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Mahmood Alsabbagh M. Congenital Ichthyosis: Current Approaches to Prenatal Diagnoses. Fetal Pediatr Pathol 2024; 43:157-175. [PMID: 38204144 DOI: 10.1080/15513815.2023.2301468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024]
Abstract
INTRODUCTION Congenital ichthyosis represents a wide spectrum of diseases. This article reviews prenatal testing for ichthyosis. METHODS We used pubmed.ncbi.nlm.nih.gov to search for 38 types of congenital ichthyosis combined with 17 words related to prenatal testing. RESULTS Search resulted in 408 publications covering 13 types of ichthyoses and four types of tests. DISCUSSION Biochemical testing is diagnostic in trichothiodystrophy, but nonspecific in X-linked ichthyosis and Refsum syndrome. Except in X-linked ichthyosis, biochemical testing requires invasive procedures to obtain fetal skin biopsy, amniocytes, or chorionic villus samples. It is superior to histological and cytological examination of fetal skin biopsy or amniocytes because keratinization occurs later in pregnancy and microscopy cannot differentiate between ichthyosis types. Imaging is more acceptable due to noninvasiveness and routine use, although ultrasonography is operator-dependent, nonspecific, and captures abnormalities at late stage. Molecular tests are described in at-risk pregnancies but testing of free fetal DNA was not described.
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Affiliation(s)
- Manahel Mahmood Alsabbagh
- Princess Al-Jawhara Center for Molecular Medicine and Inherited Disorders & Department of Molecular Medicine, Arabian Gulf University, Manama, Kingdom of Bahrain
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Identification of candidate aberrantly methylated and differentially expressed genes in Esophageal squamous cell carcinoma. Sci Rep 2020; 10:9735. [PMID: 32546690 PMCID: PMC7297810 DOI: 10.1038/s41598-020-66847-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 05/28/2020] [Indexed: 12/11/2022] Open
Abstract
Aberrant methylated genes (DMGs) play an important role in the etiology and pathogenesis of esophageal squamous cell carcinoma (ESCC). In this study, we aimed to integrate three cohorts profile datasets to ascertain aberrant methylated-differentially expressed genes and pathways associated with ESCC by comprehensive bioinformatics analysis. We downloaded data of gene expression microarrays (GSE20347, GSE38129) and gene methylation microarrays (GSE52826) from the Gene Expression Omnibus (GEO) database. Aberrantly differentially expressed genes (DEGs) were obtained by GEO2R tool. The David database was then used to perform Gene ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genome pathway enrichment analyses on selected genes. STRING and Cytoscape software were used to construct a protein-protein interaction (PPI) network, then the modules in the PPI networks were analyzed with MCODE and the hub genes chose from the PPI networks were verified by Oncomine and TCGA database. In total, 291 hypomethylation-high expression genes and 168 hypermethylation-low expression genes were identified at the screening step, and finally found six mostly changed hub genes including KIF14, CDK1, AURKA, LCN2, TGM1, and DSG1. Pathway analysis indicated that aberrantly methylated DEGs mainly associated with the P13K-AKT signaling, cAMP signaling and cell cycle process. After validation in multiple databases, most hub genes remained significant. Patients with high expression of AURKA were associated with shorter overall survival. To summarize, we have identified six feasible aberrant methylated-differentially expressed genes and pathways in ESCC by bioinformatics analysis, potentially providing valuable information for the molecular mechanisms of ESCC. Our data combined the analysis of gene expression profiling microarrays and gene methylation profiling microarrays, simultaneously, and in this way, it can shed a light for screening and diagnosis of ESCC in future.
