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Archana CA, Sekar YS, Suresh KP, Subramaniam S, Sagar N, Rani S, Anandakumar J, Pandey RK, Barman NN, Patil SS. Investigating the Influence of ANTXR2 Gene Mutations on Protective Antigen Binding for Heightened Anthrax Resistance. Genes (Basel) 2024; 15:426. [PMID: 38674361 PMCID: PMC11049084 DOI: 10.3390/genes15040426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
Bacillus anthracis is the bacterium responsible for causing the zoonotic disease called anthrax. The disease presents itself in different forms like gastrointestinal, inhalation, and cutaneous. Bacterial spores are tremendously adaptable, can persist for extended periods and occasionally endanger human health. The Anthrax Toxin Receptor-2 (ANTXR2) gene acts as membrane receptor and facilitates the entry of the anthrax toxin into host cells. Additionally, mutations in the ANTXR2 gene have been linked to various autoimmune diseases, including Hyaline Fibromatosis Syndrome (HFS), Ankylosing Spondylitis (AS), Juvenile Hyaline Fibromatosis (JHF), and Infantile Systemic Hyalinosis (ISH). This study delves into the genetic landscape of ANTXR2, aiming to comprehend its associations with diverse disorders, elucidate the impacts of its mutations, and pinpoint minimal non-pathogenic mutations capable of reducing the binding affinity of the ANTXR2 gene with the protective antigen. Recognizing the pivotal role of single-nucleotide polymorphisms (SNPs) in shaping genetic diversity, we conducted computational analyses to discern highly deleterious and tolerated non-synonymous SNPs (nsSNPs) in the ANTXR2 gene. The Mutpred2 server determined that the Arg465Trp alteration in the ANTXR2 gene leads to altered DNA binding (p = 0.22) with a probability of a deleterious mutation of 0.808; notably, among the identified deleterious SNPs, rs368288611 (Arg465Trp) stands out due to its significant impact on altering the DNA-binding ability of ANTXR2. We propose these SNPs as potential candidates for hypertension linked to the ANTXR2 gene, which is implicated in blood pressure regulation. Noteworthy among the tolerated substitutions is rs200536829 (Ala33Ser), recognized as less pathogenic; this highlights its potential as a valuable biomarker, potentially reducing side effects on the host while also reducing binding with the protective antigen protein. Investigating these SNPs holds the potential to correlate with several autoimmune disorders and mitigate the impact of anthrax disease in humans.
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Affiliation(s)
- Chamalapura Ashwathama Archana
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru 560064, India; (C.A.A.); (Y.S.S.); (N.S.); (S.R.); (J.A.); (S.S.P.)
| | - Yamini Sri Sekar
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru 560064, India; (C.A.A.); (Y.S.S.); (N.S.); (S.R.); (J.A.); (S.S.P.)
| | - Kuralayanapalya Puttahonnappa Suresh
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru 560064, India; (C.A.A.); (Y.S.S.); (N.S.); (S.R.); (J.A.); (S.S.P.)
| | | | - Ningegowda Sagar
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru 560064, India; (C.A.A.); (Y.S.S.); (N.S.); (S.R.); (J.A.); (S.S.P.)
| | - Swati Rani
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru 560064, India; (C.A.A.); (Y.S.S.); (N.S.); (S.R.); (J.A.); (S.S.P.)
| | - Jayashree Anandakumar
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru 560064, India; (C.A.A.); (Y.S.S.); (N.S.); (S.R.); (J.A.); (S.S.P.)
| | - Rajan Kumar Pandey
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Solna, Sweden;
| | - Nagendra Nath Barman
- College of Veterinary Science, Assam Agricultural University (AAU), Guwahati 781022, India;
| | - Sharanagouda S. Patil
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru 560064, India; (C.A.A.); (Y.S.S.); (N.S.); (S.R.); (J.A.); (S.S.P.)
