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Kirkham JK, Estepp JH, Weiss MJ, Rashkin SR. Genetic Variation and Sickle Cell Disease Severity: A Systematic Review and Meta-Analysis. JAMA Netw Open 2023; 6:e2337484. [PMID: 37851445 PMCID: PMC10585422 DOI: 10.1001/jamanetworkopen.2023.37484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/30/2023] [Indexed: 10/19/2023] Open
Abstract
Importance Sickle cell disease (SCD) is a monogenic disorder, yet clinical outcomes are influenced by additional genetic factors. Despite decades of research, the genetics of SCD remain poorly understood. Objective To assess all reported genetic modifiers of SCD, evaluate the design of associated studies, and provide guidelines for future analyses according to modern genetic study recommendations. Data Sources PubMed, Web of Science, and Scopus were searched through May 16, 2023, identifying 5290 publications. Study Selection At least 2 reviewers identified 571 original, peer-reviewed English-language publications reporting genetic modifiers of human SCD phenotypes, wherein the outcome was not treatment response, and the comparison was not between SCD subtypes or including healthy controls. Data Extraction and Synthesis Data relevant to all genetic modifiers of SCD were extracted, evaluated, and presented following STREGA and PRISMA guidelines. Weighted z score meta-analyses and pathway analyses were conducted. Main Outcomes and Measures Outcomes were aggregated into 25 categories, grouped as acute complications, chronic conditions, hematologic parameters or biomarkers, and general or mixed measures of SCD severity. Results The 571 included studies reported on 29 670 unique individuals (50% ≤ 18 years of age) from 43 countries. Of the 17 757 extracted results (4890 significant) in 1552 genes, 3675 results met the study criteria for meta-analysis: reported phenotype and genotype, association size and direction, variability measure, sample size, and statistical test. Only 173 results for 62 associations could be cross-study combined. The remaining associations could not be aggregated because they were only reported once or methods (eg, study design, reporting practice) and genotype or phenotype definitions were insufficiently harmonized. Gene variants regulating fetal hemoglobin and α-thalassemia (important markers for SCD severity) were frequently identified: 19 single-nucleotide variants in BCL11A, HBS1L-MYB, and HBG2 were significantly associated with fetal hemoglobin (absolute value of Z = 4.00 to 20.66; P = 8.63 × 10-95 to 6.19 × 10-5), and α-thalassemia deletions were significantly associated with increased hemoglobin level and reduced risk of albuminuria, abnormal transcranial Doppler velocity, and stroke (absolute value of Z = 3.43 to 5.16; P = 2.42 × 10-7 to 6.00 × 10-4). However, other associations remain unconfirmed. Pathway analyses of significant genes highlighted the importance of cellular adhesion, inflammation, oxidative and toxic stress, and blood vessel regulation in SCD (23 of the top 25 Gene Ontology pathways involve these processes) and suggested future research areas. Conclusions and Relevance The findings of this comprehensive systematic review and meta-analysis of all published genetic modifiers of SCD indicated that implementation of standardized phenotypes, statistical methods, and reporting practices should accelerate discovery and validation of genetic modifiers and development of clinically actionable genetic profiles.
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Affiliation(s)
- Justin K. Kirkham
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, Tennessee
| | - Jeremie H. Estepp
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, Tennessee
- Department of Global Pediatric Medicine, St Jude Children’s Research Hospital, Memphis, Tennessee
- Now with Agios Pharmaceuticals, Cambridge, Massachusetts
| | - Mitch J. Weiss
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, Tennessee
| | - Sara R. Rashkin
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, Tennessee
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Palomarez A, Jha M, Medina Romero X, Horton RE. Cardiovascular consequences of sickle cell disease. BIOPHYSICS REVIEWS 2022; 3:031302. [PMID: 38505276 PMCID: PMC10903381 DOI: 10.1063/5.0094650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/11/2022] [Indexed: 03/21/2024]
Abstract
Sickle cell disease (SCD) is an inherited blood disorder caused by a single point mutation within the beta globin gene. As a result of this mutation, hemoglobin polymerizes under low oxygen conditions causing red blood cells to deform, become more adhesive, and increase in rigidity, which affects blood flow dynamics. This process leads to enhanced red blood cell interactions with the endothelium and contributes to vaso-occlusion formation. Although traditionally defined as a red blood cell disorder, individuals with SCD are affected by numerous clinical consequences including stroke, painful crisis episodes, bone infarctions, and several organ-specific complications. Elevated cardiac output, endothelium activation along with the sickling process, and the vaso-occlusion events pose strains on the cardiovascular system. We will present a review of the cardiovascular consequences of sickle cell disease and show connections with the vasculopathy related to SCD. We will also highlight biophysical properties and engineering tools that have been used to characterize the disease. Finally, we will discuss therapies for SCD and potential implications on SCD cardiomyopathy.
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Affiliation(s)
- Alexis Palomarez
- Department of Biomedical Engineering, Cullen College of Engineering, University of Houston, Houston, Texas 77204, USA
| | - Manisha Jha
- Department of Biomedical Engineering, Cullen College of Engineering, University of Houston, Houston, Texas 77204, USA
| | - Ximena Medina Romero
- Department of Biomedical Engineering, Cullen College of Engineering, University of Houston, Houston, Texas 77204, USA
| | - Renita E. Horton
- Department of Biomedical Engineering, Cullen College of Engineering, University of Houston, Houston, Texas 77204, USA
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Rizo-de la Torre LC, Borrayo-López FJ, Perea-Díaz FJ, Aquino E, Venegas M, Hernández-Carbajal C, Espinoza-Mata LL, Ibarra-Cortés B. Fetal hemoglobin regulating genetic variants identified in homozygous (HbSS) and heterozygous (HbSA) subjects from South Mexico. J Trop Pediatr 2022; 68:6709334. [PMID: 36130307 DOI: 10.1093/tropej/fmac073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Hemoglobin S is caused by a nucleotide change in HBB gene (HBB:c.20A>T, p.Glu6Val), is presented in diverse forms: simple carriers (HbSA), homozygotes (HbSS) also known as sickle cell anemia, and compound heterozygotes with other β-hemoglobinopathies. It is worldwide distributed, in Mexico, is frequently observed in the southern states Guerrero, Oaxaca and Chiapas. Elevated fetal hemoglobin (HbF) is associated with mild phenotype; single-nucleotide variants (SNVs) in modifier genes, such as BCL11A, HBG2, HBBP1 pseudogene and HBS1L-MYB intergenic region, upregulate HbF synthesis. The aim of this study was to identify HbF regulating genetic variants in HbSS and HbSA Mexican subjects. We studied 39 individuals (HbSS = 24, 61%, HbSA = 15, 39%) from Chiapas (67%) and Guerrero (33%), peripheral blood was collected in ethylenediamine tetraacetic acid (EDTA) for molecular and hematological studies, DNA was isolated by salting-out technic and genotyping was performed through allelic discrimination by real time polymerase chain reaction (RT-PCR) using Taqman® probes for 15 SNV (in BCL11A: rs6706648, rs7557939, rs4671393, rs11886868, rs766432, rs7599488, rs1427407; HBS1L-MYB: rs28384513, rs7776054, rs9399137, rs4895441, rs9402686, rs1320963; HBG2: rs7482144; and HBBP1: rs10128556). The obtained data were analyzed using IMB SPSS v.22.0 software. All minor alleles were observed in frequencies over 0.05, the most frequent was rs9402686 (0.82), while the less frequent was rs101028556 (0.08). In HbSS group, the mean fetal hemoglobin was 11.9 ± 5.9% and was significantly elevated in BCL11A rs11886868 wildtype homozygotes and in carriers of HBS1L-MYB intergenic region rs7776054 (p = 0.04 and p = 0.03, respectively). In conclusion, in HbSS Mexican patients, two SNVs were observed related to increased HbF; BCL11A rs11886868 and HBS1L-MYB rs7776054.
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Affiliation(s)
- L C Rizo-de la Torre
- División de Medicina Molecular, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - F J Borrayo-López
- División de Medicina Molecular, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico.,Departamento de Biología Molecular y Genómica, Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara (UDG), Guadalajara, Jalisco, Mexico.,División de Genética, CIBO, IMSS, Guadalajara, Jalisco, Mexico
| | - F J Perea-Díaz
- División de Genética, CIBO, IMSS, Guadalajara, Jalisco, Mexico
| | - E Aquino
- Departamento de Hematología, Hospital de Especialidades Pediátricas, Secretaría de Salud, Tuxtla Gutiérrez, Chiapas, Mexico
| | - M Venegas
- Departamento de Hematología, Hospital Regional, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Acapulco, Guerrero, Mexico
| | - C Hernández-Carbajal
- Departamento de Hematología, Hospital General Regional No. 1, IMSS, Acapulco, Guerrero, Mexico
| | - L L Espinoza-Mata
- División de Medicina Molecular, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico.,División de Genética, CIBO, IMSS, Guadalajara, Jalisco, Mexico
| | - B Ibarra-Cortés
- Instituto de Genética Humana "Dr. Enrique Corona Rivera" CUCS, UDG, Guadalajara, Jalisco, Mexico
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Ata F, Yousaf Z, Sardar S, Javed S, Iqbal P, Khamees I, Malkawi LS, Yassin MA. Protocol for "Genetic composition of sickle cell disease in the Arab population: A systematic review". Health Sci Rep 2022; 5:e450. [PMID: 35509404 PMCID: PMC9062566 DOI: 10.1002/hsr2.450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 10/17/2021] [Accepted: 11/09/2021] [Indexed: 11/18/2022] Open
Abstract
Background Sickle Cell Disease (SCD) is a global health issue in hematology with a progressively increasing prevalence. There are recent advances in the management of SCD, with new drugs being introduced. It is essential to analyze the genetic makeup of SCD regionally to anticipate the effectiveness of management modalities. This systematic review's main objectives are (a) to combine the existing knowledge of the genetic composition of SCD in the Arab population and (b) to analyze the various phenotypes of SCD prevalent in the Arab population. Methods We will perform a systematic review and search multiple electronic databases predefined search terms to identify eligible articles. Eligible studies should report findings on the genetic testing of Sickle Cell disease in the 22 Arab countries. Case reports, case series, observational studies with cross‐sectional or prospective research design, case‐control studies, and experimental studies will be included. Study quality will be independently evaluated by two reviewers using the statistical methodology and categories guided by the Cochrane Collaboration Handbook and PRISMA guidelines. Discussion This review will explore and integrate the evidence available on the various genotypes and phenotypes of SCD in the Arab population. By acquiring and summarizing data about the genetic and phenotypic variants of the SCD patient population, this study will add to the knowledge and help find more precise treatments. Systematic review registration The protocol is registered at the International Prospective Register of Systematic Reviews (PROSPERO; registration number: CRD42020218666).
