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Hamdi Y, Boujemaa M, Ben Aissa-Haj J, Radouani F, Khyatti M, Mighri N, Hannachi M, Ghedira K, Souiai O, Hkimi C, Kammoun MS, Mejri N, Bouaziz H, Beloufa MA, Charoute H, Barakat A, Najjar I, Taniguchi H, Pietrosemoli N, Dellagi K, Abdelhak S, Boubaker MS, Chica C, Rouleau E. A regionally based precision medicine implementation initiative in North Africa:The PerMediNA consortium. Transl Oncol 2024; 44:101940. [PMID: 38537326 DOI: 10.1016/j.tranon.2024.101940] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/23/2024] [Accepted: 03/11/2024] [Indexed: 04/21/2024] Open
Abstract
Precision Medicine is being increasingly used in the developed world to improve health care. While several Precision Medicine (PM) initiatives have been launched worldwide, their implementations have proven to be more challenging particularly in low- and middle-income countries. To address this issue, the "Personalized Medicine in North Africa" initiative (PerMediNA) was launched in three North African countries namely Tunisia, Algeria and Morocco. PerMediNA is coordinated by Institut Pasteur de Tunis together with the French Ministry for Europe and Foreign Affairs, with the support of Institut Pasteur in France. The project is carried out along with Institut Pasteur d'Algérie and Institut Pasteur du Maroc in collaboration with national and international leading institutions in the field of PM including Institut Gustave Roussy in Paris. PerMediNA aims to assess the readiness level of PM implementation in North Africa, to strengthen PM infrastructure, to provide workforce training, to generate genomic data on North African populations, to implement cost effective, affordable and sustainable genetic testing for cancer patients and to inform policy makers on how to translate research knowledge into health products and services. Gender equity and involvement of young scientists in this implementation process are other key goals of the PerMediNA project. In this paper, we are describing PerMediNA as the first PM implementation initiative in North Africa. Such initiatives contribute significantly in shortening existing health disparities and inequities between developed and developing countries and accelerate access to innovative treatments for global health.
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Affiliation(s)
- Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia.
| | - Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Jihenne Ben Aissa-Haj
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia; Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Fouzia Radouani
- Chlamydiae and Mycoplasmas Laboratory, Research Department, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Meriem Khyatti
- Laboratory of Viral Oncology, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Najah Mighri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Mariem Hannachi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Chaima Hkimi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Mohamed Selim Kammoun
- Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Nesrine Mejri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia; Medical Oncology Department, Abderrahmane Mami Hospital, Faculty of Medicine, University Tunis El Manar, Tunis, Tunisia
| | - Hanen Bouaziz
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia; Department of Carcinological Surgery, Salah Azaiez Institute, Tunis, Tunisia
| | | | - Hicham Charoute
- Research unit of Epidemiology, Biostatistics and Bioinformatics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Abdelhamid Barakat
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc 20360, Casablanca, Morocco
| | - Imène Najjar
- Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Paris 75015, France
| | - Hiroaki Taniguchi
- The Polish Academy of Sciences, Poland; University Mohamed VI, Morocco
| | - Natalia Pietrosemoli
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub F-75015, Paris, France
| | - Koussay Dellagi
- Pasteur Network Association, Institut Pasteur, Paris, France
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Mohamed Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia; Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Claudia Chica
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub F-75015, Paris, France
| | - Etienne Rouleau
- Department of Biology and Pathology-Cancer Genetics Laboratory-Gustave Roussy 94805, Villejuif, France
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Jandoubi N, Boujemaa M, Mighri N, Mejri N, Ben Nasr S, Bouaziz H, Berrazega Y, Rachdi H, Daoud N, Zribi A, Ayari J, El Benna H, Labidi S, Haddaoui A, Mrad R, Ben Ahmed S, Boussen H, Abdelhak S, Boubaker S, Hamdi Y. Genetic testing for hereditary cancer syndromes in Tunisian patients: Impact on health system. Transl Oncol 2024; 43:101912. [PMID: 38387387 PMCID: PMC10900923 DOI: 10.1016/j.tranon.2024.101912] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/29/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
INTRODUCTION Cancer management in Africa faces diverse challenges due to limited resources, health system challenges, and other matters. Identifying hereditary cancer syndromic cases is crucial to improve clinical management and preventive care in these settings. This study aims to explore the clinicopathological features and genetic factors associated with hereditary cancer in Tunisia, a North African country with a rising cancer burden MATERIALS AND METHODS: Clinicopathological features and personal/family history of cancer were explored in 521 patients. Genetic analysis using Sanger and next-generation sequencing was performed for a set of patients RESULTS: Hereditary breast and ovarian cancer syndrome was the most frequent cluster in which 36 BRCA mutations were identified. We described a subgroup of patients with likely ''breast cancer-only syndrome'' among this cluster. Two cases of Li-Fraumeni syndrome with distinct TP53 mutations namely c.638G>A and c.733G>A have been identified. Genetic investigation also allowed the identification of a new BLM homozygous mutation (c.3254dupT) in one patient with multiple primary cancers. Phenotype-genotype correlation suggests the diagnosis of Bloom syndrome. A recurrent MUTYH mutation (c.1143_1144dup) was identified in three patients with different phenotypes CONCLUSION: Our study calls for comprehensive genetic education and the implementation of genetic screening in Tunisia and other African countries health systems, to reduce the burden of hereditary diseases and improve cancer outcomes in resource-stratified settings.
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Affiliation(s)
- Nouha Jandoubi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Najah Mighri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nesrine Mejri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia; Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Sonia Ben Nasr
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia; Department of Medical Oncology, Military Hospital of Tunis, Tunis, Tunisia
| | - Hanen Bouaziz
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia; Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Yosra Berrazega
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Haifa Rachdi
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Nouha Daoud
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Aref Zribi
- Department of Medical Oncology, Military Hospital of Tunis, Tunis, Tunisia
| | - Jihene Ayari
- Department of Medical Oncology, Military Hospital of Tunis, Tunis, Tunisia
| | - Houda El Benna
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia; Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Soumaya Labidi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia; Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | | | - Ridha Mrad
- Department of Human Genetics, Charles Nicolle Hospital, Tunis, Tunisia
| | - Slim Ben Ahmed
- Department of Medical Oncology, Farhat Hached University Hospital of Sousse, Faculty of Medicine of Sousse, Tunisia
| | - Hamouda Boussen
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia; Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia; Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia; Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia.
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Mkaouar R, Riahi Z, Marrakchi J, Mezzi N, Romdhane L, Boujemaa M, Dallali H, Sayeb M, Lahbib S, Jaouadi H, Boudabbous H, Zekri L, Chargui M, Messaoud O, Elyounsi M, Kraoua I, Zaouak A, Turki I, Mokni M, Boucher S, Petit C, Giraudet F, Mbarek C, Besbes G, Halayem S, Zainine R, Turki H, Tounsi A, Bonnet C, Mrad R, Abdelhak S, Trabelsi M, Charfeddine C. Current phenotypic and genetic spectrum of syndromic deafness in Tunisia: paving the way for precision auditory health. Front Genet 2024; 15:1384094. [PMID: 38711914 PMCID: PMC11072975 DOI: 10.3389/fgene.2024.1384094] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/15/2024] [Indexed: 05/08/2024] Open
Abstract
Hearing impairment (HI) is a prevalent neurosensory condition globally, impacting 5% of the population, with over 50% of congenital cases attributed to genetic etiologies. In Tunisia, HI underdiagnosis prevails, primarily due to limited access to comprehensive clinical tools, particularly for syndromic deafness (SD), characterized by clinical and genetic heterogeneity. This study aimed to uncover the SD spectrum through a 14-year investigation of a Tunisian cohort encompassing over 700 patients from four referral centers (2007-2021). Employing Sanger sequencing, Targeted Panel Gene Sequencing, and Whole Exome Sequencing, genetic analysis in 30 SD patients identified diagnoses such as Usher syndrome, Waardenburg syndrome, cranio-facial-hand-deafness syndrome, and H syndrome. This latter is a rare genodermatosis characterized by HI, hyperpigmentation, hypertrichosis, and systemic manifestations. A meta-analysis integrating our findings with existing data revealed that nearly 50% of Tunisian SD cases corresponded to rare inherited metabolic disorders. Distinguishing between non-syndromic and syndromic HI poses a challenge, where the age of onset and progression of features significantly impact accurate diagnoses. Despite advancements in local genetic characterization capabilities, certain ultra-rare forms of SD remain underdiagnosed. This research contributes critical insights to inform molecular diagnosis approaches for SD in Tunisia and the broader North-African region, thereby facilitating informed decision-making in clinical practice.
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Affiliation(s)
- Rahma Mkaouar
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Zied Riahi
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Jihene Marrakchi
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Otorhinolaryngology, District Hospital of Menzel Bourguiba, Bizerte, Tunisia
| | - Nessrine Mezzi
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Biology, Faculty of Sciences of Bizerte, Université Tunis Carthage, Tunis, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Biology, Faculty of Sciences of Bizerte, Université Tunis Carthage, Tunis, Tunisia
| | - Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Genetic Typing Service, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Marwa Sayeb
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Saida Lahbib
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hager Jaouadi
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Marseille Medical Genetics (MMG) U1251, Aix Marseille Université, INSERM, Marseille, France
| | - Hela Boudabbous
- Department of Pediatrics, La Rabta Hospital, Tunis, Tunisia
- Laboratory of Hereditary Diseases of the Metabolism Investigation and Patients Management, Faculty of Medicine in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Epidemiology and Public Health, Directorate General of Military Health, Faculty of Medicine in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Lotfi Zekri
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- ICHARA Association (International Research Institute on Sign Language), Tunis, Tunisia
| | - Mariem Chargui
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Olfa Messaoud
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Meriem Elyounsi
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital in Tunis, Tunis, Tunisia
- LR99ES10 Laboratory of Human Genetics, Faculty of Medicine in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Ichraf Kraoua
- Child and Adolescent Neurology Department of Neurology, National Institute of Neurology, Tunis, Tunisia
- LR18SP04 Department of Child Neurology, National Institute Mongi Ben Hmida of Neurology in Tunis. University of Tunis El Manar, Tunis, Tunisia
| | - Anissa Zaouak
- Department of Dermatology, Habib Thameur Hospital, Research Unit Genodermatoses and Cancers LR12SP03, Tunis, Tunisia
| | - Ilhem Turki
- Child and Adolescent Neurology Department of Neurology, National Institute of Neurology, Tunis, Tunisia
- LR18SP04 Department of Child Neurology, National Institute Mongi Ben Hmida of Neurology in Tunis. University of Tunis El Manar, Tunis, Tunisia
| | - Mourad Mokni
- Service de dermatologie, Hôpital La Rabta, Unité de recherche UR 12SP07, Hôpital La Rabta, Tunis, Tunisia
| | - Sophie Boucher
- Service d’ORL et chirurgie cervico-faciale, CHU d’Angers, Angers, France
- Equipe Mitolab, Institut Mitovasc, CNRS UMR6015, UMR Inserm 1083, Université d’Angers, Angers, France
| | - Christine Petit
- Institut Pasteur, Université Paris Cité, Inserm UA06, Institut de l’Audition, Paris, France
- Collège de France, Paris, France
| | - Fabrice Giraudet
- Unité Mixte de Recherche (UMR) 1107, INSERM, Clermont-Ferrand, France
- Centre Auditif SoluSons, Clermont-Ferrand, France
| | - Chiraz Mbarek
- ENT Department, Habib Thameur Hospital, Tunis, Tunisia
| | - Ghazi Besbes
- Department of Otorhinolaryngology and Maxillofacial Surgery - La Rabta Hospital in Tunis, Tunis, Tunisia
| | - Soumeyya Halayem
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Service de pédopsychiatrie, Hôpital Razi, Faculté de Médecine de Tunis, Université Tunis el Manar, Tunis, Tunisia
| | - Rim Zainine
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Otorhinolaryngology and Maxillofacial Surgery - La Rabta Hospital in Tunis, Tunis, Tunisia
| | - Hamida Turki
- Dermatology Department Hedi Chaker University Hospital, Sfax University Sfax Tunisia, Tunis, Tunisia
| | | | - Crystel Bonnet
- Institut Pasteur, Université Paris Cité, Inserm UA06, Institut de l’Audition, Paris, France
| | - Ridha Mrad
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital in Tunis, Tunis, Tunisia
- LR99ES10 Laboratory of Human Genetics, Faculty of Medicine in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Mediha Trabelsi
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital in Tunis, Tunis, Tunisia
- LR99ES10 Laboratory of Human Genetics, Faculty of Medicine in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Cherine Charfeddine
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
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Mezzi N, Zaouak A, Mkaouar R, Kacem I, Gouider R, Fenniche S, Mrad R, Abdelhak S, Romdhane L. Comorbidity of bathing suit ichthyosis and limb-girdle muscular dystrophy type 2 A in a Tunisian patient revealed by Whole Exome Sequencing. Gene 2024; 900:148127. [PMID: 38181929 DOI: 10.1016/j.gene.2024.148127] [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: 10/31/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024]
Abstract
Elevated rates of consanguinity and inbreeding are responsible for the high prevalence of recessively inherited diseases among inbred populations including Tunisia. In addition, the co-occurrence of two of these conditions, called also comorbidity, within the same individual or in members of the same family are often described in Tunisia which is challenging for diagnosis. The high throughput sequencing has improved the diagnosis of inherited diseases. We report here on a 32-year-old woman born to consanguineous parents. She presented with congenital ichthyosis and muscular dystrophy. She was primarily suspected as suffering from Chanarin-Dorfman syndrome (CDS) with unusual form. Screening of founder mutations allowed only the elucidation of the molecular etiology of Ichthyosis. As the result was inconclusive, Whole Exome Sequencing (WES) was conducted. WES data analysis led to the identification of a mutation in the CAPN3 gene underlying limb-girdle muscular dystrophy type 2A (LGMD2A). Sanger sequencing confirmed the familial segregation of mutations. This work presents the first case worldwide of individual comorbidity of bathing suit ichthyosis and LGMD2A. The co-occurrence of two diseases should be systematically considered when establishing a diagnosis especially in consanguineous populations. WES is a powerful tool for molecular diagnosis in particular for revealing comorbidities and rectifying the diagnosis.
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Affiliation(s)
- Nessrine Mezzi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis El Manar University, 1002 Tunis Belvédère, Tunisia; Department of Biology, Faculty of Sciences of Bizerte, Carthage University, 7021 Jarzouna, Tunisia
| | - Anissa Zaouak
- Habib Thameur Hospital, Dermatology Department, 1008 Tunis, Tunisia
| | - Rahma Mkaouar
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis El Manar University, 1002 Tunis Belvédère, Tunisia
| | - Imen Kacem
- Department of Neurology, LR18SP03, Clinical Investigation Center of Neurosciences and Mental Health, Universitary Hospital Razi-Mannouba, Tunis, Tunisia
| | - Riadh Gouider
- Department of Neurology, LR18SP03, Clinical Investigation Center of Neurosciences and Mental Health, Universitary Hospital Razi-Mannouba, Tunis, Tunisia
| | - Samy Fenniche
- Habib Thameur Hospital, Dermatology Department, 1008 Tunis, Tunisia
| | - Ridha Mrad
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis El Manar University, 1002 Tunis Belvédère, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis El Manar University, 1002 Tunis Belvédère, Tunisia; Department of Biology, Faculty of Sciences of Bizerte, Carthage University, 7021 Jarzouna, Tunisia.
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Jmel H, Sarno S, Giuliani C, Boukhalfa W, Abdelhak S, Luiselli D, Kefi R. Genetic diversity of variants involved in drug response among Tunisian and Italian populations toward personalized medicine. Sci Rep 2024; 14:5842. [PMID: 38462643 PMCID: PMC10925599 DOI: 10.1038/s41598-024-55239-7] [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: 03/01/2023] [Accepted: 02/21/2024] [Indexed: 03/12/2024] Open
Abstract
Adverse drug reactions (ADR) represent a significant contributor to morbidity and mortality, imposing a substantial financial burden. Genetic ancestry plays a crucial role in drug response. The aim of this study is to characterize the genetic variability of selected pharmacogenes involved with ADR in Tunisians and Italians, with a comparative analysis against global populations. A cohort of 135 healthy Tunisians and 737 Italians were genotyped using a SNP array. Variants located in 25 Very Important Pharmacogenes implicated in ADR were extracted from the genotyping data. Distribution analysis of common variants in Tunisian and Italian populations in comparison to 24 publicly available worldwide populations was performed using PLINK and R software. Results from Principle Component and ADMIXTURE analyses showed a high genetic similarity among Mediterranean populations, distinguishing them from Sub-Saharan African and Asian populations. The Fst comparative analysis identified 27 variants exhibiting significant differentiation between the studied populations. Among these variants, four SNPs rs622342, rs3846662, rs7294, rs5215 located in SLC22A1, HMGCR, VKORC1 and KCNJ11 genes respectively, are reported to be associated with ethnic variability in drug responses. In conclusion, correlating the frequencies of genotype risk variants with their associated ADRs would enhance drug outcomes and the implementation of personalized medicine in the studied populations.
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Affiliation(s)
- Haifa Jmel
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Genetic Typing DNA Service Pasteur Institute, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Stefania Sarno
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Wided Boukhalfa
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Donata Luiselli
- Laboratory of Ancient DNA (aDNALab), Department of Cultural Heritage (DBC), University of Bologna, Ravenna, Italy
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia.
- University of Tunis El Manar, Tunis, Tunisia.
- Genetic Typing DNA Service Pasteur Institute, Institut Pasteur de Tunis, Tunis, Tunisia.
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Romdhane L, Kefi S, Mezzi N, Abassi N, Jmel H, Romdhane S, Shan J, Chouchane L, Abdelhak S. Ethnic and functional differentiation of copy number polymorphisms in Tunisian and HapMap population unveils insights on genome organizational plasticity. Sci Rep 2024; 14:4654. [PMID: 38409353 PMCID: PMC10897484 DOI: 10.1038/s41598-024-54749-8] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 02/15/2024] [Indexed: 02/28/2024] Open
Abstract
Admixture mapping has been useful in identifying genetic variations linked to phenotypes, adaptation and diseases. Copy number variations (CNVs) represents genomic structural variants spanning large regions of chromosomes reaching several megabases. In this investigation, the "Canary" algorithm was applied to 102 Tunisian samples and 991 individuals from eleven HapMap III populations to genotype 1279 copy number polymorphisms (CNPs). In this present work, we investigate the Tunisian population structure using the CNP makers previously identified among Tunisian. The study revealed that Sub-Saharan African populations exhibited the highest diversity with the highest proportions of allelic CNPs. Among all the African populations, Tunisia showed the least diversity. Individual ancestry proportions computed using STRUCTURE analysis revealed a major European component among Tunisians with lesser contribution from Sub-Saharan Africa and Asia. Population structure analysis indicated the genetic proximity with Europeans and noticeable distance from the Sub-Saharan African and East Asian clusters. Seven genes harbouring Tunisian high-frequent CNPs were identified known to be associated with 9 Mendelian diseases and/or phenotypes. Functional annotation of genes under selection highlighted a noteworthy enrichment of biological processes to receptor pathway and activity as well as glutathione metabolism. Additionally, pathways of potential concern for health such as drug metabolism, infectious diseases and cancers exhibited significant enrichment. The distinctive genetic makeup of the Tunisians might have been influenced by various factors including natural selection and genetic drift, resulting in the development of distinct genetic variations playing roles in specific biological processes. Our research provides a justification for focusing on the exclusive genome organization of this population and uncovers previously overlooked elements of the genome.