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Casas-Alba D, Martínez-Monseny A, Pino-Ramírez RM, Alsina L, Castejón E, Navarro-Vilarrubí S, Pérez-Dueñas B, Serrano M, Palau F, García-Alix A. Hyaline fibromatosis syndrome: Clinical update and phenotype-genotype correlations. Hum Mutat 2018; 39:1752-1763. [PMID: 30176098 DOI: 10.1002/humu.23638] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 11/11/2022]
Abstract
Hyaline fibromatosis syndrome (HFS) is the unifying term for infantile systemic hyalinosis and juvenile hyaline fibromatosis. HFS is a rare autosomal recessive disorder of the connective tissue caused by mutations in the gene for anthrax toxin receptor-2 (ANTXR2). It is characterized by abnormal growth of hyalinized fibrous tissue with cutaneous, mucosal, osteoarticular, and systemic involvement. We reviewed the 84 published cases and their molecular findings, aiming to gain insight into the clinical features, prognostic factors, and phenotype-genotype correlations. Extreme pain at minimal handling in a newborn is the presentation pattern most frequently seen in grade 4 patients (life-limiting disease). Gingival hypertrophy and subcutaneous nodules are some of the disease hallmarks. Though painful joint stiffness and contractures are almost universal, weakness and hypotonia may also be present. Causes of death are intractable diarrhea, recurrent infections, and organ failure. Median age of death of grade 4 cases is 15.0 months (p25-p75: 9.5-24.0). This review provides evidence to reinforce the previous hypothesis that missense mutations in exons 1-12 and mutations leading to a premature stop codon lead to the severe form of the disease, while missense pathogenic variants in exons 13-17 lead to the mild form of the disease. Multidisciplinary team approach is recommended.
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Affiliation(s)
- Dídac Casas-Alba
- Department of Pediatrics, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
- Department of Genetic and Molecular Medicine, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Antonio Martínez-Monseny
- Department of Genetic and Molecular Medicine, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Rosa M Pino-Ramírez
- Department of Pediatrics, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Laia Alsina
- Department of Pediatric Allergy and Clinical Immunology, Hospital Sant Joan de Déu, University of Barcelona, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Esperanza Castejón
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Sergi Navarro-Vilarrubí
- Department of Pediatric Palliative Care, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Belén Pérez-Dueñas
- Department of Pediatric Neurology, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
- Department of Pediatric Neurology, Vall d'Hebron Hospital and Research Institute, Barcelona, Spain
| | - Mercedes Serrano
- Department of Genetic and Molecular Medicine, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
- Department of Pediatric Neurology, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
- CIBER de Enfermedades Raras (CIBERER-ISCIII), Madrid, Spain
| | - Francesc Palau
- Department of Genetic and Molecular Medicine, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
- CIBER de Enfermedades Raras (CIBERER-ISCIII), Madrid, Spain
- Laboratory of Neurogenetics and Molecular Medicine, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
- Division of Pediatrics, University of Barcelona School of Medicine, Barcelona, Spain
| | - Alfredo García-Alix
- Department of Genetic and Molecular Medicine, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
- CIBER de Enfermedades Raras (CIBERER-ISCIII), Madrid, Spain
- Department of Neonatology, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
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Zhang LC, Shao Y, Gao LH, Liu J, Xi YY, Xu Y, Wu C, Chen W, Chen HP, Wang YL, Duan HF, Hu XW. TEM8 functions as a receptor for uPA and mediates uPA-stimulated EGFR phosphorylation. Cell Commun Signal 2018; 16:62. [PMID: 30241478 PMCID: PMC6151050 DOI: 10.1186/s12964-018-0272-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/06/2018] [Indexed: 02/07/2023] Open
Abstract
