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Pandey H, Singh K, Ranjan R, Dass J, Tyagi S, Seth T, Saxena R, Mahapatra M. Prevalence and Impact of HMOX1 Polymorphism (rs2071746: A > T) in Indian Sickle Cell Disease Patients. J Lab Physicians 2023; 15:583-589. [PMID: 37780888 PMCID: PMC10539052 DOI: 10.1055/s-0043-1770068] [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: 06/27/2022] [Accepted: 04/17/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction Fetal hemoglobin (HbF) levels play significant role in lowering down the morbidity and mortality in sickle cell disease (SCD) patients. Coinheritance of heme oxygenase-1 (HMOX1) rs2071746:A > T polymorphism may contribute to variable HbF levels in Indian SCD patients. Objective This study was aimed to evaluate the role of HMOX1 polymorphism and its impact on HbF level in Indian SCD patients. Materials and Methods One-hundred twenty confirmed cases of SCD and 50 healthy controls were recruited. Their mean age was 11.5 ± 8.6 years (range: 3-23 years). Quantification of Hb, HbA2, HbF, and HbS was done by capillary zone electrophoresis. Allele-specific polymerase chain reaction was used to genotype HMOX1 (rs2071746:A > T) gene polymorphism. Results Out of the 120 cases of SCD, 65 were hemoglobin sickle-shaped (HbSS) and 55 were sickle-beta thalassemia (Sβ). Out of 65 HbSS patients, 29 (44.6%) were heterozygous (AT), 20 (30.76%) were homozygous (TT), and 16 (24.61%) were found wild-type (AA) genotype. Out of 55 Sβ, 22 (40%) were heterozygous, 18 (32%) were homozygous and 15 (28%) were wild-type. Patients carrying HMOX1 (rs2071746:A > T), AT, and TT genotypes had less anemia, painful crisis, splenomegaly, hepatomegaly, jaundice, and blood transfusion. HbF level was found higher in TT genotype (in HbSS the HbF levels was 25.1 ± 4.4; in sickle-beta thalassemia the HbF levels was 36.1 ± 4.7) than wild-type(AA) and was statistically significant ( p -value <0.001). Conclusion The TT genotype of the rs2071746:A > T polymorphism was associated with increased levels of Hb F ( p < 0.001). It can serve as a HbF modifier in Indian sickle cell diseases patients.
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Affiliation(s)
- Hareram Pandey
- Department of Hematology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Kanwaljeet Singh
- Lab Sciences & Molecular Medicine, Army Hospital Research and Referral, Delhi Cantt, Delhi, India
| | - Ravi Ranjan
- Department of Hematology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Jasmita Dass
- Department of Hematology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Seema Tyagi
- Department of Hematology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Tulika Seth
- Department of Hematology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Renu Saxena
- Department of Hematology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Manoranjan Mahapatra
- Department of Hematology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
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Galactéros F. Le globule rouge drépanocytaire. Données génétiques et structurelles. Rev Med Interne 2023; 44:4S2-4S6. [PMID: 38049243 DOI: 10.1016/s0248-8663(23)01302-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Sickle cell disease is syndromic, associating a hemolytic anemia, a vaso-obstructive vascular disease, and an infectious risk linked to the precocity of the splenic function loss. The willingly hyperacute and potentially fatal character of the two last elements of the pathophysiologic syndrome, has, quite rightly, focused the therapeutic researches on them. Great success in those two domains have allowed a very important gain in life expectancy. However, chronic progressive organ dysfunction began to appear in older than 25 years-old patients. It concerns mainly renal, hepatic, cardiac functions and pulmonary arterial pressure and may lead to organ failure and premature death. Since some 25 years, the clinical research demonstrated an association between such complications and intravascular hemolytic rate, and it turned to a causative relationship. This present paper try to summarize the actual knowledge on the structural and genetic aspects of sickle cell anemia hemolysis. © 2023 Société nationale française de médecine interne (SNFMI). Published by Elsevier Masson SAS. All rights reserved.
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Affiliation(s)
- F Galactéros
- Unité des maladies génétiques du globule rouge (UMGGR), médecine interne, GHU Henri-Mondor AP-HP et U-PEC, France.
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3
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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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Ranque B, Diaw M, Dembele AK, Lapoumeroulie C, Offredo L, Tessougue O, Gueye SM, Diallo D, Diop S, Colin-Aronovicz Y, Jouven X, Blanc-Brude O, Tharaux PL, Le Jeune S, Connes P, Romana M, Le Van Kim C. Association of haemolysis markers, blood viscosity and microcirculation function with organ damage in sickle cell disease in sub-Saharan Africa (the BIOCADRE study). Br J Haematol 2023; 203:319-326. [PMID: 37583261 DOI: 10.1111/bjh.19006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 06/27/2023] [Accepted: 07/18/2023] [Indexed: 08/17/2023]
Abstract
Sickle cell anaemia (SCA) is a monogenic disease with a highly variable clinical course. We aimed to investigate associations between microvascular function, haemolysis markers, blood viscosity and various types of SCA-related organ damage in a multicentric sub-Saharan African cohort of patients with SCA. In a cross-sectional study, we selected seven groups of adult patients with SS phenotype in Dakar and Bamako based on the following complications: leg ulcer, priapism, osteonecrosis, retinopathy, high tricuspid regurgitant jet velocity (TRV), macro-albuminuria or none. Clinical assessment, echocardiography, peripheral arterial tonometry, laboratory tests and blood viscosity measurement were performed. We explored statistical associations between the biological parameters and the six studied complications. Among 235 patients, 58 had high TRV, 46 osteonecrosis, 43 priapism, 33 leg ulcers, 31 retinopathy and 22 macroalbuminuria, whereas 36 had none of these complications. Multiple correspondence analysis revealed no cluster of complications. Lactate dehydrogenase levels were associated with high TRV, and blood viscosity was associated with retinopathy and the absence of macroalbuminuria. Despite extensive phenotyping of patients, no specific pattern of SCA-related complications was identified. New biomarkers are needed to predict SCA clinical expression to adapt patient management, especially in Africa, where healthcare resources are scarce.
