1
|
Weiss JS, Rapuano CJ, Seitz B, Busin M, Kivelä TT, Bouheraoua N, Bredrup C, Nischal KK, Chawla H, Borderie V, Kenyon KR, Kim EK, Møller HU, Munier FL, Berger T, Lisch W. IC3D Classification of Corneal Dystrophies-Edition 3. Cornea 2024; 43:466-527. [PMID: 38359414 PMCID: PMC10906208 DOI: 10.1097/ico.0000000000003420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/08/2023] [Accepted: 09/24/2023] [Indexed: 02/17/2024]
Abstract
PURPOSE The International Committee for the Classification of Corneal Dystrophies (IC3D) was created in 2005 to develop a new classification system integrating current information on phenotype, histopathology, and genetic analysis. This update is the third edition of the IC3D nomenclature. METHODS Peer-reviewed publications from 2014 to 2023 were evaluated. The new information was used to update the anatomic classification and each of the 22 standardized templates including the level of evidence for being a corneal dystrophy [from category 1 (most evidence) to category 4 (least evidence)]. RESULTS Epithelial recurrent erosion dystrophies now include epithelial recurrent erosion dystrophy, category 1 ( COL17A1 mutations, chromosome 10). Signs and symptoms are similar to Franceschetti corneal dystrophy, dystrophia Smolandiensis, and dystrophia Helsinglandica, category 4. Lisch epithelial corneal dystrophy, previously reported as X-linked, has been discovered to be autosomal dominant ( MCOLN1 mutations, chromosome 19). Classic lattice corneal dystrophy (LCD) results from TGFBI R124C mutation. The LCD variant group has over 80 dystrophies with non-R124C TGFBI mutations, amyloid deposition, and often similar phenotypes to classic LCD. We propose a new nomenclature for specific LCD pathogenic variants by appending the mutation using 1-letter amino acid abbreviations to LCD. Pre-Descemet corneal dystrophies include category 1, autosomal dominant, punctiform and polychromatic pre-Descemet corneal dystrophy (PPPCD) ( PRDX3 mutations, chromosome 10). Typically asymptomatic, it can be distinguished phenotypically from pre-Descemet corneal dystrophy, category 4. We include a corneal dystrophy management table. CONCLUSIONS The IC3D third edition provides a current summary of corneal dystrophy information. The article is available online at https://corneasociety.org/publications/ic3d .
Collapse
Affiliation(s)
- Jayne S Weiss
- Departments of Ophthalmology, Pathology and Pharmacology, Louisiana State University Eye Center of Excellence, Louisiana State University Health Sciences Center, New Orleans, LA
| | - Christopher J Rapuano
- Cornea Service, Wills Eye Hospital, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA
| | - Berthold Seitz
- Department of Ophthalmology, Saarland University Medical Center, Homburg/Saar, Germany
| | - Massimo Busin
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Istituto Internazionale per la Ricerca e Formazione in Oftalmologia, Forlì, Italy
| | - Tero T Kivelä
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Nacim Bouheraoua
- Department of Ophthalmology, Quinze-Vingts National Ophthalmology Hospital and Sorbonne Université, Paris, France
| | - Cecilie Bredrup
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Ken K Nischal
- Division of Pediatric Ophthalmology, Strabismus and Adult Motility, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA
| | - Harshvardhan Chawla
- Department of Ophthalmology, Louisiana State University Health Sciences Center, New Orleans, LA
| | - Vincent Borderie
- Department of Ophthalmology, Quinze-Vingts National Ophthalmology Hospital and Sorbonne Université, Paris, France
| | - Kenneth R Kenyon
- Department of Ophthalmology, Tufts University School of Medicine and Harvard Medical School, Schepens Eye Research Institute and New England Eye Center, Boston, MA
| | - Eung Kweon Kim
- Corneal Dystrophy Research Institute, Yonsei University College of Medicine, Seoul, Korea
- Saevit Eye Hospital, Goyang, Korea
| | - Hans Ulrik Møller
- Department of Pediatric Ophthalmology, Aarhus University Hospital, Aarhus, Denmark
| | - Francis L Munier
- Retinoblastoma and Oculogenetic Units, Jules-Gonin Eye Hospital and Fondation Asile des Aveugle, University of Lausanne, Lausanne, Switzerland; and
| | - Tim Berger
- Department of Ophthalmology, Saarland University Medical Center, Homburg/Saar, Germany
| | - Walter Lisch
- Department of Ophthalmology, Johannes Gutenberg University Mainz, Mainz, Germany
| |
Collapse
|
2
|
Fernández-Caballero L, Martín-Merida I, Blanco-Kelly F, Avila-Fernandez A, Carreño E, Fernandez-San Jose P, Irigoyen C, Jimenez-Rolando B, Lopez-Grondona F, Mahillo I, Martin-Gutierrez MP, Minguez P, Perea-Romero I, Del Pozo-Valero M, Riveiro-Alvarez R, Rodilla C, Rodriguez-Peña L, Sánchez-Barbero AI, Swafiri ST, Trujillo-Tiebas MJ, Zurita O, García-Sandoval B, Corton M, Ayuso C. PRPH2-Related Retinal Dystrophies: Mutational Spectrum in 103 Families from a Spanish Cohort. Int J Mol Sci 2024; 25:2913. [PMID: 38474159 PMCID: PMC10931554 DOI: 10.3390/ijms25052913] [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: 02/01/2024] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
PRPH2, one of the most frequently inherited retinal dystrophy (IRD)-causing genes, implies a high phenotypic variability. This study aims to analyze the PRPH2 mutational spectrum in one of the largest cohorts worldwide, and to describe novel pathogenic variants and genotype-phenotype correlations. A study of 220 patients from 103 families recruited from a database of 5000 families. A molecular diagnosis was performed using classical molecular approaches and next-generation sequencing. Common haplotypes were ascertained by analyzing single-nucleotide polymorphisms. We identified 56 variants, including 11 novel variants. Most of them were missense variants (64%) and were located in the D2-loop protein domain (77%). The most frequently occurring variants were p.Gly167Ser, p.Gly208Asp and p.Pro221_Cys222del. Haplotype analysis revealed a shared region in families carrying p.Leu41Pro or p.Pro221_Cys222del. Patients with retinitis pigmentosa presented an earlier disease onset. We describe the largest cohort of IRD families associated with PRPH2 from a single center. Most variants were located in the D2-loop domain, highlighting its importance in interacting with other proteins. Our work suggests a likely founder effect for the variants p.Leu41Pro and p.Pro221_Cys222del in our Spanish cohort. Phenotypes with a primary rod alteration presented more severe affectation. Finally, the high phenotypic variability in PRPH2 hinders the possibility of drawing genotype-phenotype correlations.
Collapse
Affiliation(s)
- Lidia Fernández-Caballero
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Inmaculada Martín-Merida
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Almudena Avila-Fernandez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ester Carreño
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (E.C.); (B.J.-R.); (M.P.M.-G.); (B.G.-S.)
| | - Patricia Fernandez-San Jose
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Genetics, Ramón y Cajal University Hospital, 28034 Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Cristina Irigoyen
- Ophthalmology Service, Donostia University Hospital, 20014 Donostia-San Sebastián, Spain
| | - Belen Jimenez-Rolando
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (E.C.); (B.J.-R.); (M.P.M.-G.); (B.G.-S.)
| | - Fermina Lopez-Grondona
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ignacio Mahillo
- Department of Statistics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain;
| | - María Pilar Martin-Gutierrez
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (E.C.); (B.J.-R.); (M.P.M.-G.); (B.G.-S.)
| | - Pablo Minguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Irene Perea-Romero
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Marta Del Pozo-Valero
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Rosa Riveiro-Alvarez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Cristina Rodilla
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Lidya Rodriguez-Peña
- Sección de Genética Medica, Servicio de Pediatría, HCU Virgen de la Arrixaca, 30120 Murcia, Spain
| | - Ana Isabel Sánchez-Barbero
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Saoud T. Swafiri
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - María José Trujillo-Tiebas
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Olga Zurita
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Blanca García-Sandoval
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (E.C.); (B.J.-R.); (M.P.M.-G.); (B.G.-S.)
| | - Marta Corton
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| |
Collapse
|
3
|
Darouich S, Darouich S. A novel homozygous variant in ATL1 associated with early onset spastic paraplegia 3A: Further evidence for autosomal recessive inheritance. Am J Med Genet A 2024; 194:e63464. [PMID: 37927245 DOI: 10.1002/ajmg.a.63464] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 11/07/2023]
Abstract
Spastic paraplegia 3A (SPG3A) has long been considered as an autosomal dominant disorder till the report in 2014 and 2016 of two consanguineous Arabic families, showing that ATL1 mutations may cause autosomal recessive paraplegia. Here, a third report of a consanguineous Arabic family with recessive SPG3A is described. Exome sequencing reveals homozygosity for a novel likely pathogenic ATL1 splice donor variant (c.522+1G>T) in an affected 5-year-old infant whereas the parents, heterozygous carriers, are asymptomatic. The infant's phenotype is consistent with an early onset complicated SPG3A with severe progressive spasticity of the lower limbs and intellectual disability.
Collapse
Affiliation(s)
- Sihem Darouich
- Université de Tunis El Manar, Faculté de Médecine de Tunis, Tunis, Tunisia
- CHU Habib Bougatfa, Unité de Pathologie Fœtale et Placentaire, Bizerte, Tunisia
| | - Samia Darouich
- Université de Tunis El Manar, Institut Supérieur des Sciences Humaines de Tunis, Tunis, Tunisia
| |
Collapse
|
4
|
Ju Y, Chen T, Ruan L, Zhao Y, Chang Q, Huang X. Mutations in TSPAN12 gene causing familial exudative vitreoretinopathy. Hum Genomics 2024; 18:22. [PMID: 38424652 PMCID: PMC10905792 DOI: 10.1186/s40246-024-00589-6] [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: 01/16/2024] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND To report newly found TSPAN12 mutations with a unique form of familial exudative vitreoretinopathy (FEVR) and find out the possible mechanism of a repeated novel intronic variant in TSPAN12 led to FEVR. RESULTS Nine TSPAN12 mutations with a unique form of FEVR were detected by panel-based NGS. MINI-Gene assay showed two splicing modes of mRNA that process two different bands A and B, and mutant-type shows replacement with the splicing mode of Exon11 hopping. Construction of wild-type and mutant TSPAN12 vector showed the appearance of premature termination codons (PTC). In vitro expression detection showed significant down-regulated expression level of TSPAN12 mRNAs and proteins in cells transfected with mutant vectors compared with in wild-type group. On the contrary, translation inhibitor CHX and small interfering RNA of UPF1 (si-UPF1) significantly increased mRNA or protein expression of TSPAN12 in cells transfected with the mutant vectors. CONCLUSIONS Nine mutations in TSPAN12 gene are reported in 9 FEVR patients with a unique series of ocular abnormalities. The three novel TSPAN12 mutations trigger NMD would cause the decrease of TSPAN12 proteins that participate in biosynthesis and assembly of microfibers, which might lead to FEVR, and suggest that intronic sequence analysis might be a vital tool for genetic counseling and prenatal diagnoses.
Collapse
Affiliation(s)
- Yuqiao Ju
- Department of Ophthalmology and Vision Science, Eye and ENT Hospital of Fudan University, 83 Fenyang Rd, Shanghai, 200031, China
- Key Laboratory of Myopia of State Health Ministry, and Key Laboratory of Visual Impairment and Restoration of Shanghai, Shanghai, China
| | - Tianhui Chen
- Department of Ophthalmology and Vision Science, Eye and ENT Hospital of Fudan University, 83 Fenyang Rd, Shanghai, 200031, China
- Key Laboratory of Myopia of State Health Ministry, and Key Laboratory of Visual Impairment and Restoration of Shanghai, Shanghai, China
| | - Lu Ruan
- Department of Ophthalmology and Vision Science, Eye and ENT Hospital of Fudan University, 83 Fenyang Rd, Shanghai, 200031, China
- Key Laboratory of Myopia of State Health Ministry, and Key Laboratory of Visual Impairment and Restoration of Shanghai, Shanghai, China
| | - Ye Zhao
- Department of Ophthalmology and Vision Science, Eye and ENT Hospital of Fudan University, 83 Fenyang Rd, Shanghai, 200031, China
- Key Laboratory of Myopia of State Health Ministry, and Key Laboratory of Visual Impairment and Restoration of Shanghai, Shanghai, China
| | - Qing Chang
- Department of Ophthalmology and Vision Science, Eye and ENT Hospital of Fudan University, 83 Fenyang Rd, Shanghai, 200031, China.
- Key Laboratory of Myopia of State Health Ministry, and Key Laboratory of Visual Impairment and Restoration of Shanghai, Shanghai, China.
| | - Xin Huang
- Department of Ophthalmology and Vision Science, Eye and ENT Hospital of Fudan University, 83 Fenyang Rd, Shanghai, 200031, China.
- Key Laboratory of Myopia of State Health Ministry, and Key Laboratory of Visual Impairment and Restoration of Shanghai, Shanghai, China.
| |
Collapse
|
5
|
Bianco L, Arrigo A, Antropoli A, Del Fabbro S, Mauro L, Pina A, Bandello F, Battaglia Parodi M. The Retinal Phenotype Associated with the p.Pro101Thr BEST1 Variant. Ophthalmol Retina 2024; 8:288-297. [PMID: 37717827 DOI: 10.1016/j.oret.2023.09.012] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 08/29/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
PURPOSE To describe the retinal phenotype associated with the p.Pro101Thr BEST1 variant. DESIGN Retrospective, observational case series. PARTICIPANTS Patients diagnosed with bestrophinopathies in which molecular genetic testing identified the p.Pro101Thr BEST1 as well as healthy carriers among their first-degree relatives. METHODS Medical records were reviewed to obtain data on family history and ophthalmic examinations, including retinal imaging. The imaging protocol included OCT and fundus autofluorescence using Spectralis HRA + OCT (Heidelberg Engineering). Genetic analysis was performed by next-generation sequencing. MAIN OUTCOME MEASURES Results of ophthalmic examinations and multimodal imaging features of retinal phenotypes. RESULTS The c.301C>A, p.Pro101Thr BEST1 missense variant was identified as the causative variant in 8 individuals (all men) from 5 families, accounting for 13% of cases (8/61) and 10% of pathogenic alleles (9/93) in our cohort of patients affected by bestrophinopathies. Seven individuals (14 eyes) had the variant in heterozygous status: all eyes had a hyperopic refractive error (median spherical equivalent of + 3.75 diopters [D]) and 4 individuals had a macular dystrophy with mildly reduced visual acuity (median of 20/25 Snellen), whereas the other 3 were asymptomatic carriers. On multimodal retinal imaging, 5 (36%) out of 14 eyes had subclinical bestrophinopathy, 4 (29%) had typical findings of adult-onset foveomacular vitelliform dystrophy (AOFVD), and the remaining 5 (36%) displayed a pattern dystrophy-like phenotype. Follow-up data were available for 6 subjects, demonstrating clinical stability up to 11 years, in both subclinical and clinical forms. An additional patient with autosomal recessive bestrophinopathy was found to harbor the p.Pro101Thr variant in homozygosity. CONCLUSIONS The p.Pro101Thr BEST1 variant is likely a frequent cause of bestrophinopathy in the Italian population and can result in autosomal dominant macular dystrophies with incomplete penetrance and mild clinical manifestations as well as autosomal recessive bestrophinopathy. The spectrum of autosomal dominant maculopathy includes the typical AOFVD and a pattern dystrophy-like phenotype. FINANCIAL DISCLOSURE(S) Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
Collapse
Affiliation(s)
- Lorenzo Bianco
- Department of Ophthalmology, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Alessandro Arrigo
- Department of Ophthalmology, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy.
| | - Alessio Antropoli
- Department of Ophthalmology, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Sebastiano Del Fabbro
- Department of Ophthalmology, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Luca Mauro
- Department of Ophthalmology, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Adelaide Pina
- Department of Ophthalmology, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Francesco Bandello
- Department of Ophthalmology, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | - Maurizio Battaglia Parodi
- Department of Ophthalmology, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| |
Collapse
|
6
|
Kaufmann TL, Schwarz RF. Improved identification of cancer mutational processes. Nat Genet 2024; 56:365-366. [PMID: 38454020 DOI: 10.1038/s41588-024-01679-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Affiliation(s)
- Tom L Kaufmann
- BIFOLD - Berlin Institute for the Foundations of Learning and Data, Berlin, Germany.
