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Caria CA, Faà V, Porcu S, Marongiu MF, Poddie D, Perseu L, Meloni A, Vaccargiu S, Ristaldi MS. Post-GWAS Validation of Target Genes Associated with HbF and HbA 2 Levels. Cells 2024; 13:1185. [PMID: 39056767 PMCID: PMC11274989 DOI: 10.3390/cells13141185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Genome-Wide Association Studies (GWASs) have identified a huge number of variants associated with different traits. However, their validation through in vitro and in vivo studies often lags well behind their identification. For variants associated with traits or diseases of biomedical interest, this gap delays the development of possible therapies. This issue also impacts beta-hemoglobinopathies, such as beta-thalassemia and sickle cell disease (SCD). The definitive cures for these diseases are currently bone marrow transplantation and gene therapy. However, limitations regarding their effective use restrict their worldwide application. Great efforts have been made to identify whether modulators of fetal hemoglobin (HbF) and, to a lesser extent, hemoglobin A2 (HbA2) are possible therapeutic targets. Herein, we performed the post-GWAS in vivo validation of two genes, cyclin D3 (CCND3) and nuclear factor I X (NFIX), previously associated with HbF and HbA2 levels. The absence of Ccnd3 expression in vivo significantly increased g (HbF) and d (HbA2) globin gene expression. Our data suggest that CCND3 is a possible therapeutic target in sickle cell disease. We also confirmed the association of Nfix with γ-globin gene expression and present data suggesting a possible role for Nfix in regulating Kruppel-like transcription factor 1 (Klf1), a master regulator of hemoglobin switching. This study contributes to filling the gap between GWAS variant identification and target validation for beta-hemoglobinopathies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Maria Serafina Ristaldi
- Istituto di Ricerca Genetica e Biomedica, Cittadella Universitaria di Monserrato, SS 554, Bivio Sestu Km 4,500, 09042 Cagliari, Italy; (C.A.C.); (V.F.); (S.P.); (M.F.M.); (D.P.); (L.P.); (A.M.); (S.V.)
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Alshabeeb MA, Alwadaani D, Al Qahtani FH, Abohelaika S, Alzahrani M, Al Zayed A, Al Saeed HH, Al Ajmi H, Alsomaie B, Rashid M, Daly AK. Impact of Genetic Variations on Thromboembolic Risk in Saudis with Sickle Cell Disease. Genes (Basel) 2023; 14:1919. [PMID: 37895268 PMCID: PMC10606407 DOI: 10.3390/genes14101919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Sickle cell disease (SCD) is a Mendelian disease characterized by multigenic phenotypes. Previous reports indicated a higher rate of thromboembolic events (TEEs) in SCD patients. A number of candidate polymorphisms in certain genes (e.g., FVL, PRT, and MTHFR) were previously reported as risk factors for TEEs in different clinical conditions. This study aimed to genotype these genes and other loci predicted to underlie TEEs in SCD patients. METHODOLOGY A multi-center genome-wide association study (GWAS) involving Saudi SCD adult patients with a history of TEEs (n = 65) and control patients without TEE history (n = 285) was performed. Genotyping used the 10× Affymetrix Axiom array, which includes 683,030 markers. Fisher's exact test was used to generate p-values of TEE associations with each single-nucleotide polymorphism (SNP). The haplotype analysis software tool version 1.05, designed by the University of Göttingen, Germany, was used to identify the common inherited haplotypes. RESULTS No association was identified between the targeted single-nucleotide polymorphism rs1801133 in MTHFR and TEEs in SCD (p = 0.79). The allele frequency of rs6025 in FVL and rs1799963 in PRT in our cohort was extremely low (<0.01); thus, both variants were excluded from the analysis as no meaningful comparison was possible. In contrast, the GWAS analysis showed novel genome-wide associations (p < 5 × 10-8) with seven signals; five of them were located on Chr 11 (rs35390334, rs331532, rs317777, rs147062602, and rs372091), one SNP on Chr 20 (rs139341092), and another on Chr 9 (rs76076035). The other 34 SNPs located on known genes were also detected at a signal threshold of p < 5 × 10-6. Seven of the identified variants are located in olfactory receptor family 51 genes (OR51B5, OR51V1, OR51A1P, and OR51E2), and five variants were related to family 52 genes (OR52A5, OR52K1, OR52K2, and OR52T1P). The previously reported association between rs5006884-A in OR51B5 and fetal hemoglobin (HbF) levels was confirmed in our study, which showed significantly lower levels of HbF (p = 0.002) and less allele frequency (p = 0.003) in the TEE cases than in the controls. The assessment of the haplotype inheritance pattern involved the top ten significant markers with no LD (rs353988334, rs317777, rs14788626882, rs49188823, rs139349992, rs76076035, rs73395847, rs1368823, rs8888834548, and rs1455957). A haplotype analysis revealed significant associations between two haplotypes (a risk, TT-AA-del-AA-ins-CT-TT-CC-CC-AA, and a reverse protective, CC-GG-ins-GG-del-TT-CC-TT-GG-GG) and TEEs in SCD (p = 0.024, OR = 6.16, CI = 1.34-28.24, and p = 0.019, OR = 0.33, CI = 0.13-0.85, respectively). CONCLUSIONS Seven markers showed novel genome-wide associations; two of them were exonic variants (rs317777 in OLFM5P and rs147062602 in OR51B5), and less significant associations (p < 5 × 10-6) were identified for 34 other variants in known genes with TEEs in SCD. Moreover, two 10-SNP common haplotypes were determined with contradictory effects. Further replication of these findings is needed.
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Affiliation(s)
- Mohammad A. Alshabeeb
- King Abdullah International Medical Research Center (KAIMRC), Riyadh 11426, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia (M.A.)
| | - Deemah Alwadaani
- King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia (M.A.)
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Riyadh 11481, Saudi Arabia
| | - Farjah H. Al Qahtani
- Hematology/Oncology Center, King Saud University Medical City (KSUMC), Riyadh 11411, Saudi Arabia;
| | - Salah Abohelaika
- Research Department, Qatif Central Hospital (QCH), Qatif 32654, Saudi Arabia;
- Pharmacy Department, Qatif Central Hospital (QCH), Qatif 32654, Saudi Arabia
| | - Mohsen Alzahrani
- King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia (M.A.)
- King Fahad Hospital, Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia
| | - Abdullah Al Zayed
- Hematology Department, Qatif Central Hospital (QCH), Qatif 32654, Saudi Arabia; (A.A.Z.); (H.H.A.S.)
| | - Hussain H. Al Saeed
- Hematology Department, Qatif Central Hospital (QCH), Qatif 32654, Saudi Arabia; (A.A.Z.); (H.H.A.S.)
| | - Hala Al Ajmi
- King Abdullah International Medical Research Center (KAIMRC), Riyadh 11426, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia (M.A.)
| | - Barrak Alsomaie
- King Abdullah International Medical Research Center (KAIMRC), Riyadh 11426, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia (M.A.)
| | - Mamoon Rashid
- King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia (M.A.)
- Department of AI and Bioinformatics, King Abdullah International Medical Research Center (KAIMRC), Riyadh 11481, Saudi Arabia
| | - Ann K. Daly
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK
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Adeyemo TA, Ojewunmi OO, Oyetunji IA, Kalejaiye OO, Menzel S. Fetal-haemoglobin enhancing genotype at BCL11A reduces HbA 2 levels in patients with sickle cell anaemia. EJHAEM 2021; 2:459-461. [PMID: 35844678 PMCID: PMC9175773 DOI: 10.1002/jha2.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 11/09/2022]
Abstract
Understanding the interplay of genetic factors with haemoglobin expression and pathological processes in sickle cell disease is important for pharmacological and gene-therapeutic interventions. In our nascent study cohort of Nigerian patients, we found that three major disease-modifying factors, HbF levels, α-thalassaemia deletion and BCL11A genotype, had expected beneficial haematological effects. A key BCL11A variant, while improving HbF levels (5.7%-9.0%), also led to a small, but significant decrease in HbA2. We conclude that in general, interventions boosting HbF are likely to reduce HbA2 in patients' erythroid cells and that such therapeutic strategies might benefit from a parallel stimulation of HbA2 through independent mechanisms.
