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Bhattacharya A, Parlanti P, Cavallo L, Farrow E, Spivey T, Renieri A, Mari F, Manzini MC. A novel framework for functional annotation of variants of uncertain significance in ID/ASD risk gene CC2D1A. Hum Mol Genet 2024:ddae070. [PMID: 38652285 DOI: 10.1093/hmg/ddae070] [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] [Revised: 03/07/2024] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are genetically heterogeneous with hundreds of identified risk genes, most affecting only a few patients. Novel missense variants in these genes are being discovered as clinical exome sequencing is now routinely integrated into diagnosis, yet most of them are annotated as variants of uncertain significance (VUS). VUSs are a major roadblock in using patient genetics to inform clinical action. We developed a framework to characterize VUSs in Coiled-coil and C2 domain containing 1A (CC2D1A), a gene causing autosomal recessive ID with comorbid ASD in 40% of cases. We analyzed seven VUSs (p.Pro319Leu, p.Ser327Leu, p.Gly441Val, p.Val449Met, p.Thr580Ile, p.Arg886His and p.Glu910Lys) from four cases of individuals with ID and ASD. Variants were cloned and overexpressed in HEK293 individually and in their respective heterozygous combination. CC2D1A is a signaling scaffold that positively regulates PKA-CREB signaling by repressing phosphodiesterase 4D (PDE4D) to prevent cAMP degradation. After testing multiple parameters including direct interaction between PDE4D and CC2D1A, cAMP levels and CREB activation, we found that the most sensitive readout was CREB transcriptional activity using a luciferase assay. Compared to WT CC2D1A, five VUSs (p.Pro319Leu, p.Gly441Val, p.Val449Met, p.Thr580Ile, and p.Arg886His) led to significantly blunted response to forskolin induced CREB activation. This luciferase assay approach can be scaled up to annotate ~150 CC2D1A VUSs that are currently listed in ClinVar. Since CREB activation is a common denominator for multiple ASD/ID genes, our paradigm can also be adapted for their VUSs.
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Affiliation(s)
- Aniket Bhattacharya
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Paola Parlanti
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Luca Cavallo
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Edward Farrow
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, 2121 I St NW, Washington, DC 20052, United States
| | - Tyler Spivey
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, 2121 I St NW, Washington, DC 20052, United States
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Viale Bracci 2, 53100 Siena, Italy
| | - Francesca Mari
- Medical Genetics, University of Siena, Viale Bracci 2, 53100 Siena, Italy
| | - M Chiara Manzini
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
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Fortunato F, Bianchi F, Ricci G, Torri F, Gualandi F, Neri M, Farnè M, Giannini F, Malandrini A, Volpi N, Lopergolo D, Silani V, Ticozzi N, Verde F, Pareyson D, Fenu S, Bonanno S, Nigro V, Peduto C, D'Ambrosio P, Zeuli R, Zanobio M, Picillo E, Servidei S, Primiano G, Sancricca C, Sciacco M, Brusa R, Filosto M, Cotti Piccinelli S, Pegoraro E, Mongini T, Solero L, Gadaleta G, Brusa C, Minetti C, Bruno C, Panicucci C, Sansone VA, Lunetta C, Zanolini A, Toscano A, Pugliese A, Nicocia G, Bertini E, Catteruccia M, Diodato D, Atalaia A, Evangelista T, Siciliano G, Ferlini A. Digital health and Clinical Patient Management System (CPMS) platform utility for data sharing of neuromuscular patients: the Italian EURO-NMD experience. Orphanet J Rare Dis 2023; 18:196. [PMID: 37480080 PMCID: PMC10360326 DOI: 10.1186/s13023-023-02776-5] [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: 09/15/2022] [Accepted: 06/18/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND The development of e-health technologies for teleconsultation and exchange of knowledge is one of the core purposes of European Reference Networks (ERNs), including the ERN EURO-NMD for rare neuromuscular diseases. Within ERNs, the Clinical Patient Management System (CPMS) is a web-based platform that seeks to boost active collaboration within and across the network, implementing data sharing. Through CPMS, it is possible to both discuss patient cases and to make patients' data available for registries and databases in a secure way. In this view, CPMS may be considered a sort of a temporary storage for patients' data and an effective tool for data sharing; it facilitates specialists' consultation since rare diseases (RDs) require multidisciplinary skills, specific, and outstanding clinical experience. Following European Union (EU) recommendation, and to promote the use of CPMS platform among EURO-NMD members, a twelve-month pilot project was set up to train the 15 Italian Health Care Providers (HCPs). In this paper, we report the structure, methods, and results of the teaching course, showing that tailored, ERN-oriented, training can significantly enhance the profitable use of the CPMS. RESULTS Throughout the training course, 45 professionals learned how to use the many features of the CPMS, eventually opening 98 panels of discussion-amounting to 82% of the total panels included in the EURO-NMD. Since clinical, genetic, diagnostic, and therapeutic data of patients can be securely stored within the platform, we also highlight the importance of this platform as an effective tool to discuss and share clinical cases, in order to ease both case solving and data storing. CONCLUSIONS In this paper, we discuss how similar course could help implementing the use of the platform, highlighting strengths and weaknesses of e-health for ERNs. The expected result is the creation of a "map" of neuromuscular patients across Europe that might be improved by a wider use of CPMS.