- Department of Electrical Engineering and Computer Science, Technische Universität Berlin, Berlin, Germany.
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
| | - Roland F Schwarz
- BIFOLD - Berlin Institute for the Foundations of Learning and Data, Berlin, Germany.
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
| |
Collapse
|
7
|
Wills A, Dibbern M, Frierson HF, Raghavan SS. Metastatic Undifferentiated Melanoma Mimicking a Primary Bone Tumor: A Potential Diagnostic Pitfall. Am J Dermatopathol 2024; 46:170-172. [PMID: 38170737 DOI: 10.1097/dad.0000000000002622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
ABSTRACT Undifferentiated melanoma (UM) is defined by the loss of classic morphologic and immunohistochemical melanocytic markers. Reports in the literature are rare and show that UM usually occurs as a metastasis in the setting of a known primary cutaneous melanoma. The most common mutations in UM include those involving BRAF , NRAS , and KIT , which are almost invariably present in the parent melanoma. In this study, we report a case of a primary sinonasal melanoma with metastatic UM presenting with osteoclast-like giant cells and resembling a primary bone tumor. The retention of an unusual KRAS mutation in UM that was also present in the primary lesion provided critical information for the diagnosis. Our report highlights the importance of considering mutational analysis to identify undifferentiated melanomas in patients with metastatic tumors which do not have the typical histopathologic and immunohistochemical features of melanoma.
Collapse
Affiliation(s)
- Abby Wills
- Department of Dermatology, University of Virginia Health System, Charlottesville, VA; and
| | - Megan Dibbern
- Department of Pathology, University of Virginia Health System, Charlottesville, VA
| | - Henry F Frierson
- Department of Pathology, University of Virginia Health System, Charlottesville, VA
| | - Shyam S Raghavan
- Department of Pathology, University of Virginia Health System, Charlottesville, VA
| |
Collapse
|
8
|
Kader MA, Devarajan B, Vijayan S, Ramakrishnan R, Sundaresan P, Uduman MS, Krishnadas SR, Kuppamuthu D. Myocilin Mutation N480K Leads to Early Onset Juvenile and Adult-onset Primary Open Angle Glaucoma in a Six Generation Family. J Glaucoma 2024; 33:218-224. [PMID: 37670504 DOI: 10.1097/ijg.0000000000002286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/29/2023] [Indexed: 09/07/2023]
Abstract
PRCIS A pathogenic autosomal dominant MYOC mutation N480K detected in 6 generations of an Indian family is primarily responsible for juvenile open angle glaucoma (JOAG) and adult-onset primary open angle glaucoma (POAG), emphasizing the importance of screening this mutation at a younger age. PURPOSE To screen myocilin mutations in a large South Indian family with early-onset JOAG and adult-onset POAG. METHODS In a large South Indian family with 20 members, 8 members diagnosed as JOAG, 7 members as POAG, 4 members as JOAG suspect, and 1 member as POAG suspect were screened for myocilin ( MYOC) mutations using Sanger sequencing. Whole exome sequencing was performed on clinically suspected JOAG/POAG individuals. RESULTS Myocilin gene mutation N480K (c.1440C>G) was detected in 20 family members, including proband, of whom 8 were JOAG and 7 were POAG patients, 3 were JOAG suspects, and 2 were unaffected. Among the unaffected carriers, 1 was less than 5 years old, and another was 25 years old. The earliest to develop the disease was a 10-year-old child. The penetrance of the mutation was 95% over 10 years of age. This family had JOAG/POAG suspects with no N480K MYOC mutation, and they were further screened for other mutations using whole-exome sequencing. Polymorphisms CYP1B1 L432V and MYOC R76K were detected in 3 JOAG/POAG suspects, and among these 3, one had another CYP1B1 polymorphic variant R368H. The presence of the CYP1B1 polymorphism along with an MYOC polymorphic variant among the JOAG/POAG suspects needs additional studies to explore their combined role in the onset of glaucoma. CONCLUSIONS This study reveals that MYOC mutation is primarily responsible for JOAG and adult-onset POAG in a family, emphasizing the importance of screening for this mutation at a younger age for early treatment.
Collapse
Affiliation(s)
| | | | - Saravanan Vijayan
- Department of Genetics, Aravind Medical Research Foundation, Madurai
| | | | | | | | | | | |
Collapse
|
9
|
Zhao R, Liu M, Dai E, Chen C, Lv L, Peng L, He Y, Li S, Yang M. Deciphering a crucial dimeric interface governing Norrin dimerization and the pathogenesis of familial exudative vitreoretinopathy. FASEB J 2024; 38:e23493. [PMID: 38363575 DOI: 10.1096/fj.202302387r] [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: 11/21/2023] [Revised: 01/18/2024] [Accepted: 02/02/2024] [Indexed: 02/17/2024]
Abstract
Familial exudative vitreoretinopathy (FEVR) is a hereditary eye disease that could cause blindness. It has been established that Norrin forms dimers to activate β-catenin signaling, yet the core interface for Norrin dimerization and the precise mechanism by which Norrin dimerization contributes to the pathogenesis of FEVR remain elusive. Here, we report an NDP variant, c.265T>C (p.Phe89Leu), that interrupted β-catenin signaling by disrupting Norrin dimerization. Structural and functional analysis revealed that the Phe-89 of one Norrin monomer interacts with Pro-98, Ser-101, Arg-121, and Ile-123 of another, forming two core symmetrical dimerization interfaces that are pivotal for the formation of a "hand-by-arm" dimer. Intriguingly, we proved that one of the two core symmetrical interfaces is sufficient for dimerization and activation of β-catenin signaling, with a substantial contribution from the Phe-89/Pro-98 interaction. Further functional analysis revealed that the disruption of both dimeric interfaces eliminates potential binding sites for LRP5, which could be partially restored by over-expression of TSPAN12. In conclusion, our findings unveil a core dimerization interface that regulates Norrin/LRP5 interaction, highlighting the essential role of Norrin dimerization on β-catenin signaling and providing potential therapeutic avenues for the treatment of FEVR.
Collapse
Affiliation(s)
- Rulian Zhao
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, The Department of Medical Genetics, The Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention, Chinese Academy of Medical Sciences (No.2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| | - Min Liu
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, The Department of Medical Genetics, The Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention, Chinese Academy of Medical Sciences (No.2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| | - Erkuan Dai
- Department of Ophthalmology, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chen Chen
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Liting Lv
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, The Department of Medical Genetics, The Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention, Chinese Academy of Medical Sciences (No.2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| | - Li Peng
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, The Department of Medical Genetics, The Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention, Chinese Academy of Medical Sciences (No.2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| | - Yunqi He
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, The Department of Medical Genetics, The Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention, Chinese Academy of Medical Sciences (No.2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| | - Shujin Li
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, The Department of Medical Genetics, The Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention, Chinese Academy of Medical Sciences (No.2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| | - Mu Yang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, The Department of Medical Genetics, The Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention, Chinese Academy of Medical Sciences (No.2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| |
Collapse
|
10
|
Heidari MM, Mazrouei B, Tahmasebi M, Bagheri F, Khanjankhani Z, Khatami M, Dehghani M, Khormizi FZ. Novel nucleotide variations in the thrombomodulin (THBD) gene involved in coagulation pathways can increase the risk of recurrent pregnancy loss (RPL). Gene 2024; 895:148011. [PMID: 37979949 DOI: 10.1016/j.gene.2023.148011] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/06/2023] [Accepted: 11/15/2023] [Indexed: 11/20/2023]
Abstract
Recurrent pregnancy loss (RPL) is a common but complex complication in fertility conditions, affecting about 15-20% of couples. Although several causes have been proposed for RPL, it occurs in about 35-60% of cases without a known explanation. A strong assumption is that genetic factors play a role in the etiology and pathophysiology of PRL. Therefore, several genes are proposed as candidates in the pathogenesis of RPL. The current study aimed to investigate the effects of nucleotide changes in the THBD (thrombomodulin) gene as an RPL-related candidate gene. This gene encodes a cell receptor for thrombin and is involved in reproductive loss in RPL cases. Its involvement in the natural anticoagulant system has been extensively studied. By genetic screening of the entire coding and noncoding regions of the THBD gene, we found twenty-seven heterozygous and homozygous nucleotide changes. Ten of them led to amino acid substitutions, seven variants were identified in the promoter region, and eight of them occurred in 3'UTR. Potentially, the pathogenicity effects of these variations on THBD protein were evaluated by several prediction tools. The numerous genomic variations prompted noticeable modifications of the protein's structural and functional properties. Furthermore, in-silico scores were consistent with deleterious effects for these mutations. The results of this study provide genetic information that will be useful in the future for clinicians, scientists, and students to understand the unknown causes of RPL better. It may also pave the way for developing diagnostic/prognostic approaches to help treat PRL patients.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Mohammadreza Dehghani
- Medical Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | |
Collapse
|
11
|
Dobre EG, Nichita L, Popp C, Zurac S, Neagu M. Assessment of RAS-RAF-MAPK Pathway Mutation Status in Healthy Skin, Benign Nevi, and Cutaneous Melanomas: Pilot Study Using Droplet Digital PCR. Int J Mol Sci 2024; 25:2308. [PMID: 38396984 PMCID: PMC10889428 DOI: 10.3390/ijms25042308] [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: 01/18/2024] [Revised: 02/10/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
In the present study, we employed the ddPCR and IHC techniques to assess the prevalence and roles of RAS and RAF mutations in a small batch of melanoma (n = 22), benign moles (n = 15), and normal skin samples (n = 15). Mutational screening revealed the coexistence of BRAF and NRAS mutations in melanomas and nevi and the occurrence of NRAS G12/G13 variants in healthy skin. All investigated nevi had driver mutations in the BRAF or NRAS genes and elevated p16 protein expression, indicating cell cycle arrest despite an increased mutational burden. BRAF V600 mutations were identified in 54% of melanomas, and NRAS G12/G13 mutations in 50%. The BRAF mutations were associated with the Breslow index (BI) (p = 0.029) and TIL infiltration (p = 0.027), whereas the NRAS mutations correlated with the BI (p = 0.01) and the mitotic index (p = 0.04). Here, we demonstrate that the "young" ddPCR technology is as effective as a CE-IVD marked real-time PCR method for detecting BRAF V600 hotspot mutations in tumor biopsies and recommend it for extended use in clinical settings. Moreover, ddPCR was able to detect low-frequency hotspot mutations, such as NRAS G12/G13, in our tissue specimens, which makes it a promising tool for investigating the mutational landscape of sun-damaged skin, benign nevi, and melanomas in more extensive clinical studies.
Collapse
Affiliation(s)
- Elena-Georgiana Dobre
- Doctoral School, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania;
- “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania; (L.N.); (C.P.); (S.Z.)
| | - Luciana Nichita
- “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania; (L.N.); (C.P.); (S.Z.)
- Colentina Clinical Hospital, 020125 Bucharest, Romania
- Department of Pathology, Faculty of Dental Medicine, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Cristiana Popp
- “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania; (L.N.); (C.P.); (S.Z.)
- Colentina Clinical Hospital, 020125 Bucharest, Romania
- Department of Pathology, Faculty of Dental Medicine, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Sabina Zurac
- “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania; (L.N.); (C.P.); (S.Z.)
- Colentina Clinical Hospital, 020125 Bucharest, Romania
- Department of Pathology, Faculty of Dental Medicine, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Monica Neagu
- Doctoral School, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania;
- “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania; (L.N.); (C.P.); (S.Z.)
- Colentina Clinical Hospital, 020125 Bucharest, Romania
| |
Collapse
|
12
|
Xu B, Lan Y, Luo D, Zheng Y, Ni R, Su G, Huang Q, Li Q. Highly Sensitive Detection of PIK3CA Mutations by Looping-Out Probes-Based Melting Curve Analysis. Biochem Genet 2024; 62:77-94. [PMID: 37249716 DOI: 10.1007/s10528-023-10408-7] [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: 05/05/2023] [Accepted: 05/19/2023] [Indexed: 05/31/2023]
Abstract
PIK3CA mutations have important therapeutic and prognostic implications in various cancer types. However, highly sensitive detection of PIK3CA hotspot mutations in heterogeneous tumor samples remains a challenge in clinical settings. To establish a rapid PCR assay for highly sensitive detection of multiple PIK3CA hotspot mutations. We described a novel melting curve analysis-based assay using looping-out probes that can enrich target mutations in the background of excess wild-type and concurrently reveal the presence of mutations. The analytical and clinical performance of the assay were evaluated. The developed assay could detect 10 PIK3CA hotspot mutations at a mutant allele fraction of 0.05-0.5% within 2 h in a single step. Analysis of 82 breast cancer tissue samples revealed 43 samples with PIK3CA mutations, 28 of which were confirmed by Sanger sequencing. Further testing of 175 colorectal cancer tissue samples showed that 24 samples contained PIK3CA mutations and 19 samples were confirmed by Sanger sequencing. Droplet digital PCR supported that all mutation-containing samples undetected by sequencing contained mutations with a low allele fraction. The rapidity, ease of use, high sensitivity and accuracy make the new assay a potential screening tool for PIK3CA mutations in clinical laboratories.
Collapse
Affiliation(s)
- Boheng Xu
- Department of Molecular Diagnostics, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong, China
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yanping Lan
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Danjiao Luo
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yangsi Zheng
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Runfang Ni
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Guoqiang Su
- The First Affiliated Hospital of Xiamen University, Xiamen, 361003, Fujian, China
| | - Qiuying Huang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
| |
Collapse
|
13
|
Giolito ML, Bigliani G, Meinero R, Taubas JV. Palmitoylation of CYSTM (CYSPD) proteins in yeast. J Biol Chem 2024; 300:105609. [PMID: 38159851 PMCID: PMC10840359 DOI: 10.1016/j.jbc.2023.105609] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
A superfamily of proteins called cysteine transmembrane is widely distributed across eukaryotes. These small proteins are characterized by the presence of a conserved motif at the C-terminal region, rich in cysteines, that has been annotated as a transmembrane domain. Orthologs of these proteins have been involved in resistance to pathogens and metal detoxification. The yeast members of the family are YBR016W, YDL012C, YDR034W-B, and YDR210W. Here, we begin the characterization of these proteins at the molecular level and show that Ybr016w, Ydr034w-b, and Ydr210w are palmitoylated proteins. Protein S-acylation or palmitoylation, is a posttranslational modification that consists of the addition of long-chain fatty acids to cysteine residues. We provide evidence that Ybr016w, Ydr210w, and Ydr034w-b are localized to the plasma membrane and exhibit varying degrees of polarity toward the daughter cell, which is dependent on endocytosis and recycling. We suggest the names CPP1, CPP2, and CPP3 (C terminally palmitoylated protein) for YBR016W, YDR210W, and YDR034W-B, respectively. We show that palmitoylation is responsible for the binding of these proteins to the membrane indicating that the cysteine transmembrane on these proteins is not a transmembrane domain. We propose renaming the C-terminal cysteine-rich domain as cysteine-rich palmitoylated domain. Loss of the palmitoyltransferase Erf2 leads to partial degradation of Ybr016w (Cpp1), whereas in the absence of the palmitoyltransferase Akr1, members of this family are completely degraded. For Cpp1, we show that this degradation occurs via the proteasome in an Rsp5-dependent manner, but is not exclusively due to a lack of Cpp1 palmitoylation.
