1
|
Rodrigues Alves Barbosa V, Maroilley T, Diao C, Colvin-James L, Perrier R, Tarailo-Graovac M. Single variant, yet "double trouble": TSC and KBG syndrome because of a large de novo inversion. Life Sci Alliance 2024; 7:e202302115. [PMID: 38253421 PMCID: PMC10803213 DOI: 10.26508/lsa.202302115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Despite the advances in high-throughput sequencing, many rare disease patients remain undiagnosed. In particular, the patients with well-defined clinical phenotypes and established clinical diagnosis, yet missing or partial genetic diagnosis, may hold a clue to more complex genetic mechanisms of a disease that could be missed by available clinical tests. Here, we report a patient with a clinical diagnosis of Tuberous sclerosis, combined with unusual secondary features, but negative clinical tests including TSC1 and TSC2 Short-read whole-genome sequencing combined with advanced bioinformatics analyses were successful in uncovering a de novo pericentric 87-Mb inversion with breakpoints in TSC2 and ANKRD11, which explains the TSC clinical diagnosis, and confirms a second underlying monogenic disorder, KBG syndrome. Our findings illustrate how complex variants, such as large inversions, may be missed by clinical tests and further highlight the importance of well-defined clinical diagnoses in uncovering complex molecular mechanisms of a disease, such as complex variants and "double trouble" effects.
Collapse
Affiliation(s)
- Victoria Rodrigues Alves Barbosa
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Tatiana Maroilley
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Catherine Diao
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Leslie Colvin-James
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Renee Perrier
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Maja Tarailo-Graovac
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| |
Collapse
|
2
|
Garcia ABDM, Viola GD, Corrêa BDS, Fischer TDS, Pinho MCDF, Rodrigues GM, Ashton-Prolla P, Rosset C. An overview of actionable and potentially actionable TSC1 and TSC2 germline variants in an online Database. Genet Mol Biol 2024; 46:e20230132. [PMID: 38373162 PMCID: PMC10876083 DOI: 10.1590/1678-4685-gmb-2023-0132] [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: 05/03/2023] [Accepted: 11/26/2023] [Indexed: 02/21/2024] Open
Abstract
Tuberous Sclerosis Complex (TSC) is caused by loss of function germline variants in the TSC1 or TSC2 tumor suppressor genes. Genetic testing for the detection of pathogenic variants in either TSC1 or TSC2 was implemented as a diagnostic criterion for TSC. However, TSC molecular diagnosis can be challenging due to the absence of variant hotspots and the high number of variants described. This review aimed to perform an overview of TSC1/2 variants submitted in the ClinVar database. Variants of uncertain significance (VUS), missense and single nucleotide variants were the most frequent in clinical significance (37-40%), molecular consequence (37%-39%) and variation type (82%-83%) categories in ClinVar in TSC1 and TSC2 variants, respectively. Frameshift and nonsense VUS have potential for pathogenic reclassification if further functional and segregation studies were performed. Indeed, there were few functional assays deposited in the database and literature. In addition, we did not observe hotspots for variation and many variants presented conflicting submissions regarding clinical significance. This study underscored the importance of disseminating molecular diagnostic results in a public database to render the information largely accessible and promote accurate diagnosis. We encourage the performance of functional studies evaluating the pathogenicity of TSC1/2 variants.
Collapse
Affiliation(s)
- Arthur Bandeira de Mello Garcia
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Guilherme Danielski Viola
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Bruno da Silveira Corrêa
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Taís da Silveira Fischer
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Maria Clara de Freitas Pinho
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Centro Universitário CESUCA, Cachoeirinha, RS, Brazil
| | - Grazielle Motta Rodrigues
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
| | - Patricia Ashton-Prolla
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Porto Alegre, RS, Brazil
| | - Clévia Rosset
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
| |
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
|
Chen T, Fan X, Li G, Meng Y. Multi-omics data integration reveals the molecular network of dysregulation IQGAP2-mTOR promotes cell proliferation. Hum Cell 2023:10.1007/s13577-023-00912-8. [PMID: 37154877 DOI: 10.1007/s13577-023-00912-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/02/2023] [Indexed: 05/10/2023]
Abstract
IQGAP2 as a tumor suppressor gene can influence cell proliferation in multiple tumor cell lines. However, the regulation network of cell proliferation resulting solely from the deficiency of IQGAP2 in cells was still unclear. Here, we integrated transcriptome, proteome, and phosphoproteome analyses to investigate the regulatory network of cell proliferation in IQGAP2 knockdown HaCaT and HEK293 cells. Our findings revealed that the dysregulation of the IQGAP2-mTOR molecular network led to increased cell proliferation. We demonstrated that IQGAP2 knockdown enhanced the phosphorylation levels of AKT and S6K, leading to increased cell proliferation. Additionally, we found that AKT and mTOR inhibitors partially rescued abnormal cell proliferation by reducing hyperphosphorylation. Our data suggest a potential connection between the mTOR signaling pathway and aberrant cell proliferation in IQGAP2 knockdown cells. These findings offer a new therapeutic strategy for patients with IQGAP2 deficiency.
