1
|
AlRasheed MM. Genetics of Cardiac Tumours: A Narrative Review. Heart Lung Circ 2024; 33:639-647. [PMID: 38161083 DOI: 10.1016/j.hlc.2023.11.005] [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: 04/27/2023] [Revised: 10/09/2023] [Accepted: 11/13/2023] [Indexed: 01/03/2024]
Abstract
Cardiac tumours can occur in association with genetic syndromes. Rhabdomyomas have been reported in association with tuberous sclerosis, myxomas with Carney's complex, cardiac fibromas with Gorlin syndrome, and paragangliomas with multiple endocrine neoplasm syndrome. The presentation and prognosis of cardiac tumours associated with genetic syndromes differ compared with sporadic cases. Knowledge about the associated syndromes' genetic features and extracardiac manifestations is essential for the diagnosis, prognosis, and management of cardiac neoplasms. Moreover, identifying genetic mutations in benign and malignant cardiac tumours is needed to personalise management and improve treatment outcomes. Thus, this review discusses the genetic abnormalities associated with cardiac tumours, the current genetic screening recommendations, and the effect of those genetic mutations on the outcomes.
Collapse
Affiliation(s)
- Maha M AlRasheed
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia.
| |
Collapse
|
2
|
Muñoz-Pujol G, Ugarteburu O, Segur-Bailach E, Moliner S, Jurado S, Garrabou G, Guitart-Mampel M, García-Villoria J, Artuch R, Fons C, Ribes A, Tort F. CRISPR/Cas9-based functional genomics strategy to decipher the pathogenicity of genetic variants in inherited metabolic disorders. J Inherit Metab Dis 2023; 46:1029-1042. [PMID: 37718653 DOI: 10.1002/jimd.12681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/19/2023]
Abstract
The determination of the functional impact of variants of uncertain significance (VUS) is one of the major bottlenecks in the diagnostic workflow of inherited genetic diseases. To face this problem, we set up a CRISPR/Cas9-based strategy for knock-in cellular model generation, focusing on inherited metabolic disorders (IMDs). We selected variants in seven IMD-associated genes, including seven reported disease-causing variants and four benign/likely benign variants. Overall, 11 knock-in cell models were generated via homology-directed repair in HAP1 haploid cells using CRISPR/Cas9. The functional impact of the variants was determined by analyzing the characteristic biochemical alterations of each disorder. Functional studies performed in knock-in cell models showed that our approach accurately distinguished the functional effect of pathogenic from non-pathogenic variants in a reliable manner in a wide range of IMDs. Our study provides a generic approach to assess the functional impact of genetic variants to improve IMD diagnosis and this tool could emerge as a promising alternative to invasive tests, such as muscular or skin biopsies. Although the study has been performed only in IMDs, this strategy is generic and could be applied to other genetic disorders.
Collapse
Affiliation(s)
- Gerard Muñoz-Pujol
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Olatz Ugarteburu
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Eulàlia Segur-Bailach
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Sonia Moliner
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Susana Jurado
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Glòria Garrabou
- Inherited Metabolic diseases and Muscle Disorder's lab, Cellex-IDIBAPS, Faculty of Medicine and Health Sciences, University of Barcelona, Internal Medicine Service-Hospital Clinic of Barcelona and CIBERER, Barcelona, Spain
| | - Mariona Guitart-Mampel
- Inherited Metabolic diseases and Muscle Disorder's lab, Cellex-IDIBAPS, Faculty of Medicine and Health Sciences, University of Barcelona, Internal Medicine Service-Hospital Clinic of Barcelona and CIBERER, Barcelona, Spain
| | - Judit García-Villoria
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Rafael Artuch
- Clinical Biochemistry and Molecular Medicine and Genetics Departments, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, and CIBERER, Esplúgues de Llobregat, Barcelona, Spain
| | - Carme Fons
- Neurology Department, Fetal, Neonatal Neurology and Early Epilepsy Unit, Institut de Recerca, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Antonia Ribes
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Frederic Tort
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| |
Collapse
|
3
|
Farach LS, Northrup H, Nellist M, van Unen L, Hillman P, Klonowska K, Ekong R, Crino PB, Sing Au K. Mild TSC Phenotype and Non-Penetrance Associated with a Frameshift Variant in TSC2 Prompts Caution in Evaluating Pathogenicity of Frameshift Variants. Gene 2023:147566. [PMID: 37311496 DOI: 10.1016/j.gene.2023.147566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/15/2023]
Abstract
INTRODUCTION Technological advances in genetic testing, particularly the adoption of noninvasive prenatal screening (NIPS) for single gene disorders such as tuberous sclerosis complex (TSC, OMIM# 613254), mean that putative/possible pathogenetic DNA variants can be identified prior to the appearance of a disease phenotype. Without a phenotype, accurate prediction of variant pathogenicity is crucial. Here, we report a TSC2 frameshift variant, NM_000548.5(TSC2):c.4255_4256delCA, predicted to result in nonsense-mediated mRNA decay (NMD) and cessation of TSC2 protein production and thus pathogenic according to ACMG criteria, identified by NIPS and subsequently detected in family members with few or no symptoms of TSC. Due to the lack of TSC-associated features in the family, we hypothesized that the deletion created a non-canonical 5' donor site resulting in cryptic splicing and a transcript encoding active TSC2 protein. Verifying the predicted effect of the variant was key to designating pathogenicity in this case and should be considered for other frameshift variants in other genetic disorders. METHODS Phenotypic information on the family members was collected via review of the medical records and patient reports. RNA studies were performed using proband mRNA isolated from blood lymphocytes for RT-PCR and Sanger sequencing. Functional studies were performed by transient expression of the TSC2 variant proteins in cultured cells, followed by immunoblotting. RESULTS No family members harboring the variant met any major clinical diagnostic criteria for TSC, though a few minor features non-specific to TSC were present. RNA studies supported the hypothesis that the variant caused cryptic splicing, resulting in an mRNA transcript with an in-frame deletion of 93 base pairs r.[4255_4256del, 4251_4343del], p.[(Gln1419Valfs*104), (Gln1419_Ser1449del)]. Expression studies demonstrated that the canonical function of the resulting truncated TSC2 p.Gln1419_Ser1449del protein product was maintained and similar to wildtype. CONCLUSION Although most frameshift variants are likely to result in NMD, the NM_000548.5(TSC2):c.4255_4256delCA variant creates a cryptic 5' splice donor site, resulting in an in-frame deletion that retains TSC2 function, explaining why carriers of the variant do not have typical features of TSC. The information is important for this family and others with the same variant. Equally important is the lesson that predictions can be inaccurate, and that caution should be used when designating frameshift variants as pathogenic, especially when phenotypic information to corroborate testing results is unavailable. Our work demonstrates that functional RNA- and protein-based confirmation of the effects of DNA variants improves molecular genetic diagnostics.
