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Herbst C, Bothe V, Wegler M, Axer-Schaefer S, Audebert-Bellanger S, Gecz J, Cogne B, Feldman HB, Horn AHC, Hurst ACE, Kelly MA, Kruer MC, Kurolap A, Laquerriere A, Li M, Mark PR, Morawski M, Nizon M, Pastinen T, Polster T, Saugier-Veber P, SeSong J, Sticht H, Stieler JT, Thifffault I, van Eyk CL, Marcorelles P, Vezain-Mouchard M, Abou Jamra R, Oppermann H. Heterozygous loss-of-function variants in DOCK4 cause neurodevelopmental delay and microcephaly. Hum Genet 2024; 143:455-469. [PMID: 38526744 PMCID: PMC11043173 DOI: 10.1007/s00439-024-02655-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/09/2024] [Indexed: 03/27/2024]
Abstract
Neurons form the basic anatomical and functional structure of the nervous system, and defects in neuronal differentiation or formation of neurites are associated with various psychiatric and neurodevelopmental disorders. Dynamic changes in the cytoskeleton are essential for this process, which is, inter alia, controlled by the dedicator of cytokinesis 4 (DOCK4) through the activation of RAC1. Here, we clinically describe 7 individuals (6 males and one female) with variants in DOCK4 and overlapping phenotype of mild to severe global developmental delay. Additional symptoms include coordination or gait abnormalities, microcephaly, nonspecific brain malformations, hypotonia and seizures. Four individuals carry missense variants (three of them detected de novo) and three individuals carry null variants (two of them maternally inherited). Molecular modeling of the heterozygous missense variants suggests that the majority of them affect the globular structure of DOCK4. In vitro functional expression studies in transfected Neuro-2A cells showed that all missense variants impaired neurite outgrowth. Furthermore, Dock4 knockout Neuro-2A cells also exhibited defects in promoting neurite outgrowth. Our results, including clinical, molecular and functional data, suggest that loss-of-function variants in DOCK4 probable cause a variable spectrum of a novel neurodevelopmental disorder with microcephaly.
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Affiliation(s)
- Charlotte Herbst
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Viktoria Bothe
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Meret Wegler
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Susanne Axer-Schaefer
- Department of Epileptology, Krankenhaus Mara Bethel Epilepsy Center Medical School OWL, Bielefeld University, Campus Bethel, Bielefeld, Germany
| | | | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Benjamin Cogne
- Service de Génétique Médicale, CHU Nantes, 44000, Nantes, France
- l'institut du Thorax, Nantes Université, CHU Nantes, CNRS, INSERM, 44000, Nantes, France
| | - Hagit Baris Feldman
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anselm H C Horn
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Erlangen National High Performance Computing Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Melissa A Kelly
- HudsonAlpha Clinical Services Lab, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital University of Arizona College of Medicine, Phoenix, USA
| | - Alina Kurolap
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Annie Laquerriere
- Department of Anatomy, Inserm U1245 and CHU Rouen, Univ Rouen Normandie, 76000, Rouen, France
| | - Megan Li
- Invitae Corp, San Francisco, CA, USA
| | - Paul R Mark
- Division of Medical Genetics, Helen DeVos Children's Hospital, Corewell Health, Grand Rapids, MI, USA
| | - Markus Morawski
- Center of Neuropathology and Brain Research, Medical Faculty, Paul Flechsig Institute, University of Leipzig, Leipzig, Germany
| | - Mathilde Nizon
- Service de Génétique Médicale, CHU Nantes, 44000, Nantes, France
- l'institut du Thorax, Nantes Université, CHU Nantes, CNRS, INSERM, 44000, Nantes, France
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, USA
- University of Missouri Kansas City School of Medicine, Kansas City, USA
| | - Tilman Polster
- Department of Epileptology, Krankenhaus Mara Bethel Epilepsy Center Medical School OWL, Bielefeld University, Campus Bethel, Bielefeld, Germany
| | - Pascale Saugier-Veber
- Department of Genetics and Reference Center for Developmental Disorders, Inserm U1245 and CHU Rouen, Univ Rouen Normandie, 76000, Rouen, France
| | - Jang SeSong
- Genomic Medicine Institute, Seoul National University, Seoul, Republic of Korea
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jens T Stieler
- Center of Neuropathology and Brain Research, Medical Faculty, Paul Flechsig Institute, University of Leipzig, Leipzig, Germany
| | - Isabelle Thifffault
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, USA
- University of Missouri Kansas City School of Medicine, Kansas City, USA
| | - Clare L van Eyk
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | | | - Myriam Vezain-Mouchard
- Department of Genetics and Reference Center for Developmental Disorders, Inserm U1245 and CHU Rouen, Univ Rouen Normandie, 76000, Rouen, France
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Henry Oppermann
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany.
