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Soueid J, Hamze Z, Bedran J, Chahrour M, Boustany RM. A novel autism-associated UBLCP1 mutation impacts proteasome regulation/activity. Transl Psychiatry 2023; 13:404. [PMID: 38129378 PMCID: PMC10739866 DOI: 10.1038/s41398-023-02702-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 11/16/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
The landscape of autism spectrum disorder (ASD) in Lebanon is unique because of high rates of consanguinity, shared ancestry, and increased remote consanguinity. ASD prevalence in Lebanon is 1 in 68 with a male-to-female ratio of 2:1. This study aims to investigate the impact of an inherited deletion in UBLCP1 (Ubiquitin-Like Domain-Containing CTD Phosphatase 1) on the ubiquitin-proteasome system (UPS) and proteolysis. Whole exome sequencing in a Lebanese family with ASD without pathogenic copy number variations (CNVs) uncovered a deletion in UBLCP1. Functional evaluation of the identified variant is described in fibroblasts from the affected. The deletion in UBLCP1 exon 10 (g.158,710,261CAAAG > C) generates a premature stop codon interrupting the phosphatase domain and is predicted as pathogenic. It is absent from databases of normal variation worldwide and in Lebanon. Wild-type UBLCP1 is widely expressed in mouse brains. The mutation results in decreased UBLCP1 protein expression in patient-derived fibroblasts from the autistic patient compared to controls. The truncated UBLCP1 protein results in increased proteasome activity decreased ubiquitinated protein levels, and downregulation in expression of other proteasome subunits in samples from the affected compared to controls. Inhibition of the proteasome by using MG132 in proband cells reverses alterations in gene expression due to the restoration of protein levels of the common transcription factor, NRF1. Finally, treatment with gentamicin, which promotes premature termination codon read-through, restores UBLCP1 expression and function. Discovery of an ASD-linked mutation in UBLCP1 leading to overactivation of cell proteolysis is reported. This, in turn, leads to dysregulation of proteasome subunit transcript levels as a compensatory response.
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Affiliation(s)
- Jihane Soueid
- Department of Biochemistry and Molecular Genetics, American university of Beirut, Beirut, Lebanon
| | - Zeinab Hamze
- Department of Biochemistry and Molecular Genetics, American university of Beirut, Beirut, Lebanon
| | - Joe Bedran
- Department of Biochemistry and Molecular Genetics, American university of Beirut, Beirut, Lebanon
| | - Maria Chahrour
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Rose-Mary Boustany
- Department of Biochemistry and Molecular Genetics, American university of Beirut, Beirut, Lebanon.
- Departments of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center Special Kids Clinic, Neurogenetics Program and Division of Pediatric Neurology, Beirut, Lebanon.
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Fu C, Ngo J, Zhang S, Lu L, Miron A, Schafer S, Gage FH, Jin F, Schumacher FR, Wynshaw-Boris A. Novel correlative analysis identifies multiple genomic variations impacting ASD with macrocephaly. Hum Mol Genet 2023; 32:1589-1606. [PMID: 36519762 PMCID: PMC10162433 DOI: 10.1093/hmg/ddac300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Autism spectrum disorders (ASD) display both phenotypic and genetic heterogeneity, impeding the understanding of ASD and development of effective means of diagnosis and potential treatments. Genes affected by genomic variations for ASD converge in dozens of gene ontologies (GOs), but the relationship between the variations at the GO level have not been well elucidated. In the current study, multiple types of genomic variations were mapped to GOs and correlations among GOs were measured in ASD and control samples. Several ASD-unique GO correlations were found, suggesting the importance of co-occurrence of genomic variations in genes from different functional categories in ASD etiology. Combined with experimental data, several variations related to WNT signaling, neuron development, synapse morphology/function and organ morphogenesis were found to be important for ASD with macrocephaly, and novel co-occurrence patterns of them in ASD patients were found. Furthermore, we applied this gene ontology correlation analysis method to find genomic variations that contribute to ASD etiology in combination with changes in gene expression and transcription factor binding, providing novel insights into ASD with macrocephaly and a new methodology for the analysis of genomic variation.
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Affiliation(s)
- Chen Fu
- Department of Genetics and Genomic Science, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Justine Ngo
- Department of Genetics and Genomic Science, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Shanshan Zhang
- Department of Genetics and Genomic Science, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Leina Lu
- Department of Genetics and Genomic Science, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Alexander Miron
- Department of Genetics and Genomic Science, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Simon Schafer
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Fred H Gage
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Fulai Jin
- Department of Genetics and Genomic Science, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Anthony Wynshaw-Boris
- Department of Genetics and Genomic Science, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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Exome sequencing identifies de novo splicing variant in XRCC6 in sporadic case of autism. J Hum Genet 2019; 65:287-296. [PMID: 31827253 DOI: 10.1038/s10038-019-0707-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/27/2019] [Accepted: 12/01/2019] [Indexed: 02/06/2023]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with heterogeneity in presentation, genetic etiology, and clinical outcome. Although numerous ASD susceptibility genes have been described, they only account for a small fraction of the estimated heritability, supporting the need to identify more risk variants. This study reports the whole exome sequencing for 24 simplex families with sporadic cases of ASD. These families were selected following a rigorous family history study designed to exclude families with any history of neurodevelopmental or psychiatric disease. Fifteen rare, de novo variants, including fourteen missense variants and one splicing variant, in thirteen families were identified. We describe a splicing variant in XRCC6 which was predicted to destroy the 5' splice site in intron 9 and introduce a premature stop codon. We observed intron 9 retention in XRCC6 transcripts and reduced XRCC6 expression in the proband. Reduced XRCC6 activity and function may be relevant to ASD etiology due to XRCC6's role in nonhomologous DNA repair and interactions of the C-terminal SAP domain with DEAF1, a nuclear transcriptional regulator that is important during embryonic development.
