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1. The neocortical infrastructure for language involves region-specific patterns of laminar gene expression.

Author

Wong, Maggie M. K., Zhiqiang Sha, Lütje, Lukas, Xiang-Zhen Kong, van Heukelum, Sabrina, van de Berg, Wilma D. J., Jonkman, Laura E., Fisher, Simon E., and Francks, Clyde

Subjects
TEMPORAL lobe, GENE expression, FRONTAL lobe, TRANSCRIPTOMES, MEDICAL screening, PEOPLE with schizophrenia
Abstract

The language network of the human brain has core components in the inferior frontal cortex and superior/middle temporal cortex, with left-hemisphere dominance in most people. Functional specialization and interconnectivity of these neocortical regions is likely to be reflected in their molecular and cellular profiles. Excitatory connections between cortical regions arise and innervate according to layer-specific patterns. Here, we generated a gene expression dataset from human postmortem cortical tissue samples from core language network regions, using spatial transcriptomics to discriminate gene expression across cortical layers. Integration of these data with existing single-cell expression data identified 56 genes that showed differences in laminar expression profiles between the frontal and temporal language cortex together with upregulation in layer II/III and/or layer V/VI excitatory neurons. Based on data from large-scale genome-wide screening in the population, DNA variants within these 56 genes showed set-level associations with interindividual variation in structural connectivity between the left-hemisphere frontal and temporal language cortex, and with the brain-related disorders dyslexia and schizophrenia which often involve affected language. These findings identify region-specific patterns of laminar gene expression as a feature of the brain's language network. [ABSTRACT FROM AUTHOR]

Published
2024
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3. Missense variants in ANKRD11 cause KBG syndrome by impairment of stability or transcriptional activity of the encoded protein

Author

de Boer, Elke, primary, Ockeloen, Charlotte W., additional, Kampen, Rosalie A., additional, Hampstead, Juliet E., additional, Dingemans, Alexander J.M., additional, Rots, Dmitrijs, additional, Lütje, Lukas, additional, Ashraf, Tazeen, additional, Baker, Rachel, additional, Barat-Houari, Mouna, additional, Angle, Brad, additional, Chatron, Nicolas, additional, Denommé-Pichon, Anne-Sophie, additional, Devinsky, Orrin, additional, Dubourg, Christèle, additional, Elmslie, Frances, additional, Elloumi, Houda Zghal, additional, Faivre, Laurence, additional, Fitzgerald-Butt, Sarah, additional, Geneviève, David, additional, Goos, Jacqueline A.C., additional, Helm, Benjamin M., additional, Kini, Usha, additional, Lasa-Aranzasti, Amaia, additional, Lesca, Gaetan, additional, Lynch, Sally A., additional, Mathijssen, Irene M.J., additional, McGowan, Ruth, additional, Monaghan, Kristin G., additional, Odent, Sylvie, additional, Pfundt, Rolph, additional, Putoux, Audrey, additional, van Reeuwijk, Jeroen, additional, Santen, Gijs W.E., additional, Sasaki, Erina, additional, Sorlin, Arthur, additional, van der Spek, Peter J., additional, Stegmann, Alexander P.A., additional, Swagemakers, Sigrid M.A., additional, Valenzuela, Irene, additional, Viora-Dupont, Eléonore, additional, Vitobello, Antonio, additional, Ware, Stephanie M., additional, Wéber, Mathys, additional, Gilissen, Christian, additional, Low, Karen J., additional, Fisher, Simon E., additional, Vissers, Lisenka E.L.M., additional, Wong, Maggie M.K., additional, and Kleefstra, Tjitske, additional

Published
2023
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5. Missense variants in ANKRD11 cause KBG syndrome by impairment of stability or transcriptional activity of the encoded protein