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Affiliation(s)
- Fateen Ata
- Department of Internal Medicine Hamad General Hospital, Hamad Medical Corporation Doha Qatar
| | - Zohaib Yousaf
- Department of Internal Medicine Hamad General Hospital, Hamad Medical Corporation Doha Qatar
| | - Sundus Sardar
- Department of Internal Medicine Hamad General Hospital, Hamad Medical Corporation Doha Qatar
| | - Saad Javed
- Department of Internal Medicine Allama Iqbal Medical College Lahore Pakistan
| | - Phool Iqbal
- Department of Internal Medicine Hamad General Hospital, Hamad Medical Corporation Doha Qatar
| | - Ibraheem Khamees
- Department of Internal Medicine Hamad General Hospital, Hamad Medical Corporation Doha Qatar
| | - Lujain Salahaldeen Malkawi
- Department of Internal Medicine, Faculty of Medicine Jordan University of Science and Technology Irbid Jordan
| | - Mohamed A Yassin
- Department of Medical Oncology/Hematology National Centre for Cancer Care and Research, Hamad Medical Corporation Doha Qatar
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Manu GP, Segbefia C, N’guessan BB, Coffie SA, Adjei GO. Association Between Selected Single Nucleotide Polymorphisms in Globin and Related Genes and Response to Hydroxyurea Therapy in Ghanaian Children with Sickle Cell Disease. Pharmgenomics Pers Med 2022; 15:205-214. [PMID: 35300055 PMCID: PMC8922234 DOI: 10.2147/pgpm.s351599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/17/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Gloria Pokuaa Manu
- Department of Pharmacology and Toxicology, School of Pharmacy, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Catherine Segbefia
- Department of Child Health, University of Ghana Medical School, Accra, Ghana
| | - Benoit Banga N’guessan
- Department of Pharmacology and Toxicology, School of Pharmacy, College of Health Sciences, University of Ghana, Accra, Ghana
| | | | - George Obeng Adjei
- Centre for Tropical, Clinical Pharmacology and Therapeutics, University of Ghana Medical School, College of Health Sciences, University of Ghana, Accra, Ghana
- Correspondence: George Obeng Adjei, Email
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Significance of genetic modifiers of hemoglobinopathies leading towards precision medicine. Sci Rep 2021; 11:20906. [PMID: 34686692 PMCID: PMC8536722 DOI: 10.1038/s41598-021-00169-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 09/02/2021] [Indexed: 11/17/2022] Open
Abstract
Hemoglobinopathies though a monogenic disorder, show phenotypic variability. Hence, understanding the genetics underlying the heritable sub-phenotypes of hemoglobinopathies, specific to each population, would be prognostically useful and could inform personalized therapeutics. This study aimed to evaluate the role of genetic modifiers leading to higher HbF production with cumulative impact of the modifiers on disease severity. 200 patients (100 β-thalassemia homozygotes, 100 Sickle Cell Anemia), and 50 healthy controls were recruited. Primary screening followed with molecular analysis for confirming the β-hemoglobinopathy was performed. Co-existing α-thalassemia and the polymorphisms located in 3 genetic loci linked to HbF regulation were screened. The most remarkable result was the association of SNPs with clinically relevant phenotypic groups. The γ-globin gene promoter polymorphisms [− 158 C → T, + 25 G → A],BCL11A rs1427407 G → T, − 3 bp HBS1L-MYB rs66650371 and rs9399137 T → C polymorphisms were correlated with higher HbF, in group that has lower disease severity score (P < 0.00001), milder clinical presentation, and a significant delay in the age of the first transfusion. Our study emphasizes the complex genetic interactions underlying the disease phenotype that may be a prognostic marker for predicting the clinical severity and assist in disease management.
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Schmidt F, Marx A, Baumgarten N, Hebel M, Wegner M, Kaulich M, Leisegang M, Brandes R, Göke J, Vreeken J, Schulz M. Integrative analysis of epigenetics data identifies gene-specific regulatory elements. Nucleic Acids Res 2021; 49:10397-10418. [PMID: 34508352 PMCID: PMC8501997 DOI: 10.1093/nar/gkab798] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 08/01/2021] [Accepted: 09/07/2021] [Indexed: 12/19/2022] Open
Abstract
Understanding how epigenetic variation in non-coding regions is involved in distal gene-expression regulation is an important problem. Regulatory regions can be associated to genes using large-scale datasets of epigenetic and expression data. However, for regions of complex epigenomic signals and enhancers that regulate many genes, it is difficult to understand these associations. We present StitchIt, an approach to dissect epigenetic variation in a gene-specific manner for the detection of regulatory elements (REMs) without relying on peak calls in individual samples. StitchIt segments epigenetic signal tracks over many samples to generate the location and the target genes of a REM simultaneously. We show that this approach leads to a more accurate and refined REM detection compared to standard methods even on heterogeneous datasets, which are challenging to model. Also, StitchIt REMs are highly enriched in experimentally determined chromatin interactions and expression quantitative trait loci. We validated several newly predicted REMs using CRISPR-Cas9 experiments, thereby demonstrating the reliability of StitchIt. StitchIt is able to dissect regulation in superenhancers and predicts thousands of putative REMs that go unnoticed using peak-based approaches suggesting that a large part of the regulome might be uncharted water.
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Affiliation(s)
- Florian Schmidt
- Cluster of Excellence for Multimodal Computing and Interaction, Saarland University, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Graduate School of Computer Science, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, 60 Biopolis Street, 138672 Singapore, Singapore
| | - Alexander Marx
- Cluster of Excellence for Multimodal Computing and Interaction, Saarland University, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Graduate School of Computer Science, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- International Max Planck Research School for Computer Science, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Nina Baumgarten
- Institute for Cardiovascular Regeneration, Goethe University, 60590 Frankfurt am Main, Germany
- German Center for Cardiovascular Research (DZHK), Partner site RheinMain, 60590 Frankfurt am Main, Germany
| | - Marie Hebel
- Institute of Biochemistry II, Goethe University Frankfurt - Medical Faculty, University Hospital, 60590 Frankfurt am Main, Germany
| | - Martin Wegner
- Institute of Biochemistry II, Goethe University Frankfurt - Medical Faculty, University Hospital, 60590 Frankfurt am Main, Germany
| | - Manuel Kaulich
- Institute of Biochemistry II, Goethe University Frankfurt - Medical Faculty, University Hospital, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, 60590 Frankfurt am Main, Germany
| | - Matthias S Leisegang
- German Center for Cardiovascular Research (DZHK), Partner site RheinMain, 60590 Frankfurt am Main, Germany
- Institute for Cardiovascular Physiology, Goethe University, 60590 Frankfurt am Main, Germany
| | - Ralf P Brandes
- German Center for Cardiovascular Research (DZHK), Partner site RheinMain, 60590 Frankfurt am Main, Germany
- Institute for Cardiovascular Physiology, Goethe University, 60590 Frankfurt am Main, Germany
| | - Jonathan Göke
- Laboratory of Computational Transcriptomics, Genome Institute of Singapore, 60 Biopolis Street, 138672 Singapore, Singapore
| | - Jilles Vreeken
- CISPA Helmholtz Center for Information Security, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Cluster of Excellence for Multimodal Computing and Interaction, Saarland University, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Marcel H Schulz
- Cluster of Excellence for Multimodal Computing and Interaction, Saarland University, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Institute for Cardiovascular Regeneration, Goethe University, 60590 Frankfurt am Main, Germany
- German Center for Cardiovascular Research (DZHK), Partner site RheinMain, 60590 Frankfurt am Main, Germany
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Unique Polymorphisms at BCL11A, HBS1L-MYB and HBB Loci Associated with HbF in Kuwaiti Patients with Sickle Cell Disease. J Pers Med 2021; 11:jpm11060567. [PMID: 34204365 PMCID: PMC8234980 DOI: 10.3390/jpm11060567] [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: 05/04/2021] [Revised: 06/12/2021] [Accepted: 06/14/2021] [Indexed: 11/16/2022] Open
Abstract
Patients with sickle cell disease (SCD) in Kuwait have elevated HbF levels ranging from ~10-44%; however, the modulating factors are unclear. We investigated the association of single nucleotide polymorphisms (SNPs) at BCL11A, HBS1L-MYB and HBB with HbF levels in 237 Kuwaiti SCD patients, divided into 3 subgroups according to their HbF levels. Illumina Ampliseq custom DNA panel was used for genotyping and confirmed by arrayed primer extension or Sanger sequencing. In the BCL11A locus, the CC genotype of rs7606173 [χ2 = 16.5] and (GG) of rs10195871 [χ2 = 15.0] were associated with Hb-F1 and HbF-2 subgroups, unlike rs1427404-T [χ2 = 17.3], which showed the highest association across the three subgroups. HBS1L-MYB locus revealed 2 previously-described SNPs (rs66650371 [χ2 = 9.5] and rs35795442 [χ2 = 9.2]) and 2 previously-unreported SNPs, (rs13220662 [χ2 = 6.2] and rs1406811 [χ2 = 6.7]) that were associated with the HbF-3 subgroup, making this the key locus elevating HbF to the highest levels. HBB cluster variants were associated with lower levels of HbF (β = -1.1). We report four previously-unpublished variants showing significant association with HbF. Each of the three quantitative trait loci affects HbF levels differently; unique SNPs, especially in HBS1L-MYB, elevate HbF to the highest levels.
