Genetics
Abstract
Authors
Alexander M. Loiben, Wei-Ming Chien, Ashley McKinstry, Dania Ahmed, Matthew C. Childers, Michael Regnier, Charles E. Murry, Kai-Chun Yang
Abstract
Disorders of GABRA3, the only epilepsy-associated GABA-A receptor subunit gene on the X chromosome, have eluded clinical clarity due to ambiguous inheritance patterns and variable phenotypes. The long-standing assumption that all pathogenic variants cause loss-of-function further obscured genotype-phenotype relationships and hindered progress. Here, we curated a cohort of individuals with a GABRA3 variant, integrating deep phenotyping, genotyping, family history, electrophysiology, with a targeted mouse model. Among 43 individuals with 19 GABRA3 variants, functional analyses revealed both gain- and loss-of-function effects, each linked to distinct clinical profiles. Gain-of-function variants were associated with severe, treatment-resistant epilepsy and severe-profound intellectual disability, disproportionately affecting males, who were often non-ambulant and had cortical visual impairment. Loss-of-function variants produced milder phenotypes, with epilepsy rarely observed; affected males showed behavioural issues and language delay, while females were unaffected carriers. Our gain-of-function (Gabra3Q242L/+) mouse model mirrored these sex-specific differences, showing increased seizure susceptibility, early death, and marked cortical hyperexcitability. These insights not only resolve longstanding uncertainties surrounding GABRA3 but also redefine how X-linked disorders are interpreted. They demonstrate that it is the functional impact of a variant, not its mere presence, that determines whether a condition manifests dominantly or recessively. This distinction carries important implications for genetic counselling, precision medicine, and the broader interpretation of X-linked neurodevelopmental disorders.
Authors
Katrine M. Johannesen, Khaing Phyu Aung, Vivian W.Y. Liao, Nathan L. Absalom, Han C. Chua, Xue N. Gan, Miaomiao Mao, Chaseley E. McKenzie, Hian M. Lee, Sebastian Ortiz, Rebecca C. Spillmann, Vandana Shashi, Rodney A. Radtke, Ghayda M. Mirzaa, P. Anne Weisner, Josue Flores Daboub, Caroline Hagedorn, Pinar Bayrak-Toydemir, Desiree DeMille, Jian Zhao, Nandita Bajaj, Yline Capri, Boris Keren, Miriam Schmidts, Ingrid M.B.H. van de Laar, Marjon A. van Slegtenhorst, Rafal Ploski, Marta Bogotko, Danielle K. Bourque, Ebba Alkhunaizi, Lauren Chad, Nada Quercia, Houda Elloumi, Ingrid M. Wentzensen, Michael C. Kruer, Pritha Bisarad, Carolina I. Galaz-Montoya, Violeta Rusu, Dominique Braun, Katie Angione, Jessica C. Win, Camilo Espinosa-Jovel, Pia Zacher, Konrad Platzer, Samuel F. Berkovic, Ingrid E. Scheffer, Mary Chebib, Guido Rubboli, Rikke S. Møller, Christopher A. Reid, Philip K. Ahring
Abstract
Hereditary pheochromocytoma and paraganglioma (hPPGL) is caused by pathogenic mutations in succinate dehydrogenase (SDH) genes, commonly SDHB. However, over 80% of SDHB missense variants are classified as variants of uncertain significance (VUS), limiting clinical interpretation and diagnostic utility of germline testing. To provide functional evidence of SDHB allele pathogenicity or benignity, we developed a cellular complementation assay that quantifies intracellular succinate/fumarate ratios as a readout of SDH enzymatic activity. This assay reliably distinguished pathogenic from benign alleles with high fidelity, outperforming and complementing computational predictions. Functional assessment of patient-derived VUS alleles supported reclassification of 87% of tested variants and revealed that mutations in the iron–sulfur cluster domain were amorphic, while those at or beyond the C-terminal residue Tyr273 retained function. Variants associated with Leigh syndrome retained activity, consistent with their biallelic inheritance and distinct pathogenic mechanisms from SDHB-related tumorigenesis. Notably, hypomorphic pathogenic SDHB variants correlated with increased head and neck paraganglioma occurrence, revealing a genotype–phenotype relationship. Functional characterization of SDHB missense variants supports clinical classification, informs hPPGL risk stratification, and has immediate diagnostic impact.
