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Stephanou C, Petrou M, Kountouris P, Makariou C, Christou S, Hadjigavriel M, Kleanthous M, Papasavva T. Unravelling the Complexity of the +33 C>G [HBB:c.-18C>G] Variant in Beta Thalassemia. Biomedicines 2024; 12:296. [PMID: 38397898 PMCID: PMC10886608 DOI: 10.3390/biomedicines12020296] [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: 12/04/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
The +33 C>G variant [NM_000518.5(HBB):c.-18C>G] in the 5' untranslated region (UTR) of the β-globin gene is described in the literature as both mild and silent, while it causes a phenotype of thalassemia intermedia in the presence of a severe β-thalassemia allele. Despite its potential clinical significance, the determination of its pathogenicity according to established standards requires a greater number of published cases and co-segregation evidence than what is currently available. The present study provides an extensive phenotypic characterization of +33 C>G using 26 heterozygous and 11 compound heterozygous novel cases detected in Cyprus and employs computational predictors (CADD, RegulomeDB) to better understand its impact on clinical severity. Genotype identification of globin gene variants, including α- and δ-thalassemia determinants, and rs7482144 (XmnI) was carried out using Sanger sequencing, gap-PCR, and restriction enzyme digestion methods. The heterozygous state of +33 C>G had a silent phenotype without apparent microcytosis or hypochromia, while compound heterozygosity with a β+ or β0 allele had a spectrum of clinical phenotypes. Awareness of the +33 C>G is required across Mediterranean populations where β-thalassemia is frequent, particularly in Cyprus, with significant relevance in population screening and fetal diagnostic applications.
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Affiliation(s)
- Coralea Stephanou
- Molecular Genetics Thalassemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Miranda Petrou
- Molecular Genetics Thalassemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Petros Kountouris
- Molecular Genetics Thalassemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Christiana Makariou
- Thalassemia Clinic Nicosia, Archbishop Makarios III Hospital, Nicosia 2012, Cyprus
| | - Soteroula Christou
- Thalassemia Clinic Nicosia, Archbishop Makarios III Hospital, Nicosia 2012, Cyprus
| | | | - Marina Kleanthous
- Molecular Genetics Thalassemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Thessalia Papasavva
- Molecular Genetics Thalassemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
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2
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Koniali L, Flouri C, Kostopoulou MI, Papaioannou NY, Papasavva PL, Naiisseh B, Stephanou C, Demetriadou A, Sitarou M, Christou S, Antoniou MN, Kleanthous M, Patsali P, Lederer CW. Evaluation of Mono- and Bi-Functional GLOBE-Based Vectors for Therapy of β-Thalassemia by HBBAS3 Gene Addition and Mutation-Specific RNA Interference. Cells 2023; 12:2848. [PMID: 38132168 PMCID: PMC10741507 DOI: 10.3390/cells12242848] [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: 10/15/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Therapy via the gene addition of the anti-sickling βAS3-globin transgene is potentially curative for all β-hemoglobinopathies and therefore of particular clinical and commercial interest. This study investigates GLOBE-based lentiviral vectors (LVs) for βAS3-globin addition and evaluates strategies for an increased β-like globin expression without vector dose escalation. First, we report the development of a GLOBE-derived LV, GLV2-βAS3, which, compared to its parental vector, adds anti-sickling action and a transcription-enhancing 848-bp transcription terminator element, retains high vector titers and allows for superior β-like globin expression in primary patient-derived hematopoietic stem and progenitor cells (HSPCs). Second, prompted by our previous correction of HBBIVSI-110(G>A) thalassemia based on RNApol(III)-driven shRNAs in mono- and combination therapy, we analyzed a series of novel LVs for the RNApol(II)-driven constitutive or late-erythroid expression of HBBIVSI-110(G>A)-specific miRNA30-embedded shRNAs (shRNAmiR). This included bifunctional LVs, allowing for concurrent βAS3-globin expression. LVs were initially compared for their ability to achieve high β-like globin expression in HBBIVSI-110(G>A)-transgenic cells, before the evaluation of shortlisted candidate LVs in HBBIVSI-110(G>A)-homozygous HSPCs. The latter revealed that β-globin promoter-driven designs for monotherapy with HBBIVSI-110(G>A)-specific shRNAmiRs only marginally increased β-globin levels compared to untransduced cells, whereas bifunctional LVs combining miR30-shRNA with βAS3-globin expression showed disease correction similar to that achieved by the parental GLV2-βAS3 vector. Our results establish the feasibility of high titers for LVs containing the full HBB transcription terminator, emphasize the importance of the HBB terminator for the high-level expression of HBB-like transgenes, qualify the therapeutic utility of late-erythroid HBBIVSI-110(G>A)-specific miR30-shRNA expression and highlight the exceptional potential of GLV2-βAS3 for the treatment of severe β-hemoglobinopathies.
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Affiliation(s)
- Lola Koniali
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| | - Christina Flouri
- Gene Expression and Therapy Group, Department of Medical and Molecular Genetics, King’s College London, Guy’s Hospital, London SE1 9RT, UK; (C.F.); (M.N.A.)
| | - Markela I. Kostopoulou
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| | - Nikoletta Y. Papaioannou
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| | - Panayiota L. Papasavva
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| | - Basma Naiisseh
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| | - Coralea Stephanou
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| | - Anthi Demetriadou
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| | - Maria Sitarou
- Thalassemia Clinic Larnaca, Larnaca General Hospital, 6301 Larnaca, Cyprus;
| | - Soteroula Christou
- Thalassemia Clinic Nicosia, Archbishop Makarios III Hospital, 1474 Nicosia, Cyprus;
| | - Michael N. Antoniou
- Gene Expression and Therapy Group, Department of Medical and Molecular Genetics, King’s College London, Guy’s Hospital, London SE1 9RT, UK; (C.F.); (M.N.A.)
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| | - Petros Patsali
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| | - Carsten W. Lederer
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
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3
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Xenophontos M, Minaidou A, Stephanou C, Tamana S, Kleanthous M, Kountouris P. IthaPhen: An Interactive Database of Genotype-Phenotype Data for Hemoglobinopathies. Hemasphere 2023; 7:e922. [PMID: 37359188 PMCID: PMC10289560 DOI: 10.1097/hs9.0000000000000922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 05/31/2023] [Indexed: 06/28/2023] Open
Affiliation(s)
- Maria Xenophontos
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Anna Minaidou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Coralea Stephanou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Stella Tamana
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marina Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Petros Kountouris
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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4
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Minaidou A, Tamana S, Stephanou C, Xenophontos M, Harteveld CL, Bento C, Kleanthous M, Kountouris P. A Novel Tool for the Analysis and Detection of Copy Number Variants Associated with Haemoglobinopathies. Int J Mol Sci 2022; 23:ijms232415920. [PMID: 36555557 PMCID: PMC9782104 DOI: 10.3390/ijms232415920] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Several types of haemoglobinopathies are caused by copy number variants (CNVs). While diagnosis is often based on haematological and biochemical parameters, a definitive diagnosis requires molecular DNA analysis. In some cases, the molecular characterisation of large deletions/duplications is challenging and inconclusive and often requires the use of specific diagnostic procedures, such as multiplex ligation-dependent probe amplification (MLPA). Herein, we collected and comprehensively analysed all known CNVs associated with haemoglobinopathies. The dataset of 291 CNVs was retrieved from the IthaGenes database and was further manually annotated to specify genomic locations, breakpoints and MLPA probes relevant for each CNV. We developed IthaCNVs, a publicly available and easy-to-use online tool that can facilitate the diagnosis of rare and diagnostically challenging haemoglobinopathy cases attributed to CNVs. Importantly, it facilitates the filtering of available entries based on the type of breakpoint information, on specific chromosomal and locus positions, on MLPA probes, and on affected gene(s). IthaCNVs brings together manually curated information about CNV genomic locations, functional effects, and information that can facilitate CNV characterisation through MLPA. It can help laboratory staff and clinicians confirm suspected diagnosis of CNVs based on molecular DNA screening and analysis.