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Affiliation(s)
- Fernanda Fortunato
- Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
- Medical Genetics Unit, Department of Mother and Child, Sant'Anna University Hospital of Ferrara, Ferrara, Italy
| | - Francesca Bianchi
- Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Pisa, Italy
| | - Giulia Ricci
- Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Pisa, Italy
| | - Francesca Torri
- Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Pisa, Italy
| | - Francesca Gualandi
- Medical Genetics Unit, Department of Mother and Child, Sant'Anna University Hospital of Ferrara, Ferrara, Italy
| | - Marcella Neri
- Medical Genetics Unit, Department of Mother and Child, Sant'Anna University Hospital of Ferrara, Ferrara, Italy
| | - Marianna Farnè
- Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
- Medical Genetics Unit, Department of Mother and Child, Sant'Anna University Hospital of Ferrara, Ferrara, Italy
| | - Fabio Giannini
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
| | - Alessandro Malandrini
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
| | - Nila Volpi
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
| | - Diego Lopergolo
- Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università Degli Studi Di Milano, Milan, Italy
| | - Nicola Ticozzi
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università Degli Studi Di Milano, Milan, Italy
| | - Federico Verde
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
- Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università Degli Studi Di Milano, Milan, Italy
| | - Davide Pareyson
- Unit of Rare Neurodegenerative and Neurometabolic Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Silvia Fenu
- Unit of Rare Neurodegenerative and Neurometabolic Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Silvia Bonanno
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - Cristina Peduto
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Naples, Italy
| | - Paola D'Ambrosio
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Naples, Italy
| | - Roberta Zeuli
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Naples, Italy
| | - Mariateresa Zanobio
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Naples, Italy
| | - Esther Picillo
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Naples, Italy
| | - Serenella Servidei
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Guido Primiano
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Cristina Sancricca
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Monica Sciacco
- Neuromuscular and Rare Disease Unit, Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Roberta Brusa
- Neuromuscular and Rare Disease Unit, Department of Neuroscience, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Massimiliano Filosto
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
- ASST Spedali Civili Di Brescia, Brescia, Italy
- NeMO-Brescia Clinical Center for Neuromuscular Diseases, Brescia, Italy
| | - Stefano Cotti Piccinelli
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
- ASST Spedali Civili Di Brescia, Brescia, Italy
- NeMO-Brescia Clinical Center for Neuromuscular Diseases, Brescia, Italy
| | - Elena Pegoraro
- Department of Neuroscience, University of Padova, Padua, Italy
| | - Tiziana Mongini
- Department of Neurosciences "Rita Levi Montalcini", University of Turin, Turin, Italy
| | - Luca Solero
- Department of Neurosciences "Rita Levi Montalcini", University of Turin, Turin, Italy
| | - Giulio Gadaleta
- Department of Neurosciences "Rita Levi Montalcini", University of Turin, Turin, Italy
| | - Chiara Brusa
- Department of Neurosciences "Rita Levi Montalcini", University of Turin, Turin, Italy
| | - Carlo Minetti
- Pediatric Neurology Unit and Muscle Unit, IRCCS Istituto Giannina Gaslini, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Claudio Bruno
- Center of Translational and Experimental Myology, IRCCS Istituto Giannina Gaslini, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Chiara Panicucci
- Center of Translational and Experimental Myology, IRCCS Istituto Giannina Gaslini, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Valeria A Sansone
- The NEMO (NEuroMuscular Omniservice) Clinical Center, Milan, Italy
- Neurorehabilitation Unit, University of Milan, Milan, Italy
| | | | - Alice Zanolini
- The NEMO (NEuroMuscular Omniservice) Clinical Center, Milan, Italy
| | - Antonio Toscano
- Neurology and Neuromuscular Diseases Unit, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
- ERN-NMD Center of Messina, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Alessia Pugliese
- Neurology and Neuromuscular Diseases Unit, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Giulia Nicocia
- Neurology and Neuromuscular Diseases Unit, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Michela Catteruccia
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Daria Diodato
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Antonio Atalaia
- Service of Neuromyology, APHP-GH Pitié-Salpêtrière, Sorbonne Université, Paris, France
| | - Teresinha Evangelista
- Neuromuscular Morphology Unit, Institute of Myology, GHU Pitié-Salpêtrière, Sorbonne Université, Paris, France
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Pisa, Italy
| | - Alessandra Ferlini
- Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, Ferrara, Italy.
- Medical Genetics Unit, Department of Mother and Child, Sant'Anna University Hospital of Ferrara, Ferrara, Italy.
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