Background TEM8 is a cell membrane protein predominantly expressed in tumor endothelium, which serves as a receptor for the protective antigen (PA) of anthrax toxin. However, the physiological ligands for TEM8 remain unknown. Results Here we identified uPA as an interacting partner of TEM8. Binding of uPA stimulated the phosphorylation of TEM8 and augmented phosphorylation of EGFR and ERK1/2. Finally, TEM8-Fc, a recombinant fusion protein comprising the extracellular domain of human TEM8 linked to the Fc portion of human IgG1, efficiently abrogated the interaction between uPA and TEM8, blocked uPA-induced migration of HepG2 cells in vitro and inhibited the growth and metastasis of human MCF-7 xenografts in vivo. uPA, TEM8 and EGFR overexpression and ERK1/2 phosphorylation were found co-located on frozen cancer tissue sections. Conclusions Taken together, our data provide evidence that TEM8 is a novel receptor for uPA, which may play a significant role in the regulation of tumor growth and metastasis. Electronic supplementary material The online version of this article (10.1186/s12964-018-0272-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lian-Cheng Zhang
- Laboratory of Cell Engineering, Beijing Institute of Biotechnology (BIB), No. 20, Dongdajie Street, Fengtai District, Beijing, 100071, China.,Department of Operational Medicine, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Yong Shao
- Laboratory of Cell Engineering, Beijing Institute of Biotechnology (BIB), No. 20, Dongdajie Street, Fengtai District, Beijing, 100071, China
| | - Li-Hua Gao
- Laboratory of Cell Engineering, Beijing Institute of Biotechnology (BIB), No. 20, Dongdajie Street, Fengtai District, Beijing, 100071, China
| | - Jin Liu
- Key Laboratory of Experimental Hematology, Beijing Institute of Radiation Medicine (BIRM), No. 27, Taiping Road, Haidian District, Beijing, 100850, China
| | - Yong-Yi Xi
- Laboratory of Cell Engineering, Beijing Institute of Biotechnology (BIB), No. 20, Dongdajie Street, Fengtai District, Beijing, 100071, China
| | - Yin Xu
- Key Laboratory of Experimental Hematology, Beijing Institute of Radiation Medicine (BIRM), No. 27, Taiping Road, Haidian District, Beijing, 100850, China
| | - Chutse Wu
- Key Laboratory of Experimental Hematology, Beijing Institute of Radiation Medicine (BIRM), No. 27, Taiping Road, Haidian District, Beijing, 100850, China
| | - Wei Chen
- Laboratory of Cell Engineering, Beijing Institute of Biotechnology (BIB), No. 20, Dongdajie Street, Fengtai District, Beijing, 100071, China
| | - Hui-Peng Chen
- Laboratory of Cell Engineering, Beijing Institute of Biotechnology (BIB), No. 20, Dongdajie Street, Fengtai District, Beijing, 100071, China.
| | - You-Liang Wang
- Laboratory of Cell Engineering, Beijing Institute of Biotechnology (BIB), No. 20, Dongdajie Street, Fengtai District, Beijing, 100071, China.
| | - Hai-Feng Duan
- Key Laboratory of Experimental Hematology, Beijing Institute of Radiation Medicine (BIRM), No. 27, Taiping Road, Haidian District, Beijing, 100850, China.
| | - Xian-Wen Hu
- Laboratory of Cell Engineering, Beijing Institute of Biotechnology (BIB), No. 20, Dongdajie Street, Fengtai District, Beijing, 100071, China.
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Schussler E, Linkner RV, Levitt J, Mehta L, Martignetti JA, Oishi K. Protein-losing enteropathy and joint contractures caused by a novel homozygous ANTXR2 mutation. ACTA ACUST UNITED AC 2018; 8:17-21. [PMID: 30050362 PMCID: PMC6057141 DOI: 10.2147/agg.s159077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Infantile systemic hyalinosis (ISH) is a rare autosomal recessive disorder and an allelic form of hyaline fibromatosis syndrome that is caused by mutations in the ANTRX2 gene encoding the transmembrane anthrax toxin receptor 2. Its main features include characteristic skin lesions, joint contractures, persistent diarrhea, and failure to thrive due to accumulation of hyaline material in multiple organs. The resulting severe malnutrition can cause death in early infancy. Because of its rarity and high fatality rate, timely diagnosis is difficult and ISH may be underdiagnosed. In this report, we describe a 10-month-old male with severe protein-losing enteropathy, skin lesions, and painful joint contractures, diagnosed with ISH based on skin his-topathology and identification of a novel homozygous ANTRX2 mutation, c.1127_1128delTG (p.V376Gfs*14). While its clinical outcome is poor without curative treatment, establishing a diagnosis of ISH starting from clinical suspicion to molecular analysis is important for appropriate medical management and for risk and carrier assessment of family members.