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Abstract
Fetal hemoglobin (HbF) can blunt the pathophysiology, temper the clinical course, and offer prospects for curative therapy of sickle cell disease. This review focuses on (1) HbF quantitative trait loci and the geography of β-globin gene haplotypes, especially those found in the Middle East; (2) how HbF might differentially impact the pathophysiology and many subphenotypes of sickle cell disease; (3) clinical implications of person-to-person variation in the distribution of HbF among HbF-containing erythrocytes; and (4) reactivation of HbF gene expression using both pharmacologic and cell-based therapeutic approaches. A confluence of detailed understanding of the molecular basis of HbF gene expression, coupled with the ability to precisely target by genomic editing most areas of the genome, is producing important preliminary therapeutic results that could provide new options for cell-based therapeutics with curative intent.
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Barbanera Y, Arcioni F, Lancioni H, La Starza R, Cardinali I, Matteucci C, Nofrini V, Roetto A, Piga A, Grammatico P, Caniglia M, Mecucci C, Gorello P. Comprehensive analysis of mitochondrial and nuclear DNA variations in patients affected by hemoglobinopathies: A pilot study. PLoS One 2020; 15:e0240632. [PMID: 33091040 PMCID: PMC7581000 DOI: 10.1371/journal.pone.0240632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/29/2020] [Indexed: 12/29/2022] Open
Abstract
The hemoglobin disorders are the most common single gene disorders in the world. Previous studies have suggested that they are deeply geographically structured and a variety of genetic determinants influences different clinical phenotypes between patients inheriting identical β-globin gene mutations. In order to get new insights into the heterogeneity of hemoglobin disorders, we investigated the molecular variations on nuclear genes (i.e. HBB, HBG2, BCL11A, HBS1L and MYB) and mitochondrial DNA control region. This pilot study was carried out on 53 patients belonging to different continents and molecularly classified in 4 subgroup: β-thalassemia (β+/β+, β0/β0 and β+/β0)(15), sickle cell disease (HbS/HbS)(20), sickle cell/β-thalassemia (HbS/β+ or HBS/β0)(10), and non-thalassemic compound heterozygous (HbS/HbC, HbO-Arab/HbC)(8). This comprehensive phylogenetic analysis provided a clear separation between African and European patients either in nuclear or mitochondrial variations. Notably, informing on the phylogeographic structure of affected individuals, this accurate genetic stratification, could help to optimize the diagnostic algorithm for patients with uncertain or unknown origin.
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Affiliation(s)
- Ylenia Barbanera
- Department of Medicine, Hematology, University of Perugia, Perugia, Italy
| | - Francesco Arcioni
- Pediatric Oncohematology, Hospital Santa Maria della Misericordia, Perugia, Italy
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Roberta La Starza
- Department of Medicine, Hematology, University of Perugia, Perugia, Italy
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Caterina Matteucci
- Department of Medicine, Hematology, University of Perugia, Perugia, Italy
| | - Valeria Nofrini
- Department of Medicine, Hematology, University of Perugia, Perugia, Italy
| | - Antonella Roetto
- Department of Clinical and Biological Sciences, University of Turin, Hospital San Luigi Gonzaga, Turin, Italy
| | - Antonio Piga
- Department of Clinical and Biological Sciences, University of Turin, Hospital San Luigi Gonzaga, Turin, Italy
| | - Paola Grammatico
- Department of Molecular Medicine, Laboratory of Medical Genetics, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Maurizio Caniglia
- Pediatric Oncohematology, Hospital Santa Maria della Misericordia, Perugia, Italy
| | - Cristina Mecucci
- Department of Medicine, Hematology, University of Perugia, Perugia, Italy
| | - Paolo Gorello
- Department of Medicine, Hematology, University of Perugia, Perugia, Italy
- * E-mail:
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Alpay BA, Demetci P, Istrail S, Aguiar D. Combinatorial and statistical prediction of gene expression from haplotype sequence. Bioinformatics 2020; 36:i194-i202. [PMID: 32657373 PMCID: PMC7355230 DOI: 10.1093/bioinformatics/btaa318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Genome-wide association studies (GWAS) have discovered thousands of significant genetic effects on disease phenotypes. By considering gene expression as the intermediary between genotype and disease phenotype, expression quantitative trait loci studies have interpreted many of these variants by their regulatory effects on gene expression. However, there remains a considerable gap between genotype-to-gene expression association and genotype-to-gene expression prediction. Accurate prediction of gene expression enables gene-based association studies to be performed post hoc for existing GWAS, reduces multiple testing burden, and can prioritize genes for subsequent experimental investigation. RESULTS In this work, we develop gene expression prediction methods that relax the independence and additivity assumptions between genetic markers. First, we consider gene expression prediction from a regression perspective and develop the HAPLEXR algorithm which combines haplotype clusterings with allelic dosages. Second, we introduce the new gene expression classification problem, which focuses on identifying expression groups rather than continuous measurements; we formalize the selection of an appropriate number of expression groups using the principle of maximum entropy. Third, we develop the HAPLEXD algorithm that models haplotype sharing with a modified suffix tree data structure and computes expression groups by spectral clustering. In both models, we penalize model complexity by prioritizing genetic clusters that indicate significant effects on expression. We compare HAPLEXR and HAPLEXD with three state-of-the-art expression prediction methods and two novel logistic regression approaches across five GTEx v8 tissues. HAPLEXD exhibits significantly higher classification accuracy overall; HAPLEXR shows higher prediction accuracy on approximately half of the genes tested and the largest number of best predicted genes (r2>0.1) among all methods. We show that variant and haplotype features selected by HAPLEXR are smaller in size than competing methods (and thus more interpretable) and are significantly enriched in functional annotations related to gene regulation. These results demonstrate the importance of explicitly modeling non-dosage dependent and intragenic epistatic effects when predicting expression. AVAILABILITY AND IMPLEMENTATION Source code and binaries are freely available at https://github.com/rapturous/HAPLEX. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Berk A Alpay
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Pinar Demetci
- Department of Computer Science and Center for Computational Biology, Brown University, Providence, RI 02912, USA
| | - Sorin Istrail
- Department of Computer Science and Center for Computational Biology, Brown University, Providence, RI 02912, USA
| | - Derek Aguiar
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA
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12
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Flansburg C, Balentine CM, Grieger RW, Lund J, Ciambella M, White D, Coris E, Gonzalez E, Stone AC, Madrigal L. Fetal Hemoglobin Modulators May Be Associated With Symptomology of Football Players with Sickle Cell Trait. South Med J 2019; 112:289-294. [PMID: 31050799 DOI: 10.14423/smj.0000000000000976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
OBJECTIVES This study investigates whether genetic modifiers previously shown to influence adult fetal hemoglobin (HbF) levels and glucose-6-phosphate dehydrogenase deficiency were associated with variable symptomology in a small sample of collegiate football players with sickle cell trait. METHODS Survey data on self-assessed symptoms and genotype data from five single nucleotide polymorphisms (SNPs) related to HbF production and two SNPs that cause glucose-6-phosphate dehydrogenase deficiency were collected from current and former college football players. RESULTS In this sample, SNPs found within the β-globin gene cluster were found to be associated with a previous diagnosis of exertional sickling and experience of extreme heat during and after training. rs10189857 in the BCL11A gene was associated with body mass index and weight and with experiencing extreme thirst during and after training. No significant correlations were found between the other SNPs and symptoms within this sample. CONCLUSIONS These findings show that genetic variation known to affect sickle cell disease symptomology may partly explain why some football players with sickle cell trait experience adverse clinical outcomes during periods of extreme physical exertion and others do not.
