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Nomura F, Shimizu A, Togi S, Ura H, Niida Y. SNP Array Screening and Long Range PCR-Based Targeted Next Generation Sequencing for Autosomal Recessive Disease with Consanguinity: Insight from a Case of Xeroderma Pigmentosum Group C. Genes (Basel) 2023; 14:2079. [PMID: 38003022 PMCID: PMC10671442 DOI: 10.3390/genes14112079] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 10/30/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Advances in genetic technologies have made genetic testing more accessible than ever before. However, depending on national, regional, legal, and health insurance circumstances, testing procedures may still need to be streamlined in real-world clinical practice. In cases of autosomal recessive disease with consanguinity, the mutation locus is necessarily isodisomy because both alleles originate from a common ancestral chromosome. Based on this premise, we implemented integrated genetic diagnostic methods using SNP array screening and long range PCR-based targeted NGS in a Japanese patient with xeroderma pigmentosum (XP) under the limitation of the national health insurance system. SNP array results showed isodisomy only in XPC and ERCC4 loci. NGS, with a minimal set of long-range PCR primers, detected a homozygous frameshift mutation in XPC; NM_004628.5:c.218_219insT p.(Lys73AsnfsTer9), confirmed by Sanger sequencing, leading to a rapid diagnosis of XP group C. This shortcut strategy is applicable to all autosomal recessive diseases caused by consanguineous marriages, especially in scenarios with a moderate number of genes to test, a common occurrence in clinical genetic practice.
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Affiliation(s)
- Fumie Nomura
- Department of Dermatology, Kanazawa Medical University, Uchinada 920-0293, Japan (A.S.)
| | - Akira Shimizu
- Department of Dermatology, Kanazawa Medical University, Uchinada 920-0293, Japan (A.S.)
| | - Sumihito Togi
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Uchinada 920-0293, Japan (H.U.)
- Department of Advanced Medicine, Division of Genomic Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada 920-0293, Japan
| | - Hiroki Ura
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Uchinada 920-0293, Japan (H.U.)
- Department of Advanced Medicine, Division of Genomic Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada 920-0293, Japan
| | - Yo Niida
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Uchinada 920-0293, Japan (H.U.)
- Department of Advanced Medicine, Division of Genomic Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada 920-0293, Japan
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Xeroderma Pigmentosum: A Genetic Condition Skin Cancer Correlated—A Systematic Review. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8549532. [PMID: 35898688 PMCID: PMC9313971 DOI: 10.1155/2022/8549532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022]
Abstract
Background. Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder of UV radiation-induced damage repair that is characterized by photosensitivity and a propensity for developing, among many others, skin cancers at an early age. This systematic review focused on the correlation between the clinical, pathological, and genetic aspects of XP and skin cancer. Methods. A systematic review was conducted through a literature search of online databases PubMed, Cochrane Library, SciELO, and Google Scholar. Search terms were “Xeroderma pigmentosum”, “XP”, “XPC”, “Nucleotide excision repair”, “NER”, “POLH”, “Dry pigmented skin”, and “UV sensitive syndrome” meshed with the terms “Skin cancer”, “Melanoma”, and “NMSC”. Results. After 504 abstracts screening, 13 full-text articles were assessed for eligibility, and 3 of them were excluded. Ten articles were selected for qualitative assessment. Conclusions. Patients with XP usually suffer shorter lives due to skin cancer and neurodegenerative disease. Deletion/alteration of a distinct gene allele can produce different types of cancer. The XPC and XP-E variants are more likely to have skin cancer than patients in other complement groups, and the most common cause of death for these patients is skin cancer (metastatic melanoma or invasive SCC). Still, aggressive preventative measures to minimize UV radiation exposure can retard the course of the disease and improve the quality of life.