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Affiliation(s)
- Anna Minaidou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Stella Tamana
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Coralea Stephanou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Maria Xenophontos
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Cornelis L. Harteveld
- Human and Clinical Genetics Department, Leiden University Medical Center, P.O. Box 9600, 2333 ZC Leiden, The Netherlands
| | - Celeste Bento
- Department of Haematology, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal
| | - Marina Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Petros Kountouris
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
- Correspondence: ; Tel.: +357-22392623
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5
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Omirou M, Stephanou C, Anastopoulos I, Philippot L, Ioannides IM. Differential response of N 2O emissions, N 2O-producing and N 2O-reducing bacteria to varying tetracycline doses in fertilized soil. Environ Res 2022; 214:114013. [PMID: 35964670 DOI: 10.1016/j.envres.2022.114013] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Tetracyclines are the most widely used antibiotics worldwide. Their presence in soils could affect nutrient cycling, but our knowledge regarding how they affect soil microbial communities involved in greenhouse gas emissions is limited. The objective of the current study was to evaluate how tetracycline is affecting N2O emissions and the abundance of denitrifiers in fertilized soil. For this purpose, soil mesocosms were treated with only NH4NO3 (100 mg/kg) or NH4NO3 (100 mg/kg) plus three different doses of tetracycline (0.1, 0.5 and 2 mg/kg). Soils that did not receive tetracycline or NH4NO3 were used as controls. Nitrous oxide fluxes were monitored daily for 16 days. The total bacterial (16S rRNA), the abundance of N2O-reducing and -producing bacteria were quantified by qPCR at the end of the experiment. The application of NH4NO3 caused a significant increase of N2O emissions and AOB abundance but did not affect the abundance of denitrifiers and AOA compared to control soils. Different doses of tetracycline in fertilized soils did not mitigate these N2O emissions; instead, higher cumulative emissions were noticed in soils treated with the lowest dose. In these soils the total bacterial abundance was higher compared to soils received higher tetracycline concentration. The abundances of the N2O-producing and N2O-reducing communities were also differently affected by the addition of tetracycline, which was dose-dependent. Higher doses of tetracycline favored N2O-reducers within the total bacterial community, which could be important for mitigating N2O emissions in the long term.
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Affiliation(s)
- Michalis Omirou
- Department of Agrobiotechnology, Agricultural Research Institute, Nicosia, Cyprus.
| | - Coralea Stephanou
- Department of Agrobiotechnology, Agricultural Research Institute, Nicosia, Cyprus
| | - Ioannis Anastopoulos
- Department of Agriculture, University of Ioannina,UoI, Kostakii Campus, 47040 Arta, Greece
| | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, 21000 Dijon, France
| | - Ioannis M Ioannides
- Department of Agrobiotechnology, Agricultural Research Institute, Nicosia, Cyprus
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6
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Kountouris P, Stephanou C, Lederer CW, Traeger‐Synodinos J, Bento C, Harteveld CL, Fylaktou E, Koopmann TT, Halim‐Fikri H, Michailidou K, Nfonsam LE, Waye JS, Zilfalil BA, Kleanthous M. Adapting the ACMG/AMP variant classification framework: A perspective from the ClinGen Hemoglobinopathy Variant Curation Expert Panel. Hum Mutat 2022; 43:1089-1096. [PMID: 34510646 PMCID: PMC9545675 DOI: 10.1002/humu.24280] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/10/2021] [Accepted: 09/08/2021] [Indexed: 12/29/2022]
Abstract
Accurate and consistent interpretation of sequence variants is integral to the delivery of safe and reliable diagnostic genetic services. To standardize the interpretation process, in 2015, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published a joint guideline based on a set of shared standards for the classification of variants in Mendelian diseases. The generality of these standards and their subjective interpretation between laboratories has prompted efforts to reduce discordance of variant classifications, with a focus on the expert specification of the ACMG/AMP guidelines for individual genes or diseases. Herein, we describe our experience as a ClinGen Variant Curation Expert Panel to adapt the ACMG/AMP criteria for the classification of variants in three globin genes (HBB, HBA2, and HBA1) related to recessively inherited hemoglobinopathies, including five evidence categories, as use cases demonstrating the process of specification and the underlying rationale.
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Affiliation(s)
- Petros Kountouris
- Molecular Genetics Thalassaemia DepartmentThe Cyprus Institute of Neurology and GeneticsNicosiaCyprus,Cyprus School of Molecular MedicineNicosiaCyprus
| | - Coralea Stephanou
- Molecular Genetics Thalassaemia DepartmentThe Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Carsten W. Lederer
- Molecular Genetics Thalassaemia DepartmentThe Cyprus Institute of Neurology and GeneticsNicosiaCyprus,Cyprus School of Molecular MedicineNicosiaCyprus
| | - Joanne Traeger‐Synodinos
- Laboratory of Medical Genetics, St. Sophia's Children's HospitalNational and Kapodistrian University of AthensAthensGreece
| | - Celeste Bento
- Department of HaematologyCentro Hospitalar e Universitário de CoimbraCoimbraPortugal
| | - Cornelis L. Harteveld
- Department of Clinical Genetics/LDGALeiden University Medical CenterLeidenNetherlands
| | - Eirini Fylaktou
- Laboratory of Medical Genetics, St. Sophia's Children's HospitalNational and Kapodistrian University of AthensAthensGreece
| | - Tamara T. Koopmann
- Department of Clinical Genetics/LDGALeiden University Medical CenterLeidenNetherlands
| | | | - Kyriaki Michailidou
- Cyprus School of Molecular MedicineNicosiaCyprus,Biostatistics UnitThe Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Landry E. Nfonsam
- Hamilton Regional Laboratory Medicine ProgramHamilton Health SciencesHamiltonCanada,Department of Pathology and Molecular MedicineMcMaster UniversityHamiltonCanada
| | - John S. Waye
- Hamilton Regional Laboratory Medicine ProgramHamilton Health SciencesHamiltonCanada,Department of Pathology and Molecular MedicineMcMaster UniversityHamiltonCanada
| | | | - Marina Kleanthous
- Molecular Genetics Thalassaemia DepartmentThe Cyprus Institute of Neurology and GeneticsNicosiaCyprus,Cyprus School of Molecular MedicineNicosiaCyprus
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7