Collapse
Affiliation(s)
- Tao Chen
- Guangzhou KingMed Transformative Medicine Institute Co. Ltd., No. 10 Luoxuan 3Rd Road, Guangzhou International Biotech Island, Guangzhou, China
- Guangzhou KingMed Diagnostics Group Co. Ltd., Guangzhou, China
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
| | - Xijie Fan
- Guangzhou KingMed Transformative Medicine Institute Co. Ltd., No. 10 Luoxuan 3Rd Road, Guangzhou International Biotech Island, Guangzhou, China
- Guangzhou KingMed Diagnostics Group Co. Ltd., Guangzhou, China
| | - Guibin Li
- Guangzhou KingMed Transformative Medicine Institute Co. Ltd., No. 10 Luoxuan 3Rd Road, Guangzhou International Biotech Island, Guangzhou, China
- Guangzhou KingMed Diagnostics Group Co. Ltd., Guangzhou, China
| | - Yuhuan Meng
- Guangzhou KingMed Transformative Medicine Institute Co. Ltd., No. 10 Luoxuan 3Rd Road, Guangzhou International Biotech Island, Guangzhou, China.
- Guangzhou KingMed Diagnostics Group Co. Ltd., Guangzhou, China.
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China.
| |
Collapse
|
5
|
Genotype-phenotype correlation of renal lesions in the tuberous sclerosis complex. Hum Genome Var 2022; 9:5. [PMID: 35145067 PMCID: PMC8831580 DOI: 10.1038/s41439-022-00181-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 01/15/2023] Open
Abstract
Tuberous sclerosis complex (TSC) is an autosomal dominant disease caused by loss-of-function mutations in either of two tumor suppressor genes, TSC1 and TSC2. These mutations lead to the growth of benign tumors and hamartomas in many organs, including those of the central nervous system, the skin, and the kidneys. To investigate the genotype-phenotype correlation, we performed sequence analysis of the TSC1/2 genes using next-generation sequencing. We classified 30 patients with TSC whose pathogenic variants were identified into two groups: those with mutations producing premature termination codons (PTCs) and those with missense mutations. Then, we compared the phenotypes between the two groups. Patients with a PTC were significantly more likely to manifest the major symptoms of the diagnostic criteria than those without a PTC (P = 0.035). The frequencies of subependymal nodules (P = 0.026), cortical tubers (P = 0.026), and renal cysts (P = 0.026) were significantly higher in PTC-containing variants than in cases without a PTC. When the analyses were limited to renal angiomyolipoma (AML) cases with TSC2 mutations, there was no difference in tumor size between cases with and without a PTC. However, the cases with a PTC showed a trend toward disease onset at a younger age and multiple tumors, and bilateral disease was observed in their AML lesions. TSC patients with PTC-producing mutations might potentially manifest more severe TSC phenotypes than those with missense mutations. A larger-scale study with appropriate samples deserves further investigation.