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Feltes BC, Menck CFM. Current state of knowledge of human DNA polymerase eta protein structure and disease-causing mutations. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108436. [PMID: 35952573 DOI: 10.1016/j.mrrev.2022.108436] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 06/29/2022] [Accepted: 07/31/2022] [Indexed: 01/01/2023]
Abstract
POLη, encoded by the POLH gene, is a crucial protein for replicating damaged DNA and the most studied specialized translesion synthesis polymerases. Mutations in POLη are associated with cancer and the human syndrome xeroderma pigmentosum variant, which is characterized by extreme photosensitivity and an increased likelihood of developing skin cancers. The myriad of structural information about POLη is vast, covering dozens of different mutants, numerous crucial residues, domains, and posttranslational modifications that are essential for protein function within cells. Since POLη is key vital enzyme for cell survival, and mutations in this protein are related to aggressive diseases, understanding its structure is crucial for biomedical sciences, primarily due to its similarities with other Y-family polymerases and its potential as a targeted therapy-drug for tumors. This work provides an up-to-date review on structural aspects of the human POLη: from basic knowledge about critical residues and protein domains to its mutant variants, posttranslational modifications, and our current understanding of therapeutic molecules that target POLη. Thus, this review provides lessons about POLη's structure and gathers critical discussions and hypotheses that may contribute to understanding this protein's vital roles within the cells.
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Affiliation(s)
- Bruno César Feltes
- Department of Theoretical Informatics, Institute of Informatics, Department of Theoretical Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS Brazil; Department of Genetics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Biophysics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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4
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Zamani GY, Khan R, Karim N, Ahmed ZM, Naeem M. Identification of Frameshift Variants in POLH Gene Causing Xeroderma Pigmentosum in Two Consanguineous Pakistani Families. Genes (Basel) 2022; 13:genes13030543. [PMID: 35328096 PMCID: PMC8955859 DOI: 10.3390/genes13030543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 11/16/2022] Open
Abstract
Xeroderma pigmentosum (XP) is a rare autosomal recessive genetic disorder characterized by severe sensitivity of skin to sunlight and an increased risk of skin cancer. XP variant (XPV), a milder subtype, is caused by variants in the POLH gene. POLH encodes an error-prone DNA-polymerase eta (pol eta) which performs translesion synthesis past ultraviolet photoproducts. The current study documents the clinical and genetic investigations of two large consanguineous Pakistani families affected with XPV. In family 1, whole exome sequencing (WES) revealed a novel frameshift variant, c.1723dupG (p.(Val575Glyfs*4)), of POLH, which is predicted to cause frameshift and premature truncation of the encoded enzyme. Indeed, our ex vivo studies in HEK293T cells confirmed the truncation of the encoded protein due to the c.1723dupG variant. In family 2, Sanger sequencing of POLH exons, revealed a recurrent nonsense variant, c.437dupA (p.Tyr146*). POLH forms a hetero-tetrameric POLZ complex with REV3L, REV7, POLD2 and POLD3. Next, we performed in silico analysis of POLH and other POLZ complex genes expression in publicly available single cell mRNAseq datasets from adult human healthy and aging skin. We found overlapping expression of POLH, REV3L and POLD2 in multiple cell types including differentiated and undifferentiated keratinocytes, pericytes and melanocytes in healthy skin. However, in aging human skin, POLH expression is reduced in compare to its POLZ complex partners. Insights from our study will facilitate counseling regarding the molecular and phenotypic landscape of POLH-related XPV.
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Affiliation(s)
- Ghazala Y. Zamani
- Medical Genetics Research Laboratory, Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan; (G.Y.Z.); (N.K.)
| | - Ranjha Khan
- Joint Centre for Human Reproduction and Genetics, Anhui Society for Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei 230052, China;
| | - Noreen Karim
- Medical Genetics Research Laboratory, Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan; (G.Y.Z.); (N.K.)
| | - Zubair M. Ahmed
- Laboratory of Neurogenetics and Translational Research, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Correspondence: (Z.M.A.); (M.N.); Tel.: +1-410-706-3799 (Z.M.A.); +92-51-9064-4122 (M.N.)
| | - Muhammad Naeem
- Medical Genetics Research Laboratory, Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan; (G.Y.Z.); (N.K.)
- Correspondence: (Z.M.A.); (M.N.); Tel.: +1-410-706-3799 (Z.M.A.); +92-51-9064-4122 (M.N.)
