1
|
Romano F, Haanpää MK, Pomianowski P, Peraino AR, Pollard JR, Di Feo MF, Traverso M, Severino M, Derchi M, Henzen E, Zara F, Faravelli F, Capra V, Scala M. Expanding the phenotype of UPF3B-related disorder: Case reports and literature review. Am J Med Genet A 2024; 194:e63534. [PMID: 38318947 DOI: 10.1002/ajmg.a.63534] [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: 10/16/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
UPF3B encodes the Regulator of nonsense transcripts 3B protein, a core-member of the nonsense-mediated mRNA decay pathway, protecting the cells from the potentially deleterious actions of transcripts with premature termination codons. Hemizygous variants in the UPF3B gene cause a spectrum of neuropsychiatric issues including intellectual disability, autism spectrum disorder, attention deficit hyperactivity disorder, and schizophrenia/childhood-onset schizophrenia (COS). The number of patients reported to date is very limited, often lacking an extensive phenotypical and neuroradiological description of this ultra-rare syndrome. Here we report three subjects harboring UPF3B variants, presenting with variable clinical pictures, including cognitive impairment, central hypotonia, and syndromic features. Patients 1 and 2 harbored novel UPF3B variants-the p.(Lys207*) and p.(Asp429Serfs*27) ones, respectively-while the p.(Arg225Lysfs*229) variant, identified in Patient 3, was already reported in the literature. Novel features in our patients are represented by microcephaly, midface hypoplasia, and brain malformations. Then, we reviewed pertinent literature and compared previously reported subjects to our cases, providing possible insights into genotype-phenotype correlations in this emerging condition. Overall, the detailed phenotypic description of three patients carrying UPF3B variants is useful not only to expand the genotypic and phenotypic spectrum of UPF3B-related disorders, but also to ameliorate the clinical management of affected individuals.
Collapse
Affiliation(s)
- Ferruccio Romano
- Clinical Genomics and Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Maria K Haanpää
- Department of Genomics and Clinical Genetics, Turku University Hospital, Turku, Finland
| | - Pawel Pomianowski
- Center for Medical Genetics and Genomics, Christiana Care Health System, Newark, Delaware, USA
| | - Amanda Rose Peraino
- Center for Medical Genetics and Genomics, Christiana Care Health System, Newark, Delaware, USA
| | - John R Pollard
- Epilepsy Center, Christiana Care Health System, Newark, Delaware, USA
| | - Maria Francesca Di Feo
- Clinical Genomics and Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Department of Genomics and Clinical Genetics, Turku University Hospital, Turku, Finland
- Center for Medical Genetics and Genomics, Christiana Care Health System, Newark, Delaware, USA
- Epilepsy Center, Christiana Care Health System, Newark, Delaware, USA
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Monica Traverso
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | | | - Maria Derchi
- Cardiology Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Edoardo Henzen
- Genomics Facility, Italian Institute of Technology (IIT), Genoa, Italy
| | - Federico Zara
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Francesca Faravelli
- Clinical Genomics and Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Valeria Capra
- Clinical Genomics and Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marcello Scala
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| |
Collapse
|
2
|
D'Incal C, Van Dijck A, Ibrahim J, De Man K, Bastini L, Konings A, Elinck E, Gozes L, Marusic Z, Anicic M, Vukovic J, Van der Aa N, Mateiu L, Vanden Berghe W, Kooy RF. ADNP dysregulates methylation and mitochondrial gene expression in the cerebellum of a Helsmoortel-Van der Aa syndrome autopsy case. Acta Neuropathol Commun 2024; 12:62. [PMID: 38637827 PMCID: PMC11027339 DOI: 10.1186/s40478-024-01743-w] [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: 11/23/2023] [Accepted: 02/11/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Helsmoortel-Van der Aa syndrome is a neurodevelopmental disorder in which patients present with autism, intellectual disability, and frequent extra-neurological features such as feeding and gastrointestinal problems, visual impairments, and cardiac abnormalities. All patients exhibit heterozygous de novo nonsense or frameshift stop mutations in the Activity-Dependent Neuroprotective