Authors
Sooyeon Lee, Leor Needleman, Julie Park, Rebecca C. Schugar, Qianjin Guo, James M. Ford, Justin P. Annes
Abstract
BACKGROUND. Amyotrophic lateral sclerosis (ALS), the major adult-onset motor neuron disease, is preceded by an early period unrelated to motor symptoms, including altered sleep, with increased wakefulness and decreased deep NREM. Whether these alterations in sleep macroarchitecture are associated with, or even precede abnormalities in sleep-related EEG features remains unknown. METHODS. Here, we characterised sleep microarchitecture using polysomnography in patients with ALS (n=33) and controls (n=32), and in asymptomatic carriers of SOD1 or C9ORF72 mutations (n=57) and non-carrier controls (n=30). Patients and controls with factors that could confound sleep structure, including respiratory insufficiency, were prospectively excluded. Results were complemented in three ALS mouse models (Sod1G86R , Fus∆NLS/+ and TDP-43Q331K ). RESULTS. We observed a brain-wide reduction in the density of sleep spindles, slow oscillations and K-complexes in both early-stage ALS patients and presymptomatic gene carriers. These defects in sleep spindles and slow oscillations correlate with cognitive performance in both cohorts, particularly with scores on memory, verbal fluency and language function. Alterations in sleep microarchitecture were replicated in three mouse models and decreases in sleep spindles were rescued following intracerebroventricular supplementation of MCH or by the oral administration of a dual orexin receptor antagonist. CONCLUSION. Sleep microarchitecture is associated with cognitive deficits and is causally linked to aberrant MCH and orexin signalling in ALS. FUNDING. This work was funded by Agence Nationale de la Recherche (ANR-24-CE37-4064, ANR-10-IDEX-0002, ANR-20-SFRI-0012), Fondation Thierry Latran, Association Francaise de Recherche sur la sclérose latérale amyotrophique, Association Française contre les Myopathies (#28944), TargetALS and JPND.
Authors
Christina Lang, Simon J. Guillot, Dorothee Lule, Luisa T. Balz, Antje Knehr, Patrick Weydt, Johannes Dorst, Katharina Kandler, Hans-Peter Müller, Jan Kassubek, Laura Wassermann, Sandrine Da Cruz, Francesco Roselli, Albert C. Ludolph, Matei Bolborea, Luc Dupuis
Abstract
Authors
Vinaya Simha, Mary Kate LoPiccolo, Anna Platt, Rebecca J. Brown, Xandria Johnson, Deanna Alexis Carere, Colleen Donnelly, Matthew T. Snyder, Chao Xing, Thomas P. Mathews, Purva Gopal, Stephen C. Ward, Diana R. Tomchick, Anil K. Agarwal, Ralph J. DeBerardinis, Abhimanyu Garg
Abstract
Solute carrier (SLC) transporters govern the selective transport of diverse molecules across cell membranes, controlling fundamental metabolic and cellular processes. Despite genetic evidence implicating SLC transporters in a variety of human diseases, this family of proteins represents an underexplored target class for therapeutic drug discovery. Here, we discovered a selective potentiator of SLC39A8, a metal transporter associated with inflammatory bowel disease, schizophrenia, and cardiovascular and metabolic disorders. We conducted a drug repurposing screen, identifying efavirenz as a potentiator of manganese and cadmium uptake by SLC39A8 and subsequently generated structure-activity relationships to guide design of analogs. Computational pocket identification methodology and molecular dynamic simulations revealed a ligandable, cryptic pocket that, together with functional mutagenesis, indicated direct target engagement and allosteric modulation. Our findings demonstrate how the combination of experimental data and computational tools represents a powerful synergy that can enhance scientific outcomes. This integrated approach allowed for iterative feedback where insights from experiments informed the model refinements and computational predictions guided future experimental designs. Furthermore, our data established that SLC39A8 transporter activity can be increased pharmacologically, potentially opening avenues for SLC transporter drug discovery.
