1
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Shah OS, Nasrazadani A, Foldi J, Atkinson JM, Kleer CG, McAuliffe PF, Johnston TJ, Stallaert W, da Silva EM, Selenica P, Dopeso H, Pareja F, Mandelker D, Weigelt B, Reis-Filho JS, Bhargava R, Lucas PC, Lee AV, Oesterreich S. Spatial molecular profiling of mixed invasive ductal and lobular breast cancers reveals heterogeneity in intrinsic molecular subtypes, oncogenic signatures, and mutations. Proc Natl Acad Sci U S A 2024; 121:e2322068121. [PMID: 39042692 PMCID: PMC11295029 DOI: 10.1073/pnas.2322068121] [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: 12/28/2023] [Accepted: 06/13/2024] [Indexed: 07/25/2024] Open
Abstract
Mixed invasive ductal and lobular carcinoma (MDLC) is a rare histologic subtype of breast cancer displaying both E-cadherin positive ductal and E-cadherin negative lobular morphologies within the same tumor, posing challenges with regard to anticipated clinical management. It remains unclear whether these distinct morphologies also have distinct biology and risk of recurrence. Our spatially resolved transcriptomic, genomic, and single-cell profiling revealed clinically significant differences between ductal and lobular tumor regions including distinct intrinsic subtype heterogeneity - e.g., MDLC with triple-negative breast cancer (TNBC) or basal ductal and estrogen receptor positive (ER+) luminal lobular regions, distinct enrichment of cell cycle arrest/senescence and oncogenic (ER and MYC) signatures, genetic and epigenetic CDH1 inactivation in lobular but not ductal regions, and single-cell ductal and lobular subpopulations with unique oncogenic signatures further highlighting intraregional heterogeneity. Altogether, we demonstrated that the intratumoral morphological/histological heterogeneity within MDLC is underpinned by intrinsic subtype and oncogenic heterogeneity which may result in prognostic uncertainty and therapeutic dilemma.
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MESH Headings
- Humans
- Female
- Carcinoma, Lobular/genetics
- Carcinoma, Lobular/pathology
- Carcinoma, Lobular/metabolism
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Ductal, Breast/metabolism
- Mutation
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Breast Neoplasms/metabolism
- Breast Neoplasms/classification
- Cadherins/genetics
- Cadherins/metabolism
- Gene Expression Regulation, Neoplastic
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Triple Negative Breast Neoplasms/genetics
- Triple Negative Breast Neoplasms/pathology
- Triple Negative Breast Neoplasms/metabolism
- Transcriptome
- Gene Expression Profiling/methods
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Affiliation(s)
- Osama Shiraz Shah
- Womens Cancer Research Center at University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center and Magee Women’s Research Institute, Pittsburgh, PA15213
- Integrative Systems Biology Program, University of Pittsburgh School of Medicine, PittsburghPA15260
| | - Azadeh Nasrazadani
- Womens Cancer Research Center at University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center and Magee Women’s Research Institute, Pittsburgh, PA15213
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Julia Foldi
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA15260
| | - Jennifer M. Atkinson
- Womens Cancer Research Center at University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center and Magee Women’s Research Institute, Pittsburgh, PA15213
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA15260
| | - Celina G. Kleer
- Department of Pathology and Rogel Cancer Center, University of Michigan, Ann Arbor, MI48109
| | - Priscilla F. McAuliffe
- Womens Cancer Research Center at University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center and Magee Women’s Research Institute, Pittsburgh, PA15213
- Division of Surgical Oncology, Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA15232
| | - Tyler J. Johnston
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Wayne Stallaert
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Edaise M. da Silva
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Higinio Dopeso
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Jorge S. Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Rohit Bhargava
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
| | - Peter C. Lucas
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine and Science, Rochester, MN55902
| | - Adrian V. Lee
- Womens Cancer Research Center at University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center and Magee Women’s Research Institute, Pittsburgh, PA15213
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA15260
| | - Steffi Oesterreich
- Womens Cancer Research Center at University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center and Magee Women’s Research Institute, Pittsburgh, PA15213
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA15260
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2
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Früh S, Boudkkazi S, Koppensteiner P, Sereikaite V, Chen LY, Fernandez-Fernandez D, Rem PD, Ulrich D, Schwenk J, Chen Z, Le Monnier E, Fritzius T, Innocenti SM, Besseyrias V, Trovò L, Stawarski M, Argilli E, Sherr EH, van Bon B, Kamsteeg EJ, Iascone M, Pilotta A, Cutrì MR, Azamian MS, Hernández-García A, Lalani SR, Rosenfeld JA, Zhao X, Vogel TP, Ona H, Scott DA, Scheiffele P, Strømgaard K, Tafti M, Gassmann M, Fakler B, Shigemoto R, Bettler B. Monoallelic de novo AJAP1 loss-of-function variants disrupt trans-synaptic control of neurotransmitter release. SCIENCE ADVANCES 2024; 10:eadk5462. [PMID: 38985877 PMCID: PMC11235169 DOI: 10.1126/sciadv.adk5462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
Adherens junction-associated protein 1 (AJAP1) has been implicated in brain diseases; however, a pathogenic mechanism has not been identified. AJAP1 is widely expressed in neurons and binds to γ-aminobutyric acid type B receptors (GBRs), which inhibit neurotransmitter release at most synapses in the brain. Here, we show that AJAP1 is selectively expressed in dendrites and trans-synaptically recruits GBRs to presynaptic sites of neurons expressing AJAP1. We have identified several monoallelic AJAP1 variants in individuals with epilepsy and/or neurodevelopmental disorders. Specifically, we show that the variant p.(W183C) lacks binding to GBRs, resulting in the inability to recruit them. Ultrastructural analysis revealed significantly decreased presynaptic GBR levels in Ajap1-/- and Ajap1W183C/+ mice. Consequently, these mice exhibited reduced GBR-mediated presynaptic inhibition at excitatory and inhibitory synapses, along with impaired synaptic plasticity. Our study reveals that AJAP1 enables the postsynaptic neuron to regulate the level of presynaptic GBR-mediated inhibition, supporting the clinical relevance of loss-of-function AJAP1 variants.
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Affiliation(s)
- Simon Früh
- Department of Biomedicine, Pharmazentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Sami Boudkkazi
- Institute of Physiology II, University of Freiburg, Hermann-Herderstrasse 7, 79104 Freiburg, Germany
| | - Peter Koppensteiner
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Vita Sereikaite
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Li-Yuan Chen
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Rue du Bugnon 7, 1005 Lausanne, Switzerland
| | - Diego Fernandez-Fernandez
- Department of Biomedicine, Pharmazentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Pascal D. Rem
- Department of Biomedicine, Pharmazentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Daniel Ulrich
- Department of Biomedicine, Pharmazentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Jochen Schwenk
- Institute of Physiology II, University of Freiburg, Hermann-Herderstrasse 7, 79104 Freiburg, Germany
| | - Ziyang Chen
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Elodie Le Monnier
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Thorsten Fritzius
- Department of Biomedicine, Pharmazentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | | | - Valérie Besseyrias
- Department of Biomedicine, Pharmazentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Luca Trovò
- Department of Biomedicine, Pharmazentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Michal Stawarski
- Department of Biomedicine, Pharmazentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Emanuela Argilli
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Elliott H. Sherr
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Institute of Human Genetics and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bregje van Bon
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6525, Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6525, Netherlands
| | - Maria Iascone
- Laboratorio Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | | | | | - Mahshid S. Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrés Hernández-García
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor Genetics, Houston, TX 77021, USA
| | - Tiphanie P. Vogel
- Division of Rheumatology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Human Immunobiology, Texas Children's Hospital, Houston, TX 77030, USA
| | - Herda Ona
- Division of Rheumatology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Human Immunobiology, Texas Children's Hospital, Houston, TX 77030, USA
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter Scheiffele
- Biocenter, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Mehdi Tafti
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Rue du Bugnon 7, 1005 Lausanne, Switzerland
| | - Martin Gassmann
- Department of Biomedicine, Pharmazentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Bernd Fakler
- Institute of Physiology II, University of Freiburg, Hermann-Herderstrasse 7, 79104 Freiburg, Germany
| | - Ryuichi Shigemoto
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Bernhard Bettler
- Department of Biomedicine, Pharmazentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
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3
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Falsaperla R, Sortino V, Schinocca MA, Fusto G, Rizzo R, Barberi C, Ruggieri M, Pappalardo XG. PURA-Related Neurodevelopmental Disorders with Epilepsy Treated with Ketogenic Diet: A Case-Based Review. Genes (Basel) 2024; 15:848. [PMID: 39062627 PMCID: PMC11276249 DOI: 10.3390/genes15070848] [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: 06/10/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
PURA syndrome is a congenital developmental disorder caused by de novo mutations in the PURA gene, which encodes a DNA/RNA-binding protein essential for transcriptional and translational regulation. We present the case of an 11-year-old patient with a de novo frameshift variant in the PURA gene, identified through whole exome sequencing (WES). In addition to the classical PURA deficiency phenotype, our patient exhibited pronounced sialorrhea and seizures, which were effectively treated with the ketogenic diet (KD). Our integrative approach, combining a literature review and bioinformatics data, has led to the first documented clinical case showing improvement in both sialorrhea and seizures with KD treatment, a phenomenon not previously reported. Although a direct relationship between the de novo PURA mutation and the KD was not established, we identified a novel frameshift deletion associated with a new clinical phenotype.
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Affiliation(s)
- Raffaele Falsaperla
- Neonatal Intensive Care Unit and Neonatal Accompaniment Unit, Azienda Ospedaliero-Universitaria Policlinico “Rodolico-San Marco”, San Marco Hospital, University of Catania, 95123 Catania, Italy
- Unit of Pediatrics and Pediatric Emergency, Azienda Ospedaliero-Universitaria Policlinico “Rodolico-San Marco”, San Marco Hospital, 95123 Catania, Italy;
- Department of Medical Science-Pediatrics, University of Ferrara, 44124 Ferrara, Italy
| | - Vincenzo Sortino
- Unit of Pediatrics and Pediatric Emergency, Azienda Ospedaliero-Universitaria Policlinico “Rodolico-San Marco”, San Marco Hospital, 95123 Catania, Italy;
| | - Marina Antonietta Schinocca
- Postgraduate Training Program in Pediatrics, Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy;
| | - Gaia Fusto
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95123 Catania, Italy; (G.F.); (R.R.); (X.G.P.)
| | - Roberta Rizzo
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95123 Catania, Italy; (G.F.); (R.R.); (X.G.P.)
| | - Chiara Barberi
- Postgraduate Training Program in Pediatrics, University of Palermo, 90133 Palermo, Italy;
| | - Martino Ruggieri
- Unit of Clinical Pediatrics and Unit of Rare disease AOU “Policlinico”, PO “G. Rodolico”, University of Catania, 95123 Catania, Italy;
| | - Xena Giada Pappalardo
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95123 Catania, Italy; (G.F.); (R.R.); (X.G.P.)
- National Council of Research, Institute for Research and Biomedical Innovation (IRIB), Unit of Catania, 95123 Catania, Italy
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4
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D'Incal CP, Cappuyns E, Choukri K, De Man K, Szrama K, Konings A, Bastini L, Van Meel K, Buys A, Gabriele M, Rizzuti L, Vitriolo A, Testa G, Mohn F, Bühler M, Van der Aa N, Van Dijck A, Kooy RF, Berghe WV. Tracing the invisible mutant ADNP protein in Helsmoortel-Van der Aa syndrome patients. Sci Rep 2024; 14:14710. [PMID: 38926592 PMCID: PMC11208605 DOI: 10.1038/s41598-024-65608-x] [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: 12/08/2023] [Accepted: 06/21/2024] [Indexed: 06/28/2024] Open
Abstract
Heterozygous de novo mutations in the Activity-Dependent Neuroprotective Homeobox (ADNP) gene underlie Helsmoortel-Van der Aa syndrome (HVDAS). Most of these mutations are situated in the last exon and we previously demonstrated escape from nonsense-mediated decay by detecting mutant ADNP mRNA in patient blood. In this study, wild-type and ADNP mutants are investigated at the protein level and therefore optimal detection of the protein is required. Detection of ADNP by means of western blotting has been ambiguous with reported antibodies resulting in non-specific bands without unique ADNP signal. Validation of an N-terminal ADNP antibody (Aviva Systems) using a blocking peptide competition assay allowed to differentiate between specific and non-specific signals in different sample materials, resulting in a unique band signal around 150 kDa for ADNP, above its theoretical molecular weight of 124 kDa. Detection with different C-terminal antibodies confirmed the signals at an observed molecular weight of 150 kDa. Our antibody panel was subsequently tested by immunoblotting, comparing parental and homozygous CRISPR/Cas9 endonuclease-mediated Adnp knockout cell lines and showed disappearance of the 150 kDa signal, indicative for intact ADNP. By means of both a GFPSpark and Flag-tag N-terminally fused to a human ADNP expression vector, we detected wild-type ADNP together with mutant forms after introduction of patient mutations in E. coli expression systems by site-directed mutagenesis. Furthermore, we were also able to visualize endogenous ADNP with our C-terminal antibody panel in heterozygous cell lines carrying ADNP patient mutations, while the truncated ADNP mutants could only be detected with epitope-tag-specific antibodies, suggesting that addition of an epitope-tag possibly helps stabilizing the protein. However, western blotting of patient-derived hiPSCs, immortalized lymphoblastoid cell lines and post-mortem patient brain material failed to detect a native mutant ADNP protein. In addition, an N-terminal immunoprecipitation-competent ADNP antibody enriched truncating mutants in overexpression lysates, whereas implementation of the same method failed to enrich a possible native mutant protein in immortalized patient-derived lymphoblastoid cell lines. This study aims to shape awareness for critical assessment of mutant ADNP protein analysis in Helsmoortel-Van der Aa syndrome.
