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Mitz AR, Boccuto L, Thurm A. Evidence for common mechanisms of pathology between SHANK3 and other genes of Phelan-McDermid syndrome. Clin Genet 2024; 105:459-469. [PMID: 38414139 PMCID: PMC11025605 DOI: 10.1111/cge.14503] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/18/2024] [Accepted: 02/02/2024] [Indexed: 02/29/2024]
Abstract
Chromosome 22q13.3 deletion (Phelan-McDermid) syndrome (PMS, OMIM 606232) is a rare genetic condition that impacts neurodevelopment. PMS most commonly results from heterozygous contiguous gene deletions that include the SHANK3 gene or likely pathogenic variants of SHANK3 (PMS-SHANK3 related). Rarely, chromosomal rearrangements that spare SHANK3 share the same general phenotype (PMS-SHANK3 unrelated). Very recent human and model system studies of genes that likely contribute to the PMS phenotype point to overlap in gene functions associated with neurodevelopment, synaptic formation, stress/inflammation and regulation of gene expression. In this review of recent findings, we describe the functional overlaps between SHANK3 and six partner genes of 22q13.3 (PLXNB2, BRD1, CELSR1, PHF21B, SULT4A1, and TCF20), which suggest a model that explains the commonality between PMS-SHANK3 related and PMS-SHANK3 unrelated classes of PMS. These genes are likely not the only contributors to neurodevelopmental impairments in the region, but they are the best documented to date. The review provides evidence for the overlapping and likely synergistic contributions of these genes to the PMS phenotype.
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Affiliation(s)
- Andrew R. Mitz
- Laboratory of Neuropsychology, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Luigi Boccuto
- Healthcare Genetics and Genomics Interdisciplinary Doctoral Program, School of Nursing, College of Behavioral, Social and Health Sciences, Clemson University, Clemson, SC, USA
| | - Audrey Thurm
- Neurodevelopmental and Behavioral Phenotyping Service, Office of the Clinical Director, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
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Phelan K, Boccuto L, Powell CM, Boeckers TM, van Ravenswaaij-Arts C, Rogers RC, Sala C, Verpelli C, Thurm A, Bennett WE, Winrow CJ, Garrison SR, Toro R, Bourgeron T. Phelan-McDermid syndrome: a classification system after 30 years of experience. Orphanet J Rare Dis 2022; 17:27. [PMID: 35093143 PMCID: PMC8800328 DOI: 10.1186/s13023-022-02180-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 01/16/2022] [Indexed: 01/15/2023] Open
Abstract
Phelan-McDermid syndrome (PMS) was initially called the 22q13 deletion syndrome based on its etiology as a deletion of the distal long arm of chromosome 22. These included terminal and interstitial deletions, as well as other structural rearrangements. Later, pathogenetic variants and deletions of the SHANK3 gene were found to result in a phenotype consistent with PMS. The association between SHANK3 and PMS led investigators to consider disruption/deletion of SHANK3 to be a prerequisite for diagnosing PMS. This narrow definition of PMS based on the involvement of SHANK3 has the adverse effect of causing patients with interstitial deletions of chromosome 22 to “lose” their diagnosis. It also results in underreporting of individuals with interstitial deletions of 22q13 that preserve SHANK3. To reduce the confusion for families, clinicians, researchers, and pharma, a simple classification for PMS has been devised. PMS and will be further classified as PMS-SHANK3 related or PMS-SHANK3 unrelated. PMS can still be used as a general term, but this classification system is inclusive. It allows researchers, regulatory agencies, and other stakeholders to define SHANK3 alterations or interstitial deletions not affecting the SHANK3 coding region.