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Halim-Fikri BH, Lederer CW, Baig AA, Mat-Ghani SNA, Syed-Hassan SNRK, Yusof W, Abdul Rashid D, Azman NF, Fucharoen S, Panigoro R, Silao CLT, Viprakasit V, Jalil N, Mohd Yasin N, Bahar R, Selvaratnam V, Mohamad N, Nik Hassan NN, Esa E, Krause A, Robinson H, Hasler J, Stephanou C, Raja-Sabudin RZA, Elion J, El-Kamah G, Coviello D, Yusoff N, Abdul Latiff Z, Arnold C, Burn J, Kountouris P, Kleanthous M, Ramesar R, Zilfalil BA. Global Globin Network Consensus Paper: Classification and Stratified Roadmaps for Improved Thalassaemia Care and Prevention in 32 Countries. J Pers Med 2022; 12:jpm12040552. [PMID: 35455667 PMCID: PMC9032232 DOI: 10.3390/jpm12040552] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 12/22/2021] [Revised: 03/06/2022] [Accepted: 03/23/2022] [Indexed: 11/16/2022] Open
Abstract
The Global Globin Network (GGN) is a project-wide initiative of the Human Variome/Global Variome Project (HVP) focusing on haemoglobinopathies to build the capacity for genomic diagnosis, clinical services, and research in low- and middle-income countries. At present, there is no framework to evaluate the improvement of care, treatment, and prevention of thalassaemia and other haemoglobinopathies globally, despite thalassaemia being one of the most common monogenic diseases worldwide. Here, we propose a universally applicable system for evaluating and grouping countries based on qualitative indicators according to the quality of care, treatment, and prevention of haemoglobinopathies. We also apply this system to GGN countries as proof of principle. To this end, qualitative indicators were extracted from the IthaMaps database of the ITHANET portal, which allowed four groups of countries (A, B, C, and D) to be defined based on major qualitative indicators, supported by minor qualitative indicators for countries with limited resource settings and by the overall haemoglobinopathy carrier frequency for the target countries of immigration. The proposed rubrics and accumulative scores will help analyse the performance and improvement of care, treatment, and prevention of haemoglobinopathies in the GGN and beyond. Our proposed criteria complement future data collection from GGN countries to help monitor the quality of services for haemoglobinopathies, provide ongoing estimates for services and epidemiology in GGN countries, and note the contribution of the GGN to a local and global reduction of disease burden.
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Affiliation(s)
- Bin Hashim Halim-Fikri
- Malaysian Node of the Human Variome Project Secretariat, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (B.H.H.-F.); (S.-N.R.-K.S.-H.); (W.Y.)
| | - Carsten W. Lederer
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Ayios Dometios, Nicosia 2371, Cyprus; (C.W.L.); (C.S.); (P.K.); (M.K.)
| | - Atif Amin Baig
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu 20400, Terengganu, Malaysia;
| | - Siti Nor Assyuhada Mat-Ghani
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (S.N.A.M.-G.); (N.N.N.H.)
| | - Sharifah-Nany Rahayu-Karmilla Syed-Hassan
- Malaysian Node of the Human Variome Project Secretariat, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (B.H.H.-F.); (S.-N.R.-K.S.-H.); (W.Y.)
| | - Wardah Yusof
- Malaysian Node of the Human Variome Project Secretariat, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (B.H.H.-F.); (S.-N.R.-K.S.-H.); (W.Y.)
| | - Diana Abdul Rashid
- Department of Paediatrics, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (D.A.R.); (N.F.A.); (N.M.)
| | - Nurul Fatihah Azman
- Department of Paediatrics, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (D.A.R.); (N.F.A.); (N.M.)
| | - Suthat Fucharoen
- Thalassemia Research Centre, Institute of Molecular Biosciences, Mahidol University, Nakhom Pathom 73170, Thailand;
| | - Ramdan Panigoro
- Department of Biomedical Sciences, Medical Genetics Research Centre, Faculty of Medicine, Universitas Padjadjaran, Bandung 40161, Indonesia;
| | - Catherine Lynn T. Silao
- Institute of Human Genetics, National Institutes of Health, University of the Philippines, Manila 1000, Philippines;
- Department of Pediatrics, College of Medicine, University of the Philippines, Manila 1000, Philippines
| | - Vip Viprakasit
- Department of Paediatrics & Thalassaemia Centre, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Norunaluwar Jalil
- UKM Specialist Children’s Hospital, Jalan Yaacob Latif, Bandar Tun Razak, Cheras 56000, Kuala Lumpur, Malaysia;
| | - Norafiza Mohd Yasin
- Haematology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health, No. 1, Jalan Setia Murni U13/52, Seksyen U13, Bandar Setia Alam, Shah Alam 40170, Selangor Darul Ehsan, Malaysia; (N.M.Y.); (E.E.)
| | - Rosnah Bahar
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia;
| | - Veena Selvaratnam
- Hospital Ampang, Jalan Mewah Utara, Taman Pandan Mewah, Ampang Jaya 68000, Selangor, Malaysia;
| | - Norsarwany Mohamad
- Department of Paediatrics, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (D.A.R.); (N.F.A.); (N.M.)
| | - Nik Norliza Nik Hassan
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (S.N.A.M.-G.); (N.N.N.H.)
| | - Ezalia Esa
- Haematology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health, No. 1, Jalan Setia Murni U13/52, Seksyen U13, Bandar Setia Alam, Shah Alam 40170, Selangor Darul Ehsan, Malaysia; (N.M.Y.); (E.E.)
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service (NHLS) and School of Pathology, Faculty of Health Sciences, The University of the Witwatersrand, Watkins Pitchford Building, NHLS Braamfontein, Cnr Hospital and De Korte St, Hillbrow, P.O. Box 1038, Johannesburg 2000, South Africa;
| | - Helen Robinson
- Nossal Institute for Global Health, MDDHS, University of Melbourne, Melbourne, VIC 3010, Australia;
| | - Julia Hasler
- Global Variome, Institute of Genetic Medicine, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK;
| | - Coralea Stephanou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Ayios Dometios, Nicosia 2371, Cyprus; (C.W.L.); (C.S.); (P.K.); (M.K.)
| | - Raja-Zahratul-Azma Raja-Sabudin
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, Cheras 56000, Kuala Lumpur, Malaysia;
| | - Jacques Elion
- Medical School, Université Paris Diderot, 75018 Paris, France;
| | - Ghada El-Kamah
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo 12622, Egypt;
| | - Domenico Coviello
- Laboratorio di Genetica Umana, IRCCS Istituto Giannina Gaslini, Largo Gerolamo Gaslini 5, 16147 Genova, Italy;
| | - Narazah Yusoff
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas 13200, Pulau Pinang, Malaysia;
| | - Zarina Abdul Latiff
- Department of Paediatrics, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Cheras 56000, Kuala Lumpur, Malaysia;
| | - Chris Arnold
- BioGrid Australia, Hodgson Associates, 4 Hodgson St., Kew, Melbourne, VIC 3101, Australia;
| | - John Burn
- Translational and Clinical Research Institute, International Centre for Life Times Square, Newcastle upon Tyne NE1 3BZ, UK;
| | - Petros Kountouris
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Ayios Dometios, Nicosia 2371, Cyprus; (C.W.L.); (C.S.); (P.K.); (M.K.)