Collapse
|
6
|
Kovesdi E, Ripszam R, Postyeni E, Horvath EB, Kelemen A, Fabos B, Farkas V, Hadzsiev K, Sumegi K, Magyari L, Moreno PG, Bauer P, Melegh B. Whole Exome Sequencing in a Series of Patients with a Clinical Diagnosis of Tuberous Sclerosis Not Confirmed by Targeted TSC1/TSC2 Sequencing. Genes (Basel) 2021; 12:genes12091401. [PMID: 34573383 PMCID: PMC8471884 DOI: 10.3390/genes12091401] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/05/2021] [Accepted: 09/06/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Approximately fifteen percent of patients with tuberous sclerosis complex (TSC) phenotype do not have any genetic disease-causing mutations which could be responsible for the development of TSC. The lack of a proper diagnosis significantly affects the quality of life for these patients and their families. METHODS The aim of our study was to use Whole Exome Sequencing (WES) in order to identify the genes responsible for the phenotype of nine patients with clinical signs of TSC, but without confirmed tuberous sclerosis complex 1/ tuberous sclerosis complex 2 (TSC1/TSC2) mutations using routine molecular genetic diagnostic tools. RESULTS We found previously overlooked heterozygous nonsense mutations in TSC1, and a heterozygous intronic variant in TSC2. In one patient, two heterozygous missense variants were found in polycystic kidney and hepatic disease 1 (PKHD1), confirming polycystic kidney disease type 4. A heterozygous missense mutation in solute carrier family 12 member 5 (SLC12A5) was found in one patient, which is linked to cause susceptibility to idiopathic generalized epilepsy type 14. Heterozygous nonsense variant ring finger protein 213 (RNF213) was identified in one patient, which is associated with susceptibility to Moyamoya disease type 2. In the remaining three patients WES could not reveal any variants clinically relevant to the described phenotypes. CONCLUSION Patients without appropriate diagnosis due to the lack of sensitivity of the currently used routine diagnostic methods can significantly profit from the wider application of next generation sequencing technologies in order to identify genes and variants responsible for their symptoms.
Collapse
Affiliation(s)
- Erzsebet Kovesdi
- Department of Medical Genetics, Medical School, Szentagothai Research Center, University of Pecs, 7624 Pecs, Hungary; (R.R.); (E.P.); (K.H.); (K.S.); (L.M.); (B.M.)
- Molecular Neuroendocrinology Research Group, Institute of Physiology, Center for Neuroscience, Szentagothai Research Center, Medical School, University of Pecs, 7624 Pecs, Hungary
- Correspondence:
| | - Reka Ripszam
- Department of Medical Genetics, Medical School, Szentagothai Research Center, University of Pecs, 7624 Pecs, Hungary; (R.R.); (E.P.); (K.H.); (K.S.); (L.M.); (B.M.)
| | - Etelka Postyeni
- Department of Medical Genetics, Medical School, Szentagothai Research Center, University of Pecs, 7624 Pecs, Hungary; (R.R.); (E.P.); (K.H.); (K.S.); (L.M.); (B.M.)
| | - Emese Beatrix Horvath
- Department of Medical Genetics, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary;
| | - Anna Kelemen
- National Institute of Clinical Neurosciences, 1145 Budapest, Hungary;
| | - Beata Fabos
- Somogy County Mor Kaposi Teaching Hospital, 7400 Kaposvar, Hungary;
| | - Viktor Farkas
- Department of Pediatrics, Faculty of Medicine, Semmelweis University, 1085-Budapest, Hungary;
| | - Kinga Hadzsiev
- Department of Medical Genetics, Medical School, Szentagothai Research Center, University of Pecs, 7624 Pecs, Hungary; (R.R.); (E.P.); (K.H.); (K.S.); (L.M.); (B.M.)
| | - Katalin Sumegi
- Department of Medical Genetics, Medical School, Szentagothai Research Center, University of Pecs, 7624 Pecs, Hungary; (R.R.); (E.P.); (K.H.); (K.S.); (L.M.); (B.M.)
- Departments of Biochemistry and Medical Chemistry, Medical School, University of Pecs, 7624 Pecs, Hungary
| | - Lili Magyari
- Department of Medical Genetics, Medical School, Szentagothai Research Center, University of Pecs, 7624 Pecs, Hungary; (R.R.); (E.P.); (K.H.); (K.S.); (L.M.); (B.M.)
| | | | - Peter Bauer
- CENTOGENE GmbH, 18055 Rostock, Germany; (P.B.); (P.G.M.)
| | - Bela Melegh
- Department of Medical Genetics, Medical School, Szentagothai Research Center, University of Pecs, 7624 Pecs, Hungary; (R.R.); (E.P.); (K.H.); (K.S.); (L.M.); (B.M.)
| |
Collapse
|