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Affiliation(s)
- Brigitte Ranque
- Université Paris Cité, Inserm, UMR S970, PARCC, Paris, France
- Service de Médecine Interne, Hôpital Européen Georges Pompidou, Assistance Publique des Hôpitaux de Paris, Paris, France
- LABEX GREX, Université Paris Cité, Paris, France
| | - Mor Diaw
- Laboratoire de Physiologie et Explorations Fonctionnelles, Faculté de Médecine, Pharmacie et Odontologie Université Cheikh Anta Diop de Dakar, Dakar, Senegal
- Unité Mixte Internationale (UMI 3189), "Environnement, Santé, Sociétés" CNRS, UCAD, CNRST, USTTB, UGB, Dakar, Senegal
| | | | | | - Lucile Offredo
- Université Paris Cité, Inserm, UMR S970, PARCC, Paris, France
| | - Oumar Tessougue
- Centre de Recherche et de Lutte Contre la Drépanocytose (CRLD), Bamako, Mali
| | | | - Dapa Diallo
- Centre de Recherche et de Lutte Contre la Drépanocytose (CRLD), Bamako, Mali
| | - Saliou Diop
- Centre National de Transfusion Sanguine (CNTS), Dakar, Senegal
| | - Yves Colin-Aronovicz
- LABEX GREX, Université Paris Cité, Paris, France
- Université Paris Cité and Université des Antilles, Inserm, BIGR, Paris, France
| | - Xavier Jouven
- Université Paris Cité, Inserm, UMR S970, PARCC, Paris, France
- LABEX GREX, Université Paris Cité, Paris, France
| | - Olivier Blanc-Brude
- Université Paris Cité, Inserm, UMR S970, PARCC, Paris, France
- LABEX GREX, Université Paris Cité, Paris, France
| | - Pierre-Louis Tharaux
- Université Paris Cité, Inserm, UMR S970, PARCC, Paris, France
- LABEX GREX, Université Paris Cité, Paris, France
| | - Sylvain Le Jeune
- Université Paris Cité, Inserm, UMR S970, PARCC, Paris, France
- Service de Médecine Interne, Hôpital Avicenne, Bobigny, Assistance-Publique Hôpitaux de Paris, Paris, France
| | - Philippe Connes
- LABEX GREX, Université Paris Cité, Paris, France
- Université Lyon 1, Laboratoire LIBM EA7424, Equipe «Biologie Vasculaire et du Globule Rouge», COMUE, Lyon, France
| | - Marc Romana
- LABEX GREX, Université Paris Cité, Paris, France
- Université Paris Cité and Université des Antilles, Inserm, BIGR, Paris, France
| | - Caroline Le Van Kim
- LABEX GREX, Université Paris Cité, Paris, France
- Université Paris Cité and Université des Antilles, Inserm, BIGR, Paris, France
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Heitzer AM, Longoria J, Rampersaud E, Rashkin SR, Estepp JH, Okhomina VI, Wang WC, Raches D, Potter B, Steinberg MH, King AA, Kang G, Hankins JS. Fetal hemoglobin modulates neurocognitive performance in sickle cell anemia ✰,✰✰. Curr Res Transl Med 2022; 70:103335. [PMID: 35303690 PMCID: PMC9086114 DOI: 10.1016/j.retram.2022.103335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 01/20/2022] [Accepted: 01/30/2022] [Indexed: 12/26/2022]
Abstract
PURPOSE OF THE STUDY Fetal hemoglobin (HbF) is a modifier of the clinical and hematologic phenotype of sickle cell anemia (SCA). Three quantitative trait loci (QTL) modulate HbF expression. The neurocognitive effects of variants in these QTL have yet to be explored. We evaluated the relation between 11 SNPs in the three HbF QTL: BCL11A, MYB, the HBB gene cluster, and full-scale intelligence (IQ) in SCA. PATIENTS AND METHODS The prospective longitudinal cohort study, Sickle Cell Clinical Research and Intervention Program, was used as a discovery cohort (n = 166). The genotypes for 11 SNPs were extracted through whole genome sequencing and were analyzed using an additive model. A polygenic score for HbF (PGSHbF) integrating the numbers of low HbF alleles from 11 SNPs was analyzed as a continuous variable. The Cooperative Study of Sickle Cell Disease (n = 156) and the Silent Cerebral Infarction Transfusion (n = 114) Trial were used as two independent replication cohorts. Benjamini and Hochberg approach was used to calculate false discovery rate adjusted p-value (pFDR). RESULTS HbF was positively associated with IQ (minimum raw p = 0·0018) at pFDR<0·05. HbF mediated the relationship between two BCL11A SNPs, rs1427407 and rs7606173, HBS1L-MYB: rs9494142, and PGSHbF with IQ (minimum raw p = 0·0035) at pFDR<0·05. CONCLUSION As the major modulator of the severity of SCA, HbF also influences neurocognition, which is done through mediation of its QTL. These findings have implications for early identification of neurocognitive risk and targeted intervention.