Collapse
Affiliation(s)
- Laura S Farach
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston) and Children's Memorial Hermann Hospital, Houston, Texas, USA.
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston) and Children's Memorial Hermann Hospital, Houston, Texas, USA
| | - Mark Nellist
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Leontine van Unen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Paul Hillman
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston) and Children's Memorial Hermann Hospital, Houston, Texas, USA
| | - Katarzyna Klonowska
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Rosemary Ekong
- Research Department of Genetics, Evolution and Environment, Darwin Building, University College London, London, United Kingdom
| | - Peter B Crino
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kit Sing Au
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston) and Children's Memorial Hermann Hospital, Houston, Texas, USA
| |
Collapse
|
4
|
Functional Assays Combined with Pre-mRNA-Splicing Analysis Improve Variant Classification and Diagnostics for Individuals with Neurofibromatosis Type 1 and Legius Syndrome. Hum Mutat 2023. [DOI: 10.1155/2023/9628049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Neurofibromatosis type 1 (NF1) and Legius syndrome (LS) are caused by inactivating variants in NF1 and SPRED1. NF1 encodes neurofibromin (NF), a GTPase-activating protein (GAP) for RAS that interacts with the SPRED1 product, Sprouty-related protein with an EVH (Ena/Vasp homology) domain 1 (SPRED1). Obtaining a clinical and molecular diagnosis of NF1 or LS can be challenging due to the phenotypic diversity, the size and complexity of the NF1 and SPRED1 loci, and uncertainty over the effects of some NF1 and SPRED1 variants on pre-mRNA splicing and/or protein expression and function. To improve NF1 and SPRED1 variant classification and establish pathogenicity for NF1 and SPRED1 variants identified in individuals with NF1 or LS, we analyzed patient RNA by RT-PCR and performed in vitro exon trap experiments and estimated NF and SPRED1 protein expression, RAS GAP activity, and interaction. We obtained evidence to support pathogenicity according to American College of Medical Genetics guidelines for 73/114 variants tested, demonstrating the utility of functional approaches for NF1 and SPRED1 variant classification and NF and LS diagnostics.
Collapse
|
5
|
Douben HCW, Nellist M, van Unen L, Elfferich P, Kasteleijn E, Hoogeveen-Westerveld M, Louwen J, van Veghel-Plandsoen M, de Valk W, Saris JJ, Hendriks F, Korpershoek E, Hoefsloot LH, van Vliet M, van Bever Y, van de Laar I, Aten E, Lachmeijer AMA, Taal W, van den Bersselaar L, Schuurmans J, Oostenbrink R, van Minkelen R, van Ierland Y, van Ham TJ. High-yield identification of pathogenic NF1 variants by skin fibroblast transcriptome screening after apparently normal diagnostic DNA testing. Hum Mutat 2022; 43:2130-2140. [PMID: 36251260 PMCID: PMC10099955 DOI: 10.1002/humu.24487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/29/2022] [Accepted: 09/26/2022] [Indexed: 01/25/2023]
Abstract
Neurofibromatosis type 1 (NF1) is caused by inactivating mutations in NF1. Due to the size, complexity, and high mutation rate at the NF1 locus, the identification of causative variants can be challenging. To obtain a molecular diagnosis in 15 individuals meeting diagnostic criteria for NF1, we performed transcriptome analysis (RNA-seq) on RNA obtained from cultured skin fibroblasts. In each case, routine molecular DNA diagnostics had failed to identify a disease-causing variant in NF1. A pathogenic variant or abnormal mRNA splicing was identified in 13 cases: 6 deep intronic variants and 2 transposon insertions causing noncanonical splicing, 3 postzygotic changes, 1 branch point mutation and, in 1 case, abnormal splicing for which the responsible DNA change remains to be identified. These findings helped resolve the molecular findings for an additional 17 individuals in multiple families with NF1, demonstrating the utility of skin-fibroblast-based transcriptome analysis for molecular diagnostics. RNA-seq improves mutation detection in NF1 and provides a powerful complementary approach to DNA-based methods. Importantly, our approach is applicable to other genetic disorders, particularly those caused by a wide variety of variants in a limited number of genes and specifically for individuals in whom routine molecular DNA diagnostics did not identify the causative variant.