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Tsare EPG, Klapa MI, Moschonas NK. Protein-protein interaction network-based integration of GWAS and functional data for blood pressure regulation analysis. Hum Genomics 2024; 18:15. [PMID: 38326862 DOI: 10.1186/s40246-023-00565-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/12/2023] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND It is valuable to analyze the genome-wide association studies (GWAS) data for a complex disease phenotype in the context of the protein-protein interaction (PPI) network, as the related pathophysiology results from the function of interacting polyprotein pathways. The analysis may include the design and curation of a phenotype-specific GWAS meta-database incorporating genotypic and eQTL data linking to PPI and other biological datasets, and the development of systematic workflows for PPI network-based data integration toward protein and pathway prioritization. Here, we pursued this analysis for blood pressure (BP) regulation. METHODS The relational scheme of the implemented in Microsoft SQL Server BP-GWAS meta-database enabled the combined storage of: GWAS data and attributes mined from GWAS Catalog and the literature, Ensembl-defined SNP-transcript associations, and GTEx eQTL data. The BP-protein interactome was reconstructed from the PICKLE PPI meta-database, extending the GWAS-deduced network with the shortest paths connecting all GWAS-proteins into one component. The shortest-path intermediates were considered as BP-related. For protein prioritization, we combined a new integrated GWAS-based scoring scheme with two network-based criteria: one considering the protein role in the reconstructed by shortest-path (RbSP) interactome and one novel promoting the common neighbors of GWAS-prioritized proteins. Prioritized proteins were ranked by the number of satisfied criteria. RESULTS The meta-database includes 6687 variants linked with 1167 BP-associated protein-coding genes. The GWAS-deduced PPI network includes 1065 proteins, with 672 forming a connected component. The RbSP interactome contains 1443 additional, network-deduced proteins and indicated that essentially all BP-GWAS proteins are at most second neighbors. The prioritized BP-protein set was derived from the union of the most BP-significant by any of the GWAS-based or the network-based criteria. It included 335 proteins, with ~ 2/3 deduced from the BP PPI network extension and 126 prioritized by at least two criteria. ESR1 was the only protein satisfying all three criteria, followed in the top-10 by INSR, PTN11, CDK6, CSK, NOS3, SH2B3, ATP2B1, FES and FINC, satisfying two. Pathway analysis of the RbSP interactome revealed numerous bioprocesses, which are indeed functionally supported as BP-associated, extending our understanding about BP regulation. CONCLUSIONS The implemented workflow could be used for other multifactorial diseases.
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Affiliation(s)
- Evridiki-Pandora G Tsare
- Department of General Biology, School of Medicine, University of Patras, Patras, Greece
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Patras, Greece
| | - Maria I Klapa
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Patras, Greece.
| | - Nicholas K Moschonas
- Department of General Biology, School of Medicine, University of Patras, Patras, Greece.
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Patras, Greece.