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5
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Nabouli I, Chikhaoui A, Othman H, Elouej S, Jones M, Lagarde A, Rekaya MB, Messaoud O, Zghal M, Delague V, Levy N, De Sandre-Giovannoli A, Abdelhak S, Yacoub-Youssef H. Case Report: Identification of Novel Variants in ERCC4 and DDB2 Genes in Two Tunisian Patients With Atypical Xeroderma Pigmentosum Phenotype. Front Genet 2021; 12:650639. [PMID: 34135938 PMCID: PMC8203331 DOI: 10.3389/fgene.2021.650639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
Xeroderma Pigmentosum (XP) is a rare genetic disorder affecting the nucleotide excision repair system (NER). It is characterized by an extreme sensitivity to sunlight that induces cutaneous disorders such as severe sunburn, freckling and cancers. In Tunisia, six complementation groups have been already identified. However, the genetic etiology remains unknown for several patients. In this study, we investigated clinical characteristics and genetic defects in two families with atypical phenotypes originating from the central region in Tunisia. Clinical investigation revealed mild cutaneous features in two patients who develop multiple skin cancers at later ages, with no neurological disorders. Targeted gene sequencing revealed that they carried novel variants. A homozygous variation in the ERCC4 gene c.1762G>T, p.V588F, detected in patient XP21. As for patient XP134, he carried two homozygous mutations in the DDB2 gene c.613T>C, p.C205R and c.618C>A, p.S206R. Structural modeling of the protein predicted the identified ERCC4 variant to mildly affect protein stability without affecting its functional domains. As for the case of DDB2 double mutant, the second variation seems to cause a mild effect on the protein structure unlike the first variation which does not seem to have an effect on it. This study contributes to further characterize the mutation spectrum of XP in Tunisian families. Targeted gene sequencing accelerated the identification of rare unexpected genetic defects for diagnostic testing and genetic counseling.
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Affiliation(s)
- Imen Nabouli
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, LR16IPT05, Université Tunis ElManar, Tunis, Tunisia
| | - Asma Chikhaoui
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, LR16IPT05, Université Tunis ElManar, Tunis, Tunisia
| | - Houcemeddine Othman
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Sahar Elouej
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, LR16IPT05, Université Tunis ElManar, Tunis, Tunisia.,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - Meriem Jones
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, LR16IPT05, Université Tunis ElManar, Tunis, Tunisia.,Service de dermatologie, Hôpital Charles Nicolle, Tunis, Tunisia
| | - Arnaud Lagarde
- Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - Meriem Ben Rekaya
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, LR16IPT05, Université Tunis ElManar, Tunis, Tunisia
| | - Olfa Messaoud
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, LR16IPT05, Université Tunis ElManar, Tunis, Tunisia
| | - Mohamed Zghal
- Service de dermatologie, Hôpital Charles Nicolle, Tunis, Tunisia
| | | | - Nicolas Levy
- Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France.,Departement of Medical Genetics, Assistance Publique Hôpitaux de Marseille, La Timone Children's Hospital, Marseille, France
| | - Annachiara De Sandre-Giovannoli
- Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France.,Biological Resource Center (CRB-TAC), Assistance Publique Hôpitaux de Marseille, La Timone Children's Hospital, Marseille, France
| | - Sonia Abdelhak
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, LR16IPT05, Université Tunis ElManar, Tunis, Tunisia
| | - Houda Yacoub-Youssef
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, LR16IPT05, Université Tunis ElManar, Tunis, Tunisia
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6
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Castro LP, Sahbatou M, Kehdy FSG, Farias AA, Yurchenko AA, de Souza TA, Rosa RCA, Mendes-Junior CT, Borda V, Munford V, Zanardo ÉA, Chehimi SN, Kulikowski LD, Aquino MM, Leal TP, Tarazona-Santos E, Chaibub SC, Gener B, Calmels N, Laugel V, Sarasin A, Menck CFM. The Iberian legacy into a young genetic xeroderma pigmentosum cluster in central Brazil. Mutat Res 2020; 852:503164. [PMID: 32265042 DOI: 10.1016/j.mrgentox.2020.503164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/22/2020] [Accepted: 02/25/2020] [Indexed: 10/24/2022]
Abstract
In central Brazil, in the municipality of Faina (state of Goiás), the small and isolated village of Araras comprises a genetic cluster of xeroderma pigmentosum (XP) patients. The high level of consanguinity and the geographical isolation gave rise to a high frequency of XP patients. Recently, two founder events were identified affecting that community, with two independent mutations at the POLH gene, c.764 + 1 G > A (intron 6) and c.907 C > T; p.Arg303* (exon 8). These deleterious mutations lead to the xeroderma pigmentosum variant syndrome (XP-V). Previous reports identified both mutations in other countries: the intron 6 mutation in six patients (four families) from Northern Spain (Basque Country and Cantabria) and the exon 8 mutation in two patients from different families in Europe, one of them from Kosovo. In order to investigate the ancestry of the XP patients and the age for these mutations at Araras, we generated genotyping information for 22 XP-V patients from Brazil (16), Spain (6) and Kosovo (1). The local genomic ancestry and the shared haplotype segments among the patients showed that the intron 6 mutation at Araras is associated with an Iberian genetic legacy. All patients from Goiás, homozygotes for intron 6 mutation, share with the Spanish patients identical-by-descent (IBD) genomic segments comprising the mutation. The entrance date for the Iberian haplotype at the village was calculated to be approximately 200 years old. This result is in agreement with the historical arrival of Iberian individuals at the Goiás state (BR). Patients from Goiás and the three families from Spain share 1.8 cM (family 14), 1.7 cM (family 15), and a more significant segment of 4.7 cM within family 13. On the other hand, the patients carrying the exon 8 mutation do not share any specific genetic segment, indicating an old genetic distance between them or even no common ancestry.