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Affiliation(s)
- Edith Schussler
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rita V Linkner
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jacob Levitt
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lakshmi Mehta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John A Martignetti
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kimihiko Oishi
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Haidar Z, Temanni R, Chouery E, Jitesh P, Liu W, Al-Ali R, Wang E, Marincola FM, Jalkh N, Haddad S, Haidar W, Chouchane L, Mégarbané A. Diagnosis implications of the whole genome sequencing in a large Lebanese family with hyaline fibromatosis syndrome. BMC Genet 2017; 18:3. [PMID: 28103792 PMCID: PMC5244738 DOI: 10.1186/s12863-017-0471-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 01/10/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hyaline fibromatosis syndrome (HFS) is a recently introduced alternative term for two disorders that were previously known as juvenile hyaline fibromatosis (JHF) and infantile systemic hyalinosis (ISH). These two variants are secondary to mutations in the anthrax toxin receptor 2 gene (ANTXR2) located on chromosome 4q21. The main clinical features of both entities include papular and/or nodular skin lesions, gingival hyperplasia, joint contractures and osteolytic bone lesions that appear in the first few years of life, and the syndrome typically progresses with the appearance of new lesions. METHODS We describe five Lebanese patients from one family, aged between 28 and 58 years, and presenting with nodular and papular skin lesions, gingival hyperplasia, joint contractures and bone lesions. Because of the particular clinical features and the absence of a clinical diagnosis, Whole Genome Sequencing (WGS) was carried out on DNA samples from the proband and his parents. RESULTS A mutation in ANTXR2 (p. Gly116Val) that yielded a diagnosis of HFS was noted. CONCLUSIONS The main goal of this paper is to add to the knowledge related to the clinical and radiographic aspects of HFS in adulthood and to show the importance of Next-Generation Sequencing (NGS) techniques in resolving such puzzling cases.
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Affiliation(s)
- Zahraa Haidar
- Unité de Génétique Médicale, Faculté de Médecine, Université Saint-Joseph, Beirut, Lebanon
| | - Ramzi Temanni
- Bioinformatics Division, Sidra Medical & Research Center, Doha, Qatar
| | - Eliane Chouery
- Unité de Génétique Médicale, Faculté de Médecine, Université Saint-Joseph, Beirut, Lebanon
| | - Puthen Jitesh
- Bioinformatics Division, Sidra Medical & Research Center, Doha, Qatar
| | - Wei Liu
- Genomics Core Laboratory, Translational Medicine Division, Sidra Medical & Research Center, Doha, Qatar
| | - Rashid Al-Ali
- Bioinformatics Division, Sidra Medical & Research Center, Doha, Qatar
| | - Ena Wang
- Genomics Core Laboratory, Translational Medicine Division, Sidra Medical & Research Center, Doha, Qatar
| | | | - Nadine Jalkh
- Unité de Génétique Médicale, Faculté de Médecine, Université Saint-Joseph, Beirut, Lebanon
| | - Soha Haddad
- Department of Radiology, Hotel Dieu de France University hospital–Beirut, Beirut, Lebanon
| | - Wassim Haidar
- Department of General surgery, Dar Al Amal University Hospital-Baalbeck, Baalbeck, Lebanon
| | - Lotfi Chouchane
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - André Mégarbané
- Institut Jérôme Lejeune, 37, rue des Volontaires, Paris, 75015 France
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A complex role of anthrax toxin receptor 2 polymorphisms and capillary morphogenesis protein 2 in ankylosing spondylitis pathogenesis. Clin Rheumatol 2016; 35:2243-50. [PMID: 26728147 DOI: 10.1007/s10067-015-3158-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 12/07/2015] [Accepted: 12/21/2015] [Indexed: 01/17/2023]
Abstract