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Affiliation(s)
- Andrew M Heitzer
- Departments of Psychology, St. Jude Children's Research Hospital, Memphis, TN.
| | - Jennifer Longoria
- Departments of Psychology, St. Jude Children's Research Hospital, Memphis, TN
| | - Evadnie Rampersaud
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN
| | - Sara R Rashkin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN; Hematology, St. Jude Children's Research Hospital, Memphis, TN
| | | | | | - Winfred C Wang
- Hematology, St. Jude Children's Research Hospital, Memphis, TN
| | - Darcy Raches
- Departments of Psychology, St. Jude Children's Research Hospital, Memphis, TN
| | - Brian Potter
- Departments of Psychology, St. Jude Children's Research Hospital, Memphis, TN
| | - Martin H Steinberg
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Allison A King
- Program in Occupational Therapy and Departments of Pediatrics and Medicine, Washington University, St. Louis, MO
| | - Guolian Kang
- Biostatistics, St. Jude Children's Research Hospital, Memphis, TN; Departments of Psychology, St. Jude Children's Research Hospital, Memphis, TN
| | - Jane S Hankins
- Hematology, St. Jude Children's Research Hospital, Memphis, TN
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Sporns PB, Fullerton HJ, Lee S, Kim H, Lo WD, Mackay MT, Wildgruber M. Childhood stroke. Nat Rev Dis Primers 2022; 8:12. [PMID: 35210461 DOI: 10.1038/s41572-022-00337-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/07/2022] [Indexed: 01/09/2023]
Abstract
Stroke is an important cause of neurological morbidity in children; most survivors have permanent neurological deficits that affect the remainder of their life. Stroke in childhood, the focus of this Primer, is distinguished from perinatal stroke, defined as stroke before 29 days of age, because of its unique pathogenesis reflecting the maternal-fetal unit. Although approximately 15% of strokes in adults are haemorrhagic, half of incident strokes in children are haemorrhagic and half are ischaemic. The causes of childhood stroke are distinct from those in adults. Urgent brain imaging is essential to confirm the stroke diagnosis and guide decisions about hyperacute therapies. Secondary stroke prevention strongly depends on the underlying aetiology. While the past decade has seen substantial advances in paediatric stroke research, the quality of evidence for interventions, such as the rapid reperfusion therapies that have revolutionized arterial ischaemic stroke care in adults, remains low. Substantial time delays in diagnosis and treatment continue to challenge best possible care. Effective primary stroke prevention strategies in children with sickle cell disease represent a major success, yet barriers to implementation persist. The multidisciplinary members of the International Pediatric Stroke Organization are coordinating global efforts to tackle these challenges and improve the outcomes in children with cerebrovascular disease.
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Affiliation(s)
- Peter B Sporns
- Department of Neuroradiology, Clinic of Radiology & Nuclear Medicine, University Hospital Basel, Basel, Switzerland.,Department of Diagnostic and Interventional Neuroradiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Heather J Fullerton
- Departments of Neurology and Pediatrics, Benioff Children's Hospital, University of California at San Francisco, San Francisco, CA, USA
| | - Sarah Lee
- Division of Child Neurology, Department of Neurology & Neurological Sciences, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Helen Kim
- Departments of Anesthesia and Perioperative Care, and Epidemiology and Biostatistics, Center for Cerebrovascular Research, University of California at San Francisco, San Francisco, CA, USA
| | - Warren D Lo
- Departments of Pediatrics and Neurology, Nationwide Children's Hospital and The Ohio State University, Columbus, OH, USA
| | - Mark T Mackay
- Department of Neurology, Royal Children's Hospital, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Moritz Wildgruber
- Department of Radiology, University Hospital Munich, LMU Munich, Munich, Germany.
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Kingdom R, Wright CF. Incomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts. Front Genet 2022; 13:920390. [PMID: 35983412 PMCID: PMC9380816 DOI: 10.3389/fgene.2022.920390] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 12/20/2022] Open
Abstract
The same genetic variant found in different individuals can cause a range of diverse phenotypes, from no discernible clinical phenotype to severe disease, even among related individuals. Such variants can be said to display incomplete penetrance, a binary phenomenon where the genotype either causes the expected clinical phenotype or it does not, or they can be said to display variable expressivity, in which the same genotype can cause a wide range of clinical symptoms across a spectrum. Both incomplete penetrance and variable expressivity are thought to be caused by a range of factors, including common variants, variants in regulatory regions, epigenetics, environmental factors, and lifestyle. Many thousands of genetic variants have been identified as the cause of monogenic disorders, mostly determined through small clinical studies, and thus, the penetrance and expressivity of these variants may be overestimated when compared to their effect on the general population. With the wealth of population cohort data currently available, the penetrance and expressivity of such genetic variants can be investigated across a much wider contingent, potentially helping to reclassify variants that were previously thought to be completely penetrant. Research into the penetrance and expressivity of such genetic variants is important for clinical classification, both for determining causative mechanisms of disease in the affected population and for providing accurate risk information through genetic counseling. A genotype-based definition of the causes of rare diseases incorporating information from population cohorts and clinical studies is critical for our understanding of incomplete penetrance and variable expressivity. This review examines our current knowledge of the penetrance and expressivity of genetic variants in rare disease and across populations, as well as looking into the potential causes of the variation seen, including genetic modifiers, mosaicism, and polygenic factors, among others. We also considered the challenges that come with investigating penetrance and expressivity.
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Affiliation(s)
- Rebecca Kingdom
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, Royal Devon & Exeter Hospital, University of Exeter Medical School, Exeter, United Kingdom
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8
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A polygenic score for acute vaso-occlusive pain in pediatric sickle cell disease. Blood Adv 2021; 5:2839-2851. [PMID: 34283174 DOI: 10.1182/bloodadvances.2021004634] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/05/2021] [Indexed: 12/12/2022] Open
Abstract
Individuals with monogenic disorders can experience variable phenotypes that are influenced by genetic variation. To investigate this in sickle cell disease (SCD), we performed whole-genome sequencing (WGS) of 722 individuals with hemoglobin HbSS or HbSβ0-thalassemia from Baylor College of Medicine and from the St. Jude Children's Research Hospital Sickle Cell Clinical Research and Intervention Program (SCCRIP) longitudinal cohort study. We developed pipelines to identify genetic variants that modulate sickle hemoglobin polymerization in red blood cells and combined these with pain-associated variants to build a polygenic score (PGS) for acute vaso-occlusive pain (VOP). Overall, we interrogated the α-thalassemia deletion -α3.7 and 133 candidate single-nucleotide polymorphisms (SNPs) across 66 genes for associations with VOP in 327 SCCRIP participants followed longitudinally over 6 years. Twenty-one SNPs in 9 loci were associated with VOP, including 3 (BCL11A, MYB, and the β-like globin gene cluster) that regulate erythrocyte fetal hemoglobin (HbF) levels and 6 (COMT, TBC1D1, KCNJ6, FAAH, NR3C1, and IL1A) that were associated previously with various pain syndromes. An unweighted PGS integrating all 21 SNPs was associated with the VOP event rate (estimate, 0.35; standard error, 0.04; P = 5.9 × 10-14) and VOP event occurrence (estimate, 0.42; standard error, 0.06; P = 4.1 × 10-13). These associations were stronger than those of any single locus. Our findings provide insights into the genetic modulation of VOP in children with SCD. More generally, we demonstrate the utility of WGS for investigating genetic contributions to the variable expression of SCD-associated morbidities.