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Affiliation(s)
- L P Castro
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - M Sahbatou
- Foundation Jean Dausset - CEPH, Paris, France
| | - F S G Kehdy
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - A A Farias
- Human Genome and Stem-Cell Center, Institute of Biosciences, University of São Paulo (USP), Sao Paulo, Brazil; Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, Brazil
| | - A A Yurchenko
- Inserm U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - T A de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - R C A Rosa
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - C T Mendes-Junior
- Department of Chemistry, Forensic and Genomics Research Laboratory, Faculty of Philosophy, Sciences and Letters, University of São Paulo, Ribeirão Preto, Brazil
| | - V Borda
- National Laboratory for Scientific Computation (LNCC), Petropolis, Rio de Janeiro, Brazil
| | - V Munford
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - É A Zanardo
- Cytogenomics Laboratory, Department of Pathology, School of Medicine, University of São Paulo (FMUSP), São Paulo, Brazil
| | - S N Chehimi
- Cytogenomics Laboratory, Department of Pathology, School of Medicine, University of São Paulo (FMUSP), São Paulo, Brazil
| | - L D Kulikowski
- Cytogenomics Laboratory, Department of Pathology, School of Medicine, University of São Paulo (FMUSP), São Paulo, Brazil
| | - M M Aquino
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - T P Leal
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - E Tarazona-Santos
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - S C Chaibub
- General Hospital of Goiania, Goiania, Brazil
| | - B Gener
- Osakidetza Basque Health Service, Cruces University Hospital. Department of Genetics, Bizkaia, Spain; Biocruces Bizkaia Health Research Institute, Bizkaia, Spain
| | - N Calmels
- Laboratory of Medical Genetics, Institute of Medical Genetics of Alsace (IGMA), Strasbourg, France
| | - V Laugel
- Laboratory of Medical Genetics, Institute of Medical Genetics of Alsace (IGMA), Strasbourg, France
| | - A Sarasin
- UMR8200 CNRS, Gustave Roussy Institute, University Paris-Saclay, Villejuif, France
| | - C F M Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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7
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Chikhaoui A, Elouej S, Nabouli I, Jones M, Lagarde A, Ben Rekaya M, Messaoud O, Hamdi Y, Zghal M, Delague V, Levy N, De Sandre-Giovannoli A, Abdelhak S, Yacoub-Youssef H. Identification of a ERCC5 c.2333T>C (L778P) Variant in Two Tunisian Siblings With Mild Xeroderma Pigmentosum Phenotype. Front Genet 2019; 10:111. [PMID: 30838033 PMCID: PMC6383105 DOI: 10.3389/fgene.2019.00111] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 01/30/2019] [Indexed: 11/22/2022] Open
Abstract
Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder due to a defect in the nucleotide excision repair (NER) DNA repair pathway, characterized by severe sunburn development of freckles, premature skin aging, and susceptibility to develop cancers at an average age of eight. XP is an example of accelerated photo-aging. It is a genetically and clinically heterogeneous disease. Eight complementation groups have been described worldwide. In Tunisia, five groups have been already identified. In this work, we investigated the genetic etiology in a family with an atypically mild XP phenotype. Two Tunisian siblings born from first-degree consanguineous parents underwent clinical examination in the dermatology department of the Charles Nicolle Hospital on the basis of acute sunburn reaction and mild neurological disorders. Blood samples were collected from two affected siblings after written informed consent. As all mutations reported in Tunisia have been excluded using Sanger sequencing, we carried out mutational analysis through a targeted panel of gene sequencing using the Agilent HaloPlex target enrichment system. Our clinical study shows, in both patients, the presence of achromic macula in sun exposed area with dermatological feature suggestive of Xeroderma pigmentosum disease. No developmental and neurological disorders were observed except mild intellectual disability. Genetic investigation shows that both patients were carriers of an homozygous T to C transition at the nucleotide position c.2333, causing the leucine to proline amino acid change at the position 778 (p.Leu778Pro) of the ERCC5 gene, and resulting in