Collapse
Affiliation(s)
- María Luz Giolito
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Gonzalo Bigliani
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Rocío Meinero
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Javier Valdez Taubas
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
| |
Collapse
|
14
|
D’Esposito F, Randazzo V, Vega MI, Esposito G, Maltese PE, Torregrossa S, Scibetta P, Listì F, Gagliano C, Scalia L, Pioppo A, Marino A, Piergentili M, Malvone E, Fioretti T, Vitrano A, Piccione M, Avitabile T, Salvatore F, Bertelli M, Costagliola C, Cordeiro MF, Maggio A, D’Alcamo E. RP1 Dominant p.Ser740* Pathogenic Variant in 20 Knowingly Unrelated Families Affected by Rod-Cone Dystrophy: Potential Founder Effect in Western Sicily. Medicina (Kaunas) 2024; 60:254. [PMID: 38399542 PMCID: PMC10890639 DOI: 10.3390/medicina60020254] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024]
Abstract
Background and Objectives. Retinitis pigmentosa (RP) is the most common inherited rod-cone dystrophy (RCD), resulting in nyctalopia, progressive visual field, and visual acuity decay in the late stages. The autosomal dominant form (ADRP) accounts for about 20% of RPs. Among the over 30 genes found to date related to ADRP, RP1 pathogenic variants have been identified in 5-10% of cases. In a cohort of RCD patients from the Palermo province on the island of Sicily, we identified a prevalent nonsense variant in RP1, which was associated with ADRP. The objective of our study was to analyse the clinical and molecular data of this patient cohort and to evaluate the potential presence of a founder effect. Materials and Methods. From 2005 to January 2023, 84 probands originating from Western Sicily (Italy) with a diagnosis of RCD or RP and their relatives underwent deep phenotyping, which was performed in various Italian clinical institutions. Molecular characterisation of patients and familial segregation of pathogenic variants were carried out in different laboratories using Sanger and/or next-generation sequencing (NGS). Results. Among 84 probands with RCD/RP, we found 28 heterozygotes for the RP1 variant c.2219C>G, p.Ser740* ((NM_006269.2)*, which was therefore significantly prevalent in this patient cohort. After a careful interview process, we ascertained that some of these patients shared the same pedigree. Therefore, we were ultimately able to define 20 independent family groups with no traceable consanguinity. Lastly, analysis of clinical data showed, in our patients, that the p.Ser740* nonsense variant was often associated with a late-onset and relatively mild phenotype. Conclusions. The high prevalence of the p.Ser740* variant in ADRP patients from Western Sicily suggests the presence of a founder effect, which has useful implications for the molecular diagnosis of RCD in patients coming from this Italian region. This variant can be primarily searched for in RP-affected subjects displaying compatible modes of transmission and phenotypes, with an advantage in terms of the required costs and time for analysis. Moreover, given its high prevalence, the RP1 p.Ser740* variant could represent a potential candidate for the development of therapeutic strategies based on gene editing or translational read-through therapy for suppression of nonsense variants.
Collapse
Affiliation(s)
- Fabiana D’Esposito
- Imperial College Ophthalmic Research Group (ICORG) Unit, Imperial College, London SW7 2AZ, UK;
- Eye Clinic, Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples Federico II, 80100 Naples, Italy; (E.M.); (C.C.)
- Genofta s.r.l., Sant’Agnello, 80065 Naples, Italy
| | - Viviana Randazzo
- Eye Clinic, AOOR Villa Sofia-Cervello, 90100 Palermo, Italy; (V.R.); (S.T.); (P.S.)
| | - Maria Igea Vega
- Department of Genetics, Oncohaematology and Rare Diseases, AOOR Villa Sofia-Cervello, 90100 Palermo, Italy; (M.I.V.); (F.L.); (A.V.); (M.P.); (A.M.); (E.D.)
| | - Gabriella Esposito
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80100 Naples, Italy; (G.E.); (F.S.)
- CEINGE-Advanced Biotechnologies Franco Salvatore, 80100 Naples, Italy;
| | | | | | - Paola Scibetta
- Eye Clinic, AOOR Villa Sofia-Cervello, 90100 Palermo, Italy; (V.R.); (S.T.); (P.S.)
| | - Florinda Listì
- Department of Genetics, Oncohaematology and Rare Diseases, AOOR Villa Sofia-Cervello, 90100 Palermo, Italy; (M.I.V.); (F.L.); (A.V.); (M.P.); (A.M.); (E.D.)
| | - Caterina Gagliano
- Department of Medicine and Surgery, School of Medicine, Kore University of Enna, 94100 Enna, Italy;
| | - Lucia Scalia
- Eye Clinic, Catania University, Policlinico “Rodolico”-San Marco, 95100 Catania, Italy; (L.S.); (T.A.)
| | | | - Antonio Marino
- Department of Ophthalmology, Garibaldi Hospital, 95100 Catania, Italy;
| | - Marco Piergentili
- Department of Ophthalmology, Careggi Teaching Hospital, 50100 Florence, Italy;
| | - Emanuele Malvone
- Eye Clinic, Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples Federico II, 80100 Naples, Italy; (E.M.); (C.C.)
| | - Tiziana Fioretti
- CEINGE-Advanced Biotechnologies Franco Salvatore, 80100 Naples, Italy;
| | - Angela Vitrano
- Department of Genetics, Oncohaematology and Rare Diseases, AOOR Villa Sofia-Cervello, 90100 Palermo, Italy; (M.I.V.); (F.L.); (A.V.); (M.P.); (A.M.); (E.D.)
| | - Maria Piccione
- Department of Genetics, Oncohaematology and Rare Diseases, AOOR Villa Sofia-Cervello, 90100 Palermo, Italy; (M.I.V.); (F.L.); (A.V.); (M.P.); (A.M.); (E.D.)
| | - Teresio Avitabile
- Eye Clinic, Catania University, Policlinico “Rodolico”-San Marco, 95100 Catania, Italy; (L.S.); (T.A.)
| | - Francesco Salvatore
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80100 Naples, Italy; (G.E.); (F.S.)
- CEINGE-Advanced Biotechnologies Franco Salvatore, 80100 Naples, Italy;
| | | | - Ciro Costagliola
- Eye Clinic, Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples Federico II, 80100 Naples, Italy; (E.M.); (C.C.)
| | | | - Aurelio Maggio
- Department of Genetics, Oncohaematology and Rare Diseases, AOOR Villa Sofia-Cervello, 90100 Palermo, Italy; (M.I.V.); (F.L.); (A.V.); (M.P.); (A.M.); (E.D.)
| | - Elena D’Alcamo
- Department of Genetics, Oncohaematology and Rare Diseases, AOOR Villa Sofia-Cervello, 90100 Palermo, Italy; (M.I.V.); (F.L.); (A.V.); (M.P.); (A.M.); (E.D.)
| |
Collapse
|
15
|
Pantel D, Mertens ND, Schneider R, Hölzel S, Kari JA, Desoky SE, Shalaby MA, Lim TY, Sanna-Cherchi S, Shril S, Hildebrandt F. Copy number variation analysis in 138 families with steroid-resistant nephrotic syndrome identifies causal homozygous deletions in PLCE1 and NPHS2 in two families. Pediatr Nephrol 2024; 39:455-461. [PMID: 37670083 DOI: 10.1007/s00467-023-06134-2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/06/2023] [Accepted: 08/10/2023] [Indexed: 09/07/2023]
Abstract
BACKGROUND Steroid-resistant nephrotic syndrome (SRNS) is the second most common cause of kidney failure in children and adults under the age of 20 years. Previously, we were able to detect by exome sequencing (ES) a known monogenic cause of SRNS in 25-30% of affected families. However, ES falls short of detecting copy number variants (CNV). Therefore, we hypothesized that causal CNVs could be detected in a large SRNS cohort. METHODS We performed genome-wide single nucleotide polymorphism (SNP)-based CNV analysis on a cohort of 138 SRNS families, in whom we previously did not identify a genetic cause through ES. We evaluated ES and CNV data for variants in 60 known SRNS genes and in 13 genes in which variants are known to cause a phenocopy of SRNS. We applied previously published, predefined criteria for CNV evaluation. RESULTS We detected a novel CNV in two genes in 2 out of 138 families (1.5%). The 9,673 bp homozygous deletion in PLCE1 and the 6,790 bp homozygous deletion in NPHS2 were confirmed across the breakpoints by PCR and Sanger sequencing. CONCLUSIONS We confirmed that CNV analysis can identify the genetic cause in SRNS families that remained unsolved after ES. Though the rate of detected CNVs is minor, CNV analysis can be used when there are no other genetic causes identified. Causative CNVs are less common in SRNS than in other monogenic kidney diseases, such as congenital anomalies of the kidneys and urinary tract, where the detection rate was 5.3%. A higher resolution version of the Graphical abstract is available as Supplementary information.
Collapse
Affiliation(s)
- Dalia Pantel
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Nils D Mertens
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Ronen Schneider
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Selina Hölzel
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Jameela A Kari
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Sherif El Desoky
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Mohamed A Shalaby
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Pediatric Nephrology Center of Excellence, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Tze Y Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Shirlee Shril
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115, USA.
| |
Collapse
|
16
|
Liu Y, Yang M, Fan L, He Y, Dai E, Liu M, Jiang L, Yang Z, Li S. Frameshift variants in the C-terminal of CTNNB1 cause familial exudative vitreoretinopathy by AXIN1-mediated ubiquitin-proteasome degradation condensation. Int J Biol Macromol 2024; 258:128570. [PMID: 38096938 DOI: 10.1016/j.ijbiomac.2023.128570] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/08/2023] [Accepted: 11/30/2023] [Indexed: 12/25/2023]
Abstract
The β-catenin has two intrinsically disordered regions in both C- and N-terminal domains that trigger the formation of phase-separated condensates. Variants in its C-terminus are associated with familial exudative vitreoretinopathy (FEVR), yet the pathogenesis and the role of these variants in inducing abnormal condensates, are unclear. In this study, we identified a novel heterozygous frameshift variant, c.2104-2105insCC (p.Gln703ProfsTer33), in CTNNB1 from a FEVR-affected family. This variant encodes an unstable truncated protein that was unable to activate Wnt signal transduction, which could be rescued by the inhibition of proteasome or phosphorylation. Further functional experiments revealed the propensity of the Gln703ProfsTer33 variant to form cytoplasmic condensates, exhibiting a lower turnover rate after fluorescent bleaching due to enhanced interaction with AXIN1. LiCl, which specifically blocks GSK3β-mediated phosphorylation, restored signal transduction, cell proliferation, and junctional integrity in primary human retinal microvascular endothelial cells over-expressed with Gln703ProfsTer33. Finally, experiments on two reported FEVR-associated mutations in the C-terminal domain of β-catenin exhibited several functional defects similar to the Gln703ProfsTer33. Together, our findings unravel that the C-terminal region of β-catenin is pivotal for the regulation of AXIN1/β-catenin interaction, acting as a switch to mediate nucleic and cytosolic condensates formation that is implicated in the pathogenesis of FEVR.
Collapse
Affiliation(s)
- Yining Liu
- Central Laboratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Mu Yang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China; Research Unit for Blindness Prevention, Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China; Jinfeng Laboratory, Chongqing, China
| | - Lin Fan
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China; The University of Chinese Academy of Sciences, Beijing, China
| | - Yunqi He
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China; Research Unit for Blindness Prevention, Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Erkuan Dai
- Department of Ophthalmology, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Liu
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China; Research Unit for Blindness Prevention, Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Lei Jiang
- Central Laboratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Zhenglin Yang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China; Research Unit for Blindness Prevention, Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China; Jinfeng Laboratory, Chongqing, China; Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China; The University of Chinese Academy of Sciences, Beijing, China.
| | - Shujin Li
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China; Research Unit for Blindness Prevention, Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China; Jinfeng Laboratory, Chongqing, China.
| |
Collapse
|
17
|
Dhoble P, Robson AG, Webster AR, Michaelides M. Typical best vitelliform dystrophy secondary to biallelic variants in BEST1. Ophthalmic Genet 2024; 45:38-43. [PMID: 36908234 DOI: 10.1080/13816810.2023.2188227] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/02/2023] [Indexed: 03/14/2023]
Abstract
BACKGROUND Pathogenic variants in BEST1 can cause autosomal dominant or autosomal recessive dystrophy, typically associated with distinct retinal phenotypes. In heterozygous cases, the disorder is commonly characterized by yellow sub-macular lesions in the early stages, known as Best vitelliform macular dystrophy (BVMD). Biallelic variants usually cause a more severe phenotype including diffuse retinal pigment epithelial irregularity and widespread generalized progressive retinopathy, known as autosomal recessive bestrophinopathy (ARB). This study describes three cases with clinical changes consistent with BVMD, however, unusually associated with autosomal recessive inheritance. MATERIALS AND METHODS Detailed ophthalmic workup included comprehensive ophthalmologic examination, multimodal retinal imaging, full-field and pattern electroretinography (ERG; PERG), and electrooculogram (EOG). Genetic analysis of probands and segregation testing and fundus examination of proband relatives was performed where possible. RESULTS Three unrelated cases presented with a clinical phenotype typical for BVMD and were found to have biallelic disease-causing variants in BEST1. PERG P50 and ERG were normal in all cases. The EOG was subnormal (probands 1 and 3) or normal/borderline (proband 2). Probands 1 and 2 were homozygous for the BEST1 missense variant c.139C>T, p.Arg47Cys, while proband 3 was homozygous for a deletion, c.536_538delACA, p.Asn179del. The parents of proband 1 were phenotypically normal. Parents of proband 1 and 2 were heterozygous for the same missense variant. CONCLUSIONS Individuals with biallelic variants in BEST1 can present with a phenotype indistinguishable from BVMD. The same clinical phenotype may not be evident in those harboring the same variants in the heterozygous state. This has implications for genetic counselling and prognosticationA.
Collapse
Affiliation(s)
- Pankaja Dhoble
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Anthony G Robson
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Andrew R Webster
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Michel Michaelides
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| |
Collapse
|
18
|
Zhang Q, Yang Q, Luo J, Zhou X, Yi S, Tan S, Qin Z. Clinical features and molecular genetic investigation of infantile-onset ascending hereditary spastic paralysis (IAHSP) in two Chinese siblings caused by a novel splice site ALS2 variation. BMC Med Genomics 2024; 17:44. [PMID: 38297306 PMCID: PMC10829245 DOI: 10.1186/s12920-024-01805-x] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 01/10/2024] [Indexed: 02/02/2024] Open
Abstract
OBJECTIVE ALS2-related disorder involves retrograde degeneration of the upper motor neurons of the pyramidal tracts, among which autosomal recessive Infantile-onset ascending hereditary spastic paralysis (IAHSP) is a rare phenotype. In this study, we gathered clinical data from two Chinese siblings who were affected by IAHSP. Our aim was to assess the potential pathogenicity of the identified variants and analyze their clinical and genetic characteristics. METHOD Here, Whole-exome sequencing (WES) was performed on proband to identify the candidate variants. Subsequently, Sanger sequencing was used to verify identified candidate variants and to assess co-segregation among available family members. Utilizing both silico prediction and 3D protein modeling, an analysis was conducted to evaluate the potential functional implications of the variants on the encoded protein, and minigene assays were performed to unravel the effect of the variants on the cleavage of pre-mRNA. RESULTS Both patients were characterized by slurred speech, astasia, inability to walk, scoliosis, lower limb hypertonia, ankle clonus, contracture of joint, foot pronation and no psychomotor retardation was found. Genetic analysis revealed a novel homozygous variant of ALS2, c.1815G > T(p.Lys605Asn) in two Chinese siblings. To our knowledge, it is the first confirmed case of a likely pathogenic variant leading to IAHSP in a Chinese patient. CONCLUSION This study broadens the range of ALS2 variants and has practical implications for prenatal and postnatal screening of IAHSR. Symptom-based diagnosis of IAHSP is frequently difficult for medical practitioners. WES can be a beneficial resource to identify a particular disorder when the diagnosis cannot be determined from the symptoms alone.