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Affiliation(s)
- Claudio Peter D'Incal
- Cognitive Genetics (COGNET) and Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - Elisa Cappuyns
- Cognitive Genetics (COGNET) and Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Kaoutar Choukri
- Cognitive Genetics (COGNET) and Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Kevin De Man
- Cognitive Genetics (COGNET) and Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Kristy Szrama
- Cognitive Genetics (COGNET) and Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Anthony Konings
- Cognitive Genetics (COGNET) and Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Lina Bastini
- Cognitive Genetics (COGNET) and Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Kim Van Meel
- Cognitive Genetics (COGNET) and Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Amber Buys
- Cognitive Genetics (COGNET) and Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Ludovico Rizzuti
- Neurogenomics, Human Technopole, Viale Rita Levi-Montacini 1, 20157, Milan, Italy
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141, Milan, Italy
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Alessandro Vitriolo
- Neurogenomics, Human Technopole, Viale Rita Levi-Montacini 1, 20157, Milan, Italy
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122, Milan, Italy
| | - Giuseppe Testa
- Neurogenomics, Human Technopole, Viale Rita Levi-Montacini 1, 20157, Milan, Italy
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122, Milan, Italy
| | - Fabio Mohn
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Nathalie Van der Aa
- Cognitive Genetics (COGNET) and Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Anke Van Dijck
- Family Medicine and Population Health (FAMPOP), Department of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - R Frank Kooy
- Cognitive Genetics (COGNET) and Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Wim Vanden Berghe
- Cognitive Genetics (COGNET) and Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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5
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Sue SH, Liu ST, Huang SM. Factors affecting the expression and stability of full-length and truncated SRSF3 proteins in human cancer cells. Sci Rep 2024; 14:14397. [PMID: 38909100 PMCID: PMC11193772 DOI: 10.1038/s41598-024-64640-1] [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: 03/04/2024] [Accepted: 06/11/2024] [Indexed: 06/24/2024] Open
Abstract
Alternative splicing plays a crucial role in increasing the diversity of mRNAs expressed in the genome. Serine/arginine-rich splicing factor 3 (SRSF3) is responsible for regulating the alternative splicing of its own mRNA and ensuring that its expression is balanced to maintain homeostasis. Moreover, the exon skipping of SRSF3 leads to the production of a truncated protein instead of a frameshift mutation that generates a premature termination codon (PTC). However, the precise regulatory mechanism involved in the splicing of SRSF3 remains unclear. In this study, we first established a platform for coexpressing full-length SRSF3 (SRSF3-FL) and SRSF3-PTC and further identified a specific antibody against the SRSF3-FL and truncated SRSF3 (SRSF3-TR) proteins. Next, we found that exogenously overexpressing SRSF3-FL or SRSF3-PTC failed to reverse the effects of digoxin, caffeine, or both in combination on this molecule and its targets. Endoplasmic reticulum-related pathways, transcription factors, and chemicals such as palmitic acid and phosphate were found to be involved in the regulation of SRSF3 expression. The downregulation of SRSF3-FL by palmitic acid and phosphate was mediated via different regulatory mechanisms in HeLa cells. In summary, we provide new insights into the altered expression of the SRSF3-FL and SRSF3-TR proteins for the identification of the functions of SRSF3 in cells.
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Affiliation(s)
- Sung-How Sue
- Department of Cardiovascular Surgery, Chung Shan Medical University Hospital, Chung Shan Medical University, Taichung City, 402, Taiwan, Republic of China
- Institute of Medicine, Chung Shan Medical University, Taichung City, 402, Taiwan, Republic of China
| | - Shu-Ting Liu
- Department of Biochemistry, National Defense Medical Center, Taipei City, 114, Taiwan, Republic of China
| | - Shih-Ming Huang
- Department of Biochemistry, National Defense Medical Center, Taipei City, 114, Taiwan, Republic of China.
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6
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Shafique A, Nadeem A, Aslam F, Manzoor H, Noman M, Wohler E, Witmer PD, Sobreira N, Naz S. Identification and analyses of exonic and copy number variants in spastic paraplegia. Sci Rep 2024; 14:14331. [PMID: 38906889 PMCID: PMC11192879 DOI: 10.1038/s41598-024-64922-8] [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: 03/25/2024] [Accepted: 06/14/2024] [Indexed: 06/23/2024] Open
Abstract
Hereditary spastic paraplegias are a diverse group of degenerative disorders that are clinically categorized as isolated; with involvement of lower limb spasticity, or symptomatic, where spastic paraplegia is complicated by further neurological features. We sought to identify the underlying genetic causes of these disorders in the participating patients. Three consanguineous families with multiple affected members were identified by visiting special schools in the Punjab Province. DNA was extracted from blood samples of the participants. Exome sequencing was performed for selected patients from the three families, and the data were filtered to identify rare homozygous variants. ExomeDepth was used for the delineation of the copy number variants. All patients had varying degrees of intellectual disabilities, poor speech development, spasticity, a wide-based gait or an inability to walk and hypertonia. In family RDHR07, a homozygous deletion involving multiple exons and introns of SPG11 (NC000015.9:g.44894055_449028del) was found and correlated with the phenotype of the patients who had spasticity and other complex movement disorders, but not those who exhibited ataxic or indeterminate symptoms as well. In families ANMD03 and RDFA06, a nonsense variant, c.985C > T;(p.Arg329Ter) in DDHD2 and a frameshift insertion‒deletion variant of AP4B1, c.965-967delACTinsC;p.(Tyr322SerfsTer14), were identified which were homozygous in the patients while the obligate carriers in the respective pedigrees were heterozygous. All variants were ultra-rare with none, or very few carriers identified in the public databases. The three loss of function variants are likely to cause nonsense-mediated decay of the respective transcripts. Our research adds to the genetic variability associated with the SPG11 and AP4B1 variants and emphasizes the genetic heterogeneity of hereditary spastic paraplegia.
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Affiliation(s)
- Anum Shafique
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Ayesha Nadeem
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Faiza Aslam
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Humera Manzoor
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Muhammad Noman
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
- Department of Biochemistry, Faisalabad Medical University, Faisalabad, Pakistan
| | - Elizabeth Wohler
- McKusick-Nathans Department of Genetic Medicine, Baylor Hopkins Center for Mendelian Genomics, Baltimore, MD, USA
| | - P Dane Witmer
- McKusick-Nathans Department of Genetic Medicine, Baylor Hopkins Center for Mendelian Genomics, Baltimore, MD, USA
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Baylor Hopkins Center for Mendelian Genomics, Baltimore, MD, USA
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan.
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7
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Shah OS, Nasrazadani A, Foldi J, Atkinson JM, Kleer CG, McAuliffe PF, Johnston TJ, Stallaert W, da Silva EM, Selenica P, Dopeso H, Pareja F, Mandelker D, Weigelt B, Reis-Filho JS, Bhargava R, Lucas PC, Lee AV, Oesterreich S. Spatial molecular profiling of mixed invasive ductal-lobular breast cancers reveals heterogeneity in intrinsic molecular subtypes, oncogenic signatures, and mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.09.557013. [PMID: 38915645 PMCID: PMC11195088 DOI: 10.1101/2023.09.09.557013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Mixed invasive ductal and lobular carcinoma (MDLC) is a rare histologic subtype of breast cancer displaying both E-cadherin positive ductal and E-cadherin negative lobular morphologies within the same tumor, posing challenges with regard to anticipated clinical management. It remains unclear whether these distinct morphologies also have distinct biology and risk of recurrence. Our spatially-resolved transcriptomic, genomic, and single-cell profiling revealed clinically significant differences between ductal and lobular tumor regions including distinct intrinsic subtype heterogeneity (e.g., MDLC with TNBC/basal ductal and ER+/luminal lobular regions), distinct enrichment of senescence/dormancy and oncogenic (ER and MYC) signatures, genetic and epigenetic CDH1 inactivation in lobular, but not ductal regions, and single-cell ductal and lobular sub-populations with unique oncogenic signatures further highlighting intra-regional heterogeneity. Altogether, we demonstrated that the intra-tumoral morphological/histological heterogeneity within MDLC is underpinned by intrinsic subtype and oncogenic heterogeneity which may result in prognostic uncertainty and therapeutic dilemma. Significance MDLC displays both ductal and lobular tumor regions. Our multi-omic profiling approach revealed that these morphologically distinct tumor regions harbor distinct intrinsic subtypes and oncogenic features that may cause prognostic uncertainty and therapeutic dilemma. Thus histopathological/molecular profiling of individual tumor regions may guide clinical decision making and benefit patients with MDLC, particularly in the advanced setting where there is increased reliance on next generation sequencing.
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Batt MC, Venzor LG, Gardner K, Reith RR, Roberts KA, Herrera NJ, Fuller AM, Sullivan GA, Mulliniks JT, Spangler ML, Valberg SJ, Steffen DJ, Petersen JL. An autosomal recessive variant in PYGM causes myophosphorylase deficiency in Red Angus composite cattle. BMC Genomics 2024; 25:417. [PMID: 38678201 PMCID: PMC11055281 DOI: 10.1186/s12864-024-10330-1] [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: 12/18/2023] [Accepted: 04/19/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Between 2020 and 2022, eight calves in a Nebraska herd (composite Simmental, Red Angus, Gelbvieh) displayed exercise intolerance during forced activity. In some cases, the calves collapsed and did not recover. Available sire pedigrees contained a paternal ancestor within 2-4 generations in all affected calves. Pedigrees of the calves' dams were unavailable, however, the cows were ranch-raised and retained from prior breeding seasons, where bulls used for breeding occasionally had a common ancestor. Therefore, it was hypothesized that a de novo autosomal recessive variant was causative of exercise intolerance in these calves. RESULTS A genome-wide association analysis utilizing SNP data from 6 affected calves and 715 herd mates, followed by whole-genome sequencing of 2 affected calves led to the identification of a variant in the gene PYGM (BTA29:g.42989581G > A). The variant, confirmed to be present in the skeletal muscle transcriptome, was predicted to produce a premature stop codon (p.Arg650*). The protein product of PYGM, myophosphorylase, breaks down glycogen in skeletal muscle. Glycogen concentrations were fluorometrically assayed as glucose residues demonstrating significantly elevated glycogen concentrations in affected calves compared to cattle carrying the variant and to wild-type controls. The absence of the PYGM protein product in skeletal muscle was confirmed by immunohistochemistry and label-free quantitative proteomics analysis; muscle degeneration was confirmed in biopsy and necropsy samples. Elevated skeletal muscle glycogen persisted after harvest, resulting in a high pH and dark-cutting beef, which is negatively perceived by consumers and results in an economic loss to the industry. Carriers of the variant did not exhibit differences in meat quality or any measures of animal well-being. CONCLUSIONS Myophosphorylase deficiency poses welfare concerns for affected animals and negatively impacts the final product. The association of the recessive genotype with dark-cutting beef further demonstrates the importance of genetics to not only animal health but to the quality of their product. Although cattle heterozygous for the variant may not immediately affect the beef industry, identifying carriers will enable selection and breeding strategies to prevent the production of affected calves.
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Affiliation(s)
- Mackenzie C Batt
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Leila G Venzor
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Keri Gardner
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Rachel R Reith
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Kelsey A Roberts
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Nicolas J Herrera
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Anna M Fuller
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Gary A Sullivan
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - J Travis Mulliniks
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Matthew L Spangler
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Stephanie J Valberg
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - David J Steffen
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA.
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Pan L, Wang Y, Lin H, Zhang X, Zhang R. A Novel Frameshift Mutation( HBA2:C.337delC) Associated With α-Thalassemia Trait Detected by Next-Generation Sequencing in Southern China. Hemoglobin 2024:1-3. [PMID: 38653553 DOI: 10.1080/03630269.2024.2344786] [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: 11/26/2023] [Accepted: 04/14/2024] [Indexed: 04/25/2024]
Abstract
Here, we report a novel frameshift mutation caused by a single base deletion in exon 3 of the HBA2 gene (HBA2:c.337delC) detected by next-generation sequencing. The proband was a 26-year-old Chinese pregnant woman who originates from Hunan Province. Her mean corpuscular volume(MCV) and mean corpuscular hemoglobin (MCH) had a mild decrease. Capillary electrophoresis (CE) showed that both Hb A (97.8%) and Hb F (0.0%) values were within normal range, while the Hb A2 (2.2%) value was below normal. Sequence analysis of the α and β-globin genes revealed a novel single base deletion at codon 112 (HBA2:c.337delC) in the heterozygous state, which resulted in a mild phenotype of α-thalassemia.
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Affiliation(s)
| | - Yan Wang
- Department of Medical Genetics and Prenatal Diagnosis, Baoan Women's and Children's Hospital, Shenzhen, China
| | - Haiying Lin
- Department of Medical Genetics and Prenatal Diagnosis, Baoan Women's and Children's Hospital, Shenzhen, China
| | - Xiufa Zhang
- Department of Medical Genetics and Prenatal Diagnosis, Baoan Women's and Children's Hospital, Shenzhen, China
| | - Rui Zhang
- Department of Medical Genetics and Prenatal Diagnosis, Baoan Women's and Children's Hospital, Shenzhen, China
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Tebieva IS, Mishakova PV, Gabisova YV, Khokhova AV, Kaloeva TG, Marakhonov AV, Shchagina OA, Polyakov AV, Ginter EK, Kutsev SI, Zinchenko RA. Genetic Landscape and Clinical Features of Hyperphenylalaninemia in North Ossetia-Alania: High Frequency of P281L and P211T Genetic Variants in the PAH Gene. Int J Mol Sci 2024; 25:4598. [PMID: 38731816 PMCID: PMC11083185 DOI: 10.3390/ijms25094598] [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: 03/03/2024] [Revised: 03/30/2024] [Accepted: 04/05/2024] [Indexed: 05/13/2024] Open
Abstract
This study, conducted in the Republic of North Ossetia-Alania (RNOA), aimed to explore the genetic landscape of hyperphenylalaninemia (HPA) and phenylketonuria (PKU) in the Ossetian population using data from newborn screening (NBS). Through comprehensive molecular genetic analysis of 29 patients with HPA from diverse ethnic backgrounds, two major genetic variants in the PAH gene, P281L and P211T, were identified, constituting 50% of all detected pathogenic alleles in Ossetian patients. Remarkably, these variants exhibited an exceptionally high frequency in the Ossetian population, surpassing global prevalence rates. This study unveiled a notable prevalence of mild forms of HPA (78%), underscoring the importance of genetic counseling for carriers of pathogenic variants in the PAH gene. Moreover, the findings emphasized the necessity for ongoing monitoring of patients with mild forms, as they may lack significant symptoms for diagnosis, potentially impacting offspring. Overall, this research offers valuable insights into the genetic landscape of HPA and PKU in the Ossetian population.
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Affiliation(s)
- Inna S. Tebieva
- North-Ossetian State Medical Academy, 362003 Vladikavkaz, Russia; (I.S.T.); (T.G.K.)
