is further supported by mislocalization of Rab8, a key regulator of opsin carrier vesicle trafficking, in cc2d2a mutant photoreceptors and by enhancement of the cc2d2a retinal and kidney phenotypes with partial knockdown of rab8. We demonstrate that Cc2d2a localizes to the connecting cilium in photoreceptors and to the transition zone in other ciliated cell types and that cilia are present in these cells in cc2d2a mutants, arguing against a primary function for Cc2d2a in ciliogenesis. Our data support a model where Cc2d2a, localized at the photoreceptor connecting cilium/transition zone, facilitates protein transport through a role in Rab8-dependent vesicle trafficking and fusion.
- Published
- 2011
- Full Text
- View/download PDF
45. Myhre syndrome with ataxia and cerebellar atrophy.
- Author
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Bachmann-Gagescu R, Hisama FM, and Yuen AL
- Subjects
- Ataxia diagnosis, Ataxia pathology, Atrophy pathology, Cerebellum pathology, Cryptorchidism pathology, Facies, Female, Growth Disorders pathology, Hand Deformities, Congenital pathology, Humans, Hypertrophy pathology, Intellectual Disability pathology, Joint Diseases pathology, Phenotype, Young Adult, Ataxia etiology, Cerebellar Diseases etiology, Cryptorchidism complications, Cryptorchidism diagnosis, Growth Disorders complications, Growth Disorders diagnosis, Hand Deformities, Congenital complications, Hand Deformities, Congenital diagnosis, Hypertrophy complications, Hypertrophy diagnosis, Intellectual Disability complications, Intellectual Disability diagnosis, Joint Diseases complications, Joint Diseases diagnosis
- Published
- 2011
- Full Text
- View/download PDF
46. Recurrent 200-kb deletions of 16p11.2 that include the SH2B1 gene are associated with developmental delay and obesity.
- Author
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Bachmann-Gagescu R, Mefford HC, Cowan C, Glew GM, Hing AV, Wallace S, Bader PI, Hamati A, Reitnauer PJ, Smith R, Stockton DW, Muhle H, Helbig I, Eichler EE, Ballif BC, Rosenfeld J, and Tsuchiya KD
- Subjects
- Abnormalities, Multiple genetics, Body Mass Index, Child, Preschool, Comparative Genomic Hybridization, DNA Copy Number Variations, Gene Dosage, Genome-Wide Association Study, Humans, Infant, Infant, Newborn, Intellectual Disability genetics, Nucleic Acid Hybridization, Phenotype, Segmental Duplications, Genomic, Adaptor Proteins, Signal Transducing genetics, Chromosomes, Human, Pair 16 genetics, Developmental Disabilities genetics, Obesity genetics, Sequence Deletion
- Abstract
Purpose: The short arm of chromosome 16 is rich in segmental duplications, predisposing this region of the genome to a number of recurrent rearrangements. Genomic imbalances of an approximately 600-kb region in 16p11.2 (29.5-30.1 Mb) have been associated with autism, intellectual disability, congenital anomalies, and schizophrenia. However, a separate, distal 200-kb region in 16p11.2 (28.7-28.9 Mb) that includes the SH2B1 gene has been recently associated with isolated obesity. The purpose of this study was to better define the phenotype of this recurrent SH2B1-containing microdeletion in a cohort of phenotypically abnormal patients not selected for obesity., Methods: Array comparative hybridization was performed on a total of 23,084 patients in a clinical setting for a variety of indications, most commonly developmental delay., Results: Deletions of the SH2B1-containing region were identified in 31 patients. The deletion is enriched in the patient population when compared with controls (P = 0.003), with both inherited and de novo events. Detailed clinical information was available for six patients, who all had developmental delays of varying severity. Body mass index was ≥95th percentile in four of six patients, supporting the previously described association with obesity. The reciprocal duplication, found in 17 patients, does not seem to be significantly enriched in our patient population compared with controls., Conclusions: Deletions of the 16p11.2 SH2B1-containing region are pathogenic and are associated with developmental delay in addition to obesity.
- Published
- 2010
- Full Text
- View/download PDF
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