Collapse
Affiliation(s)
- Qiang Zhang
- Maternal and Child Health Hospital of Guangxi, Nanning, China
- Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of reproductive health and birth defect prevention, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qi Yang
- Maternal and Child Health Hospital of Guangxi, Nanning, China
- Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of reproductive health and birth defect prevention, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jingsi Luo
- Maternal and Child Health Hospital of Guangxi, Nanning, China
- Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of reproductive health and birth defect prevention, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xunzhao Zhou
- Maternal and Child Health Hospital of Guangxi, Nanning, China
- Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of reproductive health and birth defect prevention, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shang Yi
- Maternal and Child Health Hospital of Guangxi, Nanning, China
- Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of reproductive health and birth defect prevention, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shuyin Tan
- Maternal and Child Health Hospital of Guangxi, Nanning, China
- Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of reproductive health and birth defect prevention, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Zailong Qin
- Maternal and Child Health Hospital of Guangxi, Nanning, China.
- Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.
- Guangxi Key Laboratory of reproductive health and birth defect prevention, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.
- Guangxi Clinical Research Center for Pediatric Diseases, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.
| |
Collapse
|
19
|
Su Y, Zhang J, Gao J, Ding G, Jiang H, Liu Y, Li Y, Yang G. Truncated FRMD7 proteins in congenital Nystagmus: novel frameshift mutations and proteasomal pathway implications. BMC Med Genomics 2024; 17:36. [PMID: 38279119 PMCID: PMC10811807 DOI: 10.1186/s12920-024-01817-7] [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: 11/01/2023] [Accepted: 01/23/2024] [Indexed: 01/28/2024] Open
Abstract
Idiopathic congenital nystagmus (ICN) manifests as involuntary and periodic eye movements. To identify the genetic defect associated with X-linked ICN, Whole Exome Sequencing (WES) was conducted in two affected families. We identified two frameshift mutations in FRMD7, c.1492dupT/p.(Y498Lfs*15) and c.1616delG/p.(R539Kfs*2). Plasmids harboring the mutated genes and qPCR analysis revealed mRNA stability, evading degradation via the NMD pathway, and corroborated truncated protein production via Western-blot analysis. Notably, both truncated proteins were degraded through the proteasomal (ubiquitination) pathway, suggesting potential therapeutic avenues targeting this pathway for similar mutations. Moreover, we conducted a comprehensive analysis, summarizing 140 mutations within the FRMD7 gene. Our findings highlight the FERM and FA structural domains as mutation-prone regions. Interestingly, exons 9 and 12 are the most mutated regions, but 90% (28/31) mutations in exon 9 are missense while 84% (21/25) mutations in exon 12 are frameshift. A predominant occurrence of shift code mutations was observed in exons 11 and 12, possibly associated with the localization of premature termination codons (PTCs), leading to the generation of deleterious truncated proteins. Additionally, our conjecture suggests that the loss of FRMD7 protein function might not solely drive pathology; rather, the emergence of aberrant protein function could be pivotal in nystagmus etiology. We propose a dependence of FRMD7 protein normal function primarily on its anterior domain. Future investigations are warranted to validate this hypothesis.
Collapse
Affiliation(s)
- Yuqing Su
- Department of Medical Genetics, School of Basic Medical Science, Wuhan University, Wuhan, China
- The First Clinical College of Wuhan University, Wuhan, China
| | - Juntao Zhang
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, 441021, China
| | - Jiahui Gao
- Department of Medical Genetics, School of Basic Medical Science, Wuhan University, Wuhan, China
| | - Guoqing Ding
- Department of Medical Genetics, School of Basic Medical Science, Wuhan University, Wuhan, China
| | - Heng Jiang
- Department of Medical Genetics, School of Basic Medical Science, Wuhan University, Wuhan, China
| | - Yang Liu
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, 441021, China
| | - Yulei Li
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, 441021, China.
- School of Basic Medicine, Hubei University of Arts and Science, Xiangyang, 441053, China.
| | - Guohua Yang
- Department of Medical Genetics, School of Basic Medical Science, Wuhan University, Wuhan, China.
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China.
| |
Collapse
|
20
|
Jiang Y, Xiao X, Sun W, Wang Y, Li S, Jia X, Wang P, Hejtmancik JF, Zhang Q. Clinical and genetic risk factors underlying severe consequence identified in 75 families with unilateral high myopia. J Transl Med 2024; 22:75. [PMID: 38243264 PMCID: PMC10797748 DOI: 10.1186/s12967-024-04886-5] [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: 09/14/2023] [Accepted: 01/11/2024] [Indexed: 01/21/2024] Open
Abstract
BACKGROUNDS Unilateral high myopia (uHM), commonly observed in patients with retinal diseases or only with high myopia, is frequently associated with amblyopia with poor prognosis. This study aims to reveal the clinical and genetic spectrum of uHM in a large Chinese cohort. METHODS A total of 75 probands with simplex uHM were included in our Pediatric and Genetic Eye Clinic. Patients with significant posterior anomalies other than myopic fundus changes were excluded. Variants were detected by exome sequencing and then analyzed through multiple-step bioinformatic and co-segregation analysis and finally confirmed by Sanger sequencing. Genetic findings were correlated with associated clinical data for analysis. RESULTS Among the 75 probands with a mean age of 6.21 ± 4.70 years at the presentation, myopic fundus of C1 and C2 was observed in 73 (97.3%) probands. Surprisingly, specific peripheral changes were identified in 63 eyes involving 36 (48.0%) probands after extensive examination, including peripheral retinal avascular zone (74.6%, 47/63 eyes), neovascularization (54.0%), fluorescein leakage (31.7%), peripheral pigmentary changes (31.7%), and others. Exome sequencing identified 21 potential pathogenic variants of 13 genes in 20 of 75 (26.7%) probands, including genes for Stickler syndrome (COL11A1 and COL2A1; 6/20), FEVR (FZD4, LRP5, and TSPAN12; 5/20), and others (FBN1, GPR179, ZEB2, PAX6, GPR143, OPN1LW, FRMD7, and CACNA1F; 9/20). For the peripheral retinal changes in the 20 probands, variants in Stickler syndrome-related genes were predominantly associated with retinal pigmentary changes, lattice degeneration, and retinal avascular region, while variants in genes related to FEVR were mainly associated with the avascular zone, neovascularization, and fluorescein leakage. CONCLUSIONS Genetic defects were identified in about one-fourth of simplex uHM patients in which significant consequences may be hidden under a classic myopic fundus in up to half. To our knowledge, this is the first systematic genetic study on simplex uHM to date. In addition to routine care of strabismus and amblyopia, careful examination of the peripheral retina and genetic screening is warranted for patients with uHM in order to identify signs of risk for retinal detachment and other complications and provide meaningful genetic counseling.
Collapse
Affiliation(s)
- Yi Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 54 Xianlie Road, Guangzhou, 510060, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 54 Xianlie Road, Guangzhou, 510060, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 54 Xianlie Road, Guangzhou, 510060, China
| | - Yingwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 54 Xianlie Road, Guangzhou, 510060, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 54 Xianlie Road, Guangzhou, 510060, China
| | - Xiaoyun Jia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 54 Xianlie Road, Guangzhou, 510060, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 54 Xianlie Road, Guangzhou, 510060, China
| | - J Fielding Hejtmancik
- Ophthalmic Molecular Genetics Section, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, Rockville, MD, 20852, USA
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 54 Xianlie Road, Guangzhou, 510060, China.
| |
Collapse
|
21
|
Goyal S, Singh R, Singh JR, Vanita V. Novel and known variants in GJA3 and LIM2 in congenital cataract families from North India. BMC Genomics 2024; 25:31. [PMID: 38178039 PMCID: PMC10765620 DOI: 10.1186/s12864-023-09880-7] [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: 07/07/2023] [Accepted: 12/07/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND To identify the underlying genetic defects in autosomal dominant (ADCC) and autosomal recessive (ARCC) congenital cataract families from North India. METHODS Detailed family histories were collected, pedigrees drawn followed by slit-lamp examination and lens photography. Mutation screening was performed using Sanger sequencing in the known candidate genes for crystallins, connexins, and membrane proteins. The pathogenicity of identified variants was assessed bioinformatically. RESULTS In two ADCC families (CC-281 and CC-3015) with posterior lenticonus cataract, a novel change c.263C > T (p.P88L) in GJA3 in CC-281 family and a previously reported substitution c.388C > T (p.R130C) in LIM2 in CC-3015 family was observed. In an ARCC family (CC-3005) having central pulverulent cataract, a novel frameshift deletion (c.764delT;p.L255R46fs) in GJA3 was detected. The observed variants segregated completely with phenotypes in the affected members and were neither present in unaffected family members nor in the ethnically matched 150 controls (tested for two novel variants), hence excluding these as polymorphisms. CONCLUSIONS Present study identified two novel mutations i.e., c.263C > T;p.P88L and c.764delT;p.L255R46fs in GJA3 in an ADCC and an ARCC family having posterior lenticonus and central pulverulent cataract, respectively. In another ADCC family with posterior lenticonus cataract, a previously reported mutation c.388C > T;p.R130C in LIM2 was observed. R130 may be a mutation hotspot as previously ADCC families from different ethnicities (UK/Czechia, China, Spain, Japan) also harbored the same substitution, however, with different phenotypes i.e., nuclear pulverulent, membranous, nuclear, lamellar, and sutural/lamellar. Findings in present study thus expand the mutation spectrum and phenotypic heterogeneity linked with GJA3 and LIM2.
Collapse
Affiliation(s)
- Shiwali Goyal
- Department of Human Genetics, Guru Nanak Dev University (GNDU), Amritsar, 143005, Punjab, India
| | - Ravijit Singh
- Dr. Daljit, Singh Eye Hospital, Amritsar, 143001, Punjab, India
| | - Jai Rup Singh
- Department of Human Genetics, Guru Nanak Dev University (GNDU), Amritsar, 143005, Punjab, India
| | - Vanita Vanita
- Department of Human Genetics, Guru Nanak Dev University (GNDU), Amritsar, 143005, Punjab, India.
| |
Collapse
|
22
|
Yu Y, Zhang J, Zhan Y, Luo G. A novel method for detecting nine hotspot mutations of deafness genes in one tube. Sci Rep 2024; 14:454. [PMID: 38172427 PMCID: PMC10764868 DOI: 10.1038/s41598-023-50928-1] [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: 07/06/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024] Open
Abstract
Deafness is a common sensory disorder. In China, approximately 70% of hereditary deafness originates from four common deafness-causing genes: GJB2, SLC26A4, GJB3, and MT-RNR1. A single-tube rapid detection method based on 2D-PCR technology was established for nine mutation sites in the aforementioned genes, and Sanger sequencing was used to verify its reliability and accuracy. The frequency of hotspot mutations in deafness genes was analysed in 116 deaf students. 2D-PCR identified 27 genotypes of nine loci according to the melting curve of the FAM, HEX, and Alexa568 fluorescence channels. Of the 116 deaf patients, 12.9% (15/116) carried SLC26A4 mutations, including c.919-2A > G and c.2168A > G (allele frequencies, 7.3% and 2.2%, respectively). The positivity rate (29.3%; 34/116) was highest for GJB2 (allele frequency, 15.9% for c.235delC, 6.0% for c.299_300delAT, and 2.6% for c.176-191del16). Sanger sequencing confirmed the consistency of results between the detection methods based on 2D-PCR and DNA sequencing. Common pathogenic mutations in patients with non-syndromic deafness in Changzhou were concentrated in GJB2 (c.235delC, c.299_300delAT, and c.176-191del16) and SLC26A4 (c.919-2A > G and c.2168 A > G). 2D-PCR is an effective method for accurately and rapidly identifying deafness-related genotypes using a single-tube reaction, and is superior to DNA sequencing, which has a high cost and long cycle.
Collapse
Affiliation(s)
- Yang Yu
- Comprehensive Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, People's Republic of China
| | - Jun Zhang
- Comprehensive Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, People's Republic of China
| | - Yuxia Zhan
- Comprehensive Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, People's Republic of China
| | - Guanghua Luo
- Comprehensive Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, People's Republic of China.
| |
Collapse
|
23
|
Ma Z, Huang W, Xu J, Qiu J, Liu Y, Ye M, Fan S. Analysis of deafness susceptibility gene of neonates in northern Guangdong, China. Sci Rep 2024; 14:362. [PMID: 38172182 PMCID: PMC10764796 DOI: 10.1038/s41598-023-49530-2] [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: 03/24/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
This study aimed to explore the molecular epidemiology characteristics of deafness susceptibility genes in neonates in northern Guangdong and provide a scientific basis for deafness prevention and control. A total of 10,183 neonates were recruited between January 2018 and December 2022 at Yuebei People's Hospital. Among these, a PCR hybridization screening group of 8276 neonates was tested for four deafness genes: GJB2, SLC26A4, mtDNA, and GJB3 by PCR hybridization. Another group used next-generation sequencing (NGS) to detect genetic susceptibility genes in 1907 neonates. In PCR hybridization screening group, 346 (4.18%) of 8276 neonates were found to be carriers of the deafness gene. Among these, 182 (2.2%) had GJB2 variants, 114 (1.38%) had SLC26A4 variants, 35 (0.42%) had mtDNA variants, and 15 (0.18%) had GJB3 variants. In NGS Screening Group, 195 out of 1907 neonates were found to be carriers of the deafness gene, with a positive rate of 10.22%. Among these, 137 (7.18%) had GJB2 variants, 41 (2.15%) had SLC26A4 variants, 11 (0.58%) had mtDNA variants, and 6 (0.31%) had GJB3 variants. The prevalence of deafness gene variants was high in Northern Guangdong Province. The most common gene for deafness was GJB2, followed by SLC26A4 and mtDNA. GJB3 variants are rare. Compared with PCR hybridization method, NGS technology can expand the screening scope and greatly improve the detection rate of deafness genes. The c.109G>A of GJB2 was found to occur at a high frequency, which should be considered. Therefore, it is important to conduct neonatal deafness gene screening to prevent and control hereditary deafness.
Collapse
Affiliation(s)
- Zhanzhong Ma
- Reproductive Medicine Center, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512026, China
| | - Wenbo Huang
- Reproductive Medicine Center, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512026, China
| | - Jing Xu
- Reproductive Medicine Center, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512026, China
| | - Jianwu Qiu
- Department of Neonatology, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512026, China
| | - Yulan Liu
- Reproductive Medicine Center, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512026, China
| | - Meixian Ye
- Department of Biobank, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512026, China
| | - Shushu Fan
- Reproductive Medicine Center, Yuebei People's Hospital, Shantou University Medical College, Shaoguan, 512026, China.
| |
Collapse
|
24
|
Xiong Y, Chen M, Wang H, Chen L, Huang H, Xu L. Mutation analysis of GJB2, SLC26A4, GJB3 and mtDNA12SrRNA genes in 251 non-syndromic hearing loss patients in Fujian, China. Int J Pediatr Otorhinolaryngol 2024; 176:111777. [PMID: 38029595 DOI: 10.1016/j.ijporl.2023.111777] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/23/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023]
Abstract
OBJECTIVES The molecular etiology of non-syndromic hearing loss (NSHL) in Southeastern China (Fujian) has not been precisely identified. our study selected patients with NSHL and analyzed their causative genes, which helped to improve the accuracy of the diagnosis of hereditary hearing loss (HHL) and its treatment. METHODS 251 unrelated patients who attended the otolaryngology clinic of Fujian Maternal and Child Health Hospital with hearing loss were enrolled to our study. All patients had genetic tests and listening tests, of which 251 were diagnosed with NSHL. In addition, we used whole-exome sequencing (WES) in a patient who has a significant family history of HHL but negative for gene chip testing, as well as in his family members. RESULT Among of 251 patients, Nucleotide changes were found in 63 cases (25.09%), including 34 located in GJB2(13.5%, including 235delC and 299_300delAT), 13 located in SLC26A4(5.18%, including c.919-2G > A and 2168 A > G), 1 located in GJB3(0.4%,538C > T) and 16 located in mtDNA12SrRNA (6.37%,1555 A > G). In addition, we discuss the process of identifying novel PLS1 mutations from 251 patients. CONCLUSION Our results demonstrate the conventional deafness gene mutation in 251 NSHL patients in Fujian, China. Compared with the other area of China, we have a lower detection rate, but GJB2 235delC remains the most common mutation in Fujian. In addition, we discuss the process of discovering novel mutation locus for deafness, which provides an understanding for deafness diagnosis and genetic testing.