Author

de Boer, Elke, Ockeloen, Charlotte, Kampen, Rosalie, Hampstead, Juliet, Dingemans, Alexander, Rots, Dmitrijs, Lütje, Lukas, Ashraf, Tazeen, Baker, Rachel, Barat-Houari, Mouna, Angle, Brad, Chatron, Nicolas, Denommé-Pichon, Anne-Sophie, Devinsky, Orrin, Dubourg, Christèle, Elmslie, Frances, Elloumi, Houda Zghal, Faivre, Laurence, Fitzgerald-Butt, Sarah, Geneviève, David, Goos, Jacqueline, Helm, Benjamin, Kini, Usha, Lasa-Aranzasti, Amaia, Lesca, Gaetan, Lynch, Sally, Mathijssen, Irene, Mcgowan, Ruth, Monaghan, Kristin, Odent, Sylvie, Pfundt, Rolph, Putoux, Audrey, van Reeuwijk, Jeroen, Santen, Gijs, Sasaki, Erina, Sorlin, Arthur, van der Spek, Peter, Stegmann, Alexander, Swagemakers, Sigrid, Valenzuela, Irene, Viora-Dupont, Eléonore, Vitobello, Antonio, Ware, Stephanie, Wéber, Mathys, Gilissen, Christian, Low, Karen, Fisher, Simon, Dingemans, Alexander J.M., Goos, Jacqueline A.C., Mathijssen, Irene M.J., Santen, Gijs W.E., Stegmann, Alexander P.A., Swagemakers, Sigrid M.A., Vissers, Lisenka E.L.M., Wong, Maggie M.K., Kleefstra, Tjitske, MUMC+: DA KG Lab Specialisten (9), RS: FHML non-thematic output, Pathology, Plastic and Reconstructive Surgery and Hand Surgery, Radboud University [Nijmegen], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Hospices Civils de Lyon (HCL), Institut NeuroMyoGène (INMG), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), CHU Pontchaillou [Rennes], Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), FHU TRANSLAD (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Cellules Souches, Plasticité Cellulaire, Médecine Régénératrice et Immunothérapies (IRMB), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Max Planck Institute for Psycholinguistics, Max-Planck-Gesellschaft, This work was financially supported by Aspasia grants of the Dutch Research Council (015.014.036 to T.K. and 015.014.066 to L.E.L.M.V.), Netherlands Organization for Health Research and Development (91718310 to T.K.), and the Max Planck Society (M.M.K.W., S.E.F.). Individual 4 was sequenced at the Scottish Genomes Partnership. The Scottish Genomes Partnership was funded by the Chief Scientist Office of the Scottish Government Health Directorates (SGP/1) and the Medical Research Council Whole Genome Sequencing for Health and Wealth Initiative (MC/PC/15080). The Deciphering Developmental Disorders study presents independent research commissioned by the Health Innovation Challenge Fund (grant number HICF-1009-003). This study makes use of Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources (https://www.deciphergenomics.org/), which is funded by Wellcome. See Deciphering Developmental Disorders study8 or https://www.ddduk.org/access.html for full acknowledgment., Institut Català de la Salut, [de Boer E, Dingemans AJM, Rots D] Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands. Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands. [Ockeloen CW] Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands. [Kampen RA] Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands. [Hampstead JE] Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands. Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands. [Lasa-Aranzasti A] Àrea de Genètica Clínica i Molecular, Vall d'Hebron Hospital Universitari, Barcelona, Spain. Grup de Recerca en Medicina Genètica, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain, and Vall d'Hebron Barcelona Hospital Campus