| | - Marina Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, Ayios Dometios, Nicosia 2371, Cyprus; (C.W.L.); (C.S.); (P.K.); (M.K.)
| | - Raj Ramesar
- Department of Pathology, University of Cape Town City of Cape Town, Cape Town 7925, South Africa;
| | - Bin Alwi Zilfalil
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Correspondence: or ; Tel.: +60-9767-6531
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8
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Tamana S, Xenophontos M, Minaidou A, Stephanou C, Harteveld CL, Bento C, Traeger-Synodinos J, Fylaktou I, Yasin NM, Abdul Hamid FS, Esa E, Halim-Fikri H, Zilfalil BA, Kakouri AC, Kleanthous M, Kountouris P. Evaluation of in silico predictors on short nucleotide variants in HBA1, HBA2, and HBB associated with haemoglobinopathies. eLife 2022; 11:79713. [PMID: 36453528 PMCID: PMC9731569 DOI: 10.7554/elife.79713] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022] Open
Abstract
Haemoglobinopathies are the commonest monogenic diseases worldwide and are caused by variants in the globin gene clusters. With over 2400 variants detected to date, their interpretation using the American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines is challenging and computational evidence can provide valuable input about their functional annotation. While many in silico predictors have already been developed, their performance varies for different genes and diseases. In this study, we evaluate 31 in silico predictors using a dataset of 1627 variants in HBA1, HBA2, and HBB. By varying the decision threshold for each tool, we analyse their performance (a) as binary classifiers of pathogenicity and (b) by using different non-overlapping pathogenic and benign thresholds for their optimal use in the ACMG/AMP framework. Our results show that CADD, Eigen-PC, and REVEL are the overall top performers, with the former reaching moderate strength level for pathogenic prediction. Eigen-PC and REVEL achieve the highest accuracies for missense variants, while CADD is also a reliable predictor of non-missense variants. Moreover, SpliceAI is the top performing splicing predictor, reaching strong level of evidence, while GERP++ and phyloP are the most accurate conservation tools. This study provides evidence about the optimal use of computational tools in globin gene clusters under the ACMG/AMP framework.
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Affiliation(s)
- Stella Tamana
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Maria Xenophontos
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Anna Minaidou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Coralea Stephanou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Cornelis L Harteveld
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus,Leiden University Medical CenterLeidenNetherlands
| | - Celeste Bento
- Centro Hospitalar e Universitário de CoimbraCoimbraPortugal
| | | | - Irene Fylaktou
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of AthensAthensGreece
| | - Norafiza Mohd Yasin
- Haematology Unit, Cancer Research Centre, Institute for Medical Research, National Health of Institutes (NIH), Ministry of Health MalaysiaSelangorMalaysia
| | - Faidatul Syazlin Abdul Hamid
- Haematology Unit, Cancer Research Centre, Institute for Medical Research, National Health of Institutes (NIH), Ministry of Health MalaysiaSelangorMalaysia
| | - Ezalia Esa
- Haematology Unit, Cancer Research Centre, Institute for Medical Research, National Health of Institutes (NIH), Ministry of Health MalaysiaSelangorMalaysia
| | - Hashim Halim-Fikri
- Malaysian Node of the Human Variome Project, School of Medical Sciences, Health Campus, Universiti Sains MalaysiaKelantanMalaysia
| | - Bin Alwi Zilfalil
- Human Genome Centre, School of Medical Sciences, Health Campus, Universiti Sains MalaysiaKelantanMalaysia
| | - Andrea C Kakouri
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | | | - Marina Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Petros Kountouris
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
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9
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Kountouris P, Stephanou C, Archer N, Bonifazi F, Giannuzzi V, Kuo KHM, Maggio A, Makani J, Mañú-Pereira MDM, Michailidou K, Nkya S, Nnodu OE, Trompeter S, Tshilolo L, Wonkam A, Zilfalil BA, Inusa BPD, Kleanthous M. The International Hemoglobinopathy Research Network (INHERENT): An international initiative to study the role of genetic modifiers in hemoglobinopathies. Am J Hematol 2021; 96:E416-E420. [PMID: 34406671 PMCID: PMC10390849 DOI: 10.1002/ajh.26323] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/02/2021] [Indexed: 01/09/2023]
Affiliation(s)
- Petros Kountouris
- The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | | | - Natasha Archer
- Pediatric Hematology/Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - Fedele Bonifazi
- Fondazione per la Ricerca Farmacologica Gianni Benzi Onlus, Bari, Italy
| | - Viviana Giannuzzi
- Fondazione per la Ricerca Farmacologica Gianni Benzi Onlus, Bari, Italy
| | - Kevin H M Kuo
- Division of Hematology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | - Julie Makani
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - María Del Mar Mañú-Pereira
- Translational Research in Child and Adolescent Cancer. Vall d'Hebron Institut de recerca, Barcelona, Spain
| | - Kyriaki Michailidou
- The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Siana Nkya
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.,Dar es Salaam University College of Education, Dar es Salaam, Tanzania
| | - Obiageli E Nnodu
- Department of Haematology and Blood Transfusion, University of Abuja, Abuja, Nigeria
| | - Sara Trompeter
- University College London Hospitals NHS Trust, London, UK.,NHS Blood and Transplant, London, UK
| | - Léon Tshilolo
- Centre Hospitalier Monkole and CEFA-Institut de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
| | | | | | - Baba P D Inusa
- Paediatric Haematology, Evelina London Children's Hospital, Guy's & St. Thomas' Hospital NHS Foundation Trust, London, UK
| | - Marina Kleanthous
- The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
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10
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Stephanou C, Omirou M, Philippot L, Zissimos AM, Christoforou IC, Trajanoski S, Oulas A, Ioannides IM. Land use in urban areas impacts the composition of soil bacterial communities involved in nitrogen cycling. A case study from Lefkosia (Nicosia) Cyprus. Sci Rep 2021; 11:8198. [PMID: 33854127 PMCID: PMC8047022 DOI: 10.1038/s41598-021-87623-y] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/31/2021] [Indexed: 01/04/2023] Open
Abstract
The different types of land-use and soil lithology in urban and peri-urban areas of modern cities compose a complex mosaic of soil ecosystems. It is largely unknown how these differences result in changes in bacterial community composition and structure as well as in functional guilds involved in N cycling. To investigate the bacterial composition and the proportion of denitrifiers in agricultural, forested, schoolyard and industrial areas, 24 samples were collected from urban and peri-urban sites of Lefkosia. Bacterial diversity and the proportion of denitrifiers were assessed by NGS and qPCR, respectively. Proteobacteria, Actinobacteria, Bacteriodetes, Chloroflexi, Acidobacteria and Planctomycetes were identified as the most dominant phyla across all sites, while agricultural sites exhibited the highest bacterial diversity. Heavy metals such as Co, Pb, V and Al were identified as key factors shaping bacterial composition in industrial and schoolyard sites, while the bacterial assemblages in agricultural and forested sites were associated with Ca. Variance partitioning analysis showed that 10.2% of the bacterial community variation was explained by land use management, 5.1% by chemical elements due to soil lithology, and 1.4% by sampling location. The proportion of denitrifiers varied with land use management. In industrial and schoolyard sites, the abundance of the nosZII bacterial community increased while nirK abundance declined. Our data showed that land use and lithology have a moderate impact on the bacterial assemblages in urban and peri-urban areas of Lefkosia. As the nosZII bacterial community is important to the N2O sink capacity of soils, it would be interesting to elucidate the factors contributing to the proliferation of the nosZII clade in these soils.