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Affiliation(s)
- Titilope A. Adeyemo
- Department of Haematology and Blood Transfusion, College of MedicineUniversity of LagosIdi‐ArabaLagosNigeria
| | - Oyesola O. Ojewunmi
- Sickle Cell Foundation NigeriaIdi‐ArabaLagosNigeria
- School of Cancer and Pharmaceutical SciencesKing's College LondonLondonUK
| | | | - Olufunto Olufela Kalejaiye
- Haematology/Oncology Unit, Department of Medicine, College of MedicineUniversity of LagosIdi‐ArabaLagosNigeria
| | - Stephan Menzel
- School of Cancer and Pharmaceutical SciencesKing's College LondonLondonUK
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Colaco S, Nadkarni A. Borderline HbA 2 levels: Dilemma in diagnosis of beta-thalassemia carriers. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108387. [PMID: 34893152 DOI: 10.1016/j.mrrev.2021.108387] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 05/27/2021] [Accepted: 06/08/2021] [Indexed: 12/17/2022]
Abstract
There is inconsistency in the exact definition of diagnostic levels of HbA2 for β thalassemia trait. While many laboratories consider HbA2 ≥4.0 % diagnostic, still others consider HbA2 ≥3.3 % or HbA2 ≥3.5 % as the cut-off for establishing β thalassemia carrier diagnosis. This is because, over the years, studies have described β thalassemia carriers showing HbA2 levels that lie above the normal range of HbA2 but below the typical carrier range of β thalassemia. These, "borderline HbA2 levels", though not detrimental to health, are significant in β thalassemia carrier diagnosis because they can lead to misinterpretation of results. In this review, we have evaluated the prevalence of borderline HbA2 levels and discussed the causes of borderline HbA2 values. We have also compiled an extensive catalogue of β globin gene defects associated with borderline HbA2 levels and have discussed strategies to avoid misdiagnosing borderline HbA2 β thalassemia carriers. Our analysis of studies that have delineated the cause of borderline HbA2 levels in different populations shows that 35.4 % [626/1766] of all individuals with borderline HbA2 levels carry a molecular defect. Among the positive samples, 17 % [299/1766] show β globin gene defects, 7.7 % [137/1766] show α thalassemia defects, 2.7 % [49/1766] show KLF1 gene mutations, 2.3 % [41/1766] show the co-inheritance of β and α thalassemia, 2.0 % [37/1766] show the co-inheritance of β and δ thalassemia and 1.8 % [32/1766] show α globin gene triplication. It appears that a comprehensive molecular work up of the β globin gene is the only definite method to detect borderline HbA2 β thalassemia carriers, especially in populations with a high prevalence of the disease. The presence of associated genetic or acquired determinants may subsequently be assessed to identify the cause of borderline HbA2.
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Affiliation(s)
- Stacy Colaco
- Department of Hematogenetics, ICMR-National Institute of Immunohematology, 13th Floor, K.E.M. Hospital Campus, Parel, Mumbai, 400 012, India
| | - Anita Nadkarni
- Department of Hematogenetics, ICMR-National Institute of Immunohematology, 13th Floor, K.E.M. Hospital Campus, Parel, Mumbai, 400 012, India.
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Cyrus C, Vatte C, Chathoth S, Sayed AA, Borgio JF, Alrubaish MA, Alfalah R, Alsaikhan J, Al Ali AK. Haemoglobin switching modulator SNPs rs5006884 is associated with increased HbA 2 in β-thalassaemia carriers. Arch Med Sci 2021; 17:1064-1074. [PMID: 34336034 PMCID: PMC8314410 DOI: 10.5114/aoms.2019.86705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/15/2018] [Indexed: 11/25/2022] Open
Abstract
INTRODUCTION Haemoglobin A2 (HbA2), the tetramer of α- and δ-globin chains, is used as a diagnostic biomarker for β-thalassaemia carriers. The HbA2 levels are regulated by the presence of HPFH, δ-thalassaemia, HbA1/2 gene triplication, and variants of KLF1, β-globin gene, and HbF regulating QTLs. Saudi Arabia has a high incidence of borderline HbA2 levels, thereby making it difficult to classify the haemoglobinopathies. This study aims to investigate the association of known HbF enhancer QTL gene SNPs with HbA2 levels. MATERIAL AND METHODS 14 Specific SNPs in BCL11A, HMIP, OR51B6, HBBP1, and HBG2 loci were genotyped in 164 Saudi β-thalassaemia carriers by TaqMan assay to validate their role as regulators of HbA2 levels. HbA2 levels were determined using the Variant II β-Thalassemia Short Program Recorder kit. The non-random association of these SNPs was tested using HaploView software. Protein interaction was assessed using 3D structure modelling for OR51B6 (rs5006884), comparative energy minimisation, and root-mean-square deviation (RMSD) prediction. RESULTS Elevated HbA2 levels were associated with SNPs in HBBP1, OR51B6, and TCT haplotype from HBG2 promoter region. The bioinformatics modelling and prediction revealed that the exonic rs5006884 had RMSD value deviations and significantly varied binding energy minimisation. α-globin variations were found in 57.92% of individuals but were not associated with elevated HbA2. CONCLUSIONS The haemoglobin switching modulators rs2071348, rs7482144, and rs5006884 are involved in regulation of HbA2 level with rs5006884 influencing the tetramer formation. Screening for haemoglobinopathies should take these SNPs into consideration, specifically in borderline HbA2 cases. Assiduous analysis of rs5006884 as HbA2 modulator for amelioration of disease severity is recommended.
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Affiliation(s)
- Cyril Cyrus
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Chittibabu Vatte
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Shahanas Chathoth
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Abdul Azeez Sayed
- Department of Genetic Research, Institute for Research and Medical Consultation, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultation, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | | | - Rawan Alfalah
- King Fahd Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Jana Alsaikhan
- King Fahd Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Amein K. Al Ali
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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Manchinu MF, Simbula M, Caria CA, Musu E, Perseu L, Porcu S, Steri M, Poddie D, Frau J, Cocco E, Manunza L, Barella S, Ristaldi MS. Delta-Globin Gene Expression Is Enhanced in vivo by Interferon Type I. Front Med (Lausanne) 2020; 7:163. [PMID: 32528964 PMCID: PMC7256663 DOI: 10.3389/fmed.2020.00163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/09/2020] [Indexed: 12/19/2022] Open
Abstract
Beta hemoglobinopathies are widely spread monogenic lethal diseases. Delta-globin gene activation has been proposed as a possible approach for curing these pathologies. The therapeutic potential of delta-globin, the non-alpha component of Hemoglobin A2 (α2δ2; HbA2), has been demonstrated in a mouse model of beta thalassemia, while its anti-sickling effect, comparable to that of gamma globin, was established some time ago. Here we show that the delta-globin mRNA level is considerably increased in a Deoxyribonuclease II-alpha knockout mouse model in which type 1 interferon (interferon beta, IFNb) is activated. IFNb activation in the fetal liver improves the delta-globin mRNA level, while the beta-globin mRNA level is significantly reduced. In addition, we show that HbA2 is significantly increased in patients with multiple sclerosis under type 1 interferon treatment. Our results represent a proof of principle that delta-globin expression can be enhanced through the use of molecules. This observation is potentially interesting in view of a pharmacological approach able to increase the HbA2 level.