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Affiliation(s)
- Carroll Flansburg
- From the Geisinger Health System, Danville, Pennsylvania, the School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, the School of Life Sciences, Arizona State University, Tempe, Arizona, the Department of Anthropology, University of South Florida, Tampa, the Morsani College of Medicine, University of South Florida, Tampa, and the Center for Evolution and Medicine and the School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Christina M Balentine
- From the Geisinger Health System, Danville, Pennsylvania, the School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, the School of Life Sciences, Arizona State University, Tempe, Arizona, the Department of Anthropology, University of South Florida, Tampa, the Morsani College of Medicine, University of South Florida, Tampa, and the Center for Evolution and Medicine and the School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Ryan W Grieger
- From the Geisinger Health System, Danville, Pennsylvania, the School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, the School of Life Sciences, Arizona State University, Tempe, Arizona, the Department of Anthropology, University of South Florida, Tampa, the Morsani College of Medicine, University of South Florida, Tampa, and the Center for Evolution and Medicine and the School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Justin Lund
- From the Geisinger Health System, Danville, Pennsylvania, the School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, the School of Life Sciences, Arizona State University, Tempe, Arizona, the Department of Anthropology, University of South Florida, Tampa, the Morsani College of Medicine, University of South Florida, Tampa, and the Center for Evolution and Medicine and the School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Michelle Ciambella
- From the Geisinger Health System, Danville, Pennsylvania, the School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, the School of Life Sciences, Arizona State University, Tempe, Arizona, the Department of Anthropology, University of South Florida, Tampa, the Morsani College of Medicine, University of South Florida, Tampa, and the Center for Evolution and Medicine and the School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Deandre White
- From the Geisinger Health System, Danville, Pennsylvania, the School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, the School of Life Sciences, Arizona State University, Tempe, Arizona, the Department of Anthropology, University of South Florida, Tampa, the Morsani College of Medicine, University of South Florida, Tampa, and the Center for Evolution and Medicine and the School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Eric Coris
- From the Geisinger Health System, Danville, Pennsylvania, the School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, the School of Life Sciences, Arizona State University, Tempe, Arizona, the Department of Anthropology, University of South Florida, Tampa, the Morsani College of Medicine, University of South Florida, Tampa, and the Center for Evolution and Medicine and the School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Eduardo Gonzalez
- From the Geisinger Health System, Danville, Pennsylvania, the School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, the School of Life Sciences, Arizona State University, Tempe, Arizona, the Department of Anthropology, University of South Florida, Tampa, the Morsani College of Medicine, University of South Florida, Tampa, and the Center for Evolution and Medicine and the School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Anne C Stone
- From the Geisinger Health System, Danville, Pennsylvania, the School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, the School of Life Sciences, Arizona State University, Tempe, Arizona, the Department of Anthropology, University of South Florida, Tampa, the Morsani College of Medicine, University of South Florida, Tampa, and the Center for Evolution and Medicine and the School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Lorena Madrigal
- From the Geisinger Health System, Danville, Pennsylvania, the School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, the School of Life Sciences, Arizona State University, Tempe, Arizona, the Department of Anthropology, University of South Florida, Tampa, the Morsani College of Medicine, University of South Florida, Tampa, and the Center for Evolution and Medicine and the School of Life Sciences, Arizona State University, Tempe, Arizona
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13
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Gueye Tall F, Martin C, Ndour EHM, Renoux C, Ly ID, Connes P, Gueye PM, Diallo RN, Diagne I, Diop PA, Cissé A, Lopez Sall P, Joly P. Combined and differential effects of alpha-thalassemia and HbF-quantitative trait loci in Senegalese hydroxyurea-free children with sickle cell anemia. Pediatr Blood Cancer 2019; 66:e27934. [PMID: 31322815 DOI: 10.1002/pbc.27934] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/16/2019] [Accepted: 07/07/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Our objective was to investigate the combined and differential effects of alpha-thalassemia -3.7 kb deletion and HbF-promoting quantitative trait loci (HbF-QTL) in Senegalese hydroxyurea (HU)-free children and young adults with sickle cell anemia (SCA). PROCEDURE Steady-state biological parameters and vaso-occlusive crises (VOC) requiring emergency admission were recorded over a 2-year period in 301 children with SCA. The age of the first hospitalized VOC was also recorded. These data were correlated with the alpha-globin and HbF-QTL genotypes. For the latter, three different genetic loci were studied (XmnI, rs7482144; BCL11A, rs1427407; and the HBS1L-MYB region, rs28384513) and a composite score was calculated, ranging from zero (none of these three polymorphisms) to six (all three polymorphisms at the homozygous state). RESULTS A positive clinical impact of the HbF-QTL score on VOC rate, HbF, leucocytes, and C-reactive protein levels was observed only for patients without alpha-thalassemia deletion. Conversely, combination of homozygous -3.7 kb deletion with three to six HbF-QTL was associated with a higher VOC rate. The age of the first hospitalized VOC was delayed for patients with one or two alpha-thalassemia deletions and at least two HbF-QTL. CONCLUSION Alpha-thalassemia -3.7 kb deletion and HbF-QTL are modulating factors of SCA clinical severity that interact with each other. They should be studied and interpreted together and not separately, at least in HU-free children.
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Affiliation(s)
- Fatou Gueye Tall
- Laboratoire de Biochimie Pharmaceutique-FMPO, Université Cheikh Anta Diop, Dakar, Sénégal.,Laboratoire Interuniversitaire de Biologie de la Motricité (LIBM) EA7424, Equipe "Biologie vasculaire et du globule rouge", Université Claude Bernard Lyon 1, COMUE, Lyon, France.,Centre Hospitalier National d'Enfants Albert Royer, Dakar, Sénégal
| | - Cyril Martin
- Laboratoire Interuniversitaire de Biologie de la Motricité (LIBM) EA7424, Equipe "Biologie vasculaire et du globule rouge", Université Claude Bernard Lyon 1, COMUE, Lyon, France.,Laboratoire d'Excellence sur le globule rouge (Labex GR-Ex), Paris, France
| | - El Hadji Malick Ndour
- Laboratoire de Biochimie Pharmaceutique-FMPO, Université Cheikh Anta Diop, Dakar, Sénégal.,Centre Hospitalier National d'Enfants Albert Royer, Dakar, Sénégal
| | - Céline Renoux
- Laboratoire Interuniversitaire de Biologie de la Motricité (LIBM) EA7424, Equipe "Biologie vasculaire et du globule rouge", Université Claude Bernard Lyon 1, COMUE, Lyon, France.,UF "Biochimie des pathologies érythrocytaires", Laboratoire de Biochimie et Biologie moléculaire Grand-Est, Groupement hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Indou Déme Ly
- Centre Hospitalier National d'Enfants Albert Royer, Dakar, Sénégal.,Service universitaire de Pédiatrie-FMPO, Université Cheikh Anta Diop, Dakar, Sénégal
| | - Philippe Connes
- Laboratoire Interuniversitaire de Biologie de la Motricité (LIBM) EA7424, Equipe "Biologie vasculaire et du globule rouge", Université Claude Bernard Lyon 1, COMUE, Lyon, France.,Laboratoire d'Excellence sur le globule rouge (Labex GR-Ex), Paris, France.,Institut Universitaire de France, Paris, France
| | - Papa Madieye Gueye
- Laboratoire de Biochimie Pharmaceutique-FMPO, Université Cheikh Anta Diop, Dakar, Sénégal
| | - Rokhaya Ndiaye Diallo
- Laboratoire de Biochimie Pharmaceutique-FMPO, Université Cheikh Anta Diop, Dakar, Sénégal
| | - Ibrahima Diagne
- Service universitaire de Pédiatrie-FMPO, Université Cheikh Anta Diop, Dakar, Sénégal.,UFR des sciences de la santé - Université Gaston Berger, Saint-Louis, Sénégal
| | - Pape Amadou Diop
- Laboratoire de Biochimie Pharmaceutique-FMPO, Université Cheikh Anta Diop, Dakar, Sénégal
| | - Aynina Cissé
- Laboratoire de Biochimie Pharmaceutique-FMPO, Université Cheikh Anta Diop, Dakar, Sénégal
| | - Philomène Lopez Sall
- Laboratoire de Biochimie Pharmaceutique-FMPO, Université Cheikh Anta Diop, Dakar, Sénégal.,Centre Hospitalier National d'Enfants Albert Royer, Dakar, Sénégal
| | - Philippe Joly
- Laboratoire Interuniversitaire de Biologie de la Motricité (LIBM) EA7424, Equipe "Biologie vasculaire et du globule rouge", Université Claude Bernard Lyon 1, COMUE, Lyon, France.,Laboratoire d'Excellence sur le globule rouge (Labex GR-Ex), Paris, France.,UF "Biochimie des pathologies érythrocytaires", Laboratoire de Biochimie et Biologie moléculaire Grand-Est, Groupement hospitalier Est, Hospices Civils de Lyon, Bron, France
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Abstract
Hemoglobinopathies include all genetic diseases of hemoglobin and are grouped into thalassemia syndromes and structural hemoglobin variants. The β-thalassemias constitute a group of severe anemias with monogenic inheritance, caused by β-globin gene mutations. This review is focused on omics studies in hemoglobinopathies and mainly β-thalassemia, and discusses genomic, epigenomic, transcriptomic, proteomic and metabolomic findings. Omics analyses have identified various disease modifiers with an impact on disease severity and efficacy of treatments. These modifiers have contributed to the understanding of globin genes regulation/hemoglobin switching and the development of novel therapies. How omics data and their integration can contribute to efficient patient stratification, therapeutic management, improvements in existing treatments and application of novel personalized therapies is discussed.
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Affiliation(s)
- Eleni Katsantoni
- Basic Research Center, Biomedical Research Foundation, Academy of Athens, Soranou tou Ephessiou 4, 115 27, Athens, Greece.