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Affiliation(s)
- Coralea Stephanou
- Department of Agrobiotechnology, Agricultural Research Institute, Nicosia, Cyprus
| | - Michalis Omirou
- Department of Agrobiotechnology, Agricultural Research Institute, Nicosia, Cyprus. .,Department of Agrobiotechnology, Agricultural Microbiology Laboratory, Agricultural Research Institute, Athalassa, Cyprus.
| | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, 21000, Dijon, France
| | - Andreas M Zissimos
- Geological Survey Department, Ministry of Agriculture, Rural Development and Environment, Nicosia, Cyprus
| | - Irene C Christoforou
- Geological Survey Department, Ministry of Agriculture, Rural Development and Environment, Nicosia, Cyprus
| | - Slave Trajanoski
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Anastasis Oulas
- Cyprus Institute of Neurology and Genetics, Bioinformatics Group, Engomi, Cyprus
| | - Ioannis M Ioannides
- Department of Agrobiotechnology, Agricultural Research Institute, Nicosia, Cyprus
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11
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Nanou A, Toumpeki C, Fanis P, Bianchi N, Cosenza LC, Zuccato C, Sentis G, Giagkas G, Stephanou C, Phylactides M, Christou S, Hadjigavriel M, Sitarou M, Lederer CW, Gambari R, Kleanthous M, Katsantoni E. Sex-specific transcriptional profiles identified in β-thalassemia patients. Haematologica 2021; 106:1207-1211. [PMID: 32817281 PMCID: PMC8018115 DOI: 10.3324/haematol.2020.248013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Indexed: 11/29/2022] Open
Affiliation(s)
- Aikaterini Nanou
- Basic Research Center, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Chrisavgi Toumpeki
- Basic Research Center, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Pavlos Fanis
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia
| | - Nicoletta Bianchi
- Department of Life Sciences and Biotechnology, Ferrara University, Ferrara, Italy
| | | | - Cristina Zuccato
- Department of Life Sciences and Biotechnology, Ferrara University, Ferrara, Italy
| | - George Sentis
- Basic Research Center, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Giorgos Giagkas
- Basic Research Center, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Coralea Stephanou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia
| | - Marios Phylactides
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia
| | | | | | - Maria Sitarou
- Thalassemia Clinic Larnaca, Larnaca General Hospital, Larnaca, Cyprus
| | - Carsten W Lederer
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Ferrara University, Ferrara, Italy
| | - Marina Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia
| | - Eleni Katsantoni
- Basic Research Center, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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12
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Affiliation(s)
- Coralea Stephanou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Petros Kountouris
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Carsten W. Lederer
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marina Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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13
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Lederer CW, Patsali P, Mussolino C, Turchiano G, Papasavva P, Romito M, Stephanou C, Cornu TI, Kolnagou A, Christou S, Sitarou M, Antoniou MN, Cathomen T, Kleanthous M. Gene Therapy Getting Personal: Mutation-Specific Editing and Gene Addition Strategies for β-Thalassaemia. Hemoglobin 2020. [DOI: 10.1080/03630269.2020.1719599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Carsten W. Lederer
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Petros Patsali
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Giandomenico Turchiano
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Panayiota Papasavva
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Marianna Romito
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Coralea Stephanou
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Tatjana I. Cornu
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Annita Kolnagou
- Thalassaemia Clinic Paphos, Paphos General Hospital, Paphos, Cyprus
| | - Soteroula Christou
- Thalassaemia Clinic Nicosia, Archbishop Makarios III Hospital, Nicosia, Cyprus
| | - Maria Sitarou
- Thalassaemia Clinic Larnaca, Larnaca General Hospital, Larnaca, Cyprus
| | - Mike N. Antoniou
- Department of Medical and Molecular Genetics, King’s College London, London, UK
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
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14
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Kountouris P, Stephanou C, Lederer CW, Tamana S, Minaidou A, Xenophontos M, Angastiniotis M, Eleftheriou A, Zilfalil BA, Ramesar RS, Elion J, Robinson HM, Kleanthous M. The ITHANET-Human Variome Project: Moving Functional Annotation Forward. Hemoglobin 2020. [DOI: 10.1080/03630269.2020.1719591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Petros Kountouris
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Coralea Stephanou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Carsten W. Lederer
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Stella Tamana
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Anna Minaidou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Maria Xenophontos
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | | | | | - Bin Alwi Zilfalil
- School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Raj S. Ramesar
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Jacques Elion
- Paris Diderot University Medical School, Paris, France
| | - Helen M. Robinson
- Human Variome Project International Coordinating Office, Melbourne, Australia
| | - Marina Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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15
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Stephanou C, Kountouris P, Tamana S, Minaidou A, Lederer CW, Kleanthous M. ITHANET: An Information and Database Community Portal for Hemoglobinopathies. Hemoglobin 2020. [DOI: 10.1080/03630269.2020.1717757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Coralea Stephanou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Petros Kountouris
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Stella Tamana
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Anna Minaidou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Carsten W. Lederer
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marina Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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16
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Anastopoulos I, Omirou M, Stephanou C, Oulas A, Vasiliades MA, Efstathiou AM, Ioannides IM. Valorization of agricultural wastes could improve soil fertility and mitigate soil direct N 2O emissions. J Environ Manage 2019; 250:109389. [PMID: 31499464 DOI: 10.1016/j.jenvman.2019.109389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/26/2019] [Accepted: 08/10/2019] [Indexed: 06/10/2023]
Abstract
The emerging need for sustainable management of the increasing quantities of urban and industrial organic wastes creates opportunities for the development of alternative strategies for the improvement of degraded soils. The current study was performed to examine the effects of agricultural wastes application on soil bacterial community as well as CO2 and N2O direct gas emissions. Untreated soils were compared with soils, which received the same amount of N (100 μg/g soil) in the form of ammonium nitrate and organic agricultural waste. In particular, soils were incubated with three different organic agricultural wastes, orange (OP), mandarin (MP) and banana peels (BP) and ammonium nitrate (F) after adjusting soil water at 70% of its holding capacity. In the current study, soil chemical characteristics, quantitative PCR of denitrifiers (nirK, nirS, nosZI and nosZII) and16s rRNA amplicon sequencing were assessed to examine the links between the soil microbial communities and short-term soil direct N2O emissions when treated with agricultural wastes. The highest soil direct N2O emissions were recorded in soils received ammonium nitrate while soils received agricultural wastes exhibited substantially lower soil direct N2O emissions. On the contrary, agricultural wastes stimulated CO2 accumulation as well as the growth of copiotrophic bacterial groups like Proteobacteria and Firmicutes. Interestingly, direct soil N2O emissions were decoupled from the density of denitrifier community while agricultural wastes caused a substantial reduction of the relative abundance of bacterial taxa associated with N2O emissions in the soil. This study proves evidence that agricultural wastes could be integrated in a waste management strategy, which inter alia includes their direct use in agricultural ecosystems resulting in reduced N2O emissions.