Collapse
Affiliation(s)
- Hannie C W Douben
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mark Nellist
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Leontine van Unen
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Peter Elfferich
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Esmee Kasteleijn
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Jesse Louwen
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Walter de Valk
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jasper J Saris
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Femke Hendriks
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Esther Korpershoek
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Lies H Hoefsloot
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Margreethe van Vliet
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Yolande van Bever
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ingrid van de Laar
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Emmelien Aten
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Augusta M A Lachmeijer
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Walter Taal
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands.,Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lisa van den Bersselaar
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Juliette Schuurmans
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rianne Oostenbrink
- ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands.,Department of General Pediatrics, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Rick van Minkelen
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Yvette van Ierland
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Tjakko J van Ham
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| |
Collapse
|
6
|
Cui M, Jiang W, Sheng J, Wu J, Zhang X. Rap_GAP Domain of TSC2 Contributes to Tumor Suppression Through mTOR Signaling in Human Hepatocellular Carcinoma. DNA Cell Biol 2022; 41:215-224. [PMID: 35143341 DOI: 10.1089/dna.2021.0769] [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] [Indexed: 11/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is an aggressive disease with a high degree of tumor heterogeneity. Genetic lesions of mTOR-related genes, including TSC2 and hyperactivation of mTOR signaling, are common in HCC. However, the association of genetic alterations with hepatocarcinogenesis remains unclear. In this study, continuous truncating mutations occurred within or upstream of the TSC2 Rap_GAP domain in clinical HCC samples. To elucidate whether hyperactivation of mTOR signaling in HCC is caused by TSC2 truncating mutations, HCC cell models carrying the TSC2 deletion (CRISPR/Cas9) or the TSC2 truncating mutation (mutagenesis) were established. Our findings showed that either TSC2 deletion or TSC2 mutant could lead to TSC2 loss-of-function and hyperactivation of mTOR signaling. Furthermore, hyperactivation of mTOR signaling was relieved by rapamycin. Immunohistochemistry of clinical samples confirmed frequent TSC2 loss in HCC. Thus, our study revealed that genetic alterations cause TSC2 loss of function and result in the hyperactivation of mTOR, and high frequency of TSC2 truncating mutations around RAP_GAP domain may be one of the reasons for the hyperactivation of mTOR in HCC patients.
Collapse
Affiliation(s)
- Mengying Cui
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, P.R. China
| | - Weibo Jiang
- Department of Orthopedic, The Second Hospital of Jilin University, Changchun, P.R. China
| | - Jiyao Sheng
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, P.R. China
| | - Jiacheng Wu
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, P.R. China
| | - Xuewen Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, P.R. China
| |
Collapse
|
7
|
Updated International Tuberous Sclerosis Complex Diagnostic Criteria and Surveillance and Management Recommendations. Pediatr Neurol 2021; 123:50-66. [PMID: 34399110 DOI: 10.1016/j.pediatrneurol.2021.07.011] [Citation(s) in RCA: 245] [Impact Index Per Article: 81.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 07/20/2021] [Indexed: 01/10/2023]
Abstract
BACKGROUND Tuberous sclerosis complex (TSC) is an autosomal dominant genetic disease affecting multiple body systems with wide variability in presentation. In 2013, Pediatric Neurology published articles outlining updated diagnostic criteria and recommendations for surveillance and management of disease manifestations. Advances in knowledge and approvals of new therapies necessitated a revision of those criteria and recommendations. METHODS Chairs and working group cochairs from the 2012 International TSC Consensus Group were invited to meet face-to-face over two days at the 2018 World TSC Conference on July 25 and 26 in Dallas, TX, USA. Before the meeting, working group cochairs worked with group members via e-mail and telephone to (1) review TSC literature since the 2013 publication, (2) confirm or amend prior recommendations, and (3) provide new recommendations as required. RESULTS Only two changes were made to clinical diagnostic criteria reported in 2013: "multiple cortical tubers and/or radial migration lines" replaced the more general term "cortical dysplasias," and sclerotic bone lesions were reinstated as a minor criterion. Genetic diagnostic criteria were reaffirmed, including highlighting recent findings that some individuals with TSC are genetically mosaic for variants in TSC1 or TSC2. Changes to surveillance and management criteria largely reflected increased emphasis on early screening for electroencephalographic abnormalities, enhanced surveillance and management of TSC-associated neuropsychiatric disorders, and new medication approvals. CONCLUSIONS Updated TSC diagnostic criteria and surveillance and management recommendations presented here should provide an improved framework for optimal care of those living with TSC and their families.
Collapse
|
8
|
Bąbol-Pokora K, Bielska M, Bobeff K, Jatczak-Pawlik I, Borkowska J, Kotulska K, Jóźwiak S, Młynarski W, Trelińska J. A multistep approach to the genotype-phenotype analysis of Polish patients with tuberous sclerosis complex. Eur J Med Genet 2021; 64:104309. [PMID: 34403804 DOI: 10.1016/j.ejmg.2021.104309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 07/23/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022]
Abstract
The aim of this study was to evaluate a cost-effective diagnostic strategy for identification of casual variants for tuberous sclerosis complex (TSC) in the Polish population and to correlate the genetic results with selected phenotypic features. Fifty-five patients, aged 3-44 years, with a clinical diagnosis of TSC were enrolled into the study. All patients received a three-step analysis: next generation sequencing screening (NGS), multiplex ligation-dependent probe amplification (MLPA) and deep sequencing. This multistep approach obtained positive results in 51/55 (93%) patients: of the 51 positives TSC1 variants were observed in 16 (31%) and TSC2 variants in 35 (69%); these included 13 novel variants and two patients with mosaicism. Four patients (7%) had no mutation identified (NMI). Among the TSC1 gene variants, there were five nonsense, four frameshift, three large deletions, two missense and two splicing variants. For the TSC2 gene, 11 were missense, eight splicing, six frameshift, four large deletions, two in-frame deletions and four nonsense variants. The patients with TSC2 changes had their clinical diagnosis of TSC at a younger age than those with TSC1 changes (one year vs three years, p = 0.041). The TSC2 group demonstrated a higher number of major symptoms per patient (p = 0.04). Subependymal giant cell astrocytoma with concomitance of other brain lesions was more common in patients with missense mutations in either gene (23% vs 0%, p = 0.02). Such a multistep molecular diagnostic strategy could increase the possibility of detecting causal variants for TSC and may allow detection of mosaicism at low levels. Missense pathogenic variants in TSC1 or TSC2 gene might be associated with a higher risk of brain lesions.