- Republican Children’s Clinical Hospital, 362003 Vladikavkaz, Russia; (Y.V.G.); (A.V.K.)
| | - Polina V. Mishakova
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (P.V.M.); (A.V.M.); (O.A.S.); (A.V.P.); (E.K.G.); (S.I.K.)
| | - Yulia V. Gabisova
- Republican Children’s Clinical Hospital, 362003 Vladikavkaz, Russia; (Y.V.G.); (A.V.K.)
| | - Alana V. Khokhova
- Republican Children’s Clinical Hospital, 362003 Vladikavkaz, Russia; (Y.V.G.); (A.V.K.)
| | - Tamara G. Kaloeva
- North-Ossetian State Medical Academy, 362003 Vladikavkaz, Russia; (I.S.T.); (T.G.K.)
| | - Andrey V. Marakhonov
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (P.V.M.); (A.V.M.); (O.A.S.); (A.V.P.); (E.K.G.); (S.I.K.)
| | - Olga A. Shchagina
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (P.V.M.); (A.V.M.); (O.A.S.); (A.V.P.); (E.K.G.); (S.I.K.)
| | - Alexander V. Polyakov
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (P.V.M.); (A.V.M.); (O.A.S.); (A.V.P.); (E.K.G.); (S.I.K.)
| | - Evgeny K. Ginter
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (P.V.M.); (A.V.M.); (O.A.S.); (A.V.P.); (E.K.G.); (S.I.K.)
| | - Sergey I. Kutsev
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (P.V.M.); (A.V.M.); (O.A.S.); (A.V.P.); (E.K.G.); (S.I.K.)
| | - Rena A. Zinchenko
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (P.V.M.); (A.V.M.); (O.A.S.); (A.V.P.); (E.K.G.); (S.I.K.)
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11
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Chen Y, Qin L, Jin Y, Xie H, Yang L, Wang M, Xie Y. Clinical and genetic characterization of a protein S deficient patient with multiple thrombotic events. Int J Lab Hematol 2024; 46:415-418. [PMID: 38238031 DOI: 10.1111/ijlh.14228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 01/05/2024] [Indexed: 03/20/2024]
Affiliation(s)
- Yuan Chen
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Langyi Qin
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Yanhui Jin
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Haixiao Xie
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Lihong Yang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Mingshan Wang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Yaosheng Xie
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
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Machida R, Ogawa T, Min Soe K, Moriyama K. Nonsense-mediated mRNA decay affects hyperactive root formation in oculo-facio-cardio-dental syndrome via up-frameshift protein 1. J Oral Biosci 2024; 66:225-231. [PMID: 38244688 DOI: 10.1016/j.job.2024.01.008] [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: 09/11/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/22/2024]
Abstract
OBJECTIVES Oculo-facio-cardio-dental (OFCD) syndrome is a rare X-linked genetic disorder caused by mutations in the BCL6 co-repressor (BCOR) and is mainly characterized by radiculomegaly (elongated dental roots). All BCOR mutations reported to date have been associated with premature termination codons, indicating that nonsense-mediated mRNA decay (NMD) might play a vital role in the pathogenesis of OFCD syndrome. However, the molecular mechanisms underlying NMD remain unclear. In this study, we investigated the involvement of up-frameshift protein 1 (UPF1), which plays a central role in NMD, in the hyperactive root formation caused by BCOR mutations. METHODS Periodontal ligament cells, isolated from a Japanese woman with a c.3668delC frameshift mutation in BCOR, and primary human periodontal ligament fibroblasts (HPdLFs) were used for an RNA immunoprecipitation assay to confirm the binding of UPF1 to mutated BCOR. Additionally, the effects of UPF1 on the BCOR transcription levels and corresponding gene expression were determined by performing relative quantitative real-time polymerase chain reactions. RESULTS RNA immunoprecipitation revealed that UPF1 binds to exon 9 of mutated BCOR. Additionally, UPF1 knockdown via siRNA upregulated the transcription of BCOR, whereas overexpression of wild-type and mutated BCOR with the same frameshift mutation in HPdLFs altered bone morphogenetic protein 2 (BMP2) expression. CONCLUSIONS Our findings indicate that BCOR mutations regulate the transcription of BCOR via UPF1, which may in turn regulate the expression of BMP2. NMD, caused by a c.3668delC mutation, potentially leads to an OFCD syndrome phenotype, including elongated dental roots.
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Affiliation(s)
- Ryoto Machida
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
| | - Takuya Ogawa
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
| | - Kyaw Min Soe
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
| | - Keiji Moriyama
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
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13
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Zheng Y, Chen S. Transcriptional precision in photoreceptor development and diseases - Lessons from 25 years of CRX research. Front Cell Neurosci 2024; 18:1347436. [PMID: 38414750 PMCID: PMC10896975 DOI: 10.3389/fncel.2024.1347436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
The vertebrate retina is made up of six specialized neuronal cell types and one glia that are generated from a common retinal progenitor. The development of these distinct cell types is programmed by transcription factors that regulate the expression of specific genes essential for cell fate specification and differentiation. Because of the complex nature of transcriptional regulation, understanding transcription factor functions in development and disease is challenging. Research on the Cone-rod homeobox transcription factor CRX provides an excellent model to address these challenges. In this review, we reflect on 25 years of mammalian CRX research and discuss recent progress in elucidating the distinct pathogenic mechanisms of four CRX coding variant classes. We highlight how in vitro biochemical studies of CRX protein functions facilitate understanding CRX regulatory principles in animal models. We conclude with a brief discussion of the emerging systems biology approaches that could accelerate precision medicine for CRX-linked diseases and beyond.
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Affiliation(s)
- Yiqiao Zheng
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
| | - Shiming Chen
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
- Department of Developmental Biology, Washington University in St. Louis, Saint Louis, MO, United States
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Fan Y, Zheng C, Ma R, Wang J, Yang S, Ye Q. MMP19 Variants in Familial and Sporadic Idiopathic Pulmonary Fibrosis. Lung 2023; 201:571-580. [PMID: 37971547 DOI: 10.1007/s00408-023-00652-4] [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: 08/17/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Gene variants have been identified in patients with familial or sporadic idiopathic pulmonary fibrosis (IPF). These variants may partially account for the genetic risk of IPF. The aim of this study was to identify potential genes involved in both familial and sporadic IPF. METHODS A Han family in northern China with four members diagnosed with IPF was investigated in this observational study. Whole-exome sequencing (WES) was used to identify germline variants underlying disease phenotypes in five members of this family. Candidate rare variants were validated by Sanger sequencing in samples from 16 family members and 119 patients with sporadic IPF. The plasma levels of proteins encoded by the above candidate genes were also examined in 16 family members, 119 other patients with sporadic IPF and 120 age- and sex-matched healthy controls. RESULTS In a Chinese Han family, MMP19 c.1222 C > T was identified in all familial IPF patients and six offspring from generations III and IV. This variant introduces a premature stop codon, which may damage protein function. Sanger sequencing revealed that 7.6% (9/119) of sporadic IPF patients harbored three MMP19 variants. The genetic risk analysis for pulmonary fibrosis showed that MMP19 c.1499 C > T and c.1316G > A were significantly associated with an increased risk of IPF (OR 3.66, p = 0.028 and OR 8.64, p < 0.001, respectively). The plasma levels of MMP19 were significantly higher in patients with sporadic or familial IPF than in healthy controls (all p < 0.001). CONCLUSIONS MMP19 variants were identified in familial or sporadic IPF, thus providing a potential new clue into IPF pathogenesis.
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Affiliation(s)
- Yali Fan
- Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, No.8 Worker's Stadium, Chaoyang District, Beijing, 100020, China
- Department of Respiratory Medicine and Critical Care, Beijing Jishuitan Hospital, Beijing, 100035, China
| | - Chunming Zheng
- Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, No.8 Worker's Stadium, Chaoyang District, Beijing, 100020, China
- Department of Medical Research Center, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, China
| | - Ruimin Ma
- Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, No.8 Worker's Stadium, Chaoyang District, Beijing, 100020, China
| | - Jingwei Wang
- Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, No.8 Worker's Stadium, Chaoyang District, Beijing, 100020, China
| | - Shuqiao Yang
- Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, No.8 Worker's Stadium, Chaoyang District, Beijing, 100020, China
- Department of Respiratory and Critical Care Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, China
| | - Qiao Ye
- Clinical Center for Interstitial Lung Diseases, Beijing Institute of Respiratory Medicine, Beijing Chaoyang Hospital, Capital Medical University, No.8 Worker's Stadium, Chaoyang District, Beijing, 100020, China.
- Department of Occupational Medicine and Toxicology, Beijing Chaoyang Hospital, Capital Medical University, No.8 Worker's Stadium, Chaoyang District, Beijing, 100020, China.
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Li Z, Cheng W, Zi F, Wang J, Huang X, Sheng X, Rong W. Four different gene-related cone-rod dystrophy: clinical and genetic findings in six Chinese families with diverse modes of inheritance. Front Genet 2023; 14:1157156. [PMID: 38028590 PMCID: PMC10652761 DOI: 10.3389/fgene.2023.1157156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose: To investigate pathogenic variants in six families with cone-rod dystrophy (CORD) presenting various inheritance patterns by using whole-exome sequencing (WES) and analyzing phenotypic features. Methods: A total of six families with CORD were enrolled in Ningxia Eye Hospital for this study. The probands and their family members received comprehensive ophthalmic examinations, and DNA was abstracted from patients and family members. Whole-exome sequencing was performed on probands to screen the causative variants, and all suspected pathogenic variants were determined via Sanger sequencing. Furthermore, co-segregation analysis was performed on available family members. The pathogenicity of novel variants was predicted using in silico analysis and evaluated according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Results: Of the six families, two families were assigned as X-linked recessive (XL), two families were assigned as autosomal recessive (AR), and two families were assigned as autosomal dominant (AD). Pathogenic variants were detected in CACNA1F in two X-linked recessive probands, among which family 1 had a hemizygous frameshift variant c.2201del (p.Val734Glyfs*17) and family 2 had a hemizygous missense variant c.245G>A (p.Arg82Gln). Both probands had high myopia, with fundus tessellation accompanied by abnormalities in the outer structure of the macular area. The homozygous splice variant c.2373 + 5G>T in PROM1 and the homozygous nonsense variant c.604C>T (p.Arg202Ter) in ADAM9 were detected in two autosomal recessive families of the probands. Both probands showed different degrees of atrophy in the macular area, and the lesions showed hypofluorescence changes in autofluorescence. The heterozygous variation in CRX c.682C>T (p.Gln228Ter) was detected in two autosomal dominant families. The onset age of the two probands was late, with better vision and severe macular atrophy. According to ACMG guidelines and the analysis of online in silico tools, all variations were labeled as potentially harmful or pathogenic. Conclusion: Pathogenic variants in CACNA1F, PROM1, ADAM9, and CRX genes were identified in six families affected by the diverse inheritance patterns of CORD. Furthermore, the potential impact of the nonsense-mediated decay (NMD) mechanism on the manifestation of CORD phenotypes was examined and addressed. Simultaneously, the spectrum of pathogenic variants and clinical phenotypes associated with the CORD gene was extended.
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Affiliation(s)
- Zhen Li
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Wanyu Cheng
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Feiyin Zi
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Juan Wang
- Department of Ophthalmology, Qingdao West Coast New District Central Hospital, Qingdao, China
| | - Xiaoyu Huang
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | | | - Weining Rong
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
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Ahmed R, Saba AA, Paul A, Nur J, Alam MS, Chakraborty S, Howlader MZH, Islam LN, Nabi AHMN. Intronic Variants of the Angiotensin-Converting Enzyme 2 Gene Modulate Plasma ACE2 Levels and Possibly Confer Protection against Severe COVID-19. BIOMED RESEARCH INTERNATIONAL 2023; 2023:5705076. [PMID: 37929242 PMCID: PMC10622595 DOI: 10.1155/2023/5705076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/24/2023] [Accepted: 10/07/2023] [Indexed: 11/07/2023]
Abstract
Membrane-bound angiotensin-converting enzyme 2 (ACE2) receptor acts as the entry point for the novel coronavirus, SARS-CoV-2. Polymorphisms in the ACE2 gene may alter viral binding, regulate the expression of ACE2, and thus, affect disease severity. In this study, 68 COVID-19 patients with varying degrees of severity and 40 healthy controls were enrolled. The genetic landscape of the ACE2 gene was explored by whole exome sequencing of 29 individuals, and specific regions of ACE2 were analyzed for the rest of the participants via PCR, followed by barcode-tagged sequencing. The mean soluble ACE2 level in the plasma of healthy controls and patients did not vary significantly but was higher in the patient group (3.77 ± 1.55 ng/mL vs. 3.94 ± 1.42 ng/mL). Analysis of exon 1, exon 2, and exon 8 of the ACE2 gene revealed that these regions are highly conserved in our population. Investigation of exon 11 and its flanking intronic region revealed that deletions in a stretch of 18T nucleotides in the noncoding region significantly decrease ACE2 levels in plasma, as individuals harboring wild-type variants had higher plasma ACE2 levels compared to those harboring T1del, T2del, and T3del variants. However, the intronic variants were not found to be significantly associated with disease severity.
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Affiliation(s)
- Rubaiat Ahmed
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Abdullah Al Saba
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Anik Paul
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Jasmin Nur
- Department of Immunology, Bangladesh Institute of Research and Rehabilitation in Diabetes, Endocrine and Metabolic Disorders, Shahbag, Dhaka, Bangladesh
| | - Md Sohrab Alam
- Department of Immunology, Bangladesh Institute of Research and Rehabilitation in Diabetes, Endocrine and Metabolic Disorders, Shahbag, Dhaka, Bangladesh
| | - Sajib Chakraborty
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Md. Zakir Hossain Howlader
- Laboratory of Nutrition and Health Research, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Laila N. Islam
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - A. H. M. Nurun Nabi
- Laboratory of Population Genetics, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
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Pantaleo A, Forte G, Cariola F, Valentini AM, Fasano C, Sanese P, Grossi V, Buonadonna AL, De Marco K, Lepore Signorile M, Guglielmi AF, Manghisi A, Gigante G, Armentano R, Disciglio V, Simone C. Tumor Testing and Genetic Analysis to Identify Lynch Syndrome Patients in an Italian Colorectal Cancer Cohort. Cancers (Basel) 2023; 15:5061. [PMID: 37894428 PMCID: PMC10605602 DOI: 10.3390/cancers15205061] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Lynch syndrome (LS) is an inherited cancer susceptibility syndrome caused by germline mutations in a DNA mismatch repair (MMR) gene or in the EPCAM gene. LS is associated with an increased lifetime risk of colorectal cancer (CRC) and other malignancies. The screening algorithm for LS patient selection is based on the identification of CRC specimens that have MMR loss/high microsatellite instability (MSI-H) and are wild-type for BRAFV600. Here, we sought to clinically and molecularly characterize patients with these features. From 2017 to 2023, 841 CRC patients were evaluated for MSI and BRAFV600E mutation status, 100 of which showed MSI-H. Of these, 70 were wild-type for BRAFV600. Among these 70 patients, 30 were genetically tested for germline variants in hereditary cancer predisposition syndrome genes. This analysis showed that 19 of these 30 patients (63.3%) harbored a germline pathogenic or likely pathogenic variant in MMR genes, 2 (6.7%) harbored a variant of unknown significance (VUS) in MMR genes, 3 (10%) harbored a VUS in other cancer-related genes, and 6 (20%) were negative to genetic testing. These findings highlight the importance of personalized medicine for tailored genetic counseling, management, and surveillance of families with LS and other hereditary cancer syndromes.