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Dyar B, Meaddough E, Sarasua SM, Rogers C, Phelan K, Boccuto L. Genetic Findings as the Potential Basis of Personalized Pharmacotherapy in Phelan-McDermid Syndrome. Genes (Basel) 2021; 12:1192. [PMID: 34440366 PMCID: PMC8392667 DOI: 10.3390/genes12081192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/26/2021] [Accepted: 07/29/2021] [Indexed: 12/13/2022] Open
Abstract
Phelan-McDermid syndrome (PMS) is a genetic disorder often characterized by autism or autistic-like behavior. Most cases are associated with haploinsufficiency of the SHANK3 gene resulting from deletion of the gene at 22q13.3 or from a pathogenic variant in the gene. Treatment of PMS often targets SHANK3, yet deletion size varies from <50 kb to >9 Mb, potentially encompassing dozens of genes and disrupting regulatory elements altering gene expression, inferring the potential for multiple therapeutic targets. Repurposed drugs have been used in clinical trials investigating therapies for PMS: insulin-like growth factor 1 (IGF-1) for its effect on social and aberrant behaviors, intranasal insulin for improvements in cognitive and social ability, and lithium for reversing regression and stabilizing behavior. The pharmacogenomics of PMS is complicated by the CYP2D6 enzyme which metabolizes antidepressants and antipsychotics often used for treatment. The gene coding for CYP2D6 maps to 22q13.2 and is lost in individuals with deletions larger than 8 Mb. Because PMS has diverse neurological and medical symptoms, many concurrent medications may be prescribed, increasing the risk for adverse drug reactions. At present, there is no single best treatment for PMS. Approaches to therapy are necessarily complex and must target variable behavioral and physical symptoms of PMS.
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Affiliation(s)
- Brianna Dyar
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC 29634, USA; (B.D.); (E.M.); (S.M.S.)
| | - Erika Meaddough
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC 29634, USA; (B.D.); (E.M.); (S.M.S.)
| | - Sara M. Sarasua
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC 29634, USA; (B.D.); (E.M.); (S.M.S.)
| | | | - Katy Phelan
- Florida Cancer Specialists & Research Institute, Fort Myers, FL 33905, USA;
| | - Luigi Boccuto
- Healthcare Genetics Program, School of Nursing, Clemson University, Clemson, SC 29634, USA; (B.D.); (E.M.); (S.M.S.)
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Srikanth S, Jain L, Zepeda-Mendoza C, Cascio L, Jones K, Pauly R, DuPont B, Rogers C, Sarasua S, Phelan K, Morton C, Boccuto L. Position effects of 22q13 rearrangements on candidate genes in Phelan-McDermid syndrome. PLoS One 2021; 16:e0253859. [PMID: 34228749 PMCID: PMC8259982 DOI: 10.1371/journal.pone.0253859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/15/2021] [Indexed: 11/19/2022] Open
Abstract
Phelan-McDermid syndrome (PMS) is a multi-system disorder characterized by significant variability in clinical presentation. The genetic etiology is also variable with differing sizes of deletions in the chromosome 22q13 region and types of genetic abnormalities (e.g., terminal or interstitial deletions, translocations, ring chromosomes, or SHANK3 variants). Position effects have been shown to affect gene expression and function and play a role in the clinical presentation of various genetic conditions. This study employed a topologically associating domain (TAD) analysis approach to investigate position effects of chromosomal rearrangements on selected candidate genes mapped to 22q13 in 81 individuals with PMS. Data collected were correlated with clinical information from these individuals and with expression and metabolic profiles of lymphoblastoid cells from selected cases. The data confirmed TAD predictions for genes encompassed in the deletions and the clinical and molecular data indicated clear differences among individuals with different 22q13 deletion sizes. The results of the study indicate a positive correlation between deletion size and phenotype severity in PMS and provide evidence of the contribution of other genes to the clinical variability in this developmental disorder by reduced gene expression and altered metabolomics.