Collapse
Affiliation(s)
- Katarzyna Bąbol-Pokora
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, ul. Sporna 36/50, 91-738, Lodz, Poland
| | - Marta Bielska
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, ul. Sporna 36/50, 91-738, Lodz, Poland
| | - Katarzyna Bobeff
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, ul. Sporna 36/50, 91-738, Lodz, Poland
| | - Izabela Jatczak-Pawlik
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, ul. Sporna 36/50, 91-738, Lodz, Poland
| | - Julita Borkowska
- Department of Neurology & Epileptology, The Children's Memorial Health Institute, ul. Dzieci Polskich 20, 04-730, Warsaw, Poland
| | - Katarzyna Kotulska
- Department of Neurology & Epileptology, The Children's Memorial Health Institute, ul. Dzieci Polskich 20, 04-730, Warsaw, Poland
| | - Sergiusz Jóźwiak
- Department of Child Neurology, Medical University of Warsaw, ul. Zwirki I Wigury 63A, 02-097, Warsaw, Poland
| | - Wojciech Młynarski
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, ul. Sporna 36/50, 91-738, Lodz, Poland
| | - Joanna Trelińska
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, ul. Sporna 36/50, 91-738, Lodz, Poland.
| |
Collapse
|
9
|
Cochran M, East K, Greve V, Kelly M, Kelley W, Moore T, Myers RM, Odom K, Schroeder MC, Bick D. A study of elective genome sequencing and pharmacogenetic testing in an unselected population. Mol Genet Genomic Med 2021; 9:e1766. [PMID: 34313030 PMCID: PMC8457704 DOI: 10.1002/mgg3.1766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 04/08/2021] [Accepted: 07/09/2021] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Genome sequencing (GS) of individuals without a medical indication, known as elective GS, is now available at a number of centers around the United States. Here we report the results of elective GS and pharmacogenetic panel testing in 52 individuals at a private genomics clinic in Alabama. METHODS Individuals seeking elective genomic testing and pharmacogenetic testing were recruited through a private genomics clinic in Huntsville, AL. Individuals underwent clinical genome sequencing with a separate pharmacogenetic testing panel. RESULTS Six participants (11.5%) had pathogenic or likely pathogenic variants that may explain one or more aspects of their medical history. Ten participants (19%) had variants that altered the risk of disease in the future, including two individuals with clonal hematopoiesis of indeterminate potential. Forty-four participants (85%) were carriers of a recessive or X-linked disorder. All individuals with pharmacogenetic testing had variants that affected current and/or future medications. CONCLUSION Our study highlights the importance of collecting detailed phenotype information to interpret results in elective GS.
Collapse
Affiliation(s)
- Meagan Cochran
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Kelly East
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Veronica Greve
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Melissa Kelly
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Whitley Kelley
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Troy Moore
- Kailos Genetics, Huntsville, Alabama, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Katherine Odom
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Molly C Schroeder
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| |
Collapse
|
10
|
Functional and structural analyses of novel Smith-Kingsmore Syndrome-Associated MTOR variants reveal potential new mechanisms and predictors of pathogenicity. PLoS Genet 2021; 17:e1009651. [PMID: 34197453 PMCID: PMC8279410 DOI: 10.1371/journal.pgen.1009651] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/14/2021] [Accepted: 06/08/2021] [Indexed: 12/31/2022] Open
Abstract
Smith-Kingsmore syndrome (SKS) is a rare neurodevelopmental disorder characterized by macrocephaly/megalencephaly, developmental delay, intellectual disability, hypotonia, and seizures. It is caused by dominant missense mutations in MTOR. The pathogenicity of novel variants in MTOR in patients with neurodevelopmental disorders can be difficult to determine and the mechanism by which variants cause disease remains poorly understood. We report 7 patients with SKS with 4 novel MTOR variants and describe their phenotypes. We perform in vitro functional analyses to confirm MTOR activation and interrogate disease mechanisms. We complete structural analyses to understand the 3D properties of pathogenic variants. We examine the accuracy of relative accessible surface area, a quantitative measure of amino acid side-chain accessibility, as a predictor of MTOR variant pathogenicity. We describe novel clinical features of patients with SKS. We confirm MTOR Complex 1 activation and identify MTOR Complex 2 activation as a new potential mechanism of disease in SKS. We find that pathogenic MTOR variants disproportionately cluster in hotspots in the core of the protein, where they disrupt alpha helix packing due to the insertion of bulky amino acid side chains. We find that relative accessible surface area is significantly lower for SKS-associated variants compared to benign variants. We expand the phenotype of SKS and demonstrate that additional pathways of activation may contribute to disease. Incorporating 3D properties of MTOR variants may help in pathogenicity classification. We hope these findings may contribute to improving the precision of care and therapeutic development for individuals with SKS. Smith-Kingsmore Syndrome is a rare disease caused by damage in a gene named MTOR that is associated with excessive growth of the head and brain, delays in development and deficits in intellectual functioning. We report 7 patients who have changes in MTOR that have never been reported before. We describe new medical findings in these patients that may be common in Smith-Kingsmore Syndrome more broadly. We then identify how these new gene changes impact the function of the MTOR protein and thus cell function downstream. Lastly, we show that changes in the gene that lie deep inside the 3D structure of the MTOR protein are more likely to cause disease than those changes that lie on the surface of the protein. We may be able to use the 3D properties of MTOR gene changes to predict if future changes we see are likely to cause disease or not.