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Affiliation(s)
- Lilia Romdhane
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.
- Department of Biology, Faculty of Sciences of Bizerte, University of Carthage, Zarzouna, Tunisia.
| | - Sameh Kefi
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nessrine Mezzi
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Najla Abassi
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Haifa Jmel
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Safa Romdhane
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Jingxuan Shan
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Education City-Qatar Foundation, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Lotfi Chouchane
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Education City-Qatar Foundation, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Sonia Abdelhak
- Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
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7
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Boujemaa M, Nouira F, Jandoubi N, Mejri N, Bouaziz H, Charfeddine C, Ben Nasr S, Labidi S, El Benna H, Berrazega Y, Rachdi H, Daoud N, Benna F, Haddaoui A, Abdelhak S, Samir Boubaker M, Boussen H, Hamdi Y. Uncovering the clinical relevance of unclassified variants in DNA repair genes: a focus on BRCA negative Tunisian cancer families. Front Genet 2024; 15:1327894. [PMID: 38313678 PMCID: PMC10834681 DOI: 10.3389/fgene.2024.1327894] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/02/2024] [Indexed: 02/06/2024] Open
Abstract
Introduction: Recent advances in sequencing technologies have significantly increased our capability to acquire large amounts of genetic data. However, the clinical relevance of the generated data continues to be challenging particularly with the identification of Variants of Uncertain Significance (VUSs) whose pathogenicity remains unclear. In the current report, we aim to evaluate the clinical relevance and the pathogenicity of VUSs in DNA repair genes among Tunisian breast cancer families. Methods: A total of 67 unsolved breast cancer cases have been investigated. The pathogenicity of VUSs identified within 26 DNA repair genes was assessed using different in silico prediction tools including SIFT, PolyPhen2, Align-GVGD and VarSEAK. Effects on the 3D structure were evaluated using the stability predictor DynaMut and molecular dynamics simulation with NAMD. Family segregation analysis was also performed. Results: Among a total of 37 VUSs identified, 11 variants are likely deleterious affecting ATM, BLM, CHEK2, ERCC3, FANCC, FANCG, MSH2, PMS2 and RAD50 genes. The BLM variant, c.3254dupT, is novel and seems to be associated with increased risk of breast, endometrial and colon cancer. Moreover, c.6115G>A in ATM and c.592+3A>T in CHEK2 were of keen interest identified in families with multiple breast cancer cases and their familial cosegregation with disease has been also confirmed. In addition, functional in silico analyses revealed that the ATM variant may lead to protein immobilization and rigidification thus decreasing its activity. We have also shown that FANCC and FANCG variants may lead to protein destabilization and alteration of the structure compactness which may affect FANCC and FANCG protein activity. Conclusion: Our findings revealed that VUSs in DNA repair genes might be associated with increased cancer risk and highlight the need for variant reclassification for better disease management. This will help to improve the genetic diagnosis and therapeutic strategies of cancer patients not only in Tunisia but also in neighboring countries.
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Affiliation(s)
- Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Fatma Nouira
- Laboratory of Bioactive Substances, Center of Biotechnology of Borj Cedria, University of Tunis El Manar, Hamam, Tunisia
| | - Nouha Jandoubi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nesrine Mejri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Hanen Bouaziz
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Cherine Charfeddine
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- High Institute of Biotechnology of Sidi Thabet, Biotechpole of Sidi Thabet, University of Manouba, Ariana, Tunisia
| | - Sonia Ben Nasr
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Medical Oncology, Military Hospital of Tunis, Tunis, Tunisia
| | - Soumaya Labidi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Houda El Benna
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Yosra Berrazega
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Haifa Rachdi
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Nouha Daoud
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Farouk Benna
- Radiation Oncology Department, Salah Azaiez Institute, Tunis, Tunisia
| | | | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Mohamed Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Hamouda Boussen
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
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Zaouak A, Abdessalem G, Chamli A, Messoud O, Trabelsi M, Fenniche S, Abdelhak S, Hammami H. Coexistence of Ichthyosis, Yellowish Keratoderma, and Neurologic Manifestations: Think About Sjogren-Larsson Syndrome. Skinmed 2023; 21:457-458. [PMID: 38051253] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Affiliation(s)
- Anissa Zaouak
- Department of Dermatology, Habib Thameur Hospital, Tunis, Tunisia
| | - Ghaith Abdessalem
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Amal Chamli
- Department of Dermatology, Habib Thameur Hospital, Tunis, Tunisia
| | - Olfa Messoud
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Mediha Trabelsi
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, Tunisia
| | - Samy Fenniche
- Department of Dermatology, Habib Thameur Hospital, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Houda Hammami
- Department of Dermatology, Habib Thameur Hospital, Tunis, Tunisia
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Fassatoui M, Saffarian A, Mulet C, Jamoussi H, Gamoudi A, Ben Halima Y, Hechmi M, Abdelhak S, Abid A, Sansonetti P, Pedron T, Kefi R. Gut microbiota profile and the influence of nutritional status on bacterial distribution in diabetic and healthy Tunisian subjects. Biosci Rep 2023; 43:BSR20220803. [PMID: 37669144 PMCID: PMC10500226 DOI: 10.1042/bsr20220803] [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: 04/11/2022] [Revised: 06/01/2022] [Accepted: 06/22/2022] [Indexed: 09/07/2023] Open
Abstract
Gut microbiota plays a key role in the regulation of metabolism and immunity. We investigated the profile of gut microbiota and the impact of dietary intake on gut bacterial distribution in diabetic and healthy Tunisian subjects, aiming to identify a dysbiotic condition, hence opening the way to restore eubiosis and facilitate return to health. In the present research, we enrolled 10 type 1 diabetic (T1D), 10 type 2 diabetic (T2D) patients and 13 healthy (H) subjects. Illumina Miseq technology was used to sequence V3-V4 hypervariable regions of bacterial 16SrRNA gene. Data were analyzed referring to QIIME 2 pipeline. RStudio software was used to explore the role of nutrition in gut bacterial distribution. At the phylum level, we identified an imbalanced gut microbiota composition in diabetic patients marked by a decrease in the proportion of Firmicutes and an increase in the abundance of Bacteroidetes compared with H subjects. We observed higher amounts of Fusobacteria and a decline in the levels of TM7 phyla in T1D patients compared with H subjects. However, we revealed a decrease in the proportions of Verrucomicrobia in T2D patients compared with H subjects. At the genus level, T2D subjects were more affected by gut microbiota alteration, showing a reduction in the relative abundance of Faecalibacterium, Akkermansia, Clostridium, Blautia and Oscillibacter, whereas T1D group shows a decrease in the proportion of Blautia. The gut bacteria distribution was mainly affected by fats and carbohydrates consumption. Gut microbiota composition was altered in Tunisian diabetic patients and affected by dietary habits.
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Affiliation(s)
- Meriem Fassatoui
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Campus Universitaire Farhat Hached, Tunis, Tunisia
| | - Azadeh Saffarian
- Unité de Pathogénie Microbienne Moléculaire, INSERM U1202, Institut Pasteur, Paris, France
| | - Céline Mulet
- Unité de Pathogénie Microbienne Moléculaire, INSERM U1202, Institut Pasteur, Paris, France
| | - Henda Jamoussi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Research Unit on Obesity UR18ES01, Faculty of Medicine, University Tunis El Manar, Tunis, Tunisia
| | - Amel Gamoudi
- Department of Nutritional Diseases A. National Institute of Nutrition and Food Technology, Tunis, Tunisia
| | - Yosra Ben Halima
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Meriem Hechmi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Carthage, National Institute of Applied Science and Technology, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Campus Universitaire Farhat Hached, Tunis, Tunisia
| | - Abdelmajid Abid
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Philippe J. Sansonetti
- Unité de Pathogénie Microbienne Moléculaire, INSERM U1202, Institut Pasteur, Paris, France
- Chaire de Microbiologie et Maladies Infectieuses, Collège de France, Paris, France
| | - Thierry Pedron
- Unité de Pathogénie Microbienne Moléculaire, INSERM U1202, Institut Pasteur, Paris, France
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Campus Universitaire Farhat Hached, Tunis, Tunisia
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10
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Kheriji N, Dakhlaoui T, Kamoun Rebai W, Maatoug S, Thabet MT, Mellah T, Mrad M, Trabelsi H, Soltani M, Kabbage M, Hassine HB, Hadj Salah Bahlous A, Mahjoub F, Jamoussi H, Abid A, Abdelhak S, Kefi R. Prevalence and risk factors of diabetes mellitus and hypertension in North East Tunisia calling for efficient and effective actions. Sci Rep 2023; 13:12706. [PMID: 37543635 PMCID: PMC10404238 DOI: 10.1038/s41598-023-39197-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 08/31/2022] [Accepted: 07/21/2023] [Indexed: 08/07/2023] Open
Abstract
Diabetes and hypertension are a serious public health problem worldwide. In the last decades, prevalence of these two metabolic diseases has dramatically increased in the Middle East and North Africa region, especially in Tunisia. This study aimed to determine the prevalence of type 2 diabetes (T2D) and High Blood Pressure (HBP) in Zaghouan, a North-East region of Tunisia. To this end, an exploratory study with stratified random sampling of 420 participants has been carried out. Various data were collected. Blood samples and urine were drawn for biochemical assay. Then, all data were analyzed using the statistical R software. Results showed an alarming situation with an inter-regional difference in prevalence of obesity (50.0%, CI 95.0%), HBP (39.0%, CI 95.0%) and T2D (32.0%, CI 95.0%). This study allowed the discovery of 24, 17 and 2 new cases of T2D, HBP and T2D&HBP respectively. The association of some socio-economic factors and biochemical parameters with these chronic diseases has been highlighted. To conclude, the health situation in the governorate of Zaghouan requires urgent interventions to better manage the growing epidemic of non-communicable diseases (NCD) in the region. This study demonstrated the importance of engaging health policy makers in road mapping and implementing national NCD prevention programs.
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Affiliation(s)
- Nadia Kheriji
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, Belvédère Tunisie, B.P. 74, 1002, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
| | - Thouraya Dakhlaoui
- Regional Association of Diabetics of Zaghouan-Regional Hospital of Zaghouan, Zaghouan, Tunisia
| | - Wafa Kamoun Rebai
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, Belvédère Tunisie, B.P. 74, 1002, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Sonia Maatoug
- University of Tunis El Manar, Tunis, Tunisia
- Science Shop (Communication, Science and Society Unit)"Science Together-العلم مع بعضنا", Institut Pasteur de Tunis, Tunis, Tunisia
| | - Mohamed Taher Thabet
- Regional Association of Diabetics of Zaghouan-Regional Hospital of Zaghouan, Zaghouan, Tunisia
| | - Thouraya Mellah
- Higher School of Digital Economy (ESEN-UMA), University of Manouba, Manouba, Tunisia
- Association La Recherche en Action (REACT), Tunis, Tunisia
| | - Mehdi Mrad
- University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Hajer Trabelsi
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Manel Soltani
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Maria Kabbage
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, Belvédère Tunisie, B.P. 74, 1002, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Hichem Ben Hassine
- University of Tunis El Manar, Tunis, Tunisia
- Science Shop (Communication, Science and Society Unit)"Science Together-العلم مع بعضنا", Institut Pasteur de Tunis, Tunis, Tunisia
| | - Afef Hadj Salah Bahlous
- University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Faten Mahjoub
- University of Tunis El Manar, Tunis, Tunisia
- National Institute of Nutrition & Food Technology of Tunis, Tunis, Tunisia
- Research Unit UR18ES01 on "Obesity", Faculty of Medicine of Tunis, Tunis, Tunisia
| | - Henda Jamoussi
- University of Tunis El Manar, Tunis, Tunisia
- National Institute of Nutrition & Food Technology of Tunis, Tunis, Tunisia
- Research Unit UR18ES01 on "Obesity", Faculty of Medicine of Tunis, Tunis, Tunisia
| | - Abdelmajid Abid
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, Belvédère Tunisie, B.P. 74, 1002, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, Belvédère Tunisie, B.P. 74, 1002, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, Belvédère Tunisie, B.P. 74, 1002, Tunis, Tunisia.
- University of Tunis El Manar, Tunis, Tunisia.
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11
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Khalat N, Messaoud O, Ben Rekaya M, Chargui M, Zghal M, Zendah B, Saqer N, Mokni M, Abdelhak S, Mohamed OA. First genetic characterization of Xeroderma pigmentosum in Libya: High frequency of XP-C founder mutation. Mol Genet Genomic Med 2023:e2158. [PMID: 36812379 DOI: 10.1002/mgg3.2158] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/18/2023] [Accepted: 02/09/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Xeroderma pigmentosum is an autosomal recessive disease characterized by a high sensitivity to UV radiations. The disease is clinically and genetically heterogeneous, thus making accurate early clinical diagnosis difficult. Although the disease is considered rare worldwide, previous studies have shown that it is more frequent in Maghreb countries. So far, no genetic study has been published on Libyan patients, except three reports limited to clinical descriptions. METHODS Our study, which represents the first genetic characterization of XP in Libya, was conducted on 14 unrelated families including 23 Libyan XP patients with a consanguinity rate of 93%. Blood samples were collected from 201 individuals including patients and their relatives. Patients were screened for founder mutations already described in Tunisia. RESULTS The two founder Maghreb XP mutations, XPA p.Arg228* associated with the neurological form and XPC p.Val548Alafs*25 in patients with only cutaneous manifestations, were homozygously identified. The latter was predominant (19 of 23 patients). In addition, another XPC homozygous mutation (p.Arg220*) has been identified in only one patient. For the remaining patient, the absence of founder XPA, XPC, XPD, and XPG mutations suggests mutational heterogeneity of XP in Libya. CONCLUSION Identification of common mutations with other Maghreb populations is in favor of a common ancestor in North-African populations.
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Affiliation(s)
| | - Olfa Messaoud
- Institut Pasteur de Tunis, Biomedical Genomics and Oncogenetics Laboratory, University Tunis El Manar, Tunis, Tunisia
| | - Mariem Ben Rekaya
- Institut Pasteur de Tunis, Biomedical Genomics and Oncogenetics Laboratory, University Tunis El Manar, Tunis, Tunisia
| | - Mariem Chargui
- Institut Pasteur de Tunis, Biomedical Genomics and Oncogenetics Laboratory, University Tunis El Manar, Tunis, Tunisia
| | - Mohamed Zghal
- Dermatology Department, Charles Nicolle Hospital, Tunis, Tunisia
| | - Bashir Zendah
- Dermatology Department, Medical Tripoli Centre (MTC), Tripoli, Libya
| | - Najat Saqer
- Dermatology Department, Central Tripoli Hospital, Tripoli, Libya
| | - Mourad Mokni
- Dermatology Department, La Rabta Hospital, Tunis, Tunisia
| | - Sonia Abdelhak
- Institut Pasteur de Tunis, Biomedical Genomics and Oncogenetics Laboratory, University Tunis El Manar, Tunis, Tunisia
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12
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Mighri N, Mejri N, Boujemaa M, Berrazega Y, Rachdi H, El Benna H, Labidi S, Benna F, Boubaker S, Boussen H, Abdelhak S, Hamdi Y. Association between epidemiological and clinico-pathological features of breast cancer with prognosis, family history, Ki-67 proliferation index and survival in Tunisian breast cancer patients. PLoS One 2022; 17:e0269732. [PMID: 36094928 PMCID: PMC9467370 DOI: 10.1371/journal.pone.0269732] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 05/26/2022] [Indexed: 11/19/2022] Open
Abstract
Breast cancer has different epidemio-clinical characteristics in Middle East and North-African populations compared to those reported in the Western countries. The aim of this study is to analyze the epidemiological and clinico-pathological features of breast cancer in Tunisia and to determine prognostic factors with special interest to family history, Ki-67 proliferation index and comorbidity. We retrospectively reviewed epidemiological and clinico-pathological data from patients’ medical records, treated in the Medical Oncology Department at Abderrahmane Mami Hospital, in the period 2011–2015. Data has been collected on 602 breast cancer patients and analyzed using SPSS software V.23.0. Our study showed high fractions of young breast cancer patients and cases with dense breasts. The most prevalent comorbidities observed in the studied cohort were cardiovascular diseases and diabetes. Familial breast cancer was found in 23.3% of cases and was associated with younger age at diagnosis (p<0.001) and advanced stage (p = 0.015). Ki-67 index >20% was significantly associated with early age at diagnosis, lymph node involvement (p = 0.002), advanced tumor grade (p<0.001) and high risk of relapse (p = 0.007). Ki-67 cut-off 30% predicted survival in luminal cases. Survival was worse in patients with triple negative breast cancer compared to non-triple negative breast cancer, inflammatory breast cancer compared to non-inflammatory breast cancer, moderately to poorly differentiated tumors compared to well-differentiated tumors and with positive lymph nodes compared to pN0 (p<0.05). Our study showed new insights into epidemiological and clinico-pathological characteristics of breast cancer that are not well explored in Tunisian population. Considering our findings along with the implementation of electronic health record system may improve patient health care quality and disease management.
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Affiliation(s)
- Najah Mighri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nesrine Mejri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Yosra Berrazega
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Haifa Rachdi
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Houda El Benna
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Soumaya Labidi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Farouk Benna
- Department of Radiation Oncology, University of Tunis, Tunis, Tunisia
| | - Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Hamouda Boussen
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
- * E-mail:
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Zaouak A, Abdessalem G, Messaoud O, Ebdelli W, Chamli A, Abdelhak S, Hammami H, Fenniche S. When to Recommend a Peripheral Blood Smear to Patients with Congenital Ichthyosiform Erythroderma. Skinmed 2022; 20:305-306. [PMID: 35976023] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A 4-year-old boy born from a consanguineous marriage was referred to our department for congenital ichthyosis. He was a collodion baby at birth and progressively developed a generalized erythroderma with fine whitish scales covering his body. Initially, he was diagnosed as having congenital ichthyosiform erythroderma. Physical examination revealed fine white grayish scales with an erythematous background involving the scalp and flexural areas (Figure 1a). His palms and soles depicted hyperlinearity (Figure 1b). His hair, teeth, nails, and mucosa were normal. Abdominal examination revealed hepatomegaly, and the liver was enlarged by 4 cm below the right costal margin. He had a normal motor and mental development, and his neurologic examination was normal. There was no muscular weakness. (SKINmed. 2022;20:305-306).