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Alnafie AN, Alateeq SA, Al-Muhanna FA, Alsulaiman AM, Alfarhan M, Buali W, Vatte CB, Cyrus C, Keating B, Al-Ali AK, Steinberg MH. Exome sequencing in high and low fetal haemoglobin Arab-Indian haplotype sickle cell disease. Br J Haematol 2021; 194:e61-e64. [PMID: 34041755 DOI: 10.1111/bjh.17542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/17/2022]
Affiliation(s)
- Awatif N Alnafie
- Department of Pathology, College of Medicine, King Fahad Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Suad A Alateeq
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Fahad A Al-Muhanna
- Department of Internal Medicine, College of Medicine, King Fahad Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | | | - Mohammed Alfarhan
- Department of Orthopedic Surgery, College of Medicine, King Faisal University, Alahssa, Saudi Arabia
| | - Waleed Buali
- Department of Pediatrics, College of Medicine, King Fahad Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Chitti Babu Vatte
- Department of Internal Medicine, College of Medicine, King Fahad Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Cyril Cyrus
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Brendan Keating
- Department of Surgery, Division of Transplantation, Perelman School of Medicine, Penn Transplant Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Amein K Al-Ali
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Martin H Steinberg
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
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Al‐Ali AK, Alsulaiman A, Alfarhan M, Safaya S, Vatte CB, Albuali WM, Qutub HO, Alzahrani AJ, Milton JN, Steinberg MH. Sickle cell disease in the Eastern Province of Saudi Arabia: Clinical and laboratory features. Am J Hematol 2021; 96:E117-E121. [PMID: 33460474 DOI: 10.1002/ajh.26096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/12/2021] [Accepted: 01/12/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Amein K. Al‐Ali
- Alomran Scientific Chair, King Faisal University Al‐Ahsa Saudi Arabia
- Department of Clinical Biochemistry College of Medicine, Imam Abdulrahman bin Faisal University Dammam Saudi Arabia
| | - Ahmed Alsulaiman
- Alomran Scientific Chair, King Faisal University Al‐Ahsa Saudi Arabia
- Department of Internal Medicine King Fahd Hospital Al‐Ahsa Saudi Arabia
| | - Mohammed Alfarhan
- Alomran Scientific Chair, King Faisal University Al‐Ahsa Saudi Arabia
- Department of Orthopedic Surgery College of Medicine, King Faisal University Al‐Ahsa Saudi Arabia
| | - Surinder Safaya
- Alomran Scientific Chair, King Faisal University Al‐Ahsa Saudi Arabia
| | - Chitti Babu Vatte
- Department of Clinical Biochemistry College of Medicine, Imam Abdulrahman bin Faisal University Dammam Saudi Arabia
| | - Waleed M. Albuali
- Alomran Scientific Chair, King Faisal University Al‐Ahsa Saudi Arabia
| | - Hatem O. Qutub
- Alomran Scientific Chair, King Faisal University Al‐Ahsa Saudi Arabia
| | | | - Jacqueline N. Milton
- Department of Statistics Boston University School of Public Health Boston Massachusetts
| | - Martin H. Steinberg
- Department of Medicine, Center of Excellence in Sickle Cell Disease Boston University and Boston Medical Center Boston Massachusetts
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11
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Rao S, Yao Y, Bauer DE. Editing GWAS: experimental approaches to dissect and exploit disease-associated genetic variation. Genome Med 2021; 13:41. [PMID: 33691767 PMCID: PMC7948363 DOI: 10.1186/s13073-021-00857-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/12/2021] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association studies (GWAS) have uncovered thousands of genetic variants that influence risk for human diseases and traits. Yet understanding the mechanisms by which these genetic variants, mainly noncoding, have an impact on associated diseases and traits remains a significant hurdle. In this review, we discuss emerging experimental approaches that are being applied for functional studies of causal variants and translational advances from GWAS findings to disease prevention and treatment. We highlight the use of genome editing technologies in GWAS functional studies to modify genomic sequences, with proof-of-principle examples. We discuss the challenges in interrogating causal variants, points for consideration in experimental design and interpretation of GWAS locus mechanisms, and the potential for novel therapeutic opportunities. With the accumulation of knowledge of functional genetics, therapeutic genome editing based on GWAS discoveries will become increasingly feasible.
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Affiliation(s)
- Shuquan Rao
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; Broad Institute; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Yao Yao
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; Broad Institute; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; Broad Institute; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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12
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Steinberg MH. Fetal Hemoglobin in Sickle Hemoglobinopathies: High HbF Genotypes and Phenotypes. J Clin Med 2020; 9:jcm9113782. [PMID: 33238542 PMCID: PMC7700170 DOI: 10.3390/jcm9113782] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 12/30/2022] Open
Abstract
Fetal hemoglobin (HbF) usually consists of 4 to 10% of total hemoglobin in adults of African descent with sickle cell anemia. Rarely, their HbF levels reach more than 30%. High HbF levels are sometimes a result of β-globin gene deletions or point mutations in the promoters of the HbF genes. Collectively, the phenotype caused by these mutations is called hereditary persistence of fetal hemoglobin, or HPFH. The pancellularity of HbF associated with these mutations inhibits sickle hemoglobin polymerization in most sickle erythrocytes so that these patients usually have inconsequential hemolysis and few, if any, vasoocclusive complications. Unusually high HbF can also be associated with variants of the major repressors of the HbF genes, BCL11A and MYB. Perhaps most often, we lack an explanation for very high HbF levels in sickle cell anemia.