Collapse
|
11
|
Kuroda K, Moriya K, Nakano T, Saito R, Sato D, Katayama S, Niizuma H, Watanuki M, Uematsu M, Sasahara Y, Kure S. A pediatric case of osteosarcoma and tuberous sclerosis complex with a novel germline mutation in the TSC2 gene and a somatic mutation in the TP53 gene. Pediatr Blood Cancer 2021; 68:e28960. [PMID: 33694273 DOI: 10.1002/pbc.28960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/25/2021] [Accepted: 02/01/2021] [Indexed: 11/08/2022]
Affiliation(s)
- Kaoru Kuroda
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kunihiko Moriya
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tomohiro Nakano
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ryoko Saito
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Daichi Sato
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Saori Katayama
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hidetaka Niizuma
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Munenori Watanuki
- Department of Orthopedic Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mitsugu Uematsu
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoji Sasahara
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shigeo Kure
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| |
Collapse
|
12
|
Proietti Onori M, Koene LMC, Schäfer CB, Nellist M, de Brito van Velze M, Gao Z, Elgersma Y, van Woerden GM. RHEB/mTOR hyperactivity causes cortical malformations and epileptic seizures through increased axonal connectivity. PLoS Biol 2021; 19:e3001279. [PMID: 34038402 PMCID: PMC8186814 DOI: 10.1371/journal.pbio.3001279] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 06/08/2021] [Accepted: 05/10/2021] [Indexed: 01/03/2023] Open
Abstract
Hyperactivation of the mammalian target of rapamycin (mTOR) pathway can cause malformation of cortical development (MCD) with associated epilepsy and intellectual disability (ID) through a yet unknown mechanism. Here, we made use of the recently identified dominant-active mutation in Ras Homolog Enriched in Brain 1 (RHEB), RHEBp.P37L, to gain insight in the mechanism underlying the epilepsy caused by hyperactivation of the mTOR pathway. Focal expression of RHEBp.P37L in mouse somatosensory cortex (SScx) results in an MCD-like phenotype, with increased mTOR signaling, ectopic localization of neurons, and reliable generalized seizures. We show that in this model, the mTOR-dependent seizures are caused by enhanced axonal connectivity, causing hyperexcitability of distally connected neurons. Indeed, blocking axonal vesicle release from the RHEBp.P37L neurons alone completely stopped the seizures and normalized the hyperexcitability of the distally connected neurons. These results provide new evidence of the extent of anatomical and physiological abnormalities caused by mTOR hyperactivity, beyond local malformations, which can lead to generalized epilepsy. Hyperactivation of the mTOR pathway can cause cortical malformations and epilepsy. This study reveals that these effects can be uncoupled and that mTOR hyperactivity in a limited set of neurons induces hyperexcitability in non-targeted, healthy neurons, suggesting that it is actually these changes that may underlie mTOR-driven epileptogenesis.
Collapse
Affiliation(s)
- Martina Proietti Onori
- Department of Neuroscience, Erasmus Medical Center, Rotterdam, the Netherlands
- The ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Linda M. C. Koene
- Department of Neuroscience, Erasmus Medical Center, Rotterdam, the Netherlands
- The ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Carmen B. Schäfer
- Department of Neuroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mark Nellist
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, Zuid Holland, the Netherlands
| | | | - Zhenyu Gao
- Department of Neuroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Ype Elgersma
- Department of Neuroscience, Erasmus Medical Center, Rotterdam, the Netherlands
- The ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, Zuid Holland, the Netherlands
- * E-mail: (YE); (GMvW)
| | - Geeske M. van Woerden
- Department of Neuroscience, Erasmus Medical Center, Rotterdam, the Netherlands
- The ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, Zuid Holland, the Netherlands
- * E-mail: (YE); (GMvW)
| |
Collapse
|
13
|
TSC1 binding to lysosomal PIPs is required for TSC complex translocation and mTORC1 regulation. Mol Cell 2021; 81:2705-2721.e8. [PMID: 33974911 DOI: 10.1016/j.molcel.2021.04.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/13/2021] [Accepted: 04/19/2021] [Indexed: 11/21/2022]
Abstract
The TSC complex is a critical negative regulator of the small GTPase Rheb and mTORC1 in cellular stress signaling. The TSC2 subunit contains a catalytic GTPase activating protein domain and interacts with multiple regulators, while the precise function of TSC1 is unknown. Here we provide a structural characterization of TSC1 and define three domains: a C-terminal coiled-coil that interacts with TSC2, a central helical domain that mediates TSC1 oligomerization, and an N-terminal HEAT repeat domain that interacts with membrane phosphatidylinositol phosphates (PIPs). TSC1 architecture, oligomerization, and membrane binding are conserved in fungi and humans. We show that lysosomal recruitment of the TSC complex and subsequent inactivation of mTORC1 upon starvation depend on the marker lipid PI3,5P2, demonstrating a role for lysosomal PIPs in regulating TSC complex and mTORC1 activity via TSC1. Our study thus identifies a vital role of TSC1 in TSC complex function and mTORC1 signaling.
Collapse
|
14
|
Yang H, Yu Z, Chen X, Li J, Li N, Cheng J, Gao N, Yuan HX, Ye D, Guan KL, Xu Y. Structural insights into TSC complex assembly and GAP activity on Rheb. Nat Commun 2021; 12:339. [PMID: 33436626 PMCID: PMC7804450 DOI: 10.1038/s41467-020-20522-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/04/2020] [Indexed: 12/13/2022] Open
Abstract
Tuberous sclerosis complex (TSC) integrates upstream stimuli and regulates cell growth by controlling the activity of mTORC1. TSC complex functions as a GTPase-activating protein (GAP) towards small GTPase Rheb and inhibits Rheb-mediated activation of mTORC1. Mutations in TSC genes cause tuberous sclerosis. In this study, the near-atomic resolution structure of human TSC complex reveals an arch-shaped architecture, with a 2:2:1 stoichiometry of TSC1, TSC2, and TBC1D7. This asymmetric complex consists of two interweaved TSC1 coiled-coil and one TBC1D7 that spans over the tail-to-tail TSC2 dimer. The two TSC2 GAP domains are symmetrically cradled within the core module formed by TSC2 dimerization domain and central coiled-coil of TSC1. Structural and biochemical analyses reveal TSC2 GAP-Rheb complimentary interactions and suggest a catalytic mechanism, by which an asparagine thumb (N1643) stabilizes γ-phosphate of GTP and accelerate GTP hydrolysis of Rheb. Our study reveals mechanisms of TSC complex assembly and GAP activity.