an XP-G phenotype. The same variation was previously reported at the heterozygous state in a patient cell line in Europe, for which no clinical data were available and was suggested to confer an XP/CS phenotype based on functional tests. This study contributes to further characterization of the mutation spectrum of XP in consanguineous Tunisian families and is potentially helpful for early diagnosis. It also indicates that the genotype-phenotype correlation is not always coherent for patients with mild clinical features. These data therefore suggest that targeted NGS is a highly informative diagnostic strategy, which can be used for XP molecular etiology determination.
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Affiliation(s)
- Asma Chikhaoui
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Sahar Elouej
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia.,Aix Marseille Univ, Inserm, MMG, U 1251, Marseille, France
| | - Imen Nabouli
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Meriem Jones
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia.,Service de Dermatologie, Hôpital Charles Nicolle, Tunis, Tunisia
| | - Arnaud Lagarde
- Aix Marseille Univ, Inserm, MMG, U 1251, Marseille, France
| | - Meriem Ben Rekaya
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Olfa Messaoud
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Yosr Hamdi
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Mohamed Zghal
- Service de Dermatologie, Hôpital Charles Nicolle, Tunis, Tunisia
| | | | - Nicolas Levy
- Aix Marseille Univ, Inserm, MMG, U 1251, Marseille, France.,Département de Génétique Médicale, AP-HM, Hôpital la Timone, Marseille, France
| | - Annachiara De Sandre-Giovannoli
- Aix Marseille Univ, Inserm, MMG, U 1251, Marseille, France.,Département de Génétique Médicale, AP-HM, Hôpital la Timone, Marseille, France
| | - Sonia Abdelhak
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Houda Yacoub-Youssef
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
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8
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Elloumi-Zghal H, Chaabouni Bouhamed H. Genetics and genomic medicine in Tunisia. Mol Genet Genomic Med 2018; 6:134-159. [PMID: 29663716 PMCID: PMC5902400 DOI: 10.1002/mgg3.392] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 03/07/2018] [Indexed: 01/19/2023] Open
Abstract
Genetics and genomic medicine in Tunisia.
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9
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Ben Rekaya M, Naouali C, Messaoud O, Jones M, Bouyacoub Y, Nagara M, Pippucci T, Jmel H, Chargui M, Jerbi M, Alibi M, Dallali H, Bashamboo A, McElreavey K, Romeo G, Barakat A, Zghal M, Yacoub-Youssef H, Abdelhak S. Whole Exome Sequencing allows the identification of two novel groups of Xeroderma pigmentosum in Tunisia, XP-D and XP-E: Impact on molecular diagnosis. J Dermatol Sci 2018; 89:172-180. [DOI: 10.1016/j.jdermsci.2017.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 08/02/2017] [Accepted: 10/31/2017] [Indexed: 12/17/2022]
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10
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De Palma A, Morren MA, Ged C, Pouvelle C, Taïeb A, Aoufouchi S, Sarasin A. Diagnosis of Xeroderma pigmentosum variant in a young patient with two novel mutations in the POLH gene. Am J Med Genet A 2017; 173:2511-2516. [PMID: 28688171 DOI: 10.1002/ajmg.a.38340] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/01/2017] [Accepted: 06/06/2017] [Indexed: 12/13/2022]
Abstract
We describe the characterization of Xeroderma Pigmentosum variant (XPV) in a young Caucasian patient with phototype I, who exhibited a high sensitivity to sunburn and multiple cutaneous tumors at the age of 15 years. Two novel mutations in the POLH gene, which encodes the translesion DNA polymerase η, with loss of function due to two independent exon skippings, are reported to be associated as a compound heterozygous state in the patient. Western blot analysis performed on proteins from dermal fibroblasts derived from the patient and analysis of the mutation spectrum on immunoglobulin genes produced during the somatic hypermutation process in his memory B cells, show the total absence of translesion polymerase η activity in the patient. The total lack of Polη activity, necessary to bypass in an error-free manner UVR-induced pyrimidine dimers following sun exposure, explains the early unusual clinical appearance of this patient.