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Affiliation(s)
- Maria Francesca Manchinu
- Istituto Di Ricerca Genetica e Biomedica Del Consiglio Nazionale Delle Ricerche, Monserrato, Italy
| | - Michela Simbula
- Istituto Di Ricerca Genetica e Biomedica Del Consiglio Nazionale Delle Ricerche, Monserrato, Italy
| | - Cristian Antonio Caria
- Istituto Di Ricerca Genetica e Biomedica Del Consiglio Nazionale Delle Ricerche, Monserrato, Italy
| | - Ester Musu
- Istituto Di Ricerca Genetica e Biomedica Del Consiglio Nazionale Delle Ricerche, Monserrato, Italy
| | - Lucia Perseu
- Istituto Di Ricerca Genetica e Biomedica Del Consiglio Nazionale Delle Ricerche, Monserrato, Italy
| | - Susanna Porcu
- Istituto Di Ricerca Genetica e Biomedica Del Consiglio Nazionale Delle Ricerche, Monserrato, Italy
| | - Maristella Steri
- Istituto Di Ricerca Genetica e Biomedica Del Consiglio Nazionale Delle Ricerche, Monserrato, Italy
| | - Daniela Poddie
- Istituto Di Ricerca Genetica e Biomedica Del Consiglio Nazionale Delle Ricerche, Monserrato, Italy
| | - Jessica Frau
- Department of Medical Science and Public Health, Centro Sclerosi Multipla, University of Cagliari, Cagliari, Italy
| | - Eleonora Cocco
- Department of Medical Science and Public Health, Centro Sclerosi Multipla, University of Cagliari, Cagliari, Italy
| | - Laura Manunza
- Ospedale Microcitemico "A. Cao" - A.O. "G. Brotzu", Cagliari, Italy
| | - Susanna Barella
- Ospedale Microcitemico "A. Cao" - A.O. "G. Brotzu", Cagliari, Italy
| | - Maria Serafina Ristaldi
- Istituto Di Ricerca Genetica e Biomedica Del Consiglio Nazionale Delle Ricerche, Monserrato, Italy
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Kingchaiyaphum B, Sanchaisuriya K, Fucharoen G, Chaibunruang A, Hess SY, Hinnouho GM, Barffour MA, Wessells KR, Kounnavong S, Fucharoen S. Hemoglobins F, A 2 , and E levels in Laotian children aged 6-23 months with Hb E disorders: Effect of age, sex, and thalassemia types. Int J Lab Hematol 2020; 42:277-283. [PMID: 32048804 PMCID: PMC7318314 DOI: 10.1111/ijlh.13164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/21/2019] [Accepted: 01/24/2020] [Indexed: 11/29/2022]
Abstract
Introduction Determination of hemoglobins (Hbs) F, A2, and E is crucial for diagnosis of thalassemia. This study determined the levels of Hbs F, A2, and E in children aged 6‐23 months and investigated the effect of age, sex, and types of thalassemia on the expression of these Hbs. Methods A total of 698 blood samples of Laotian children including 272 non‐Hb E, 271 Hb E heterozygotes, and 155 Hb E homozygotes were collected. Hb profiles were determined using the capillary zone electrophoresis. Coinheritance of α‐thalassemia and the homozygosity for Hb E mutation were checked by PCR‐based assay. Results Children heterozygous and homozygous for Hb E had significantly higher Hb F and A2 levels than non‐Hb E children (median Hb F = 1.1% for non‐Hb E group, 2.7% for Hb E heterozygotes, and 9.4% for Hb E homozygotes; median Hb A2 = 2.6% for non‐Hb E group, 3.8% for Hb E heterozygotes, and 5.2% for Hb E homozygotes). The median Hb E levels were 21.9% for Hb E heterozygotes and 85.3% for Hb E homozygotes. Comparing within group, there was a statistically significant difference between children with and without an α‐gene defect for Hb A2 and E, but not Hb F. Based on a multiple regression analysis, age and sex were significantly associated with the expression of Hb F and A2 but not Hb E. Conclusions Our findings can guide the development of a diagnostic approach to thalassemia in children aged 6‐23 months.
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Affiliation(s)
| | - Kanokwan Sanchaisuriya
- Center for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Goonnapa Fucharoen
- Center for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Attawut Chaibunruang
- Center for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Sonja Y Hess
- Institute for Global Nutrition, University of California, Davis, CA, USA
| | | | - Maxwell A Barffour
- Institute for Global Nutrition, University of California, Davis, CA, USA
| | - Kimbery R Wessells
- Institute for Global Nutrition, University of California, Davis, CA, USA
| | | | - Supan Fucharoen
- Center for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
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Oikonomidis IL, Tsouloufi TK, Mylonakis ME, Kritsepi-Konstantinou M. Capillary hemoglobin electrophoresis of healthy and anemic dogs: Quantification, validation, and reference intervals of hemoglobin fractions. PLoS One 2019; 14:e0217258. [PMID: 31483782 PMCID: PMC6726222 DOI: 10.1371/journal.pone.0217258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/17/2019] [Indexed: 11/19/2022] Open
Abstract
Despite the advances in canine medicine and the rapid gaining of attention of canine models in biomedical field and particularly in hemoglobin genes research, the studies on canine hemoglobin composition are sparse with ambiguous findings. Our aim was: i) to investigate the electrophoretic pattern of canine hemoglobin and the possible effects of age, sex, and anemia using a capillary electrophoresis assay, and ii) to validate this assay and calculate reference intervals (RIs) for canine hemoglobin fractions. Blood samples were collected from 53 healthy and 42 dogs with regenerative and non-regenerative anemias. The Sebia Capillarys 2 flex-piercing was used for hemoglobin analysis and it was validated using canine blood samples. R statistical language was employed for the statistical analyses. A major hemoglobin fraction (named HbA0) and a minor one (named HbA2) were identified in 100% and 47.4% of samples, respectively. The within-run and between-run CV was 0.1% for HbA0, and 9.1% and 11.2% for HbA2, respectively. The extremely narrow range of HbA0 and HbA2 values hampered a linearity study using canine blood samples. The RIs for HbA0 and HbA2 were 98.9-100% and 0-1.1%, respectively. HbA0 and HbA2 values were not significantly correlated with age (P = 0.866) or reticulocyte count (P = 0.731). No differences were observed in the median HbA0 and HbA2 between the two sexes (P = 0.887), and healthy and anemic dogs (P = 0.805). In conclusion, the capillary electrophoresis revealed a major hemoglobin fraction and an inconsistently present minor fraction. No effect of age, sex, anemia, or regenerative status of anemia was detected. The assay used was validated and RIs were generated, so as to be suitable for use in future investigations.
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Affiliation(s)
- Ioannis L. Oikonomidis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Theodora K. Tsouloufi
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Mathios E. Mylonakis
- Clinic of Companion Animal Medicine, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria Kritsepi-Konstantinou
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Barrera-Reyes PK, Tejero ME. Genetic variation influencing hemoglobin levels and risk for anemia across populations. Ann N Y Acad Sci 2019; 1450:32-46. [PMID: 31385320 DOI: 10.1111/nyas.14200] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 06/30/2019] [Accepted: 07/05/2019] [Indexed: 01/19/2023]
Abstract
Hemoglobin (Hb) concentration is the outcome of the interaction between genetic variation and environmental factors, including nutritional status, sex, age, and altitude. Genetic diversity influencing this protein is complex and varies widely across populations. Variants related to abnormal Hb or altered characteristics of the erythrocytes increase the risk for anemia. The most prevalent are related to the inherited globin abnormalities affecting Hb production and structure. Malaria-endemic regions harbor the highest frequencies of variants associated with the most frequent monogenic diseases and the risk for nonnutritional anemia and are considered as public health problems. Variation in genes encoding for enzymes and membrane proteins in red blood cells also influence erythrocyte life span and risk for anemia. Most of these variants are rare. Interindividual variability of hematological parameters is also influenced by common genetic variation across the whole genome. Some of the identified variants are associated with Hb production, erythropoiesis, and iron metabolism. Specialized databases have been developed to organize and update the large body of available information on genetic variation related to Hb variation, their frequency, geographical distribution, and clinical significance. Our present review analyzed the underlying genetic factors that affect Hb concentrations, their clinical relevance, and geographical distribution across populations.