Collapse
Affiliation(s)
- Huirong Yang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Zishuo Yu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Jiabei Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Jiaxuan Cheng
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Hai-Xin Yuan
- The Molecular and Cell Biology Research Lab, The Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Dan Ye
- The Molecular and Cell Biology Research Lab, The Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Kun-Liang Guan
- Department of Pharmacology and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| |
Collapse
|
15
|
Cheah PS, Prabhakar S, Yellen D, Beauchamp RL, Zhang X, Kasamatsu S, Bronson RT, Thiele EA, Kwiatkowski DJ, Stemmer-Rachamimov A, György B, Ling KH, Kaneki M, Tannous BA, Ramesh V, Maguire CA, Breakefield XO. Gene therapy for tuberous sclerosis complex type 2 in a mouse model by delivery of AAV9 encoding a condensed form of tuberin. SCIENCE ADVANCES 2021; 7:eabb1703. [PMID: 33523984 PMCID: PMC7793581 DOI: 10.1126/sciadv.abb1703] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 11/18/2020] [Indexed: 05/06/2023]
Abstract
Tuberous sclerosis complex (TSC) results from loss of a tumor suppressor gene - TSC1 or TSC2, encoding hamartin and tuberin, respectively. These proteins formed a complex to inhibit mTORC1-mediated cell growth and proliferation. Loss of either protein leads to overgrowth lesions in many vital organs. Gene therapy was evaluated in a mouse model of TSC2 using an adeno-associated virus (AAV) vector carrying the complementary for a "condensed" form of human tuberin (cTuberin). Functionality of cTuberin was verified in culture. A mouse model of TSC2 was generated by AAV-Cre recombinase disruption of Tsc2-floxed alleles at birth, leading to a shortened lifespan (mean 58 days) and brain pathology consistent with TSC. When these mice were injected intravenously on day 21 with AAV9-cTuberin, the mean survival was extended to 462 days with reduction in brain pathology. This demonstrates the potential of treating life-threatening TSC2 lesions with a single intravenous injection of AAV9-cTuberin.
Collapse
Affiliation(s)
- Pike-See Cheah
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital, and Program in Neuroscience, Harvard Medical School, Boston, MA, USA
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Shilpa Prabhakar
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital, and Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - David Yellen
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital, and Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Roberta L Beauchamp
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Xuan Zhang
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital, and Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Shingo Kasamatsu
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
- Shriners Hospitals for Children, Boston, MA, USA
| | - Roderick T Bronson
- Rodent Histopathology Core Facility, Harvard Medical School, Boston, MA, USA
| | - Elizabeth A Thiele
- Herscot Center for Tuberous Sclerosis Complex, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- The Pediatric Epilepsy Program, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Bence György
- Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - King-Hwa Ling
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Masao Kaneki
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
- Shriners Hospitals for Children, Boston, MA, USA
| | - Bakhos A Tannous
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital, and Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Vijaya Ramesh
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Casey A Maguire
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital, and Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Xandra O Breakefield
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital, and Program in Neuroscience, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
16
|
Mongrain V, van Doesburg NH, Rypens F, Fallet-Bianco C, Maassen J, Dufort-Gervais J, Côté L, Major P. A case report of severe tuberous sclerosis complex detected in utero and linked to a novel duplication in the TSC2 gene. BMC Neurol 2020; 20:324. [PMID: 32873234 PMCID: PMC7460776 DOI: 10.1186/s12883-020-01905-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 08/23/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Disease severity is tremendously variable in tuberous sclerosis complex (TSC). In contrast with the detailed guidelines available for TSC diagnosis and management, clinical practice lacks adequate tools to evaluate the prognosis, especially in the case of in utero diagnosis. In addition, the correlation between genotypes and phenotypes remains a challenge, in part due to the large number of mutations linked to TSC. In this report, we describe a case of severe TSC diagnosed in utero and associated with a specific mutation in the gene tuberous sclerosis complex 2 (TSC2). CASE PRESENTATION A mother was referred for a thorough investigation following the observation by ultrasound of cardiac abnormalities in her fetus. The mother was healthy and reported frequent, intense and long-lasting hiccups/spasms in the fetus. The fetus of gestational age 33 weeks and 4 days was found to have multiple cardiac tumors with cardiac ultrasound. Brain magnetic resonance imaging (MRI) performed in utero revealed the presence of sub-ependymal nodules and of abnormal signals disseminated in the white matter, in the cerebral cortex and in the cerebellum. Following diagnosis of definite TSC, pregnancy interruption was chosen by the parents. Genetic testing of the fetus exposed a duplication in exon 41 of TSC2 (c.5169dupA), which was absent in the parents. The autopsy ascertained the high severity of brain damage characterized by an extensive disorganisation of white and grey matter in most cerebral lobes. CONCLUSIONS This case presentation is the first to depict the association between a de novo TSC2 c.5169dupA and multi-organ manifestation together with indications of a particularly high disease severity. This report can help physicians to perform early clinical diagnosis of TSC and to evaluate the prognosis.