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Affiliation(s)
- Armando De Palma
- Department of Dermatology, University hospitals Leuven, Leuven, Belgium
| | - Marie-Anne Morren
- Department of Dermatology, University hospitals Leuven, Leuven, Belgium
| | - Cécile Ged
- Unité INSERM U1035 and Center de Référence pour les Maladies Rares de la Peau, CHU de Bordeaux, Bordeaux, France
| | - Caroline Pouvelle
- Laboratory of Genetic Instability and Oncogenesis, UMR8200 CNRS, Gustave Roussy, Université Paris-Sud, Villejuif, France
| | - Alain Taïeb
- Unité INSERM U1035 and Center de Référence pour les Maladies Rares de la Peau, CHU de Bordeaux, Bordeaux, France
| | - Said Aoufouchi
- Laboratory of Genetic Instability and Oncogenesis, UMR8200 CNRS, Gustave Roussy, Université Paris-Sud, Villejuif, France.,Université Pierre et Marie Curie, Paris, France
| | - Alain Sarasin
- Laboratory of Genetic Instability and Oncogenesis, UMR8200 CNRS, Gustave Roussy, Université Paris-Sud, Villejuif, France
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Calmels N, Greff G, Obringer C, Kempf N, Gasnier C, Tarabeux J, Miguet M, Baujat G, Bessis D, Bretones P, Cavau A, Digeon B, Doco-Fenzy M, Doray B, Feillet F, Gardeazabal J, Gener B, Julia S, Llano-Rivas I, Mazur A, Michot C, Renaldo-Robin F, Rossi M, Sabouraud P, Keren B, Depienne C, Muller J, Mandel JL, Laugel V. Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing. Orphanet J Rare Dis 2016; 11:26. [PMID: 27004399 PMCID: PMC4804614 DOI: 10.1186/s13023-016-0408-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 03/16/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Deficient nucleotide excision repair (NER) activity causes a variety of autosomal recessive diseases including xeroderma pigmentosum (XP) a disorder which pre-disposes to skin cancer, and the severe multisystem condition known as Cockayne syndrome (CS). In view of the clinical overlap between NER-related disorders, as well as the existence of multiple phenotypes and the numerous genes involved, we developed a new diagnostic approach based on the enrichment of 16 NER-related genes by multiplex amplification coupled with next-generation sequencing (NGS). METHODS Our test cohort consisted of 11 DNA samples, all with known mutations and/or non pathogenic SNPs in two of the tested genes. We then used the same technique to analyse samples from a prospective cohort of 40 patients. Multiplex amplification and sequencing were performed using AmpliSeq protocol on the Ion Torrent PGM (Life Technologies). RESULTS We identified causative mutations in 17 out of the 40 patients (43%). Four patients showed biallelic mutations in the ERCC6(CSB) gene, five in the ERCC8(CSA) gene: most of them had classical CS features but some had very mild and incomplete phenotypes. A small cohort of 4 unrelated classic XP patients from the Basque country (Northern Spain) revealed a common splicing mutation in POLH (XP-variant), demonstrating a new founder effect in this population. Interestingly, our results also found ERCC2(XPD), ERCC3(XPB) or ERCC5(XPG) mutations in two cases of UV-sensitive syndrome and in two cases with mixed XP/CS phenotypes. CONCLUSIONS Our study confirms that NGS is an efficient technique for the analysis of NER-related disorders on a molecular level. It is particularly useful for phenotypes with combined features or unusually mild symptoms. Targeted NGS used in conjunction with DNA repair functional tests and precise clinical evaluation permits rapid and cost-effective diagnosis in patients with NER-defects.
