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Iacomino M, Houerbi N, Fortuna S, Howe J, Li S, Scorrano G, Riva A, Cheng KW, Steiman M, Peltekova I, Yusuf A, Baldassari S, Tamburro S, Scudieri P, Musante I, Di Ludovico A, Guerrisi S, Balagura G, Corsello A, Efthymiou S, Murphy D, Uva P, Verrotti A, Fiorillo C, Delvecchio M, Accogli A, Elsabbagh M, Houlden H, Scherer SW, Striano P, Zara F, Chou TF, Salpietro V. Allelic heterogeneity and abnormal vesicle recycling in PLAA-related neurodevelopmental disorders. Front Mol Neurosci 2024; 17:1268013. [PMID: 38650658 PMCID: PMC11033462 DOI: 10.3389/fnmol.2024.1268013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/16/2024] [Indexed: 04/25/2024] Open
Abstract
The human PLAA gene encodes Phospholipase-A2-Activating-Protein (PLAA) involved in trafficking of membrane proteins. Through its PUL domain (PLAP, Ufd3p, and Lub1p), PLAA interacts with p97/VCP modulating synaptic vesicles recycling. Although few families carrying biallelic PLAA variants were reported with progressive neurodegeneration, consequences of monoallelic PLAA variants have not been elucidated. Using exome or genome sequencing we identified PLAA de-novo missense variants, affecting conserved residues within the PUL domain, in children affected with neurodevelopmental disorders (NDDs), including psychomotor regression, intellectual disability (ID) and autism spectrum disorders (ASDs). Computational and in-vitro studies of the identified variants revealed abnormal chain arrangements at C-terminal and reduced PLAA-p97/VCP interaction, respectively. These findings expand both allelic and phenotypic heterogeneity associated to PLAA-related neurological disorders, highlighting perturbed vesicle recycling as a potential disease mechanism in NDDs due to genetic defects of PLAA.
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Affiliation(s)
- Michele Iacomino
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Nadia Houerbi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Sara Fortuna
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Jennifer Howe
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Giovanna Scorrano
- Department of Pediatrics, Sant'Annunziata Hospital, University "G. D'Annunzio", Chieti, Italy
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Antonella Riva
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy
| | - Kai-Wen Cheng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Mandy Steiman
- Montreal Neurological Institute-Hospital, Azrieli Centre for Autism Research, McGill University, Montreal, QC, Canada
| | - Iskra Peltekova
- McGill University Health Centre, McGill University, Montreal, QC, Canada
| | - Afiqah Yusuf
- Montreal Neurological Institute-Hospital, Azrieli Centre for Autism Research, McGill University, Montreal, QC, Canada
| | - Simona Baldassari
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Serena Tamburro
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Paolo Scudieri
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy
| | - Ilaria Musante
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Armando Di Ludovico
- Department of Pediatrics, Sant'Annunziata Hospital, University "G. D'Annunzio", Chieti, Italy
| | - Sara Guerrisi
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Ganna Balagura
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Antonio Corsello
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
| | - David Murphy
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
| | - Paolo Uva
- Clinical Bioinformatics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | | | - Chiara Fiorillo
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Maurizio Delvecchio
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Andrea Accogli
- Division of Medical Genetics, Department of Specialized Medicine, McGill University, Montreal, QC, Canada
| | - Mayada Elsabbagh
- Montreal Neurological Institute-Hospital, Azrieli Centre for Autism Research, McGill University, Montreal, QC, Canada
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
| | - Stephen W Scherer
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy
| | - Federico Zara
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, United States
| | - Vincenzo Salpietro
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
- Department of Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
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Kaplow IM, Lawler AJ, Schäffer DE, Srinivasan C, Sestili HH, Wirthlin ME, Phan BN, Prasad K, Brown AR, Zhang X, Foley K, Genereux DP, Karlsson EK, Lindblad-Toh K, Meyer WK, Pfenning AR. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science 2023; 380:eabm7993. [PMID: 37104615 PMCID: PMC10322212 DOI: 10.1126/science.abm7993] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/23/2023] [Indexed: 04/29/2023]
Abstract
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.
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Affiliation(s)
- Irene M. Kaplow
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alyssa J. Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Daniel E. Schäffer
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Chaitanya Srinivasan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Heather H. Sestili
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Morgan E. Wirthlin
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - BaDoi N. Phan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kavya Prasad
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ashley R. Brown
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaomeng Zhang
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kathleen Foley
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Diane P. Genereux
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Elinor K. Karlsson
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute, Cambridge, MA, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Wynn K. Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Andreas R. Pfenning
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
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