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Whole exome sequencing reveals inherited and de novo variants in autism spectrum disorder: a trio study from Saudi families. Sci Rep 2017; 7:5679. [PMID: 28720891 PMCID: PMC5515956 DOI: 10.1038/s41598-017-06033-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/06/2017] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with genetic and clinical heterogeneity. The interplay of de novo and inherited rare variants has been suspected in the development of ASD. Here, we applied whole exome sequencing (WES) on 19 trios from singleton Saudi families with ASD. We developed an analysis pipeline that allows capturing both de novo and inherited rare variants predicted to be deleterious. A total of 47 unique rare variants were detected in 17 trios including 38 which are newly discovered. The majority were either autosomal recessive or X-linked. Our pipeline uncovered variants in 15 ASD-candidate genes, including 5 (GLT8D1, HTATSF1, OR6C65, ITIH6 and DDX26B) that have not been reported in any human condition. The remaining variants occurred in genes formerly associated with ASD or other neurological disorders. Examples include SUMF1, KDM5B and MXRA5 (Known-ASD genes), PRODH2 and KCTD21 (implicated in schizophrenia), as well as USP9X and SMS (implicated in intellectual disability). Consistent with expectation and previous studies, most of the genes implicated herein are enriched for biological processes pertaining to neuronal function. Our findings underscore the private and heterogeneous nature of the genetic architecture of ASD even in a population with high consanguinity rates.
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Fang H, Wu Y, Yang H, Yoon M, Jiménez-Barrón LT, Mittelman D, Robison R, Wang K, Lyon GJ. Whole genome sequencing of one complex pedigree illustrates challenges with genomic medicine. BMC Med Genomics 2017; 10:10. [PMID: 28228131 PMCID: PMC5322674 DOI: 10.1186/s12920-017-0246-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/14/2017] [Indexed: 12/18/2022] Open
Abstract
Background Human Phenotype Ontology (HPO) has risen as a useful tool for precision medicine by providing a standardized vocabulary of phenotypic abnormalities to describe presentations of human pathologies; however, there have been relatively few reports combining whole genome sequencing (WGS) and HPO, especially in the context of structural variants. Methods We illustrate an integrative analysis of WGS and HPO using an extended pedigree, which involves Prader–Willi Syndrome (PWS), hereditary hemochromatosis (HH), and dysautonomia-like symptoms. A comprehensive WGS pipeline was used to ensure reliable detection of genomic variants. Beyond variant filtering, we pursued phenotypic prioritization of candidate genes using Phenolyzer. Results Regarding PWS, WGS confirmed a 5.5 Mb de novo deletion of the parental allele at 15q11.2 to 15q13.1. Phenolyzer successfully returned the diagnosis of PWS, and pinpointed clinically relevant genes in the deletion. Further, Phenolyzer revealed how each of the genes is linked with the phenotypes represented by HPO terms. For HH, WGS identified a known disease variant (p.C282Y) in HFE of an affected female. Analysis of HPO terms alone fails to provide a correct diagnosis, but Phenolyzer successfully revealed the phenotype-genotype relationship using a disease-centric approach. Finally, Phenolyzer also revealed the complexity behind dysautonomia-like symptoms, and seven variants that might be associated with the phenotypes were identified by manual filtering based on a dominant inheritance model. Conclusions The integration of WGS and HPO can inform comprehensive molecular diagnosis for patients, eliminate false positives and reveal novel insights into undiagnosed diseases. Due to extreme heterogeneity and insufficient knowledge of human diseases, it is also important that phenotypic and genomic data are standardized and shared simultaneously. Electronic supplementary material The online version of this article (doi:10.1186/s12920-017-0246-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Han Fang
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Stony Brook University, 100 Nicolls Rd, Stony Brook, NY, USA.,Simons Center for Quantitative Biology, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yiyang Wu
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Stony Brook University, 100 Nicolls Rd, Stony Brook, NY, USA
| | - Hui Yang
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA, USA.,Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA
| | - Margaret Yoon
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Laura T Jiménez-Barrón
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, MX, Mexico
| | | | - Reid Robison
- Tute, Genomics Inc., 150 S 100 W, Provo, UT, USA.,Utah Foundation for Biomedical Research, Salt Lake City, UT, USA
| | - Kai Wang
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA, USA.,Department of Psychiatry, University of Southern California, Los Angeles, CA, USA.,Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA.,Present Address: Department of Biomedical Informatics and Institute for Genomic Medicine, Columbia University Medical Center, New York, 10032, NY, USA
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, One Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. .,Stony Brook University, 100 Nicolls Rd, Stony Brook, NY, USA. .,Utah Foundation for Biomedical Research, Salt Lake City, UT, USA.
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