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Affiliation(s)
- Martin H Steinberg
- Department of Medicine, Division of Hematology/Oncology, Center of Excellence for Sickle Cell Disease, Center for Regenerative Medicine, Genome Science Institute, Boston University School of Medicine and Boston Medical Center, 72 E. Concord St., Boston, MA 02118, USA
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13
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Gordeuk VR, Shah BN, Zhang X, Thuma PE, Zulu S, Moono R, Reading NS, Song J, Zhang Y, Nouraie M, Campbell A, Minniti CP, Rana SR, Darbari DS, Kato GJ, Niu M, Castro OL, Machado R, Gladwin MT, Prchal JT. The CYB5R3 c .350C>G and G6PD A alleles modify severity of anemia in malaria and sickle cell disease. Am J Hematol 2020; 95:1269-1279. [PMID: 32697331 PMCID: PMC8095369 DOI: 10.1002/ajh.25941] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 07/08/2020] [Indexed: 12/18/2022]
Abstract
Genetic modifiers of anemia in Plasmodium falciparum infection and sickle cell disease (SCD) are not fully known. Both conditions are associated with oxidative stress, hemolysis and anemia. The CYB5R3 gene encodes cytochrome b5 reductase 3, which converts methemoglobin to hemoglobin through oxidation of NADH. CYB5R3c.350C > G encoding CYB5R3T117S , the most frequent recognized African-specific polymorphism, does not have known functional significance, but its high allele frequency (23% in African Americans) suggests a selection advantage. Glucose-6-phosphate dehydrogenase (G6PD) is essential for protection from oxidants; its African-polymorphic X-linked A+ and A- alleles, and other variants with reduced activity, coincide with endemic malaria distribution, suggesting protection from lethal infection. We examined the association of CYB5R3c.350C > G with severe anemia (hemoglobin <5 g/dL) in the context of G6PD A+ and A- status among 165 Zambian children with malaria. CYB5R3c.350C > G offered protection against severe malarial anemia in children without G6PD deficiency (G6PD wild type or A+/A- heterozygotes) (odds ratio 0.29, P = .022) but not in G6PD A+ or A- hemizygotes/homozygotes. We also examined the relationship of CYB5R3c.350C > G with hemoglobin concentration among 267 children and 321 adults and adolescents with SCD in the US and UK and found higher hemoglobin in SCD patients without G6PD deficiency (β = 0.29, P = .022 children; β = 0.33, P = .004 adults). Functional studies in SCD erythrocytes revealed mildly lower activity of native CYB5R3T117S compared to wildtype CYB5R3 and higher NADH/NAD+ ratios. In conclusion, CYB5R3c.350C > G appears to ameliorate anemia severity in malaria and SCD patients without G6PD deficiency, possibly accounting for CYB5R3c.350C > G selection and its high prevalence.
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Affiliation(s)
- Victor R. Gordeuk
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Binal N. Shah
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Xu Zhang
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | | | | | | | | | - Jihyun Song
- University of Utah and ARUP Laboratories, Salt Lake City, Utah
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Mehdi Nouraie
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Andrew Campbell
- Children’s National Medical Center, Washington, District of Columbia
| | - Caterina P. Minniti
- Center for Sickle Cell Disease, Montefiore Medical Center, New York, New York
| | - Sohail R. Rana
- Department of Pediatrics and Child Health, Howard University Hospital, Washington, District of Columbia
| | | | | | - Mei Niu
- Center for Sickle Cell Disease, Howard University, Washington, District of Columbia
| | - Oswaldo L. Castro
- Center for Sickle Cell Disease, Howard University, Washington, District of Columbia
| | | | - Mark T. Gladwin
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
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14
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El-Ghamrawy M, Yassa ME, Tousson AMS, El-Hady MA, Mikhaeil E, Mohamed NB, Khorshied MM. Association between BCL11A, HSB1L-MYB, and XmnI γG-158 (C/T) gene polymorphism and hemoglobin F level in Egyptian sickle cell disease patients. Ann Hematol 2020; 99:2279-2288. [PMID: 32772141 DOI: 10.1007/s00277-020-04187-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 07/15/2020] [Indexed: 01/17/2023]
Abstract
Sickle cell disease (SCD) is a monogenic disease characterized by multisystem morbidity and highly variable clinical course. Inter-individual variability in hemoglobin F (HbF) levels is one of the main modifiers that account for the clinical heterogeneity in SCD. HbF levels are affected by, among other factors, single nucleotide polymorphisms (SNPs) at the BCL11A gene and the HBS1L-MYB intergenic region and Xmn1 gene. Our aim was to investigate HbF-enhancer haplotypes at these loci to obtain a first overview of the genetic situation of SCD patients in Egypt and its impact on the severity of the disease. The study included 100 SCD patients and 100 matched controls. Genotyping of BCL11A (rs1886868 C/T), HBS1L-MYB (rs9389268 A/G) and Xmn1 γG158 (rs7842144 C/T) SNPs showed no statistically significant difference between SCD patients and controls except for the hetero-mutant genotypes of BCL11A which was significantly higher in SCD patients compared with controls. Baseline HbF levels were significantly higher in those with co-inheritance of polymorphic genotypes of BCL11A + HSB1L-MYB and BCL11A + Xmn1. Steady-state HbF levels, used as an indicator of disease severity, were significantly higher in SCD-Sβ patients having the polymorphic genotypes of HSB1L-MYB. Fold change of HbF in both patient groups did not differ between those harboring the wild and the polymorphic genotypes of the studied SNPs. In conclusion, BCL11A, HSB1L, and Xmn1 genetic polymorphisms had no positive impact on baseline HbF levels solely but had if coexisted. Discovery of the molecular mechanisms controlling HbF production could provide a more effective strategy for HbF induction.