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15
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Biological impact of α genes, β haplotypes, and G6PD activity in sickle cell anemia at baseline and with hydroxyurea. Blood Adv 2019; 2:626-637. [PMID: 29555644 DOI: 10.1182/bloodadvances.2017014555] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/20/2018] [Indexed: 12/17/2022] Open
Abstract
Sickle cell anemia (SCA), albeit monogenic, has heterogeneous phenotypic expression, mainly related to the level of hemoglobin F (HbF). No large cohort studies have ever compared biological parameters in patients with major β-globin haplotypes; ie, Senegal (SEN), Benin (BEN), and Bantu/Central African Republic (CAR). The aim of this study was to evaluate the biological impact of α genes, β haplotypes, and glucose-6-phosphate dehydrogenase (G6PD) activity at baseline and with hydroxyurea (HU). Homozygous HbS patients from the Créteil pediatric cohort with available α-gene and β-haplotype data were included (n = 580; 301 females and 279 males) in this retrospective study. Homozygous β-haplotype patients represented 74% of cases (37.4% CAR/CAR, 24.3% BEN/BEN, and 12.1% SEN/SEN). HU was given to 168 cohort SCA children. Hematological parameters were recorded when HbF was maximal, and changes (ΔHU-T0) were calculated. At baseline, CAR-haplotype and α-gene numbers were independently and negatively correlated with Hb and positively correlated with lactate dehydrogenase. HbF was negatively correlated with CAR-haplotype numbers and positively with BEN- and SEN-haplotype numbers. The BCL11A/rs1427407 "T" allele, which is favorable for HbF expression, was positively correlated with BEN- and negatively correlated with CAR-haplotype numbers. With HU treatment, Δ and HbF values were positively correlated with the BEN-haplotype number. BEN/BEN patients had higher HbF and Hb levels than CAR/CAR and SEN/SEN patients. In conclusion, we show that BEN/BEN patients have the best response on HU and suggest that this could be related to the higher prevalence of the favorable BCL11A/rs1427407/T/allele for HbF expression in these patients.
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16
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Hassan FM, Al-Zahrani FM. BCL11A rs1427407 Genotypes in Sickle Cell Anemia Patients Undergo to Stroke Problems in Sudan. Korean J Fam Med 2018; 40:53-57. [PMID: 30563311 PMCID: PMC6351796 DOI: 10.4082/kjfm.17.0144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/16/2018] [Indexed: 11/24/2022] Open
Abstract
Background Sickle cell disease is an autosomal recessive condition that results from the presence of a mutated form of hemoglobin. Some genetic variants of BCL11A are amenable to therapeutic manipulation. The present study investigated the relationship of a BCL11A variant (rs1427407) and its plasma levels with vaso-occlusive crises and stroke complications among patients in Sudan with sickle cell disease. Methods This cross-sectional study was performed between June 2014 and October 2016. The subjects included 166 patients who were diagnosed with sickle cell disease and 35 healthy control subjects, who were grouped according to sex and age (<15 years, 15–25 years, and >25 years). All patients and/or their guardians provided informed consent. Blood samples were collected from the patients and controls under aseptic conditions. Results Plasma BCL11A levels were elevated in cases with vaso-occlusive crises that lasted for >3 years. In addition, plasma BCL11A levels were high in cases with the GG genotype (vs. GT and TT) at rs1427407. Furthermore, the BCL11A rs1427407 GG/GT genotypes increased the risk of vaso-occlusive crisis and stroke in the patients with sickle cell disease. Conclusion The BCL11A variant (rs1427407) and its plasma levels were associated with vaso-occlusive crisis and stroke in patients with sickle cell disease.
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Affiliation(s)
- Fathelrahman Mahdi Hassan
- Department of Clinical Laboratory Science, College of Applied Medical Science, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Faisal Mousa Al-Zahrani
- Department of Clinical Laboratory Science, College of Applied Medical Science, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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17
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Al-Allawi N, Qadir SMA, Puehringer H, Chui DHK, Farrell JJ, Oberkanins C. The association of HBG2, BCL11A, and HMIP polymorphisms with fetal hemoglobin and clinical phenotype in Iraqi Kurds with sickle cell disease. Int J Lab Hematol 2018; 41:87-93. [PMID: 30216683 DOI: 10.1111/ijlh.12927] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/14/2018] [Accepted: 08/14/2018] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Fetal hemoglobin (HbF) is the major modifier for sickle cell disease (SCD) severity. HbF is modulated mainly by three major quantitative trait loci (QTL) on chromosomes 2, 6, and 11. METHODS Five SNPs in the three QTLs (HBG2, rs7482144; BCL11A, rs1427407 and rs10189857; and HBS1L-MYB intergenic region, rs28384513 and rs9399137) were investigated by multiplex PCR and reverse hybridization, and their roles in HbF and clinical phenotype variability in Iraqi Kurds with SCD were assessed. RESULTS HBG2 rs7482144 with minor allele frequency (MAF) of 0.133 was the most significant contributor to HbF variability, contributing 18.1%, followed by rs1427407 (MAF of 0.266) and rs9399137 (MAF of 0.137) at 14.3% and 8.8%, respectively. The other two SNPs were not significant contributors. Furthermore, when the cumulative numbers of minor alleles in the three contributing SNPs were assessed, HbF% and hemoglobin concentration increased with increasing number of minor alleles (P < 0.0005 and 0.001, respectively), while serum lactic dehydrogenase, reticulocytes, leukocytes, transfusion, and pain frequencies decreased (P = 0.003, 0.004, <0.0005, <0.0005, and 0.017, respectively). CONCLUSIONS It was demonstrated that SNPs in all three major HbF QTLs contribute significantly to HbF and clinical variability in Iraqi Kurds with SCD and that the cumulative number of minor alleles at contributing SNPs may serve as a better predictor of such variability in this population.
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Affiliation(s)
- Nasir Al-Allawi
- Department of Pathology, College of Medicine, University of Duhok, Duhok, Iraq
| | | | | | - David H K Chui
- Departments of Medicine, Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - John J Farrell
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts
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18
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Kesornsit A, Jeenduang N, Horpet D, Plyduang T, Nuinoon M. Quantitative Trait Loci Influencing Hb F Levels in Southern Thai Hb E (HBB: c.79G>A) Heterozygotes. Hemoglobin 2018; 42:23-29. [DOI: 10.1080/03630269.2018.1429281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Aumpika Kesornsit
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
| | - Nutjaree Jeenduang
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
- Research Excellence Centre for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat, Thailand
| | - Dararat Horpet
- The Centre for Scientific and Technological Equipments, Walailak University, Nakhon Si Thammarat, Thailand
| | - Thunyaluk Plyduang
- The Centre for Scientific and Technological Equipments, Walailak University, Nakhon Si Thammarat, Thailand
| | - Manit Nuinoon
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand
- Research Excellence Centre for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat, Thailand
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19
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Lohani N, Bhargava N, Munshi A, Ramalingam S. Pharmacological and molecular approaches for the treatment of β-hemoglobin disorders. J Cell Physiol 2017; 233:4563-4577. [PMID: 29159826 DOI: 10.1002/jcp.26292] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/07/2017] [Indexed: 12/25/2022]
Abstract
β-hemoglobin disorders, such as β-thalassemia and sickle cell anemia are among the most prevalent inherited genetic disorders worldwide. These disorders are caused by mutations in the gene encoding hemoglobin-β (HBB), a vital protein found in red blood cells (RBCs) that carries oxygen from lungs to all parts of the human body. As a consequence, there has been an enduring interest in this field in formulating therapeutic strategies for the treatment of these diseases. Currently, there is no cure available for hemoglobin disorders, although, some patients have been treated with bone marrow transplantation, whose scope is limited because of the difficulty in finding a histocompatible donor and also due to transplant-associated clinical complications that can arise during the treatment. On account of these constraints, reactivation of fetal hemoglobin (HbF) synthesis holds immense promise and is a viable strategy to alleviate the symptoms of β-hemoglobin disorders. Development of new genomic tools has led to the identification of important natural genetic modifiers of hemoglobin switching which include BCL11A, KLF1, HBSIL-MYB, LRF, LSD1, LDB1, histone deacetylases 1 and 2 (HDAC1 and HDAC2). miRNAs are also promising therapeutic targets for development of more effective strategies for the induction of HbF production. Many new small molecule pharmacological inducers of HbF production are already under pre-clinical and clinical development. Furthermore, recent advancements in gene and cell therapy includes targeted genome editing and iPS cell technologies, both of which utilizes a patient's own cells, are emerging as extremely promising approaches for significantly reducing the burden of β-hemoglobin disorders.
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Affiliation(s)
- Neelam Lohani
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Nupur Bhargava
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Anjana Munshi
- Centre for Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India
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20
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Habara AH, Shaikho EM, Steinberg MH. Fetal hemoglobin in sickle cell anemia: The Arab-Indian haplotype and new therapeutic agents. Am J Hematol 2017; 92:1233-1242. [PMID: 28736939 PMCID: PMC5647233 DOI: 10.1002/ajh.24872] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/18/2017] [Accepted: 07/21/2017] [Indexed: 12/28/2022]
Abstract
Fetal hemoglobin (HbF) has well-known tempering effects on the symptoms of sickle cell disease and its levels vary among patients with different haplotypes of the sickle hemoglobin gene. Compared with sickle cell anemia haplotypes found in patients of African descent, HbF levels in Saudi and Indian patients with the Arab-Indian (AI) haplotype exceed that in any other haplotype by nearly twofold. Genetic association studies have identified some loci associated with high HbF in the AI haplotype but these observations require functional confirmation. Saudi patients with the Benin haplotype have HbF levels almost twice as high as African patients with this haplotype but this difference is unexplained. Hydroxyurea is still the only FDA approved drug for HbF induction in sickle cell disease. While most patients treated with hydroxyurea have an increase in HbF and some clinical improvement, 10 to 20% of adults show little response to this agent. We review the genetic basis of HbF regulation focusing on sickle cell anemia in Saudi Arabia and discuss new drugs that can induce increased levels of HbF.