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Affiliation(s)
- Anissa Zaouak
- Department of Dermatology, Habib Thameur Hospital, Tunis, Tunisia;
| | - Ghaith Abdessalem
- Research Unit "Genodermatoses and Cancers" LR-12SP03, Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Olfa Messaoud
- Research Unit "Genodermatoses and Cancers" LR-12SP03, Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Wissal Ebdelli
- Department of Dermatology, Habib Thameur Hospital, Tunis, Tunisia
| | - Amal Chamli
- Department of Dermatology, Habib Thameur Hospital, Tunis, Tunisia
| | - Sonia Abdelhak
- Research Unit "Genodermatoses and Cancers" LR-12SP03, Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Houda Hammami
- Department of Dermatology, Habib Thameur Hospital, Tunis, Tunisia
| | - Samy Fenniche
- Department of Dermatology, Habib Thameur Hospital, Tunis, Tunisia
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Chikhaoui A, Jones M, Režen T, Ben Ahmed M, Naouali C, Komel R, Zghal M, Boubaker S, Abdelhak S, Yacoub-Youssef H. Inflammatory landscape in Xeroderma pigmentosum patients with cutaneous melanoma. Sci Rep 2022; 12:13854. [PMID: 35974070 PMCID: PMC9381529 DOI: 10.1038/s41598-022-17928-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 08/02/2022] [Indexed: 11/09/2022] Open
Abstract
Xeroderma pigmentosum (XP) is a DNA repair disease that predisposes to early skin cancers as cutaneous melanoma. Melanoma microenvironment contains inflammatory mediators, which would be interesting biomarkers for the prognosis or for the identification of novel therapeutic targets. We used a PCR array to evaluate the transcriptional pattern of 84 inflammatory genes in melanoma tumors obtained from XP patients (XP-Mel) and in sporadic melanoma (SP-Mel) compared to healthy skin. Commonly expressed inflammatory genes were further explored via GTEx and GEPIA databases. The differentially expressed inflammatory genes in XP were compared to their expression in skin exposed to UVs, and evaluated on the basis of the overall survival outcomes of patients with melanoma. Monocyte subsets of patients with SP-Mel, XP and healthy donors were also assessed. PCR array data revealed that 34 inflammatory genes were under-expressed in XP-Mel compared to SP-Mel. Differentially expressed genes that were common in XP-Mel and SP-Mel were correlated with the transcriptomic datasets from GEPIA and GTEx and highlighted the implication of KLK1 and IL8 in the tumorigenesis. We showed also that in XP-Mel tumors, there was an overexpression of KLK6 and KLK10 genes, which seems to be associated with a bad survival rate. As for the innate immunity, we observed a decrease of intermediate monocytes in patients with SP-Mel and in XP. We highlight an alteration in the immune response in XP patients. We identified candidate biomarkers involved in the tumorigenesis, and in the survival of patients with melanoma. Intermediate monocyte's in patients at risk could be a prognostic biomarker for melanoma outcome.
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Affiliation(s)
- Asma Chikhaoui
- Laboratoire de Génomique Biomédicale Et Oncogénétique (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia.,Université Tunis El Manar, Tunis, Tunisia
| | - Meriem Jones
- Département de Dermatologie, Hôpital Charles Nicolle de Tunis, Tunis, Tunisia
| | - Tadeja Režen
- Faculty of Medicine, Centre for Functional Genomics and Bio-Chips and Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana, Slovenia
| | - Melika Ben Ahmed
- Laboratoire de Transmission, Contrôle Et Immunobiologie de L'infection, LR16IPT02, Institut Pasteur de Tunis Université de Tunis El Manar I, 2092, Tunis, Tunisia
| | - Chokri Naouali
- Laboratoire de Génomique Biomédicale Et Oncogénétique (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia.,Université Tunis El Manar, Tunis, Tunisia
| | - Radovan Komel
- Faculty of Medicine, Centre for Functional Genomics and Bio-Chips and Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana, Slovenia
| | - Mohamed Zghal
- Département de Dermatologie, Hôpital Charles Nicolle de Tunis, Tunis, Tunisia
| | - Samir Boubaker
- Laboratoire de Génomique Biomédicale Et Oncogénétique (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia.,Université Tunis El Manar, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratoire de Génomique Biomédicale Et Oncogénétique (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia.,Université Tunis El Manar, Tunis, Tunisia
| | - Houda Yacoub-Youssef
- Laboratoire de Génomique Biomédicale Et Oncogénétique (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia. .,Université Tunis El Manar, Tunis, Tunisia.
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15
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Kabbage M, Ben Aissa-Haj J, Othman H, Jaballah-Gabteni A, Laarayedh S, Elouej S, Medhioub M, Kettiti HT, Khsiba A, Mahmoudi M, BelFekih H, Maaloul A, Touinsi H, Hamzaoui L, Chelbi E, Abdelhak S, Boubaker MS, Azzouz MM. A Rare MSH2 Variant as a Candidate Marker for Lynch Syndrome II Screening in Tunisia: A Case of Diffuse Gastric Carcinoma. Genes (Basel) 2022; 13:genes13081355. [PMID: 36011265 PMCID: PMC9407052 DOI: 10.3390/genes13081355] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/17/2022] [Accepted: 07/21/2022] [Indexed: 12/24/2022] Open
Abstract
Several syndromic forms of digestive cancers are known to predispose to early-onset gastric tumors such as Hereditary Diffuse Gastric Cancer (HDGC) and Lynch Syndrome (LS). LSII is an extracolonic cancer syndrome characterized by a tumor spectrum including gastric cancer (GC). In the current work, our main aim was to identify the mutational spectrum underlying the genetic predisposition to diffuse gastric tumors occurring in a Tunisian family suspected of both HDGC and LS II syndromes. We selected the index case “JI-021”, which was a woman diagnosed with a Diffuse Gastric Carcinoma and fulfilling the international guidelines for both HDGC and LSII syndromes. For DNA repair, a custom panel targeting 87 candidate genes recovering the four DNA repair pathways was used. Structural bioinformatics analysis was conducted to predict the effect of the revealed variants on the functional properties of the proteins. DNA repair genes panel screening identified two variants: a rare MSH2 c.728G>A classified as a variant with uncertain significance (VUS) and a novel FANCD2 variant c.1879G>T. The structural prediction model of the MSH2 variant and electrostatic potential calculation showed for the first time that MSH2 c.728G>A is likely pathogenic and is involved in the MSH2-MLH1 complex stability. It appears to affect the MSH2-MLH1 complex as well as DNA-complex stability. The c.1879G>T FANCD2 variant was predicted to destabilize the protein structure. Our results showed that the MSH2 p.R243Q variant is likely pathogenic and is involved in the MSH2-MLH1 complex stability, and molecular modeling analysis highlights a putative impact on the binding with MLH1 by disrupting the electrostatic potential, suggesting the revision of its status from VUS to likely pathogenic. This variant seems to be a shared variant in the Mediterranean region. These findings emphasize the importance of testing DNA repair genes for patients diagnosed with diffuse GC with suspicion of LSII and colorectal cancer allowing better clinical surveillance for more personalized medicine.
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Affiliation(s)
- Maria Kabbage
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (J.B.A.-H.); (A.J.-G.); (S.L.); (H.T.K.); (A.M.); (M.S.B.)
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis 1002, Tunisia; (M.M.); (A.K.); (M.M.); (H.B.); (L.H.); (E.C.); (S.A.); (M.M.A.)
- Correspondence:
| | - Jihenne Ben Aissa-Haj
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (J.B.A.-H.); (A.J.-G.); (S.L.); (H.T.K.); (A.M.); (M.S.B.)
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis 1002, Tunisia; (M.M.); (A.K.); (M.M.); (H.B.); (L.H.); (E.C.); (S.A.); (M.M.A.)
| | - Houcemeddine Othman
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg 2000, South Africa;
| | - Amira Jaballah-Gabteni
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (J.B.A.-H.); (A.J.-G.); (S.L.); (H.T.K.); (A.M.); (M.S.B.)
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis 1002, Tunisia; (M.M.); (A.K.); (M.M.); (H.B.); (L.H.); (E.C.); (S.A.); (M.M.A.)
| | - Sarra Laarayedh
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (J.B.A.-H.); (A.J.-G.); (S.L.); (H.T.K.); (A.M.); (M.S.B.)
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis 1002, Tunisia; (M.M.); (A.K.); (M.M.); (H.B.); (L.H.); (E.C.); (S.A.); (M.M.A.)
| | - Sahar Elouej
- Marseille Medical Genetics, Aix Marseille University, INSERM, 13007 Marseille, France;
| | - Mouna Medhioub
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis 1002, Tunisia; (M.M.); (A.K.); (M.M.); (H.B.); (L.H.); (E.C.); (S.A.); (M.M.A.)
- Gastroenterology Department, Mohamed Tahar Maamouri Hospital, Nabeul 8000, Tunisia
| | - Haifa Tounsi Kettiti
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (J.B.A.-H.); (A.J.-G.); (S.L.); (H.T.K.); (A.M.); (M.S.B.)
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis 1002, Tunisia; (M.M.); (A.K.); (M.M.); (H.B.); (L.H.); (E.C.); (S.A.); (M.M.A.)
| | - Amal Khsiba
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis 1002, Tunisia; (M.M.); (A.K.); (M.M.); (H.B.); (L.H.); (E.C.); (S.A.); (M.M.A.)
- Gastroenterology Department, Mohamed Tahar Maamouri Hospital, Nabeul 8000, Tunisia
| | - Moufida Mahmoudi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis 1002, Tunisia; (M.M.); (A.K.); (M.M.); (H.B.); (L.H.); (E.C.); (S.A.); (M.M.A.)
- Gastroenterology Department, Mohamed Tahar Maamouri Hospital, Nabeul 8000, Tunisia
| | - Houda BelFekih
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis 1002, Tunisia; (M.M.); (A.K.); (M.M.); (H.B.); (L.H.); (E.C.); (S.A.); (M.M.A.)
- Department of Oncology, Mohamed Tahar Maamouri Hospital, Nabeul 8000, Tunisia
| | - Afifa Maaloul
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (J.B.A.-H.); (A.J.-G.); (S.L.); (H.T.K.); (A.M.); (M.S.B.)
| | - Hassen Touinsi
- Department of Surgery, Mohamed Tahar Maamouri Hospital, Nabeul 8000, Tunisia;
| | - Lamine Hamzaoui
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis 1002, Tunisia; (M.M.); (A.K.); (M.M.); (H.B.); (L.H.); (E.C.); (S.A.); (M.M.A.)
- Gastroenterology Department, Mohamed Tahar Maamouri Hospital, Nabeul 8000, Tunisia
| | - Emna Chelbi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis 1002, Tunisia; (M.M.); (A.K.); (M.M.); (H.B.); (L.H.); (E.C.); (S.A.); (M.M.A.)
- Department of Pathology, Mohamed Tahar Maamouri Hospital, Nabeul 8000, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis 1002, Tunisia; (M.M.); (A.K.); (M.M.); (H.B.); (L.H.); (E.C.); (S.A.); (M.M.A.)
| | - Mohamed Samir Boubaker
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (J.B.A.-H.); (A.J.-G.); (S.L.); (H.T.K.); (A.M.); (M.S.B.)
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis 1002, Tunisia; (M.M.); (A.K.); (M.M.); (H.B.); (L.H.); (E.C.); (S.A.); (M.M.A.)
| | - Mohamed Mousaddak Azzouz
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis 1002, Tunisia; (M.M.); (A.K.); (M.M.); (H.B.); (L.H.); (E.C.); (S.A.); (M.M.A.)
- Gastroenterology Department, Mohamed Tahar Maamouri Hospital, Nabeul 8000, Tunisia
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Hamdi Y, Mulder N, Abdelhak S. Women in Systems Science and Gender Parity: Why and How to Democratize the "Technology, Innovation, and Society Nexus". OMICS 2022; 26:329-338. [PMID: 35666517 DOI: 10.1089/omi.2022.0055] [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] [Indexed: 06/15/2023]
Abstract
A career in systems science offers exciting prospects as well as challenges around the world, which are often underexplored or unknown. Gender parity, diversity, inclusion, and equity are essential for knowledge production, systems science research, and innovation to be representative, democratic, and critically informed. By virtue of its focus on systems, omics science is ideally poised to understand and respond to systemic and structural issues that hinder gender parity, equity, and democracy in science and society. In this context, voices from women in systems science in resource-limited countries are often inaudible, a gap that this article aims to bridge. We present here some of the pressing issues and possible ways forward for equitable representation of women in science. We highlight emerging frontiers of systems science such as digital transformation, Industry 4.0, and cyber-physical systems where gender parity and equity are crucial. This article also examines some of the challenges faced by women scientists in Africa. All in all, much work is needed across communities and countries worldwide for diversity and gender equity in Science, Technology, Engineering, Mathematics (STEM)-based programs. Adapting a critical lens that examines power asymmetries in STEM in Africa and around the world, and new ways of thinking for bringing women scientists in Africa to leadership positions in traditional STEM fields such as computer science and engineering where large gender equity gaps exist, is a timely and principled necessity in 21st century science and society.
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Affiliation(s)
- Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM University of Cape Town Faculty of Health Sciences, Cape Town, South Africa
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
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Boujemaa M, Mighri N, Chouchane L, Boubaker MS, Abdelhak S, Boussen H, Hamdi Y. Health influenced by genetics: A first comprehensive analysis of breast cancer high and moderate penetrance susceptibility genes in the Tunisian population. PLoS One 2022; 17:e0265638. [PMID: 35333900 PMCID: PMC8956157 DOI: 10.1371/journal.pone.0265638] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/04/2022] [Indexed: 12/03/2022] Open
Abstract
Significant advances have been made to understand the genetic basis of breast cancer. High, moderate and low penetrance variants have been identified with inter-ethnic variability in mutation frequency and spectrum. Genome wide association studies (GWAS) are widely used to identify disease-associated SNPs. Understanding the functional impact of these risk-SNPs will help the translation of GWAS findings into clinical interventions. Here we aim to characterize the genetic patterns of high and moderate penetrance breast cancer susceptibility genes and to assess the functional impact of non-coding SNPs. We analyzed BRCA1/2, PTEN, STK11, TP53, ATM, BRIP1, CHEK2 and PALB2 genotype data obtained from 135 healthy participants genotyped using Affymetrix Genome-Wide Human SNP-Array 6.0. Haplotype analysis was performed using Haploview.V4.2 and PHASE.V2.1. Population structure and genetic differentiation were assessed using principal component analysis (PCA) and fixation index (FST). Functional annotation was performed using In Silico web-based tools including RegulomeDB and VARAdb. Haplotype analysis showed distinct LD patterns with high levels of recombination and haplotype blocks of moderate to small size. Our findings revealed also that the Tunisian population tends to have a mixed origin with European, South Asian and Mexican footprints. Functional annotation allowed the selection of 28 putative regulatory variants. Of special interest were BRCA1_ rs8176318 predicted to alter the binding sites of a tumor suppressor miRNA hsa-miR-149 and PALB2_ rs120963 located in tumorigenesis-associated enhancer and predicted to strongly affect the binding of P53. Significant differences in allele frequencies were observed with populations of African and European ancestries for rs8176318 and rs120963 respectively. Our findings will help to better understand the genetic basis of breast cancer by guiding upcoming genome wide studies in the Tunisian population. Putative functional SNPs may be used to develop an efficient polygenic risk score to predict breast cancer risk leading to better disease prevention and management.
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Affiliation(s)
- Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Najah Mighri
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medicine, New York, New York, United States of America
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, United States of America
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Mohamed Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hamouda Boussen
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
- * E-mail:
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18
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Chikhaoui A, Kraoua I, Calmels N, Bouchoucha S, Obringer C, Zayoud K, Montagne B, M’rad R, Abdelhak S, Laugel V, Ricchetti M, Turki I, Yacoub-Youssef H. Heterogeneous clinical features in Cockayne syndrome patients and siblings carrying the same CSA mutations. Orphanet J Rare Dis 2022; 17:121. [PMID: 35248096 PMCID: PMC8898519 DOI: 10.1186/s13023-022-02257-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 02/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background Cockayne syndrome (CS) is a rare autosomal recessive disorder caused by mutations in ERCC6/CSB or ERCC8/CSA that participate in the transcription-coupled nucleotide excision repair (TC-NER) of UV-induced DNA damage. CS patients display a large heterogeneity of clinical symptoms and severities, the reason of which is not fully understood, and that cannot be anticipated in the diagnostic phase. In addition, little data is available for affected siblings, and this disease is largely undiagnosed in North Africa. Methods We report here the clinical description as well as genetic and functional characterization of eight Tunisian CS patients, including siblings. These patients, who belonged to six unrelated families, underwent complete clinical examination and biochemical analyses. Sanger sequencing was performed for the recurrent mutation in five families, and targeted gene sequencing was done for one patient of the sixth family. We also performed Recovery RNA Synthesis (RRS) to confirm the functional impairment of DNA repair in patient-derived fibroblasts. Results Six out of eight patients carried a homozygous indel mutation (c.598_600delinsAA) in exon 7 of ERCC8, and displayed a variable clinical spectrum including between siblings sharing the same mutation. The other two patients were siblings who carried a homozygous splice-site variant in ERCC8 (c.843+1G>C). This last pair presented more severe clinical manifestations, which are rarely associated with CSA mutations, leading to gastrostomy and hepatic damage. Impaired TC-NER was confirmed by RRS in six tested patients. Conclusions This study provides the first deep characterization of case series of CS patients carrying CSA mutations in North Africa. These mutations have been described only in this region and in the Middle-East. We also provide the largest characterization of multiple unrelated patients, as well as siblings, carrying the same mutation, providing a framework for dissecting elusive genotype–phenotype correlations in CS. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02257-1.
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Ben Aissa-Haj J, Kabbage M, Othmen H, Saulnier P, Kettiti HT, Jaballah-Gabteni A, Ferah A, Medhioub M, Khsiba A, Mahmoudi M, Maaloul A, Ben Nasr S, Chelbi E, Abdelhak S, Boubaker MS, Azzouz MM, Rouleau E. CDH1 Germline Variants in a Tunisian Cohort with Hereditary Diffuse Gastric Carcinoma. Genes (Basel) 2022; 13:genes13030400. [PMID: 35327954 PMCID: PMC8950196 DOI: 10.3390/genes13030400] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 12/24/2022] Open
Abstract
Mutational screening of the CDH1 gene is a standard treatment for patients who fulfill Hereditary Diffuse Gastric Cancer (HDGC) testing criteria. In this framework, the classification of variants found in this gene is a crucial step for the clinical management of patients at high risk for HDGC. The aim of our study was to identify CDH1 as well as CTNNA1 mutational profiles predisposing to HDGC in Tunisia. Thirty-four cases were included for this purpose. We performed Sanger sequencing for the entire coding region of both genes and MLPA (Multiplex Ligation Probe Amplification) assays to investigate large rearrangements of the CDH1 gene. As a result, three cases, all with the HDGC inclusion criteria (8.82% of the entire cohort), carried pathogenic and likely pathogenic variants of the CDH1 gene. These variants involve a novel splicing alteration, a missense c.2281G > A detected by Sanger sequencing, and a large rearrangement detected by MLPA. No pathogenic CTNNA1 variants were found. The large rearrangement is clearly pathogenic, implicating a large deletion of two exons. The novel splicing variant creates a cryptic site. The missense variant is a VUS (Variant with Uncertain Significance). With ACMG (American College of Medical Genetics and Genomics) classification and the evidence available, we thus suggest a revision of its status to likely pathogenic. Further functional studies or cosegregation analysis should be performed to confirm its pathogenicity. In addition, molecular exploration will be needed to understand the etiology of the other CDH1- and CTNNA1-negative cases fulfilling the HDGC inclusion criteria.