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Affiliation(s)
- Antonino Pantaleo
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.P.); (G.F.); (F.C.); (C.F.); (P.S.); (V.G.); (A.L.B.); (K.D.M.); (M.L.S.); (A.F.G.); (A.M.)
| | - Giovanna Forte
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.P.); (G.F.); (F.C.); (C.F.); (P.S.); (V.G.); (A.L.B.); (K.D.M.); (M.L.S.); (A.F.G.); (A.M.)
| | - Filomena Cariola
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.P.); (G.F.); (F.C.); (C.F.); (P.S.); (V.G.); (A.L.B.); (K.D.M.); (M.L.S.); (A.F.G.); (A.M.)
| | - Anna Maria Valentini
- Department of Pathology, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.M.V.); (R.A.)
| | - Candida Fasano
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.P.); (G.F.); (F.C.); (C.F.); (P.S.); (V.G.); (A.L.B.); (K.D.M.); (M.L.S.); (A.F.G.); (A.M.)
| | - Paola Sanese
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.P.); (G.F.); (F.C.); (C.F.); (P.S.); (V.G.); (A.L.B.); (K.D.M.); (M.L.S.); (A.F.G.); (A.M.)
| | - Valentina Grossi
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.P.); (G.F.); (F.C.); (C.F.); (P.S.); (V.G.); (A.L.B.); (K.D.M.); (M.L.S.); (A.F.G.); (A.M.)
| | - Antonia Lucia Buonadonna
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.P.); (G.F.); (F.C.); (C.F.); (P.S.); (V.G.); (A.L.B.); (K.D.M.); (M.L.S.); (A.F.G.); (A.M.)
| | - Katia De Marco
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.P.); (G.F.); (F.C.); (C.F.); (P.S.); (V.G.); (A.L.B.); (K.D.M.); (M.L.S.); (A.F.G.); (A.M.)
| | - Martina Lepore Signorile
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.P.); (G.F.); (F.C.); (C.F.); (P.S.); (V.G.); (A.L.B.); (K.D.M.); (M.L.S.); (A.F.G.); (A.M.)
| | - Anna Filomena Guglielmi
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.P.); (G.F.); (F.C.); (C.F.); (P.S.); (V.G.); (A.L.B.); (K.D.M.); (M.L.S.); (A.F.G.); (A.M.)
| | - Andrea Manghisi
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.P.); (G.F.); (F.C.); (C.F.); (P.S.); (V.G.); (A.L.B.); (K.D.M.); (M.L.S.); (A.F.G.); (A.M.)
| | - Gianluigi Gigante
- Department of General Surgery, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy;
| | - Raffaele Armentano
- Department of Pathology, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.M.V.); (R.A.)
| | - Vittoria Disciglio
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.P.); (G.F.); (F.C.); (C.F.); (P.S.); (V.G.); (A.L.B.); (K.D.M.); (M.L.S.); (A.F.G.); (A.M.)
| | - Cristiano Simone
- Medical Genetics, National Institute of Gastroenterology-IRCCS “Saverio de Bellis” Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.P.); (G.F.); (F.C.); (C.F.); (P.S.); (V.G.); (A.L.B.); (K.D.M.); (M.L.S.); (A.F.G.); (A.M.)
- Medical Genetics, Department of Precision and Regenerative Medicine and Jonic Area (DiMePRe-J), University of Bari Aldo Moro, 70124 Bari, Italy
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18
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Zi F, Li Z, Cheng W, Huang X, Sheng X, Rong W. Novel mutations of the X-linked genes associated with early-onset high myopia in five Chinese families. BMC Med Genomics 2023; 16:223. [PMID: 37749571 PMCID: PMC10521526 DOI: 10.1186/s12920-023-01665-x] [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: 03/12/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
PURPOSE To report novel pathogenic variants of X-linked genes in five Chinese families with early-onset high myopia (eoHM) by using whole-exome sequencing and analyzing the phenotypic features. METHODS 5 probands with X-linked recessive related eoHM were collected in Ningxia Eye Hospital from January 2021 to June 2022. The probands and their family members received comprehensive ophthalmic examinations,and DNA was abstracted from patients and family members. Whole-exome sequencing was performed on probands to screen the causative variants, and all suspected pathogenic variants were determined by Sanger sequencing and co-segregation analysis was performed on available family members. The pathogenicity of novel variants was predicted using silico analysis and evaluated according to ACMG guidelines. RT-qPCR was used to detect differences in the relative mRNAs expression of candidate gene in mRNAs available with the proband and family members in the pedigree 2. The relationship between genetic variants and clinical features was analyzed. RESULTS All probands were male, and all pedigrees conformed to an X-linked recessive inheritance pattern. They were diagnosed with high myopia at their first visits between 4 and 7 years old. Spherical equivalent ranged between - 6.00D and - 11.00D.The five novel hemizygous variants were found in the probands, containing frameshift deletion variant c.797_801del (p.Val266Alafs*75) of OPN1LW gene in the pedigree 1, nonsense variant c.513G > A (p.Trp171Ter)of RP2 gene in the pedigree 2, missense variant c.98G > T (p.Cys33Phe) of GPR143 gene in the pedigree 3, frameshift deletion variant c.1876_1877del (p.Met626Valfs*22) of FRMD7 gene in the pedigree 4 and inframe deletion variant c.670_ 675del (p.Glu192_ Glu193del) of HMGB3 gene in the pedigree 5. All variants were classified as pathogenic or likely pathogenic by the interpretation principles of HGMD sequence variants and ACMG guidelines. In family 2, RT-qPCR showed that the mRNA expression of RP2 gene was lower in the proband than in other normal family members, indicating that such variant caused an effect on gene function at the mRNA expression level. Further clinical examination showed that pedigrees 1, 2, 3, and 4 were diagnosed as X-linked recessive hereditary eye disease with early-onset high myopia, including quiescent cone dysfunction, retinitis pigmentosa, ocular albinism, and idiopathic congenital nystagmus respectively. The pedigree 5 had eoHM in the right eye and ptosis in both eyes. CONCLUSION In this paper,we are the first to report five novel hemizygous variants in OPN1LW, RP2, GPR143, FRMD7, HMGB3 genes are associated with eoHM. Our study extends the genotypic spectrums for eoHM and better assists ophthalmologists in assessing, diagnosing, and conducting genetic screening for eoHM.
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Affiliation(s)
- Feiyin Zi
- Clinical Medical College, Ningxia Medical University, Yinchuan, 750001, China
| | - Zhen Li
- Department of Ophthalmology, Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, 936 Huanghe East Road, Jinfeng District, Yinchuan, 750001, China
| | - Wanyu Cheng
- Clinical Medical College, Ningxia Medical University, Yinchuan, 750001, China
| | - Xiaoyu Huang
- Clinical Medical College, Ningxia Medical University, Yinchuan, 750001, China
| | - Xunlun Sheng
- Gansu Aier Ophthalmiology and Optometry Hospital, 1228 Guazhou Road, Qilihe District, Lanzhou, 730050, China.
| | - Weining Rong
- Department of Ophthalmology, Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, 936 Huanghe East Road, Jinfeng District, Yinchuan, 750001, China.
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Yang W, Chen SC, Wang TE, Tsai PS, Chen JC, Chen PL. L1cam alternative shorter transcripts encoding the extracellular domains were overexpressed in the intestine of L1cam knockdown mice. Gene 2023; 881:147643. [PMID: 37453721 DOI: 10.1016/j.gene.2023.147643] [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: 05/07/2023] [Revised: 06/25/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Hirschsprung disease (HSCR) is a congenital disorder of functional bowel obstruction due to the absence of enteric ganglia in distal bowel. Different L1cam variants were reportedly associated with L1cam syndrome and HSCR, whose phenotypes lacked predictable relevance to their genotypes. Using next-generation sequencing (NGS), we found an L1CAM de novo frameshift mutation in a female with mild hydrocephalus and skip-type HSCR. A nearly identical L1cam variant was introduced into FVB/NJ mice via the CRISPR-EZ method. A silent mutation was created via ssODN to gain an artificial Ncol restriction enzyme site for easier genotyping. Six L1cam protein-coding alternative transcripts were quantitatively measured. Immunofluorescence staining with polyclonal and monoclonal L1cam antibodies was used to characterize L1cam isoform proteins in enteric ganglia. Fifteen mice, seven males and eight females, generated via CRISPR-EZ, were confirmed to carry the L1cam frameshift variant, resulting in a premature stop codon. There was no prominent hydrocephalus nor HSCR-like presentation in these mice, but male infertility was noticed after observation for three generations in a total of 176 mice. Full-length L1cam transcripts were detected at a very low level in the intestinal tissues and almost none in the brain of these mice. Alternative shorter transcripts encoding the extracellular domains were overexpressed in the intestine of L1cam knockdown mice. Immunofluorescence confirmed no fulllength L1cam protein in enteric ganglia. These shorter L1cam isoform proteins might play a role in protecting L1cam knockdown mice from HSCR.
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Affiliation(s)
- Wendy Yang
- Department of Surgery, Chang Gung Children's Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Pediatric Research Center, Chang Gung Children's Hospital, Taoyuan, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Szu-Chieh Chen
- Pediatric Research Center, Chang Gung Children's Hospital, Taoyuan, Taiwan
| | - Tse-En Wang
- Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, 10617 Taipei, Taiwan
| | - Pei-Shiue Tsai
- Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, 10617 Taipei, Taiwan; Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, 10617 Taipei, Taiwan
| | - Jeng-Chang Chen
- Department of Surgery, Chang Gung Children's Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Pediatric Research Center, Chang Gung Children's Hospital, Taoyuan, Taiwan.
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taiwan; Departments of Medical Genetics, National Taiwan University Hospital, Taiwan; Departments of Internal Medicine, National Taiwan University Hospital, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
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20
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Klonowski J, Liang Q, Coban-Akdemir Z, Lo C, Kostka D. aenmd: annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants. Bioinformatics 2023; 39:btad556. [PMID: 37688563 PMCID: PMC10534055 DOI: 10.1093/bioinformatics/btad556] [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: 03/17/2023] [Revised: 07/13/2023] [Accepted: 09/07/2023] [Indexed: 09/11/2023] Open
Abstract
SUMMARY DNA changes that cause premature termination codons (PTCs) represent a large fraction of clinically relevant pathogenic genomic variation. Typically, PTCs induce transcript degradation by nonsense-mediated mRNA decay (NMD) and render such changes loss-of-function alleles. However, certain PTC-containing transcripts escape NMD and can exert dominant-negative or gain-of-function (DN/GOF) effects. Therefore, systematic identification of human PTC-causing variants and their susceptibility to NMD contributes to the investigation of the role of DN/GOF alleles in human disease. Here we present aenmd, a software for annotating PTC-containing transcript-variant pairs for predicted escape from NMD. aenmd is user-friendly and self-contained. It offers functionality not currently available in other methods and is based on established and experimentally validated rules for NMD escape; the software is designed to work at scale, and to integrate seamlessly with existing analysis workflows. We applied aenmd to variants in the gnomAD, Clinvar, and GWAS catalog databases and report the prevalence of human PTC-causing variants in these databases, and the subset of these variants that could exert DN/GOF effects via NMD escape. AVAILABILITY AND IMPLEMENTATION aenmd is implemented in the R programming language. Code is available on GitHub as an R-package (github.com/kostkalab/aenmd.git), and as a containerized command-line interface (github.com/kostkalab/aenmd_cli.git).
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Affiliation(s)
- Jonathan Klonowski
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, United States
| | - Qianqian Liang
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, United States
| | - Zeynep Coban-Akdemir
- Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX 77030, United States
| | - Cecilia Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, United States
| | - Dennis Kostka
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, United States
- Department of Computational & Systems Biology and Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260,United States
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Giardoglou P, Deloukas P, Dedoussis G, Beis D. Cfdp1 Is Essential for Cardiac Development and Function. Cells 2023; 12:1994. [PMID: 37566073 PMCID: PMC10417793 DOI: 10.3390/cells12151994] [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: 05/16/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the prevalent cause of mortality worldwide. A combination of environmental and genetic effectors modulates the risk of developing them. Thus, it is vital to identify candidate genes and elucidate their role in the manifestation of the disease. Large-scale human studies have revealed the implication of Craniofacial Development Protein 1 (CFDP1) in Coronary Artery Disease (CAD). CFDP1 belongs to the evolutionary conserved Bucentaur (BCNT) family, and to date, its function and mechanism of action in Cardiovascular Development are still unclear. We utilized zebrafish to investigate the role of cfdp1 in the developing heart due to the high genomic homology, similarity in heart physiology, and ease of experimental manipulations. We showed that cfdp1 was expressed during development, and we tested two morpholinos and generated a cfdp1 mutant line. The cfdp1-/- embryos developed arrhythmic hearts and exhibited defective cardiac performance, which led to a lethal phenotype. Findings from both knockdown and knockout experiments showed that abrogation of cfdp1 leads to downregulation of Wnt signaling in embryonic hearts during valve development but without affecting Notch activation in this process. The cfdp1 zebrafish mutant line provides a valuable tool for unveiling the novel mechanism of regulating cardiac physiology and function. cfdp1 is essential for cardiac development, a previously unreported phenotype most likely due to early lethality in mice. The detected phenotype of bradycardia and arrhythmias is an observation with potential clinical relevance for humans carrying heterozygous CFDP1 mutations and their risk of developing CAD.
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Affiliation(s)
- Panagiota Giardoglou
- Zebrafish Disease Model Laboratory, Center for Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece;
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, 17676 Athens, Greece;
| | - Panos Deloukas
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London Medical School, Queen Mary University of London, London E1 4NS, UK;
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, 17676 Athens, Greece;
| | - Dimitris Beis
- Zebrafish Disease Model Laboratory, Center for Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece;
- Laboratory of Biological Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
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Wang D, Wu J. A novel variant in the QRICH1 gene was identified in a patient with severe developmental delay. Mol Genet Genomic Med 2023; 11:e2227. [PMID: 37331002 PMCID: PMC10422060 DOI: 10.1002/mgg3.2227] [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: 02/22/2023] [Revised: 05/08/2023] [Accepted: 05/31/2023] [Indexed: 06/20/2023] Open
Abstract
BACKGROUND QRICH1 encodes the glutamine-rich protein 1, which contains one caspase activation recruitment domain and is likely to be involved in apoptosis and inflammation. However, the function of the QRICH1 gene was largely unknown. Recently, several studies have reported de novo variants in QRICH1, and the variants have been associated with Ververi-Brady syndrome characterized by developmental delay, nonspecific facial dysmorphism, and hypotonia. MATERIALS AND METHODS Whole exome sequencing, clinical examinations, and functional experiments were performed to identify the etiology of our patient. RESULTS Here, we added another patient with severe growth retardation, atrial septal defect, and slurred speech. Whole exome sequencing identified a novel truncation variant in the QRICH1 gene (MN_017730.3: c.1788dupC, p.Tyr597Leufs*9). Furthermore, the functional experiments confirmed the effect of genetic variation. CONCLUSION Our findings expand the QRICH1 variant spectrum in developmental disorders and provide evidence for the application of whole exome sequencing in Ververi-Brady syndrome.