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Affiliation(s)
- Alawi H Habara
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, 02118
| | - Elmutaz M Shaikho
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, 02118
| | - Martin H Steinberg
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, 02118
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21
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Antoniani C, Romano O, Miccio A. Concise Review: Epigenetic Regulation of Hematopoiesis: Biological Insights and Therapeutic Applications. Stem Cells Transl Med 2017; 6:2106-2114. [PMID: 29080249 PMCID: PMC5702521 DOI: 10.1002/sctm.17-0192] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/28/2017] [Indexed: 12/25/2022] Open
Abstract
Hematopoiesis is the process of blood cell formation starting from hematopoietic stem/progenitor cells (HSPCs). The understanding of regulatory networks involved in hematopoiesis and their impact on gene expression is crucial to decipher the molecular mechanisms that control hematopoietic development in physiological and pathological conditions, and to develop novel therapeutic strategies. An increasing number of epigenetic studies aim at defining, on a genome‐wide scale, the cis‐regulatory sequences (e.g., promoters and enhancers) used by human HSPCs and their lineage‐restricted progeny at different stages of development. In parallel, human genetic studies allowed the discovery of genetic variants mapping to cis‐regulatory elements and associated with hematological phenotypes and diseases. Here, we summarize recent epigenetic and genetic studies in hematopoietic cells that give insights into human hematopoiesis and provide a knowledge basis for the development of novel therapeutic approaches. As an example, we discuss the therapeutic approaches targeting cis‐regulatory regions to reactivate fetal hemoglobin for the treatment of β‐hemoglobinopathies. Epigenetic studies allowed the definition of cis‐regulatory sequences used by human hematopoietic cells. Promoters and enhancers are targeted by transcription factors and are characterized by specific histone modifications. Genetic variants mapping to cis‐regulatory elements are often associated with hematological phenotypes and diseases. In some cases, these variants can alter the binding of transcription factors, thus changing the expression of the target genes. Targeting cis‐regulatory sequences represents a promising therapeutic approach for many hematological diseases. Stem Cells Translational Medicine2017;6:2106–2114
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Affiliation(s)
- Chiara Antoniani
- Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR1163, Imagine Institute, Paris, France.,Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Oriana Romano
- Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR1163, Imagine Institute, Paris, France.,Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Annarita Miccio
- Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR1163, Imagine Institute, Paris, France.,Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France
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22
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Lai Y, Chen Y, Chen B, Zheng H, Yi S, Li G, Wei H, He S, Zheng C. Genetic Variants at BCL11A and HBS1L-MYB loci Influence Hb F Levels in Chinese Zhuang β-Thalassemia Intermedia Patients. Hemoglobin 2017; 40:405-410. [PMID: 28361591 DOI: 10.1080/03630269.2016.1253586] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Increased Hb F levels can ameliorate the symptoms of β-thalassemia (β-thal). Due to the genetic heterogenicity of β-thal, the relationship between genetic variants in modifier genes and Hb F level has been studied in different populations. The Chinese Zhuang has the second largest population in China and has 6.78% prevalence of β-thal. However, the effects of these single nucleotide polymorphism (SNP) variants on the Hb F levels of β-thal intermedia (β-TI) patients in this population have not been reported. To explore the association between modifier loci (β-globin gene cluster, HBS1L-MYB intergenic region and BCL11A) and Hb F levels in Chinese Zhuang β-TI patients, 96 unrelated β-TI patients (50 males and 46 females) with different Hb F levels were recruited and genotyped by mass spectrometry. A total of 13 SNPs were confirmed to be in a significant relationship with Hb F levels in this population. Of these, high-risk genotypes of six Hb F-associated SNPs, rs9376090, rs7776054, rs9399137, rs9389268, rs9402685 in the HBS1L-MYB intergenic region and rs189984760 in the BCL11A locus, showed association with high Hb F levels, especially for SNPs in linkage disequilibrium. One novel Hb F-associated SNP, rs189984760, was identified in our study. Our findings will be of valuable reference for correlation between modifier genes and Hb F in Chinese Zhuang populations and may lead to better understand the modifying mechanisms for β-thal.
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Affiliation(s)
- Yunli Lai
- a Genetic and Metabolic Central Laboratory , Guangxi Zhuang Autonomous Region Women and Children Care Hospital , Nanning , Guangxi Province , People's Republic of China
| | - Yun Chen
- a Genetic and Metabolic Central Laboratory , Guangxi Zhuang Autonomous Region Women and Children Care Hospital , Nanning , Guangxi Province , People's Republic of China
| | - Biyan Chen
- a Genetic and Metabolic Central Laboratory , Guangxi Zhuang Autonomous Region Women and Children Care Hospital , Nanning , Guangxi Province , People's Republic of China
| | - Haiyang Zheng
- a Genetic and Metabolic Central Laboratory , Guangxi Zhuang Autonomous Region Women and Children Care Hospital , Nanning , Guangxi Province , People's Republic of China
| | - Sheng Yi
- a Genetic and Metabolic Central Laboratory , Guangxi Zhuang Autonomous Region Women and Children Care Hospital , Nanning , Guangxi Province , People's Republic of China
| | - Guojian Li
- b Guangxi Health and Family Planning Commission , Nanning , Guangxi Province , People's Republic of China
| | - Hongwei Wei
- a Genetic and Metabolic Central Laboratory , Guangxi Zhuang Autonomous Region Women and Children Care Hospital , Nanning , Guangxi Province , People's Republic of China
| | - Sheng He
- a Genetic and Metabolic Central Laboratory , Guangxi Zhuang Autonomous Region Women and Children Care Hospital , Nanning , Guangxi Province , People's Republic of China
| | - Chenguang Zheng
- a Genetic and Metabolic Central Laboratory , Guangxi Zhuang Autonomous Region Women and Children Care Hospital , Nanning , Guangxi Province , People's Republic of China
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Mikobi TM, Tshilobo Lukusa P, Aloni MN, Lumaka AZ, Kaba DK, Devriendt K, Matthijs G, Mbuyi Muamba JM, Race V. Protective BCL11A and HBS1L-MYB polymorphisms in a cohort of 102 Congolese patients suffering from sickle cell anemia. J Clin Lab Anal 2017; 32. [PMID: 28332727 DOI: 10.1002/jcla.22207] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/21/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND We aimed to investigate the distribution of selected BCL11A and HMIP polymorphisms (SNP's), and to assess the correlation with HPFH in a cohort of sickle cell patients. METHODS A preliminary cross-sectional study was conducted in 102 patients. Group 1 was composed of patients with HPFH and Group 2 consisted of patients without HbF. We assessed 8 SNPs previously associated with HPFH in cohorts genetically close to the Congolese population. Observed frequencies were compared to expected frequencies. RESULTS In the group 1, at rs7606173, the observed frequency for the genotype GG was significantly higher and the genotype GC was significantly lower than their respective expected frequencies. At rs9399137, the observed frequency of the genotype TT was significantly lower than expected. Conversely, the observed frequency of the genotype TC was significantly higher than expected. The observed frequency of the genotype TT at rs11886868 was significantly lower than the expected whereas the frequency of the genotype TC was significantly higher than observed. The lowest HbF level was recorded in patients with genotype CC at rs11886868. CONCLUSION In this preliminary study, the results demonstrate that alleles of some of the 8 studied SNPs are not randomly distributed among patients with or without HPFH in this cohort.