Authors
Kelly L. Damm-Ganamet, Clara Moon, Alan D. Wickenden, Mark Tichenor, Yunhui Ge, Eduardo V. Mercado-Marin, Brian Chiou, Ayla Manughian-Peter, Taraneh Mirzadegan, Jennifer D. Venable, Ramnik J. Xavier, Jennifer E. Towne, Daniel B. Graham, Jacqueline Perrigoue
Abstract
Ciliary dysfunction results in multi-organ involved developmental diseases, collectively known as ciliopathies. The B9D1-B9D2-MKS1 protein complex maintains the gatekeeper function at the ciliary transition zone (TZ). However, the function of B9 proteins and the mechanisms underlying why different variants in the same B9 gene cause different ciliopathies are not fully understood. Here, we investigated the function of B9 proteins and revealed two critical functions. First, the B9 complex interacted with and anchored TMEM67 to the TZ membrane. Disruption of the B9-TMEM67 complex reduced posttranslational-modifications of axonemal microtubules due to deregulation of tubulin-modifying enzymes within cilia. Second, B9 proteins localized to centrioles prior to ciliogenesis, where they facilitated the initiation of ciliogenesis. Finally, we identified B9D2 variants in a cohort of patients with Joubert syndrome (JBTS). Consistent with the dual functions, we found that the JBTS-associated B9D2 variants primarily affected axonemal microtubule modifications without disrupting ciliogenesis, whereas the Meckel syndrome (MKS)-associated B9D2 variant disrupted both ciliogenesis and axonemal microtubule modifications. Thus, besides its role as a gatekeeper for ciliary membrane proteins, the B9 complex also controls axonemal microtubule post-translational modifications and early stages of ciliogenesis, providing insights into the distinct pathologies arising from different variants of the same gene.
Authors
Ruida He, Yan Li, Minjun Jin, Huike Jiao, Yue Shen, Qize Han, Xilang Pan, Suning Wang, Zaisheng Lin, Jingshi Li, Chao Lu, Dan Meng, Zongfu Cao, Qing Shang, Nan Lv, Kai Wan, Huafang Gao, Xu Ma, Haiyan Yin, Haishuang Chang, Liang Wang, Minna Luo, Junmin Pan, Chengtian Zhao, Muqing Cao
Abstract
Chromosome 8 (chr8) gains are common in cancer, but their contribution to tumor heterogeneity is largely unexplored. Ewing sarcoma (EwS) is defined by FET::ETS fusions with few other recurrent mutations to explain clinical diversity. In EwS, chr8 gains are the second most frequent alteration, making it an ideal model to study their relevance in an otherwise silent genomic context. We report that chr8 gain-driven expression patterns correlate with poor overall survival of EwS patients. This effect is mainly mediated by increased expression of the translation initiation factor binding protein 4E-BP1, encoded by EIF4EBP1 on chr8. Among all chr8-encoded genes, EIF4EBP1 expression showed the strongest association with poor survival and correlated with chr8 gains in EwS tumors. Similar findings emerged across multiple TCGA cancer entities. Multi-omics profiling revealed that 4E-BP1 orchestrates a pro-proliferative proteomic network. Silencing 4E-BP1 reduced proliferation, clonogenicity, spheroidal growth in vitro, and tumor growth in vivo. Drug screens demonstrated that high 4E-BP1 expression sensitizes EwS to pharmacological CDK4/6-inhibition. Chr8 gains and elevated 4E-BP1 emerge as prognostic biomarkers in EwS, with poor outcomes driven by 4E-BP1-mediated pro-proliferative networks that sensitize tumors to CDK4/6 inhibitors. Testing for chr8 gains may enhance risk stratification and therapy in EwS and other cancers.
Authors
Cornelius M. Funk, Anna C. Ehlers, Martin F. Orth, Karim Aljakouch, Jing Li, Tilman L.B. Hoelting, Rainer Will, Florian H. Geyer, A. Katharina Ceranski, Franziska Willis, Endrit Vinca, Shunya Ohmura, Roland Imle, Jana Siebenlist, Angelina Yershova, Maximilian M.L. Knott, Felina Zahnow, Ana Sastre, Javier Alonso, Felix Sahm, Heike Peterziel, Anna Loboda, Martin Schneider, Ana Banito, Gabriel Leprivier, Wolfgang Hartmann, Uta Dirksen, Olaf Witt, Ina Oehme, Stefan M. Pfister, Laura Romero-Pérez, Jeroen Krijgsveld, Florencia Cidre-Aranaz, Thomas G.P. Grünewald, Julian Musa
Abstract
CD24 promotes prostate cancer progression and metastasis by disrupting the ARF-NPM interaction and impairing p53 signaling. However, the mechanisms underlying CD24-driven metastasis remain unclear. This study identifies a novel interaction between CD24 and Regulator of Chromosome Condensation 2 (RCC2), a protein involved in cell proliferation and migration. IHC analysis of prostate adenocarcinoma samples showed frequent coexpression of CD24 (49%) and RCC2 (82%) with a positive correlation between coexpression of CD24 (49%) and RCC2 (82%). Functional assays revealed complex roles: RCC2 KO suppressed proliferation but increased migration and invasion, while CD24 KO reduced both proliferation and migration. Dual KO of CD24 and RCC2 further inhibited proliferation but had varied effects on migration. In mouse xenografts, RCC2 KO increased lung metastasis without significantly affecting primary tumor growth, while CD24 KO reduced both tumor growth and metastasis. Mechanistically, RCC2 controls migration by promoting ubiquitination and degradation of vimentin, affecting cytoskeletal dynamics. In contrast, CD24 targets RCC2 for degradation, thereby regulating β-catenin signaling. Notably, RCC2 KO enhances β-catenin activity by suppressing inhibitors AXIN2 and APC, whereas CD24 KO inhibits this pathway. These findings reveal a regulatory loop where CD24 and RCC2 reciprocally control proliferation and metastasis, positioning the CD24-RCC2 axis as a promising therapeutic target in prostate cancer.