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Montalván-Suárez M, Esperón-Moldes US, Rodríguez-Pazos L, Ordóñez-Ugalde A, Moscoso F, Ugalde-Noritz N, Santomé L, Fachal L, Tettamanti-Miranda D, Ruiz JC, Ginarte M, Vega A. A novel ABCA12 pathologic variant identified in an Ecuadorian harlequin ichthyosis patient: A step forward in genotype-phenotype correlations. Mol Genet Genomic Med 2019; 7:e608. [PMID: 30916489 PMCID: PMC6503032 DOI: 10.1002/mgg3.608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 01/10/2019] [Accepted: 01/24/2019] [Indexed: 11/22/2022] Open
Abstract
Background Autosomal recessive congenital ichthyoses (ARCI) have been associated with different phenotypes including: harlequin ichthyosis (HI), congenital ichthyosiform erythroderma (CIE), and lamellar ichthyosis (LI). While pathogenic variants in all ARCI genes are associated with LI and CIE phenotypes, the unique gene associated with HI is ABCA12. In HI, the most severe ARCI form, pathogenic variants in both ABCA12 gene alleles usually have a severe impact on protein function. The presence of at least one non‐truncating variant frequently causes a less severe congenital ichthyosis phenotype (LI and CIE). Methods We report the case of a 4‐year‐old Ecuadorian boy with a severe skin disease. Genetic diagnosis was performed by NGS. In silico predictions were performed using Alamut software v2.11. A review of the literature was carried out to identify all patients carrying ABCA12 splice‐site and missense variants, and to explore their genotype‐phenotype correlations. Results Genetic testing revealed a nonsense substitution, p.(Arg2204*), and a new missense variant, p.(Val1927Leu), in the ABCA12 gene. After performing in silico analysis and a comprehensive review of the literature, we conclude that p.(Val1927Leu) affects a well conserved residue which could either disturb the protein function or alter the splicing process, both alternatives could explain the severe phenotype of our patient. Conclusion This case expands the spectrum of ABCA12 reported disease‐causing variants which is important to unravel genotype‐phenotype correlations and highlights the importance of missense variants in the development of HI.
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Affiliation(s)
- Martha Montalván-Suárez
- Sistema de Investigación y Desarrollo SINDE, Universidad Católica de Santiago de Guayaquil and Universidad de Guayaquil, Guayaquil, Ecuador
| | - Uxia Saraiva Esperón-Moldes
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain.,Departamento de Ciencias Forenses, Anatomía Patolóxica, Xinecoloxía, Obstetricia e Pediatría, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Laura Rodríguez-Pazos
- Servicio de Dermatología del Complejo Hospitalario Universitario de Vigo, Vigo, Spain
| | - Andrés Ordóñez-Ugalde
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain.,Laboratorio Biomolecular, Cuenca, Ecuador.,Unidad de Genética y Molecular del Hospital de Especialidades José Carrasco Arteaga, Cuenca, Ecuador
| | | | - Nora Ugalde-Noritz
- Unidad de Genética y Molecular del Hospital de Especialidades José Carrasco Arteaga, Cuenca, Ecuador
| | - Luis Santomé
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Laura Fachal
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | | | - Juan Carlos Ruiz
- Universidad Espíritu Santo and Hospital Luis Vernaza, Guayaquil, Ecuador.,Instituto de Biomedicina Universidad Católica de Santiago de Guayaquil and Centro de Investigación, Universidad Espíritu Santo, Guayaquil, Ecuador
| | - Manuel Ginarte
- Servicio de Dermatología del Complexo Hospitalario Universitario de Santiago, Facultad de Medicina, Santiago de Compostela, Spain
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
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Lima Cunha D, Alakloby OM, Gruber R, Kakar N, Ahmad J, Alawbathani S, Plank R, Eckl K, Krabichler B, Altmüller J, Nürnberg P, Zschocke J, Borck G, Schmuth M, Alabdulkareem AS, Abdulaziz Alnutaifi K, Hennies HC. Unknown mutations and genotype/phenotype correlations of autosomal recessive congenital ichthyosis in patients from Saudi Arabia and Pakistan. Mol Genet Genomic Med 2019; 7:e539. [PMID: 30600594 PMCID: PMC6418373 DOI: 10.1002/mgg3.539] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/26/2018] [Accepted: 11/15/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Autosomal recessive congenital ichthyosis (ARCI) is a genetically and phenotypically heterogeneous skin disease, associated with defects in the skin permeability barrier. Several but not all genes with underlying mutations have been identified, but a clear correlation between genetic causes and clinical picture has not been described to date. METHODS Our study included 19 families from Saudi Arabia, Yemen, and Pakistan. All patients were born to consanguineous parents and diagnosed with ARCI. Mutations were analyzed by homozygosity mapping and direct sequencing. RESULTS We have detected mutations in all families in five different genes: TGM1, ABCA12, CYP4F22, NIPAL4, and ALOXE3. Five likely pathogenic variants were unknown so far, a splice site and a missense variant in TGM1, a splice site variant in NIPAL4, and missense variants in ABCA12 and CYP4F22. We attributed TGM1 and ABCA12 mutations to the most severe forms of lamellar and erythematous ichthyoses, respectively, regardless of treatment. Other mutations highlighted the presence of a phenotypic spectrum in ARCI. CONCLUSION Our results contribute to expanding the mutational spectrum of ARCI and revealed new insights into genotype/phenotype correlations. The findings are instrumental for a faster and more precise diagnosis, a better understanding of the pathophysiology, and the definition of targets for more specific therapies for ARCI.