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Affiliation(s)
- Jihenne Ben Aissa-Haj
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (M.K.); (H.T.K.); (A.J.-G.); (A.M.); (M.S.B.)
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia;
- Correspondence:
| | - Maria Kabbage
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (M.K.); (H.T.K.); (A.J.-G.); (A.M.); (M.S.B.)
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia;
| | - Houcemeddine Othmen
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg 2000, South Africa;
| | - Patrick Saulnier
- Genomic Platform Molecular Biopathology Unit, URA3655 Inserm, US23 CNRS, Gustave Roussy, 94805 Villejuif, France;
| | - Haifa Tounsi Kettiti
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (M.K.); (H.T.K.); (A.J.-G.); (A.M.); (M.S.B.)
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia;
| | - Amira Jaballah-Gabteni
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (M.K.); (H.T.K.); (A.J.-G.); (A.M.); (M.S.B.)
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia;
| | - Azer Ferah
- Laboratory of Venoms and Therapeutic Biomolecules, LR16IPT08 Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia;
| | - Mouna Medhioub
- Gastroenterology Department, Mohamed Tahar Maamouri Hospital, Nabeul 8000, Tunisia; (M.M.); (A.K.); (M.M.); (M.M.A.)
- Faculty of Medicine Tunis, University of Tunis El Manar, Tunis 1068, Tunisia
| | - Amal Khsiba
- Gastroenterology Department, Mohamed Tahar Maamouri Hospital, Nabeul 8000, Tunisia; (M.M.); (A.K.); (M.M.); (M.M.A.)
- Faculty of Medicine Tunis, University of Tunis El Manar, Tunis 1068, Tunisia
| | - Moufida Mahmoudi
- Gastroenterology Department, Mohamed Tahar Maamouri Hospital, Nabeul 8000, Tunisia; (M.M.); (A.K.); (M.M.); (M.M.A.)
- Faculty of Medicine Tunis, University of Tunis El Manar, Tunis 1068, Tunisia
| | - Afifa Maaloul
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (M.K.); (H.T.K.); (A.J.-G.); (A.M.); (M.S.B.)
| | - Sonia Ben Nasr
- Oncology Department, Military Hospital of Tunis, Tunis 1008, Tunisia;
| | - Emna Chelbi
- Department of Pathology, Mohamed Tahar Maamouri Hospital, Nabeul 8000, Tunisia;
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia;
| | - M. Samir Boubaker
- Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia; (M.K.); (H.T.K.); (A.J.-G.); (A.M.); (M.S.B.)
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia;
| | - Mohamed Mousaddak Azzouz
- Gastroenterology Department, Mohamed Tahar Maamouri Hospital, Nabeul 8000, Tunisia; (M.M.); (A.K.); (M.M.); (M.M.A.)
- Faculty of Medicine Tunis, University of Tunis El Manar, Tunis 1068, Tunisia
| | - Etienne Rouleau
- Department of Biology and Pathology-Cancer Genetics Laboratory-Gustave Roussy, 94805 Villejuif, France;
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20
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Jaouadi H, Chabrak S, Lahbib S, Abdelhak S, Zaffran S. Identification of two variants in
AGRN
and
RPL3L
genes in a patient with catecholaminergic polymorphic ventricular tachycardia suggesting new candidate disease genes and digenic inheritance. Clin Case Rep 2022; 10:e05339. [PMID: 35341025 PMCID: PMC8858789 DOI: 10.1002/ccr3.5339] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/03/2022] [Accepted: 01/14/2022] [Indexed: 11/30/2022] Open
Abstract
Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an arrhythmogenic syndrome characterized by life‐threatening arrhythmias, a normal resting electrocardiogram and the absence of overt structural heart abnormalities. Mutations in RyR2 gene account for the large part of CPVT cases. Less frequently, mutations in CASQ2 gene have been linked to the recessive form of the disease. Overall, approximately 35% of CPVT patients remain without a genetic etiology implying that other genes might be found causative of the disease. Here, we present a 6‐year‐old boy born to first‐degree related parents, with a typical phenotype of CPVT and a family history of sudden cardiac death of his brother at 7 years. A trio‐based whole exome sequencing was performed, and we identified a homozygous variant in AGRN gene and a heterozygous variant in RPL3L gene. We hypothesized that the presence of the homozygous variant in AGRN accounts for the CPVT phenotype in this family and the heterozygous variant in RPL3L gene may act as a modifier gene. Further studies are needed to determine the role of these genes in CPVT.
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Affiliation(s)
- Hager Jaouadi
- Biomedical Genomics and Oncogenetics Laboratory LR16IPT05 Institut Pasteur de Tunis Tunis Tunisia
- Aix Marseille Université INSERM, Marseille Medical Genetics Marseille France
| | - Sonia Chabrak
- Faculty of Medicine of Tunis Université Tunis El Manar Tunis Tunisia
| | - Saida Lahbib
- Biomedical Genomics and Oncogenetics Laboratory LR16IPT05 Institut Pasteur de Tunis Tunis Tunisia
| | - Sonia Abdelhak
- Biomedical Genomics and Oncogenetics Laboratory LR16IPT05 Institut Pasteur de Tunis Tunis Tunisia
| | - Stéphane Zaffran
- Aix Marseille Université INSERM, Marseille Medical Genetics Marseille France
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21
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Dallali H, Hechmi M, Morjane I, Elouej S, Jmel H, Ben Halima Y, Abid A, Bahlous A, Barakat A, Jamoussi H, Abdelhak S, Kefi R. Association of HNF1A gene variants and haplotypes with metabolic syndrome: a case-control study in the Tunisian population and a meta-analysis. Diabetol Metab Syndr 2022; 14:25. [PMID: 35109885 PMCID: PMC8812021 DOI: 10.1186/s13098-022-00794-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/15/2022] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Variants in the Hepatocyte Nuclear Factor 1 Alpha gene (HNF1A) are associated with lipoproteins levels and type 2 diabetes. In this study, we aimed to assess the association of HNF1A gene and haplotypes with the metabolic syndrome (MetS) and its components through an association study in the Tunisian population as well as by a meta-analysis. METHODS A total of 594 Tunisian individuals were genotyped for three variants (rs1169288, rs2464196 and rs735396) located in HNF1A gene using KASPar technology. Statistical analyses were performed with R software. The association was furthermore evaluated through a meta-analysis of our results with those obtained in a Moroccan population. RESULTS Our results showed no association between HNF1A variants and MetS in the Tunisian population. However, a significant association was observed between the variant rs735396 and a higher waist circumference. The stratified analysis according to the sex highlighted a significant association between the variant rs1169288 and high cholesterol levels only in women. Similarly, Haplotype analysis showed an association between the HNF1A minor haplotype and high total cholesterol mainly in women. Finally, our meta-analysis showed no association between HNF1A variants and MetS. CONCLUSIONS Our findings exclude the involvement of the three HNF1A variants rs1169288, rs2464196 and rs735396 in the susceptibility to MetS in our studied Tunisian population but emphasize the role of these variants in the cholesterol homeostasis with sex-specific differences, which may serve to rise clinical consideration to early statin therapy in women carrying these genetic variants.
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Affiliation(s)
- Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, BP 74, 13 Place Pasteur, Belvedere, 1002, Tunis, Tunisia
| | - Meriem Hechmi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, BP 74, 13 Place Pasteur, Belvedere, 1002, Tunis, Tunisia
- University of Carthage, National Institute of Applied Science and Technology, Tunis, Tunisia
| | - Imane Morjane
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, Place Louis Pasteur, Casablanca, Morocco
| | - Sahar Elouej
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, BP 74, 13 Place Pasteur, Belvedere, 1002, Tunis, Tunisia
| | - Haifa Jmel
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, BP 74, 13 Place Pasteur, Belvedere, 1002, Tunis, Tunisia
| | - Yosra Ben Halima
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, BP 74, 13 Place Pasteur, Belvedere, 1002, Tunis, Tunisia
| | - Abdelmajid Abid
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, BP 74, 13 Place Pasteur, Belvedere, 1002, Tunis, Tunisia
- National Institute of Nutrition and Food Technology, 11 rue Jebel Lakhdar, Bab Saadoun, 1007, Tunis, Tunisia
| | - Afef Bahlous
- Central Laboratory of Medical Biology, Institut Pasteur in Tunis, 13 Place Pasteur, BP 74, 1002, Tunis, Tunisia
| | - Abdelhamid Barakat
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, Place Louis Pasteur, Casablanca, Morocco
| | - Henda Jamoussi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, BP 74, 13 Place Pasteur, Belvedere, 1002, Tunis, Tunisia
- National Institute of Nutrition and Food Technology, 11 rue Jebel Lakhdar, Bab Saadoun, 1007, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, BP 74, 13 Place Pasteur, Belvedere, 1002, Tunis, Tunisia
- University of Tunis El Manar, 2092, El Manar I Tunis, Tunisia
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, BP 74, 13 Place Pasteur, Belvedere, 1002, Tunis, Tunisia.
- University of Tunis El Manar, 2092, El Manar I Tunis, Tunisia.
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22
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Mezzi N, Messaoud O, Mkaouar R, Zitouna N, Romdhane S, Abdessalem G, Charfeddine C, Maazoul F, Ouerteni I, Hamdi Y, Zaouak A, Mrad R, Abdelhak S, Romdhane L. Spectrum of Genetic Diseases in Tunisia: Current Situation and Main Milestones Achieved. Genes (Basel) 2021; 12:1820. [PMID: 34828426 PMCID: PMC8617973 DOI: 10.3390/genes12111820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/30/2021] [Accepted: 11/03/2021] [Indexed: 02/06/2023] Open
Abstract
Genetic diseases in Tunisia are a real public health problem given their chronicity and the lack of knowledge concerning their prevalence and etiology, and the high rates of consanguinity. Hence, we performed systematic reviews of the literature in order to provide a more recent spectrum of these disorders and to expose the challenges that still exist to tackle these kinds of diseases. A manual textual data mining was conducted using MeSH and PubMed databases. Collected data were classified according to the CIM-10 classification and the transmission mode. The spectrum of these diseases is estimated to be 589 entities. This suggests remarkable progress through the development of biomedical health research activities and building capacities. Sixty percent of the reported disorders are autosomal recessive, which could be explained by the high prevalence of endogamous mating. Congenital malformations (29.54%) are the major disease group, followed by metabolic diseases (22%). Sixty percent of the genetic diseases have a known molecular etiology. We also reported additional cases of comorbidity that seem to be a common phenomenon in our population. We also noticed that epidemiological data are scarce. Newborn and carrier screening was only limited to pilot projects for a few genetic diseases. Collected data are being integrated into a database under construction that will be a valuable decision-making tool. This study provides the current situation of genetic diseases in Tunisia and highlights their particularities. Early detection of the disease is important to initiate critical intervention and to reduce morbidity and mortality.
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Affiliation(s)
- Nessrine Mezzi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
- Department of Biology, Faculty of Sciences of Bizerte, Université Tunis Carthage, Jarzouna 7021, Tunisia
| | - Olfa Messaoud
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Rahma Mkaouar
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Nadia Zitouna
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Safa Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Ghaith Abdessalem
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Cherine Charfeddine
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
- High Institute of Biotechnology of Sidi Thabet, Biotechpole of Sidi Thabet, University of Manouba, Ariana 2080, Tunisia
| | - Faouzi Maazoul
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis 1002, Tunisia
| | - Ines Ouerteni
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis 1002, Tunisia
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Anissa Zaouak
- Department of Dermatology, Research Unit Genodermatosis and Cancer LR12SP03, Habib Thameur Hospital, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Ridha Mrad
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis 1002, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis 1002, Tunisia
- Department of Biology, Faculty of Sciences of Bizerte, Université Tunis Carthage, Jarzouna 7021, Tunisia
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23
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Charfeddine C, Laroussi N, Mkaouar R, Jouini R, Khayat O, Redissi A, Mosbah A, Dallali H, Chedly Debbiche A, Zaouak A, Fenniche S, Abdelhak S, Hammami-Ghorbel H. Expanding the clinical phenotype associated with NIPAL4 mutation: Study of a Tunisian consanguineous family with erythrokeratodermia variabilis-Like Autosomal Recessive Congenital Ichthyosis. PLoS One 2021; 16:e0258777. [PMID: 34669720 PMCID: PMC8528321 DOI: 10.1371/journal.pone.0258777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 10/05/2021] [Indexed: 11/19/2022] Open
Abstract
Erythrokeratodermia variabilis (EKV) is a rare disorder of cornification usually associated with dominant mutations in the GJB3 and GJB4 genes encoding connexins (Cx)31 and 30.3. Genetic heterogeneity of EKV has already been suggested. We investigated at the clinical and genetic level a consanguineous Tunisian family with 2 sisters presenting an autosomal recessive form of EKV to better characterize this disease. Mutational analysis initially screened the connexin genes and Whole-exome sequencing (WES) was performed to identify the molecular aetiology of the particular EKV phenotype in the proband. Migratory shaped erythematous areas are the initial presenting sign followed by relatively stable hyperkeratotic plaques are the two predominates characteristics in both patients. However, remarkable variability of morphological and dominating features of the disease were observed between patients. In particular, the younger sister (proband) exhibited ichthyosiform-like appearance suggesting Autosomal Recessive Congenital Ichthyosis (ARCI) condition. No causative mutations were detected in the GJB3 and GJB4 genes. WES results revealed a novel missense homozygous mutation in NIPAL4 gene (c.835C>G, p.Pro279Ala) in both patients. This variant is predicted to be likely pathogenic. In addition, in silico analysis of the mutated 3D domain structure predicted that this variant would result in NIPA4 protein destabilization and Mg2+ transport perturbation, pointing out the potential role of NIPAL4 gene in the development and maintenance of the barrier function of the epidermis. Taken togheter, these results expand the clinical phenotype associated with NIPAL4 mutation and reinforce our hypothesis of NIPAL4 as the main candidate gene for the EKV-like ARCI phenotype.
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Affiliation(s)
- Cherine Charfeddine
- University Tunis El Manar, Institut Pasteur de Tunis, Biomedical Genomics and Oncogenetics Laboratory, LR20IPT05, Tunis, Tunisia
- Université de la Manouba, Institut de Biotechnologie de Sidi Thabet, Ariana, Tunisia
- * E-mail:
| | - Nadia Laroussi
- University Tunis El Manar, Institut Pasteur de Tunis, Biomedical Genomics and Oncogenetics Laboratory, LR20IPT05, Tunis, Tunisia
| | - Rahma Mkaouar
- University Tunis El Manar, Institut Pasteur de Tunis, Biomedical Genomics and Oncogenetics Laboratory, LR20IPT05, Tunis, Tunisia
| | - Raja Jouini
- Department of Pathology, Habib Thameur Hospital, Tunis, Tunisia
| | - Olfa Khayat
- Department of Pathology, Habib Thameur Hospital, Tunis, Tunisia
| | - Aladin Redissi
- BVBGR-LR11ES31, ISBST, Université de la Manouba, Institut de Biotechnologie de Sidi Thabet, Ariana, Tunisia
| | - Amor Mosbah
- BVBGR-LR11ES31, ISBST, Université de la Manouba, Institut de Biotechnologie de Sidi Thabet, Ariana, Tunisia
| | - Hamza Dallali
- University Tunis El Manar, Institut Pasteur de Tunis, Biomedical Genomics and Oncogenetics Laboratory, LR20IPT05, Tunis, Tunisia
| | | | - Anissa Zaouak
- Department of Dermatology, Genodermatosis and Cancers Laboratory LR12SP03, Habib Thameur Hospital, Tunis, Tunisia
| | - Sami Fenniche
- Department of Dermatology, Genodermatosis and Cancers Laboratory LR12SP03, Habib Thameur Hospital, Tunis, Tunisia
| | - Sonia Abdelhak
- University Tunis El Manar, Institut Pasteur de Tunis, Biomedical Genomics and Oncogenetics Laboratory, LR20IPT05, Tunis, Tunisia
| | - Houda Hammami-Ghorbel
- Department of Dermatology, Genodermatosis and Cancers Laboratory LR12SP03, Habib Thameur Hospital, Tunis, Tunisia
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24
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Dallali H, Kheriji N, Kammoun W, Mrad M, Soltani M, Trabelsi H, Hamdi W, Bahlous A, Ben Ahmed M, Mahjoub F, Jamoussi H, Abdelhak S, Kefi R. Multiallelic Rare Variants in BBS Genes Support an Oligogenic Ciliopathy in a Non-obese Juvenile-Onset Syndromic Diabetic Patient: A Case Report. Front Genet 2021; 12:664963. [PMID: 34691137 PMCID: PMC8526562 DOI: 10.3389/fgene.2021.664963] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 08/31/2021] [Indexed: 01/28/2023] Open
Abstract
Juvenile-onset diabetes may occur in the context of a rare syndromic presentation, suggesting a monogenic etiology rather than a common multifactorial diabetes. In the present study, we report the case of a young diabetic Tunisian patient presenting learning problems, speech deficits, short stature, brachydactyly, and a normal weight. Whole exome sequencing analysis revealed five heterozygous genetic variants in BBS1, BBS4, BBS8, MKS1, and CEP290. These genes are involved in the regulation of cilium biogenesis and function. We analyzed variant combinations pathogenicity using the recently developed ORVAL tool, and we hypothesized that cumulative synergetic effects of these variants could explain the syndromic phenotype observed in our patient. Therefore, our investigation suggested a genetic diagnosis of Bardet-Biedl syndrome with an oligogenic inheritance pattern rather than a monogenic diabetes. Although there is no curative therapy for this ciliopathy at the moment, a genetic diagnosis may offer other supportive care options, including the prevention of other possible clinical manifestations of this syndrome, mainly renal abnormalities, obesity, liver fibrosis, and hypertension, as well as the genetic counseling for family members.