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Affiliation(s)
- Dong Wang
- Department of Oral and Maxillofacial Surgery, affiliated Dongguan HospitalSouthern Medical University (Dongguan people's Hospital)DongguanChina
| | - Jin Wu
- Department of Pediatric Endocrinology and Metabolism, Key Laboratory of Birth Defects and Related Diseases of Women and ChildrenWest China Second Hospital of Sichuan UniversityChengduChina
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Huang HL, Zhang QX, Huang F, Long XY, Song Z, Xiao B, Li GL, Ma CY, Liu D. TMEM151A variants associated with paroxysmal kinesigenic dyskinesia. Hum Genet 2023; 142:1017-1028. [PMID: 36856871 DOI: 10.1007/s00439-023-02535-3] [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: 12/18/2022] [Accepted: 02/16/2023] [Indexed: 03/02/2023]
Abstract
TMEM151A, located at 11q13.2 and encoding transmembrane protein 151A, was recently reported as causative for autosomal dominant paroxysmal kinesigenic dyskinesia (PKD). Here, through comprehensive analysis of sporadic and familial cases, we expand the clinical and mutation spectrum of PKD. In doing so, we clarify the clinical and genetic features of Chinese PKD patients harboring TMEM151A variants and further explore the relationship between TMEM151A mutations and PKD. Whole exome sequencing was performed on 26 sporadic PKD patients and nine familial PKD pedigrees without PRRT2 variants. Quantitative real-time PCR was used to assess the gene expression of frameshift mutant TMEM151A in a PKD patient. TMEM151A variants reported to date were reviewed. Four TMEM151A variants were detected in four unrelated families with 12 individuals, including a frameshift mutation [c.606_607insA (p.Val203fs)], two missense mutations [c.166G > A (p.Gly56Arg) and c.791T > C (p.Val264Ala)], and a non-pathogenic variant [c.994G > A (p.Gly332Arg)]. The monoallelic frameshift mutation [c.606_607insA (p.Val203fs)] may cause TMEM151A mRNA decay, suggesting a potential pathogenic mechanism of haploinsufficiency. Patients with TMEM151A variants had short-duration attacks and presented with dystonia. Our study provides a detailed clinical description of PKD patients with TMEM151A mutations and reports a new disease-causing mutation, expanding the known phenotypes caused by TMEM151A mutations and providing further detail about the pathoetiology of PKD.
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Affiliation(s)
- Hua Lin Huang
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qing Xia Zhang
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fei Huang
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiao Yan Long
- Department of Neurology, The Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhi Song
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bo Xiao
- Department of Neurology, The Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guo Liang Li
- Department of Neurology, The Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Cai Yu Ma
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Ding Liu
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.
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Sun B, Chen L. Mapping genetic variants for nonsense-mediated mRNA decay regulation across human tissues. Genome Biol 2023; 24:164. [PMID: 37434206 PMCID: PMC10337212 DOI: 10.1186/s13059-023-03004-w] [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: 03/04/2022] [Accepted: 06/30/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Nonsense-mediated mRNA decay (NMD) was originally conceived as an mRNA surveillance mechanism to prevent the production of potentially deleterious truncated proteins. Research also shows NMD is an important post-transcriptional gene regulation mechanism selectively targeting many non-aberrant mRNAs. However, how natural genetic variants affect NMD and modulate gene expression remains elusive. RESULTS Here we elucidate NMD regulation of individual genes across human tissues through genetical genomics. Genetic variants corresponding to NMD regulation are identified based on GTEx data through unique and robust transcript expression modeling. We identify genetic variants that influence the percentage of NMD-targeted transcripts (pNMD-QTLs), as well as genetic variants regulating the decay efficiency of NMD-targeted transcripts (dNMD-QTLs). Many such variants are missed in traditional expression quantitative trait locus (eQTL) mapping. NMD-QTLs show strong tissue specificity especially in the brain. They are more likely to overlap with disease single-nucleotide polymorphisms (SNPs). Compared to eQTLs, NMD-QTLs are more likely to be located within gene bodies and exons, especially the penultimate exons from the 3' end. Furthermore, NMD-QTLs are more likely to be found in the binding sites of miRNAs and RNA binding proteins. CONCLUSIONS We reveal the genome-wide landscape of genetic variants associated with NMD regulation across human tissues. Our analysis results indicate important roles of NMD in the brain. The preferential genomic positions of NMD-QTLs suggest key attributes for NMD regulation. Furthermore, the overlap with disease-associated SNPs and post-transcriptional regulatory elements implicates regulatory roles of NMD-QTLs in disease manifestation and their interactions with other post-transcriptional regulators.
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Affiliation(s)
- Bo Sun
- Department of Quantitative and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Liang Chen
- Department of Quantitative and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA.
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25
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Wagner RN, Wießner M, Friedrich A, Zandanell J, Breitenbach-Koller H, Bauer JW. Emerging Personalized Opportunities for Enhancing Translational Readthrough in Rare Genetic Diseases and Beyond. Int J Mol Sci 2023; 24:6101. [PMID: 37047074 PMCID: PMC10093890 DOI: 10.3390/ijms24076101] [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: 02/16/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Nonsense mutations trigger premature translation termination and often give rise to prevalent and rare genetic diseases. Consequently, the pharmacological suppression of an unscheduled stop codon represents an attractive treatment option and is of high clinical relevance. At the molecular level, the ability of the ribosome to continue translation past a stop codon is designated stop codon readthrough (SCR). SCR of disease-causing premature termination codons (PTCs) is minimal but small molecule interventions, such as treatment with aminoglycoside antibiotics, can enhance its frequency. In this review, we summarize the current understanding of translation termination (both at PTCs and at cognate stop codons) and highlight recently discovered pathways that influence its fidelity. We describe the mechanisms involved in the recognition and readthrough of PTCs and report on SCR-inducing compounds currently explored in preclinical research and clinical trials. We conclude by reviewing the ongoing attempts of personalized nonsense suppression therapy in different disease contexts, including the genetic skin condition epidermolysis bullosa.
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Affiliation(s)
- Roland N. Wagner
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Michael Wießner
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Andreas Friedrich
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Johanna Zandanell
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | | | - Johann W. Bauer
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
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26
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Wang H, Guo M, Wei H, Chen Y. Targeting p53 pathways: mechanisms, structures, and advances in therapy. Signal Transduct Target Ther 2023; 8:92. [PMID: 36859359 PMCID: PMC9977964 DOI: 10.1038/s41392-023-01347-1] [Citation(s) in RCA: 96] [Impact Index Per Article: 96.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/19/2022] [Accepted: 02/07/2023] [Indexed: 03/03/2023] Open
Abstract
The TP53 tumor suppressor is the most frequently altered gene in human cancers, and has been a major focus of oncology research. The p53 protein is a transcription factor that can activate the expression of multiple target genes and plays critical roles in regulating cell cycle, apoptosis, and genomic stability, and is widely regarded as the "guardian of the genome". Accumulating evidence has shown that p53 also regulates cell metabolism, ferroptosis, tumor microenvironment, autophagy and so on, all of which contribute to tumor suppression. Mutations in TP53 not only impair its tumor suppressor function, but also confer oncogenic properties to p53 mutants. Since p53 is mutated and inactivated in most malignant tumors, it has been a very attractive target for developing new anti-cancer drugs. However, until recently, p53 was considered an "undruggable" target and little progress has been made with p53-targeted therapies. Here, we provide a systematic review of the diverse molecular mechanisms of the p53 signaling pathway and how TP53 mutations impact tumor progression. We also discuss key structural features of the p53 protein and its inactivation by oncogenic mutations. In addition, we review the efforts that have been made in p53-targeted therapies, and discuss the challenges that have been encountered in clinical development.
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Affiliation(s)
- Haolan Wang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Ming Guo
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Hudie Wei
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
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27
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Manjunath LE, Singh A, Som S, Eswarappa SM. Mammalian proteome expansion by stop codon readthrough. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1739. [PMID: 35570338 DOI: 10.1002/wrna.1739] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 04/11/2022] [Accepted: 04/16/2022] [Indexed: 12/20/2022]
Abstract
Recognition of a stop codon by translation machinery as a sense codon results in translational readthrough instead of termination. This recoding process, termed stop codon readthrough (SCR) or translational readthrough, is found in all domains of life including mammals. The context of the stop codon, local mRNA topology, and molecules that interact with the mRNA region downstream of the stop codon determine SCR. The products of SCR can have localization, stability, and function different from those of the canonical isoforms. In this review, we discuss how recent technological and computational advances have increased our understanding of the SCR process in the mammalian system. Based on the known molecular events that occur during SCR of multiple mRNAs, we propose transient molecular roadblocks on an mRNA downstream of the stop codon as a possible mechanism for the induction of SCR. We argue, with examples, that the insights gained from the natural SCR events can guide us to develop novel strategies for the treatment of diseases caused by premature stop codons. This article is categorized under: Translation > Regulation.
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Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Saubhik Som
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
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28
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Yuan S, Huang X, Zhang S, Yang S, Rui X, Qi X, Wang X, Zheng Y, Rong W, Sheng X. Two novel variations in LRP2 cause Donnai-Barrow syndrome in a Chinese family with severe early-onset high myopia. Front Genet 2023; 14:1107347. [PMID: 36777721 PMCID: PMC9911814 DOI: 10.3389/fgene.2023.1107347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/17/2023] [Indexed: 02/14/2023] Open
Abstract
Donnai-Barrow syndrome (DBS) is a rare autosomal recessive disorder caused by mutation in the low density lipoprotein receptor-related protein 2 gene (LRP2). Defects in this protein may lead to clinical multiple organ malformations by affecting the development of organs such as the nervous system, eyes, ears, and kidneys. Although some variations on LRP2 have been found to be associated with DBS, early diagnosis and prevention of patients with atypical DBS remains a challenge for many physicians because of their clinical heterogeneity. The objective of this study is to explore the association between the clinical presentation and the genotype of a DBS patient who was initially diagnosed with early-onset high myopia (eoHM) from a healthy Chinese family. To this end, we tested the patient of this family via whole exome sequencing and further verified the results among other family members by Sanger sequencing. Comprehensive ophthalmic tests as well as other systemic examinations were also performed on participants with various genotypes. Genetic assessment revealed that two novel variations in LRP2, a de novo missense variation (c.9032G>A; p.Arg3011Lys) and a novel splicing variation (c.2909-2A>T) inherited from the father, were both carried by the proband in this family, and they are strongly associated with the typical clinical features of DBS patients. Therefore, in this paper we are the first to report two novel compound heterozygous variations in LPR2 causing DBS. Our study extends the genotypic spectrums for LPR2-DBS and better assists physicians in predicting, diagnosing, and conducting gene therapy for DBS.
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Affiliation(s)
- Shiqin Yuan
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Xiaoyu Huang
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China,Clinical Medical College, Ningxia Medical University, Yinchuan, China
| | - Shuang Zhang
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Shangying Yang
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China,Clinical Medical College, Ningxia Medical University, Yinchuan, China
| | - Xue Rui
- Gansu Aier Ophthalmology and Optometry Hospital, Lanzhou, China
| | - Xiaolong Qi
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Xuhui Wang
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Yali Zheng
- Department of Kidney Internal Medicine, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Weining Rong
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China,*Correspondence: Xunlun Sheng, ; Weining Rong,
| | - Xunlun Sheng
- Gansu Aier Ophthalmology and Optometry Hospital, Lanzhou, China,*Correspondence: Xunlun Sheng, ; Weining Rong,
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29
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Li C, Wang X, Li F, Ding H, Liu L, Xiong Y, Yang C, Zhang Y, Wu J, Yin A. A novel non-sense variant in the OFD1 gene caused Joubert syndrome. Front Genet 2023; 13:1064762. [PMID: 36704348 PMCID: PMC9871390 DOI: 10.3389/fgene.2022.1064762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/13/2022] [Indexed: 01/12/2023] Open
Abstract
Background: Joubert syndrome (JBS) is a rare neurodevelopmental disorder associated with progressive renal, liver, and retinal involvement that exhibits heterogeneity in both clinical manifestations and genetic etiology. Therefore, it is difficult to make a definite prenatal diagnosis. Methods: Whole-exome sequencing and Sanger sequencing were performed to screen the causative gene variants in a suspected JBS family. RNA-seq and protein model prediction were performed to clarify the potential pathogenic mechanism. A more comprehensive review of previously reported cases with OFD1 variants is presented and may help to establish a genotype-phenotype. Results: We identified a novel non-sense variant in the OFD1 gene, OFD1 (NM_003611.3): c.2848A>T (p.Lys950Ter). Sanger sequencing confirmed cosegregation among this family. RNA-seq confirmed that partial degradation of mutant transcripts, which was predicted to be caused by the non-sense-mediated mRNA decay (NMD) mechanism, may explain the reduction in the proportion of mutant transcripts. Protein structure prediction of the non-sense variant transcript revealed that this variant may lead to a change in the OFD1 protein structure. Conclusion: The genetic variation spectrum of JBS10 caused by OFD1 was broadened. The novel variants further deepened our insight into the molecular mechanism of the disease.
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Affiliation(s)
- Chen Li
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Xingwang Wang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Fake Li
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Hongke Ding
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Ling Liu
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Ying Xiong
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Chaoxiang Yang
- Medical Imaging Department, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yan Zhang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Jing Wu
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China,*Correspondence: Jing Wu, ; Aihua Yin,
| | - Aihua Yin
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China,*Correspondence: Jing Wu, ; Aihua Yin,
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30
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Guo R, Zhang X, Liu A, Ji J, Liu W. Novel clinical presentation and PAX6 mutation in families with congenital aniridia. Front Med (Lausanne) 2022; 9:1042588. [PMID: 36582291 PMCID: PMC9792480 DOI: 10.3389/fmed.2022.1042588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
Purpose To explore the clinical phenotype and genetic defects of families with congenital aniridia. Methods Four Chinese families with aniridia were enrolled in this study. The detailed ocular presentations of the patients were recorded. Whole exome sequencing (BGI MGIEasy V4 chip) was used to detect the gene mutation. Sanger sequencing was performed to validate the potential pathogenic variants, and segregation analysis was performed on all available family members. Results By whole exome sequencing and Sanger sequencing, three recurrent mutations (c.112del, p.Arg38Glyfs*16; c.299G > A, p.Trp100* and c.718C > T, p.Arg240*) and one novel mutation (c.278_281del, p.Glu93Alafs*30) of PAX6 were identified. All the mutations were co-segregated with the phenotype in the families. We also observed spontaneous anterior lens capsule rupture in aniridia for the first time. Conclusion We report spontaneous anterior lens capsule rupture as a novel phenotype of aniridia and three recurrent mutations and one novel mutation of PAX6 in families with aniridia. Our results expanded the phenotype and genotype spectra of aniridia and can help us better understand the disease.