Collapse
Affiliation(s)
- Valérie Mongrain
- Department of Neuroscience, Université de Montréal, Montreal, QC, Canada. .,Center for Advanced Research in Sleep Medicine, Recherche CIUSSS-NIM (site Hôpital du Sacré-Coeur de Montréal), 5400 Gouin West blvd., Montreal, QC, H4J1C5, Canada.
| | - Nicolaas H van Doesburg
- Centre intégré de diagnostic prénatal (CIDP) and Pediatric Neurology Service, Centre Hospitalier Universitaire (CHU) Ste-Justine, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T1C5, Canada
| | - Françoise Rypens
- Centre intégré de diagnostic prénatal (CIDP) and Pediatric Neurology Service, Centre Hospitalier Universitaire (CHU) Ste-Justine, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T1C5, Canada
| | - Catherine Fallet-Bianco
- Centre intégré de diagnostic prénatal (CIDP) and Pediatric Neurology Service, Centre Hospitalier Universitaire (CHU) Ste-Justine, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T1C5, Canada
| | - Justine Maassen
- Centre intégré de diagnostic prénatal (CIDP) and Pediatric Neurology Service, Centre Hospitalier Universitaire (CHU) Ste-Justine, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T1C5, Canada
| | - Julien Dufort-Gervais
- Center for Advanced Research in Sleep Medicine, Recherche CIUSSS-NIM (site Hôpital du Sacré-Coeur de Montréal), 5400 Gouin West blvd., Montreal, QC, H4J1C5, Canada
| | - Lucie Côté
- Centre intégré de diagnostic prénatal (CIDP) and Pediatric Neurology Service, Centre Hospitalier Universitaire (CHU) Ste-Justine, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T1C5, Canada
| | - Philippe Major
- Department of Neuroscience, Université de Montréal, Montreal, QC, Canada. .,Centre intégré de diagnostic prénatal (CIDP) and Pediatric Neurology Service, Centre Hospitalier Universitaire (CHU) Ste-Justine, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T1C5, Canada.
| |
Collapse
|
17
|
Rosengren T, Nanhoe S, de Almeida LGD, Schönewolf-Greulich B, Larsen LJ, Hey CAB, Dunø M, Ek J, Risom L, Nellist M, Møller LB. Mutational analysis of TSC1 and TSC2 in Danish patients with tuberous sclerosis complex. Sci Rep 2020; 10:9909. [PMID: 32555378 PMCID: PMC7303179 DOI: 10.1038/s41598-020-66588-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 05/19/2020] [Indexed: 02/07/2023] Open
Abstract
Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterized by hamartomas in the skin and other organs, including brain, heart, lung, kidney and bones. TSC is caused by mutations in TSC1 and TSC2. Here, we present the TSC1 and TSC2 variants identified in 168 Danish individuals out of a cohort of 327 individuals suspected of TSC. A total of 137 predicted pathogenic or likely pathogenic variants were identified: 33 different TSC1 variants in 42 patients, and 104 different TSC2 variants in 126 patients. In 40 cases (24%), the identified predicted pathogenic variant had not been described previously. In total, 33 novel variants in TSC2 and 7 novel variants in TSC1 were identified. To assist in the classification of 11 TSC2 variants, we investigated the effects of these variants in an in vitro functional assay. Based on the functional results, as well as population and genetic data, we classified 8 variants as likely to be pathogenic and 3 as likely to be benign.
Collapse
Affiliation(s)
- Thomas Rosengren
- Clinical Genetics Clinic, Copenhagen University Hospital, Rigshospitalet. Address 1: Kennedy Center, Gl landevej 7, DK-2600, Glostrup, Denmark. Address 2: 4062, Blegdamsvej 9, DK-2100, Østerbro, Denmark
| | - Santoesha Nanhoe
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Luis Gustavo Dufner de Almeida
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Bitten Schönewolf-Greulich
- Clinical Genetics Clinic, Copenhagen University Hospital, Rigshospitalet. Address 1: Kennedy Center, Gl landevej 7, DK-2600, Glostrup, Denmark. Address 2: 4062, Blegdamsvej 9, DK-2100, Østerbro, Denmark
| | - Lasse Jonsgaard Larsen
- Clinical Genetics Clinic, Copenhagen University Hospital, Rigshospitalet. Address 1: Kennedy Center, Gl landevej 7, DK-2600, Glostrup, Denmark. Address 2: 4062, Blegdamsvej 9, DK-2100, Østerbro, Denmark
| | - Caroline Amalie Brunbjerg Hey
- Clinical Genetics Clinic, Copenhagen University Hospital, Rigshospitalet. Address 1: Kennedy Center, Gl landevej 7, DK-2600, Glostrup, Denmark. Address 2: 4062, Blegdamsvej 9, DK-2100, Østerbro, Denmark
| | - Morten Dunø
- Clinical Genetics Clinic, Copenhagen University Hospital, Rigshospitalet. Address 1: Kennedy Center, Gl landevej 7, DK-2600, Glostrup, Denmark. Address 2: 4062, Blegdamsvej 9, DK-2100, Østerbro, Denmark
| | - Jakob Ek
- Clinical Genetics Clinic, Copenhagen University Hospital, Rigshospitalet. Address 1: Kennedy Center, Gl landevej 7, DK-2600, Glostrup, Denmark. Address 2: 4062, Blegdamsvej 9, DK-2100, Østerbro, Denmark
| | - Lotte Risom
- Clinical Genetics Clinic, Copenhagen University Hospital, Rigshospitalet. Address 1: Kennedy Center, Gl landevej 7, DK-2600, Glostrup, Denmark. Address 2: 4062, Blegdamsvej 9, DK-2100, Østerbro, Denmark
| | - Mark Nellist
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lisbeth Birk Møller
- Clinical Genetics Clinic, Copenhagen University Hospital, Rigshospitalet. Address 1: Kennedy Center, Gl landevej 7, DK-2600, Glostrup, Denmark. Address 2: 4062, Blegdamsvej 9, DK-2100, Østerbro, Denmark.
