Browsing by Author "Undiagnosed Diseases Network"

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    HNRNPC haploinsufficiency affects alternative splicing of intellectual disability-associated genes and causes a neurodevelopmental disorder
    (Elsevier, 2023) Niggl, Eva; Bouman, Arjan; Briere, Lauren C.; Hoogenboezem, Remco M.; Wallaard, Ilse; Park, Joohyun; Admard, Jakob; Wilke, Martina; Harris-Mostert, Emilio D. R. O.; Elgersma, Minetta; Bain, Jennifer; Balasubramanian, Meena; Banka, Siddharth; Benke, Paul J.; Bertrand, Miriam; Blesson, Alyssa E.; Clayton-Smith, Jill; Ellingford, Jamie M.; Gillentine, Madelyn A.; Goodloe, Dana H.; Haack, Tobias B.; Jain, Mahim; Krantz, Ian; Luu, Sharon M.; McPheron, Molly; Muss, Candace L.; Raible, Sarah E.; Robin, Nathaniel H.; Spiller, Michael; Starling, Susan; Sweetser, David A.; Thiffault, Isabelle; Vetrini, Francesco; Witt, Dennis; Woods, Emily; Zhou, Dihong; Genomics England Research Consortium; Undiagnosed Diseases Network; Elgersma, Ype; van Esbroeck, Annelot C. M.; Medical and Molecular Genetics, School of Medicine
    Heterogeneous nuclear ribonucleoprotein C (HNRNPC) is an essential, ubiquitously abundant protein involved in mRNA processing. Genetic variants in other members of the HNRNP family have been associated with neurodevelopmental disorders. Here, we describe 13 individuals with global developmental delay, intellectual disability, behavioral abnormalities, and subtle facial dysmorphology with heterozygous HNRNPC germline variants. Five of them bear an identical in-frame deletion of nine amino acids in the extreme C terminus. To study the effect of this recurrent variant as well as HNRNPC haploinsufficiency, we used induced pluripotent stem cells (iPSCs) and fibroblasts obtained from affected individuals. While protein localization and oligomerization were unaffected by the recurrent C-terminal deletion variant, total HNRNPC levels were decreased. Previously, reduced HNRNPC levels have been associated with changes in alternative splicing. Therefore, we performed a meta-analysis on published RNA-seq datasets of three different cell lines to identify a ubiquitous HNRNPC-dependent signature of alternative spliced exons. The identified signature was not only confirmed in fibroblasts obtained from an affected individual but also showed a significant enrichment for genes associated with intellectual disability. Hence, we assessed the effect of decreased and increased levels of HNRNPC on neuronal arborization and neuronal migration and found that either condition affects neuronal function. Taken together, our data indicate that HNRNPC haploinsufficiency affects alternative splicing of multiple intellectual disability-associated genes and that the developing brain is sensitive to aberrant levels of HNRNPC. Hence, our data strongly support the inclusion of HNRNPC to the family of HNRNP-related neurodevelopmental disorders.
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    Macrocephaly and developmental delay caused by missense variants in RAB5C
    (Oxford University Press, 2023) Koop, Klaas; Yuan, Weimin; Tessadori, Federico; Rodriguez-Polanco, Wilmer R.; Grubbs, Jeremy; Zhang, Bo; Osmond, Matt; Graham, Gail; Sawyer, Sarah; Conboy, Erin; Vetrini, Francesco; Treat, Kayla; Płoski, Rafal; Pienkowski, Victor Murcia; Kłosowska, Anna; Fieg, Elizabeth; Krier, Joel; Mallebranche, Coralie; Alban, Ziegler; Aldinger, Kimberly A.; Ritter, Deborah; Macnamara, Ellen; Sullivan, Bonnie; Herriges, John; Alaimo, Joseph T.; Helbig, Catherine; Ellis, Colin A.; van Eyk, Clare; Gecz, Jozef; Farrugia, Daniel; Osei-Owusu, Ikeoluwa; Adès, Lesley; van den Boogaard, Marie-Jose; Fuchs, Sabine; Bakker, Jeroen; Duran, Karen; Dawson, Zachary D.; Lindsey, Anika; Huang, Huiyan; Baldridge, Dustin; Silverman, Gary A.; Grant, Barth D.; Raizen, David; Undiagnosed Diseases Network; van Haaften, Gijs; Pak, Stephen C.; Rehmann, Holger; Schedl, Tim; van Hasselt, Peter; Medical and Molecular Genetics, School of Medicine