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Affiliation(s)
- Tite Minga Mikobi
- Center for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo.,Department des Sciences de Bases, Laboratory of Biochemistry and Molecular Biology, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo.,Sickle Cell Center of Yolo, Kinshasa, Democratic Republic of Congo
| | - Prosper Tshilobo Lukusa
- Center for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo.,Department of Pediatrics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo.,Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
| | - Michel Ntetani Aloni
- Division of Hemato-oncology and Nephrology, Department of Pediatrics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Aimé Zola Lumaka
- Center for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo.,Department of Pediatrics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo.,Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo.,Center for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Didine Kinkodi Kaba
- Division of Biostatistics and Epidemiology, School of Public Health, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Koenraad Devriendt
- Center for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Gert Matthijs
- Center for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jean Marie Mbuyi Muamba
- Division of Hemato-Immuno-Rheumatology, Department of Internal Medicine, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Valérie Race
- Center for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
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24
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Existence of HbF Enhancer Haplotypes at HBS1L-MYB Intergenic Region in Transfusion-Dependent Saudi β-Thalassemia Patients. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1972429. [PMID: 28280727 PMCID: PMC5322420 DOI: 10.1155/2017/1972429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 12/14/2016] [Accepted: 01/16/2017] [Indexed: 12/21/2022]
Abstract
Background and Objectives. β-Thalassemia and sickle cell disease are genetic disorders characterized by reduced and abnormal β-globin chain production, respectively. The elevation of fetal hemoglobin (HbF) can ameliorate the severity of these disorders. In sickle cell disease patients, the HbF level elevation is associated with three quantitative trait loci (QTLs), BCL11A, HBG2 promoter, and HBS1L-MYB intergenic region. This study elucidates the existence of the variants in these three QTLs to determine their association with HbF levels of transfusion-dependent Saudi β-thalassemia patients. Materials and Methods. A total of 174 transfusion-dependent β-thalassemia patients and 164 healthy controls from Eastern Province of Saudi Arabia were genotyped for fourteen single nucleotide polymorphisms (SNPs) from the three QTL regions using TaqMan assay on real-time PCR. Results. Genotype analysis revealed that six alleles of HBS1L-MYB QTL (rs9376090C p = 0.0009, rs9399137C p = 0.008, rs4895441G p = 0.004, rs9389269C p = 0.008, rs9402686A p = 0.008, and rs9494142C p = 0.002) were predominantly associated with β-thalassemia. In addition, haplotype analysis revealed that haplotypes of HBS1L-MYB (GCCGCAC p = 0.022) and HBG2 (GTT p = 0.009) were also predominantly associated with β-thalassemia. Furthermore, the HBS1L-MYB region also exhibited association with the high HbF cohort. Conclusion. The stimulation of HbF gene expression may provide alternative therapies for the amelioration of the disease severity of β-thalassemia.
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25
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Vathipadiekal V, Farrell JJ, Wang S, Edward HL, Shappell H, Al-Rubaish A, Al-Muhanna F, Naserullah Z, Alsuliman A, Qutub HO, Simkin I, Farrer LA, Jiang Z, Luo HY, Huang S, Mostoslavsky G, Murphy GJ, Patra PK, Chui DH, Alsultan A, Al-Ali AK, Sebastiani P, Steinberg MH. A candidate transacting modulator of fetal hemoglobin gene expression in the Arab-Indian haplotype of sickle cell anemia. Am J Hematol 2016; 91:1118-1122. [PMID: 27501013 DOI: 10.1002/ajh.24527] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 08/02/2016] [Accepted: 08/03/2016] [Indexed: 12/30/2022]
Abstract
Fetal hemoglobin (HbF) levels are higher in the Arab-Indian (AI) β-globin gene haplotype of sickle cell anemia compared with African-origin haplotypes. To study genetic elements that effect HbF expression in the AI haplotype we completed whole genome sequencing in 14 Saudi AI haplotype sickle hemoglobin homozygotes-seven selected for low HbF (8.2% ± 1.3%) and seven selected for high HbF (23.5% ± 2.6%). An intronic single nucleotide polymorphism (SNP) in ANTXR1, an anthrax toxin receptor (chromosome 2p13), was associated with HbF. These results were replicated in two independent Saudi AI haplotype cohorts of 120 and 139 patients, but not in 76 Saudi Benin haplotype, 894 African origin haplotype and 44 AI haplotype patients of Indian origin, suggesting that this association is effective only in the Saudi AI haplotype background. ANTXR1 variants explained 10% of the HbF variability compared with 8% for BCL11A. These two genes had independent, additive effects on HbF and together explained about 15% of HbF variability in Saudi AI sickle cell anemia patients. ANTXR1 was expressed at mRNA and protein levels in erythroid progenitors derived from induced pluripotent stem cells (iPSCs) and CD34+ cells. As CD34+ cells matured and their HbF decreased ANTXR1 expression increased; as iPSCs differentiated and their HbF increased, ANTXR1 expression decreased. Along with elements in cis to the HbF genes, ANTXR1 contributes to the variation in HbF in Saudi AI haplotype sickle cell anemia and is the first gene in trans to HBB that is associated with HbF only in carriers of the Saudi AI haplotype. Am. J. Hematol. 91:1118-1122, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Vinod Vathipadiekal
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - John J. Farrell
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Shuai Wang
- Department of Biostatistics; Boston University School of Public Health; Boston Massachusetts
| | - Heather L. Edward
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Heather Shappell
- Department of Biostatistics; Boston University School of Public Health; Boston Massachusetts
| | - A.M. Al-Rubaish
- Department of Internal Medicine; College of Medicine, University of Dammam; Dammam Kingdom of Saudi Arabia
| | - Fahad Al-Muhanna
- Department of Internal Medicine; College of Medicine, University of Dammam; Dammam Kingdom of Saudi Arabia
| | - Z. Naserullah
- Al-Omran Scientific Chair for Hematological Diseases; King Faisal University; Al-Ahsa Kingdom of Saudi Arabia
- Department of Pediatrics; Maternity and Child Hospital; Dammam Kingdom of Saudi Arabia
| | - A. Alsuliman
- Alomran Scientific Chair; King Faisal University, King Fahd Hospital; Hafof Al-Ahsa Kingdom of Saudi Arabia
| | - Hatem Othman Qutub
- Alomran Scientific Chair; King Faisal University; Al-Ahsa Kingdom of Saudi Arabia
| | - Irene Simkin
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Lindsay A. Farrer
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Zhihua Jiang
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Hong-Yuan Luo
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Shengwen Huang
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Gustavo Mostoslavsky
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - George J. Murphy
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Pradeep K. Patra
- Department of Biochemistry; Pt. J. N. M. Medical College; Raipur Chattisgarh India
| | - David H.K. Chui
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Abdulrahman Alsultan
- Sickle Cell Disease Research Center and Department of Pediatrics; College of Medicine, King Saud University; Riyadh Saudi Arabia
| | - Amein K. Al-Ali
- Center for Research and Medical Consultation; University of Dammam; Dammam Kingdom of Saudi Arabia
| | - Paola Sebastiani
- Department of Biostatistics; Boston University School of Public Health; Boston Massachusetts
| | - Martin H. Steinberg
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
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26
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Vathipadiekal V, Alsultan A, Baltrusaitis K, Farrell JJ, Al-Rubaish AM, Al-Muhanna F, Naserullah Z, Suliman A, Patra P, Milton JN, Farrer LA, Chui DH, Al-Ali AK, Sebastiani P, Steinberg MH. Homozygosity for a haplotype in the HBG2-OR51B4 region is exclusive to Arab-Indian haplotype sickle cell anemia. Am J Hematol 2016; 91:E308-11. [PMID: 27185208 DOI: 10.1002/ajh.24368] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/10/2016] [Accepted: 03/13/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Vinod Vathipadiekal
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Abdulrahman Alsultan
- Sickle Cell Disease Research Center and Department of Pediatrics; College of Medicine, King Saud University; Riyadh Saudi Arabia
| | - Kristin Baltrusaitis
- Department of Biostatistics; Boston University School of Public Health; Boston Massachusetts
| | - John J. Farrell
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Abdullah M. Al-Rubaish
- Department of Internal Medicine; College of Medicine, University of Dammam; Dammam Kingdom of Saudi Arabia
| | - Fahad Al-Muhanna
- Department of Internal Medicine; College of Medicine, University of Dammam; Dammam Kingdom of Saudi Arabia
| | - Zaki Naserullah
- Alomran Scientific Chair for Hematological Diseases, King Faisal University, King Faisal University, King Fahd Hospital; Hafof Al-Ahsa Kingdom of Saudi Arabia
- Department of Pediatrics, Maternity & Child Hospital; Dammam Kingdom of Saudi Arabia
| | - Ahmed Suliman
- Alomran Scientific Chair; King Faisal University, King Fahd Hospital; Hafof Al-Ahsa Kingdom of Saudi Arabia
| | - P.K. Patra
- Department of Biochemistry; Pt. J.N.M. Medical College; Raipur Chhattisgarh India
| | - Jacqueline N. Milton
- Department of Biostatistics; Boston University School of Public Health; Boston Massachusetts
| | - Lindsay A. Farrer
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - David H.K. Chui
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Amein K. Al-Ali
- Center for Research & Medical Consultation; University of Dammam; Dammam Saudi Arabia
| | - Paola Sebastiani
- Department of Biostatistics; Boston University School of Public Health; Boston Massachusetts
| | - Martin. H. Steinberg
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
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27
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Liu L, Pertsemlidis A, Ding LH, Story MD, Steinberg MH, Sebastiani P, Hoppe C, Ballas SK, Pace BS. Original Research: A case-control genome-wide association study identifies genetic modifiers of fetal hemoglobin in sickle cell disease. Exp Biol Med (Maywood) 2016; 241:706-18. [PMID: 27022141 DOI: 10.1177/1535370216642047] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Sickle cell disease (SCD) is a group of inherited blood disorders that have in common a mutation in the sixth codon of the β-globin (HBB) gene on chromosome 11. However, people with the same genetic mutation display a wide range of clinical phenotypes. Fetal hemoglobin (HbF) expression is an important genetic modifier of SCD complications leading to milder symptoms and improved long-term survival. Therefore, we performed a genome-wide association study (GWAS) using a case-control experimental design in 244 African Americans with SCD to discover genetic factors associated with HbF expression. The case group consisted of subjects with HbF≥8.6% (133 samples) and control group subjects with HbF≤£3.1% (111 samples). Our GWAS results replicated SNPs previously identified in an erythroid-specific enhancer region located in the second intron of the BCL11A gene associated with HbF expression. In addition, we identified SNPs in the SPARC, GJC1, EFTUD2 and JAZF1 genes as novel candidates associated with HbF levels. To gain insights into mechanisms of globin gene regulation in the HBB locus, linkage disequilibrium (LD) and haplotype analyses were conducted. We observed strong LD in the low HbF group in contrast to a loss of LD and greater number of haplotypes in the high HbF group. A search of known HBB locus regulatory elements identified SNPs 5' of δ-globin located in an HbF silencing region. In particular, SNP rs4910736 created a binding site for a known transcription repressor GFi1 which is a candidate protein for further investigation. Another HbF-associated SNP, rs2855122 in the cAMP response element upstream of Gγ-globin, was analyzed for functional relevance. Studies performed with siRNA-mediated CREB binding protein (CBP) knockdown in primary erythroid cells demonstrated γ-globin activation and HbF induction, supporting a repressor role for CBP. This study identifies possible molecular determinants of HbF production.