This study investigated the role of anthrax toxin receptor 2 (ANTXR2) gene polymorphisms and capillary morphogenesis protein 2 (CMG2) expression in susceptibility and pathogenesis to ankylosing spondylitis (AS) in the Han Chinese in Beijing. A case-control study was performed using 602 AS patient samples meeting the revised New York criterion and 619 matched controls from Han Chinese individuals. Nineteen single-nucleotide polymorphisms (SNPs) of ANTXR2 genes were selected and genotyped using the Sequenom iPlex platform. Real-time polymerase chain reaction and flow cytometry were performed to investigate the impact of SNP polymorphisms on ANTXR2 transcription and CMG2 expression, respectively. The association of variants with AS was examined with UNPHASED 3.1.5. A novel association was observed between AS and three SNPs in the ANTXR2 gene (rs4690127, rs6823031, and rs4333130; P = 0.004, 0.011, and 0.013, respectively), confirming the association between rs433130 and AS in the Han Chinese. The strongest haplotype association was observed with rs4690127-rs6823031-rs4333130 (P = 2.5 × 10(-4)). rs6534639 and rs4333130 showed a cis-interaction (P = 0.027) in AS. ANTXR2 messenger RNA (mRNA) expression was significantly higher in the AS group than in the control group (P = 0.039). CMG2 expression in the lipopolysaccharide (LPS)-stimulated group was significantly lower than that in the control group (P = 0.018). This study reports a novel association between ANTXR2 and AS in the Han Chinese. ANTXR2 genetic polymorphisms affect ANTXR2 mRNA transcription and CMG2 expression. The opposing results observed for ANTXR2 transcription and CMG2 expression suggest a complex role of ANTXR2 polymorphisms in AS pathogenesis.
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7
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Marques SA, Stolf HO, Polizel JO, Munhoz T, Brandão MC, Marques MEA. Hyaline fibromatosis syndrome: cutaneous manifestations. An Bras Dermatol 2016; 91:226-9. [PMID: 27192526 PMCID: PMC4861574 DOI: 10.1590/abd1806-4841.20163799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 10/13/2014] [Indexed: 11/22/2022] Open
Abstract
Hyaline fibromatosis syndrome is the current name for clinical manifestations of diseases previously known as "infantile systemic hyalinosis" and "juvenile hyaline fibromatosis". The authors report representative clinical cases of each one of the above subtypes with emphasis on cutaneous manifestations and difficulties for early diagnosis in this syndrome, essentially of multidisciplinary approach.
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Affiliation(s)
- Silvio Alencar Marques
- Universidade Estadual Paulista “Júlio de
Mesquita Filho” (Unesp) – Botucatu (SP), Brazil
| | - Hamilton Ometto Stolf
- Universidade Estadual Paulista “Júlio de
Mesquita Filho” (Unesp) – Botucatu (SP), Brazil
| | - Juliana Ocanha Polizel
- Universidade Estadual Paulista “Júlio de
Mesquita Filho” (Unesp) – Botucatu (SP), Brazil
| | - Tânia Munhoz
- Universidade Estadual Paulista “Júlio de
Mesquita Filho” (Unesp) – Botucatu (SP), Brazil
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Caminsky NG, Mucaki EJ, Rogan PK. Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis. F1000Res 2015. [DOI: 10.12688/f1000research.5654.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The interpretation of genomic variants has become one of the paramount challenges in the post-genome sequencing era. In this review we summarize nearly 20 years of research on the applications of information theory (IT) to interpret coding and non-coding mutations that alter mRNA splicing in rare and common diseases. We compile and summarize the spectrum of published variants analyzed by IT, to provide a broad perspective of the distribution of deleterious natural and cryptic splice site variants detected, as well as those affecting splicing regulatory sequences. Results for natural splice site mutations can be interrogated dynamically with Splicing Mutation Calculator, a companion software program that computes changes in information content for any splice site substitution, linked to corresponding publications containing these mutations. The accuracy of IT-based analysis was assessed in the context of experimentally validated mutations. Because splice site information quantifies binding affinity, IT-based analyses can discern the differences between variants that account for the observed reduced (leaky) versus abolished mRNA splicing. We extend this principle by comparing predicted mutations in natural, cryptic, and regulatory splice sites with observed deleterious phenotypic and benign effects. Our analysis of 1727 variants revealed a number of general principles useful for ensuring portability of these analyses and accurate input and interpretation of mutations. We offer guidelines for optimal use of IT software for interpretation of mRNA splicing mutations.