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Affiliation(s)
- Ruru Guo
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Xiaotian Zhang
- Department of Ophthalmology, Nankai University Eye Hospital, Tianjin, China,Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin Eye Hospital, Clinical College of Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Aihua Liu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Jian Ji
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Wei Liu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China,*Correspondence: Wei Liu,
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31
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Ivanenko AV, Evtushenko NA, Gurskaya NG. Genome Editing in Therapy of Genodermatoses. Mol Biol 2022. [DOI: 10.1134/s0026893322060085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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32
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Novel Compound Heterozygous Variations in MPDZ Gene Caused Isolated Bilateral Macular Coloboma in a Chinese Family. Cells 2022; 11:cells11223602. [PMID: 36429029 PMCID: PMC9688216 DOI: 10.3390/cells11223602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
Macular coloboma (MC) is a rare congenital retinochoroidal defect characterized by lesions of different sizes in the macular region. The pathological mechanism underlying congenital MC is unknown. Novel compound heterozygous variations, c.4301delA (p.Asp1434fs*3) and c.5255C>G (p.Ser1752Ter), in the multiple PDZ domain (MPDZ) proteins were identified via whole-exome analysis on the proband with isolated bilateral macular coloboma in a Chinese family. Segregation analysis revealed that each of the unaffected parents was heterozygous for one of the two variants. The results of the in silico and bioinformatics analysis were aligned with the experimental data. The knockdown of MPDZ in zebrafish caused a decrease in the ellipsoid zone, a destruction of the outer limiting membrane, and the subsequent RPE degeneration. Overall, the loss of MPDZ in zebrafish contributed to retinal development failure. These results indicate that MPDZ plays an essential role in the occurrence and maintenance of the macula, and the novel compound heterozygous variations were responsible for an autosomal recessive macular deficiency in this Chinese family.
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33
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Ropero Gradilla P, Raya JM, González FA, Rochas S, Ferrer-Benito S, Nieto JM, Martín-Santos T, Barrios M, Gutiérrez-Murillo L, Villegas A, Benavente C. Hb Nivaria: A New Hemoglobin Variant with a Shortened α-Globin Chain [ α139(HC1)Lys →Stop; HBA1: c.418A>T]. Hemoglobin 2022; 46:344-346. [PMID: 36847654 DOI: 10.1080/03630269.2023.2172430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
We report a novel hemoglobin (Hb) variant found in a Spanish individual from Santa Cruz de Tenerife, the Canary Islands in Spain. The proband was a 39-year-old male. High performance liquid chromatography (HPLC) displayed an unknown peak (19.3%) at a retention time of 1.3 min. eluting before Hb A0. Capillary zone electrophoresis (CZE) showed an abnormal peak (20.0%) in zone 12. Direct DNA sequencing of the α-globin genes revealed heterozygosity for a nonsense mutation at codon 139 (AAA>TAA), causing a lysine to stop codon substitution [α139(HC1)Lys→Stop; HBA1: c.418A>T]. We decided to name the variant Hb Nivaria (Tenerife) for the place of birth and residence of the proband.
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Affiliation(s)
- Paloma Ropero Gradilla
- Servicio de Hematología y Hemoterapia. Hospital Clínico San Carlos, Madrid, España.,Instituto de Investigación Sanitaria Hospital Clínico San Carlos, Madrid, España
| | - José María Raya
- Servicio de Hematología y Hemoterapia, Hospital Universitario de Canarias, Santa Cruz de Tenerife, Islas Canarias, España
| | - Fernando Ataúlfo González
- Servicio de Hematología y Hemoterapia. Hospital Clínico San Carlos, Madrid, España.,Instituto de Investigación Sanitaria Hospital Clínico San Carlos, Madrid, España
| | - Sara Rochas
- Servicio de Hematología y Hemoterapia. Hospital Clínico San Carlos, Madrid, España.,Instituto de Investigación Sanitaria Hospital Clínico San Carlos, Madrid, España
| | - Sara Ferrer-Benito
- Servicio de Hematología y Hemoterapia. Hospital Clínico San Carlos, Madrid, España.,Instituto de Investigación Sanitaria Hospital Clínico San Carlos, Madrid, España
| | - Jorge M Nieto
- Servicio de Hematología y Hemoterapia. Hospital Clínico San Carlos, Madrid, España.,Instituto de Investigación Sanitaria Hospital Clínico San Carlos, Madrid, España
| | - Taida Martín-Santos
- Servicio de Hematología y Hemoterapia, Hospital Universitario de Canarias, Santa Cruz de Tenerife, Islas Canarias, España
| | - Marcelo Barrios
- Servicio de Hematología y Hemoterapia, Hospital Universitario de Canarias, Santa Cruz de Tenerife, Islas Canarias, España
| | - Lorena Gutiérrez-Murillo
- Servicio de Hematología y Hemoterapia, Hospital Universitario de Canarias, Santa Cruz de Tenerife, Islas Canarias, España
| | - Ana Villegas
- Servicio de Hematología y Hemoterapia. Hospital Clínico San Carlos, Madrid, España
| | - Celina Benavente
- Servicio de Hematología y Hemoterapia. Hospital Clínico San Carlos, Madrid, España.,Instituto de Investigación Sanitaria Hospital Clínico San Carlos, Madrid, España
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Martin H, Rupkey J, Asthana S, Yoon J, Patel S, Mott J, Pei Z, Mao Y. Diverse Roles of the Exon Junction Complex Factors in the Cell Cycle, Cancer, and Neurodevelopmental Disorders-Potential for Therapeutic Targeting. Int J Mol Sci 2022; 23:ijms231810375. [PMID: 36142288 PMCID: PMC9499366 DOI: 10.3390/ijms231810375] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 12/04/2022] Open
Abstract
The exon junction complex (EJC) plays a crucial role in regulating gene expression at the levels of alternative splicing, translation, mRNA localization, and nonsense-mediated decay (NMD). The EJC is comprised of three core proteins: RNA-binding motif 8A (RBM8A), Mago homolog (MAGOH), eukaryotic initiation factor 4A3 (eIF4A3), and a peripheral EJC factor, metastatic lymph node 51 (MLN51), in addition to other peripheral factors whose structural integration is activity-dependent. The physiological and mechanistic roles of the EJC in contribution to molecular, cellular, and organismal level function continue to be explored for potential insights into genetic or pathological dysfunction. The EJC’s specific role in the cell cycle and its implications in cancer and neurodevelopmental disorders prompt enhanced investigation of the EJC as a potential target for these diseases. In this review, we highlight the current understanding of the EJC’s position in the cell cycle, its relation to cancer and developmental diseases, and potential avenues for therapeutic targeting.
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Affiliation(s)
- Hannah Martin
- Department of Biology, Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Julian Rupkey
- Department of Biology, Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Shravan Asthana
- Department of Biology, Pennsylvania State University, University Park, State College, PA 16802, USA
- Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Chicago, IL 60611, USA
| | - Joy Yoon
- Department of Biology, Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Shray Patel
- Department of Biology, Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Jennifer Mott
- Department of Biology, Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Zifei Pei
- Department of Biology, Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Yingwei Mao
- Department of Biology, Pennsylvania State University, University Park, State College, PA 16802, USA
- Correspondence:
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35
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Testa MF, Lombardi S, Bernardi F, Ferrarese M, Belvini D, Radossi P, Castaman G, Pinotti M, Branchini A. Translational readthrough at F8 nonsense variants in the factor VIII B domain contributes to residual expression and lowers inhibitor association. Haematologica 2022; 108:472-482. [PMID: 35924581 PMCID: PMC9890017 DOI: 10.3324/haematol.2022.281279] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Indexed: 02/03/2023] Open
Abstract
In hemophilia A, F8 nonsense variants, and particularly those affecting the large factor VIII (FVIII) B domain that is dispensable for coagulant activity, display lower association with replacement therapy-related anti-FVIII inhibitory antibodies as retrieved from multiple international databases. Since null genetic conditions favor inhibitor development, we hypothesized that translational readthrough over premature termination codons (PTC) may contribute to immune tolerance by producing full-length proteins through the insertion of amino acid subset(s). To quantitatively evaluate the readthrough output in vitro, we developed a very sensitive luciferase-based system to detect very low full-length FVIII synthesis from a wide panel (n=45; ~60% patients with PTC) of F8 nonsense variants. PTC not associated with inhibitors displayed higher readthrough-driven expression levels than inhibitor-associated PTC, a novel observation. Particularly, higher levels were detected for B-domain variants (n=20) than for variants in other domains (n=25). Studies on plasma from six hemophilia A patients with PTC, integrated by expression of the corresponding nonsense and readthrough-deriving missense variants, consistently revealed higher FVIII levels for B-domain variants. Only one B-domain PTC (Arg814*) was found among the highly represented PTC not sporadically associated with inhibitors, but with the lowest proportion of inhibitor cases (4 out of 57). These original insights into the molecular genetics of hemophilia A, and particularly into genotype-phenotype relationships related with disease treatment, demonstrate that B-domain features favor PTC readthrough output. This provides a potential molecular mechanism contributing to differential PTC-associated inhibitor occurrence, with translational implications for a novel, experimentally based classification of F8 nonsense variants.
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Affiliation(s)
- Maria Francesca Testa
- Department of Life Sciences and Biotechnology and LTTA Center, University of Ferrara, Ferrara
| | - Silvia Lombardi
- Department of Life Sciences and Biotechnology and LTTA Center, University of Ferrara, Ferrara,°Current address: Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology and LTTA Center, University of Ferrara, Ferrara
| | - Mattia Ferrarese
- Department of Life Sciences and Biotechnology and LTTA Center, University of Ferrara, Ferrara
| | - Donata Belvini
- Transfusion Service, Hemophilia Center and Hematology, Castelfranco Veneto Hospital, Castelfranco Veneto
| | - Paolo Radossi
- Oncohematology-Oncologic Institute of Veneto, Castelfranco Veneto Hospital, Castelfranco Veneto
| | - Giancarlo Castaman
- Center for Bleeding Disorders and Coagulation, Careggi University Hospital, Florence, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology and LTTA Center, University of Ferrara, Ferrara.
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology and LTTA Center, University of Ferrara, Ferrara.
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36
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Lombardi S, Testa MF, Pinotti M, Branchini A. Translation termination codons in protein synthesis and disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 132:1-48. [PMID: 36088072 DOI: 10.1016/bs.apcsb.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Fidelity of protein synthesis, a process shaped by several mechanisms involving specialized ribosome regions and external factors, ensures the precise reading of sense as well as stop codons (UGA, UAG, UAA), which are usually localized at the 3' of mRNA and drive the release of the polypeptide chain. However, either natural (NTCs) or premature (PTCs) termination codons, the latter arising from nucleotide changes, can undergo a recoding process named ribosome or translational readthrough, which insert specific amino acids (NTCs) or subset(s) depending on the stop codon type (PTCs). This process is particularly relevant for nonsense mutations, a relatively frequent cause of genetic disorders, which impair gene expression at different levels by potentially leading to mRNA degradation and/or synthesis of truncated proteins. As a matter of fact, many efforts have been made to develop efficient and safe readthrough-inducing compounds, which have been challenged in several models of human disease to provide with a therapy. In this view, the dissection of the molecular determinants shaping the outcome of readthrough, namely nucleotide and protein contexts as well as their interplay and impact on protein structure/function, is crucial to identify responsive nonsense mutations resulting in functional full-length proteins. The interpretation of experimental and mechanistic findings is also important to define a possibly clear picture of potential readthrough-favorable features useful to achieve rescue profiles compatible with therapeutic thresholds typical of each targeted disorder, which is of primary importance for the potential translatability of readthrough into a personalized and mutation-specific, and thus patient-oriented, therapeutic strategy.
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Affiliation(s)
- Silvia Lombardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Maria Francesca Testa
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
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Molecular Basis of Pathogenic Variants in the Fibrillar Collagens. Genes (Basel) 2022; 13:genes13071199. [PMID: 35885981 PMCID: PMC9320522 DOI: 10.3390/genes13071199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/26/2022] [Accepted: 06/28/2022] [Indexed: 12/04/2022] Open
Abstract
The fibrillar collagen family is comprised of the quantitatively major types I, II and III collagens and the quantitatively minor types V and XI. These form heterotypic collagen fibrils (composed of more than a single collagen type) where the minor collagens have a regulatory role in controlling fibril formation and diameter. The structural pre-requisites for normal collagen biosynthesis and fibrillogenesis result in many places where this process can be disrupted, and consequently a wide variety of phenotypes result when pathogenic changes occur in these fibrillar collagen genes. Another contributing factor is alternative splicing, both naturally occurring and as the result of pathogenic DNA alterations. This article will discuss how these factors should be taken into account when assessing DNA sequencing results from a patient.
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Tibrewal S, Ratna R, Gour A, Agarkar S, Dubey S, Ganesh S, Kekunnaya R, Sangwan V, Liu Y, Vanita V. Clinical and molecular aspects of congenital aniridia - A review of current concepts. Indian J Ophthalmol 2022; 70:2280-2292. [PMID: 35791108 PMCID: PMC9426064 DOI: 10.4103/ijo.ijo_2255_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Congenital aniridia is a pan ocular disorder characterized by partial or total loss of iris tissue as the defining feature. Classic aniridia, however, has a spectrum of ocular findings, including foveal hypoplasia, optic nerve hypoplasia, nystagmus, late-onset cataract, glaucoma, and keratopathy. The latter three are reasons for further visual compromise in such patients. This entity is often due to mutations in the PAX6 (Paired box protein Pax-6) gene. Recently, aniridia-like phenotypes have been reported due to non-PAX6 mutations as in PITX2, FOXC1, FOXD3, TRIM44, and CYP1B1 as well wherein there is an overlap of aniridia, such as iris defects with congenital glaucoma or anterior segment dysgenesis. In this review, we describe the various clinical features of classic aniridia, the comorbidities and their management, the mutation spectrum of the genes involved, genotype-phenotype correlation of PAX6 and non-PAX6 mutations, and the genetic testing plan. The various systemic associations and their implications in screening and genetic testing have been discussed. Finally, the future course of aniridia treatment in the form of drugs (such as ataluren) and targeted gene therapy has been discussed.