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Yap P, Riley LG, Kakadia PM, Bohlander SK, Curran B, Rahimi MJ, Alburaiky S, Hayes I, Oppermann H, Print C, Cooper ST, Le Quesne Stabej P. Biallelic ATP2B1 variants as a likely cause of a novel neurodevelopmental malformation syndrome with primary hypoparathyroidism. Eur J Hum Genet 2024; 32:125-129. [PMID: 37926713 PMCID: PMC10772071 DOI: 10.1038/s41431-023-01484-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/22/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Abstract
ATP2B1 encodes plasma membrane calcium-transporting-ATPase1 and plays an essential role in maintaining intracellular calcium homeostasis that regulates diverse signaling pathways. Heterozygous de novo missense and truncating ATP2B1 variants are associated with a neurodevelopmental phenotype of variable expressivity. We describe a proband with distinctive craniofacial gestalt, Pierre-Robin sequence, neurodevelopmental and growth deficit, periventricular heterotopia, brachymesophalangy, cutaneous syndactyly, and persistent hypocalcemia from primary hypoparathyroidism. Proband-parent trio exome sequencing identified compound heterozygous ATP2B1 variants: a maternally inherited splice-site (c.3060+2 T > G) and paternally inherited missense c.2938 G > T; p.(Val980Leu). Reverse-transcription-PCR on the proband's fibroblast-derived mRNA showed aberrantly spliced ATP2B1 transcripts targeted for nonsense-mediated decay. All correctly-spliced ATP2B1 mRNA encoding p.(Val980Leu) functionally causes decreased cellular Ca2+ extrusion. Immunoblotting showed reduced fibroblast ATP2B1. We conclude that biallelic ATP2B1 variants are the likely cause of the proband's phenotype, strengthening the association of ATP2B1 as a neurodevelopmental gene and expanding the phenotypic characterization of a biallelic loss-of-function genotype.
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Affiliation(s)
- Patrick Yap
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand.
- Genetic Health Service New Zealand - Northern hub, Auckland, New Zealand.
| | - Lisa G Riley
- Rare Diseases Functional Genomics, Kids Research, The Children's Hospital at Westmead and The Children's Medical Research Institute, Sydney, NSW, 2145, Australia
- Specialty of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Purvi M Kakadia
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Stefan K Bohlander
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Ben Curran
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Meer Jacob Rahimi
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, 04103, Germany
| | - Salam Alburaiky
- Genetic Health Service New Zealand - Northern hub, Auckland, New Zealand
| | - Ian Hayes
- Genetic Health Service New Zealand - Northern hub, Auckland, New Zealand
| | - Henry Oppermann
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, 04103, Germany
| | - Cristin Print
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Sandra T Cooper
- Specialty of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Sydney, NSW, 2145, Australia
- The Children's Medical Research Institute, 214 Hawkesbury Road, Westmead, NSW, 2145, Australia
| | - Polona Le Quesne Stabej
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
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Brechtmann F, Bechtler T, Londhe S, Mertes C, Gagneur J. Evaluation of input data modality choices on functional gene embeddings. NAR Genom Bioinform 2023; 5:lqad095. [PMID: 37942285 PMCID: PMC10629286 DOI: 10.1093/nargab/lqad095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/07/2023] [Accepted: 09/28/2023] [Indexed: 11/10/2023] Open
Abstract
Functional gene embeddings, numerical vectors capturing gene function, provide a promising way to integrate functional gene information into machine learning models. These embeddings are learnt by applying self-supervised machine-learning algorithms on various data types including quantitative omics measurements, protein-protein interaction networks and literature. However, downstream evaluations comparing alternative data modalities used to construct functional gene embeddings have been lacking. Here we benchmarked functional gene embeddings obtained from various data modalities for predicting disease-gene lists, cancer drivers, phenotype-gene associations and scores from genome-wide association studies. Off-the-shelf predictors trained on precomputed embeddings matched or outperformed dedicated state-of-the-art predictors, demonstrating their high utility. Embeddings based on literature and protein-protein interactions inferred from low-throughput experiments outperformed embeddings derived from genome-wide experimental data (transcriptomics, deletion screens and protein sequence) when predicting curated gene lists. In contrast, they did not perform better when predicting genome-wide association signals and were biased towards highly-studied genes. These results indicate that embeddings derived from literature and low-throughput experiments appear favourable in many existing benchmarks because they are biased towards well-studied genes and should therefore be considered with caution. Altogether, our study and precomputed embeddings will facilitate the development of machine-learning models in genetics and related fields.