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Affiliation(s)
- Nadège Calmels
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France.
| | - Géraldine Greff
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France
| | - Cathy Obringer
- Laboratoire de Génétique Médicale - INSERM U1112, Institut de Génétique Médicale d'Alsace (IGMA), Faculté de médecine de Strasbourg, 11 rue Humann, Strasbourg, France
| | - Nadine Kempf
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France
| | - Claire Gasnier
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France
| | - Julien Tarabeux
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France
| | - Marguerite Miguet
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France
| | - Geneviève Baujat
- Centre de Référence Maladies Osseuses Constitutionnelles, Département de Génétique, Hôpital Necker-Enfants malades, Paris, France
| | - Didier Bessis
- Département de Dermatologie, Hôpital Saint-Éloi, 80 avenue Augustin-Fliche, 34295, Montpellier, France
| | - Patricia Bretones
- Service d'Endocrinologie Pédiatrique, diabète et maladies héréditaires du métabolisme, Hôpital Femme Mère enfant, GH Est, 59 boulevard Pinel, Bron, France
| | - Anne Cavau
- Service de Pédiatrie Générale, Hôpital Necker-Enfants malades, Paris, France
| | - Béatrice Digeon
- Service de Pédiatrie, CHU de Reims, Hôpital Maison Blanche, 45 rue Cognacq-Jay, Reims, France
| | - Martine Doco-Fenzy
- Service de Génétique et Biologie de la Reproduction CHU de Reims, Hôpital Maison Blanche, 45 rue Cognacq-Jay, Reims, France
| | - Bérénice Doray
- Service de Génétique, CHU La Réunion, Hôpital Félix Guyon, Allée des Topazes, Saint-Denis, France
| | - François Feillet
- Centre de Référence des Maladies Héréditaires du Métabolisme, Service de Médecine Infantile, INSERM NGERE 954, CHU Brabois Enfants, Allée du Morvan, Vandœuvre les Nancy, France
| | - Jesus Gardeazabal
- Servicio de Dermatología, Cruces University Hospital, BioCruces Health Research Institute, Baracaldo Vizcaya, Spain
| | - Blanca Gener
- Servicio de Genética, Cruces University Hospital, BioCruces Health Research Institute, Baracaldo Vizcaya, Spain
| | - Sophie Julia
- Service de Génétique Médicale, CHU de Toulouse - Hôpital Purpan, Place du Docteur Baylac, Toulouse, France
| | - Isabel Llano-Rivas
- Servicio de Genética, Cruces University Hospital, BioCruces Health Research Institute, Baracaldo Vizcaya, Spain
| | - Artur Mazur
- Department of Pediatrics, Pediatric Endocrinology and Diabetes, Faculty of Medicine, University of Rzeszów, Rzeszów, Poland
| | - Caroline Michot
- Service de Génétique Médicale, Hôpital Necker Enfants-Malades, 24 Bd du Montparnasse, Paris, France
| | | | - Massimiliano Rossi
- Centre de Référence des Anomalies du Développement, Service de Génétique, Hospices Civils de Lyon, Lyon, France.,INSERM U1028; CNRS UMR5292; CNRL TIGER Team, Lyon, France
| | - Pascal Sabouraud
- Service de Pédiatrie A - Neurologie pédiatrique, CHU de Reims - American Memorial Hospital, 47 rue Cognacq Jay, Reims, France
| | - Boris Keren
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, UM 75, U 1127, UMR 7225, ICM, F-75013, Paris, France
| | - Christel Depienne
- AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, UM 75, U 1127, UMR 7225, ICM, F-75013, Paris, France
| | - Jean Muller
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France.,Laboratoire de Génétique Médicale - INSERM U1112, Institut de Génétique Médicale d'Alsace (IGMA), Faculté de médecine de Strasbourg, 11 rue Humann, Strasbourg, France
| | - Jean-Louis Mandel
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France
| | - Vincent Laugel
- Laboratoire de Génétique Médicale - INSERM U1112, Institut de Génétique Médicale d'Alsace (IGMA), Faculté de médecine de Strasbourg, 11 rue Humann, Strasbourg, France.,Service de Pédiatrie, Hôpitaux Universitaires de Strasbourg, 1 avenue Molière, Strasbourg, France
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