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Affiliation(s)
- Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, Tunis, Tunisia
| | - Nadia Kheriji
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, Tunis, Tunisia
| | - Wafa Kammoun
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, Tunis, Tunisia
| | - Mehdi Mrad
- Central Laboratory of Medical Biology, Institut Pasteur in Tunis, Tunis, Tunisia
| | - Manel Soltani
- Central Laboratory of Medical Biology, Institut Pasteur in Tunis, Tunis, Tunisia
| | - Hajer Trabelsi
- Central Laboratory of Medical Biology, Institut Pasteur in Tunis, Tunis, Tunisia
| | - Walid Hamdi
- Laboratory of Transmission, Control and Immunobiology of Infections, Institut Pasteur in Tunis, Tunis, Tunisia
| | - Afef Bahlous
- Central Laboratory of Medical Biology, Institut Pasteur in Tunis, Tunis, Tunisia
| | - Melika Ben Ahmed
- Laboratory of Transmission, Control and Immunobiology of Infections, Institut Pasteur in Tunis, Tunis, Tunisia
| | - Faten Mahjoub
- Research Unit on Obesity, National Institute of Nutrition and Food Technology, Tunis, Tunisia
| | - Henda Jamoussi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, Tunis, Tunisia
- Research Unit on Obesity, National Institute of Nutrition and Food Technology, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur in Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
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25
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Mkaouar R, Abdallah LCB, Naouali C, Lahbib S, Turki Z, Elouej S, Bouyacoub Y, Somai M, Mcelreavey K, Bashamboo A, Abdelhak S, Messaoud O. Oligogenic Inheritance Underlying Incomplete Penetrance of PROKR2 Mutations in Hypogonadotropic Hypogonadism. Front Genet 2021; 12:665174. [PMID: 34539727 PMCID: PMC8446458 DOI: 10.3389/fgene.2021.665174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 07/05/2021] [Indexed: 11/17/2022] Open
Abstract
The role of the prokineticin 2 pathway in human reproduction, olfactory bulb morphogenesis, and gonadotropin-releasing hormone secretion is well established. Recent studies have highlighted the implication of di/oligogenic inheritance in this disorder. In the present study, we aimed to identify the genetic mechanisms that could explain incomplete penetrance in hypogonadotropic hypogonadism (HH). This study involved two unrelated Tunisian patients with HH, which was triggered by identifying a homozygous p.(Pro290Ser) mutation in the PROKR2 gene in a girl (HH1) with Kallmann syndrome (KS). The functional effect of this variant has previously been well demonstrated. Unexpectedly, her unaffected father (HH1P) and brother (HH1F) also carried this genetic variation at a homozygous state. In the second family, we identified a heterozygous p.(Lys205del) mutation in PROKR2, both in a male patient with normosmic idiopathic IHH (HH12) and his asymptomatic mother. Whole-exome sequencing in the three HH1 family members allowed the identification of additional variants in the prioritized genes. We then carried out digenic combination predictions using the oligogenic resource for variant analysis (ORVAL) software. For HH1, we found the highest number of disease-causing variant pairs. Notably, a CCDC141 variant (c.2803C > T) was involved in 18 pathogenic digenic combinations. The CCDC141 variant acts in an autosomal recessive inheritance mode, based on the digenic effect prediction data. For the second patient (HH12), prediction by ORVAL allowed the identification of an interesting pathogenic digenic combination between DUSP6 and SEMA7A genes, predicted as “dual molecular diagnosis.” The SEMA7A variant p.(Glu436Lys) is novel and predicted as a VUS by Varsome. Sanger validation revealed the absence of this variant in the healthy mother. We hypothesize that disease expression in HH12 could be induced by the digenic transmission of the SEMA7A and DUSP6 variants or a monogenic inheritance involving only the SEMA7A VUS if further functional assays allow its reclassification into pathogenic. Our findings confirm that homozygous loss-of-function genetic variations are insufficient to cause KS, and that oligogenism is most likely the main transmission mode involved in Congenital Hypogonadotropic Hypogonadism.
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Affiliation(s)
- Rahma Mkaouar
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Tunis, Tunisia.,Faculté des Sciences Mathématiques, Physiques et Naturelles de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | | | - Chokri Naouali
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Saida Lahbib
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Zinet Turki
- Département d'Endocrinologie et de Technologie Alimentaire, Institut de Nutrition, Tunis, Tunisia
| | - Sahar Elouej
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Yosra Bouyacoub
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Maali Somai
- Département d'Endocrinologie et de Technologie Alimentaire, Institut de Nutrition, Tunis, Tunisia
| | | | - Anu Bashamboo
- Génétique du Développement Humain, Institut Pasteur, Paris, France
| | - Sonia Abdelhak
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Olfa Messaoud
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Tunis, Tunisia
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26
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Hamdi Y, Mighri N, Boujemaa M, Mejri N, Ben Nasr S, Ben Rekaya M, Messaoud O, Bouaziz H, Berrazega Y, Rachdi H, Jaidane O, Daoud N, Zribi A, Ayari J, El Benna H, Labidi S, Ben Hassouna J, Haddaoui A, Rahal K, Benna F, Mrad R, Ben Ahmed S, Boussen H, Boubaker S, Abdelhak S. Identification of Eleven Novel BRCA Mutations in Tunisia: Impact on the Clinical Management of BRCA Related Cancers. Front Oncol 2021; 11:674965. [PMID: 34490083 PMCID: PMC8417726 DOI: 10.3389/fonc.2021.674965] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/27/2021] [Indexed: 12/20/2022] Open
Abstract
Background Breast cancer is the world's most common cancer among women. It is becoming an increasingly urgent problem in low- and middle-income countries (LMICs) where a large fraction of women is diagnosed with advanced-stage disease and have no access to treatment or basic palliative care. About 5-10% of all breast cancers can be attributed to hereditary genetic components and up to 25% of familial cases are due to mutations in BRCA1/2 genes. Since their discovery in 1994 and 1995, as few as 18 mutations have been identified in BRCA genes in the Tunisian population. The aim of this study is to identify additional BRCA mutations, to estimate their contribution to the hereditary breast and ovarian cancers in Tunisia and to investigate the clinicopathological signatures associated with BRCA mutations. Methods A total of 354 patients diagnosed with breast and ovarian cancers, including 5 male breast cancer cases, have been investigated for BRCA1/2 mutations using traditional and/or next generation sequencing technologies. Clinicopathological signatures associated with BRCA mutations have also been investigated. Results In the current study, 16 distinct mutations were detected: 10 in BRCA1 and 6 in BRCA2, of which 11 are described for the first time in Tunisia including 3 variations that have not been reported previously in public databases namely BRCA1_c.915T>A; BRCA2_c.-227-?_7805+? and BRCA2_c.249delG. Early age at onset, family history of ovarian cancer and high tumor grade were significantly associated with BRCA status. BRCA1 carriers were more likely to be triple negative breast cancer compared to BRCA2 carriers. A relatively high frequency of contralateral breast cancer and ovarian cancer occurrence was observed among BRCA carriers and was more frequent in patients carrying BRCA1 mutations. Conclusion Our study provides new insights into breast and ovarian cancer genetic landscape in the under-represented North African populations. The prevalence assessment of novel and recurrent BRCA1/2 pathogenic mutations will enhance the use of personalized treatment and precise screening strategies by both affected and unaffected North African cancer cases.
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Affiliation(s)
- Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Najah Mighri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nesrine Mejri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Sonia Ben Nasr
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Department of Medical Oncology, Military Hospital of Tunis, Tunis, Tunisia
| | - Mariem Ben Rekaya
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,UR17ES15, Oncotheranostic Biomarkers, Faculty of Medicine of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Olfa Messaoud
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hanen Bouaziz
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Yosra Berrazega
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Haifa Rachdi
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Olfa Jaidane
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Nouha Daoud
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Aref Zribi
- Department of Medical Oncology, Military Hospital of Tunis, Tunis, Tunisia
| | - Jihene Ayari
- Department of Medical Oncology, Military Hospital of Tunis, Tunis, Tunisia
| | - Houda El Benna
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Soumaya Labidi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Jamel Ben Hassouna
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | | | - Khaled Rahal
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Farouk Benna
- Department of Radiation Oncology, University of Tunis, Tunis, Tunisia
| | - Ridha Mrad
- Department of Human Genetics, Charles Nicolle Hospital, Tunis, Tunisia
| | - Slim Ben Ahmed
- Faculty of Medicine of Sousse Department of Medical Oncology Farhat Hached University Hospital University of Sousse, Sousse, Tunisia
| | - Hamouda Boussen
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
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27
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Hamdi Y, Boujemaa M, Mighri N, Mejri N, Jaidane O, Ben Nasr S, Bouaziz H, Hassouna JB, Zribi A, Berrazaga Y, Rachdi H, Daoud N, El Benna H, Labidi S, Haddaoui A, Rahal K, Benna F, Boussen H, Abdelhak S, Boubaker S. Identification of BRCA2 Cis Double Heterozygous Breast Cancer Cases Using Whole Exome Sequencing: Phenotypic Expression and Impact on Personalized Oncology. Front Genet 2021; 12:674990. [PMID: 34456966 PMCID: PMC8397457 DOI: 10.3389/fgene.2021.674990] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 07/08/2021] [Indexed: 12/24/2022] Open
Abstract
BRCA1 and BRCA2 are the most commonly mutated breast cancer susceptibility genes that convey a high risk of breast and ovarian cancer. Most BRCA1 or BRCA2 mutation carriers have inherited a single heterozygous mutation. In recent years, very rare cases with biallelic or trans double heterozygous mutations on BRCA1 and or BRCA2 have been identified and seem to be associated with distinctive phenotypes. Given that this genotype-phenotype correlation in cancer predisposing hereditary conditions is of relevance for oncological prevention and genetic testing, it is important to investigate these rare BRCA genotypes for better clinical management of BRCA mutation carriers. Here we present the first report on Cis double heterozygosity (Cis DH) on BRCA2 gene identified using Whole exome sequencing (WES) in a Tunisian family with two BRCA2 mutations namely: c.632-1G>A and c.1310_1313DelAAGA that are both reported as pathogenic in ClinVar database. Subsequent analysis in 300 high-risk Tunisian breast cancer families detected this Cis double heterozygous genotype in 8 additional individuals belonging to 5 families from the same geographic origin suggesting a founder effect. Moreover, the observed Cis DH seems to be associated with an early age of onset (mean age = 35.33 years) and severe phenotype of the disease with high breast cancer grade and multiple cancer cases in the family. The identification of unusual BRCA genotypes in this Tunisian cohort highlights the importance of performing genetic studies in under-investigated populations. This will also potentially help avoiding erroneous classifications of genetic variants in African population and therefore avoiding clinical misdiagnosis of BRCA related cancers. Our findings will also have an impact on the genetic testing and the clinical management of North African breast cancer patients as well as patients from different other ethnic groups in regard to several emerging target therapies such as PARP inhibitors.
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Affiliation(s)
- Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Najah Mighri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nesrine Mejri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Olfa Jaidane
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Sonia Ben Nasr
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Department of Medical Oncology, Military Hospital, Tunis, Tunisia
| | - Hanen Bouaziz
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Jamel Ben Hassouna
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Aref Zribi
- Department of Medical Oncology, Military Hospital, Tunis, Tunisia
| | - Yossra Berrazaga
- Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Haifa Rachdi
- Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Nouha Daoud
- Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Houda El Benna
- Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Soumaya Labidi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | | | - Khaled Rahal
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Farouk Benna
- Department of Radiation Oncology, University of Tunis, Tunis, Tunisia
| | - Hamouda Boussen
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
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28
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Kraoua I, Bouyacoub Y, Drissi C, Chargui M, Rebai I, Chebil A, Klaa H, Benrhouma H, Hassen A, Gouider-Khouja N, Abdelhak S, Boespflug-Tanguy O, Youssef-Turki IB, Dorboz I. Hypomyelination and Congenital Cataract: Clinical, Imaging, and Genetic Findings in Three Tunisian Families and Literature Review. Neuropediatrics 2021; 52:302-309. [PMID: 34192786 DOI: 10.1055/s-0041-1728654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Hypomyelination and congenital cataract (HCC) is characterized by congenital cataract, progressive neurologic impairment, and diffuse myelin deficiency. This autosomal recessive disorder is caused by homozygous variant in the FAM126A gene. Five consanguineous Tunisian patients, belonging to three unrelated families, underwent routine blood tests, electroneuromyography, and magnetic resonance imaging of the brain. The direct sequencing of FAM126A exons was performed for the patients and their relatives. We summarized the 30 previously published HCC cases. All of our patients were carriers of a previously reported c.414 + 1G > T (IVS5 + 1G > T) variant, but the clinical spectrum was variable. Despite the absence of a phenotype-genotype correlation in HCC disease, screening of this splice site variant should be performed in family members at risk.
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Affiliation(s)
- Ichraf Kraoua
- LR18SP04, Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, University of Tunis El Manar, Tunis, Tunisia
| | - Yosra Bouyacoub
- LR11IPT05, Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Cyrine Drissi
- Department of Neuroradiology, National Institute Mongi Ben Hmida of Neurology, Tunis, Tunisia
| | - Mariem Chargui
- LR11IPT05, Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Ibtihel Rebai
- LR18SP04, Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, University of Tunis El Manar, Tunis, Tunisia
| | - Ahmed Chebil
- Department B of Ophthalmology, Hedi Rais Institute of Ophthalmology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hédia Klaa
- LR18SP04, Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, University of Tunis El Manar, Tunis, Tunisia
| | - Hanene Benrhouma
- LR18SP04, Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, University of Tunis El Manar, Tunis, Tunisia
| | - Aida Hassen
- LR18SP04, Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, University of Tunis El Manar, Tunis, Tunisia
| | - Neziha Gouider-Khouja
- LR18SP04, Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, University of Tunis El Manar, Tunis, Tunisia
| | - Sonia Abdelhak
- LR11IPT05, Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Odile Boespflug-Tanguy
- Université de Paris, NeuroDiderot, UMR 1141, INSERM, Neuropédiatrie, LEUKOFRANCE, APHP, Hôpital Robert Debré, France
| | - Ilhem Ben Youssef-Turki
- LR18SP04, Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, University of Tunis El Manar, Tunis, Tunisia
| | - Imen Dorboz
- Université de Paris, NeuroDiderot, UMR 1141, INSERM, Neuropédiatrie, LEUKOFRANCE, APHP, Hôpital Robert Debré, France
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29
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Chouikha A, Ghrabi A, Ghodbane A, Hammemi W, Khedhiri M, Sadraoui A, Touzi H, Hassine HB, Maatoug S, Bensaoud C, Abdelhak S, Bouarrouj S, Gdoura M, Chaouachi H, Triki H. Distribution of HCV Genotypes Among People Who Inject Drugs in Tunisia: New Evidence for Scaling Up Prevention and Treatment Toward National Elimination Goal. Front Microbiol 2021; 12:697859. [PMID: 34385988 PMCID: PMC8353188 DOI: 10.3389/fmicb.2021.697859] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022] Open
Abstract
Little is known about the distribution of hepatitis C virus (HCV) genotypes among people who inject drugs (PWID) in North African countries, including Tunisia. This study aims to describe HCV genotypes circulating among Tunisian PWID. A cross-sectional study was conducted, and 128 HCV-positive PWID were recruited between 2018 and 2019 from community-based harm reduction centers. After informed consent, sociodemographic characteristics and risk behavior data were obtained using an interviewer-administrated questionnaire. Blood samples were collected for further serological and molecular testing. Overall, five women and 123 men were included. The median age was 39.5 years. The majority of PWID (56.3%) had less than a secondary level of education, were single (57%), were unemployed (65.6%), were incarcerated at least once (93.0%), and had a history of residency in at least one foreign country (50.8%). During the previous 12 months, 82.0% reported having reused syringes at least once, 43.8% shared syringes at least once, while 56.2% had at least one unprotected sexual relation, and 28.1% had more than two different sexual partners. Tattooing was reported among 60.2%. All positive results for HCV-infection by rapid testing were confirmed by enzyme-linked immunosorbent assay (ELISA). HCV-RNA was detectable in 79.7%. Genotyping showed a predominance of genotype 1 (52%) followed by genotype 3 (34%) and genotype 4 (10%). Four patients (4%) had an intergenotype mixed infection. Subtyping showed the presence of six different HCV subtypes as follows: 1a (53.2%), 1b (6.4%), 3a (33.0%), 4a (3.2%), and 4d (4.3%). This is the first study describing circulating HCV genotypes among PWID in Tunisia. The distribution of HCV genotypes is distinct from the general population with a predominance of subtypes 1a and 3a. These findings can be used to guide national efforts aiming to optimize the access of PWID to relevant HCV prevention and treatment measures including pangenotypic regimens for patients infected with HCV genotype 3.
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Affiliation(s)
- Anissa Chouikha
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, Tunis El Manar University, Tunis, Tunisia
| | - Amine Ghrabi
- Association Tunisienne d'Information et d'Orientation sur le SIDA et la Toxicomanie (Tunisian Association for Information and Orientation on HIV/AIDS and Toxicomania - ATIOST), Tunis, Tunisia
| | - Amira Ghodbane
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, Tunis El Manar University, Tunis, Tunisia
| | - Walid Hammemi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, Tunis El Manar University, Tunis, Tunisia
| | - Marwa Khedhiri
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, Tunis El Manar University, Tunis, Tunisia
| | - Amel Sadraoui
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, Tunis El Manar University, Tunis, Tunisia
| | - Henda Touzi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, Tunis El Manar University, Tunis, Tunisia
| | | | - Sonia Maatoug
- Science Shop, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Chaima Bensaoud
- Science Shop, Institut Pasteur de Tunis, Tunis, Tunisia.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czechia
| | | | - Samir Bouarrouj
- Association Tunisienne d'Information et d'Orientation sur le SIDA et la Toxicomanie (Tunisian Association for Information and Orientation on HIV/AIDS and Toxicomania - ATIOST), Tunis, Tunisia
| | - Mariem Gdoura
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, Tunis El Manar University, Tunis, Tunisia
| | - Hedia Chaouachi
- Association Tunisienne d'Information et d'Orientation sur le SIDA et la Toxicomanie (Tunisian Association for Information and Orientation on HIV/AIDS and Toxicomania - ATIOST), Tunis, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, Tunis El Manar University, Tunis, Tunisia
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30
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Hamdi Y, Abdeljaoued-Tej I, Zatchi AA, Abdelhak S, Boubaker S, Brown JS, Benkahla A. Cancer in Africa: The Untold Story. Front Oncol 2021; 11:650117. [PMID: 33937056 PMCID: PMC8082106 DOI: 10.3389/fonc.2021.650117] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/12/2021] [Indexed: 12/13/2022] Open
Abstract
Background Despite rising incidence and mortality rates in Africa, cancer has been given low priority in the research field and in healthcare services. Indeed, 57% of all new cancer cases around the world occur in low income countries exacerbated by lack of awareness, lack of preventive strategies, and increased life expectancies. Despite recent efforts devoted to cancer epidemiology, statistics on cancer rates in Africa are often dispersed across different registries. In this study our goal included identifying the most promising prevention and treatment approaches available in Africa. To do this, we collated and analyzed the incidence and fatality rates for the 10 most common and fatal cancers in 56 African countries grouped into 5 different regions (North, West, East, Central and South) over 16-years (2002–2018). We examined temporal and regional trends by investigating the most important risk factors associated to each cancer type. Data were analyzed by cancer type, African region, gender, measures of socioeconomic status and the availability of medical devices. Results We observed that Northern and Southern Africa were most similar in their cancer incidences and fatality rates compared to other African regions. The most prevalent cancers are breast, bladder and liver cancers in Northern Africa; prostate, lung and colorectal cancers in Southern Africa; and esophageal and cervical cancer in East Africa. In Southern Africa, fatality rates from prostate cancer and cervical cancer have increased. In addition, these three cancers are less fatal in Northern and Southern Africa compared to other regions, which correlates with the Human Development Index and the availability of medical devices. With the exception of thyroid cancer, all other cancers have higher incidences in males than females. Conclusion Our results show that the African continent suffers from a shortage of medical equipment, research resources and epidemiological expertise. While recognizing that risk factors are interconnected, we focused on risk factors more or less specific to each cancer type. This helps identify specific preventive and therapeutic options in Africa. We see a need for implementing more accurate preventive strategies to tackle this disease as many cases are likely preventable. Opportunities exist for vaccination programs for cervical and liver cancer, genetic testing and use of new targeted therapies for breast and prostate cancer, and positive changes in lifestyle for lung, colorectal and bladder cancers. Such recommendations should be tailored for the different African regions depending on their disease profiles and specific needs.