Protein (ADNP) gene, accounting for a prevalence of 0.2% of all autism cases worldwide. ADNP fulfills an essential chromatin remodeling function during brain development. In this study, we investigated the cerebellum of a died 6-year-old male patient with the c.1676dupA/p.His559Glnfs*3 ADNP mutation. RESULTS The clinical presentation of the patient was representative of the Helsmoortel-Van der Aa syndrome. During his lifespan, he underwent two liver transplantations after which the child died because of multiple organ failure. An autopsy was performed, and various tissue samples were taken for further analysis. We performed a molecular characterization of the cerebellum, a brain region involved in motor coordination, known for its highest ADNP expression and compared it to an age-matched control subject. Importantly, epigenome-wide analysis of the ADNP cerebellum identified CpG methylation differences and expression of multiple pathways causing neurodevelopmental delay. Interestingly, transcription factor motif enrichment analysis of differentially methylated genes showed that the ADNP binding motif was the most significantly enriched. RNA sequencing of the autopsy brain further identified downregulation of the WNT signaling pathway and autophagy defects as possible causes of neurodevelopmental delay. Ultimately, label-free quantification mass spectrometry identified differentially expressed proteins involved in mitochondrial stress and sirtuin signaling pathways amongst others. Protein-protein interaction analysis further revealed a network including chromatin remodelers (ADNP, SMARCC2, HDAC2 and YY1), autophagy-related proteins (LAMP1, BECN1 and LC3) as well as a key histone deacetylating enzyme SIRT1, involved in mitochondrial energy metabolism. The protein interaction of ADNP with SIRT1 was further biochemically validated through the microtubule-end binding proteins EB1/EB3 by direct co-immunoprecipitation in mouse cerebellum, suggesting important mito-epigenetic crosstalk between chromatin remodeling and mitochondrial energy metabolism linked to autophagy stress responses. This is further supported by mitochondrial activity assays and stainings in patient-derived fibroblasts which suggest mitochondrial dysfunctions in the ADNP deficient human brain. CONCLUSION This study forms the baseline clinical and molecular characterization of an ADNP autopsy cerebellum, providing novel insights in the disease mechanisms of the Helsmoortel-Van der Aa syndrome. By combining multi-omic and biochemical approaches, we identified a novel SIRT1-EB1/EB3-ADNP protein complex which may contribute to autophagic flux alterations and impaired mitochondrial metabolism in the Helsmoortel-Van der Aa syndrome and holds promise as a new therapeutic target.
Collapse
Affiliation(s)
- Claudio D'Incal
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Antwerp, Belgium
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Antwerp, Belgium
| | - Anke Van Dijck
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Antwerp, Belgium
- Family Medicine and Population Health (FAMPOP), Department of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Joe Ibrahim
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Antwerp, Belgium
| | - Kevin De Man
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Antwerp, Belgium
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Antwerp, Belgium
| | - Lina Bastini
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Antwerp, Belgium
| | - Anthony Konings
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Antwerp, Belgium
| | - Ellen Elinck
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Antwerp, Belgium
| | - Lllana Gozes
- The Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Adams Super Center for Brain Studies and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Zlatko Marusic
- Clinical Department of Pathology and Cytology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Mirna Anicic
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, School of Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Jurica Vukovic
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, School of Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Nathalie Van der Aa
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Antwerp, Belgium
| | - Ligia Mateiu
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Antwerp, Belgium
| | - Wim Vanden Berghe
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Antwerp, Belgium.