Authors
Xuelian Cui, Yicun Wang, Chao Zhang, Zhichao Liu, Haiyan Yu, Lizhong Wang, Jiangbing Zhou, Runhua Liu
Abstract
Charcot-Marie-Tooth Disease is a clinically and genetically heterogeneous group of hereditary neuropathies. Despite progress in genetic sequencing, around a quarter of patients remain unsolved. Here, we identify 16 recessive variants in the RhoGTPase activating protein 19 gene (ARHGAP19) causing motor-predominant neuropathy in 25 individuals from 20 unrelated families. The ARHGAP19 protein acts as a negative regulator of the RhoA GTPase. In vitro biochemical and cellular assays revealed that patient variants impair the GTPase-activating protein (GAP) activity of ARHGAP19 and reduce ARHGAP19 protein levels. Combined in vitro and in vivo studies reveal that human ARHGAP19, and conserved ARHGAP19 orthologs in Drosophila and Zebrafish, influence motoneuron morphology and promote locomotor capacity. Transcriptomic studies further demonstrate that ARHGAP19 regulates cellular pathways associated with motor proteins and the cell cycle. Taken together, our findings establish ARHGAP19 variants as a cause of inherited neuropathy acting through a loss-of-function mechanism.
Authors
Natalia Dominik, Stephanie Efthymiou, Christopher J. Record, Xinyu Miao, Renee Q. Lin, Jevin M. Parmar, Annarita Scardamaglia, Reza Maroofian, Simon A. Lowe, Gabriel N. Aughey, Abigail D. Wilson, Riccardo Curro, Ricardo P. Schnekenberg, Shahryar Alavi, Leif Leclaire, Yi He, Kristina Zhelcheska, Yohanns Bellaiche, Isabelle Gaugué, Mariola Skorupinska, Liedewei Van de Vondel, Sahar I. Da'as, Valentina Turchetti, Serdal Güngör, Gavin V. Monahan, Ehsan Ghayoor Karimiani, Yalda Jamshidi, Phillipa J. Lamont, Camila Armirola-Ricaurte, Haluk Topaloglu, Albena Jordanova, Mashaya Zaman, Selina H. Banu, Wilson Marques, Pedro J. Tomaselli, Busra Aynekin, Ali Cansu, Huseyin Per, Ayten Güleç, Javeria Raza Alvi, Tipu Sultan, Arif Khan, Giovanni Zifarelli, Shahnaz Ibrahim, Grazia M. S. Mancini, M.M. Motazacker, Esther Brusse, Vincenzo Lupo, Teresa Sevilla, A. Nazli Başak, Seyma Tekgul, Robin J. Palvadeau, Jonathan Baets, Yesim Parman, Arman Çakar, Rita Horvath, Tobias B. Haack, Jan-Hendrik Stahl, Kathrin Grundmann-Hauser, Joohyun Park, Stephan Zuchner, Nigel G. Laing, Lindsay A. Wilson, Alexander M. Rossor, James Polke, Fernanda Barbosa Figueiredo, André Pessoa, Fernando Kok, Antônio Rodrigues Coimbra-Neto, Marcondes C. Franca Jr, Gianina Ravenscroft, Sherifa A. Hamed, Wendy K. Chung, Alan M. Pittman, Daniel P. Osborn, Michael Hanna, Andrea Cortese, Mary M. Reilly, James E.C. Jepson, Nathalie Lamarche-Vane, Henry Houlden
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ISSN: 0021-9738 (print), 1558-8238 (online)