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Affiliation(s)
- Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Ines Abdeljaoued-Tej
- Laboratory of BioInformatics bioMathematics, and bioStatistics (BIMS), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Engineering School of Statistics and Information Analysis, University of Carthage, Ariana, Tunisia
| | - Afzal Ali Zatchi
- Laboratory of BioInformatics bioMathematics, and bioStatistics (BIMS), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Engineering School of Statistics and Information Analysis, University of Carthage, Ariana, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Joel S Brown
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, United States
| | - Alia Benkahla
- Laboratory of BioInformatics bioMathematics, and bioStatistics (BIMS), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
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Kraoua I, Ben Younes T, Dorboz I, Rouissi A, Abdelhak S, Boespflug-Tanguy O, Youssef-Turki IB. Étude clinique et génétique des leucodystrophies en Tunisie. Rev Neurol (Paris) 2021. [DOI: 10.1016/j.neurol.2021.02.195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Yaiche H, Tounsi-Kettiti H, Ben Jemii N, Jaballah Gabteni A, Mezghanni N, Ardhaoui M, Fehri E, Maaloul A, Abdelhak S, Boubaker S. New insights in the clinical implication of HOXA5 as prognostic biomarker in patients with colorectal cancer. Cancer Biomark 2021; 30:213-221. [PMID: 33136093 DOI: 10.3233/cbm-201758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Homeobox A5 (HOXA5) is a member of the HOX protein family which is involved in several carcinogenesis pathways, and is dysregulated in many cancer types. However, its expression and function in human colorectal cancer (CRC) is still largely unknown. OBJECTIVE This study aimed to evaluate HOXA5 expression in Tunisian patients with CRC in order to define new potential biomarker. METHODS An immunohistochemical labeling using an HOXA5 antibody was performed on 85 formalin fixed paraffin embedded specimens from patients with CRC. Six normal colon mucosa cases were used as controls. RESULTS HOXA5 expression showed a cytoplasmic staining in both tumor and stromal/endothelial cells. Loss or low HOXA5 expression was seen in tumor cells in 74/85 cases (87.06%) and in stromal/endothelial cells, in 77/85 (90.59%). In control group of normal colon mucosa HOXA5 was moderately expressed in all the cases. The abnormal expression, was significantly associated to lymph nodes metastasis in tumor cells (p= 0.043) and in stromal/endothelial cells (p= 0.024). CONCLUSION HOXA5 immunostaining results suggest the valuable role of this protein in colorectal carcinogenesis. Moreover, the association of lymph node metastasis to HOXA5 abnormal expression underlies its crucial role in colorectal cancer dissemination and prognosis.
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Affiliation(s)
- Hamza Yaiche
- Laboratory of Human and Experimental Pathology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Haifa Tounsi-Kettiti
- Laboratory of Human and Experimental Pathology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Nadia Ben Jemii
- Laboratory of Human and Experimental Pathology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Amira Jaballah Gabteni
- Laboratory of Human and Experimental Pathology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Najla Mezghanni
- Laboratory of Human and Experimental Pathology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Monia Ardhaoui
- Laboratory of Human and Experimental Pathology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Emna Fehri
- Laboratory of Human and Experimental Pathology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Afifa Maaloul
- Laboratory of Human and Experimental Pathology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Samir Boubaker
- Laboratory of Human and Experimental Pathology, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia
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Ben Haj Ali A, Messaoud O, Elouej S, Talmoudi F, Ayed W, Mellouli F, Ouederni M, Hadiji S, De Sandre-Giovannoli A, Delague V, Lévy N, Bogliolo M, Surrallés J, Abdelhak S, Amouri A. FANCA Gene Mutations in North African Fanconi Anemia Patients. Front Genet 2021; 12:610050. [PMID: 33679882 PMCID: PMC7933650 DOI: 10.3389/fgene.2021.610050] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/22/2021] [Indexed: 11/27/2022] Open
Abstract
Populations in North Africa (NA) are characterized by a high rate of consanguinity. Consequently, the proportion of founder mutations might be higher than expected and could be a major cause for the high prevalence of recessive genetic disorders like Fanconi anemia (FA). We report clinical, cytogenetic, and molecular characterization of FANCA in 29 North African FA patients from Tunisia, Libya, and Algeria. Cytogenetic tests revealed high rates of spontaneous chromosome breakages for all patients except two of them. FANCA molecular analysis was performed using three different molecular approaches which allowed us to identify causal mutations as homozygous or compound heterozygous forms. It included a nonsense mutation (c.2749C > T; p.Arg917Ter), one reported missense mutation (c.1304G > A; p.Arg435His), a novel missense variant (c.1258G > A; p.Asp409Glu), and the FANCA most common reported mutation (c.3788_3790delTCT; p.Phe1263del). Furthermore, three founder mutations were identified in 86.7% of the 22 Tunisian patients: (1) a deletion of exon 15, in 36.4% patients (8/22); (2), a deletion of exons 4 and 5 in 23% (5/22) and (3) an intronic mutation c.2222 + 166G > A, in 27.3% (6/22). Despite the relatively small number of patients studied, our results depict the mutational landscape of FA among NA populations and it should be taken into consideration for appropriate genetic counseling.
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Affiliation(s)
- Abir Ben Haj Ali
- Department of Histology and Cytogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Olfa Messaoud
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Sahar Elouej
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,INSERM, MMG, UMR 1251, Aix Marseille University, Marseille, France
| | - Faten Talmoudi
- Department of Histology and Cytogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Wiem Ayed
- Department of Histology and Cytogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Fethi Mellouli
- Department of Peadiatric Immuno-Haematology, National Bone Marrow Transplantation, Tunis, Tunisia
| | - Monia Ouederni
- Department of Peadiatric Immuno-Haematology, National Bone Marrow Transplantation, Tunis, Tunisia
| | - Sondes Hadiji
- Haematology Department, Hedi Chaker Hospital, University of Sfax, Sfax, Tunisia
| | | | - Valérie Delague
- INSERM, MMG, UMR 1251, Aix Marseille University, Marseille, France
| | - Nicolas Lévy
- INSERM, MMG, UMR 1251, Aix Marseille University, Marseille, France
| | - Massimo Bogliolo
- Research Institute IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Jordi Surrallés
- Research Institute IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Ahlem Amouri
- Department of Histology and Cytogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
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Boujemaa M, Hamdi Y, Mejri N, Romdhane L, Ghedira K, Bouaziz H, El Benna H, Labidi S, Dallali H, Jaidane O, Ben Nasr S, Haddaoui A, Rahal K, Abdelhak S, Boussen H, Boubaker MS. Germline copy number variations in BRCA1/2 negative families: Role in the molecular etiology of hereditary breast cancer in Tunisia. PLoS One 2021; 16:e0245362. [PMID: 33503040 PMCID: PMC7840007 DOI: 10.1371/journal.pone.0245362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/28/2020] [Indexed: 12/24/2022] Open
Abstract
Hereditary breast cancer accounts for 5-10% of all breast cancer cases. So far, known genetic risk factors account for only 50% of the breast cancer genetic component and almost a quarter of hereditary cases are carriers of pathogenic mutations in BRCA1/2 genes. Hence, the genetic basis for a significant fraction of familial cases remains unsolved. This missing heritability may be explained in part by Copy Number Variations (CNVs). We herein aimed to evaluate the contribution of CNVs to hereditary breast cancer in Tunisia. Whole exome sequencing was performed for 9 BRCA negative cases with a strong family history of breast cancer and 10 matched controls. CNVs were called using the ExomeDepth R-package and investigated by pathway analysis and web-based bioinformatic tools. Overall, 483 CNVs have been identified in breast cancer patients. Rare CNVs affecting cancer genes were detected, of special interest were those disrupting APC2, POU5F1, DOCK8, KANSL1, TMTC3 and the mismatch repair gene PMS2. In addition, common CNVs known to be associated with breast cancer risk have also been identified including CNVs on APOBECA/B, UGT2B17 and GSTT1 genes. Whereas those disrupting SULT1A1 and UGT2B15 seem to correlate with good clinical response to tamoxifen. Our study revealed new insights regarding CNVs and breast cancer risk in the Tunisian population. These findings suggest that rare and common CNVs may contribute to disease susceptibility. Those affecting mismatch repair genes are of interest and require additional attention since it may help to select candidates for immunotherapy leading to better outcomes.
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Affiliation(s)
- Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Nesrine Mejri
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Biology, Faculty of Science of Bizerte, University of Carthage, Jarzouna, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hanen Bouaziz
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Houda El Benna
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Soumaya Labidi
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Olfa Jaidane
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Sonia Ben Nasr
- Department of Medical Oncology, Military Hospital of Tunis, Tunis, Tunisia
| | | | - Khaled Rahal
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hamouda Boussen
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Mohamed Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
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Romdhane L, Mezzi N, Dallali H, Messaoud O, Shan J, Fakhro KA, Kefi R, Chouchane L, Abdelhak S. A map of copy number variations in the Tunisian population: a valuable tool for medical genomics in North Africa. NPJ Genom Med 2021; 6:3. [PMID: 33420067 PMCID: PMC7794582 DOI: 10.1038/s41525-020-00166-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/18/2020] [Indexed: 11/24/2022] Open
Abstract
Copy number variation (CNV) is considered as the most frequent type of structural variation in the human genome. Some CNVs can act on human phenotype diversity, encompassing rare Mendelian diseases and genomic disorders. The North African populations remain underrepresented in public genetic databases in terms of single-nucleotide variants as well as for larger genomic mutations. In this study, we present the first CNV map for a North African population using the Affymetrix Genome-Wide SNP (single-nucleotide polymorphism) array 6.0 array genotyping intensity data to call CNVs in 102 Tunisian healthy individuals. Two softwares, PennCNV and Birdsuite, were used to call CNVs in order to provide reliable data. Subsequent bioinformatic analyses were performed to explore their features and patterns. The CNV map of the Tunisian population includes 1083 CNVs spanning 61.443 Mb of the genome. The CNV length ranged from 1.017 kb to 2.074 Mb with an average of 56.734 kb. Deletions represent 57.43% of the identified CNVs, while duplications and the mixed loci are less represented. One hundred and three genes disrupted by CNVs are reported to cause 155 Mendelian diseases/phenotypes. Drug response genes were also reported to be affected by CNVs. Data on genes overlapped by deletions and duplications segments and the sequence properties in and around them also provided insights into the functional and health impacts of CNVs. These findings represent valuable clues to genetic diversity and personalized medicine in the Tunisian population as well as in the ethnically similar populations from North Africa.
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Affiliation(s)
- Lilia Romdhane
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia.
- Department of Biology, Faculty of Science of Bizerte, Jarzouna, Tunisia.
| | - Nessrine Mezzi
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Hamza Dallali
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Olfa Messaoud
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Jingxuan Shan
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Khalid A Fakhro
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Rym Kefi
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
- Genetic Intelligence Laboratory, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Sonia Abdelhak
- Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia
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Ben Jemii N, Tounsi-Kettiti H, Yaiche H, Mezghanni N, Jaballah Gabteni A, Fehri E, Ben Fayala C, Abdelhak S, Boubaker S. Dysregulated PDGFR alpha expression and novel somatic mutations in colorectal cancer: association to RAS wild type status and tumor size. J Transl Med 2020; 18:440. [PMID: 33213472 PMCID: PMC7678118 DOI: 10.1186/s12967-020-02614-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/06/2020] [Indexed: 12/11/2022] Open
Abstract
Background Platelet derived growth factor receptor alpha (PDGFRα) has been considered as a relevant factor in tumor proliferation, angiogenesis and metastatic dissemination. It was a target of tyrosine kinase (TK) inhibitors emerged in the therapy of diverse cancers. In colorectal cancer, the commonly used therapy is anti-epithelial growth factor receptor (EGFR). However, both RAS mutated and a subgroup of RAS wild type patients resist to such therapy. The aim of this study is to investigate PDGFRα protein expression and mutational status in colorectal adenocarcinoma and their association with clinicopathological features and molecular RAS status to provide useful information for the identification of an effective biomarker that might be implicated in prognosis and treatment prediction. Methods Our study enrolled 103 formalin fixed paraffin-embedded (FFPE) colorectal adenocarcinoma. PDGFRα expression was investigated by immunohistochemistry (IHC). Hotspot exon 18 of PDGFRA was studied by PCR followed by Sanger sequencing and RAS status was determined by real time quantitative PCR. Thirteen normal colon tissues were used as negative controls. Results PDGFRα staining was detected in the cytoplasm of all tissues. Low expression was observed in all normal colon mucosa. In adenocarcinoma, 45% (45/100) of cases showed PDGFRα overexpression. This overexpression was significantly associated with mutations in exon 18 (P = 0.024), RAS wild type status (P < 10–3), tumor diameter (P = 0.048), whereas there was no association with tumor side (P = 0.13) and other clinicopathological features. Conclusion Overexpression of PDGFRα in adenocarcinoma suggests its potential role in tumor cells growth and invasion. The association between PDGFRα overexpression in both tumor and stromal adenocarcinoma cells with RAS wild type status suggests its potential role in anti-EGFR therapy resistance and the relevance of using it as specific or adjuvant therapeutic target.
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Affiliation(s)
- Nadia Ben Jemii
- Laboratory of Human and Experimental Pathology, Faculty of Science of Tunis, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia. .,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.
| | - Haifa Tounsi-Kettiti
- Laboratory of Human and Experimental Pathology, Faculty of Medicine of Tunis, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Hamza Yaiche
- Laboratory of Human and Experimental Pathology, Faculty of Science of Tunis, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Najla Mezghanni
- Laboratory of Human and Experimental Pathology, Faculty of Science of Tunis, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Amira Jaballah Gabteni
- Laboratory of Human and Experimental Pathology, Faculty of Science of Tunis, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Emna Fehri
- Laboratory of Human and Experimental Pathology, Faculty of Science of Tunis, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Chayma Ben Fayala
- Laboratory of Human and Experimental Pathology, Faculty of Science of Tunis, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Samir Boubaker
- Laboratory of Human and Experimental Pathology, Faculty of Medicine of Tunis, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University Tunis El Manar, Tunis, Tunisia
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Mighri N, Hamdi Y, Boujemaa M, Othman H, Ben Nasr S, El Benna H, Mejri N, Labidi S, Ayari J, Jaidene O, Bouaziz H, Ben Rekaya M, M'rad R, Haddaoui A, Rahal K, Boussen H, Boubaker S, Abdelhak S. Identification of Novel BRCA1 and RAD50 Mutations Associated With Breast Cancer Predisposition in Tunisian Patients. Front Genet 2020; 11:552971. [PMID: 33240314 PMCID: PMC7677579 DOI: 10.3389/fgene.2020.552971] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022] Open
Abstract
Background Deleterious mutations on BRCA1/2 genes are known to confer high risk of developing breast and ovarian cancers. The identification of these mutations not only helped in selecting high risk individuals that need appropriate prevention approaches but also led to the development of the PARP-inhibitors targeted therapy. This study aims to assess the prevalence of the most frequent BRCA1 mutation in Tunisia, c.211dupA, and provide evidence of its common origin as well as its clinicopathological characteristics. We also aimed to identify additional actionable variants using classical and next generation sequencing technologies (NGS) which would allow to implement cost-effective genetic testing in limited resource countries. Patients and Methods Using sanger sequencing, 112 breast cancer families were screened for c.211dupA. A set of patients that do not carry this mutation were investigated using NGS. Haplotype analysis was performed to assess the founder effect and to estimate the age of this mutation. Correlations between genetic and clinical data were also performed. Results The c.211dupA mutation was identified in 8 carriers and a novel private BRCA1 mutation, c.2418dupA, was identified in one carrier. Both mutations are likely specific to North-Eastern Tunisia. Haplotype analysis supported the founder effect of c.211dupA and showed its recent origin. Phenotype-genotype correlation showed that both BRCA1 mutations seem to be associated with a severe phenotype. Whole Exome Sequencing (WES) analysis of a BRCA negative family revealed a Variant of Unknown Significance, c.3647C > G on RAD50. Molecular modeling showed that this variant could be classified as deleterious as it is responsible for destabilizing the RAD50 protein structure. Variant prioritization and pathway analysis of the WES data showed additional interesting candidate genes including MITF and ANKS6. Conclusion We recommend the prioritization of BRCA1-c.211dupA screening in high risk breast cancer families originating from the North-East of Tunisia. We also highlighted the importance of NGS in detecting novel mutations, such as RAD50-c.3647C > G. In addition, we strongly recommend using data from different ethnic groups to review the pathogenicity of this variant and reconsider its classification in ClinVar.
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Affiliation(s)
- Najah Mighri
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Houcemeddine Othman
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Sonia Ben Nasr
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,The Military Hospital of Tunis, Department of Medical Oncology, Tunis, Tunisia
| | - Houda El Benna
- Department of Medical Oncology, Abderrahmane Mami Hospital, Ariana, Tunisia
| | - Nesrine Mejri
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Department of Medical Oncology, Abderrahmane Mami Hospital, Ariana, Tunisia
| | - Soumaya Labidi
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Department of Medical Oncology, Abderrahmane Mami Hospital, Ariana, Tunisia
| | - Jihen Ayari
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,The Military Hospital of Tunis, Department of Medical Oncology, Tunis, Tunisia
| | - Olfa Jaidene
- Department of Carcinological Surgery, Salah Azaiez Institute, Tunis, Tunisia
| | - Hanen Bouaziz
- Department of Carcinological Surgery, Salah Azaiez Institute, Tunis, Tunisia
| | - Mariem Ben Rekaya
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Ridha M'rad
- Service des Maladies Congénitales et Héréditaires, Hôpital Charles Nicolle, Tunis, Tunisia
| | - Abderrazek Haddaoui
- The Military Hospital of Tunis, Department of Medical Oncology, Tunis, Tunisia
| | - Khaled Rahal
- Department of Carcinological Surgery, Salah Azaiez Institute, Tunis, Tunisia
| | - Hamouda Boussen
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Department of Medical Oncology, Abderrahmane Mami Hospital, Ariana, Tunisia
| | - Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
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El Jeni R, Ghedira K, El Bour M, Abdelhak S, Benkahla A, Bouhaouala-Zahar B. High-quality genome sequence assembly of R.A73 Enterococcus faecium isolated from freshwater fish mucus. BMC Microbiol 2020; 20:322. [PMID: 33096980 PMCID: PMC7584074 DOI: 10.1186/s12866-020-01980-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/18/2020] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Whole-genome sequencing using high throughput technologies has revolutionized and speeded up the scientific investigation of bacterial genetics, biochemistry, and molecular biology. Lactic acid bacteria (LABs) have been extensively used in fermentation and more recently as probiotics in food products that promote health. Genome sequencing and functional genomics investigations of LABs varieties provide rapid and important information about their diversity and their evolution, revealing a significant molecular basis. This study investigated the whole genome sequences of the Enterococcus faecium strain (HG937697), isolated from the mucus of freshwater fish in Tunisian dams. Genomic DNA was extracted using the Quick-GDNA kit and sequenced using the Illumina HiSeq2500 system. Sequences quality assessment was performed using FastQC software. The complete genome annotation was carried out with the Rapid Annotation using Subsystem Technology (RAST) web server then NCBI PGAAP. RESULTS The Enterococcus faecium R.A73 assembled in 28 contigs consisting of 2,935,283 bps. The genome annotation revealed 2884 genes in total including 2834 coding sequences and 50 RNAs containing 3 rRNAs (one rRNA 16 s, one rRNA 23 s and one rRNA 5 s) and 47 tRNAs. Twenty-two genes implicated in bacteriocin production are identified within the Enterococcus faecium R.A73 strain. CONCLUSION Data obtained provide insights to further investigate the effective strategy for testing this Enterococcus faecium R.A73 strain in the industrial manufacturing process. Studying their metabolism with bioinformatics tools represents the future challenge and contribution to improving the utilization of the multi-purpose bacteria in food.