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Affiliation(s)
- Shailja Tibrewal
- Department of Ocular Genetics; Department of Pediatric Ophthalmology, Strabismus and Neuro-ophthalmology, Dr Shroff's Charity Eye Hospital, Daryaganj, New Delhi, India
| | - Ria Ratna
- Department of Ocular Genetics, Dr Shroff's Charity Eye Hospital, Daryaganj, New Delhi, India
| | - Abha Gour
- Department of Cornea and Anterior Segment, Dr Shroff's Charity Eye Hospital, Daryaganj, New Delhi, India
| | - Sumita Agarkar
- Department of Pediatric Ophthalmology and Strabismus, Medical Research Foundation, Sankara Netralaya, Chennai, Tamil Nadu, India
| | - Suneeta Dubey
- Department of Glaucoma, Dr Shroff's Charity Eye Hospital, Daryaganj, New Delhi, India
| | - Suma Ganesh
- Department of Pediatric Ophthalmology, Strabismus and Neuro-ophthalmology, Dr Shroff's Charity Eye Hospital, Daryaganj, New Delhi, India
| | - Ramesh Kekunnaya
- Child Sight Institute, Jasti V Ramanamma Children's Eye Care Centre, L V Prasad Eye Institute, KAR Campus, Hyderabad, Telangana, India
| | - Virender Sangwan
- Department of Cornea and Anterior Segment, Dr Shroff's Charity Eye Hospital, Daryaganj, New Delhi, India
| | - Yutao Liu
- Department of Cellular Biology and Anatomy, Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, USA
| | - Vanita Vanita
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
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Hu TM, Wu CL, Hsu SH, Tsai HY, Cheng FY, Cheng MC. Ultrarare Loss-of-Function Mutations in the Genes Encoding the Ionotropic Glutamate Receptors of Kainate Subtypes Associated with Schizophrenia Disrupt the Interaction with PSD95. J Pers Med 2022; 12:783. [PMID: 35629206 PMCID: PMC9144110 DOI: 10.3390/jpm12050783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 02/01/2023] Open
Abstract
Schizophrenia is a complex mental disorder with a genetic component. The GRIK gene family encodes ionotropic glutamate receptors of the kainate subtype, which are considered candidate genes for schizophrenia. We screened for rare and pathogenic mutations in the protein-coding sequences of the GRIK gene family in 516 unrelated patients with schizophrenia using the ion semiconductor sequencing method. We identified 44 protein-altered variants, and in silico analysis indicated that 36 of these mutations were rare and damaging or pathological based on putative protein function. Notably, we identified four truncating mutations, including two frameshift deletion mutations (GRIK1p.Phe24fs and GRIK1p.Thr882fs) and two nonsense mutations (GRIK2p.Arg300Ter and GRIK4p.Gln342Ter) in four unrelated patients with schizophrenia. They exhibited minor allele frequencies of less than 0.01% and were absent in 1517 healthy controls from Taiwan Biobank. Functional analysis identified these four truncating mutants as loss-of-function (LoF) mutants in HEK-293 cells. We also showed that three mutations (GRIK1p.Phe24fs, GRIK1p.Thr882fs, and GRIK2p.Arg300Ter) weakened the interaction with the PSD95 protein. The results suggest that the GRIK gene family harbors ultrarare LoF mutations in some patients with schizophrenia. The identification of proteins that interact with the kainate receptors will be essential to determine kainate receptor-mediated signaling in the brain.
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Affiliation(s)
- Tsung-Ming Hu
- Department of Psychiatry, Yuli Branch, Taipei Veterans General Hospital, Hualien 98142, Taiwan; (T.-M.H.); (C.-L.W.); (S.-H.H.); (H.-Y.T.); (F.-Y.C.)
- Department of Future Studies and LOHAS Industry, Fo Guang University, Jiaosi, Yilan County 26247, Taiwan
| | - Chia-Liang Wu
- Department of Psychiatry, Yuli Branch, Taipei Veterans General Hospital, Hualien 98142, Taiwan; (T.-M.H.); (C.-L.W.); (S.-H.H.); (H.-Y.T.); (F.-Y.C.)
| | - Shih-Hsin Hsu
- Department of Psychiatry, Yuli Branch, Taipei Veterans General Hospital, Hualien 98142, Taiwan; (T.-M.H.); (C.-L.W.); (S.-H.H.); (H.-Y.T.); (F.-Y.C.)
| | - Hsin-Yao Tsai
- Department of Psychiatry, Yuli Branch, Taipei Veterans General Hospital, Hualien 98142, Taiwan; (T.-M.H.); (C.-L.W.); (S.-H.H.); (H.-Y.T.); (F.-Y.C.)
| | - Fu-Yu Cheng
- Department of Psychiatry, Yuli Branch, Taipei Veterans General Hospital, Hualien 98142, Taiwan; (T.-M.H.); (C.-L.W.); (S.-H.H.); (H.-Y.T.); (F.-Y.C.)
| | - Min-Chih Cheng
- Department of Psychiatry, Yuli Branch, Taipei Veterans General Hospital, Hualien 98142, Taiwan; (T.-M.H.); (C.-L.W.); (S.-H.H.); (H.-Y.T.); (F.-Y.C.)
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Potapova NA. Nonsense Mutations in Eukaryotes. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:400-412. [PMID: 35790376 DOI: 10.1134/s0006297922050029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/14/2022] [Accepted: 03/22/2022] [Indexed: 06/15/2023]
Abstract
Nonsense mutations are a type of mutations which results in a premature termination codon occurrence. In general, these mutations have been considered to be among the most harmful ones which lead to premature protein translation termination and result in shortened nonfunctional polypeptide. However, there is evidence that not all nonsense mutations are harmful as well as some molecular mechanisms exist which allow to avoid pathogenic effects of these mutations. This review addresses relevant information on nonsense mutations in eukaryotic genomes, characteristics of these mutations, and different molecular mechanisms preventing or mitigating harmful effects thereof.
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Affiliation(s)
- Nadezhda A Potapova
- Kharkevich Institute for Information Transmission Problems (IITP), Russian Academy of Sciences, Moscow, 127051, Russia.
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41
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The Physiological Roles of the Exon Junction Complex in Development and Diseases. Cells 2022; 11:cells11071192. [PMID: 35406756 PMCID: PMC8997533 DOI: 10.3390/cells11071192] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/19/2022] [Accepted: 03/24/2022] [Indexed: 01/12/2023] Open
Abstract
The exon junction complex (EJC) becomes an increasingly important regulator of early gene expression in the central nervous system (CNS) and other tissues. The EJC is comprised of three core proteins: RNA-binding motif 8A (RBM8A), Mago homolog (MAGOH), eukaryotic initiation factor 4A3 (EIF4A3), and a peripheral EJC factor, metastatic lymph node 51 (MLN51), together with various auxiliary factors. The EJC is assembled specifically at exon-exon junctions on mRNAs, hence the name of the complex. The EJC regulates multiple levels of gene expression, from splicing to translation and mRNA degradation. The functional roles of the EJC have been established as crucial to the normal progress of embryonic and neurological development, with wide ranging implications on molecular, cellular, and organism level function. Dysfunction of the EJC has been implicated in multiple developmental and neurological diseases. In this review, we discuss recent progress on the EJC’s physiological roles.
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Brunklaus A, Pérez-Palma E, Ghanty I, Xinge J, Brilstra E, Ceulemans B, Chemaly N, de Lange I, Depienne C, Guerrini R, Mei D, Møller RS, Nabbout R, Regan BM, Schneider AL, Scheffer IE, Schoonjans AS, Symonds JD, Weckhuysen S, Kattan MW, Zuberi SM, Lal D. Development and Validation of a Prediction Model for Early Diagnosis of SCN1A-Related Epilepsies. Neurology 2022; 98:e1163-e1174. [PMID: 35074891 PMCID: PMC8935441 DOI: 10.1212/wnl.0000000000200028] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 01/03/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Pathogenic variants in the neuronal sodium channel α1 subunit gene (SCN1A) are the most frequent monogenic cause of epilepsy. Phenotypes comprise a wide clinical spectrum, including severe childhood epilepsy; Dravet syndrome, characterized by drug-resistant seizures, intellectual disability, and high mortality; and the milder genetic epilepsy with febrile seizures plus (GEFS+), characterized by normal cognition. Early recognition of a child's risk for developing Dravet syndrome vs GEFS+ is key for implementing disease-modifying therapies when available before cognitive impairment emerges. Our objective was to develop and validate a prediction model using clinical and genetic biomarkers for early diagnosis of SCN1A-related epilepsies. METHODS We performed a retrospective multicenter cohort study comprising data from patients with SCN1A-positive Dravet syndrome and patients with GEFS+ consecutively referred for genetic testing (March 2001-June 2020) including age at seizure onset and a newly developed SCN1A genetic score. A training cohort was used to develop multiple prediction models that were validated using 2 independent blinded cohorts. Primary outcome was the discriminative accuracy of the model predicting Dravet syndrome vs other GEFS+ phenotypes. RESULTS A total of 1,018 participants were included. The frequency of Dravet syndrome was 616/743 (83%) in the training cohort, 147/203 (72%) in validation cohort 1, and 60/72 (83%) in validation cohort 2. A high SCN1A genetic score (133.4 [SD 78.5] vs 52.0 [SD 57.5]; p < 0.001) and young age at onset (6.0 [SD 3.0] vs 14.8 [SD 11.8] months; p < 0.001) were each associated with Dravet syndrome vs GEFS+. A combined SCN1A genetic score and seizure onset model separated Dravet syndrome from GEFS+ more effectively (area under the curve [AUC] 0.89 [95% CI 0.86-0.92]) and outperformed all other models (AUC 0.79-0.85; p < 0.001). Model performance was replicated in both validation cohorts 1 (AUC 0.94 [95% CI 0.91-0.97]) and 2 (AUC 0.92 [95% CI 0.82-1.00]). DISCUSSION The prediction model allows objective estimation at disease onset whether a child will develop Dravet syndrome vs GEFS+, assisting clinicians with prognostic counseling and decisions on early institution of precision therapies (http://scn1a-prediction-model.broadinstitute.org/). CLASSIFICATION OF EVIDENCE This study provides Class II evidence that a combined SCN1A genetic score and seizure onset model distinguishes Dravet syndrome from other GEFS+ phenotypes.
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Affiliation(s)
- Andreas Brunklaus
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA.
| | - Eduardo Pérez-Palma
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ismael Ghanty
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ji Xinge
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Eva Brilstra
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Berten Ceulemans
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Nicole Chemaly
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Iris de Lange
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Christel Depienne
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Renzo Guerrini
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Davide Mei
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Rikke S Møller
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Rima Nabbout
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Brigid M Regan
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Amy L Schneider
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ingrid E Scheffer
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - An-Sofie Schoonjans
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Joseph D Symonds
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Sarah Weckhuysen
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Michael W Kattan
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Sameer M Zuberi
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
| | - Dennis Lal
- From the Pediatric Neurosciences Research Group (A.B., I.G., J.D.S., S.M.Z.), Royal Hospital for Children, Glasgow; Institute of Health and Wellbeing (A.B., I.G., J.D.S., S.M.Z.), University of Glasgow, UK; Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana (E.P.-P.), Universidad del Desarrollo, Santiago, Chile; Genomic Medicine Institute, Lerner Research Institute (E.P.-P., D.L.), Department of Quantitative Health Sciences (J.X., M.W.K.), and Epilepsy Center, Neurological Institute (D.L.), Cleveland Clinic, OH; Department of Genetics (E.B., I.d.L.), University Medical Centre, Utrecht, the Netherlands; Department of Child Neurology (B.C., A.-S.S.), University Hospital Antwerp, Belgium; Reference Centre for Rare Epilepsies, Department of Pediatric Neurology (N.C., R.N.), Hôpital Necker-Enfants Malades, Université de Paris, France; Institute of Human Genetics (C.D.), University Hospital Essen, University of Duisburg-Essen, Germany; Neuroscience Department (R.G., D.M.), Children's Hospital A. Meyer-University of Florence, Italy; The Danish Epilepsy Centre (R.S.M.), Dianalund, Denmark; Institute for Regional Health Services (R.S.M.), University of Southern Denmark, Odense; Department of Medicine, Epilepsy Research Centre, Austin Health (B.M.R., A.L.S., I.E.S.), and Florey and Murdoch Children's Research Institutes, Royal Children's Hospital (I.E.S.), University of Melbourne, Australia; Applied and Translational Neurogenomics Group (S.W.), VIB-Center for Molecular Neurology, VIB, Antwerp; Neurology Department (S.W.), University Hospital Antwerp; Institute Born-Bunge (S.W.), University of Antwerp, Belgium; Cologne Center for Genomics (D.L.), University of Cologne, Germany; and Stanley Center for Psychiatric Genetics (D.L.), Broad Institute of MIT and Harvard, Cambridge, MA
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Zhao J, Li Z, Puri R, Liu K, Nunez I, Chen L, Zheng S. Molecular profiling of individual FDA-approved clinical drugs identifies modulators of nonsense-mediated mRNA decay. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:304-318. [PMID: 35024243 PMCID: PMC8718828 DOI: 10.1016/j.omtn.2021.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 12/07/2021] [Indexed: 12/12/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) degrades transcripts with premature stop codons. Given the prevalence of nonsense single nucleotide polymorphisms (SNPs) in the general population, it is urgent to catalog the effects of clinically approved drugs on NMD activity: any interference could alter the expression of nonsense SNPs, inadvertently inducing adverse effects. This risk is higher for patients with disease-causing nonsense mutations or an illness linked to dysregulated nonsense transcripts. On the other hand, hundreds of disorders are affected by cellular NMD efficiency and may benefit from NMD-modulatory drugs. Here, we profiled individual FDA-approved drugs for their impact on cellular NMD efficiency using a sensitive method that directly probes multiple endogenous NMD targets for a robust readout of NMD modulation. We found most FDA-approved drugs cause unremarkable effects on NMD, while many elicit clear transcriptional responses. Besides several potential mild NMD modulators, the anticancer drug homoharringtonine (HHT or omacetaxine mepesuccinate) consistently upregulates various endogenous NMD substrates in a dose-dependent manner in multiple cell types. We further showed translation inhibition mediates HHT's NMD effect. In summary, many FDA drugs induce transcriptional changes, and a few impact global NMD, and direct measurement of endogenous NMD substrate expression is robust to monitor cellular NMD.