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Affiliation(s)
- Felix Brechtmann
- TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - Thibault Bechtler
- TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Shubhankar Londhe
- TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | - Christian Mertes
- TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Munich Data Science Institute, Technical University of Munich, Garching, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Julien Gagneur
- TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
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5
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Poggio E, Barazzuol L, Salmaso A, Milani C, Deligiannopoulou A, Cazorla ÁG, Jang SS, Juliá-Palacios N, Keren B, Kopajtich R, Lynch SA, Mignot C, Moorwood C, Neuhofer C, Nigro V, Oostra A, Prokisch H, Saillour V, Schuermans N, Torella A, Verloo P, Yazbeck E, Zollino M, Jech R, Winkelmann J, Necpal J, Calì T, Brini M, Zech M. ATP2B2 de novo variants as a cause of variable neurodevelopmental disorders that feature dystonia, ataxia, intellectual disability, behavioral symptoms, and seizures. Genet Med 2023; 25:100971. [PMID: 37675773 DOI: 10.1016/j.gim.2023.100971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/08/2023] Open
Abstract
PURPOSE ATP2B2 encodes the variant-constrained plasma-membrane calcium-transporting ATPase-2, expressed in sensory ear cells and specialized neurons. ATP2B2/Atp2b2 variants were previously linked to isolated hearing loss in patients and neurodevelopmental deficits with ataxia in mice. We aimed to establish the association between ATP2B2 and human neurological disorders. METHODS Multinational case recruitment, scrutiny of trio-based genomics data, in silico analyses, and functional variant characterization were performed. RESULTS We assembled 7 individuals harboring rare, predicted deleterious heterozygous ATP2B2 variants. The alleles comprised 5 missense substitutions that affected evolutionarily conserved sites and 2 frameshift variants in the penultimate exon. For 6 variants, a de novo status was confirmed. Unlike described patients with hearing loss, the individuals displayed a spectrum of neurological abnormalities, ranging from ataxia with dystonic features to complex neurodevelopmental manifestations with intellectual disability, autism, and seizures. Two cases with recurrent amino-acid variation showed distinctive overlap with cerebellar atrophy-associated ataxia and epilepsy. In cell-based studies, all variants caused significant alterations in cytosolic calcium handling with both loss- and gain-of-function effects. CONCLUSION Presentations in our series recapitulate key phenotypic aspects of Atp2b2-mouse models and underline the importance of precise calcium regulation for neurodevelopment and cerebellar function. Our study documents a role for ATP2B2 variants in causing heterogeneous neurodevelopmental and movement-disorder syndromes.
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Affiliation(s)
- Elena Poggio
- Department of Biology, University of Padua, Padua, Italy
| | - Lucia Barazzuol
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Andrea Salmaso
- Department of Biology, University of Padua, Padua, Italy
| | - Celeste Milani
- Department of Biology, University of Padua, Padua, Italy
| | | | - Ángeles García Cazorla
- European Reference Network for Hereditary Metabolic Diseases (MetabERN), Madrid, Spain; Neurometabolic Unit and Synaptic Metabolism Laboratory, Neurology Department Sant Joan de Déu Hospital, IPR, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Se Song Jang
- Seoul National University (SNU) College of Medicine, Seoul, South Korea
| | - Natalia Juliá-Palacios
- Neurology Department, Neurometabolic Unit, Institut de Recerca, CIBERER and MetabERN, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Boris Keren
- APHP.Sorbonne Université, Department of Medical Genetics, Pitié-Salpêtrière University Hospital, and Centre de Référence Maladies Rares Déficiences Intellectuelles de Causes Rares, Paris, France
| | - Robert Kopajtich
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Sally Ann Lynch
- Department of Clinical Genetics, Temple Street Children's University Hospital, Dublin, Ireland
| | - Cyril Mignot