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Affiliation(s)
- Rim El Jeni
- Laboratory of Microbiology and Pathology of Aquatic Organisms, Institut National des Sciences et Technologies de la Mer (INSTM), Tunis, Tunisia
- Laboratory of Venoms and Therapeutic Molecules, Pasteur Institute of Tunis, Tunis, Tunisia
| | - Kais Ghedira
- Bioinformatics and Biostatistics Laboratory (LR16IPT09), Pasteur Institute of Tunis, Tunis, Tunisia
| | - Monia El Bour
- Laboratory of Microbiology and Pathology of Aquatic Organisms, Institut National des Sciences et Technologies de la Mer (INSTM), Tunis, Tunisia
| | - Sonia Abdelhak
- Biomedical Genomics and Oncogenetics Laboratory LR16IPT05, Pasteur Institute of Tunis, Tunis, Tunisia
| | - Alia Benkahla
- Bioinformatics and Biostatistics Laboratory (LR16IPT09), Pasteur Institute of Tunis, Tunis, Tunisia
| | - Balkiss Bouhaouala-Zahar
- Laboratory of Venoms and Therapeutic Molecules, Pasteur Institute of Tunis, Tunis, Tunisia
- Medical School of Tunis, University of Tunis El Manar, 1007 Tunis, Tunisia
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Romdhane L, Bouhamed H, Ghedira K, Ben Hamda C, Louhichi A, Jmel H, Romdhane S, Charfeddine C, Mokni M, Abdelhak S, Rebai A. The morbid cutaneous anatomy of the human genome revealed by a bioinformatic approach. Genomics 2020; 112:4232-4241. [PMID: 32650097 DOI: 10.1016/j.ygeno.2020.07.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 03/28/2020] [Accepted: 07/02/2020] [Indexed: 01/05/2023]
Abstract
Computational approaches have been developed to prioritize candidate genes in disease gene identification. They are based on different pieces of evidences associating each gene with the given disease. In this study, 648 genes underlying genodermatoses have been compared to 1808 genes involved in other genetic diseases using a bioinformatic approach. These genes were studied at the structural, evolutionary and functional levels. Results show that genes underlying genodermatoses present longer CDS and have more exons. Significant differences were observed in nucleotide motif and amino-acid compositions. Evolutionary conservation analysis revealed that genodermatoses genes have less paralogs, more orthologs in Mouse and Dog and are less conserved. Functional analysis revealed that genodermatosis genes seem to be involved in immune system and skin layers. The Bayesian network model returned a rate of good classification of around 80%. This computational approach could help investigators working in the field of dermatology by prioritizing positional candidate genes for mutation screening.
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Affiliation(s)
- Lilia Romdhane
- Biomedical Genomics and Oncogenetics Laboratory LR11IPT05, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia; Department of Biology, Faculty of Sciences of Bizerte, Jarzouna, Université Tunis Carthage, Tunis, Tunisia.
| | - Heni Bouhamed
- Molecular and Cellular Screening Process Laboratory, Centre of Biotechnology of Sfax, Sfax, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Cherif Ben Hamda
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Amel Louhichi
- Molecular and Cellular Screening Process Laboratory, Centre of Biotechnology of Sfax, Sfax, Tunisia
| | - Haifa Jmel
- Biomedical Genomics and Oncogenetics Laboratory LR11IPT05, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Safa Romdhane
- Biomedical Genomics and Oncogenetics Laboratory LR11IPT05, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Chérine Charfeddine
- Biomedical Genomics and Oncogenetics Laboratory LR11IPT05, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia; High Institut of Biotechnology of Sidi Thabet, University of Manouba, BiotechPole of Sidi Thabet, Ariana, Tunisia
| | - Mourad Mokni
- Department of Dermatology, CHU La Rabta Tunis, Tunis, Tunisia; Public health and infection Research Laboratory, La Rabta Hospital, Tunis, Tunisia
| | - Sonia Abdelhak
- Biomedical Genomics and Oncogenetics Laboratory LR11IPT05, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Ahmed Rebai
- Molecular and Cellular Screening Process Laboratory, Centre of Biotechnology of Sfax, Sfax, Tunisia
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El-Kamah GY, Mohamed AM, Gad YZ, Abdelhak S, Hennig BJ, Ramesar RS, Landouré G, Gaye A, Newport MJ, Williams SM, Ramsay M. Developing a Road Map to Spread Genomic Knowledge in Africa: 10th Conference of the African Society of Human Genetics, Cairo, Egypt. Am J Trop Med Hyg 2020; 102:719-723. [PMID: 32124726 DOI: 10.4269/ajtmh.19-0408] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The tenth conference of the African Society of Human Genetics was held in Egypt with the theme "Human Genetics and Genomics in Africa: Challenges for Both Rare and Common Genetic Disorders." Current research was presented, and we discussed visions for the future of genomic research on the African continent. In this report, we summarize the presented scientific research within and relevant to Africa as presented by both African and non-African scientists. We also discuss the current situation concerning genomic medicine and genomic research within the continent, difficulties in implementing genetic services and genomic medicine in Africa, and a road map to overcome those difficulties and meet the needs of the African researchers and patients.
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Affiliation(s)
- Ghada Y El-Kamah
- Human Genetics and Genome Research Division, Centre of Scientific Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Amal M Mohamed
- Human Genetics and Genome Research Division, Centre of Scientific Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Yehia Z Gad
- Human Genetics and Genome Research Division, Centre of Scientific Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | | | - Raj S Ramesar
- Division of Human Genetics, Department of Pathology, Faculty of Health Science, University of Cape Town and Affiliated Hospitals, Cape Town, South Africa
| | - Guida Landouré
- Service de Neurologie, Centre Hospitalier Universitaire du Point G, Bamako, Mali.,Human Genetics and Genome Research Division, Centre of Scientific Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Amadou Gaye
- National Institutes of Health, National Human Genome Research, Bethesda, Maryland.,Service de Neurologie, Centre Hospitalier Universitaire du Point G, Bamako, Mali
| | - Melanie J Newport
- Brighton and Sussex Centre for Global Health Research, Brighton and Sussex Medical School, University of Sussex, Falmer, United Kingdom
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Institute of Computational Biology, Case Western Reserve University, Cleveland, Ohio
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Mejri N, El Benna H, Rachdi H, Labidi S, Benna M, Daoud N, Hamdi Y, Abdelhak S, Boussen H. Reproductive Risk Factors of Inflammatory Breast Cancer according to Luminal, HER2-Overexpressing, and Triple-Negative Subtypes: A Case Comparison Study. Oncol Res Treat 2020; 43:204-210. [DOI: 10.1159/000506691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 02/19/2020] [Indexed: 11/19/2022]
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Radouani F, Zass L, Hamdi Y, Rocha JD, Sallam R, Abdelhak S, Ahmed S, Azzouzi M, Benamri I, Benkahla A, Bouhaouala-Zahar B, Chaouch M, Jmel H, Kefi R, Ksouri A, Kumuthini J, Masilela P, Masimirembwa C, Othman H, Panji S, Romdhane L, Samtal C, Sibira R, Ghedira K, Fadlelmola F, Kassim SK, Mulder N. A review of clinical pharmacogenetics Studies in African populations. Per Med 2020; 17:155-170. [PMID: 32125935 PMCID: PMC8093600 DOI: 10.2217/pme-2019-0110] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Effective interventions and treatments for complex diseases have been implemented globally, however, coverage in Africa has been comparatively lower due to lack of capacity, clinical applicability and knowledge on the genetic contribution to disease and treatment. Currently, there is a scarcity of genetic data on African populations, which have enormous genetic diversity. Pharmacogenomics studies have the potential to revolutionise treatment of diseases, therefore, African populations are likely to benefit from these approaches to identify likely responders, reduce adverse side effects and optimise drug dosing. This review discusses clinical pharmacogenetics studies conducted in African populations, focusing on studies that examined drug response in complex diseases relevant to healthcare. Several pharmacogenetics associations have emerged from African studies, as have gaps in knowledge.
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Affiliation(s)
- Fouzia Radouani
- Research Department, Chlamydiae & Mycoplasmas Laboratory, Institut Pasteur du Maroc, Casablanca 20360, Morocco
| | - Lyndon Zass
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, South Africa
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002 Tunis, Belvédère, Tunisie
| | - Jorge da Rocha
- Sydney Brenner Institute for Molecular Bioscience, University of The Witwatersrand, Johannesburg, South Africa
| | - Reem Sallam
- Medical Biochemistry & Molecular Biology Department, Faculty of Medicine, Ain Shams University, Abbaseya, Cairo 11381, Egypt
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002 Tunis, Belvédère, Tunisie
| | - Samah Ahmed
- Centre for Bioinformatics & Systems Biology, Faculty of Science, University of Khartoum, 321 Khartoum, Sudan.,Faculty of Clinical & Industrial Pharmacy, National University, Khartoum, Sudan
| | - Maryame Azzouzi
- Research Department, Chlamydiae & Mycoplasmas Laboratory, Institut Pasteur du Maroc, Casablanca 20360, Morocco
| | - Ichrak Benamri
- Research Department, Chlamydiae & Mycoplasmas Laboratory, Institut Pasteur du Maroc, Casablanca 20360, Morocco.,Systems & Data Engineering Team, National School of Applied Sciences of Tangier, Morocco
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics & Biostatistics LR 16 IPT 09, Institute Pasteur de Tunis, Tunisia
| | - Balkiss Bouhaouala-Zahar
- Laboratory of Venoms & Therapeutic Molecules, Pasteur Institute of Tunis, 13 Place Pasteur, BP74, Tunis Belvedere- University of Tunis El Manar, Tunisia
| | - Melek Chaouch
- Laboratory of Bioinformatics, Biomathematics & Biostatistics LR 16 IPT 09, Institute Pasteur de Tunis, Tunisia
| | - Haifa Jmel
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002 Tunis, Belvédère, Tunisie
| | - Rym Kefi
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002 Tunis, Belvédère, Tunisie
| | - Ayoub Ksouri
- Laboratory of Bioinformatics, Biomathematics & Biostatistics LR 16 IPT 09, Institute Pasteur de Tunis, Tunisia.,Laboratory of Venoms & Therapeutic Molecules, Pasteur Institute of Tunis, 13 Place Pasteur, BP74, Tunis Belvedere- University of Tunis El Manar, Tunisia
| | - Judit Kumuthini
- H3ABioNet, Bioinformatics Department, Centre for Proteomic & Genomic Research, Cape Town, South Africa
| | - Phumlani Masilela
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, South Africa
| | - Collen Masimirembwa
- Sydney Brenner Institute for Molecular Bioscience, University of The Witwatersrand, Johannesburg, South Africa.,DMPK Department, African Institute of Biomedical Science & Technology, Harare, Zimbabwe
| | - Houcemeddine Othman
- Sydney Brenner Institute for Molecular Bioscience, University of The Witwatersrand, Johannesburg, South Africa
| | - Sumir Panji
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, South Africa
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002 Tunis, Belvédère, Tunisie.,Département des Sciences de la Vie, Faculté des Sciences de Bizerte, Université Carthage, 7021 Jarzouna, BP 21, Tunisie
| | - Chaimae Samtal
- Biotechnology Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohammed Ben Abdellah University, Fez 30000, Morocco.,Department of Biology, University of Mohammed Premier, Oujda, Morocco.,Department of Biology Faculty of Sciences, University of Sidi Mohamed Ben Abdellah, Fez, Morocco
| | - Rania Sibira
- Centre for Bioinformatics & Systems Biology, Faculty of Science, University of Khartoum, 321 Khartoum, Sudan.,Department of Neurosurgery, National Center For Neurological Sciences, Khartoum, Sudan
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics & Biostatistics LR 16 IPT 09, Institute Pasteur de Tunis, Tunisia
| | - Faisal Fadlelmola
- Centre for Bioinformatics & Systems Biology, Faculty of Science, University of Khartoum, 321 Khartoum, Sudan
| | - Samar Kamal Kassim
- Medical Biochemistry & Molecular Biology Department, Faculty of Medicine, Ain Shams University, Abbaseya, Cairo 11381, Egypt
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, South Africa
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Jaouadi H, Bouyacoub Y, Chabrak S, Kraoua L, Zaroui A, Elouej S, Nagara M, Dallali H, Delague V, Levy N, Benkhalifa R, Mechmeche R, Zaffran S, Abdelhak S. Multiallelic rare variants support an oligogenic origin of sudden cardiac death in the young. Herz 2020; 46:94-102. [PMID: 31970460 DOI: 10.1007/s00059-019-04883-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/20/2019] [Accepted: 12/06/2019] [Indexed: 12/16/2022]
Abstract
Unexplained sudden death in the young is cardiovascular in most cases. Structural and conduction defects in cardiac-related genes can conspire to underlie sudden cardiac death. Here we report a clinical investigation and an extensive genetic assessment of a Tunisian family with sudden cardiac death in young members. In order to identify the family-genetic basis of sudden cardiac death, we performed Whole Exome Sequencing (WES), read depth copy-number-variation (CNV) screening and segregation analysis. We identify 6 ultra-rare pathogenic heterozygous variants in OBSCN, RYR2, DSC2, AKAP9, CACNA1C and RBM20 genes, and one homozygous splicing variant in TECRL gene consistent with an oligogenic model of inheritance. CNV analysis did not reveal any causative CNV consistent with the family phenotype. Overall, our results are highly suggestive for a cumulative effect of heterozygous missense variants as disease causation and to account for a greater disease severity among offspring. Our study further confirms the complexity of the inheritance of sudden cardiac death and highlights the utility of family-based WES and segregation analysis in the identification of family specific mutations within different cardiac genes pathways.
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Affiliation(s)
- Hager Jaouadi
- Biomedical Genomics and Oncogenetics Laboratory LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, 13 Place Pasteur, BP74-1002, Tunis, belvédère, Tunisia.
| | - Yosra Bouyacoub
- Biomedical Genomics and Oncogenetics Laboratory LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, 13 Place Pasteur, BP74-1002, Tunis, belvédère, Tunisia
| | - Sonia Chabrak
- Department of Cardiology, La Rabta Hospital, Tunis, Tunisia.,Faculty of Medicine of Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Lilia Kraoua
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, Tunisia
| | - Amira Zaroui
- Faculty of Medicine of Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Sahar Elouej
- Aix Marseille University, INSERM, U1251, Marseille Medical Genetics, Marseille, France
| | - Majdi Nagara
- Biomedical Genomics and Oncogenetics Laboratory LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, 13 Place Pasteur, BP74-1002, Tunis, belvédère, Tunisia
| | - Hamza Dallali
- Biomedical Genomics and Oncogenetics Laboratory LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, 13 Place Pasteur, BP74-1002, Tunis, belvédère, Tunisia
| | - Valérie Delague
- Aix Marseille University, INSERM, U1251, Marseille Medical Genetics, Marseille, France
| | - Nicolas Levy
- Aix Marseille University, INSERM, U1251, Marseille Medical Genetics, Marseille, France
| | - Rym Benkhalifa
- Venoms and Therapeutic Biomolecules Laboratory LR16IPT08, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Rachid Mechmeche
- Department of Cardiology, La Rabta Hospital, Tunis, Tunisia.,Faculty of Medicine of Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Stéphane Zaffran
- Aix Marseille University, INSERM, U1251, Marseille Medical Genetics, Marseille, France
| | - Sonia Abdelhak
- Biomedical Genomics and Oncogenetics Laboratory LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, 13 Place Pasteur, BP74-1002, Tunis, belvédère, Tunisia
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45
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Bouchoucha S, Chikhaoui A, Najjar D, Dallali H, Khammessi M, Abdelhak S, Nessibe N, Shboul M, Kircher SG, Al Kaissi A, Yacoub-Youssef H. Clinical and Genetic Heterogeneity in Six Tunisian Families With Horizontal Gaze Palsy With Progressive Scoliosis: A Retrospective Study of 13 Cases. Front Pediatr 2020; 8:172. [PMID: 32373565 PMCID: PMC7179758 DOI: 10.3389/fped.2020.00172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 03/25/2020] [Indexed: 11/13/2022] Open
Abstract
Background: Horizontal Gaze Palsy with Progressive Scoliosis (HGPPS) is a rare autosomal recessive congenital disorder characterized by the absence of conjugate horizontal eye movements, and progressive debilitating scoliosis during childhood and adolescence. HGPPS is associated with mutations of the ROBO3 gene. In this study, the objective is to identify pathogenic variants in a cohort of Tunisian patients with HGPPS and to further define ROBO3 genotype-phenotype correlations. Methods: Thirteen Tunisian patients from six unrelated consanguineous families all manifesting HGPPS were genetically investigated. We searched for the causative variants for HGPPS using classical Sanger and whole exome sequencing. Results: Four distinct homozygous mutations were identified in ROBO3 gene. Two of these were newly identified homozygous and non-synonymous mutations, causing effectively damage to the protein by in silico analysis. The other two mutations were previously reported in Tunisian patients with HGPPS. Mutations were validated by Sanger sequencing in parents and affected individuals. Conclusion: To the best of our knowledge, this is the largest ever reported cohort on families with HGPPS in whom ROBO3 mutations were identified. These molecular findings have expanded our knowledge of the ROBO3 mutational spectrum. The relevance of our current study is two-fold; first to assist proper management of the scoliosis and second to protect families at risk.