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Affiliation(s)
| | - Michalis Omirou
- Agricultural Research Institute, Department of Agrobiotechnology, Cyprus.
| | - Coralea Stephanou
- Agricultural Research Institute, Department of Agrobiotechnology, Cyprus
| | - Anastasios Oulas
- Cyprus Institute of Neurology and Genetics, Bioinformatics Group, Cyprus
| | - Michalis A Vasiliades
- University of Cyprus, Department of Chemistry, Heterogeneous Catalysis Laboratory, Cyprus
| | - Angelos M Efstathiou
- University of Cyprus, Department of Chemistry, Heterogeneous Catalysis Laboratory, Cyprus
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17
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Stephanou C, Tamana S, Minaidou A, Papasavva P, Kleanthous M, Kountouris P. Genetic Modifiers at the Crossroads of Personalised Medicine for Haemoglobinopathies. J Clin Med 2019; 8:jcm8111927. [PMID: 31717530 PMCID: PMC6912721 DOI: 10.3390/jcm8111927] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 09/20/2019] [Revised: 10/25/2019] [Accepted: 11/05/2019] [Indexed: 12/20/2022] Open
Abstract
Haemoglobinopathies are common monogenic disorders with diverse clinical manifestations, partly attributed to the influence of modifier genes. Recent years have seen enormous growth in the amount of genetic data, instigating the need for ranking methods to identify candidate genes with strong modifying effects. Here, we present the first evidence-based gene ranking metric (IthaScore) for haemoglobinopathy-specific phenotypes by utilising curated data in the IthaGenes database. IthaScore successfully reflects current knowledge for well-established disease modifiers, while it can be dynamically updated with emerging evidence. Protein–protein interaction (PPI) network analysis and functional enrichment analysis were employed to identify new potential disease modifiers and to evaluate the biological profiles of selected phenotypes. The most relevant gene ontology (GO) and pathway gene annotations for (a) haemoglobin (Hb) F levels/Hb F response to hydroxyurea included urea cycle, arginine metabolism and vascular endothelial growth factor receptor (VEGFR) signalling, (b) response to iron chelators included xenobiotic metabolism and glucuronidation, and (c) stroke included cytokine signalling and inflammatory reactions. Our findings demonstrate the capacity of IthaGenes, together with dynamic gene ranking, to expand knowledge on the genetic and molecular basis of phenotypic variation in haemoglobinopathies and to identify additional candidate genes to potentially inform and improve diagnosis, prognosis and therapeutic management.
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Affiliation(s)
| | | | | | | | - Marina Kleanthous
- Correspondence: (M.K.); (P.K.); Tel.:+357-2239-2652 (M.K.); +357-2239-2623 (P.K.)
| | - Petros Kountouris
- Correspondence: (M.K.); (P.K.); Tel.:+357-2239-2652 (M.K.); +357-2239-2623 (P.K.)
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18
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Bento C, Kountouris P, Stephanou C, Lederer CW, Kleanthous M. Variant Scoring Based on ClinGen Tools and Hemoglobinopathy-Specific Criteria. Hemoglobin 2019. [DOI: 10.1080/03630269.2020.1719589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Celeste Bento
- Haematology Department, Central Hospital and University of Coimbra, Coimbra, Portugal
- Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Petros Kountouris
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Coralea Stephanou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Carsten W. Lederer
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marina Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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19
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Dong A, Ghiaccio V, Motta I, Guo S, Peralta R, Freier SM, Watt A, Damle S, Ikawa Y, Jarocha D, Chappell M, Stephanou C, Delbini P, Chen C, Christou S, Kleanthous M, Smith-Whitley K, Manwani D, Casu C, Abdulmalik O, Cappellini MD, Rivella S, Breda L. 2'-O-methoxyethyl splice-switching oligos correct splicing from IVS2-745 β-thalassemia patient cells restoring HbA production and chain rebalance. Haematologica 2019; 106:1433-1442. [PMID: 32439726 PMCID: PMC8094087 DOI: 10.3324/haematol.2019.226852] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Indexed: 01/13/2023] Open
Abstract
β-thalassemia is a disorder caused by altered hemoglobin protein synthesis which affects individuals worldwide. Severe forms of the disease, left untreated, can result in death before the age of 3 years.1 The standard of care consists of chronic and costly palliative treatment by blood transfusion combined with iron chelation. This dual approach suppresses anemia and reduces iron-related toxicities in patients. Allogeneic bone marrow transplant is an option, but limited by the availability of a highly compatible hematopoietic stem cell donor. While gene therapy is being explored in several trials, its use is highly limited to developed regions with centers of excellence and well-established healthcare systems. 2 Hence, there remains a tremendous unmet medical need to develop alternative treatment strategies for b-thalassemia.3 Occurrence of aberrant splicing is one of the processes that affects b-globin synthesis in b-thalassemia. The (C>G) IVS2-745 is a splicing mutation within intron 2 of the b-globin (HBB) gene. It leads to an aberrantly spliced mRNA that incorporates an intron fragment. This results in an in-frame premature termination codon that inhibits b-globin production. Here, we propose the use of uniform 2'-O-methoxyethyl (2'-MOE) splice switching oligos (SSO) to reverse this aberrant splicing in the pre-mRNA. With these SSO we show aberrant to wild-type splice switching. This switching leads to an increase of adult hemoglobin up to 80% in erythroid cells from patients with the IVS2-745 HBB mutation. Furthermore, we demonstrate a restoration of the balance between b-like- and α-globin chains, and up to an 87% reduction in toxic heme aggregates. While examining the potential benefit of 2'-MOE-SSO in a mixed sickle-thalassemic phenotypic setting, we found reduced sickle hemoglobin synthesis and sickle cell formation due to HbA induction. In summary, 2'-MOE-SSO are a promising therapy for forms of b-thalassemia caused by mutations leading to aberrant splicing.