Collapse
Affiliation(s)
- Yikang Xiong
- The Frist Department of Clinical Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, Fujian Province, China
| | - Meihuan Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, China
| | - Haiwei Wang
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, China
| | - Lingji Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, China.
| | - Liangpu Xu
- The Frist Department of Clinical Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, Fujian Province, China; Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, China.
| |
Collapse
|
25
|
Li H, Wei X, Wu S, Zhu T, Sun Z, Li H, Han X, Zou X, Yao F, Sui R. Clinical and genetic characterization of a large cohort of Chinese patients with Bietti crystalline retinopathy. Graefes Arch Clin Exp Ophthalmol 2024; 262:337-351. [PMID: 37584790 DOI: 10.1007/s00417-023-06178-y] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 07/10/2023] [Accepted: 07/16/2023] [Indexed: 08/17/2023] Open
Abstract
PURPOSE To investigate the clinical and genetic characteristics for a large cohort of Chinese patients with Bietti crystalline retinopathy (BCR). METHODS A total of 208 Chinese BCR patients from 175 families were recruited. Comprehensive clinical evaluations and genetic analysis were performed. Genotype-phenotype correlations were evaluated through statistical analysis. RESULTS The patients' median age was 37 years (range, 20-76 years). The median best corrected visual acuity (BCVA) was 0.8 LogMAR unit (range, 2.8 to -0.12). A significant decline of BCVA was revealed in patients over 40 years old (P<0.001). Two clinical types were observed: peripheral type (type P) and central type (type C). Significantly more type C patients had a worse central visual acuity, but a more preserved retinal function (P<0.05). Molecular screening detected biallelic CYP4V2 pathogenic variants in 98.3% (172/175) of the families, including 19 novel ones. The most frequent pathogenic variant was c.802-8_810del17insGC, with the allele frequency of 55.7% (195/350), followed by c.992A>C (28/350, 8%) and c.1091-2A>G (23/350, 6.6%). BCR patients with one c.802-8_810del17insGC and one truncating variant (IVS6-8/Tru) had BCVA>1.3 LogMAR unit (Snellen equivalent<20/400) at a younger age than those with homozygous c.802-8_810del17insGC variants (homo IVS6-8) (P=0.031). CONCLUSIONS BCR patients preserved relatively good vision before 40 years old. Two distinct clinical types of BCR were observed. BCR patients with IVS6-8/Tru had an earlier decline in visual acuity than those with homo IVS6-8. Our findings enhance the knowledge of BCR and will be helpful in patient selection for gene therapy.
Collapse
Affiliation(s)
- Huajin Li
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Department of Ophthalmology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xing Wei
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Shijing Wu
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Tian Zhu
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zixi Sun
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Hui Li
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoxu Han
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xuan Zou
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Fengxia Yao
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
| |
Collapse
|
26
|
Le Gall J, Dehainault C, Boutte M, Petitalot A, Caputo SM, Courtois L, Vacher S, Bieche I, Radvanyi F, Pacquement H, Doz F, Lumbroso-Le Rouic L, Gauthier Villars M, Stoppa-Lyonnet D, Lallemand F, Houdayer C, Golmard L. Germline HPF1 retrogene insertion in RB1 gene involved in cancer predisposition. J Med Genet 2023; 61:78-83. [PMID: 37541786 DOI: 10.1136/jmg-2022-109105] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 07/23/2023] [Indexed: 08/06/2023]
Abstract
About half of the human genome is composed of repeated sequences derived from mobile elements, mainly retrotransposons, generally without pathogenic effect. Familial forms of retinoblastoma are caused by germline pathogenic variants in RB1 gene. Here, we describe a family with retinoblastoma affecting a father and his son. No pathogenic variant was identified after DNA analysis of RB1 gene coding sequence and exon-intron junctions. However, RB1 mRNA analysis showed a chimeric transcript with insertion of 114 nucleotides from HPF1 gene inside RB1 gene. This chimeric transcript led to an insertion of 38 amino acids in functional domain of retinoblastoma protein. Subsequent DNA analysis in RB1 intron 17 revealed the presence of a full-length HPF1 retrogene insertion in opposite orientation. Functional assay shows that this insertion has a deleterious impact on retinoblastoma protein function. This is the first report of a full-length retrogene insertion involved in human Mendelian disease leading to a chimeric transcript and a non-functional chimeric protein. Some retrogene insertions may be missed by standard diagnostic genetic testing, so contribution of retrogene insertions to human disease may be underestimated. The increasing use of whole genome sequencing in diagnostic settings will help to get a more comprehensive view of retrogenes.
Collapse
Affiliation(s)
- Jessica Le Gall
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - Catherine Dehainault
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - Matteo Boutte
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - Ambre Petitalot
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - Sandrine M Caputo
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - Laura Courtois
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - Sophie Vacher
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - Ivan Bieche
- Department of Genetics, Institut Curie, Paris, France
- Université de Paris, Paris, France
| | - François Radvanyi
- Department of Genetics, PSL University, Paris, France
- Molecular Oncology Team, UMR144, Paris, France
| | - Hélène Pacquement
- Department of Genetics, PSL University, Paris, France
- Oncology Center SIREDO, Institut Curie, Paris, France
| | - François Doz
- Molecular Oncology Team, UMR144, Paris, France
- Oncology Center SIREDO, Institut Curie, Paris, France
| | - Livia Lumbroso-Le Rouic
- Department of Genetics, PSL University, Paris, France
- Department of Ophthalmology, Institut Curie, Paris, France
| | - Marion Gauthier Villars
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - François Lallemand
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| | - Claude Houdayer
- Department of Genetics, University Hospital Centre Rouen, Rouen, France
| | - Lisa Golmard
- Department of Genetics, Institut Curie, Paris, France
- Department of Genetics, PSL University, Paris, France
| |
Collapse
|
27
|
Rao Y, Ahmed N, Pritchard J, O'Brien EP. Incorporating mutational heterogeneity to identify genes that are enriched for synonymous mutations in cancer. BMC Bioinformatics 2023; 24:462. [PMID: 38062391 PMCID: PMC10704839 DOI: 10.1186/s12859-023-05521-8] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/05/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Synonymous mutations, which change the DNA sequence but not the encoded protein sequence, can affect protein structure and function, mRNA maturation, and mRNA half-lives. The possibility that synonymous mutations might be enriched in cancer has been explored in several recent studies. However, none of these studies control for all three types of mutational heterogeneity (patient, histology, and gene) that are known to affect the accurate identification of non-synonymous cancer-associated genes. Our goal is to adopt the current standard for non-synonymous mutations in an investigation of synonymous mutations. RESULTS Here, we create an algorithm, MutSigCVsyn, an adaptation of MutSigCV, to identify cancer-associated genes that are enriched for synonymous mutations based on a non-coding background model that takes into account the mutational heterogeneity across these levels. Using MutSigCVsyn, we first analyzed 2572 cancer whole-genome samples from the Pan-cancer Analysis of Whole Genomes (PCAWG) to identify non-synonymous cancer drivers as a quality control. Indicative of the algorithm accuracy we find that 58.6% of these candidate genes were also found in Cancer Census Gene (CGC) list, and 66.2% were found within the PCAWG cancer driver list. We then applied it to identify 30 putative cancer-associated genes that are enriched for synonymous mutations within the same samples. One of the promising gene candidates is the B cell lymphoma 2 (BCL-2) gene. BCL-2 regulates apoptosis by antagonizing the action of proapoptotic BCL-2 family member proteins. The synonymous mutations in BCL2 are enriched in its anti-apoptotic domain and likely play a role in cancer cell proliferation. CONCLUSION Our study introduces MutSigCVsyn, an algorithm that accounts for mutational heterogeneity at patient, histology, and gene levels, to identify cancer-associated genes that are enriched for synonymous mutations using whole genome sequencing data. We identified 30 putative candidate genes that will benefit from future experimental studies on the role of synonymous mutations in cancer biology.
Collapse
Affiliation(s)
- Yiyun Rao
- Huck Institute of the Life Sciences, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Nabeel Ahmed
- Huck Institute of the Life Sciences, Pennsylvania State University, University Park, State College, PA, 16802, USA
- Moderna, Inc., Cambridge, USA
| | - Justin Pritchard
- Department of Biomedical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA.
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, State College, PA, 16802, USA.
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, State College, PA, 16802, USA.
| |
Collapse
|
28
|
Sylla MM, Kolesinkova M, da Costa BL, Maumenee IH, Tsang SH, Quinn PMJ. A novel pathogenic CRB1 variant presenting as Leber Congenital Amaurosis 8 and evaluation of gene editing feasibility. Doc Ophthalmol 2023; 147:217-224. [PMID: 37804373 DOI: 10.1007/s10633-023-09951-w] [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: 02/27/2023] [Accepted: 08/25/2023] [Indexed: 10/09/2023]
Abstract
INTRODUCTION Leber Congenital Amaurosis (LCA) is an inherited retinal disease that presents in infancy with severely decreased vision, nystagmus, and extinguished electroretinography findings. LCA8 is linked to variants in the Crumbs homolog 1 (CRB1) gene. CASE DESCRIPTION We report a novel CRB1 variant in a 14-year-old male presenting with nystagmus, worsening vision, and inability to fixate on toys in his infancy. Color fundus photography revealed nummular pigments in the macula and periphery. Imaging studies revealed thickened retina on standard domain optical coherence tomography and widespread atrophy of the retinal pigment epithelium on autofluorescence. Full-field electroretinography revealed extinguished scotopic and significantly reduced photopic responses. Genetic testing demonstrated a novel homozygous variant, c.3057 T > A; p.(Tyr1019Ter), in the CRB1 gene. This variant is not currently amenable to base editing, however, in silico analysis revealed several potential prime editing strategies for correction. CONCLUSION This case presentation is consistent with LCA8, suggesting pathogenicity of this novel variant and expanding our knowledge of disease-causing CRB1 variants.
Collapse
Affiliation(s)
- Mohamed M Sylla
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
- Jonas Children's Vision Care, and Bernard and Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University, New York, NY, USA
- State University of New York at Downstate Health Sciences University, Brooklyn, NY, USA
| | - Masha Kolesinkova
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
- Jonas Children's Vision Care, and Bernard and Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University, New York, NY, USA
- State University of New York at Downstate Health Sciences University, Brooklyn, NY, USA
| | | | - Irene H Maumenee
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
- Jonas Children's Vision Care, and Bernard and Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University, New York, NY, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
- Jonas Children's Vision Care, and Bernard and Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University, New York, NY, USA
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Peter M J Quinn
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Ophthalmology, Columbia University Irving Medical Center, Hammer Health Sciences Building, 701 West 168th Street, New York, NY, 10032, USA.
| |
Collapse
|
29
|
Kwon R, Cheng HH, Pritchard CC. Tumor Mutational Burden Testing in Solid Tumors. JAMA Oncol 2023; 9:1725-1726. [PMID: 37883072 DOI: 10.1001/jamaoncol.2023.4293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
A 58-year-old man with diabetes, chronic kidney disease, and JAK2-positive myeloproliferative neoplasm is referred for newly diagnosed oligometastatic prostate cancer with substantial urinary symptoms. What would you do next?
Collapse
Affiliation(s)
- Regina Kwon
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle
| | - Heather H Cheng
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Colin C Pritchard
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle
- VA Puget Sound Health Care System, Seattle, Washington
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
| |
Collapse
|
30
|
Fu M, Duan S, Zhang X, Wang J, Wang S, Chi ZL. A Novel Heterozygous TGFBI c.1613C>A Pathogenic Variant is Associated With Lattice Corneal Dystrophy in a Chinese Family. Am J Ophthalmol 2023; 256:138-145. [PMID: 37567434 DOI: 10.1016/j.ajo.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023]
Abstract
PURPOSE To investigate the gene mutations and relationship of clinical manifestation in a Chinese family with familial lattice corneal dystrophy (LCD). DESIGN Single-family case-control study. METHODS A family with familial LCD was recruited for this study. A total of 10 affected and 13 healthy family members participated in this research. Clinical features were examined by slit-lamp examination and anterior segment optical coherence tomography (AS-OCT). Peripheral blood samples were collected from each participant, and genomic DNA was extracted. Whole-exome sequencing (WES) analysis was performed, and the pathogenic variants of LCD were identified using bioinformatics tools and confirmed by Sanger sequencing. RESULTS Slit-lamp examination revealed diffuse grayish-white punctate, linear, and "lattice-like" opacities in the corneal epithelium and superficial corneal stroma. AS-OCT revealed an irregularly shaped cornea. The corneal epithelium and anterior corneal stroma showed high-reflective deposits and bulges. The clinical appearance of the patients fit the pattern and features of autosomal dominant inheritance of LCD type I (LCD I). A novel pathogenic variant of exon 12 in TGFBI was found by WES analysis, in which cytosine at position 1613 was substituted by adenine (c.1613C>A), and the amino acid was changed from threonine to lysine (p.T538K). Mutated genes and proteins were predicted to be deleterious. CONCLUSION A novel heterozygous pathogenic variant (c.1613C>A) of TGFBI was identified in the Chinese family with LCD I.
Collapse
Affiliation(s)
- Mengjun Fu
- From the State Key Laboratory of Ophthalmology (M.F., X.Z., Z-L.C.), Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China; National Clinical Research Center for Ocular Diseases (M.F., X.Z., Z-L.C.), Eye Hospital, Wenzhou Medical University, Wenzhou, China; Weifang Eye Institute (M.F., J.W., S.W.), National Key Clinical Specialty, Weifang Eye Hospital, Zhengda Guangming Eye Group, Weifang, China
| | - Shan Duan
- Laboratory of Molecular Medicine (S.D.), Institute of Maternal and Child Medicine, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Xiaobo Zhang
- From the State Key Laboratory of Ophthalmology (M.F., X.Z., Z-L.C.), Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China; National Clinical Research Center for Ocular Diseases (M.F., X.Z., Z-L.C.), Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jiahao Wang
- Weifang Eye Institute (M.F., J.W., S.W.), National Key Clinical Specialty, Weifang Eye Hospital, Zhengda Guangming Eye Group, Weifang, China
| | - Sheng Wang
- Weifang Eye Institute (M.F., J.W., S.W.), National Key Clinical Specialty, Weifang Eye Hospital, Zhengda Guangming Eye Group, Weifang, China
| | - Zai-Long Chi
- From the State Key Laboratory of Ophthalmology (M.F., X.Z., Z-L.C.), Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China; National Clinical Research Center for Ocular Diseases (M.F., X.Z., Z-L.C.), Eye Hospital, Wenzhou Medical University, Wenzhou, China.
| |
Collapse
|
31
|
Mullie GA, Javidi S, Soucy JF, Lesk MR, Hamel P. Variable phenotypic expression of MYOC mutations in a family with inherited pediatric glaucoma. Can J Ophthalmol 2023; 58:e269-e270. [PMID: 37247815 DOI: 10.1016/j.jcjo.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/10/2023] [Indexed: 05/31/2023]
Affiliation(s)
| | | | - Jean-François Soucy
- University of Montreal, Montreal, QC; Sainte-Justine University Hospital Center, Montreal, QC
| | - Mark R Lesk
- University of Montreal, Montreal, QC; University Ophthalmology Center of the University of Montreal Maisonneuve-Rosemont Hospital, Montreal, QC
| | - Patrick Hamel
- University of Montreal, Montreal, QC; Sainte-Justine University Hospital Center, Montreal, QC.
| |
Collapse
|
32
|
Ali A, Abdullah, Bilal M, Mis EK, Lakhani SA, Ahmad W, Ullah I. Sequence variants in different genes underlying Bardet-Biedl syndrome in four consanguineous families. Mol Biol Rep 2023; 50:9963-9970. [PMID: 37897612 DOI: 10.1007/s11033-023-08816-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/11/2023] [Indexed: 10/30/2023]
Abstract
BACKGROUND Bardet-Biedl Syndrome (BBS) is a rare (1:13,500-1-160,000) heterogeneous congenital disorder, characterized by postaxial polydactyly, obesity, hypogonadism, rod-cone dystrophy, cognitive impairment, and renal abnormalities (renal cystic dysplasia, anatomical malformation). To date about twenty-five genes have been identified to cause BBS, which accounts for about 80% of BBS diagnosis. METHODS In the current study, we have performed mutational screening of four Pakistani consanguineous families (A-D) with clinical manifestation of BBS by microsatellite-based genotyping and whole exome sequencing. RESULTS Analysis of the data revealed four variants, including a novel/unique inheritance pattern of compound heterozygous variants, p.(Ser40*) and p.(Thr259Leufs*21), in MKKS gene, novel homozygous variant, p.(Gly251Val)] in BBS7 gene and two previously reported p.(Thr259Leufs*21) in MKKS and p.(Met1Lys) in BBS5 gene. The variants were found segregated with the disorder within the families. CONCLUSION The study not only expanded mutations spectrum in the BBS genes, but this will facilitate diagnosis and genetic counselling of families carrying BBS related phenotypes in Pakistani population.