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Affiliation(s)
- Jingrong Zhao
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 91709, USA
| | - Zhelin Li
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 91709, USA
| | - Ruchira Puri
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 91709, USA
| | - Kelvin Liu
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 91709, USA
| | - Israel Nunez
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 91709, USA
| | - Liang Chen
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Sika Zheng
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 91709, USA
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Udy DB, Bradley RK. Nonsense-mediated mRNA decay uses complementary mechanisms to suppress mRNA and protein accumulation. Life Sci Alliance 2022; 5:e202101217. [PMID: 34880103 PMCID: PMC8711849 DOI: 10.26508/lsa.202101217] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/13/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is an essential, highly conserved quality control pathway that detects and degrades mRNAs containing premature termination codons. Although the essentiality of NMD is frequently ascribed to its prevention of truncated protein accumulation, the extent to which NMD actually suppresses proteins encoded by NMD-sensitive transcripts is less well-understood than NMD-mediated suppression of mRNA. Here, we describe a reporter system that permits accurate quantification of both mRNA and protein levels via stable integration of paired reporters encoding NMD-sensitive and NMD-insensitive transcripts into the AAVS1 safe harbor loci in human cells. We use this system to demonstrate that NMD suppresses proteins encoded by NMD-sensitive transcripts by up to eightfold more than the mRNA itself. Our data indicate that NMD limits the accumulation of proteins encoded by NMD substrates by mechanisms beyond mRNA degradation, such that even when NMD-sensitive mRNAs escape destruction, their encoded proteins are still effectively suppressed.
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Affiliation(s)
- Dylan B Udy
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Małachowska B, Janikiewicz J, Pietrowska K, Wyka K, Madzio J, Wypyszczak K, Tkaczyk M, Chrul S, Zwiech R, Hogendorf A, Małecki MT, Borowiec M, Krętowski A, Młynarski W, Dobrzyń A, Ciborowski M, Fendler W. Elevated level of lysophosphatidic acid among patients with HNF1B mutations and its role in RCAD syndrome: a multiomic study. Metabolomics 2022; 18:15. [PMID: 35179657 PMCID: PMC8857088 DOI: 10.1007/s11306-022-01873-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 02/01/2022] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Patients with hepatocyte nuclear factor-1 beta (HNF1B) mutations present a variable phenotype with two main symptoms: maturity onset diabetes of the young (MODY) and polycystic kidney disease (PKD). OBJECTIVES Identification of serum metabolites specific for HNF1Bmut and evaluation of their role in disease pathogenesis. METHODS We recruited patients with HNF1Bmut (N = 10), HNF1Amut (N = 10), PKD: non-dialyzed and dialyzed (N = 8 and N = 13); and healthy controls (N = 12). Serum fingerprinting was performed by LC-QTOF-MS. Selected metabolite was validated by ELISA (enzyme-linked immunosorbent assay) measurements and then biologically connected with HNF1B by in silico analysis. HepG2 were stimulated with lysophosphatidic acid (LPA) and HNF1B gene was knocked down (kd) by small interfering RNA. Transcriptomic analysis with microarrays and western blot measurements were performed. RESULTS Serum levels of six metabolites including: arachidonic acid, hydroxyeicosatetraenoic acid, linoleamide and three LPA (18:1, 18:2 and 20:4), had AUC (the area under the curve) > 0.9 (HNF1Bmut vs comparative groups). The increased level of LPA was confirmed by ELISA measurements. In HepG2HNF1Bkd cells LPA stimulation lead to downregulation of many pathways associated with cell cycle, lipid metabolism, and upregulation of steroid hormone metabolism and Wnt signaling. Also, increased intracellular protein level of autotaxin was detected in the cells. GSK-3alpha/beta protein level and its phosphorylated ratio were differentially affected by LPA stimulation in HNF1Bkd and control cells. CONCLUSIONS LPA is elevated in sera of patients with HNF1Bmut. LPA contributes to the pathogenesis of HNF1B-MODY by affecting Wnt/GSK-3 signaling.
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Affiliation(s)
- Beata Małachowska
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 15 Mazowiecka Street, 92-215, Lodz, Poland
| | - Justyna Janikiewicz
- Laboratory of Cell Signaling and Metabolic Disorders, Nencki Institute of Experimental Biology PAS, 3 Pasteur Street, 02-093, Warsaw, Poland
| | - Karolina Pietrowska
- Clinical Research Centre, Medical University of Bialystok, 24a Sklodowska-Curie Street, 15-276, Bialystok, Poland
| | - Krystyna Wyka
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 36/50 Sporna Street, 91-738, Lodz, Poland
| | - Joanna Madzio
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 36/50 Sporna Street, 91-738, Lodz, Poland
| | - Kamila Wypyszczak
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 36/50 Sporna Street, 91-738, Lodz, Poland
| | - Marcin Tkaczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, 281/289 Rzgowska Street, 93-338, Lodz, Poland
- Department of Pediatrics Nephrology and Immunology, Medical University of Lodz, 281/289 Rzgowska Street, 93-338, Lodz, Poland
| | - Sławomir Chrul
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, 281/289 Rzgowska Street, 93-338, Lodz, Poland
| | - Rafał Zwiech
- Department of Kidney Transplantation/Dialysis Department, Barlicki Memorial Teaching Hospital No. 1, Medical University of Lodz, 22 Kopcinskiego Street, 90-153, Lodz, Poland
| | - Anna Hogendorf
- Department of Pediatrics, Diabetology, Endocrinology, and Nephrology, Medical University of Lodz, 36/50 Sporna Street, 91-738, Lodz, Poland
| | - Maciej T Małecki
- Department of Metabolic Diseases, Medical College, Jagiellonian University, 2 Jakubowskiego Street, 30-688, Cracov, Poland
| | - Maciej Borowiec
- Department of Clinical Genetics, Medical University of Lodz, 251 Pomorska Street, 92-213, Lodz, Poland
| | - Adam Krętowski
- Clinical Research Centre, Medical University of Bialystok, 24a Sklodowska-Curie Street, 15-276, Bialystok, Poland
- Department of Endocrinology, Diabetology, and Internal Medicine, Medical University of Bialystok, 24a Sklodowska-Curie Street, 15-276, Bialystok, Poland
| | - Wojciech Młynarski
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 36/50 Sporna Street, 91-738, Lodz, Poland
| | - Agnieszka Dobrzyń
- Laboratory of Cell Signaling and Metabolic Disorders, Nencki Institute of Experimental Biology PAS, 3 Pasteur Street, 02-093, Warsaw, Poland
| | - Michał Ciborowski
- Clinical Research Centre, Medical University of Bialystok, 24a Sklodowska-Curie Street, 15-276, Bialystok, Poland
| | - Wojciech Fendler
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 15 Mazowiecka Street, 92-215, Lodz, Poland.
- Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.
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Palazzo AF, Kejiou NS. Non-Darwinian Molecular Biology. Front Genet 2022; 13:831068. [PMID: 35251134 PMCID: PMC8888898 DOI: 10.3389/fgene.2022.831068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/24/2022] [Indexed: 12/14/2022] Open
Abstract
With the discovery of the double helical structure of DNA, a shift occurred in how biologists investigated questions surrounding cellular processes, such as protein synthesis. Instead of viewing biological activity through the lens of chemical reactions, this new field used biological information to gain a new profound view of how biological systems work. Molecular biologists asked new types of questions that would have been inconceivable to the older generation of researchers, such as how cellular machineries convert inherited biological information into functional molecules like proteins. This new focus on biological information also gave molecular biologists a way to link their findings to concepts developed by genetics and the modern synthesis. However, by the late 1960s this all changed. Elevated rates of mutation, unsustainable genetic loads, and high levels of variation in populations, challenged Darwinian evolution, a central tenant of the modern synthesis, where adaptation was the main driver of evolutionary change. Building on these findings, Motoo Kimura advanced the neutral theory of molecular evolution, which advocates that selection in multicellular eukaryotes is weak and that most genomic changes are neutral and due to random drift. This was further elaborated by Jack King and Thomas Jukes, in their paper “Non-Darwinian Evolution”, where they pointed out that the observed changes seen in proteins and the types of polymorphisms observed in populations only become understandable when we take into account biochemistry and Kimura’s new theory. Fifty years later, most molecular biologists remain unaware of these fundamental advances. Their adaptionist viewpoint fails to explain data collected from new powerful technologies which can detect exceedingly rare biochemical events. For example, high throughput sequencing routinely detects RNA transcripts being produced from almost the entire genome yet are present less than one copy per thousand cells and appear to lack any function. Molecular biologists must now reincorporate ideas from classical biochemistry and absorb modern concepts from molecular evolution, to craft a new lens through which they can evaluate the functionality of transcriptional units, and make sense of our messy, intricate, and complicated genome.
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Wang JM, Ho DV, Kritzer A, Chan JY. A novel nonsense variant in the NFE2L1 transcription factor in a patient with developmental delay, hypotonia, genital anomalies, and failure to thrive. Hum Mutat 2022; 43:471-476. [PMID: 35112409 PMCID: PMC8960367 DOI: 10.1002/humu.24337] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/25/2022] [Accepted: 01/30/2022] [Indexed: 11/08/2022]
Abstract
The NFE2L1 transcription factor (also known as Nrf1 for nuclear factor erythroid 2-related factor-1) is a broadly expressed basic leucine zipper protein that performs a critical role in the cellular stress response pathway. Here, we identified a heterozygous nonsense mutation located in the last exon of the gene that terminates translation prematurely, resulting in the production of a truncated peptide devoid of the carboxyl-terminal region containing the DNA-binding and leucine-zipper dimerization interface of the protein. Variant derivatives were well expressed in vitro, and they inhibited the transactivation function of wild-type proteins in luciferase reporter assays. Our studies suggest that this dominant-negative effect of truncated variants is through the formation of inactive heterodimers with wild-type proteins preventing the expression of its target genes. These findings suggest the potential role of diminished NFE2L1 function as an explanation for the developmental delay, hypotonia, hypospadias, bifid scrotum, and failure to thrive observed in the patient.
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Affiliation(s)
- Julia M Wang
- Department of Laboratory Medicine and Pathology, University of California, Irvine, Irvine, California, USA
| | - Daniel V Ho
- Department of Laboratory Medicine and Pathology, University of California, Irvine, Irvine, California, USA
| | - Amy Kritzer
- Division of Genetics and Genomics, Boston Children Hospital, Boston, Massachusetts, USA
| | - Jefferson Y Chan
- Department of Laboratory Medicine and Pathology, University of California, Irvine, Irvine, California, USA
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Swamy H, Glading AJ. Is Location Everything? Regulation of the Endothelial CCM Signaling Complex. Front Cardiovasc Med 2022; 9:954780. [PMID: 35898265 PMCID: PMC9309484 DOI: 10.3389/fcvm.2022.954780] [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: 05/27/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Recent advances have steadily increased the number of proteins and pathways known to be involved in the development of cerebral cavernous malformation (CCM). Our ability to synthesize this information into a cohesive and accurate signaling model is limited, however, by significant gaps in our knowledge of how the core CCM proteins, whose loss of function drives development of CCM, are regulated. Here, we review what is known about the regulation of the three core CCM proteins, the scaffolds KRIT1, CCM2, and CCM3, with an emphasis on binding interactions and subcellular location, which frequently control scaffolding protein function. We highlight recent work that challenges the current model of CCM complex signaling and provide recommendations for future studies needed to address the large number of outstanding questions.
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Affiliation(s)
- Harsha Swamy
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY, United States
| | - Angela J Glading
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY, United States
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Kingdom R, Wright CF. Incomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts. Front Genet 2022; 13:920390. [PMID: 35983412 PMCID: PMC9380816 DOI: 10.3389/fgene.2022.920390] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 12/20/2022] Open
Abstract
The same genetic variant found in different individuals can cause a range of diverse phenotypes, from no discernible clinical phenotype to severe disease, even among related individuals. Such variants can be said to display incomplete penetrance, a binary phenomenon where the genotype either causes the expected clinical phenotype or it does not, or they can be said to display variable expressivity, in which the same genotype can cause a wide range of clinical symptoms across a spectrum. Both incomplete penetrance and variable expressivity are thought to be caused by a range of factors, including common variants, variants in regulatory regions, epigenetics, environmental factors, and lifestyle. Many thousands of genetic variants have been identified as the cause of monogenic disorders, mostly determined through small clinical studies, and thus, the penetrance and expressivity of these variants may be overestimated when compared to their effect on the general population. With the wealth of population cohort data currently available, the penetrance and expressivity of such genetic variants can be investigated across a much wider contingent, potentially helping to reclassify variants that were previously thought to be completely penetrant. Research into the penetrance and expressivity of such genetic variants is important for clinical classification, both for determining causative mechanisms of disease in the affected population and for providing accurate risk information through genetic counseling. A genotype-based definition of the causes of rare diseases incorporating information from population cohorts and clinical studies is critical for our understanding of incomplete penetrance and variable expressivity. This review examines our current knowledge of the penetrance and expressivity of genetic variants in rare disease and across populations, as well as looking into the potential causes of the variation seen, including genetic modifiers, mosaicism, and polygenic factors, among others. We also considered the challenges that come with investigating penetrance and expressivity.
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Affiliation(s)
- Rebecca Kingdom
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
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Abstract
Introduction Valid prediction models or predictors of disease progression in children and young patients with autosomal dominant polycystic kidney disease (ADPKD) are lacking. Although total kidney volume (TKV) and Mayo imaging classification are generally used to predict disease progression in patients with ADPKD, it remains unclear whether germline mutation types are associated with these factors. We therefore investigated the association between mutation type and TKV and Mayo imaging classification among patients with ADPKD. Methods A total of 129 patients with ADPKD who underwent genetic analyses were enrolled in the study. The associations between the severity of PKD (TKV ≥ 1000 ml and Mayo classes 1C–1E) and the PKD1 mutation types (nonsense mutation, frameshift or splicing mutation, and substitution) were evaluated. Results Among the mutation types, only PKD1 splicing/frameshift mutation had significant associations with TKV ≥ 1000 ml in sex-adjusted and multivariable logistic analyses. Similarly, only the PKD1 splicing/frameshift mutation was significantly associated with Mayo 1C–1E in sex-adjusted and multivariable logistic analyses. PKD1 nonsense mutation, PKD1 substitution, or PKD1 mutation position had no significant association with TKV ≥ 1000 ml or Mayo 1C–1E. Conclusion Kidney cyst severity differs according to the mutation types in PKD1. Patients with PKD1 splicing mutations or PKD1 frameshift mutations are associated with TKV ≥ 1000 ml or Mayo 1C–1E. Detailed assessment of mutation types may be useful for predicting renal prognosis in patients with ADPKD and may especially contribute to the care of a high-risk group of children with ADPKD.
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