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Affiliation(s)
- Paloma K Barrera-Reyes
- Laboratorio de Nutrigenómica y Nutrigenética, Instituto Nacional de Medicina Genómica, Ciudad de, México, Mexico.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de, México, Mexico
| | - M Elizabeth Tejero
- Laboratorio de Nutrigenómica y Nutrigenética, Instituto Nacional de Medicina Genómica, Ciudad de, México, Mexico
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Özbolat G. Heterozigot β-talasemili kadınlarda gebelik değişkeninin HbA2 değeri üzerine etkisi. CUKUROVA MEDICAL JOURNAL 2019. [DOI: 10.17826/cumj.440755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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11
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Chaweephisal P, Phusua A, Fanhchaksai K, Sirichotiyakul S, Charoenkwan P. Borderline hemoglobin A2 levels in northern Thai population: HBB genotypes and effects of coinherited alpha-thalassemia. Blood Cells Mol Dis 2019; 74:13-17. [DOI: 10.1016/j.bcmd.2018.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/01/2018] [Accepted: 10/03/2018] [Indexed: 01/13/2023]
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12
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Han WP, Huang L, Li YY, Han YY, Li D, An BQ, Huang SW. Reference intervals for HbA 2 and HbF and cut-off value of HbA 2 for β-thalassemia carrier screening in a Guizhou population of reproductive age. Clin Biochem 2018; 65:24-28. [PMID: 30503531 DOI: 10.1016/j.clinbiochem.2018.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 11/02/2018] [Accepted: 11/17/2018] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The aims of this study were to establish the reference intervals for HbA2 and HbF in a Guizhou population of reproductive age, and to determine the cut-off value of HbA2 for β-thalassemia carrier screening. METHODS Hemoglobin analysis was performed on 832 individuals without hypochromic microcytic anemia to calculate the reference intervals for HbA2 and HbF. Three hundred and ninety one β-thalassemia carriers and non β-thalassemia individuals were analyzed for their HbA2 levels followed by detecting β-globin gene mutations, then cut-off value of HbA2 for β-thalassemia carrier screening was determined using ROC curve analysis. RESULTS The reference interval for HbA2 in overall normal individuals was 2.3%-3.1%, and reference intervals for HbF in normal males and females (including normal females and pregnant women) were 0-0.5% and 0-1.0% respectively. The cut-off values of HbA2 for β-thalassemia carrier screening in males, non-pregnant women, pregnant women and the overall set were 4.40%, 3.75%, 3.70% and 3.95% respectively. CONCLUSION Gender and pregnancy status had no obvious influence on reference interval for HbA2. The HbF level was higher in females than in males, but pregnancy status had no obvious influence on HbF level. Cut-off value of HbA2 for β-thalassemia carrier screening was obviously affected by gender but not by pregnancy status.
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Affiliation(s)
- Wen-Ping Han
- Department of Laboratory, Guizhou Provincial People's Hospital, No.83 East Zhongshan Road, Guiyang 550002, Guizhou, PR China; Nanjing Red Cross Blood Center, Nanjing 210003, Jiangsu, PR China
| | - Ling Huang
- Department of Laboratory, Guizhou Provincial People's Hospital, No.83 East Zhongshan Road, Guiyang 550002, Guizhou, PR China
| | - Yuan-Yuan Li
- Department of Laboratory, Guizhou Provincial People's Hospital, No.83 East Zhongshan Road, Guiyang 550002, Guizhou, PR China
| | - Yuan-Yuan Han
- Department of Laboratory, Guizhou Provincial People's Hospital, No.83 East Zhongshan Road, Guiyang 550002, Guizhou, PR China; Medical college, Guizhou University, South Jiaxiu Road, Guiyang 550025, Guizhou, PR China
| | - Di Li
- Department of Laboratory, Guizhou Provincial People's Hospital, No.83 East Zhongshan Road, Guiyang 550002, Guizhou, PR China
| | - Bang-Quan An
- Department of Laboratory, Guizhou Provincial People's Hospital, No.83 East Zhongshan Road, Guiyang 550002, Guizhou, PR China.
| | - Sheng-Wen Huang
- Department of Laboratory, Guizhou Provincial People's Hospital, No.83 East Zhongshan Road, Guiyang 550002, Guizhou, PR China; Medical college, Guizhou University, South Jiaxiu Road, Guiyang 550025, Guizhou, PR China.
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13
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Jiang F, Qu YX, Chen GL, Li J, Zhou JY, Zuo LD, Liao C, Li DZ. KFL1 Gene Variants in α-Thalassemia Individuals with Increased Fetal Hemoglobin in a Chinese Population. Hemoglobin 2018; 42:161-165. [PMID: 30205725 DOI: 10.1080/03630269.2018.1486325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Krüppel-like factor 1 (KLF1) is a pleiotropic erythroid transcription factor that is a regulator of definitive erythropoiesis. The aim of this study was to detect KLF1 gene variants in α-thalassemia (α-thal) carriers with an increased Hb F level in a Chinese population, and determine the changes of hematological parameters as a result of interactions between KLF1 gene mutations and α-thal. Subjects with α-thal and Hb F levels of ≥1.0% were selected for further investigation. Direct sequencing was used to detect KLF1 gene mutations. Hematological parameters of subjects with α-thal and concomitant KLF1 gene mutations and those with α-thal alone were compared. The KLF1 gene variants were detected in 46 of 275 (16.7%) individuals with α-thal and Hb F levels of ≥1.0%. The detection rate of KLF1 gene mutations rose correspondingly when the Hb F level increased. For α0-thal carriers, significantly lower mean corpuscular volume (MCV) and mean corpuscular hemoglobin (Hb) (MCH) values were observed in KLF1 gene mutation-positive carriers than that in KLF1 gene mutation-free carriers; conversely, significantly higher Hb A2 and Hb F levels were observed in the former condition rather than in the latter condition. The results of this study indicate that KLF1 gene variants are common in Chinese subjects with α-thal and increased Hb F levels, and KLF1 gene mutations decreased the red blood cell (RBC) indices in α-thal carriers as that in normal adults.
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Affiliation(s)
- Fan Jiang
- a Guangzhou Women and Children's Medical Center , Guangzhou Medical University , Guangzhou , Guangdong Province , People's Republic of China
| | - Yan-Xia Qu
- a Guangzhou Women and Children's Medical Center , Guangzhou Medical University , Guangzhou , Guangdong Province , People's Republic of China
| | - Gui-Lan Chen
- a Guangzhou Women and Children's Medical Center , Guangzhou Medical University , Guangzhou , Guangdong Province , People's Republic of China
| | - Jian Li
- a Guangzhou Women and Children's Medical Center , Guangzhou Medical University , Guangzhou , Guangdong Province , People's Republic of China
| | - Jian-Ying Zhou
- a Guangzhou Women and Children's Medical Center , Guangzhou Medical University , Guangzhou , Guangdong Province , People's Republic of China
| | - Lian-Dong Zuo
- a Guangzhou Women and Children's Medical Center , Guangzhou Medical University , Guangzhou , Guangdong Province , People's Republic of China
| | - Can Liao
- a Guangzhou Women and Children's Medical Center , Guangzhou Medical University , Guangzhou , Guangdong Province , People's Republic of China
| | - Dong-Zhi Li
- a Guangzhou Women and Children's Medical Center , Guangzhou Medical University , Guangzhou , Guangdong Province , People's Republic of China
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14
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Yu S, Chen Y, Lai K, Dewan RK, He Y. A Novel Variant with Positive Natural Selection Influenced Hb A 2 Levels in Chinese Individuals with β-Thalassemia. Hemoglobin 2017; 41:193-197. [PMID: 28747083 DOI: 10.1080/03630269.2017.1358177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
β-Thalassemia (β-thal) is the most common inherited hemolytic anemia worldwide. Elevated Hb A2 is a mark of β-thal carriers. The aim of this study was to identify the pathogenic variants associated with the Hb A2 levels. One thousand and thirty β-thal carriers were recruited for this study. Using positive natural expression quantitative trait loci (eQTL) analysis, a significant variant was selected. Genotyping for the rs231841 polymorphism was performed by the Sequenom MassARRAY IPLEX platform. All genetic association analyses were performed with the PLINK program. The linear regression analysis showed that rs231841 in the intron region of the potassium voltage-gated channel subfamily Q member 1 (KCNQ1) gene on chromosome 11p15 was significantly associated with Hb A2 levels. The presence of the C allele was associated with elevated Hb A2 levels. Our results suggest that rs231841 on the KCNQ1 gene with positive natural selection is related to Hb A2 levels in Chinese β-thal carriers, and KCNQ1 is probably associated with the expression of the β-like globin gene cluster.