Collapse
Affiliation(s)
- Amjad Ali
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Pediatric Genome Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Emily Kathryn Mis
- Pediatric Genome Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Saquib Ali Lakhani
- Pediatric Genome Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Imran Ullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.
| |
Collapse
|
33
|
Li J, Wang C, Zhang S, Cai B, Pan B, Sun C, Qi X, Ma C, Fang W, Jin K, Bi X, Jin Z, Zhuang W. Genetic detection of two novel LRP5 pathogenic variants in patients with familial exudative vitreoretinopathy. BMC Ophthalmol 2023; 23:489. [PMID: 38030997 PMCID: PMC10685552 DOI: 10.1186/s12886-023-03243-2] [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: 12/31/2022] [Accepted: 11/23/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Familial exudative vitreoretinopathy (FEVR) is a genetic eye disorder that leads to abnormal development of retinal blood vessels, resulting in vision impairment. This study aims to identify pathogenic variants by targeted exome sequencing in 9 independent pedigrees with FEVR and characterize the novel pathogenic variants by molecular dynamics simulation. METHODS Clinical data were collected from 9 families with FEVR. The causative genes were screened by targeted next-generation sequencing (TGS) and verified by Sanger sequencing. In silico analyses (SIFT, Polyphen2, Revel, MutationTaster, and GERP + +) were carried out to evaluate the pathogenicity of the variants. Molecular dynamics was simulated to predict protein conformation and flexibility transformation alterations on pathogenesis. Furthermore, molecular docking techniques were employed to explore the interactions and binding properties between LRP5 and DKK1 proteins relevant to the disease. RESULTS A 44% overall detection rate was achieved with four variants including c.4289delC: p.Pro1431Argfs*8, c.2073G > T: p.Trp691Cys, c.1801G > A: p.Gly601Arg in LRP5 and c.633 T > A: p.Tyr211* in TSPAN12 in 4 unrelated probands. Based on in silico analysis and ACMG standard, two of them, c.4289delC: p.Pro1431Argfs*8 and c.2073G > T: p.Trp691Cys of LRP5 were identified as novel pathogenic variants. Based on computational predictions using molecular dynamics simulations and molecular docking, there are indications that these two variants might lead to alterations in the secondary structure and spatial conformation of the protein, potentially impacting its rigidity and flexibility. Furthermore, these pathogenic variants are speculated to potentially influence hydrogen bonding interactions and could result in an increased binding affinity with the DKK1 protein. CONCLUSIONS Two novel genetic variants of the LRP5 gene were identified, expanding the range of mutations associated with FEVR. Through molecular dynamics simulations and molecular docking, the potential impact of these variants on protein structure and their interactions with the DKK1 protein has been explored. These findings provide further support for the involvement of these variants in the pathogenesis of the disease.
Collapse
Affiliation(s)
- Jiayu Li
- Third Clinical Medical College of Ningxia Medical University, Shengli Street, Yinchuan, 750004, Ningxia, China
- Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, Huanghe Road, Yinchuan, 750011, Ningxia, China
| | - Chanjuan Wang
- Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, Huanghe Road, Yinchuan, 750011, Ningxia, China
| | - Shaochi Zhang
- Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, Huanghe Road, Yinchuan, 750011, Ningxia, China
| | - Bo Cai
- Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, Huanghe Road, Yinchuan, 750011, Ningxia, China
| | - Bo Pan
- Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, Huanghe Road, Yinchuan, 750011, Ningxia, China
| | - Caihong Sun
- Third Clinical Medical College of Ningxia Medical University, Shengli Street, Yinchuan, 750004, Ningxia, China
- Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, Huanghe Road, Yinchuan, 750011, Ningxia, China
| | - Xiaolong Qi
- Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, Huanghe Road, Yinchuan, 750011, Ningxia, China
| | - Chunmei Ma
- Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, Huanghe Road, Yinchuan, 750011, Ningxia, China
| | - Wei Fang
- Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, Huanghe Road, Yinchuan, 750011, Ningxia, China
| | - Kangxin Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, 100005, China
| | - Xiaojun Bi
- Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, Huanghe Road, Yinchuan, 750011, Ningxia, China.
| | - Zibing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, 100005, China.
| | - Wenjuan Zhuang
- Third Clinical Medical College of Ningxia Medical University, Shengli Street, Yinchuan, 750004, Ningxia, China.
- Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, Huanghe Road, Yinchuan, 750011, Ningxia, China.
| |
Collapse
|
34
|
Han JH, Cancellieri F, Perea-Romero I, Ayuso C, Quinodoz M, Rivolta C. The p.C759F Variant in USH2A Is a Pathogenic Mutation: Systematic Literature Review and Meta-Analysis of 667 Genotypes. Ophthalmic Res 2023; 67:107-114. [PMID: 38016437 DOI: 10.1159/000535545] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 11/14/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND Although the p.C759F (c.2276G>T, p.Cys759Phe) variant in the USH2A gene has been identified in association with retinal degeneration by several authors, its pathogenicity has been questioned once by the publication of two unaffected homozygotes from a single family. OBJECTIVES The objective of the study was to ascertain the role of p.C759F in hereditary retinal disease. METHODS We examined 87 research articles reporting on patients carrying this variant and then used this information as primary data for a series of meta-analytical tests. RESULTS Independent statistical analyses showed that p.C759F (i) is highly enriched in patients with respect to healthy individuals, (ii) represents a clear-cut recessive allele causing disease when it is in trans with other mutations, (iii) is pathogenic in homozygotes. CONCLUSIONS Our results confirm that p.C759F is a bona fide mutation, leading to retinal blindness according to a recessive pattern of inheritance.
Collapse
Affiliation(s)
- Ji Hoon Han
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Irene Perea-Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| |
Collapse
|
35
|
Millan-Esteban D, García-Casado Z, Macià A, de la Rosa I, Torrecilla-Vall-Llossera C, Penin RM, Manrique-Silva E, Pellegrini S, Biasin MR, Rizzolo P, Gavillero A, Di Stefani A, Pellegrini C, Requena C, Fargnoli MC, Peris K, Cota C, Menin C, Landi MT, Nagore E. Molecular Profile of Subungual Melanoma: A MelaNostrum Consortium Study of 68 Cases Reporting BRAF, NRAS, KIT, and TERT Promoter Status. Dermatology 2023; 240:164-169. [PMID: 37918362 DOI: 10.1159/000534955] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 08/31/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND Subungual melanoma (SM) is an unusual type of melanocytic tumor affecting the nail apparatus. The mutational prevalence of the most prominently mutated genes in melanoma has been reported in small cohorts of SM, with unclear conclusions on whether SM is different from the rest of melanomas arising in acral locations or not. Hence, the molecular profile of a large series of SM is yet to be described. OBJECTIVES The aim of this study was to describe the molecular characteristics of a large series of SM and their association with demographic and histopathological features. METHODS Patients diagnosed with SM between 2001 and 2021 were identified from six Spanish and Italian healthcare centers. The mutational status for BRAF, NRAS, KIT, and the promoter region of TERT (TERTp) were determined either by Sanger sequencing or next-generation sequencing. Clinical data were retrieved from the hospital databases to elucidate potential associations. RESULTS A total of 68 SM cases were included. Mutations were most common in BRAF (10.3%) and KIT (10%), followed by NRAS (7.6%), and TERTp (3.8%). Their prevalence was similar to that of non-subungual acral melanoma but higher in SM located on the hand than on the foot. CONCLUSIONS To date, this study represents the largest cohort of SM patients with data on the known driver gene mutations. The low mutation rate supports a different etiopathogenic mechanism for SM in comparison of non-acral cutaneous melanoma, particularly for SM of the foot.
Collapse
Affiliation(s)
- David Millan-Esteban
- School of Medicine, Universidad Católica de València San Vicente Mártir, València, Spain
- Department of Dermatology, Fundación Instituto Valenciano de Oncología, València, Spain
| | - Zaida García-Casado
- Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología, València, Spain
| | - Anna Macià
- Department of Experimental Medicine, Oncological Pathology Group, Institut de Recerca Biomèdica de Lleida, University of Lleida, Lleida, Spain
| | - Inés de la Rosa
- Department of Experimental Medicine, Oncological Pathology Group, Institut de Recerca Biomèdica de Lleida, University of Lleida, Lleida, Spain
| | | | - Rosa Maria Penin
- Department of Dermatology, Hospital Universitari de Bellvitge, Bellvitge, Spain
| | | | - Stefania Pellegrini
- Pathology Unit, Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | - Maria Raffaella Biasin
- Pathology Unit, Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | - Piera Rizzolo
- Department of Dermatopathology, San Gallicano Dermatological Institute IRCCS, Rome, Italy
| | - Alicia Gavillero
- School of Medicine, Universidad Católica de València San Vicente Mártir, València, Spain
| | - Alessandro Di Stefani
- Dermatologia, Dipartimento Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Dermatologia, Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Cristina Pellegrini
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Celia Requena
- Department of Dermatology, Fundación Instituto Valenciano de Oncología, València, Spain
| | - Maria Concetta Fargnoli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
- Dermatology Unit, Osppedale San Salvatore, L'Aquila, Italy
| | - Ketty Peris
- Dermatologia, Dipartimento Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Dermatologia, Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Carlo Cota
- Department of Dermatopathology, San Gallicano Dermatological Institute IRCCS, Rome, Italy
| | - Chiara Menin
- Pathology Unit, Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Eduardo Nagore
- School of Medicine, Universidad Católica de València San Vicente Mártir, València, Spain
- Department of Dermatology, Fundación Instituto Valenciano de Oncología, València, Spain
| |
Collapse
|
36
|
Tsai ASH, Kang EYC, Wang NK, Lee H, Seo GH, Khang R, Wu WC. LONG-TERM CLINICAL OUTCOMES AND GENOTYPE-PHENOTYPE CORRELATION IN FAMILIAL EXUDATIVE VITREORETINOPATHY IN A TERTIARY REFERRAL CENTER. Retina 2023; 43:1945-1950. [PMID: 37339455 DOI: 10.1097/iae.0000000000003868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
BACKGROUND/PURPOSE To evaluate clinical outcomes and assess genotype-phenotype correlations in patients with familial exudative vitreoretinopathy (FEVR). METHODS Clinical charts of 40 patients with FEVR were reviewed. FEVR was staged per Pendergast and Trese, and retinal dragging and folds further classified per Yaguchi et al. We performed whole-exome sequencing and compared clinical characteristics between genetic-positive and genetic-negative groups. RESULTS The mean duration of follow-up was 5.4 years (range: 0.33, 15) for genetic-positive and 6.9 (range: 1, 20) for genetic-negative patients. The mean age at diagnosis was 5.6 years (0.25, 27) for genetic-positive and 6.0 (0, 32) for genetic-negative patients. Genetic-positive patients reported 100% full-term births and genetic-negative patients reported 45% full-term births ( P = 0.0012). There were more patients with retinal folds with all major vessels affected (Yaguchi's Group 4) in genetic-positive compared with genetic-negative patients (21.4% vs. 2.6%, P = 0.045). TSPAN12 was the most common (57.1%) genetic mutation in our population of which 50% exhibited asymmetric presentation. CONCLUSION Patients who test positive for a typical FEVR gene mutation reported more term births and had more severe disease by Yaguchi's classification. TSPAN12 was the most common genetic mutation in our population and had highly asymmetrical disease.
Collapse
Affiliation(s)
- Andrew S H Tsai
- Singapore National Eye Centre, Singapore
- DUKE NUS Medical School, Singapore
| | - Eugene Y C Kang
- Department of Ophthalmology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Nan-Kai Wang
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, Columbia University, New York, New York; and
| | - Hane Lee
- Division of Medical Genetics, 3billion Inc., Seoul, South Korea
| | - Go Hun Seo
- Division of Medical Genetics, 3billion Inc., Seoul, South Korea
| | - Rin Khang
- Division of Medical Genetics, 3billion Inc., Seoul, South Korea
| | - Wei-Chi Wu
- Department of Ophthalmology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| |
Collapse
|
37
|
Boese EA, Alward WLM, Kwon YH, Roos BR, Stone EM, Scheetz TE, Fingert JH. Thrombospondin Mutations and Patients With Primary Congenital Glaucoma in a United States Population. J Glaucoma 2023; 32:e156-e160. [PMID: 37327471 DOI: 10.1097/ijg.0000000000002254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/02/2023] [Indexed: 06/18/2023]
Abstract
Mutations in the thrombospondin 1 ( THBS1 ) gene have been previously reported in primary congenital glaucoma (PCG) pedigrees that exhibit autosomal dominant inheritance with low penetrance. We sought to determine the role of THBS1 mutations in a cohort of 20 patients with PCG and 362 normal controls from Iowa using a combination of Sanger sequencing and whole exome sequencing. We detected 16 different THBS1 variants, including 4 rare, nonsynonymous variants (p.Thr611Met, p.Asn708Lys, p.Gln1089His, and p.Glu1166Lys). However, none of these variants were judged to be disease-causing mutations based on: 1) prevalence in cases and controls from Iowa, 2) prevalence in the public database gnomAD, 3) mutation analysis algorithms, and 4) THBS1 DNA sequence conservation. These results indicate THBS1 mutations are not a common cause of PCG in patients from Iowa and may be a rare cause of PCG overall.