    Rab GTPases are important regulators of intracellular vesicular trafficking. RAB5C is a member of the Rab GTPase family that plays an important role in the endocytic pathway, membrane protein recycling and signaling. Here we report on 12 individuals with nine different heterozygous de novo variants in RAB5C. All but one patient with missense variants (n = 9) exhibited macrocephaly, combined with mild-to-moderate developmental delay. Patients with loss of function variants (n = 2) had an apparently more severe clinical phenotype with refractory epilepsy and intellectual disability but a normal head circumference. Four missense variants were investigated experimentally. In vitro biochemical studies revealed that all four variants were damaging, resulting in increased nucleotide exchange rate, attenuated responsivity to guanine exchange factors and heterogeneous effects on interactions with effector proteins. Studies in C. elegans confirmed that all four variants were damaging in vivo and showed defects in endocytic pathway function. The variant heterozygotes displayed phenotypes that were not observed in null heterozygotes, with two shown to be through a dominant negative mechanism. Expression of the human RAB5C variants in zebrafish embryos resulted in defective development, further underscoring the damaging effects of the RAB5C variants. Our combined bioinformatic, in vitro and in vivo experimental studies and clinical data support the association of RAB5C missense variants with a neurodevelopmental disorder characterized by macrocephaly and mild-to-moderate developmental delay through disruption of the endocytic pathway.
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    TNPO2 variants associate with human developmental delays, neurologic deficits, and dysmorphic features and alter TNPO2 activity in Drosophila
    (Elsevier, 2021) Goodman, Lindsey D.; Cope, Heidi; Nil, Zelha; Ravenscroft, Thomas A.; Charng, Wu-Lin; Lu, Shenzhao; Tien, An-Chi; Pfundt, Rolph; Koolen, David A.; Haaxma, Charlotte A.; Veenstra-Knol, Hermine E.; Klein Wassink-Ruiter, Jolien S.; Wevers, Marijke R.; Jones, Melissa; Walsh, Laurence E.; Klee, Victoria H.; Theunis, Miel; Legius, Eric; Steel, Dora; Barwick, Katy E.S.; Kurian, Manju A.; Mohammad, Shekeeb. S.; Dale, Russell C.; Terhal, Paulien A.; van Binsbergen, Ellen; Kirmse, Brian; Robinette, Bethany; Cogné, Benjamin; Isidor, Bertrand; Grebe, Theresa A.; Kulch, Peggy; Hainline, Bryan E.; Sapp, Katherine; Morava, Eva; Klee, Eric W.; Macke, Erica L.; Trapane, Pamela; Spencer, Christopher; Si, Yue; Begtrup, Amber; Moulton, Matthew J.; Dutta, Debdeep; Kanca, Oguz; Undiagnosed Diseases Network; Wangler, Michael F.; Yamamoto, Shinya; Bellen, Hugo J.; Tan, Queenie K.G.; Pediatrics, School of Medicine
    Transportin-2 (TNPO2) mediates multiple pathways including non-classical nucleocytoplasmic shuttling of >60 cargoes, such as developmental and neuronal proteins. We identified 15 individuals carrying de novo coding variants in TNPO2 who presented with global developmental delay (GDD), dysmorphic features, ophthalmologic abnormalities, and neurological features. To assess the nature of these variants, functional studies were performed in Drosophila. We found that fly dTnpo (orthologous to TNPO2) is expressed in a subset of neurons. dTnpo is critical for neuronal maintenance and function as downregulating dTnpo in mature neurons using RNAi disrupts neuronal activity and survival. Altering the activity and expression of dTnpo using mutant alleles or RNAi causes developmental defects, including eye and wing deformities and lethality. These effects are dosage dependent as more severe phenotypes are associated with stronger dTnpo loss. Interestingly, similar phenotypes are observed with dTnpo upregulation and ectopic expression of TNPO2, showing that loss and gain of Transportin activity causes developmental defects. Further, proband-associated variants can cause more or less severe developmental abnormalities compared to wild-type TNPO2 when ectopically expressed. The impact of the variants tested seems to correlate with their position within the protein. Specifically, those that fall within the RAN binding domain cause more severe toxicity and those in the acidic loop are less toxic. Variants within the cargo binding domain show tissue-dependent effects. In summary, dTnpo is an essential gene in flies during development and in neurons. Further, proband-associated de novo variants within TNPO2 disrupt the function of the encoded protein. Hence, TNPO2 variants are causative for neurodevelopmental abnormalities.