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Affiliation(s)
- Sami Bouchoucha
- Laboratoire de Génomique Biomédicale et Oncogénétique, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Service Orthopédie, Hôpital d'enfant Béchir Hamza, Tunis, Tunisia
| | - Asma Chikhaoui
- Laboratoire de Génomique Biomédicale et Oncogénétique, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Dorra Najjar
- Laboratoire de Génomique Biomédicale et Oncogénétique, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Hamza Dallali
- Laboratoire de Génomique Biomédicale et Oncogénétique, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Maleke Khammessi
- Laboratoire de Génomique Biomédicale et Oncogénétique, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratoire de Génomique Biomédicale et Oncogénétique, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Nabil Nessibe
- Service Orthopédie, Hôpital d'enfant Béchir Hamza, Tunis, Tunisia
| | - Mohammad Shboul
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Susanne G Kircher
- Institute of Medical Chemistry, Medical University of Vienna, Vienna, Austria
| | - Ali Al Kaissi
- First Medical Department, Ludwig Boltzmann Institute of Osteology, Hanusch Hospital of WGKK, AUVA Trauma Centre Meidling, Hanusch Hospital, Vienna, Austria.,Pediatric Department, Orthopaedic Hospital of Speising, Vienna, Austria
| | - Houda Yacoub-Youssef
- Laboratoire de Génomique Biomédicale et Oncogénétique, LR16IPT05, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
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46
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Kraoua I, Karkar A, Drissi C, Benrhouma H, Klaa H, Samaan S, Renaldo F, Elmaleh M, Ben Hamouda M, Abdelhak S, Boespflug-Tanguy O, Ben Youssef-Turki I, Dorboz I. Novel POLR1C mutation in RNA polymerase III-related leukodystrophy with severe myoclonus and dystonia. Mol Genet Genomic Med 2019; 7:e914. [PMID: 31368241 PMCID: PMC6732337 DOI: 10.1002/mgg3.914] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/16/2019] [Accepted: 07/22/2019] [Indexed: 11/15/2022] Open
Abstract
Introduction RNA polymerase III (Pol III)‐related leukodystrophies are a group of autosomal recessive neurodegenerative disorders caused by mutations in POLR3A and POLR3B. Recently a recessive mutation in POLR1C causative of Pol III‐related leukodystrophies was identified. Methods We report the case of a Tunisian girl of 14 years of age who was referred to our department for evaluation of progressive ataxia that began at the age of 5. Genetic diagnosis was performed by NGS and Sanger analysis. In silico predictions were performed using SIFT, PolyPhen‐2, and Mutation Taster. Results Neurological examination showed cerebellar and tetrapyramidal syndrome, mixed movement disorders with generalized dystonia and severe myoclonus leading to death at 25 years. Brain MRI scans showed diffuse hypomyelination associated with cerebellar atrophy. It also showed bilateral T2 hypointensity of the ventrolateral thalamus, part of the posterior limb of the internal capsule, the substantia nigra and the subthalamic nucleus. Next generation sequencing leukodystrophy panel including POLR3A and POLR3B was negative. Sanger sequencing of the coding regions of POLR1C revealed a novel homozygous mutation. Conclusion The clinical and imaging findings of patients with POLR1C hypomyelinating leukodystrophy are reviewed. Interestingly, severe myoclonic dystonia and T2 hypointensity of the substantia nigra and the subthalamic nucleus are not reported yet and could be helpful for the diagnosis of POLR1C hypomyelinating leukodystrophy.
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Affiliation(s)
- Ichraf Kraoua
- Department of Child and Adolescent Neurology, LR18SP04, National Institute Mongi Ben Hmida of Neurology, University of Tunis El Manar, Tunis, Tunisia
| | - Adnane Karkar
- Genetics and Molecular Pathology Laboratory, Medical School of Casablanca, Hassan II University, Casablanca, Morocco.,INSERM UMR1141, Sorbonne Paris Cité, DHU PROTECT, Paris Diderot University, Robert Debré Hospital, Paris, France
| | - Cyrine Drissi
- Department of Neuroradiology, National Institute Mongi Ben Hmida of Neurology, Tunis, Tunisia
| | - Hanene Benrhouma
- Department of Child and Adolescent Neurology, LR18SP04, National Institute Mongi Ben Hmida of Neurology, University of Tunis El Manar, Tunis, Tunisia
| | - Hedia Klaa
- Department of Child and Adolescent Neurology, LR18SP04, National Institute Mongi Ben Hmida of Neurology, University of Tunis El Manar, Tunis, Tunisia
| | - Simon Samaan
- Molecular Biology, Genetic Department, Robert Debré Hospital, Paris, France
| | - Florence Renaldo
- INSERM UMR1141, Sorbonne Paris Cité, DHU PROTECT, Paris Diderot University, Robert Debré Hospital, Paris, France.,Department of Neuropediatrics and Metabolic Diseases, Reference Center for Leukodystrophies, Robert Debré Hospital, AP-HP, Paris, France
| | | | - Mohamed Ben Hamouda
- Department of Neuroradiology, National Institute Mongi Ben Hmida of Neurology, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR11IPT05, Pasteur Institute of Tunisia, University of Tunis El Manar, Tunis, Tunisia
| | - Odile Boespflug-Tanguy
- INSERM UMR1141, Sorbonne Paris Cité, DHU PROTECT, Paris Diderot University, Robert Debré Hospital, Paris, France.,Department of Neuropediatrics and Metabolic Diseases, Reference Center for Leukodystrophies, Robert Debré Hospital, AP-HP, Paris, France
| | - Ilfghem Ben Youssef-Turki
- Department of Child and Adolescent Neurology, LR18SP04, National Institute Mongi Ben Hmida of Neurology, University of Tunis El Manar, Tunis, Tunisia
| | - Imen Dorboz
- INSERM UMR1141, Sorbonne Paris Cité, DHU PROTECT, Paris Diderot University, Robert Debré Hospital, Paris, France
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Bouyacoub Y, Falfoul Y, Ouederni M, Sayeb M, Chedli A, Chargui M, Sassi H, Chakroun Chenguel I, Munier FL, El Matri L, Abdelhak S, Cheour M. Granular type I corneal dystrophy in a large consanguineous Tunisian family with homozygous p.R124S mutation in the TGFBI gene. Ophthalmic Genet 2019; 40:329-337. [PMID: 31322463 DOI: 10.1080/13816810.2019.1639202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Purpose: We report the clinical features and the mutational analysis in a large Tunisian family with granular corneal dystrophy type I (GCD1). Patients and Methods: Thirty-three members of the Tunisian family underwent a complete ophthalmologic examination. DNA extraction and direct Sanger sequencing of the exons 4 and 12 of transforming growth factor β Induced (TGFBI) gene was performed for 42 members. For the molecular modeling of TGFBI protein, we used pGenTHREADER method to identify templates, 3D-EXPRESSO program to align sequences, MODELLER to get a homology model for the FAS1 (fasciclin-like) domains and finally NOMAD-ref web server for the energy minimization. Results: The diagnosis of GCD1 was clinically and genetically confirmed. Sequencing of exon 4 of TGFBI gene revealed the p.[R124S] mutation at heterozygous and homozygous states in patients with different clinical severities. Visual acuity was severely affected in the homozygous patients leading to a first penetrating keratoplasty. Recurrence occurred rapidly, began in the seat of the corneal stitches and remained superficial up to 40 years after the graft. For heterozygous cases, visual acuity ranged from 6/10 to 10/10. Corneal opacities were deeper and predominating in the stromal center. According to bioinformatic analysis, this mutation likely perturbs the protein physicochemical properties and reduces its solubility without structural modification. Conclusions: Our study describes for the first time phenotype-genotype correlation in a large Tunisian family with GCDI and illustrates for the first time clinical and histopathological presentation of homozygous p.[R124S] mutation. These results help to understand pathophysiology of the disease.
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Affiliation(s)
- Yosra Bouyacoub
- Laboratory of Biomedical Genetics and Oncogenetics, Université Tunis El Manar, Institut Pasteur de Tunis, LR16IPT05 , Tunis , Tunisia.,Institut Supérieur de Biotechnologie, Université de Monastir , Monastir , Tunisia
| | - Yousra Falfoul
- B Department, Hedi Raies Institute of Ophthalmology , Tunis , Tunisia.,Oculogenetic Laboratory, LR14SP01, Hedi Raies Institute of Ophthalmology , Tunis , Tunisia
| | - Mariem Ouederni
- Department of Ophthalmology, Habib Thameur Hospital , Tunis , Tunisia
| | - Marwa Sayeb
- Laboratory of Biomedical Genetics and Oncogenetics, Université Tunis El Manar, Institut Pasteur de Tunis, LR16IPT05 , Tunis , Tunisia
| | - Aschraf Chedli
- Department of Anatomopathology, Habib Thameur Hospital , Tunis , Tunisia
| | - Mariem Chargui
- Laboratory of Biomedical Genetics and Oncogenetics, Université Tunis El Manar, Institut Pasteur de Tunis, LR16IPT05 , Tunis , Tunisia
| | - Hela Sassi
- Department of Ophthalmology, Habib Thameur Hospital , Tunis , Tunisia
| | | | - Francis L Munier
- Jules-Gonin Eye Hospital, University of Lausanne , Lausanne , Switzerland
| | - Leila El Matri
- B Department, Hedi Raies Institute of Ophthalmology , Tunis , Tunisia.,Oculogenetic Laboratory, LR14SP01, Hedi Raies Institute of Ophthalmology , Tunis , Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genetics and Oncogenetics, Université Tunis El Manar, Institut Pasteur de Tunis, LR16IPT05 , Tunis , Tunisia
| | - Monia Cheour
- Department of Ophthalmology, Habib Thameur Hospital , Tunis , Tunisia
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Fassatoui M, Lopez-Siles M, Díaz-Rizzolo DA, Jmel H, Naouali C, Abdessalem G, Chikhaoui A, Nadal B, Jamoussi H, Abid A, Gomis R, Abdelhak S, Martinez-Medina M, Kefi R. Gut microbiota imbalances in Tunisian participants with type 1 and type 2 diabetes mellitus. Biosci Rep 2019; 39:BSR20182348. [PMID: 31147456 PMCID: PMC6579978 DOI: 10.1042/bsr20182348] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 12/22/2022] Open
Abstract
Gut microbiota plays an important role in the regulation of the immune system and host's metabolism. We aimed to characterize the gut microbiota of Tunisian participants with and without diabetes.We enrolled ten participants with type 1 diabetes mellitus (T1DM), ten patients with type 2 diabetes mellitus (T2DM), and 11 subjects without diabetes. Bacteria was quantified in fecal samples by quantitative PCR (qPCR). Statistical tests and multivariate analysis were performed using RStudio program.Results showed that the proportions of Firmicutes, Akkermansia muciniphila, and Faecalibacterium prausnitzii (P≤0.041), as well as, the ratio Firmicutes/Bacteroidetes decreased in participants with T1DM compared with those without diabetes (p = 0.036). Participants with T2DM presented a reduction in the amounts of A. muciniphila and F. prausnitzii compared with those without diabetes (P≤0.036). Furthermore, A. muciniphila is negatively correlated with glucose level (P=0.022) and glycated hemoglobin (HbA1c) (P=0.035). Multivariate analysis revealed that participants with diabetes formed a cluster apart compared with those without diabetes.In conclusion the gut bacteria of Tunisian participants with diabetes was altered. The gut bacterial profile, especially the distribution of A muciniphila in participants with diabetes was affected by glycemic dysregulation. The investigation of the gut microbiota may help clinicians to improve diagnosis and treatment of diabetes and its complications.
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Affiliation(s)
- Meriem Fassatoui
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, B.P.74, 1002, Belvédère, Tunis, Tunisia
- University of Tunis El Manar, Campus Universitaire Farhat Hached, BP n° 94, Rommana, 1068, Tunis, Tunisia
| | - Mireia Lopez-Siles
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Maria Aurèlia Capmany, 40, 17003, Girona, Spain
| | - Diana A Díaz-Rizzolo
- Diabetes and Obesity Research Laboratory, Institut d'Investigations Biomèdiques, August Pi I Sunyer (IDIBAPS), Hospital Clinic, Rosselló 149-153, 08036, Barcelona Spain
| | - Haifa Jmel
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, B.P.74, 1002, Belvédère, Tunis, Tunisia
| | - Chokri Naouali
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, B.P.74, 1002, Belvédère, Tunis, Tunisia
- University of Tunis El Manar, Campus Universitaire Farhat Hached, BP n° 94, Rommana, 1068, Tunis, Tunisia
| | - Ghaith Abdessalem
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, B.P.74, 1002, Belvédère, Tunis, Tunisia
- University of Tunis El Manar, Campus Universitaire Farhat Hached, BP n° 94, Rommana, 1068, Tunis, Tunisia
| | - Asma Chikhaoui
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, B.P.74, 1002, Belvédère, Tunis, Tunisia
- University of Tunis El Manar, Campus Universitaire Farhat Hached, BP n° 94, Rommana, 1068, Tunis, Tunisia
| | - Belén Nadal
- Diabetes and Obesity Research Laboratory, Institut d'Investigations Biomèdiques, August Pi I Sunyer (IDIBAPS), Hospital Clinic, Rosselló 149-153, 08036, Barcelona Spain
| | - Henda Jamoussi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, B.P.74, 1002, Belvédère, Tunis, Tunisia
- Department of Nutritional Diseases A, National Institute of Nutrition and Food Technology, 11, Rue Djebel Lakhdar, Bab Saâdoun, 1007, Tunis, Tunisia
| | - Abdelmajid Abid
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, B.P.74, 1002, Belvédère, Tunis, Tunisia
- Department of External Consultation, National Institute of Nutrition and Food Technology, 11, Rue Djebel Lakhdar, Bab Saâdoun, 1007, Tunis, Tunisia
| | - Ramon Gomis
- Diabetes and Obesity Research Laboratory, Institut d'Investigations Biomèdiques, August Pi I Sunyer (IDIBAPS), Hospital Clinic, Rosselló 149-153, 08036, Barcelona Spain
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, B.P.74, 1002, Belvédère, Tunis, Tunisia
- University of Tunis El Manar, Campus Universitaire Farhat Hached, BP n° 94, Rommana, 1068, Tunis, Tunisia
| | - Margarita Martinez-Medina
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Maria Aurèlia Capmany, 40, 17003, Girona, Spain
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, B.P.74, 1002, Belvédère, Tunis, Tunisia
- University of Tunis El Manar, Campus Universitaire Farhat Hached, BP n° 94, Rommana, 1068, Tunis, Tunisia
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49
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Jaballah-Gabteni A, Tounsi H, Kabbage M, Hamdi Y, Elouej S, Ben Ayed I, Medhioub M, Mahmoudi M, Dallali H, Yaiche H, Ben Jemii N, Maaloul A, Mezghani N, Abdelhak S, Hamzaoui L, Azzouz M, Boubaker S. Identification of novel pathogenic MSH2 mutation and new DNA repair genes variants: investigation of a Tunisian Lynch syndrome family with discordant twins. J Transl Med 2019; 17:212. [PMID: 31248416 PMCID: PMC6598283 DOI: 10.1186/s12967-019-1961-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 06/21/2019] [Indexed: 02/08/2023] Open
Abstract
Background Lynch syndrome (LS) is a highly penetrant inherited cancer predisposition syndrome, characterized by autosomal dominant inheritance and germline mutations in DNA mismatch repair genes. Despite several genetic variations that have been identified in various populations, the penetrance is highly variable and the reasons for this have not been fully elucidated. This study investigates whether, besides pathogenic mutations, environment and low penetrance genetic risk factors may result in phenotype modification in a Tunisian LS family. Patients and methods A Tunisian family with strong colorectal cancer (CRC) history that fulfill the Amsterdam I criteria for the diagnosis of Lynch syndrome was proposed for oncogenetic counseling. The index case was a man, diagnosed at the age of 33 years with CRC. He has a monozygotic twin diagnosed at the age of 35 years with crohn disease. Forty-seven years-old was the onset age of his paternal uncle withCRC. An immunohistochemical (IHC) labeling for the four proteins (MLH1, MSH2, MSH6 and PMS2) of the MisMatchRepair (MMR) system was performed for the index case. A targeted sequencing of MSH2, MLH1 and a panel of 85 DNA repair genes was performed for the index case and for his unaffected father. Results The IHC results showed a loss of MSH2 but not MLH1, MSH6 and PMS2 proteins expression. Genomic DNA screening, by targeted DNA repair genes sequencing, revealed an MSH2 pathogenic mutation (c.1552C>T; p.Q518X), confirmed by Sanger sequencing. This mutation was suspected to be a causal mutation associated to the loss of MSH2 expression and it was found in first and second degree relatives. The index case has smoking and alcohol consumption habits. Moreover, he harbors extensive genetic variations in other DNA-repair genes not shared with his unaffected father. Conclusion In our investigated Tunisian family, we confirmed the LS by IHC, molecular and in silico investigations. We identified a novel pathogenic mutation described for the first time in Tunisia. These results come enriching the previously reported pathogenic mutations in LS families. Our study brings new arguments to the interpretation of MMR expression pattern and highlights new risk modifiers genes eventually implicated in CRC. Twins discordance reported in this work underscore that disease penetrance could be influenced by both genetic background and environmental factors. Electronic supplementary material The online version of this article (10.1186/s12967-019-1961-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amira Jaballah-Gabteni
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia. .,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis, Tunisia.
| | - Haifa Tounsi
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis, Tunisia
| | - Maria Kabbage
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis, Tunisia
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis, Tunisia
| | - Sahar Elouej
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis, Tunisia.,Marseille Medical Genetics, Aix Marseille University, INSERM, Marseille, France
| | - Ines Ben Ayed
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis, Tunisia
| | - Mouna Medhioub
- Gastroenterology Department, Mohamed Tahar Maamouri Hospital, 8000, Nabeul, Tunisia
| | - Moufida Mahmoudi
- Gastroenterology Department, Mohamed Tahar Maamouri Hospital, 8000, Nabeul, Tunisia
| | - Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis, Tunisia
| | - Hamza Yaiche
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis, Tunisia
| | - Nadia Ben Jemii
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis, Tunisia
| | - Afifa Maaloul
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Najla Mezghani
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis, Tunisia
| | - Lamine Hamzaoui
- Gastroenterology Department, Mohamed Tahar Maamouri Hospital, 8000, Nabeul, Tunisia
| | - Mousaddak Azzouz
- Gastroenterology Department, Mohamed Tahar Maamouri Hospital, 8000, Nabeul, Tunisia
| | - Samir Boubaker
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis EL Manar University, Tunis, Tunisia
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Zaouak A, Jaouadi H, Chamli A, Jouini R, Abdelhak S, Hammami H, Fenniche S. H‐like syndrome successfully treated with methotrexate. Dermatol Ther 2019; 32:e12994. [DOI: 10.1111/dth.12994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 05/29/2019] [Accepted: 06/10/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Anissa Zaouak
- Dermatology Department, Research Unit “Genodermatoses and cancers LR12SP03”HabibThameur Hospital Tunis Tunisia
| | - Hager Jaouadi
- Laboratory of Biomedical Genomics and OncogeneticsInstitut Pasteur de Tunis Tunis Tunisia
| | - Amal Chamli
- Dermatology Department, Research Unit “Genodermatoses and cancers LR12SP03”HabibThameur Hospital Tunis Tunisia
| | - Raja Jouini
- Anatomopathology DepartmentHabibThameur Hospital Tunis Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and OncogeneticsInstitut Pasteur de Tunis Tunis Tunisia
| | - Houda Hammami
- Dermatology Department, Research Unit “Genodermatoses and cancers LR12SP03”HabibThameur Hospital Tunis Tunisia
| | - Samy Fenniche
- Dermatology Department, Research Unit “Genodermatoses and cancers LR12SP03”HabibThameur Hospital Tunis Tunisia
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