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Affiliation(s)
- Dulce Lima Cunha
- Department of Biological and Geographical Sciences, University of Huddersfield, Huddersfield, UK.,Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria.,Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Omar Mohammed Alakloby
- Department of Dermatology, College of Medicine, Imam Abdulrahman Bin Faisal University (formerly University of Dammam), Dammam, Saudi Arabia
| | - Robert Gruber
- Department of Dermatology, Medical University of Innsbruck, Innsbruck, Austria
| | - Naseebullah Kakar
- Institute of Human Genetics, University of Ulm, Ulm, Germany.,Department of Biotechnology, BUITEMS, Quetta, Pakistan
| | - Jamil Ahmad
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
| | - Salem Alawbathani
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Roswitha Plank
- Department of Biological and Geographical Sciences, University of Huddersfield, Huddersfield, UK.,Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Katja Eckl
- Department of Biological and Geographical Sciences, University of Huddersfield, Huddersfield, UK.,Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria.,Department of Biology, Edge Hill University, Ormskirk, UK
| | - Birgit Krabichler
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.,CECAD Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases, University of Cologne, Cologne, Germany
| | - Johannes Zschocke
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Guntram Borck
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Matthias Schmuth
- Department of Dermatology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Kholood Abdulaziz Alnutaifi
- Department of Dermatology, College of Medicine, Imam Abdulrahman Bin Faisal University (formerly University of Dammam), Dammam, Saudi Arabia
| | - Hans Christian Hennies
- Department of Biological and Geographical Sciences, University of Huddersfield, Huddersfield, UK.,Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria.,Cologne Center for Genomics, University of Cologne, Cologne, Germany.,CECAD Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases, University of Cologne, Cologne, Germany
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Alallasi SR, Kokandi AA, Banagnapali B, Shaik NA, Al-Shehri BA, Alrayes NM, Al-Aama JY, Jelani M. Exome Analysis Identifies a Novel Compound Heterozygous Alteration in TGM1 Gene Leading to Lamellar Ichthyosis in a Child From Saudi Arabia: Case Presentation. Front Pediatr 2019; 7:44. [PMID: 30847336 PMCID: PMC6393366 DOI: 10.3389/fped.2019.00044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/01/2019] [Indexed: 11/26/2022] Open
Abstract
Background: Lamellar ichthyosis is an autosomal recessive type of rare skin disorders characterized with defective epidermis leading hyperkeratosis with brownish-gray scales over the body. These patients are born as collodion babies and may also exhibit additional features like erythema, ectropion, and eclabium. This disease is mainly caused by homozygous and compound heterozygous alterations in transglutaminase 1 encoding gene (TGM1), which is located on 14q12. Case presentation: This study reports the genetic analysis of a 4-year Saudi girl presenting lamellar ichthyosis. She was the first child of unrelated parents. The family had no previous history of the disease phenotype. She was born as a collodion baby without any prenatal complications. At the time of this study she had developed rough scaly skin on her legs, arms and trunk regions with thick palms and soles. Whole exome sequencing (WES) followed by Sanger sequence validation identified a novel compound heterozygous variant in TGM1 gene. The paternal variant was a missense transition (c.1141G>A; p.Ala381Thr) present at exon 7, while maternal variant (c.758-1G>C) was present at the intron4-exon5 boundary. To the best of our knowledge these variants had not been reported before in TGM1 gene. Conclusion: In isolated and inbred populations, homozygous variants are identified more frequently; however, our results suggest that compound heterozygous variants should also be considered especially when the marriages are not consanguineous.