Subjects
Neuroinformatics, Proteasome Endopeptidase Complex, [SDV]Life Sciences [q-bio], fenómenos genéticos::variación genética::mutación::mutación de sentido erróneo [FENÓMENOS Y PROCESOS], Mutation, Missense, Genotype-phenotype study, enfermedades musculoesqueléticas::enfermedades óseas::enfermedades óseas del desarrollo [ENFERMEDADES], Ossos - Malalties - Aspectes genètics, ANKRD11, All institutes and research themes of the Radboud University Medical Center, Missense variants, Intellectual Disability, Other subheadings::Other subheadings::/genetics [Other subheadings], Humans, Genotype–phenotype study, Musculoskeletal Diseases::Bone Diseases::Bone Diseases, Developmental [DISEASES], Abnormalities, Multiple, Genetics (clinical), [SDV.GEN]Life Sciences [q-bio]/Genetics, Bone Diseases, Developmental, Congenital, Hereditary, and Neonatal Diseases and Abnormalities::Congenital Abnormalities::Stomatognathic System Abnormalities::Tooth Abnormalities [DISEASES], Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Otros calificadores::Otros calificadores::/genética [Otros calificadores], Tooth Abnormalities, Neurodevelopmental disorders, Facies, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], KBG syndrome, Repressor Proteins, Anomalies cromosòmiques, Phenotype, enfermedades y anomalías neonatales congénitas y hereditarias::anomalías congénitas::anomalías del sistema estomatognático::anomalías dentarias [ENFERMEDADES], Genetic Phenomena::Genetic Variation::Mutation::Mutation, Missense [PHENOMENA AND PROCESSES], Chromosome Deletion, Dents - Malformacions - Aspectes genètics, Transcription Factors
Abstract

KBG syndrome; Missense variants; Neurodevelopmental disorders Síndrome KBG; Variants de missense; Trastorns del neurodesenvolupament Síndrome KBG; Variantes de missense; Trastornos del neurodesarrollo Purpose Although haploinsufficiency of ANKRD11 is among the most common genetic causes of neurodevelopmental disorders, the role of rare ANKRD11 missense variation remains unclear. We characterized clinical, molecular, and functional spectra of ANKRD11 missense variants. Methods We collected clinical information of individuals with ANKRD11 missense variants and evaluated phenotypic fit to KBG syndrome. We assessed pathogenicity of variants through in silico analyses and cell-based experiments. Results We identified 20 unique, mostly de novo, ANKRD11 missense variants in 29 individuals, presenting with syndromic neurodevelopmental disorders similar to KBG syndrome caused by ANKRD11 protein truncating variants or 16q24.3 microdeletions. Missense variants significantly clustered in repression domain 2 at the ANKRD11 C-terminus. Of the 10 functionally studied missense variants, 6 reduced ANKRD11 stability. One variant caused decreased proteasome degradation and loss of ANKRD11 transcriptional activity. Conclusion Our study indicates that pathogenic heterozygous ANKRD11 missense variants cause the clinically recognizable KBG syndrome. Disrupted transrepression capacity and reduced protein stability each independently lead to ANKRD11 loss-of-function, consistent with haploinsufficiency. This highlights the diagnostic relevance of ANKRD11 missense variants, but also poses diagnostic challenges because the KBG-associated phenotype may be mild and inherited pathogenic ANKRD11 (missense) variants are increasingly observed, warranting stringent variant classification and careful phenotyping.

Published
2022
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7. FriendlyClearMap: an optimized toolkit for mouse brain mapping and analysis.

Author

Negwer, Moritz, Bosch, Bram, Bormann, Maren, Hesen, Rick, Lütje, Lukas, Aarts, Lynn, Rossing, Carleen, Nadif Kasri, Nael, and Schubert, Dirk

Subjects
INTERNEURONS, BRAIN mapping, CELL imaging, MICE, IMAGE analysis, VASOACTIVE intestinal peptide
Abstract

Background Tissue clearing is currently revolutionizing neuroanatomy by enabling organ-level imaging with cellular resolution. However, currently available tools for data analysis require a significant time investment for training and adaptation to each laboratory's use case, which limits productivity. Here, we present FriendlyClearMap, an integrated toolset that makes ClearMap1 and ClearMap2's CellMap pipeline easier to use, extends its functions, and provides Docker Images from which it can be run with minimal time investment. We also provide detailed tutorials for each step of the pipeline. Findings For more precise alignment, we add a landmark-based atlas registration to ClearMap's functions as well as include young mouse reference atlases for developmental studies. We provide an alternative cell segmentation method besides ClearMap's threshold-based approach: Ilastik's Pixel Classification, importing segmentations from commercial image analysis packages and even manual annotations. Finally, we integrate BrainRender, a recently released visualization tool for advanced 3-dimensional visualization of the annotated cells. Conclusions As a proof of principle, we use FriendlyClearMap to quantify the distribution of the 3 main GABAergic interneuron subclasses (parvalbumin+ [PV+], somatostatin+, and vasoactive intestinal peptide+) in the mouse forebrain and midbrain. For PV+ neurons, we provide an additional dataset with adolescent vs. adult PV+ neuron density, showcasing the use for developmental studies. When combined with the analysis pipeline outlined above, our toolkit improves on the state-of-the-art packages by extending their function and making them easier to deploy at scale. [ABSTRACT FROM AUTHOR]