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Antwerp, Belgium.
| |
Collapse
|
3
|
Sun L, Mailliot J, Schaffitzel C. Nonsense-Mediated mRNA Decay Factor Functions in Human Health and Disease. Biomedicines 2023; 11:722. [PMID: 36979701 PMCID: PMC10045457 DOI: 10.3390/biomedicines11030722] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a cellular surveillance mechanism that degrades mRNAs with a premature stop codon, avoiding the synthesis of C-terminally truncated proteins. In addition to faulty mRNAs, NMD recognises ~10% of endogenous transcripts in human cells and downregulates their expression. The up-frameshift proteins are core NMD factors and are conserved from yeast to human in structure and function. In mammals, NMD diversified into different pathways that target different mRNAs employing additional NMD factors. Here, we review our current understanding of molecular mechanisms and cellular roles of NMD pathways and the involvement of more specialised NMD factors. We describe the consequences of mutations in NMD factors leading to neurodevelopmental diseases, and the role of NMD in cancer. We highlight strategies of RNA viruses to evade recognition and decay by the NMD machinery.
Collapse
Affiliation(s)
- Lingling Sun
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Justine Mailliot
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Christiane Schaffitzel
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK
- Bristol Engineering Biology Centre BrisEngBio, 24 Tyndall Ave, Bristol BS8 1TQ, UK
| |
Collapse
|
4
|
Implementing computational methods in tandem with synonymous gene recoding for therapeutic development. Trends Pharmacol Sci 2023; 44:73-84. [PMID: 36307252 DOI: 10.1016/j.tips.2022.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 12/24/2022]
Abstract
Synonymous gene recoding, the substitution of synonymous variants into the genetic sequence, has been used to overcome many production limitations in therapeutic development. However, the safety and efficacy of recoded therapeutics can be difficult to evaluate because synonymous codon substitutions can result in subtle, yet impactful changes in protein features and require sensitive methods for detection. Given that computational approaches have made significant leaps in recent years, we propose that machine-learning (ML) tools may be leveraged to assess gene-recoded therapeutics and foresee an opportunity to adapt codon contexts to enhance some powerful existing tools. Here, we examine how synonymous gene recoding has been used to address challenges in therapeutic development, explain the biological mechanisms underlying its effects, and explore the application of computational platforms to improve the surveillance of functional variants in therapeutic design.
Collapse
|
5
|
Wallmeroth D, Lackmann JW, Kueckelmann S, Altmüller J, Dieterich C, Boehm V, Gehring NH. Human UPF3A and UPF3B enable fault-tolerant activation of nonsense-mediated mRNA decay. EMBO J 2022; 41:e109191. [PMID: 35451084 PMCID: PMC9108619 DOI: 10.15252/embj.2021109191] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 03/18/2022] [Accepted: 03/31/2022] [Indexed: 12/14/2022] Open
Abstract
The paralogous human proteins UPF3A and UPF3B are involved in recognizing mRNAs targeted by nonsense‐mediated mRNA decay (NMD). UPF3B has been demonstrated to support NMD, presumably by bridging an exon junction complex (EJC) to the NMD factor UPF2. The role of UPF3A has been described either as a weak NMD activator or an NMD inhibitor. Here, we present a comprehensive functional analysis of UPF3A and UPF3B in human cells using combinatory experimental approaches. Overexpression or knockout of UPF3A as well as knockout of UPF3B did not substantially change global NMD activity. In contrast, the co‐depletion of UPF3A and UPF3B resulted in a marked NMD inhibition and a transcriptome‐wide upregulation of NMD substrates, demonstrating a functional redundancy between both NMD factors. In rescue experiments, UPF2 or EJC binding‐deficient UPF3B largely retained NMD activity. However, combinations of different mutants, including deletion of the middle domain, showed additive or synergistic effects and therefore failed to maintain NMD. Collectively, UPF3A and UPF3B emerge as fault‐tolerant, functionally redundant NMD activators in human cells.