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Affiliation(s)
- Shanjuan Yu
- a Department of Pediatrics , The First Affiliated Hospital of Guangxi Medical University , Nanning , Guangxi Province , People's Republic of China
| | - Yang Chen
- b School of Public Health, Guangxi Medical University , Nanning , Guangxi Province , People's Republic of China
| | - Ketong Lai
- c Guangxi Key Laboratory of Thalassemia Research , The First Affiliated Hospital of Guangxi Medical University , Nanning , Guangxi Province , People's Republic of China
| | - Roma Kajal Dewan
- a Department of Pediatrics , The First Affiliated Hospital of Guangxi Medical University , Nanning , Guangxi Province , People's Republic of China
| | - Yunyan He
- a Department of Pediatrics , The First Affiliated Hospital of Guangxi Medical University , Nanning , Guangxi Province , People's Republic of China
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15
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Molecular basis of β thalassemia and potential therapeutic targets. Blood Cells Mol Dis 2017; 70:54-65. [PMID: 28651846 DOI: 10.1016/j.bcmd.2017.06.001] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 06/09/2017] [Accepted: 06/09/2017] [Indexed: 12/15/2022]
Abstract
The remarkable phenotypic diversity of β thalassemia that range from severe anemia and transfusion-dependency, to a clinically asymptomatic state exemplifies how a spectrum of disease severity can be generated in single gene disorders. While the genetic basis for β thalassemia, and how severity of the anemia could be modified at different levels of its pathophysiology have been well documented, therapy remains largely supportive with bone marrow transplant being the only cure. Identification of the genetic variants modifying fetal hemoglobin (HbF) production in combination with α globin genotype provide some prediction of disease severity for β thalassemia but generation of a personalized genetic risk score to inform prognosis and guide management requires a larger panel of genetic modifiers yet to be discovered. Nonetheless, genetic studies have been successful in characterizing the key variants and pathways involved in HbF regulation, providing new therapeutic targets for HbF reactivation. BCL11A has been established as a quantitative repressor, and progress has been made in manipulating its expression using genomic and gene-editing approaches for therapeutic benefits. Recent discoveries and understanding in the mechanisms associated with ineffective and abnormal erythropoiesis have also provided additional therapeutic targets, a couple of which are currently being tested in clinical trials.
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16
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Southam L, Gilly A, Süveges D, Farmaki AE, Schwartzentruber J, Tachmazidou I, Matchan A, Rayner NW, Tsafantakis E, Karaleftheri M, Xue Y, Dedoussis G, Zeggini E. Whole genome sequencing and imputation in isolated populations identify genetic associations with medically-relevant complex traits. Nat Commun 2017; 8:15606. [PMID: 28548082 PMCID: PMC5458552 DOI: 10.1038/ncomms15606] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 03/28/2017] [Indexed: 01/26/2023] Open
Abstract
Next-generation association studies can be empowered by sequence-based imputation and by studying founder populations. Here we report ∼9.5 million variants from whole-genome sequencing (WGS) of a Cretan-isolated population, and show enrichment of rare and low-frequency variants with predicted functional consequences. We use a WGS-based imputation approach utilizing 10,422 reference haplotypes to perform genome-wide association analyses and observe 17 genome-wide significant, independent signals, including replicating evidence for association at eight novel low-frequency variant signals. Two novel cardiometabolic associations are at lead variants unique to the founder population sequences: chr16:70790626 (high-density lipoprotein levels beta −1.71 (SE 0.25), P=1.57 × 10−11, effect allele frequency (EAF) 0.006); and rs145556679 (triglycerides levels beta −1.13 (SE 0.17), P=2.53 × 10−11, EAF 0.013). Our findings add empirical support to the contribution of low-frequency variants in complex traits, demonstrate the advantage of including population-specific sequences in imputation panels and exemplify the power gains afforded by population isolates. Isolated populations can provide useful information on low-frequency variants for dissecting genetic architecture of complex traits. Here, Zeggini and colleagues show enrichment of rare and low-frequency variants and 8 novel low-frequency variant signals for cardiometabolic traits in two Greek isolated populations
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Affiliation(s)
- Lorraine Southam
- Wellcome Trust Sanger Institute, Human Genetics, Hinxton CB10 1SA, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Arthur Gilly
- Wellcome Trust Sanger Institute, Human Genetics, Hinxton CB10 1SA, UK
| | - Dániel Süveges
- Wellcome Trust Sanger Institute, Human Genetics, Hinxton CB10 1SA, UK
| | - Aliki-Eleni Farmaki
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens 17671, Greece
| | | | | | - Angela Matchan
- Wellcome Trust Sanger Institute, Human Genetics, Hinxton CB10 1SA, UK
| | - Nigel W Rayner
- Wellcome Trust Sanger Institute, Human Genetics, Hinxton CB10 1SA, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.,Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Churchill Hospital, Oxford OX3 7LE, UK
| | | | | | - Yali Xue
- Wellcome Trust Sanger Institute, Human Genetics, Hinxton CB10 1SA, UK
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens 17671, Greece
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17
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Lai Y, Zhou L, Yi S, Chen Y, Tang Y, Yi S, Yang Z, Wei H, Zheng C, He S. The association between four SNPs (rs7482144, rs4671393, rs28384513 and rs4895441) and fetal hemoglobin levels in Chinese Zhuang β-thalassemia intermedia patients. Blood Cells Mol Dis 2017; 63:52-57. [DOI: 10.1016/j.bcmd.2017.01.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 01/17/2017] [Accepted: 01/20/2017] [Indexed: 11/25/2022]
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18
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Canver MC, Lessard S, Pinello L, Wu Y, Ilboudo Y, Stern EN, Needleman AJ, Galactéros F, Brugnara C, Kutlar A, McKenzie C, Reid M, Chen DD, Das PP, A Cole M, Zeng J, Kurita R, Nakamura Y, Yuan GC, Lettre G, Bauer DE, Orkin SH. Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci. Nat Genet 2017; 49:625-634. [PMID: 28218758 PMCID: PMC5374001 DOI: 10.1038/ng.3793] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/25/2017] [Indexed: 02/06/2023]
Abstract
Cas9-mediated, high-throughput, saturating in situ mutagenesis permits fine-mapping of function across genomic segments. Disease- and trait-associated variants from genome-wide association studies largely cluster in regulatory DNA. Here we demonstrate the use of multiple designer nucleases and variant-aware library design to interrogate trait-associated regulatory DNA at high resolution. We developed a computational tool for the creation of saturating mutagenesis libraries with single or combinatorial nucleases with incorporation of variants. We applied this methodology to the HBS1L-MYB intergenic region, a locus associated with red blood cell traits, including fetal hemoglobin levels. This approach identified putative regulatory elements that control MYB expression. Analysis of genomic copy number highlighted potential false positive regions, which emphasizes the importance of off-target analysis in design of saturating mutagenesis experiments. Taken together, these data establish a widely applicable high-throughput and high-resolution methodology to reliably identify minimal functional sequences within large regions of disease- and trait-associated DNA.