- APHP.Sorbonne Université, Department of Medical Genetics, Pitié-Salpêtrière University Hospital, and Centre de Référence Maladies Rares Déficiences Intellectuelles de Causes Rares, Paris, France
| | - Catherine Moorwood
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | - Christiane Neuhofer
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania, Luigi Vanvitelli, Napoli, Italy
| | - Anna Oostra
- Department of Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Virginie Saillour
- Laboratoire de biologie médicale multisites Seqoia - FMG2025, Paris, France
| | - Nika Schuermans
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University Hospital, Ghent, Belgium
| | - Annalaura Torella
- Department of Precision Medicine, University of Campania, Luigi Vanvitelli, Napoli, Italy
| | - Patrick Verloo
- Department of Pediatric Neurology, Center for Inherited Metabolic Disorders and metabERN, University Hospital Ghent, Ghent, Belgium
| | - Elise Yazbeck
- Pediatric Neurology Department, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Paris Saclay, Bicêtre Hospital, Le Kremlin Bicêtre, France
| | - Marcella Zollino
- Unit of Medical Genetics, Section of Genomic Medicine, Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Robert Jech
- Department of Neurology, Charles University in Prague, 1st Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany; Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Jan Necpal
- 2nd Department of Neurology, Faculty of Medicine, Comenius University, Bratislava, Slovakia; Department of Neurology, Zvolen Hospital, Zvolen, Slovakia
| | - Tito Calì
- Department of Biomedical Sciences, University of Padua, Padua, Italy; Centro Studi per la Neurodegenerazione (CESNE), University of Padua, Padua, Italy; Neuroscience Center (PNC), University of Padua, Padua, Italy
| | - Marisa Brini
- Department of Biology, University of Padua, Padua, Italy; Centro Studi per la Neurodegenerazione (CESNE), University of Padua, Padua, Italy
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany; Institute for Advanced Study, Technical University of Munich, Garching, Germany.
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6
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Kou M, Li X, Shao X, Grundberg E, Wang X, Ma H, Heianza Y, Martinez JA, Bray GA, Sacks FM, Qi L. DNA Methylation of Birthweight-Blood Pressure Genes and Changes of Blood Pressure in Response to Weight-Loss Diets in the POUNDS Lost Trial. Hypertension 2023; 80:1223-1230. [PMID: 37039021 PMCID: PMC10192077 DOI: 10.1161/hypertensionaha.123.20864] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/26/2023] [Indexed: 04/12/2023]
Abstract
BACKGROUND DNA methylation (DNAm) may play a critical role in bridging prenatal adverse events and cardiometabolic disorders including hypertension in later life. METHODS We included 672 adult participants with overweight or obesity, who participated in a 2-year randomized weight-loss dietary intervention study. We defined the regional DNAm levels as the average methylation level of 5'-cytosine-phosphate-guanine-3' within 500 bp of LINC00319 (cg01820192), ATP2B1 (cg00508575), and LMNA (cg12593793), respectively. Generalized linear regression models were used to assess the association between the regional DNAm and 2-year blood pressure changes. Trajectory analysis was used to identify subgroups that shared a similar underlying trajectory of 2-year blood pressure changes. RESULTS The regional DNAm at LINC00319, showed significantly different associations with 2-year changes in systolic blood pressure and diastolic blood pressure among participants assigned to low- or high-fat diets (P for interaction<0.05 for all). In response to the low-fat diet, per SD higher regional DNAm at LINC00319 was associated with greater reductions in both 2-year changes in systolic blood pressure (β, -1.481; P=0.020) and diastolic blood pressure (β, -1.096; P=0.009). Three trajectories of changes in systolic blood pressure or diastolic blood pressure were identified, and participants with higher regional DNAm at LINC00319 were more likely to experience and maintain decreased systolic blood pressure and diastolic blood pressure (odds ratio of being in decrease-stable versus stable [95% CI], 1.542 [1.146-2.076] and 1.463 [1.125-1.902]). CONCLUSIONS Our findings suggest that DNAm could be a metabolic memory bridging early and later life, and an indicator of more benefits from eating a low-fat weight-loss diet.