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Affiliation(s)
- Alisa Dong
- Weill Cornell Medical College of Cornell University, New York, USA
| | - Valentina Ghiaccio
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, USA
| | - Irene Motta
- University of Milan - Fondazione IRCCS Ca' Granda Ospedale Policlinico, Milan, Italy
| | | | | | | | - Andy Watt
- Ionis Pharmaceuticals, Carlsbad, CA, USA
| | | | - Yasuhiro Ikawa
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, USA
| | - Danuta Jarocha
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, USA
| | - Maxwell Chappell
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, USA
| | - Coralea Stephanou
- Dept. of Molecular Genetics Thalassaemia, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Paola Delbini
- University of Milan - Fondazione IRCCS Ca' Granda Ospedale Policlinico, Milan, Italy
| | - Connie Chen
- Graduate School of Medical Sciences, Weill Cornell Medical College of Cornell University, New York
| | - Soteroula Christou
- Dept. of Molecular Genetics Thalassaemia, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marina Kleanthous
- Dept. of Molecular Genetics Thalassaemia, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kim Smith-Whitley
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, USA
| | | | - Carla Casu
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, USA
| | - Osheiza Abdulmalik
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, USA
| | | | - Stefano Rivella
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, USA
| | - Laura Breda
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, USA
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20
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Patsali P, Turchiano G, Papasavva P, Romito M, Loucari CC, Stephanou C, Christou S, Sitarou M, Mussolino C, Cornu TI, Antoniou MN, Lederer CW, Cathomen T, Kleanthous M. Correction of IVS I-110(G>A) β-thalassemia by CRISPR/Cas-and TALEN-mediated disruption of aberrant regulatory elements in human hematopoietic stem and progenitor cells. Haematologica 2019; 104:e497-e501. [PMID: 31004018 DOI: 10.3324/haematol.2018.215178] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Petros Patsali
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Giandomenico Turchiano
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Freiburg, Germany
| | - Panayiota Papasavva
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Marianna Romito
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Freiburg, Germany
| | - Constantinos C Loucari
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Coralea Stephanou
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Department of Medical and Molecular Genetics, King's College London, London, UK
| | | | - Maria Sitarou
- Thalassemia Center, Cyprus Ministry of Health, Cyprus
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Freiburg, Germany
| | - Tatjana I Cornu
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Freiburg, Germany
| | - Michael N Antoniou
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Carsten W Lederer
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus .,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany .,Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus .,Cyprus School of Molecular Medicine, Nicosia, Cyprus
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21
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Kashiouris M, Zemore Z, Kimball Z, Stephanou C, de Wit M, Fowler A, Fisher B, Sessler C. SUPPLY CHAIN DELAYS IN ANTIMICROBIAL ADMINISTRATION AFTER THE INITIAL CLINICIAN ORDER AND MORTALITY IN PATIENTS WITH SEPSIS. Chest 2019. [DOI: 10.1016/j.chest.2019.02.106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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22
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Patsali P, Papasavva P, Stephanou C, Christou S, Sitarou M, Antoniou MN, Lederer CW, Kleanthous M. Short-hairpin RNA against aberrant HBBIVSI-110(G>A) mRNA restores β-globin levels in a novel cell model and acts as mono- and combination therapy for β-thalassemia in primary hematopoietic stem cells. Haematologica 2018; 103:e419-e423. [PMID: 29700171 DOI: 10.3324/haematol.2018.189357] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Petros Patsali
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Department of Medical and Molecular Genetics, King's College London, UK
| | - Panayiota Papasavva
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Coralea Stephanou
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Department of Medical and Molecular Genetics, King's College London, UK
| | | | | | | | - Carsten W Lederer
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus .,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
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23
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Loucari CC, Patsali P, van Dijk TB, Stephanou C, Papasavva P, Zanti M, Kurita R, Nakamura Y, Christou S, Sitarou M, Philipsen S, Lederer CW, Kleanthous M. Rapid and Sensitive Assessment of Globin Chains for Gene and Cell Therapy of Hemoglobinopathies. Hum Gene Ther Methods 2018; 29:60-74. [PMID: 29325430 PMCID: PMC5806072 DOI: 10.1089/hgtb.2017.190] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 10/01/2017] [Accepted: 01/09/2018] [Indexed: 02/06/2023] Open
Abstract
The β-hemoglobinopathies sickle cell anemia and β-thalassemia are the focus of many gene-therapy studies. A key disease parameter is the abundance of globin chains because it indicates the level of anemia, likely toxicity of excess or aberrant globins, and therapeutic potential of induced or exogenous β-like globins. Reversed-phase high-performance liquid chromatography (HPLC) allows versatile and inexpensive globin quantification, but commonly applied protocols suffer from long run times, high sample requirements, or inability to separate murine from human β-globin chains. The latter point is problematic for in vivo studies with gene-addition vectors in murine disease models and mouse/human chimeras. This study demonstrates HPLC-based measurements of globin expression (1) after differentiation of the commonly applied human umbilical cord blood-derived erythroid progenitor-2 cell line, (2) in erythroid progeny of CD34+ cells for the analysis of clustered regularly interspaced short palindromic repeats/Cas9-mediated disruption of the globin regulator BCL11A, and (3) of transgenic mice holding the human β-globin locus. At run times of 8 min for separation of murine and human β-globin chains as well as of human γ-globin chains, and with routine measurement of globin-chain ratios for 12 nL of blood (tested for down to 0.75 nL) or of 300,000 in vitro differentiated cells, the methods presented here and any variant-specific adaptations thereof will greatly facilitate evaluation of novel therapy applications for β-hemoglobinopathies.
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Affiliation(s)
- Constantinos C. Loucari
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Petros Patsali
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Thamar B. van Dijk
- Erasmus University Medical Center, Department of Cell Biology, Rotterdam, The Netherlands
| | - Coralea Stephanou
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Panayiota Papasavva
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Maria Zanti
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Ryo Kurita
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | | | | | - Sjaak Philipsen
- Erasmus University Medical Center, Department of Cell Biology, Rotterdam, The Netherlands
| | - Carsten W. Lederer
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
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24
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Stephanou C, Papasavva P, Zachariou M, Patsali P, Epitropou M, Ladas P, Al-Abdulla R, Christou S, Antoniou MN, Lederer CW, Kleanthous M. Suitability of small diagnostic peripheral-blood samples for cell-therapy studies. Cytotherapy 2017; 19:311-326. [PMID: 28088294 DOI: 10.1016/j.jcyt.2016.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 09/01/2016] [Revised: 11/07/2016] [Accepted: 11/07/2016] [Indexed: 01/20/2023]
Abstract
BACKGROUND AIMS Primary hematopoietic stem and progenitor cells (HSPCs) are key components of cell-based therapies for blood disorders and are thus the authentic substrate for related research. We propose that ubiquitous small-volume diagnostic samples represent a readily available and as yet untapped resource of primary patient-derived cells for cell- and gene-therapy studies. METHODS In the present study we compare isolation and storage methods for HSPCs from normal and thalassemic small-volume blood samples, considering genotype, density-gradient versus lysis-based cell isolation and cryostorage media with different serum contents. Downstream analyses include viability, recovery, differentiation in semi-solid media and performance in liquid cultures and viral transductions. RESULTS We demonstrate that HSPCs isolated either by ammonium-chloride potassium (ACK)-based lysis or by gradient isolation are suitable for functional analyses in clonogenic assays, high-level HSPC expansion and efficient lentiviral transduction. For cryostorage of cells, gradient isolation is superior to ACK lysis, and cryostorage in freezing media containing 50% fetal bovine serum demonstrated good results across all tested criteria. For assays on freshly isolated cells, ACK lysis performed similar to, and for thalassemic samples better than, gradient isolation, at a fraction of the cost and hands-on time. All isolation and storage methods show considerable variation within sample groups, but this is particularly acute for density gradient isolation of thalassemic samples. DISCUSSION This study demonstrates the suitability of small-volume blood samples for storage and preclinical studies, opening up the research field of HSPC and gene therapy to any blood diagnostic laboratory with corresponding bioethics approval for experimental use of surplus material.