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Affiliation(s)
- Li Liu
- Department of Biological Sciences, University of Texas at Dallas, Dallas, TX 75083, USA
| | - Alexander Pertsemlidis
- Departments of Pediatrics and Cellular & Structural Biology, Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Liang-Hao Ding
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael D Story
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Martin H Steinberg
- Center of Excellence in Sickle Cell Disease Boston Medical Center, Pediatrics, Pathology and Laboratory Medicine, Boston University, Boston, MA 02215, USA
| | - Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02215, USA
| | - Carolyn Hoppe
- Department of Hematology/Oncology, UCSF Benioff Children's Hospital, Oakland, CA 94609, USA
| | - Samir K Ballas
- Cardeza Foundation for Hematologic Research, Department of Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Betty S Pace
- Department of Pediatrics, Augusta University, Augusta, GA 30912, USA
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28
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Leonardo FC, Brugnerotto AF, Domingos IF, Fertrin KY, de Albuquerque DM, Bezerra MAC, Araújo AS, Saad STO, Costa FF, Menzel S, Conran N, Thein SL. Reduced rate of sickle-related complications in Brazilian patients carrying HbF-promoting alleles at the BCL11A and HMIP-2 loci. Br J Haematol 2016; 173:456-60. [PMID: 26888013 DOI: 10.1111/bjh.13961] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/08/2015] [Indexed: 11/28/2022]
Abstract
The presence of high levels of fetal haemoglobin (HbF) provides well-validated clinical benefits to patients with sickle cell anaemia (SCA). Nevertheless it has been difficult to show clear direct effects of the known genetic HbF modifiers, such as the enhancer polymorphisms for haematopoietic transcription factors BCL11A and MYB, on SCA severity. Investigating SCA patients from Brazil, with a high degree of European genetic admixture, we have detected strong effects of these variants on HbF levels. Critically, we have shown, for the first time, that the presence of such HbF-promoting variants leads to a reduced rate of SCA complications, especially stroke.
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Affiliation(s)
- Flávia C Leonardo
- Haematology Centre, School of Medicine, University of Campinas- UNICAMP, Campinas, Brazil
| | - Ana F Brugnerotto
- Haematology Centre, School of Medicine, University of Campinas- UNICAMP, Campinas, Brazil
| | - Igor F Domingos
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil
| | - Kleber Y Fertrin
- Haematology Centre, School of Medicine, University of Campinas- UNICAMP, Campinas, Brazil
| | | | - Marcos A C Bezerra
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil
| | - Aderson S Araújo
- Haematology and Haemotherapy Foundation of Pernambuco (HEMOPE), Recife, Brazil
| | - Sara T O Saad
- Haematology Centre, School of Medicine, University of Campinas- UNICAMP, Campinas, Brazil
| | - Fernando F Costa
- Haematology Centre, School of Medicine, University of Campinas- UNICAMP, Campinas, Brazil
| | - Stephan Menzel
- Department of Molecular Haematology, Division of Cancer Studies, King's College London Faculty of Life Sciences & Medicine, London, UK
| | - Nicola Conran
- Haematology Centre, School of Medicine, University of Campinas- UNICAMP, Campinas, Brazil
| | - Swee Lay Thein
- Department of Molecular Haematology, Division of Cancer Studies, King's College London Faculty of Life Sciences & Medicine, London, UK.,Sickle Cell Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
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29
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Yao L, Berman BP, Farnham PJ. Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. Crit Rev Biochem Mol Biol 2015; 50:550-73. [PMID: 26446758 PMCID: PMC4666684 DOI: 10.3109/10409238.2015.1087961] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Enhancers are short regulatory sequences bound by sequence-specific transcription factors and play a major role in the spatiotemporal specificity of gene expression patterns in development and disease. While it is now possible to identify enhancer regions genomewide in both cultured cells and primary tissues using epigenomic approaches, it has been more challenging to develop methods to understand the function of individual enhancers because enhancers are located far from the gene(s) that they regulate. However, it is essential to identify target genes of enhancers not only so that we can understand the role of enhancers in disease but also because this information will assist in the development of future therapeutic options. After reviewing models of enhancer function, we discuss recent methods for identifying target genes of enhancers. First, we describe chromatin structure-based approaches for directly mapping interactions between enhancers and promoters. Second, we describe the use of correlation-based approaches to link enhancer state with the activity of nearby promoters and/or gene expression. Third, we describe how to test the function of specific enhancers experimentally by perturbing enhancer–target relationships using high-throughput reporter assays and genome editing. Finally, we conclude by discussing as yet unanswered questions concerning how enhancers function, how target genes can be identified, and how to distinguish direct from indirect changes in gene expression mediated by individual enhancers.
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Affiliation(s)
- Lijing Yao
- a Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California , Los Angeles , CA , USA and
| | - Benjamin P Berman
- b Department of Biomedical Sciences , Bioinformatics and Computational Biology Research Center, Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Peggy J Farnham
- a Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California , Los Angeles , CA , USA and
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30
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Pule GD, Ngo Bitoungui VJ, Chetcha Chemegni B, Kengne AP, Antonarakis S, Wonkam A. Association between Variants at BCL11A Erythroid-Specific Enhancer and Fetal Hemoglobin Levels among Sickle Cell Disease Patients in Cameroon: Implications for Future Therapeutic Interventions. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:627-31. [PMID: 26393293 DOI: 10.1089/omi.2015.0124] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Variants in BCL11A were previously associated with fetal hemoglobin (HbF) levels among Cameroonian sickle cell disease (SCD) patients, however explaining only ∼2% of the variance. In the same patients, we have investigated the relationship between HbF and two SNPs in a BCL11A erythroid-specific enhancer (N=626). Minor allele frequencies in rs7606173 and rs1427407 were 0.42 and 0.24, respectively. Both variants were significantly associated with HbF levels (p=3.11e-08 and p=6.04e-06, respectively) and explained 8% and 6.2% variations, respectively. These data have confirmed a stronger effect on HbF of genomic variations at the BCL11A erythroid-specific enhancer among patients with SCD in Cameroon, the first report on a West African population. The relevance of these findings is of prime importance because the disruption of this enhancer would alter BCL11A expression in erythroid precursors and thus HbF expression, while sparing the induced functional challenges of any alterations on the expression of this transcription factor in non-erythroid lineages, thus providing an attractive approach for new treatment strategies of SCD.
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Affiliation(s)
- Gift Dineo Pule
- 1 Division of Human Genetics, Department of Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
| | | | | | - Andre Pascal Kengne
- 3 Non-Communicable Diseases Research Unit, South African Medical Research Council , Cape Town, South Africa
| | - Stylianos Antonarakis
- 4 Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva , Switzerland
| | - Ambroise Wonkam
- 1 Division of Human Genetics, Department of Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
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31
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Achigbu KI, Odetunde OI, Chinawa JM, Achigbu EO, Ikefuna AN, Emodi IJ, Ibe BC. Pulmonary function indices in children with sickle cell anemia in Enugu, south-east Nigeria. Saudi Med J 2015. [PMID: 26219442 PMCID: PMC4549588 DOI: 10.15537/smj.2015.8.11525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Objectives: To determine the pulmonary function indices of children with sickle cell anemia (SCA) attending the pediatric sickle cell clinic at the University of Nigeria Teaching Hospital, Enugu, south-east Nigeria and to compare these indices with the results obtained from other regions. Methods: A case control study of lung function in children with SCA aged 6-20 years. The study was carried out in the University of Nigeria/University of Nigeria Teaching Hospital, Enugu State, Nigeria between October 2014 and January 2015. Measurements of the peak expiratory flow rate, forced vital capacity (FVC), and forced expiratory volume in one second (FEV1) were evaluated. Results: A total of 80 subjects were recruited into the study, comprising 40 homozygous HbSS (hemoglobin SS) patients and an equal number of controls. Children with SCA had statistically lower values of FEV1 (1.6±0.52), FVC (1.76±0.95), and peak expiratory flow rate (PEFR) (309.00±82.64) when compared with normal hemoglobin genotype FEV1 (12.01±0.53), FVC (2.12±0.54), and PEFR (364.10±87.85). The mean FVC, FEV1/FVC, and PEFR were also higher in the male control group compared with the HbSS male group, but these differences were not statistically significant. Female controls had significantly larger FEV1, FVC, and PEFR values compared with the HbSS females. Conclusion: The lung function indices were significantly lower in children and adolescents with SCA compared with the matched controls with a hemoglobin genotype AA.
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Affiliation(s)
- Kingsley I Achigbu
- Department of Pediatrics, Federal Medical Centre, Owerri, Imo State, Nigeria. E-mail.
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32
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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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