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Affiliation(s)
- Minghao Kou
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Xiang Li
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Elin Grundberg
- Department of Pediatrics, Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO, United States
| | - Xuan Wang
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Hao Ma
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - Yoriko Heianza
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
| | - J. Alfredo Martinez
- Madrid Institute of Advance Studies (IMDEA), Research Institute on Food & Health Sciences, Precision Nutrition Program, Madrid, Spain
| | - George A. Bray
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA, United States
| | - Frank M. Sacks
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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7
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Gharbi T, Liu C, Khan H, Zhang Z, Yang GY, Tang Y. Hypoxic Preconditioned Neural Stem Cell-Derived Extracellular Vesicles Contain Distinct Protein Cargo from Their Normal Counterparts. Curr Issues Mol Biol 2023; 45:1982-1997. [PMID: 36975497 PMCID: PMC10047917 DOI: 10.3390/cimb45030127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Hypoxic preconditioning has been demonstrated to increase the resistance of neural stem cells (NSCs) to hypoxic conditions, as well as to improve their capacity for differentiation and neurogenesis. Extracellular vesicles (EVs) have recently emerged as critical mediators of cell–cell communication, but their role in this hypoxic conditioning is presently unknown. Here, we demonstrated that three hours of hypoxic preconditioning triggers significant neural stem cell EV release. Proteomic profiling of EVs from normal and hypoxic preconditioned neural stem cells identified 20 proteins that were upregulated and 22 proteins that were downregulated after hypoxic preconditioning. We also found an upregulation of some of these proteins by qPCR, thus indicating differences also at the transcript level within the EVs. Among the upregulated proteins are CNP, Cyfip1, CASK, and TUBB5, which are well known to exhibit significant beneficial effects on neural stem cells. Thus, our results not only show a significant difference of protein cargo in EVs consequent to hypoxic exposure, but identify several candidate proteins that might play a pivotal role in the cell-to-cell mediated communication underlying neuronal differentiation, protection, maturation, and survival following exposure to hypoxic conditions.
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Calcium signaling and genetic rare diseases: An auditory perspective. Cell Calcium 2023; 110:102702. [PMID: 36791536 DOI: 10.1016/j.ceca.2023.102702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/07/2023]
Abstract
Deafness is a highly heterogeneous disorder which stems, for 50%, from genetic origins. Sensory transduction relies mainly on sensory hair cells of the cochlea, in the inner ear. Calcium is key for the function of these cells and acts as a fundamental signal transduction. Its homeostasis depends on three factors: the calcium influx, through the mechanotransduction channel at the apical pole of the hair cell as well as the voltage-gated calcium channel at the base of the cells; the calcium buffering via Ca2+-binding proteins in the cytoplasm, but also in organelles such as mitochondria and the reticulum endoplasmic mitochondria-associated membranes with specialized proteins; and the calcium extrusion through the Ca-ATPase pump, located all over the plasma membrane. In addition, the synaptic transmission to the central nervous system is also controlled by calcium. Genetic studies of inherited deafness have tremendously helped understand the underlying molecular pathways of calcium signaling. In this review, we discuss these different factors in light of the associated genetic diseases (syndromic and non-syndromic deafness) and the causative genes.
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Beckmann D, Langnaese K, Gottfried A, Hradsky J, Tedford K, Tiwari N, Thomas U, Fischer KD, Korthals M. Ca 2+ Homeostasis by Plasma Membrane Ca 2+ ATPase (PMCA) 1 Is Essential for the Development of DP Thymocytes. Int J Mol Sci 2023; 24:ijms24021442. [PMID: 36674959 PMCID: PMC9865543 DOI: 10.3390/ijms24021442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/13/2023] Open
Abstract
The strength of Ca2+ signaling is a hallmark of T cell activation, yet the role of Ca2+ homeostasis in developing T cells before expressing a mature T cell receptor is poorly understood. We aimed to unveil specific functions of the two plasma membrane Ca2+ ATPases expressed in T cells, PMCA1 and PMCA4. On a transcriptional and protein level we found that PMCA4 was expressed at low levels in CD4-CD8- double negative (DN) thymocytes and was even downregulated in subsequent stages while PMCA1 was present throughout development and upregulated in CD4+CD8+ double positive (DP) thymocytes. Mice with a targeted deletion of Pmca1 in DN3 thymocytes had an almost complete block of DP thymocyte development with an accumulation of DN4 thymocytes but severely reduced numbers of CD8+ immature single positive (ISP) thymocytes. The DN4 thymocytes of these mice showed strongly elevated basal cytosolic Ca2+ levels and a pre-mature CD5 expression, but in contrast to the DP thymocytes they were only mildly prone to apoptosis. Surprisingly, mice with a germline deletion of Pmca4 did not show any signs of altered progression through the developmental thymocyte stages, nor altered Ca2+ homeostasis throughout this process. PMCA1 is, therefore, non-redundant in keeping cellular Ca2+ levels low in the early thymocyte development required for the DN to DP transition.