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Affiliation(s)
- Mona El-Ghamrawy
- Pediatric Department, Pediatric Hematology & BMT Unit, Kasr Al-Ainy School of Medicine, Cairo University, Kasr Al-Ainy St, Cairo, 11562, Egypt
| | - Marianne E Yassa
- Clinical and Chemical Pathology Department, KasrAl-Ainy Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Angie M S Tousson
- Pediatric Department, KasrAl-Ainy Faculty of Medicine, Cairo University, Kasr Al-Ainy St, Cairo, 11562, Egypt
| | - Marwa Abd El-Hady
- Pediatric Department, KasrAl-Ainy Faculty of Medicine, Cairo University, Kasr Al-Ainy St, Cairo, 11562, Egypt
| | - Erini Mikhaeil
- Pediatric and Neonatology, Ministry of Health, Cairo, Egypt
| | - Nada B Mohamed
- Misr University for Science and Technology, 6th of October City, Egypt
| | - Mervat Mamdooh Khorshied
- Clinical and Chemical Pathology Department, KasrAl-Ainy Faculty of Medicine, Cairo University, Cairo, Egypt.
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15
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Association of HMIP1 C-893A polymorphism and disease severity in patients with sickle cell anemia. Hematol Transfus Cell Ther 2020; 43:243-248. [PMID: 32665180 PMCID: PMC8446232 DOI: 10.1016/j.htct.2020.03.006] [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: 12/13/2019] [Revised: 03/03/2020] [Accepted: 03/16/2020] [Indexed: 11/23/2022] Open
Abstract
Introduction Sickle cell anemia (SCA) is a Mendelian disorder with a heterogeneous clinical course. The reasons for this phenotypic diversity are not entirely established, but it is known that high fetal hemoglobin levels lead to a milder course of the disease. Additionally, genetic variants in the intergenic region HBS1L-MYB promote high levels of fetal hemoglobin into adulthood. Objective In the present study, we investigated the HMIP1 C-839A (rs9376092) polymorphism, located at the HBS1L-MYB intergenic region block 1, in SCA patients. Method We analyzed 299 SCA patients followed in two reference centers in Brazil. The HMIP1 C-839A (rs9376092) genotypes were determined by allele specific polymerase chain reactions. Clinical and laboratory data were obtained from patient interviews and medical records. Results The median fetal hemoglobin levels were higher in patients with the HMIP1 C-839A (rs9376092) AA genotype (CC = 6.4%, CA = 5.6% and AA = 8.6%), but this difference did not reach significance (p = 0.194). No association between HMIP1 C-839A (rs9376092) genotypes and other clinical and laboratorial features was detected (p > 0.05). Conclusion In summary, our data could not support the previously related association between the HMIP1 C-893A (rs9376092) polymorphism and differential fetal hemoglobin levels.
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16
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Sales RR, Belisário AR, Faria G, Mendes F, Luizon MR, Viana MB. Functional polymorphisms of BCL11A and HBS1L-MYB genes affect both fetal hemoglobin level and clinical outcomes in a cohort of children with sickle cell anemia. Ann Hematol 2020; 99:1453-1463. [PMID: 32447424 DOI: 10.1007/s00277-020-04079-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/04/2020] [Indexed: 01/28/2023]
Abstract
Fetal hemoglobin (HbF) ameliorates clinical severity of sickle cell anemia (SCA). The major loci regulating HbF levels are HBB cluster, BCL11A, and HMIP-2 (HBS1L-MYB). However, the impact of noncoding single-nucleotide polymorphisms (SNPs) in these loci on clinical outcomes and their functional role on regulating HbF levels should be better elucidated. Therefore, we performed comprehensive association analyses of 14 noncoding SNPs in five loci with HbF levels and with clinical outcomes in a cohort of 250 children with SCA from Southeastern Brazil, and further performed functional annotation of these SNPs. We found SNPs independently associated with HbF levels: rs4671393 in BCL11A (β-coefficient = 0.28), rs9399137 in HMIP-2A (β-coefficient = 0.16), and rs4895441 in HMIP-2B (β-coefficient = 0.15). Patients carrying minor (HbF-boosting) alleles for rs1427407, rs93979137, rs4895441, rs9402686, and rs9494145 showed reduced count of reticulocytes (p < 0.01), while those carrying the T allele of rs9494145 showed lower white blood cell count (p = 0.002). Carriers of the minor allele for rs9402686 showed higher peripheral saturation of oxygen (p = 0.002). Patients carrying minor alleles in BCL11A showed lower risk of transfusion incidence rate ratio (IRR ≥ 1.3; p < 0.0001). This effect was independent of HbF effect (p = 0.005). Carriers of minor alleles for rs9399137 and rs9402686 showed lower risk of acute chest syndrome (IRR > 1.3; p ≤ 0.01). Carriers of the reference allele for rs4671393 showed lower risk of infections (IRR = 1.16; p = 0.01). In conclusion, patients carrying HbF-boosting alleles of BCL11A and HMIP-2 were associated with milder clinical phenotypes. Higher HbF concentration may underlie this effect.