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Caminsky N, Mucaki EJ, Rogan PK. Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis. F1000Res 2014; 3:282. [PMID: 25717368 PMCID: PMC4329672 DOI: 10.12688/f1000research.5654.1] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/10/2014] [Indexed: 12/14/2022] Open
Abstract
The interpretation of genomic variants has become one of the paramount challenges in the post-genome sequencing era. In this review we summarize nearly 20 years of research on the applications of information theory (IT) to interpret coding and non-coding mutations that alter mRNA splicing in rare and common diseases. We compile and summarize the spectrum of published variants analyzed by IT, to provide a broad perspective of the distribution of deleterious natural and cryptic splice site variants detected, as well as those affecting splicing regulatory sequences. Results for natural splice site mutations can be interrogated dynamically with Splicing Mutation Calculator, a companion software program that computes changes in information content for any splice site substitution, linked to corresponding publications containing these mutations. The accuracy of IT-based analysis was assessed in the context of experimentally validated mutations. Because splice site information quantifies binding affinity, IT-based analyses can discern the differences between variants that account for the observed reduced (leaky) versus abolished mRNA splicing. We extend this principle by comparing predicted mutations in natural, cryptic, and regulatory splice sites with observed deleterious phenotypic and benign effects. Our analysis of 1727 variants revealed a number of general principles useful for ensuring portability of these analyses and accurate input and interpretation of mutations. We offer guidelines for optimal use of IT software for interpretation of mRNA splicing mutations.
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Affiliation(s)
- Natasha Caminsky
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Eliseos J Mucaki
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Peter K Rogan
- Departments of Biochemistry and Computer Science, Western University, London, ON, N6A 2C1, Canada
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10
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Al Sinani S, Al Murshedy F, Abdwani R. Infantile systemic hyalinosis: a case report with a novel mutation. Oman Med J 2013; 28:53-5. [PMID: 23386947 DOI: 10.5001/omj.2013.12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Accepted: 11/12/2012] [Indexed: 11/03/2022] Open
Abstract
Infantile Systemic Hyalinosis (ISH) (OMIM 236490) is a rare, progressive and fatal autosomal recessive disorder characterized by multiple subcutaneous skin nodules, gingival hypertrophy, osteopenia, joint contractures, failure to thrive, diarrhea with protein losing enteropathy, and frequent infections. There is diffuse deposition of hyaline material in the skin, gastrointestinal tract, muscle and endocrine glands. It is caused by mutations in the ANTXR2 (also known as CMG2) gene, which encodes a trans-membranous protein involved in endothelial development and basement membrane-extracellular matrix assembly. We describe a child with classical features of ISH presenting in infancy with severe chronic debilitating pain and progressive joint contractures. The diagnosis was confirmed by molecular DNA sequencing of ANTXR2 gene which revealed a novel homozygous mutation not previously reported; 79 bp deletion of the entire exon 11 (c.867_945del, p.E289DfsX22). Although this is the first reported case of ISH in Oman, we believe that the disease is under-diagnosed since children affected with this lethal disease pass away early in infancy prior to establishing a final diagnosis.
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Affiliation(s)
- Siham Al Sinani
- Department of Child Health, Sultan Qaboos University Hospital, Al Khoud, Sultanate of Oman
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