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Affiliation(s)
- Coralea Stephanou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus; Gene Expression and Therapy Group, King's College London, United Kingdom
| | - Panayiota Papasavva
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus; Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Myria Zachariou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Petros Patsali
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus; Gene Expression and Therapy Group, King's College London, United Kingdom
| | - Marilena Epitropou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Petros Ladas
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Ruba Al-Abdulla
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Soteroulla Christou
- Thalassaemia Centre, Ministry of Health, Archbishop Makarios III Hospital, Nicosia, Cyprus
| | - Michael N Antoniou
- Gene Expression and Therapy Group, King's College London, United Kingdom
| | - Carsten W Lederer
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus; Cyprus School of Molecular Medicine, Nicosia, Cyprus.
| | - Marina Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus; Cyprus School of Molecular Medicine, Nicosia, Cyprus
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25
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Patsali P, Mussolino C, Loucari C, Stephanou C, Antoniou M, Cathomen T, Lederer CW, Kleanthous M. 692. Genome Editing for Personalized Gene Therapy of IVSI-110 Beta-Thalassemia. Mol Ther 2016. [DOI: 10.1016/s1525-0016(16)33500-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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26
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Christodoulou I, Patsali P, Stephanou C, Antoniou M, Kleanthous M, Lederer CW. Measurement of lentiviral vector titre and copy number by cross-species duplex quantitative PCR. Gene Ther 2015. [PMID: 26202078 PMCID: PMC4705430 DOI: 10.1038/gt.2015.60] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [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] [Indexed: 01/05/2023]
Abstract
Lentiviruses are the vectors of choice for many preclinical studies and clinical applications of gene therapy. Accurate measurement of biological vector titre before treatment is a prerequisite for vector dosing, and the calculation of vector integration sites per cell after treatment is as critical to the characterisation of modified cell products as it is to long-term follow-up and the assessment of risk and therapeutic efficiency in patients. These analyses are typically based on quantitative real-time PCR (qPCR), but as yet compromise accuracy and comparability between laboratories and experimental systems, the former by using separate simplex reactions for the detection of endogene and lentiviral sequences and the latter by designing different PCR assays for analyses in human cells and animal disease models. In this study, we validate in human and murine cells a qPCR system for the single-tube assessment of lentiviral vector copy numbers that is suitable for analyses in at least 33 different mammalian species, including human and other primates, mouse, pig, cat and domestic ruminants. The established assay combines the accuracy of single-tube quantitation by duplex qPCR with the convenience of one-off assay optimisation for cross-species analyses and with the direct comparability of lentiviral transduction efficiencies in different species.
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Affiliation(s)
| | - P Patsali
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,King's College London, Gene Expression and Therapy Group London, UK
| | - C Stephanou
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,King's College London, Gene Expression and Therapy Group London, UK
| | - M Antoniou
- King's College London, Gene Expression and Therapy Group London, UK
| | - M Kleanthous
- Cyprus School of Molecular Medicine, Nicosia, Cyprus.,Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - C W Lederer
- Cyprus School of Molecular Medicine, Nicosia, Cyprus.,Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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27
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Maubaret CG, Salpea KD, Romanoski CE, Folkersen L, Cooper JA, Stephanou C, Wah Li K, Palmen J, Hamsten A, Neil A, Stephens JW, Lusis AJ, Eriksson P, Talmud PJ, Humphries SE. Association of TERC and OBFC1 haplotypes with mean leukocyte telomere length and risk for coronary heart disease. PLoS One 2013; 8:e83122. [PMID: 24349443 PMCID: PMC3861448 DOI: 10.1371/journal.pone.0083122] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [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: 06/07/2013] [Accepted: 10/31/2013] [Indexed: 12/21/2022] Open
Abstract
Objective To replicate the associations of leukocyte telomere length (LTL) with variants at four loci and to investigate their associations with coronary heart disease (CHD) and type II diabetes (T2D), in order to examine possible causal effects of telomere maintenance machinery on disease aetiology. Methods Four SNPs at three loci BICD1 (rs2630578 GγC), 18q12.2 (rs2162440 GγT), and OBFC1 (rs10786775 CγG, rs11591710 AγC) were genotyped in four studies comprised of 2353 subjects out of which 1148 had CHD and 566 T2D. Three SNPs (rs12696304 CγG, rs10936601G>T and rs16847897 GγC) at the TERC locus were genotyped in these four studies, in addition to an offspring study of 765 healthy students. For all samples, LTL had been measured using a real-time PCR-based method. Results Only one SNP was associated with a significant effect on LTL, with the minor allele G of OBFC1 rs10786775 SNP being associated with longer LTL (β=0.029, P=0.04). No SNPs were significantly associated with CHD or T2D. For OBFC1 the haplotype carrying both rare alleles (rs10786775G and rs11591710C, haplotype frequency 0.089) was associated with lower CHD prevalence (OR: 0.77; 95% CI: 0.61–0.97; P= 0.03). The TERC haplotype GTC (rs12696304G, rs10936601T and rs16847897C, haplotype frequency 0.210) was associated with lower risk for both CHD (OR: 0.86; 95% CI: 0.75-0.99; P=0.04) and T2D (OR: 0.74; 95% CI: 0.61–0.91; P= 0.004), with no effect on LTL. Only the last association remained after adjusting for multiple testing. Conclusion Of reported associations, only that between the OBFC1 rs10786775 SNP and LTL was confirmed, although our study has a limited power to detect modest effects. A 2-SNP OBFC1 haplotype was associated with higher risk of CHD, and a 3-SNP TERC haplotype was associated with both higher risk of CHD and T2D. Further work is required to confirm these results and explore the mechanisms of these effects.
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Affiliation(s)
- Cécilia G. Maubaret
- Cardiovascular Genetics, BHF Laboratories,University College London (UCL), London, United Kingdom
- ISPED, Université Bordeaux Ségalen/INSERM u.897, Bordeaux, France
- * E-mail:
| | - Klelia D. Salpea
- Cardiovascular Genetics, BHF Laboratories,University College London (UCL), London, United Kingdom
- Institute of Molecular Biology & Genetics, Biomedical Sciences Research Center "Alexander Fleming", Athens, Greece
| | - Casey E. Romanoski
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Lasse Folkersen
- Atherosclerosis Research Unit, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jackie A. Cooper
- Cardiovascular Genetics, BHF Laboratories,University College London (UCL), London, United Kingdom
| | - Coralea Stephanou
- Cardiovascular Genetics, BHF Laboratories,University College London (UCL), London, United Kingdom
| | - Ka Wah Li
- Cardiovascular Genetics, BHF Laboratories,University College London (UCL), London, United Kingdom
| | - Jutta Palmen
- Cardiovascular Genetics, BHF Laboratories,University College London (UCL), London, United Kingdom
| | - Anders Hamsten
- Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Andrew Neil
- Division Public Health & Primary Health Care, University of Oxford, Oxford, United Kingdom
| | - Jeffrey W. Stephens
- Diabetes Research Group, School of Medicine, Swansea University, Swansea, United Kingdom
| | - Aldons J. Lusis
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Per Eriksson
- Atherosclerosis Research Unit, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Philippa J. Talmud
- Cardiovascular Genetics, BHF Laboratories,University College London (UCL), London, United Kingdom
| | - Steve E. Humphries
- Cardiovascular Genetics, BHF Laboratories,University College London (UCL), London, United Kingdom
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28
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Stephanou C. [Mucogingival surgery for dental prosthesis. A new method]. Odontiatriki 1972; 5:308-11. [PMID: 4569335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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