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Affiliation(s)
- Matthew C Canver
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Samuel Lessard
- Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Luca Pinello
- Department of Molecular Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Yuxuan Wu
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Yann Ilboudo
- Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Emily N Stern
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Austen J Needleman
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Frédéric Galactéros
- Red Cell Genetic Disease Unit, Hôpital Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), UPeC, IMRB U955 Equipe no. 2, Créteil, France
| | - Carlo Brugnara
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Abdullah Kutlar
- Department of Medicine, Sickle Cell Center, Augusta University, Augusta, Georgia, USA
| | - Colin McKenzie
- The Caribbean Institute for Health Research, University of the West Indies, Mona, Kingston, Jamaica
| | - Marvin Reid
- The Caribbean Institute for Health Research, University of the West Indies, Mona, Kingston, Jamaica
| | - Diane D Chen
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Partha Pratim Das
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Mitchel A Cole
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Japan.,Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Boston, Massachusetts, USA
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19
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Thein SL. Genetic Basis and Genetic Modifiers of β-Thalassemia and Sickle Cell Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1013:27-57. [PMID: 29127676 DOI: 10.1007/978-1-4939-7299-9_2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
β-thalassemia and sickle cell disease (SCD) are prototypical Mendelian single gene disorders, both caused by mutations affecting the adult β-globin gene. Despite the apparent genetic simplicity, both disorders display a remarkable spectrum of phenotypic severity and share two major genetic modifiers-α-globin genotype and innate ability to produce fetal hemoglobin (HbF, α2γ2).This article provides an overview of the genetic basis for SCD and β-thalassemia, and genetic modifiers identified through phenotype correlation studies. Identification of the genetic variants modifying HbF production in combination with α-globin genotype provide some prediction of disease severity for β-thalassemia and SCD but generation of a personalized genetic risk score to inform prognosis and guide management requires a larger panel of genetic modifiers yet to be discovered.Nonetheless, genetic studies have been successful in characterizing some of the key variants and pathways involved in HbF regulation, providing new therapeutic targets for HbF reactivation.
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Affiliation(s)
- Swee Lay Thein
- Sickle Cell Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Building 10, Room 6S241 MSC 1589, 10 Center Dr., Bethesda, MD, 20892-1589, USA.
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20
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Maharry SE, Walker CJ, Liyanarachchi S, Mehta S, Patel M, Bainazar MA, Huang X, Lankenau MA, Hoag KW, Ranganathan P, Garzon R, Blachly JS, Guttridge DC, Bloomfield CD, de la Chapelle A, Eisfeld AK. Dissection of the Major Hematopoietic Quantitative Trait Locus in Chromosome 6q23.3 Identifies miR-3662 as a Player in Hematopoiesis and Acute Myeloid Leukemia. Cancer Discov 2016; 6:1036-51. [PMID: 27354268 DOI: 10.1158/2159-8290.cd-16-0023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 06/23/2016] [Indexed: 12/14/2022]
Abstract
UNLABELLED Chromosomal aberrations and multiple genome-wide association studies (GWAS) have established a major hematopoietic quantitative trait locus in chromosome 6q23.3. The locus comprises an active enhancer region, in which some of the associated SNPs alter transcription factor binding. We now identify miR-3662 as a new functional driver contributing to the associated phenotypes. The GWAS SNPs are strongly associated with higher miR-3662 expression. Genome editing of rs66650371, a three-base-pair deletion, suggests a functional link between the SNP genotype and the abundance of miR-3662. Increasing miR-3662's abundance increases colony formation in hematopoietic progenitor cells, particularly the erythroid lineage. In contrast, miR-3662 is not expressed in acute myeloid leukemia cells, and its overexpression has potent antileukemic effects in vitro and in vivo Mechanistically, miR-3662 directly targets NF-κB-mediated transcription. Thus, miR-3662 is a new player of the hematopoietic 6q23.3 locus. SIGNIFICANCE The characterization of miR-3662 has identified a new actor in the prominent hematopoietic quantitative trait locus in chromosome 6q23.3. The mechanistic insights into miR-3662's function may reveal novel or only partially known pathways for normal and malignant hematopoietic cell proliferation. Cancer Discov; 6(9); 1036-51. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 932.
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Affiliation(s)
- Sophia E Maharry
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | | | | | - Sujay Mehta
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Mitra Patel
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Maryam A Bainazar
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Xiaomeng Huang
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Malori A Lankenau
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Kevin W Hoag
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | | | - Ramiro Garzon
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - James S Blachly
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Denis C Guttridge
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
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21
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Paglietti ME, Satta S, Sollaino MC, Barella S, Ventrella A, Desogus MF, Demartis FR, Manunza L, Origa R. The Problem of Borderline Hemoglobin A2 Levels in the Screening for β-Thalassemia Carriers in Sardinia. Acta Haematol 2016; 135:193-9. [PMID: 26794457 DOI: 10.1159/000442194] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/04/2015] [Indexed: 01/08/2023]
Abstract
BACKGROUND The increase in HbA2 is the most important parameter for the identification of thalassemia carriers. However, in routine screening for hemoglobinopathies, some cases are difficult to classify because the level of HbA2 is not typically elevated. In this work, we report the results of a molecular investigation on a cohort of subjects with borderline HbA2. METHODS All subjects with a β-thalassemia carrier partner and a borderline percentage level of HbA2 were investigated for the presence of a pathological mutation in the β-globin gene. All negative subjects were screened for both the KLF1 mutation and the presence of ααα/ or αααα/ alleles. The subjects with reduced MCV and/or MCH were also screened for deletional and nondeletional α-globin gene defects. RESULTS Various β-globin mutations and KLF1 gene defects are the most common genetic determinants responsible for this phenotype in our population. CONCLUSION KLF1 mutations are important in a screening program for hemoglobinopathies. An increase in HbF in association with borderline HbA2 levels is a useful but not exclusive marker that suggests the investigation of this gene. On the basis of our findings, we are able to suggest the molecular procedure to use in a population characterized by a high prevalence of thalassemia carriers.
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Affiliation(s)
- Maria Elisabetta Paglietti
- Dipartimento di Sanitx00E0; Pubblica, Medicina Clinica e Molecolare, Universitx00E0; degli Studi di Cagliari, Ospedale Microcitemico, Cagliari, Italy
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22
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Genome-wide association analyses based on whole-genome sequencing in Sardinia provide insights into regulation of hemoglobin levels. Nat Genet 2015; 47:1264-71. [PMID: 26366553 PMCID: PMC4627580 DOI: 10.1038/ng.3307] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 04/23/2015] [Indexed: 12/20/2022]
Abstract
We report genome-wide association study results for the levels of A1, A2 and fetal hemoglobins, analyzed for the first time concurrently. Integrating high-density array genotyping and whole-genome sequencing in a large general population cohort from Sardinia, we detected 23 associations at 10 loci. Five signals are due to variants at previously undetected loci: MPHOSPH9, PLTP-PCIF1, ZFPM1 (FOG1), NFIX and CCND3. Among the signals at known loci, ten are new lead variants and four are new independent signals. Half of all variants also showed pleiotropic associations with different hemoglobins, which further corroborated some of the detected associations and identified features of coordinated hemoglobin species production.
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23
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Abstract
Sickle cell disease and β thalassemia are common severe diseases with little effective pathophysiologically-based treatment. Their phenotypic heterogeneity prompted genomic approaches to identify modifiers that ultimately might be exploited therapeutically. Fetal hemoglobin (HbF) is the major modulator of the phenotype of the β hemoglobinopathies. HbF inhibits deoxyHbS polymerization and in β thalassemia compensates for the reduction of HbA. The major success of genomics has been a better understanding the genetic regulation of HbF by identifying the major quantitative trait loci for this trait. If the targets identified can lead to means of increasing HbF to therapeutic levels in sufficient numbers of sickle or β-thalassemia erythrocytes, the pathophysiology of these diseases would be reversed. The availability of new target loci, high-throughput drug screening, and recent advances in genome editing provide the opportunity for new approaches to therapeutically increasing HbF production.
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Affiliation(s)
- Duyen A Ngo
- Department of Medicine, Boston University School of Medicine, 820 Harrison Ave., FGH 1st Floor, Boston, MA, 02118, USA.
| | - Martin H Steinberg
- Departments of Medicine, Pediatrics, Pathology and Laboratory Medicine, Boston University School of Medicine, 72 E. Concord Street, Boston, MA, 02118, USA.
