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Accogli A, Park YN, Lenk GM, Severino M, Scala M, Denecke J, Hempel M, Lessel D, Kortüm F, Salpietro V, de Marco P, Guerrisi S, Torella A, Nigro V, Srour M, Turro E, Labarque V, Freson K, Piatelli G, Capra V, Kitzman JO, Meisler MH. Biallelic loss-of-function variants of SLC12A9 cause lysosome dysfunction and a syndromic neurodevelopmental disorder. Genet Med 2024; 26:101097. [PMID: 38334070 DOI: 10.1016/j.gim.2024.101097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/10/2024] Open
Abstract
PURPOSE Pathogenic variants of FIG4 generate enlarged lysosomes and neurological and developmental disorders. To identify additional genes regulating lysosomal volume, we carried out a genome-wide activation screen to detect suppression of enlarged lysosomes in FIG4-/- cells. METHODS The CRISPR-a gene activation screen utilized sgRNAs from the promoters of protein-coding genes. Fluorescence-activated cell sorting separated cells with correction of the enlarged lysosomes from uncorrected cells. Patient variants of SLC12A9 were identified by exome or genome sequencing and studied by segregation analysis and clinical characterization. RESULTS Overexpression of SLC12A9, a solute co-transporter, corrected lysosomal swelling in FIG4-/- cells. SLC12A9 (NP_064631.2) colocalized with LAMP2 at the lysosome membrane. Biallelic variants of SLC12A9 were identified in 3 unrelated probands with neurodevelopmental disorders. Common features included intellectual disability, skeletal and brain structural abnormalities, congenital heart defects, and hypopigmented hair. Patient 1 was homozygous for nonsense variant p.(Arg615∗), patient 2 was compound heterozygous for p.(Ser109Lysfs∗20) and a large deletion, and proband 3 was compound heterozygous for p.(Glu290Glyfs∗36) and p.(Asn552Lys). Fibroblasts from proband 1 contained enlarged lysosomes that were corrected by wild-type SLC12A9 cDNA. Patient variant p.(Asn552Lys) failed to correct the lysosomal defect. CONCLUSION Impaired function of SLC12A9 results in enlarged lysosomes and a recessive disorder with a recognizable neurodevelopmental phenotype.
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Affiliation(s)
- Andrea Accogli
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre (MUHC), Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Young N Park
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | - Guy M Lenk
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | | | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università Degli Studi di Genova, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Jonas Denecke
- University Children's Hospital, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, United Kingdom; Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | | | | | - Annalaura Torella
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Myriam Srour
- Department of Human Genetics, McGill University, Montreal, QC, Canada; Department of Pediatrics, Division of Pediatric Neurology, McGill University, Montreal, QC, Canada; McGill University Health Center (MUHC) Research Institute, Montreal, QC, Canada; Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Ernest Turro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY; Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Veerle Labarque
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium; Paediatric Hemato-Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Kathleen Freson
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven, Belgium
| | - Gianluca Piatelli
- Department of Neurosurgery, Gaslini Children's Hospital, Genoa, Italy
| | - Valeria Capra
- Genomics and Clinical Genetics, IRCCS Instituto G. Gaslini, Genoa, Italy
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | - Miriam H Meisler
- Department of Human Genetics, University of Michigan, Ann Arbor, MI.
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Calzetta L, Ludovica Ritondo B, de Marco P, Cazzola M, Rogliani P. Reply to Han et al.: impact on mortality of triple ICS/LABA/LAMA therapy in a population of COPD patients including also subjects with asthma-like profile. Expert Rev Respir Med 2020; 15:579-581. [PMID: 33332207 DOI: 10.1080/17476348.2021.1866835] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Luigino Calzetta
- Department of Medicine and Surgery, Respiratory Disease and Lung Function Unit, University of Parma, Parma, Italy
| | - Beatrice Ludovica Ritondo
- Unit of Respiratory Medicine, Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Patrizia de Marco
- Unit of Respiratory Medicine, Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Mario Cazzola
- Unit of Respiratory Medicine, Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Paola Rogliani
- Unit of Respiratory Medicine, Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
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Calzetta L, Ritondo BL, de Marco P, Cazzola M, Rogliani P. Evaluating triple ICS/LABA/LAMA therapies for COPD patients: a network meta-analysis of ETHOS, KRONOS, IMPACT, and TRILOGY studies. Expert Rev Respir Med 2020; 15:143-152. [DOI: 10.1080/17476348.2020.1816830] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Luigino Calzetta
- Department of Medicine and Surgery, Respiratory Disease and Lung Function Unit, University of Parma, Parma, Italy
| | - Beatrice Ludovica Ritondo
- Unit of Respiratory Medicine, Department of Experimental Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Patrizia de Marco
- Unit of Respiratory Medicine, Department of Experimental Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Mario Cazzola
- Unit of Respiratory Medicine, Department of Experimental Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Paola Rogliani
- Unit of Respiratory Medicine, Department of Experimental Medicine, University of Rome “Tor Vergata”, Rome, Italy
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