Published
2023
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8. Missense variants in ANKRD11cause KBG syndrome by impairment of stability or transcriptional activity of the encoded protein

Author

de Boer, Elke, Ockeloen, Charlotte W., Kampen, Rosalie A., Hampstead, Juliet E., Dingemans, Alexander J.M., Rots, Dmitrijs, Lütje, Lukas, Ashraf, Tazeen, Baker, Rachel, Barat-Houari, Mouna, Angle, Brad, Chatron, Nicolas, Denommé-Pichon, Anne-Sophie, Devinsky, Orrin, Dubourg, Christèle, Elmslie, Frances, Elloumi, Houda Zghal, Faivre, Laurence, Fitzgerald-Butt, Sarah, Geneviève, David, Goos, Jacqueline A.C., Helm, Benjamin M., Kini, Usha, Lasa-Aranzasti, Amaia, Lesca, Gaetan, Lynch, Sally A., Mathijssen, Irene M.J., McGowan, Ruth, Monaghan, Kristin G., Odent, Sylvie, Pfundt, Rolph, Putoux, Audrey, van Reeuwijk, Jeroen, Santen, Gijs W.E., Sasaki, Erina, Sorlin, Arthur, van der Spek, Peter J., Stegmann, Alexander P.A., Swagemakers, Sigrid M.A., Valenzuela, Irene, Viora-Dupont, Eléonore, Vitobello, Antonio, Ware, Stephanie M., Wéber, Mathys, Gilissen, Christian, Low, Karen J., Fisher, Simon E., Vissers, Lisenka E.L.M., Wong, Maggie M.K., and Kleefstra, Tjitske

Abstract

Although haploinsufficiency of ANKRD11is among the most common genetic causes of neurodevelopmental disorders, the role of rare ANKRD11missense variation remains unclear. We characterized clinical, molecular, and functional spectra of ANKRD11missense variants.

Published
2022
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9. Missense variants in ANKRD11cause KBG syndrome by impairment of stability or transcriptional activity of the encoded protein

Author

de Boer, Elke, Ockeloen, Charlotte W., Kampen, Rosalie A., Hampstead, Juliet E., Dingemans, Alexander J.M., Rots, Dmitrijs, Lütje, Lukas, Ashraf, Tazeen, Baker, Rachel, Barat-Houari, Mouna, Angle, Brad, Chatron, Nicolas, Denommé-Pichon, Anne-Sophie, Devinsky, Orrin, Dubourg, Christèle, Elmslie, Frances, Elloumi, Houda Zghal, Faivre, Laurence, Fitzgerald-Butt, Sarah, Geneviève, David, Goos, Jacqueline A.C., Helm, Benjamin M., Kini, Usha, Lasa-Aranzasti, Amaia, Lesca, Gaetan, Lynch, Sally A., Mathijssen, Irene M.J., McGowan, Ruth, Monaghan, Kristin G., Odent, Sylvie, Pfundt, Rolph, Putoux, Audrey, van Reeuwijk, Jeroen, Santen, Gijs W.E., Sasaki, Erina, Sorlin, Arthur, van der Spek, Peter J., Stegmann, Alexander P.A., Swagemakers, Sigrid M.A., Valenzuela, Irene, Viora-Dupont, Eléonore, Vitobello, Antonio, Ware, Stephanie M., Wéber, Mathys, Gilissen, Christian, Low, Karen J., Fisher, Simon E., Vissers, Lisenka E.L.M., Wong, Maggie M.K., and Kleefstra, Tjitske

Published
2023
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