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Steinberg MH, Rodgers GP. HbA2: biology, clinical relevance and a possible target for ameliorating sickle cell disease. Br J Haematol 2015; 170:781-7. [DOI: 10.1111/bjh.13570] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Griffin P. Rodgers
- National Institute of Diabetes and Digestive and Kidney Diseases; National Institutes of Health; Bethesda MD USA
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25
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Panoutsopoulou K, Hatzikotoulas K, Xifara DK, Colonna V, Farmaki AE, Ritchie GRS, Southam L, Gilly A, Tachmazidou I, Fatumo S, Matchan A, Rayner NW, Ntalla I, Mezzavilla M, Chen Y, Kiagiadaki C, Zengini E, Mamakou V, Athanasiadis A, Giannakopoulou M, Kariakli VE, Nsubuga RN, Karabarinde A, Sandhu M, McVean G, Tyler-Smith C, Tsafantakis E, Karaleftheri M, Xue Y, Dedoussis G, Zeggini E. Genetic characterization of Greek population isolates reveals strong genetic drift at missense and trait-associated variants. Nat Commun 2014; 5:5345. [PMID: 25373335 PMCID: PMC4242463 DOI: 10.1038/ncomms6345] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 09/22/2014] [Indexed: 11/09/2022] Open
Abstract
Isolated populations are emerging as a powerful study design in the search for low-frequency and rare variant associations with complex phenotypes. Here we genotype 2,296 samples from two isolated Greek populations, the Pomak villages (HELIC-Pomak) in the North of Greece and the Mylopotamos villages (HELIC-MANOLIS) in Crete. We compare their genomic characteristics to the general Greek population and establish them as genetic isolates. In the MANOLIS cohort, we observe an enrichment of missense variants among the variants that have drifted up in frequency by more than fivefold. In the Pomak cohort, we find novel associations at variants on chr11p15.4 showing large allele frequency increases (from 0.2% in the general Greek population to 4.6% in the isolate) with haematological traits, for example, with mean corpuscular volume (rs7116019, P=2.3 × 10(-26)). We replicate this association in a second set of Pomak samples (combined P=2.0 × 10(-36)). We demonstrate significant power gains in detecting medical trait associations.
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Affiliation(s)
| | | | - Dionysia Kiara Xifara
- 1] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK [2] Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
| | - Vincenza Colonna
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', National Research Council (CNR), Naples 80131, Italy
| | - Aliki-Eleni Farmaki
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens 17671, Greece
| | - Graham R S Ritchie
- 1] Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK [2] European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | - Lorraine Southam
- 1] Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK [2] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Arthur Gilly
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
| | - Ioanna Tachmazidou
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
| | - Segun Fatumo
- 1] Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK [2] H3Africa Bioinformatics Network (H3ABioNet) Node, National Biotechnology Development Agency (NABDA), Federal Ministry of Science and Technology (FMST), Abuja 900107, Nigeria [3] International Health Research Group, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8NR, UK
| | - Angela Matchan
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
| | - Nigel W Rayner
- 1] Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK [2] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK [3] Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK
| | - Ioanna Ntalla
- 1] Department of Nutrition and Dietetics, Harokopio University of Athens, Athens 17671, Greece [2] Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Massimo Mezzavilla
- 1] Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK [2] Division of Medical Genetics, Department of Reproductive Sciences and Development, IRCCS-Burlo Garofolo, University of Trieste, Trieste 34137, Italy
| | - Yuan Chen
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
| | | | - Eleni Zengini
- 1] Dromokaiteio Psychiatric Hospital of Athens, Chaidari, Athens 12461, Greece [2] Department of Human Metabolism, University of Sheffield, Sheffield S10 2TN, UK
| | - Vasiliki Mamakou
- 1] Dromokaiteio Psychiatric Hospital of Athens, Chaidari, Athens 12461, Greece [2] School of Medicine, National and Kapodistrian University of Athens, Goudi, Athens 11527, Greece
| | | | - Margarita Giannakopoulou
- School of Health Sciences, Faculty of Nursing, National and Kapodistrian University of Athens, Goudi, Athens 11527, Greece
| | | | - Rebecca N Nsubuga
- Medical Research Council/Uganda Virus Research Institute, Uganda Research Unit on AIDS, PO Box 49, Entebbe, Uganda
| | - Alex Karabarinde
- Medical Research Council/Uganda Virus Research Institute, Uganda Research Unit on AIDS, PO Box 49, Entebbe, Uganda
| | - Manjinder Sandhu
- 1] Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK [2] International Health Research Group, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8NR, UK
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Chris Tyler-Smith
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
| | | | | | - Yali Xue
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
| | - George Dedoussis
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens 17671, Greece
| | - Eleftheria Zeggini
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1HH, UK
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26
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Griffin PJ, Sebastiani P, Edward H, Baldwin CT, Gladwin M, Gordeuk V, Chui DH, Steinberg MH. The genetics of hemoglobin A2 regulation in sickle cell anemia. Am J Hematol 2014; 89:1019-23. [PMID: 25042611 PMCID: PMC4298130 DOI: 10.1002/ajh.23811] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 07/15/2014] [Accepted: 07/16/2014] [Indexed: 02/02/2023]
Abstract
Hemoglobin A2 , a tetramer of α- and δ-globin chains, comprises less than 3% of total hemoglobin in normal adults. In northern Europeans, single nucleotide polymorphisms (SNPs) in the HBS1L-MYB locus on chromosome 6q and the HBB cluster on chromosome 11p were associated with HbA2 levels. We examined the genetic basis of HbA2 variability in sickle cell anemia using genome-wide association studies. HbA2 levels were associated with SNPs in the HBS1L-MYB interval and SNPs in BCL11A. These effects are mediated by the association of these loci with γ-globin gene expression and fetal hemoglobin (HbF) levels. The association of polymorphisms downstream of the β-globin gene (HBB) cluster on chromosome 11 with HbA2 was not mediated by HbF. In sickle cell anemia, levels of HbA2 appear to be modulated by trans-acting genes that affect HBG expression and perhaps also elements within the β-globin gene cluster. HbA2 is expressed pancellularly and can inhibit HbS polymerization. It remains to be seen if genetic regulators of HbA2 can be exploited for therapeutic purposes.
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Affiliation(s)
- Paula J. Griffin
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Heather Edward
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Clinton T. Baldwin
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Mark Gladwin
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Victor Gordeuk
- Department of Medicine and Comprehensive Sickle Cell Center, University of Illinois, Chicago, IL
| | - David H.K. Chui
- Department of Medicine, Boston University School of Medicine, Boston, MA
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27
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Chen P, Takeuchi F, Lee JY, Li H, Wu JY, Liang J, Long J, Tabara Y, Goodarzi MO, Pereira MA, Kim YJ, Go MJ, Stram DO, Vithana E, Khor CC, Liu J, Liao J, Ye X, Wang Y, Lu L, Young TL, Lee J, Thai AC, Cheng CY, van Dam RM, Friedlander Y, Heng CK, Koh WP, Chen CH, Chang LC, Pan WH, Qi Q, Isono M, Zheng W, Cai Q, Gao Y, Yamamoto K, Ohnaka K, Takayanagi R, Kita Y, Ueshima H, Hsiung CA, Cui J, Sheu WHH, Rotter JI, Chen YDI, Hsu C, Okada Y, Kubo M, Takahashi A, Tanaka T, van Rooij FJA, Ganesh SK, Huang J, Huang T, Yuan J, Hwang JY, Gross MD, Assimes TL, Miki T, Shu XO, Qi L, Chen YT, Lin X, Aung T, Wong TY, Teo YY, Kim BJ, Kato N, Tai ES. Multiple nonglycemic genomic loci are newly associated with blood level of glycated hemoglobin in East Asians. Diabetes 2014; 63:2551-62. [PMID: 24647736 PMCID: PMC4284402 DOI: 10.2337/db13-1815] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/08/2014] [Indexed: 11/13/2022]
Abstract
Glycated hemoglobin A1c (HbA1c) is used as a measure of glycemic control and also as a diagnostic criterion for diabetes. To discover novel loci harboring common variants associated with HbA1c in East Asians, we conducted a meta-analysis of 13 genome-wide association studies (GWAS; N = 21,026). We replicated our findings in three additional studies comprising 11,576 individuals of East Asian ancestry. Ten variants showed associations that reached genome-wide significance in the discovery data set, of which nine (four novel variants at TMEM79 [P value = 1.3 × 10(-23)], HBS1L/MYB [8.5 × 10(-15)], MYO9B [9.0 × 10(-12)], and CYBA [1.1 × 10(-8)] as well as five variants at loci that had been previously identified [CDKAL1, G6PC2/ABCB11, GCK, ANK1, and FN3KI]) showed consistent evidence of association in replication data sets. These variants explained 1.76% of the variance in HbA1c. Several of these variants (TMEM79, HBS1L/MYB, CYBA, MYO9B, ANK1, and FN3K) showed no association with either blood glucose or type 2 diabetes. Among individuals with nondiabetic levels of fasting glucose (<7.0 mmol/L) but elevated HbA1c (≥6.5%), 36.1% had HbA1c <6.5% after adjustment for these six variants. Our East Asian GWAS meta-analysis has identified novel variants associated with HbA1c as well as demonstrated that the effects of known variants are largely transferable across ethnic groups. Variants affecting erythrocyte parameters rather than glucose metabolism may be relevant to the use of HbA1c for diagnosing diabetes in these populations.