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Affiliation(s)
- Rahyssa Rodrigues Sales
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil. .,Programa de Pós-Graduação em Saúde da Criança e do Adolescente, Faculdade de Medicina, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil. .,Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil.
| | - André Rolim Belisário
- Centro de Tecidos Biológicos de Minas Gerais, Fundação Hemominas, Lagoa Santa, Minas Gerais, 33400-000, Brazil
| | - Gabriela Faria
- Serviço de Pesquisa, Fundação Hemominas, Belo Horizonte, Minas Gerais, Brazil
| | - Fabiola Mendes
- Serviço de Pesquisa, Fundação Hemominas, Belo Horizonte, Minas Gerais, Brazil
| | - Marcelo Rizzatti Luizon
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil.,Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Marcos Borato Viana
- Faculdade de Medicina/NUPAD, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
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17
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High levels of proinflammatory cytokines IL-6 and IL-8 are associated with a poor clinical outcome in sickle cell anemia. Ann Hematol 2020; 99:947-953. [PMID: 32140892 DOI: 10.1007/s00277-020-03978-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/25/2020] [Indexed: 11/22/2022]
Abstract
Sickle cell anemia (SCA) pathophysiology is characterized by the activation of sickle red blood cells, reticulocytes, leukocytes, platelets, and endothelial cells, and with the expression of several inflammatory molecules. Therefore, it is conceivable that variations in levels of proinflammatory cytokines may act as a signaling of differential clinical course in SCA. Here, we evaluated the clinical impact of proinflammatory cytokines interleukin 1-β (IL-1β), interleukin 6 (IL-6), and interleukin 8 (IL-8) in 79 patients with SCA, followed in a single reference center from northeastern Brazil. The main clinical/laboratory data were obtained from patient interview and medical records. The proinflammatory markers IL-1β, IL-6, and IL-8 were evaluated by using commercially available enzyme-linked immunosorbent assay kits. According to levels of the proinflammatory markers, we observed that patients who had a higher frequency of VOC per year (P = 0.0236), acute chest syndrome (P = 0.01), leg ulcers (P = 0.0001), osteonecrosis (P = 0.0006), stroke (P = 0.0486), and priapism (P = 0.0347) had higher IL-6 levels compared with patients without these clinical complications. Furthermore, increased levels of IL-8 were found in patients who presented leg ulcers (P = 0.0184). No significant difference was found for IL-1β levels (P > 0.05). In summary, the present study emphasizes the role of inflammation in SCA pathophysiology, reveals an association of IL-8 levels and leg ulcer occurrence, and indicates that IL-6 levels can be used as a useful predictor for poor outcomes in SCA.
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18
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Dai Y, Shaikho EM, Perez J, Wilson CA, Liu LY, White MR, Farrell JJ, Chui DHK, Sebastiani P, Steinberg MH. BCL2L1 is associated with γ-globin gene expression. Blood Adv 2019; 3:2995-3001. [PMID: 31648320 PMCID: PMC6849934 DOI: 10.1182/bloodadvances.2019032243] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/11/2019] [Indexed: 11/20/2022] Open
Abstract
Fetal hemoglobin (HbF) expression is partially governed by the trans-acting quantitative trait loci BCL11A and MYB and a cis-acting locus linked to the HBB gene cluster. Our previous analysis of the Genotype-Tissue Expression database suggested that BCL2L1 was associated with HbF gene expression. In erythroid progenitors from patients with sickle cell disease, BCL2L1 messenger RNA (mRNA) levels were positively correlated with HBG mRNA and total HbF concentration (r2 = 0.72, P = .047 and r2 = 0.68, P = .01, respectively). Inhibition of BCL2L1 protein activity in HbF-expressing HUDEP-1 cells decreased HBG expression in a dose-dependent manner. Overexpression of BCL2L1 in these cells increased HBG expression fourfold (P < .05) and increased F cells by 13% (P < .05). Overexpression of BCL2L1 in erythroid progenitors derived from primary adult CD34+ cells upregulated HBG expression 11-fold (P < .05), increased F cells by 18% (P < .01), did not significantly affect cell differentiation or proliferation, and had a minor effect on survival. Although the mechanism remains unknown, our results suggest that BCL2L1 is associated with HbF gene activation.
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Affiliation(s)
- Yan Dai
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Elmutaz M Shaikho
- Department of Medicine, Boston University School of Medicine, Boston, MA
- Bioinformatics Program, Boston University, Boston, MA; and
| | - Jessica Perez
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Carolyn A Wilson
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Lesley Y Liu
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Mitchell R White
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - John J Farrell
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - David H K Chui
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Martin H Steinberg
- Department of Medicine, Boston University School of Medicine, Boston, MA
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19
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Nicolau M, Vargas S, Silva M, Coelho A, Ferreira E, Mendonça J, Vieira L, Kjöllerström P, Maia R, Silva R, Dias A, Ferreira T, Morais A, Soares IM, Lavinha J, Faustino P. Genetic modulators of fetal hemoglobin expression and ischemic stroke occurrence in African descendant children with sickle cell anemia. Ann Hematol 2019; 98:2673-2681. [PMID: 31478061 DOI: 10.1007/s00277-019-03783-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/11/2019] [Indexed: 02/06/2023]
Abstract
Sickle cell anemia (SCA) is an autosomal recessive monogenic disease with significant clinical variability. Cerebrovascular disease, particularly ischemic stroke, is one of the most severe complications of SCA in children. This study aimed to investigate the influence of genetic variants on the levels of fetal hemoglobin (Hb F) and biochemical parameters related with chronic hemolysis, as well as on ischemic stroke risk, in ninety-one unrelated SCA patients, children of sub-Saharan progenitors. Our results show that a higher Hb F level has an inverse relationship with the occurrence of stroke, since the group of patients who suffered stroke presents a significantly lower mean Hb F level (5.34 ± 4.57% versus 9.36 ± 6.48%; p = 0.024). Furthermore, the co-inheritance of alpha-thalassemia improves the chronic hemolytic pattern, evidenced by a decreased reticulocyte count (8.61 ± 3.58% versus 12.85 ± 4.71%; p < 0.001). In addition, our findings have confirmed the importance of HBG2 and BCL11A loci in the regulation of Hb F expression in sub-Saharan African SCA patients, as rs7482144_A, rs11886868_C, and rs4671393_A alleles are significantly associated with a considerable increase in Hb F levels (p = 0.019, p = 0.026, and p = 0.028, respectively). Concerning KLF1, twelve different variants were identified, two of them novel. Seventy-three patients (80.2%) presented at least one variant in this gene. However, no correlation was observed between the presence of these variants and Hb F level, severity of hemolysis, or stroke occurrence, which is consistent with their in silico-predicted minor functional consequences. Thus, we conclude that the prevalence of functional KLF1 variants in a sub-Saharan African background does not seem to be relevant to SCA clinical modulation.