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Affiliation(s)
- Sujata Srikanth
- Greenwood Genetic Center, Greenwood, SC, United States of America
| | - Lavanya Jain
- School of Nursing, Healthcare Genetics Program, Clemson University, Clemson, SC, United States of America
| | - Cinthya Zepeda-Mendoza
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
| | - Lauren Cascio
- Greenwood Genetic Center, Greenwood, SC, United States of America
| | - Kelly Jones
- Greenwood Genetic Center, Greenwood, SC, United States of America
| | - Rini Pauly
- Greenwood Genetic Center, Greenwood, SC, United States of America
| | - Barb DuPont
- Greenwood Genetic Center, Greenwood, SC, United States of America
| | - Curtis Rogers
- Greenwood Genetic Center, Greenwood, SC, United States of America
| | - Sara Sarasua
- School of Nursing, Healthcare Genetics Program, Clemson University, Clemson, SC, United States of America
| | - Katy Phelan
- Genetics Laboratory, Florida Cancer Specialists and Research Institute, Fort Myers, FL, United States of America
| | - Cynthia Morton
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women’s Hospital, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, United States of America
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States of America
- Division of Human Communication, Development and Hearing, School of Biological Sciences, Manchester Academic Health Science Center, Manchester, United Kingdom
| | - Luigi Boccuto
- Greenwood Genetic Center, Greenwood, SC, United States of America
- School of Nursing, College of Behavioral, Social and Health Sciences, Clemson University, Clemson, SC, United States of America
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Ziats CA, Grosvenor LP, Sarasua SM, Thurm AE, Swedo SE, Mahfouz A, Rennert OM, Ziats MN. Functional genomics analysis of Phelan-McDermid syndrome 22q13 region during human neurodevelopment. PLoS One 2019; 14:e0213921. [PMID: 30875393 PMCID: PMC6420160 DOI: 10.1371/journal.pone.0213921] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/04/2019] [Indexed: 12/02/2022] Open
Abstract
Phelan-McDermid syndrome (PMS) is a neurodevelopmental disorder characterized by varying degrees of intellectual disability, severely delayed language development and specific facial features, and is caused by a deletion within chromosome 22q13.3. SHANK3, which is located at the terminal end of this region, has been repeatedly implicated in other neurodevelopmental disorders and deletion of this gene specifically is thought to cause much of the neurologic symptoms characteristic of PMS. However, it is still unclear to what extent SHANK3 deletions contribute to the PMS phenotype, and what other genes nearby are causal to the neurologic disease. In an effort to better understand the functional landscape of the PMS region during normal neurodevelopment, we assessed RNA-sequencing (RNA-seq) expression data collected from post-mortem brain tissue from developmentally normal subjects over the course of prenatal to adolescent age and analyzed expression changes of 65 genes on 22q13. We found that the majority of genes within this region were expressed in the brain, with ATNX10, MLC1, MAPK8IP2, and SULT4A1 having the highest overall expression. Analysis of the temporal profiles of the highest expressed genes revealed a trend towards peak expression during the early post-natal period, followed by a drop in expression later in development. Spatial analysis revealed significant region specific differences in the expression of SHANK3, MAPK8IP2, and SULT4A1. Region specific expression over time revealed a consistently unique gene expression profile within the cerebellum, providing evidence for a distinct developmental program within this region. Exon-specific expression of SHANK3 showed higher expression within exons contributing to known brain specific functional isoforms. Overall, we provide an updated roadmap of the PMS region, implicating several genes and time periods as important during neurodevelopment, with the hope that this information can help us better understand the phenotypic heterogeneity of PMS.
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Affiliation(s)
- Catherine A. Ziats
- Division of Intramural Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Luke P. Grosvenor
- Pediatrics and Developmental Neuroscience Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, United States of America
- Simons Foundation Autism Research Initiative, New York, New York, United States of America
| | - Sara M. Sarasua
- School of Nursing, Clemson University, Clemson, South Carolina, United States of America
| | - Audrey E. Thurm
- Pediatrics and Developmental Neuroscience Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Susan E. Swedo
- Pediatrics and Developmental Neuroscience Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ahmed Mahfouz
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Owen M. Rennert
- Division of Intramural Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- Pediatrics and Developmental Neuroscience Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mark N. Ziats
- Division of Intramural Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Internal Medicine, Michigan Medicine, Ann Arbor, Michigan, United States of America
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