Collapse
Affiliation(s)
- Damaris Wallmeroth
- Institute for Genetics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | | | - Sabrina Kueckelmann
- Institute for Genetics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg University Hospital, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Volker Boehm
- Institute for Genetics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| |
Collapse
|
6
|
Yi Z, Arvola RM, Myers S, Dilsavor CN, Abu Alhasan R, Carter BN, Patton RD, Bundschuh R, Singh G. Mammalian UPF3A and UPF3B can activate nonsense-mediated mRNA decay independently of their exon junction complex binding. EMBO J 2022; 41:e109202. [PMID: 35451102 PMCID: PMC9108626 DOI: 10.15252/embj.2021109202] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 03/21/2022] [Accepted: 03/31/2022] [Indexed: 12/30/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is governed by the three conserved factors-UPF1, UPF2, and UPF3. While all three are required for NMD in yeast, UPF3B is dispensable for NMD in mammals, and its paralog UPF3A is suggested to only weakly activate or even repress NMD due to its weaker binding to the exon junction complex (EJC). Here, we characterize the UPF3A/B-dependence of NMD in human cell lines deleted of one or both UPF3 paralogs. We show that in human colorectal cancer HCT116 cells, NMD can operate in a UPF3B-dependent and -independent manner. While UPF3A is almost dispensable for NMD in wild-type cells, it strongly activates NMD in cells lacking UPF3B. Notably, NMD remains partially active in cells lacking both UPF3 paralogs. Complementation studies in these cells show that EJC-binding domain of UPF3 paralogs is dispensable for NMD. Instead, the conserved "mid" domain of UPF3 paralogs is consequential for their NMD activity. Altogether, our results demonstrate that the mammalian UPF3 proteins play a more active role in NMD than simply bridging the EJC and the UPF complex.
Collapse
Affiliation(s)
- Zhongxia Yi
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - René M Arvola
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Sean Myers
- Department of Physics, The Ohio State University, Columbus, OH, USA
| | - Corinne N Dilsavor
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Rabab Abu Alhasan
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Bayley N Carter
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Robert D Patton
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Physics, The Ohio State University, Columbus, OH, USA
| | - Ralf Bundschuh
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Physics, The Ohio State University, Columbus, OH, USA.,Department of Chemistry and Biochemistry, The Ohio State University , Columbus, OH, USA.,Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Guramrit Singh
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
7
|
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.
Collapse
|
8
|
Highly efficient prime editing by introducing same-sense mutations in pegRNA or stabilizing its structure. Nat Commun 2022; 13:1669. [PMID: 35351879 PMCID: PMC8964725 DOI: 10.1038/s41467-022-29339-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/11/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractPrime editor (PE), which is developed by combining Cas9 nickase and an engineered reverse transcriptase, can mediate all twelve types of base substitutions and small insertions or deletions in living cells but its efficiency remains low. Here, we develop spegRNA by introducing same-sense mutations at proper positions in the reverse-transcription template of pegRNA to increase PE’s base-editing efficiency up-to 4,976-fold (on-average 353-fold). We also develop apegRNA by altering the pegRNA secondary structure to increase PE’s indel-editing efficiency up-to 10.6-fold (on-average 2.77-fold). The spegRNA and apegRNA can be combined to further enhance editing efficiency. When spegRNA and apegRNA are used in PE3 and PE5 systems, the efficiencies of sPE3, aPE3, sPE5 and aPE5 systems are all enhanced significantly. The strategies developed in this study realize highly efficient prime editing at certain previously uneditable sites.