Collapse
Affiliation(s)
- Erin A Boese
- Institute for Vision Research
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Wallace L M Alward
- Institute for Vision Research
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Young H Kwon
- Institute for Vision Research
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Ben R Roos
- Institute for Vision Research
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Edwin M Stone
- Institute for Vision Research
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Todd E Scheetz
- Institute for Vision Research
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - John H Fingert
- Institute for Vision Research
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA
| |
Collapse
|
38
|
Pérez-Pérez M, Agostino A, de Sola-Llamas CG, Ruvolo M, Vilches-Arenas A, Relimpio-López MI, Espejo-Arjona F, Macías-García L, De Miguel-Rodríguez M, García-Escudero A, Idoate MA, Ríos-Martín JJ. Next-generation sequencing of uveal melanoma with clinical and histological correlations: Prognostic value of new mutations in the PI3K/AKT/mTOR pathway. Clin Exp Ophthalmol 2023; 51:822-834. [PMID: 37803816 DOI: 10.1111/ceo.14302] [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: 06/04/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND Uveal melanoma (UM) is the eye's most common primary malignancy and there are no effective therapies for disseminated disease. It is important to try to know the patient's prognosis. The aim of this study was to reflect genetic variants, studied using NGS, of a series of 69 cases of UM and its correlation with histopathology and clinical progression. METHODS We performed targeted NGS using a 519-gene panel. RESULTS There were selected 28 different mutated genes, showing a total of 231 genetic variants that affected the function of the protein. The most common secondary mutations occurred in SF3B1 (in 26%), followed by BAP1 (in 23%), LRP1B (22%) and FGFR4 (20%). BAP1 mutation was associated with a greater likelihood of metastases and with greater presence of epithelioid cells. LRP1B was also associated with presence of epithelioid cells SF3B1 mutation was significantly associated with a spindle morphology. We found variants in the RAD51B, TOP2A, PTPRD, TSC2, DHX9, PDK1 and MTOR that have not been previously reported in consulted databases. The presence of a mutation in: CHEK2, DHX9 and PDK1 was associated with metastases. CONCLUSIONS BAP1 is the most solid biomarker of a poor prognosis in UM and mutations can be detected using NGS. SF3B1 is associated with the spindle cell subtype of UM, which gives it probably a favourable prognostic value. Our study suggests that mutations in DHX9 and PDK1 can have prognostic value. These potential biomarkers are related to the PI3K/AKT/mTOR pathway and makes them candidates for developing new directed therapies.
Collapse
Affiliation(s)
- Manuel Pérez-Pérez
- Department of Anatomic Pathology, Virgen Macarena University Hospital, Seville, Spain
| | - Alessandro Agostino
- Diagnostics and Genomics Division, Agilent Technologies Italia S.p.A. Cernusco sul Naviglio, Milan, Italy
| | | | - Michael Ruvolo
- Diagnostics and Genomics Division, Agilent Technologies, Inc., Santa Clara, California, USA
| | - Angel Vilches-Arenas
- Department of Preventive Medicine and Public Health, Faculty of Medicine, University of Seville, Seville, Spain
| | | | | | - Laura Macías-García
- Department of Normal and Pathological Histology and Cytology, Faculty of Medicine, University of Seville, Seville, Spain
| | - Manuel De Miguel-Rodríguez
- Department of Normal and Pathological Histology and Cytology, Faculty of Medicine, University of Seville, Seville, Spain
| | | | - Miguel A Idoate
- Department of Anatomic Pathology, Virgen Macarena University Hospital, Seville, Spain
- Department of Normal and Pathological Histology and Cytology, Faculty of Medicine, University of Seville, Seville, Spain
| | - Juan J Ríos-Martín
- Department of Anatomic Pathology, Virgen Macarena University Hospital, Seville, Spain
| |
Collapse
|
39
|
Kaur A, Banday AZ, Dawman L, Rawat A, Tiewsoh K. Factors predicting the occurrence of disease-causing variants on next-generation sequencing in children with steroid-resistant nephrotic syndrome - implications for resource-constrained settings. Pediatr Nephrol 2023; 38:3663-3670. [PMID: 37335381 DOI: 10.1007/s00467-023-06042-5] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/25/2023] [Accepted: 05/15/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND Enhanced availability of high-throughput sequencing (at progressively reducing costs) has revolutionized the identification of monogenic SRNS. However, in resource-poor settings, it may not be possible to perform next-generation sequencing (NGS) in all children wherein monogenic SRNS is suspected. Besides, the optimal strategy of genetic evaluation (in patients with SRNS) in routine clinical practice in resource-limited settings is unknown. METHODS Patients with newly diagnosed SRNS were recruited from our center and followed up prospectively. We analyzed the factor(s) independently predicting the occurrence of disease-causing variants in these patients. RESULTS In our study, 36 children/adolescents with SRNS were included (initial steroid resistance in 53%). On targeted NGS, pathogenic/likely pathogenic variants were identified in 31% (n = 11). These included homozygous or compound heterozygous variants in the following genes: ALOX12B, COL4A3, CRB2, NPHS1, NPHS2, PLCE1, and heterozygous variant in WT1 gene. Overall, 14 variants were identified of which 5 (36%) were novel. Age of < 1 or < 2 years and presence of family history of nephrotic syndrome independently predicted the occurrence of monogenic SRNS on multivariate analysis. CONCLUSIONS While NGS-based genetic testing in SRNS is increasingly being incorporated in routine clinical practice the world over, the scenario is far from optimal in resource-limited settings. Our study highlights that resources for genetic testing in SRNS should be prioritized for patients with early age at disease onset and presence of family history. Larger studies composed of diverse multi-ethnic cohorts of patients with SRNS are required to further delineate the optimal strategy of genetic evaluation in resource-poor settings. A higher resolution version of the Graphical abstract is available as Supplementary information.
Collapse
Affiliation(s)
- Anit Kaur
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Center, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Aaqib Zaffar Banday
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Center, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Lesa Dawman
- Nephrology Unit, Department of Pediatrics, Advanced Pediatrics Center, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Amit Rawat
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Center, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Karalanglin Tiewsoh
- Nephrology Unit, Department of Pediatrics, Advanced Pediatrics Center, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India.
| |
Collapse
|
40
|
Goyal S, Singh R, Singh JR, Vanita V. Mutation screening in autosomal dominant congenital cataract families from North India. Mol Genet Genomics 2023; 298:1279-1288. [PMID: 37458831 DOI: 10.1007/s00438-023-02053-x] [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: 12/21/2022] [Accepted: 07/01/2023] [Indexed: 11/19/2023]
Abstract
Congenital cataract an opacity of the eye lens is present at birth and results in visual impairment during early childhood. If left untreated, it can lead to permanent blindness. Its prevalence is ten times higher in developing countries like India. Thus, we aimed to investigate the underlying genetic defects in three autosomal dominant congenital cataract (ADCC) families from North India. Detailed family histories were collected, pedigrees drawn followed by slit-lamp examination and lens photography. Mutation screening was performed in the candidate genes for crystallins, connexins, and membrane proteins by Sanger sequencing. Pathogenicity of novel variant was assessed bioinformatically. In an ADCC (CC-3006) family with bilateral membranous cataract and microcornea, a novel change (c.1114C>T;p.P372S) in GJA3 has been detected. In other two ADCC families affected with subcapsular (CC-286) and shrunken membranous hypermature cataract (CC-3014), a nonsense mutation (c.463C>T;p.Q155X) in CRYβB2 and a frameshift deletion (c.590_591delAG;p.E197VfsX22) in CRYβA1/A3 respectively, are observed. These variants segregated completely with the phenotypes in respective families and were absent in their unaffected family members and unrelated controls (tested for novel variant in GJA3). Earlier p.Q155X (CRYβB2) and p.E197VfsX22 (CRYβA1/A3) are reported with entirely different phenotypes. Thus, findings in present study expand the mutation spectrum and phenotypic heterogeneity linked with GJA3, CRYβB2, and CRYβA1/A3 for congenital cataracts. Identifying underlying genetic defects is essential for disease management and appropriate genetic counseling.
Collapse
Affiliation(s)
- Shiwali Goyal
- Department of Human Genetics, Guru Nanak Dev University (GNDU), Amritsar, 143005, Punjab, India
| | - Ravijit Singh
- Dr. Daljit Singh Eye Hospital, Amritsar, 143001, Punjab, India
| | - Jai Rup Singh
- Department of Human Genetics, Guru Nanak Dev University (GNDU), Amritsar, 143005, Punjab, India
| | - Vanita Vanita
- Department of Human Genetics, Guru Nanak Dev University (GNDU), Amritsar, 143005, Punjab, India.
| |
Collapse
|
41
|
Lu Y, Guo X, Yang M, Wang K, Cao G, Liu Y, Hou X, Chen L, Liang K. BRAF V600E genetic testing should be recommended for Bethesda III or V thyroid nodules based on fine-needle aspiration. Sci Rep 2023; 13:17129. [PMID: 37816788 PMCID: PMC10564976 DOI: 10.1038/s41598-023-44464-1] [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: 03/25/2023] [Accepted: 10/09/2023] [Indexed: 10/12/2023] Open
Abstract
The preoperative diagnosis of thyroid nodules now routinely includes BRAFV600E genetic testing in most provincial and municipal hospitals in China. This study identified the most suitable patients of thyroid nodule for BRAFV600E genetic testing. We retrospectively collected data of patients from the Hospital Information System that had undergone fine needle aspiration biopsy (FNAB) from May 2019 to December 2021. Data of FNAB, BRAFV600E genetic testing, and post-surgical pathological diagnosis were collected. A total of 12,392 patients were included in this study. Among them, 7,010 patients underwent solely FNAB, while 5,382 patients had both FNAB and BRAFV600E genetic testing. In the FNAB group, 2,065 thyroid nodules were surgically removed, with a 93.12% malignancy rate. In the FNAB + BRAF group, 2,005 nodules were dissected, and the malignancy rate was 98.20%. However, it was evident that in the subgroups, the combination of FNAB and BRAFV600E genetic testing only benefited Bethesda III (p < 0.001) and V (p = 0.001) nodules. Overall, the combination of FNAB with BRAFV600E genetic testing significantly improved the malignancy rate of surgical thyroid nodes at our hospital when compared to FNAB alone. The subgroup analysis showed that BRAFV600E genetic testing only benefited Bethesda III and V nodules. These findings provide a clinical reference for rationally selecting the most suitable population for BRAFV600E genetic testing.
Collapse
Affiliation(s)
- Yiran Lu
- Department of Endocrine and Metabolic Diseases, Qilu Hospital of Shandong University, Jinan, China
| | - Xinghong Guo
- Department of Endocrine and Metabolic Diseases, Qilu Hospital of Shandong University, Jinan, China
- Institute of Endocrine and Metabolic Diseases of Shandong University, Jinan, China
- Key Laboratory of Endocrine and Metabolic Diseases, Shandong Province Medicine & Health, Jinan, China
- Jinan Clinical Research Center for Endocrine and Metabolic Diseases, Jinan, China
| | - Mengmeng Yang
- Department of Endocrine and Metabolic Diseases, Qilu Hospital of Shandong University, Jinan, China
| | - Kewei Wang
- Department of Endocrine and Metabolic Diseases, Qilu Hospital of Shandong University, Jinan, China
| | - Guanglei Cao
- Department of Endocrine and Metabolic Diseases, Qilu Hospital of Shandong University, Jinan, China
| | - Yan Liu
- Department of Endocrine and Metabolic Diseases, Qilu Hospital of Shandong University, Jinan, China
| | - Xinguo Hou
- Department of Endocrine and Metabolic Diseases, Qilu Hospital of Shandong University, Jinan, China
- Institute of Endocrine and Metabolic Diseases of Shandong University, Jinan, China
- Key Laboratory of Endocrine and Metabolic Diseases, Shandong Province Medicine & Health, Jinan, China
- Jinan Clinical Research Center for Endocrine and Metabolic Diseases, Jinan, China
| | - Li Chen
- Department of Endocrine and Metabolic Diseases, Qilu Hospital of Shandong University, Jinan, China.
- Institute of Endocrine and Metabolic Diseases of Shandong University, Jinan, China.
- Key Laboratory of Endocrine and Metabolic Diseases, Shandong Province Medicine & Health, Jinan, China.
- Jinan Clinical Research Center for Endocrine and Metabolic Diseases, Jinan, China.
| | - Kai Liang
- Department of Endocrine and Metabolic Diseases, Qilu Hospital of Shandong University, Jinan, China.
- Institute of Endocrine and Metabolic Diseases of Shandong University, Jinan, China.
- Key Laboratory of Endocrine and Metabolic Diseases, Shandong Province Medicine & Health, Jinan, China.
- Jinan Clinical Research Center for Endocrine and Metabolic Diseases, Jinan, China.
| |
Collapse
|
42
|
Liu L, Guo D, Yang F, Qi H, Zhou Y, Zheng D, Jin G. Identification and phenotypic analysis of novel LTBP2 mutations in a Chinese cohort with congenital ectopia lentis. Mol Vis 2023; 29:169-179. [PMID: 38222456 PMCID: PMC10784221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/10/2023] [Indexed: 01/16/2024] Open
Abstract
Purpose To evaluate the frequency of LTBP2 mutations and to elaborate on LTBP2-related clinical phenotypes in a Chinese congenital ectopia lentis (CEL) cohort. Methods In total, 145 Chinese probands with CEL were recruited for this study and underwent ocular and systemic examinations. Whole-exome sequencing was used to identify mutations, and Sanger sequencing and bioinformatics analysis were further performed to verify pathogenic mutations. Results Overall, biallelic mutations in LTBP2 involving eight novel mutations (c.4370-7_4370-9delTCT, c.4370-5C>G, c.3452G>A, c.2253delG, c.4114T>C, c.1251G>A, c.4760G>A, and c.620G>A) were identified in four CEL probands (4/145, 2.76%). Patients with LTBP2 mutations were characterized by a megalocornea, spherophakia, high myopia, and glaucoma instead of a flat cornea, high corneal astigmatism, cardiovascular and skeletal abnormalities that were reported in other gene mutations. A novel homozygous frameshift mutation was detected, and this type of mutation was found to cause more complicated ocular symptoms than others, ranging from the anterior segment to the fundus. Conclusion This study reported the mutation frequency of the LTBP2 gene in a Chinese CEL cohort and provided novel insight into LTBP2-related genotype-phenotype associations in CEL.
Collapse
Affiliation(s)
- Liyan Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Dongwei Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Fengmei Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Haotian Qi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Yijing Zhou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Danying Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Guangming Jin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| |
Collapse
|
43
|
Kim V, Guberina M, Bechrakis NE, Lohmann DR, Zeschnigk M, Le Guin CHD. Release of Cell-Free Tumor DNA in the Plasma of Uveal Melanoma Patients Under Radiotherapy. Invest Ophthalmol Vis Sci 2023; 64:35. [PMID: 37862025 PMCID: PMC10599159 DOI: 10.1167/iovs.64.13.35] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 10/01/2023] [Indexed: 10/21/2023] Open
Abstract
Purpose Uveal melanoma (UM) is a tumor of the eye that metastasizes in approximately half of cases. Prognostic testing requires accessibility to tumor tissue, which is usually not available with eye-preserving therapies. Noninvasive approaches to prognostic testing that provide valuable information for patient care are therefore needed. The aim of this study was to evaluate the use of circulating cell-free plasma DNA analysis in UM patients undergoing brachytherapy. Methods The study recruited 26 uveal melanoma patients referred to the department between February and October 2020. Blood samples were collected at various time points before, during, and after treatment, and deep amplicon sequencing was used to identify oncogenic variant alleles of the GNAQ and GNA11 genes, which serve as indicators for the presence of circulating tumor DNA (ctDNA). Results The results showed that all patients were ctDNA negative before brachytherapy. In 31% of patients, ctDNA was detected during therapy. The variant allele fraction of GNAQ or GNA11 alleles in ctDNA positive samples ranged from 0.24% to 2% and correlates with the largest basal diameter and thickness of the tumor. Conclusions The findings suggest that brachytherapy increases the presence of tumor DNA in the plasma of UM patients. Thus ctDNA analysis may offer a noninvasive approach for prognostic testing. However, efforts are still required to lower the limit of detection for tumor-specific genetic alterations.