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Affiliation(s)
- David Beckmann
- Institute for Biochemistry and Cell Biology, Medical Faculty, Otto-von-Guericke-University Magdeburg, 39120 Magdeburg, Germany
| | - Kristina Langnaese
- Institute for Biochemistry and Cell Biology, Medical Faculty, Otto-von-Guericke-University Magdeburg, 39120 Magdeburg, Germany
| | - Anna Gottfried
- Institute for Biochemistry and Cell Biology, Medical Faculty, Otto-von-Guericke-University Magdeburg, 39120 Magdeburg, Germany
| | - Johannes Hradsky
- Institute for Biochemistry and Cell Biology, Medical Faculty, Otto-von-Guericke-University Magdeburg, 39120 Magdeburg, Germany
| | - Kerry Tedford
- Institute for Biochemistry and Cell Biology, Medical Faculty, Otto-von-Guericke-University Magdeburg, 39120 Magdeburg, Germany
| | - Nikhil Tiwari
- Department of Cellular Neuroscience, Leibniz Institute for Neurobiology, 39120 Magdeburg, Germany
| | - Ulrich Thomas
- Department of Cellular Neuroscience, Leibniz Institute for Neurobiology, 39120 Magdeburg, Germany
| | - Klaus-Dieter Fischer
- Institute for Biochemistry and Cell Biology, Medical Faculty, Otto-von-Guericke-University Magdeburg, 39120 Magdeburg, Germany
- Correspondence:
| | - Mark Korthals
- Institute for Biochemistry and Cell Biology, Medical Faculty, Otto-von-Guericke-University Magdeburg, 39120 Magdeburg, Germany
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The ataxia-linked E1081Q mutation affects the sub-plasma membrane Ca 2+-microdomains by tuning PMCA3 activity. Cell Death Dis 2022; 13:855. [PMID: 36207321 PMCID: PMC9546857 DOI: 10.1038/s41419-022-05300-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 01/23/2023]
Abstract
Calcium concentration must be finely tuned in all eukaryotic cells to ensure the correct performance of its signalling function. Neuronal activity is exquisitely dependent on the control of Ca2+ homeostasis: its alterations ultimately play a pivotal role in the origin and progression of many neurodegenerative processes. A complex toolkit of Ca2+ pumps and exchangers maintains the fluctuation of cytosolic Ca2+ concentration within the appropriate threshold. Two ubiquitous (isoforms 1 and 4) and two neuronally enriched (isoforms 2 and 3) of the plasma membrane Ca2+ATPase (PMCA pump) selectively regulate cytosolic Ca2+ transients by shaping the sub-plasma membrane (PM) microdomains. In humans, genetic mutations in ATP2B1, ATP2B2 and ATP2B3 gene have been linked with hearing loss, cerebellar ataxia and global neurodevelopmental delay: all of them were found to impair pump activity. Here we report three additional mutations in ATP2B3 gene corresponding to E1081Q, R1133Q and R696H amino acids substitution, respectively. Among them, the novel missense mutation (E1081Q) immediately upstream the C-terminal calmodulin-binding domain (CaM-BD) of the PMCA3 protein was present in two patients originating from two distinct families. Our biochemical and molecular studies on PMCA3 E1081Q mutant have revealed a splicing variant-dependent effect of the mutation in shaping the sub-PM [Ca2+]. The E1081Q substitution in the full-length b variant abolished the capacity of the pump to reduce [Ca2+] in the sub-PM microdomain (in line with the previously described ataxia-related PMCA mutations negatively affecting Ca2+ pumping activity), while, surprisingly, its introduction in the truncated a variant selectively increased Ca2+ extrusion activity in the sub-PM Ca2+ microdomains. These results highlight the importance to set a precise threshold of [Ca2+] by fine-tuning the sub-PM microdomains and the different contribution of the PMCA splice variants in this regulation.
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