Collapse
|
9
|
Marques AR, Santos JX, Martiniano H, Vilela J, Rasga C, Romão L, Vicente AM. Gene Variants Involved in Nonsense-Mediated mRNA Decay Suggest a Role in Autism Spectrum Disorder. Biomedicines 2022; 10:biomedicines10030665. [PMID: 35327467 PMCID: PMC8945030 DOI: 10.3390/biomedicines10030665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 02/07/2023] Open
Abstract
Autism Spectrum Disorder (ASD) is a heterogeneous neurodevelopmental condition with unclear etiology. Many genes have been associated with ASD risk, but the underlying mechanisms are still poorly understood. An important post-transcriptional regulatory mechanism that plays an essential role during neurodevelopment, the Nonsense-Mediated mRNA Decay (NMD) pathway, may contribute to ASD risk. In this study, we gathered a list of 46 NMD factors and regulators and investigated the role of genetic variants in these genes in ASD. By conducting a comprehensive search for Single Nucleotide Variants (SNVs) in NMD genes using Whole Exome Sequencing data from 1828 ASD patients, we identified 270 SNVs predicted to be damaging in 28.7% of the population. We also analyzed Copy Number Variants (CNVs) from two cohorts of ASD patients (N = 3570) and discovered 38 CNVs in 1% of cases. Importantly, we discovered 136 genetic variants (125 SNVs and 11 CNVs) in 258 ASD patients that were located within protein domains required for NMD. These gene variants are classified as damaging using in silico prediction tools, and therefore may interfere with proper NMD function in ASD. The discovery of NMD genes as candidates for ASD in large patient genomic datasets provides evidence supporting the involvement of the NMD pathway in ASD pathophysiology.
Collapse
Affiliation(s)
- Ana Rita Marques
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (A.R.M.); (J.X.S.); (H.M.); (J.V.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
| | - João Xavier Santos
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (A.R.M.); (J.X.S.); (H.M.); (J.V.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
| | - Hugo Martiniano
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (A.R.M.); (J.X.S.); (H.M.); (J.V.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
| | - Joana Vilela
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (A.R.M.); (J.X.S.); (H.M.); (J.V.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
| | - Célia Rasga
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (A.R.M.); (J.X.S.); (H.M.); (J.V.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
| | - Luísa Romão
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal
| | - Astrid Moura Vicente
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (A.R.M.); (J.X.S.); (H.M.); (J.V.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal;
- Correspondence:
| |
Collapse
|
10
|
Yuan Y, Zhou Q, Wang C, Zhou W, Gu W, Zheng B. Clinical and molecular characterization of a patient with MBTPS1 related spondyloepiphyseal dysplasia: Evidence of pathogenicity for a synonymous variant. Front Pediatr 2022; 10:1056141. [PMID: 36714646 PMCID: PMC9874673 DOI: 10.3389/fped.2022.1056141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND A novel autosomal recessive skeletal dysplasia resulting from pathogenic variants in membrane-bound transcription factor peptidase, site 1 (MBTPS1) has been recently delineated. To date, only three patients have been reported. METHODS In this study, we reported the clinical and molecular features of a Chinese boy who was diagnosed with spondyloepiphyseal dysplasia. The effects of variants on mRNA splicing were analyzed through transcript analysis in vivo and minigene splice assay in vitro. RESULTS The proband mainly showed short stature, special facial features, cataract, hernias, and serious sleep apnea syndrome. Growth hormone stimulation tests suggested the boy had growth hormone deficiency. Imaging examinations suggested abnormal thoracolumbar vertebrae and severely decreased bone mineral density. Genetic analysis of MBTPS1 gene revealed two novel heterozygous variants, a nonsense mutation c.2656C > T (p.Q886*, 167) in exon 20 and a synonymous variant c.774C > T (p.A258=) in exon 6. The transcript analysis in vivo exhibited that the synonymous variant c.774C > T caused exon 6 skipping. The minigene splice assay in vitro confirmed the alteration of MBTPS1 mRNA splicing and the exon skipping was partially restored by an antisense oligonucleotide (ASO) treatment. CONCLUSION Notably, we report a Chinese rare case of spondyloepiphyseal dysplasia and validate its pathogenic synonymous variant in the MBTPS1 gene.
Collapse
Affiliation(s)
- Yeqing Yuan
- Department of Endocrinology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Qiaoli Zhou
- Department of Endocrinology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Chunli Wang
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Zhou
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Gu
- Department of Endocrinology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Bixia Zheng
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| |
Collapse
|