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Affiliation(s)
- Sami Raja Alallasi
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amal A Kokandi
- Department of Dermatology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Babajan Banagnapali
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.,Princess Al-Jawhara Albrahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noor Ahmad Shaik
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.,Princess Al-Jawhara Albrahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Bandar Ali Al-Shehri
- Princess Al-Jawhara Albrahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nuha Mohammad Alrayes
- Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jumana Yousuf Al-Aama
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.,Princess Al-Jawhara Albrahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Musharraf Jelani
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.,Centre for Omic Sciences, Islamia College Peshawar, Peshawar, Pakistan
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Assessment of coding region variants in Kuwaiti population: implications for medical genetics and population genomics. Sci Rep 2018; 8:16583. [PMID: 30409984 PMCID: PMC6224454 DOI: 10.1038/s41598-018-34815-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 10/16/2018] [Indexed: 02/07/2023] Open
Abstract
Consanguineous populations of the Arabian Peninsula have been underrepresented in global efforts that catalogue human exome variability. We sequenced 291 whole exomes of unrelated, healthy native Arab individuals from Kuwait to a median coverage of 45X and characterised 170,508 single-nucleotide variants (SNVs), of which 21.7% were ‘personal’. Up to 12% of the SNVs were novel and 36% were population-specific. Half of the SNVs were rare and 54% were missense variants. The study complemented the Greater Middle East Variome by way of reporting many additional Arabian exome variants. The study corroborated Kuwaiti population genetic substructures previously derived using genome-wide genotype data and illustrated the genetic relatedness among Kuwaiti population subgroups, Middle Eastern, European and Ashkenazi Jewish populations. The study mapped 112 rare and frequent functional variants relating to pharmacogenomics and disorders (recessive and common) to the phenotypic characteristics of Arab population. Comparative allele frequency data and carrier distributions of known Arab mutations for 23 disorders seen among Arabs, of putative OMIM-listed causal mutations for 12 disorders observed among Arabs but not yet characterized for genetic basis in Arabs, and of 17 additional putative mutations for disorders characterized for genetic basis in Arab populations are presented for testing in future Arab studies.
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Bastaki F, Mohamed M, Nair P, Saif F, Mustafa EM, Bizzari S, Al-Ali MT, Hamzeh AR. Summary of mutations underlying autosomal recessive congenital ichthyoses (ARCI) in Arabs with four novel mutations in ARCI-related genes from the United Arab Emirates. Int J Dermatol 2017; 56:514-523. [PMID: 28236338 DOI: 10.1111/ijd.13568] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 11/24/2016] [Accepted: 01/10/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND Clinical and molecular heterogeneity is a prominent characteristic of congenital ichthyoses, with the involvement of numerous causative loci. Mutations in these loci feature in autosomal recessive congenital ichthyoses (ARCIs) quite variably, with certain genes/mutations being more frequently uncovered in particular populations. METHODS In this study, we used whole exome sequencing as well as direct Sanger sequencing to uncover four novel mutations in ARCI-related genes, which were found in families from the United Arab Emirates. In silico tools such as CADD and SIFT Indel were used to predict the functional consequences of these mutations. RESULTS The here-presented mutations occurred in three genes (ALOX12B, TGM1, ABCA12), and these are a mixture of missense and indel variants with damaging functional consequences on their encoded proteins. CONCLUSIONS This study presents an overview of the mutations that were found in ARCI-related genes in Arabs and discusses molecular and clinical details pertaining to the above-mentioned Emirati cases and their novel mutations with special emphasis on the resulting protein changes.
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Affiliation(s)
- Fatma Bastaki
- Pediatric Department, Latifa Hospital, Dubai Health Authority, Dubai, UAE
| | - Madiha Mohamed
- Pediatric Department, Latifa Hospital, Dubai Health Authority, Dubai, UAE
| | | | - Fatima Saif
- Pediatric Department, Latifa Hospital, Dubai Health Authority, Dubai, UAE
| | - Ethar M Mustafa
- Pediatric Department, Latifa Hospital, Dubai Health Authority, Dubai, UAE
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