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Affiliation(s)
- Peng Chen
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | | | - Jong-Young Lee
- Center for Genome Science, National Institute of Health, Osong Health Technology Administration Complex, Chungcheongbuk-do, Republic of Korea
| | - Huaixing Li
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, TaiwanSchool of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Jun Liang
- Department of Endocrinology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College, Affiliated Hospital of Southeast University, Xuzhou, Jiangsu, China
| | - Jirong Long
- Vanderbilt Epidemiology Center and Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto, Japan
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Mark A Pereira
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN
| | - Young Jin Kim
- Center for Genome Science, National Institute of Health, Osong Health Technology Administration Complex, Chungcheongbuk-do, Republic of Korea
| | - Min Jin Go
- Center for Genome Science, National Institute of Health, Osong Health Technology Administration Complex, Chungcheongbuk-do, Republic of Korea
| | - Daniel O Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Eranga Vithana
- Singapore Eye Research Institute, Singapore National Eye Centre, SingaporeNeuroscience and Behavioural Disorders (NBD) Program, Duke-National University of Singapore Graduate Medical School, Singapore
| | - Chiea-Chuen Khor
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, SingaporeDepartment of Ophthalmology, National University of Singapore, SingaporeGenome Institute of Singapore, Agency for Science, Technology and Research, Singapore, SingaporeDepartment of Paediatrics, National University of Singapore, Singapore
| | - Jianjun Liu
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, SingaporeGenome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jiemin Liao
- Singapore Eye Research Institute, Singapore National Eye Centre, SingaporeDepartment of Ophthalmology, National University of Singapore, Singapore
| | - Xingwang Ye
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yiqin Wang
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ling Lu
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Terri L Young
- Neuroscience and Behavioural Disorders (NBD) Program, Duke-National University of Singapore Graduate Medical School, SingaporeDuke Eye Center, Duke University Medical Center, Durham, NC
| | - Jeannette Lee
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Ah Chuan Thai
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ching-Yu Cheng
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, SingaporeSingapore Eye Research Institute, Singapore National Eye Centre, SingaporeDepartment of Ophthalmology, National University of Singapore, SingaporeCentre for Quantitative Medicine, Office of Clinical Sciences, Duke-National University of Singapore Graduate Medical School, Singapore
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, SingaporeDepartment of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Chew-Kiat Heng
- Department of Paediatrics, National University of Singapore, Singapore
| | - Woon-Puay Koh
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, SingaporeDuke-National University of Singapore Graduate Medical School, Singapore
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, TaiwanSchool of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Li-Ching Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Wen-Harn Pan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY
| | - Masato Isono
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Wei Zheng
- Vanderbilt Epidemiology Center and Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Qiuyin Cai
- Vanderbilt Epidemiology Center and Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Yutang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Ken Yamamoto
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Keizo Ohnaka
- Department of Geriatric Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ryoichi Takayanagi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshikuni Kita
- Department of Health Science, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Japan
| | - Hirotsugu Ueshima
- Department of Health Science, and Center for Epidemiologic Research in Asia, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Japan
| | - Chao A Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Jinrui Cui
- Division of Endocrinology, Diabetes, and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Wayne H-H Sheu
- Division of Endocrine and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, TaiwanSchool of Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Jerome I Rotter
- Institute for Translational Genomics and Biomedical Sciences, Los Angeles Biomedical Research Institute, Harbor-University of California, Los Angeles Medical Center, Torrance, CA
| | - Yii-Der I Chen
- Institute for Translational Genomics and Biomedical Sciences, Los Angeles Biomedical Research Institute, Harbor-University of California, Los Angeles Medical Center, Torrance, CA
| | - Chris Hsu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Yukinori Okada
- Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, JapanLaboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Toshihiro Tanaka
- Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, JapanLaboratory for Cardiovascular Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Frank J A van Rooij
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Santhi K Ganesh
- Departments of Internal Medicine and Human Genetics, University of Michigan, Ann Arbor, MI
| | - Jinyan Huang
- Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - Tao Huang
- Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - Jianmin Yuan
- University of Pittsburgh Cancer Institute, Pittsburgh, PA
| | - Joo-Yeon Hwang
- Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea
| | - Myron D Gross
- Department of Laboratory Medicine and Pathology, Medical School, University of Minnesota, Minneapolis, MN
| | | | - Tetsuro Miki
- Department of Geriatric Medicine, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Xiao-Ou Shu
- Vanderbilt Epidemiology Center and Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Lu Qi
- Department of Nutrition, Harvard School of Public Health, Boston, MAChanning Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Yuan-Tson Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, TaiwanDepartment of Pediatrics, Duke University Medical Center, Durham, NC
| | - Xu Lin
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, SingaporeDepartment of Ophthalmology, National University of Singapore, Singapore
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, SingaporeSingapore Eye Research Institute, Singapore National Eye Centre, SingaporeGenome Institute of Singapore, Agency for Science, Technology and Research, Singapore, SingaporeNUS Graduate School for Integrative Science and Engineering, National University of Singapore, SingaporeDepartment of Statistics and Applied Probability, National University of Singapore, Singapore
| | - Bong-Jo Kim
- Center for Genome Science, National Institute of Health, Osong Health Technology Administration Complex, Chungcheongbuk-do, Republic of Korea
| | - Norihiro Kato
- National Center for Global Health and Medicine, Tokyo, Japan
| | - E-Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, SingaporeDepartment of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, SingaporeDuke-National University of Singapore Graduate Medical School, Singapore
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28
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Stadhouders R, Aktuna S, Thongjuea S, Aghajanirefah A, Pourfarzad F, van Ijcken W, Lenhard B, Rooks H, Best S, Menzel S, Grosveld F, Thein SL, Soler E. HBS1L-MYB intergenic variants modulate fetal hemoglobin via long-range MYB enhancers. J Clin Invest 2014; 124:1699-710. [PMID: 24614105 DOI: 10.1172/jci71520] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 01/09/2014] [Indexed: 01/21/2023] Open
Abstract
Genetic studies have identified common variants within the intergenic region (HBS1L-MYB) between GTP-binding elongation factor HBS1L and myeloblastosis oncogene MYB on chromosome 6q that are associated with elevated fetal hemoglobin (HbF) levels and alterations of other clinically important human erythroid traits. It is unclear how these noncoding sequence variants affect multiple erythrocyte characteristics. Here, we determined that several HBS1L-MYB intergenic variants affect regulatory elements that are occupied by key erythroid transcription factors within this region. These elements interact with MYB, a critical regulator of erythroid development and HbF levels. We found that several HBS1L-MYB intergenic variants reduce transcription factor binding, affecting long-range interactions with MYB and MYB expression levels. These data provide a functional explanation for the genetic association of HBS1L-MYB intergenic polymorphisms with human erythroid traits and HbF levels. Our results further designate MYB as a target for therapeutic induction of HbF to ameliorate sickle cell and β-thalassemia disease severity.
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