| |
Collapse
|
18
|
Hansmann P, Brückner A, Kiontke S, Berkenfeld B, Seebohm G, Brouillard P, Vikkula M, Jansen FE, Nellist M, Oeckinghaus A, Kümmel D. Structure of the TSC2 GAP Domain: Mechanistic Insight into Catalysis and Pathogenic Mutations. Structure 2020; 28:933-942.e4. [PMID: 32502382 DOI: 10.1016/j.str.2020.05.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/06/2020] [Accepted: 05/15/2020] [Indexed: 12/17/2022]
Abstract
The TSC complex is the cognate GTPase-activating protein (GAP) for the small GTPase Rheb and a crucial regulator of the mechanistic target of rapamycin complex 1 (mTORC1). Mutations in the TSC1 and TSC2 subunits of the complex cause tuberous sclerosis complex (TSC). We present the crystal structure of the catalytic asparagine-thumb GAP domain of TSC2. A model of the TSC2-Rheb complex and molecular dynamics simulations suggest that TSC2 Asn1643 and Rheb Tyr35 are key active site residues, while Rheb Arg15 and Asp65, previously proposed as catalytic residues, contribute to the TSC2-Rheb interface and indirectly aid catalysis. The TSC2 GAP domain is further stabilized by interactions with other TSC2 domains. We characterize TSC2 variants that partially affect TSC2 functionality and are associated with atypical symptoms in patients, suggesting that mutations in TSC1 and TSC2 might predispose to neurological and vascular disorders without fulfilling the clinical criteria for TSC.
Collapse
Affiliation(s)
- Patrick Hansmann
- Westfälische Wilhelms-Universität, Institute of Biochemistry, Wilhelm Klemm-Str. 2, 48149 Münster, Germany
| | - Anne Brückner
- Westfälische Wilhelms-Universität, Institute of Biochemistry, Wilhelm Klemm-Str. 2, 48149 Münster, Germany; Westfälische Wilhelms-Universität, Institute of Molecular Tumor Biology, Robert-Koch-Str. 43, 48149 Münster, Germany
| | - Stephan Kiontke
- Philipps-Universität Marburg, Faculty of Biology, Department of Plant Physiology and Photobiology, Karl-von-Frisch-Str. 8, 35032 Marburg, Germany
| | - Bianca Berkenfeld
- Westfälische Wilhelms-Universität, Institute of Biochemistry, Wilhelm Klemm-Str. 2, 48149 Münster, Germany
| | - Guiscard Seebohm
- University Hospital Münster, Institute for Genetics of Heart Diseases, Department of Cardiovascular Medicine, Robert-Koch-Str. 45, 48149 Münster, Germany
| | - Pascal Brouillard
- Université Catholique de Louvain, de Duve Institute, Human Molecular Genetics, Brussels, Belgium
| | - Miikka Vikkula
- Université Catholique de Louvain, de Duve Institute, Human Molecular Genetics, Brussels, Belgium; WELBIO (Walloon Excellence in Lifesciences and Biotechnology), de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Floor E Jansen
- Department of Child Neurology, Brain Center UMC Utrecht, Utrecht, the Netherlands
| | - Mark Nellist
- Department of Clinical Genetics, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands
| | - Andrea Oeckinghaus
- Westfälische Wilhelms-Universität, Institute of Molecular Tumor Biology, Robert-Koch-Str. 43, 48149 Münster, Germany
| | - Daniel Kümmel
- Westfälische Wilhelms-Universität, Institute of Biochemistry, Wilhelm Klemm-Str. 2, 48149 Münster, Germany.
| |
Collapse
|
19
|
Dufner Almeida LG, Nanhoe S, Zonta A, Hosseinzadeh M, Kom-Gortat R, Elfferich P, Schaaf G, Kenter A, Kümmel D, Migone N, Povey S, Ekong R, Nellist M. Comparison of the functional and structural characteristics of rare TSC2 variants with clinical and genetic findings. Hum Mutat 2019; 41:759-773. [PMID: 31799751 PMCID: PMC7154745 DOI: 10.1002/humu.23963] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/31/2019] [Accepted: 11/27/2019] [Indexed: 01/09/2023]
Abstract
The TSC1 and TSC2 gene products interact to form the tuberous sclerosis complex (TSC), an important negative regulator of the mechanistic target of rapamycin complex 1 (TORC1). Inactivating mutations in TSC1 or TSC2 cause TSC, and the identification of a pathogenic TSC1 or TSC2 variant helps establish a diagnosis of TSC. However, it is not always clear whether TSC1 and TSC2 variants are inactivating. To determine whether TSC1 and TSC2 variants of uncertain clinical significance affect TSC complex function and cause TSC, in vitro assays of TORC1 activity can be employed. Here we combine genetic, functional, and structural approaches to try and classify a series of 15 TSC2 VUS. We investigated the effects of the variants on the formation of the TSC complex, on TORC1 activity and on TSC2 pre‐mRNA splicing. In 13 cases (87%), the functional data supported the hypothesis that the identified TSC2 variant caused TSC. Our results illustrate the benefits and limitations of functional testing for TSC.
Collapse
Affiliation(s)
- Luiz G Dufner Almeida
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Santoesha Nanhoe
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Andrea Zonta
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Mitra Hosseinzadeh
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Regina Kom-Gortat
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Peter Elfferich
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Gerben Schaaf
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Annegien Kenter
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Daniel Kümmel
- Biochemistry and Structural Biology Section, Institute of Biochemistry, University of Munster, Munster, Germany
| | - Nicola Migone
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Sue Povey
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Rosemary Ekong
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Mark Nellist
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| |
Collapse
|