Collapse
Affiliation(s)
- Viktoria Kim
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Maja Guberina
- Department of Radiotherapy, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Nikolaos E Bechrakis
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Dietmar R Lohmann
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Michael Zeschnigk
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Claudia H D Le Guin
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| |
Collapse
|
44
|
Bui Quoc E. [Phenotype of an autosomal dominant congenital cataract in siblings]. J Fr Ophtalmol 2023; 46:966-967. [PMID: 37481451 DOI: 10.1016/j.jfo.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/04/2023] [Indexed: 07/24/2023]
Affiliation(s)
- E Bui Quoc
- Hôpital universitaire Robert-Debré, AP-HP, Paris, France.
| |
Collapse
|
45
|
Khalifa E, Chapusot C, Tournier B, Sentis J, Marion E, Remond A, Aubry M, Pioche C, Bergeron A, Primois C, Blanchard L, Millière A, Boucheix M, Léger Y, Bairrao M, Brouste V, Martin L, Soubeyran I. Idylla EGFR assay on extracted DNA: advantages, limits and place in molecular screening according to the latest guidelines for non-small-cell lung cancer (NSCLC) patients. J Clin Pathol 2023; 76:698-704. [PMID: 35820776 DOI: 10.1136/jcp-2022-208325] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/28/2022] [Indexed: 11/04/2022]
Abstract
AIMS Idylla epidermal growth factor receptor (EGFR) is a fast and fully automated mutation assay that is easy to implement. However, under the Biocartis-recommended technical conditions, tissue sections are directly introduced into the cartridge, at the risk of exhausting the tumour sample. In this study, we evaluate the performance of Idylla EGFR on extracted DNA and discuss its place within the global non-small-cell lung cancer (NSCLC) screening strategy. METHODS 577 comparative tests between Idylla EGFR on extracted DNA and next-generation sequencing (NGS) were performed across two centres. RESULTS Preanalytical thresholds were established (20% tumour cell content, 50 ng DNA input) and challenged prospectively in routine practice. 16.8% of samples referred for screening were considered non eligible for Idylla EGFR testing. Due to discordant by design cases, Idylla EGFR sensitivity was 86.9% for currently actionable EGFR mutations. Idylla EGFR specificity was 100% in first-line screening. NGS was always feasible on the same DNA. CONCLUSION Idylla EGFR on extracted DNA is feasible and enables tumour material to be saved compared with tissue section use. It is not necessary to replace the analytical thresholds of the Biocartis algorithm. Due to both the limits of the mutational repertoire and the high increase of targetable genes in NSCLC, the use of Idylla EGFR should be restricted to clinical emergency situations accompanied by NGS.
Collapse
Affiliation(s)
| | - Caroline Chapusot
- Platform of Somatic Oncology of Burgundy, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Benjamin Tournier
- Platform of Somatic Oncology of Burgundy, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Julie Sentis
- Biopathology, Institut Bergonié, Bordeaux, France
| | | | - Alicia Remond
- Platform of Somatic Oncology of Burgundy, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Manon Aubry
- Platform of Somatic Oncology of Burgundy, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Célia Pioche
- Platform of Somatic Oncology of Burgundy, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Anthony Bergeron
- Department of Pathology, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | | | | | - Alice Millière
- Department of Pathology, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | | | | | | | - Véronique Brouste
- Research and Clinical Epidemiology Unit - Biostatistics, Institut Bergonié, Bordeaux, France
| | - Laurent Martin
- Platform of Somatic Oncology of Burgundy, Centre Hospitalier Universitaire de Dijon, Dijon, France
- Department of Pathology, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | | |
Collapse
|
46
|
Chan CM, Tan TE, Jain K, Bylstra Y, Mathur RS, Tang RWC, Lee BJH, Jamuar SS, Kam S, Vithana EN, Lim WK, Fenner BJ. RETINITIS PIGMENTOSA ASSOCIATED WITH THE EYS C2139Y VARIANT : An Important Cause of Blindness in East Asian Populations. Retina 2023; 43:1788-1796. [PMID: 37418643 DOI: 10.1097/iae.0000000000003874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
PURPOSE The study aimed to describe the phenotypic features of retinitis pigmentosa (RP) associated with the previously described EYS C2139Y variant in Singaporeans and establish the importance of this variant as a prevalent cause of RP among East Asians. METHODS A clinical phenotyping and exome-sequencing study was conducted on consecutive patients with nonsyndromic RP. Epidemiological analysis was performed using Singaporean and global population-based genetic data. RESULTS A study of 150 consecutive unrelated individuals with nonsyndromic RP found that 87 (58%) of cases had plausible genotypes. A previously described missense variant in the EYS gene, 6416G>A (C2139Y), occurred heterozygously or homozygously in 17 of 150 families (11.3%), all with autosomal recessive RP. Symptom onset in EYS C2139Y-related RP ranged from 6 to 45 years, with visual acuity ranging from 20/20 at 21 years to no light perception by 48 years. C2139Y-related RP had typical findings, including sectoral RP in cases with EYS E2703X in trans . The median age at presentation was 45 years and visual fields declined to less than 20° (Goldmann V4e isopter) by age 65 years. Intereye correlation for visual acuity, fields, and ellipsoid band width was high (r 2 = 0.77-0.95). Carrier prevalence was 0.66% (allele frequency of 0.33%) in Singaporean Chinese and 0.34% in East Asians, suggesting a global disease burden exceeding 10,000 individuals. CONCLUSION The EYS C2139Y variant is common in Singaporean RP patients and other ethnic Chinese populations. Targeted molecular therapy for this single variant could potentially treat a significant proportion of RP cases worldwide.
Collapse
Affiliation(s)
- Choi Mun Chan
- Singapore National Eye Centre, Singapore Eye Research Institute, and the Ophthalmology and Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Graduate Medical School, Singapore
| | - Tien-En Tan
- Singapore National Eye Centre, Singapore Eye Research Institute, and the Ophthalmology and Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Graduate Medical School, Singapore
| | - Kanika Jain
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Yasmin Bylstra
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
| | - Ranjana S Mathur
- Singapore National Eye Centre, Singapore Eye Research Institute, and the Ophthalmology and Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Graduate Medical School, Singapore
| | - Rachael W C Tang
- Singapore National Eye Centre, Singapore Eye Research Institute, and the Ophthalmology and Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Graduate Medical School, Singapore
| | - Brian J H Lee
- Lee Kong Chian Medical School, Nanyang Technological University, Singapore; and
| | - Saumya S Jamuar
- Department of Paediatrics, KK Women's and Children's Hospital and the SingHealth Duke-NUS Genomic Medicine Center, Singapore
| | - Sylvia Kam
- Department of Paediatrics, KK Women's and Children's Hospital and the SingHealth Duke-NUS Genomic Medicine Center, Singapore
| | - Eranga N Vithana
- Singapore National Eye Centre, Singapore Eye Research Institute, and the Ophthalmology and Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Graduate Medical School, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
| | - Beau J Fenner
- Singapore National Eye Centre, Singapore Eye Research Institute, and the Ophthalmology and Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Graduate Medical School, Singapore
| |
Collapse
|
47
|
Khan S, Rana N, Nasir H, Rahim T, Aslam S, Khan F, Rahman G, Hussain MZ, Khan L, Khan M. Mutational analysis of CRYAA gene of cataract and investigating risk assessment factors responsible for eye diseases in district buner, KPK, Pakistan. Cell Mol Biol (Noisy-le-grand) 2023; 69:1-7. [PMID: 37807341 DOI: 10.14715/cmb/2023.69.9.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Indexed: 10/10/2023]
Abstract
This research has been designed to analyze the risk factors of major eye diseases and the genetic alterations contributing to the manifestation of such disease. For this purpose, data was collected from 256 patients diagnosed by an ophthalmologist by using a specialized questionnaire. Blood samples were collected from 100 patients to perform a genetic investigation of cataracts. Whole genomic DNA was extracted from blood samples via the phenol-chloroform method. The purified DNA was used as the template for the amplification of about 400 bp fragments amplifying exons 1 and 2 of the CRYAA gene. The statistical analysis showed that 68% of individuals were blind due to cataracts. During molecular analysis, nucleotide sequences obtained have resulted in one silent mutation that occured at 20 positions in exon 2. It was replacing A>G which in turn substitutes the Lysine at position 70 for Arginine. It was interpreted by statistical analysis that this mutation did not result in a significant change in the CRYAA gene. In addition, protein analysis showed no significant changes in the structure of normal and mutated genes. At last, it is concluded that environmental risk factors play a major role in the studied diseases as compared to genetic factors. It is recommended to extend the study to a larger population to study all exons of the CRYAA gene as well as develop better estimates of the magnitude of the problems of visual loss and eye diseases in the Pakistani population.
Collapse
Affiliation(s)
- Sarmir Khan
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, KP, Pakistan.
| | - Nehal Rana
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore-54590, Pakistan.
| | - Hilal Nasir
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, KP, Pakistan.
| | - Triq Rahim
- Department of Biosciences, COMSATS University, Islamabad, Pakistan.
| | - Summan Aslam
- Department of Biosciences, COMSATS University, Islamabad, Pakistan.
| | - Feroz Khan
- Department of Zoology Wild Life and Fisheries, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan.
| | - Gohar Rahman
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, KP, Pakistan.
| | - Muhammad Zawar Hussain
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, KP, Pakistan.
| | - Luqman Khan
- Faculty of Medicine, University of Rijeka, Croatia.
| | - Muhammad Khan
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, KP, Pakistan.
| |
Collapse
|
48
|
Wang Y, Lai Y, Jiang Z, Li S, Ding X. Five novel dysfunctional variants in the TSPAN12 gene in familial exudative vitreoretinopathy. Exp Eye Res 2023; 234:109574. [PMID: 37451565 DOI: 10.1016/j.exer.2023.109574] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/08/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Familial exudative vitreoretinopathy (FEVR) is an inheritable vitreoretinal disease characterized by incomplete retinal vascular development, which often leads to multiple retinal complications and causes severe vision loss in children. We reported the TSPAN12 variants' frequency in a cohort of FEVR and five novel TSPAN12 variants and related clinical features in six Chinese families. Seven hundred thirty-four families' genetic in-house data were reviewed. Whole-exome sequencing (WES) was performed in all probands; Sanger sequencing was conducted in the family members. Five novel variants from six families were noted, and clinical data were collected. Luciferase assays were applied to test the activity of the Norrin/β-catenin signal caused by the mutant TSPAN12 genes. The frequency of TSPAN12 variants in FEVR is 8.79% (50/569). Five novel variants in TSPAN12 were identified in six families, including two missense variants, c.476G > A(p.Cys159Tyr) and c.81T > G(p.Ser27Arg), two frameshift variants, c.628_629insA(p.Met210Asnfs*42) and c.251delG(p.Gly84Glufs*3) and one nonsense, c.352G > T(p.Glu118*). Low vision, high myopia, nystagmus, and leukocoria are the common symptom at the first presentation. All variants were also predicted as pathogenic in silico. Moreover, the luciferase assay demonstrated that all variants caused severely compromised Norrin/β-catenin signaling activity. In conclusion, the frequency of TSPAN12 variants in FEVR was 8.79% in our cohort. Five novel variants of TSPAN12 were identified. Moreover, we demonstrated the dysfunction of mutant variants via the downregulation of Norrin/β-catenin signaling. These findings expanded the genetic and clinical spectrum of FEVR with TSPAN12 variants.
Collapse
Affiliation(s)
- You Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Yanting Lai
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Zhaoxin Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Songshan Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
| | - Xiaoyan Ding
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
| |
Collapse
|
49
|
Deng B, Liu C. Two tests of peripheral blood by standard methods were negative for Von Hippel-Lindau mutations: A case report. Asian J Surg 2023; 46:4101-4102. [PMID: 37147258 DOI: 10.1016/j.asjsur.2023.04.079] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 04/18/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND Von Hippel-Lindau disease (VHL) is an autosomal dominant, inherited syndrome with variants in the VHL gene causing predisposition to multi-organ benign and malignant neoplasms. Approximately 95-100% of individuals with clinical VHL receive a positive result when they undergo standard genetic testing on DNA extracted from blood. Here, we present the case of an individual with a clinical diagnosis of VHL disease where peripheral blood DNA analysis did not detect a VHL variant. CASE PRESENTATION Our patient is a-38-year-old male whose chief complaints are right shoulder and back pain for almost a year. Cranial Magnetic Resonance Imaging (MRI) showed multiple space occupying lesions in cerebellar hemisphere. Spine MRI showed the formation of intraspinal cavities in cervical 5 to thoracic 10 plane, enhanced lesions in the thoracic 8 vertebral plane. Abdominal MRI showed very weakly enhanced nodules on the left kidney and multiple cystic lesions of pancreas. Our case, without a family history, fulfilled clinical criteria for VHL but initially received negative germline VHL results through multigene panel testing on DNA extracted from peripheral blood leukocytes. One year later, the second peripheral blood send for germline molecular genetic testing was also negative. CONCLUSION Although the patient tested negative for the classic VHL gene, the possibility of somatic mosaicism could not be ruled out. Instead of repeating classic testing, next-generation sequencing, multi-tissue analysis or/and genetic testing of offspring is an efficient tool to identify VHL mosaic mutation.
Collapse
Affiliation(s)
- Bing Deng
- Department of Neurosurgery, Chengdu Second People's Hospital, Chengdu, Sichuan, 610017, China.
| | - Chunguang Liu
- Department of Emergency, Da Ping Hospital, Army Military Medical University, Chongqing, 400042, China.
| |
Collapse
|
50
|
Ajami N, Soleimani A, Jafarzadeh‐Esfehani R, Hasanpour M, Rashid Shomali R, Abbaszadegan MR. Mutational landscape of phenylketonuria in Iran. J Cell Mol Med 2023; 27:2457-2466. [PMID: 37525467 PMCID: PMC10468661 DOI: 10.1111/jcmm.17865] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 06/11/2023] [Accepted: 06/28/2023] [Indexed: 08/02/2023] Open
Abstract
To date more than 1000 different variants in the PAH gene have been identified in patients with phenylketonuria (PKU). In Iran, several studies have been performed to investigate the genetics bases of the PKU in different parts of the country. In this study, we have analysed and present an update of the mutational landscape of the PAH gene as well as the population genetics and frequencies of detected variants for each cohort. Published articles on PKU mutations in Iran were identified through a comprehensive PubMed, Google Scholar, Web of Science (ISI), SCOPUS, Elsevier, Wiley Online Library and SID literature search using the terms: "phenylketonuria", "hyperphenylalaninemia", and "PKU" in combination with "Iran", "Iranian population", "mutation analysis", and "Molecular genetics". Among the literature-related to genetics of PKU, 18 studies were on the PKU mutations. According to these studies, in different populations of Iran 1497 patients were included for mutation detection that resulted in detection of 129 different mutations. Results of genetic analysis of the different cohorts of Iranian PKU patients show that the most prevalent mutation in Iran is the pathogenic splice variant c.1066-11G > A, occurring in 19.54% of alleles in the cohort. Four other common mutations were p.Arg261Gln, p.Pro281Leu, c.168 + 5G > C and p.Arg243Ter (8.18%, 6.45%, 5.88% and 3.7%, respectively). One notable feature of the studied populations is its high rate of consanguineous marriages. Considering this feature, determining the prevalent PKU mutations could be advantageous for designing screening and diagnostic panels in Iran.
Collapse
Affiliation(s)
- Naser Ajami
- Department of Medical Genetics and Molecular Medicine, School of MedicineMashhad University of Medical SciencesMashhadIran
- Medical Genetics Research Center, School of MedicineMashhad University of Medical SciencesMashhadIran
| | - Anvar Soleimani
- Department of Medical Microbiology, College of Health SciencesCihan University‐ SulaimaniyaSulaimaniyaIraq
| | - Reza Jafarzadeh‐Esfehani
- Blood Borne Infections Research Center, Academic Center for EducationCulture and Research (ACECR)‐ Khorasan RazaviMashhadIran
| | - Mojtaba Hasanpour
- Department of Biology, Faculty of SciencesUniversity of GuilanRashtIran
| | - Romina Rashid Shomali
- Reproductive Health Research Center, Department of Obstetrics and Gynecology, Alzahra HospitalGuilan University of Medical SciencesRashtIran
| | - Mohammad Reza Abbaszadegan
- Department of Medical Genetics and Molecular Medicine, School of MedicineMashhad University of Medical SciencesMashhadIran
- Immunology Research CenterMashhad University of Medical SciencesMashhadIran
| |
Collapse
|