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Affiliation(s)
- Marta Nicolau
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal
| | - Sofia Vargas
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal
| | - Marisa Silva
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal
| | - Andreia Coelho
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal
| | - Emanuel Ferreira
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal
| | - Joana Mendonça
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal
| | - Luís Vieira
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal.,ToxOmics, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Paula Kjöllerström
- Unidade de Hematologia, Hospital de Dona Estefânia, Centro Hospitalar Universitário de Lisboa Central (CHULC), Lisbon, Portugal
| | - Raquel Maia
- Unidade de Hematologia, Hospital de Dona Estefânia, Centro Hospitalar Universitário de Lisboa Central (CHULC), Lisbon, Portugal
| | - Rita Silva
- Unidade de Neuropediatria, Hospital de Dona Estefânia, CHULC, Lisbon, Portugal
| | - Alexandra Dias
- Núcleo de Hematologia, Departamento de Pediatria, Hospital Prof. Doutor Fernando Fonseca, Amadora, Portugal
| | - Teresa Ferreira
- Núcleo de Hematologia, Departamento de Pediatria, Hospital Prof. Doutor Fernando Fonseca, Amadora, Portugal
| | - Anabela Morais
- Departamento de Pediatria, Hospital de Santa Maria, Centro Hospitalar Universitário de Lisboa Norte, Lisbon, Portugal
| | | | - João Lavinha
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal.,BioISI, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Paula Faustino
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal. .,Instituto de Saúde Ambiental (ISAMB), Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal. .,Unidade de Investigação e Desenvolvimento, Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Avenida Padre Cruz, 1649-016, Lisbon, Portugal.
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20
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Houwing ME, de Pagter PJ, van Beers EJ, Biemond BJ, Rettenbacher E, Rijneveld AW, Schols EM, Philipsen JNJ, Tamminga RYJ, van Draat KF, Nur E, Cnossen MH. Sickle cell disease: Clinical presentation and management of a global health challenge. Blood Rev 2019; 37:100580. [PMID: 31128863 DOI: 10.1016/j.blre.2019.05.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 01/12/2023]
Abstract
Sickle cell disease is an autosomal recessive, multisystem disorder, characterised by chronic haemolytic anaemia, painful episodes of vaso-occlusion, progressive organ failure and a reduced life expectancy. Sickle cell disease is the most common monogenetic disease, with millions affected worldwide. In well-resourced countries, comprehensive care programs have increased life expectancy of sickle cell disease patients, with almost all infants surviving into adulthood. Therapeutic options for sickle cell disease patients are however, still scarce. Predictors of sickle cell disease severity and a better understanding of pathophysiology and (epi)genetic modifiers are warranted and could lead to more precise management and treatment. This review provides an extensive summary of the pathophysiology and management of sickle cell disease and encompasses the characteristics, complications and current and future treatment options of the disease.
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Affiliation(s)
- M E Houwing
- Department of Paediatric Haematology, Erasmus University Medical Center - Sophia Children's Hospital, Wytemaweg 80, 3015, CN, Rotterdam, the Netherlands.
| | - P J de Pagter
- Department of Paediatric Haematology, Erasmus University Medical Center - Sophia Children's Hospital, Wytemaweg 80, 3015, CN, Rotterdam, the Netherlands.
| | - E J van Beers
- Department of Internal Medicine and Dermatology, Van Creveldkliniek, University Medical Center Utrecht, Internal mail no C.01.412, 3508, GA, Utrecht, the Netherlands.
| | - B J Biemond
- Department of Internal Medicine and Clinical Haematology, Amsterdam University Medical Centers, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands.
| | - E Rettenbacher
- Department of Paediatric Haematology, Radboud University Medical Center - Amalia Children's Hospital, Geert Grooteplein Zuid 10, 6500, HB, Nijmegen, the Netherlands.
| | - A W Rijneveld
- Department of Haematology, Erasmus University Medical Center, Wytemaweg 80, 3015, CN, Rotterdam, the Netherlands.
| | - E M Schols
- Department of Haematology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands.
| | - J N J Philipsen
- Department of Cell Biology, Erasmus University Medical Center, Wytemaweg 80, 3015, CN, Rotterdam, the Netherlands.
| | - R Y J Tamminga
- Department of Paediatric Oncology and Haematology, University Medical Center Groningen - Beatrix Children's Hospital, Postbus 30001, 9700, RB, Groningen, the Netherlands..
| | - K Fijn van Draat
- Department of Paediatric Haematology, Amsterdam University Medical Centers - Emma Children's Hospital, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Department of Plasma Proteins, Sanquin Research, the Netherlands.
| | - E Nur
- Department of Internal Medicine and Clinical Haematology, Amsterdam University Medical Centers, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands.
| | - M H Cnossen
- Department of Paediatric Haematology, Erasmus University Medical Center - Sophia Children's Hospital, Wytemaweg 80, 3015, CN, Rotterdam, the Netherlands.
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21
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g(HbF): a genetic model of fetal hemoglobin in sickle cell disease. Blood Adv 2019; 2:235-239. [PMID: 29437638 DOI: 10.1182/bloodadvances.2017009811] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 12/12/2017] [Indexed: 11/20/2022] Open
Abstract
Fetal hemoglobin (HbF) is a strong modifier of sickle cell disease (SCD) severity and is associated with 3 common genetic loci. Quantifying the genetic effects of the 3 loci would specifically address the benefits of HbF increases in patients. Here, we have applied statistical methods using the most representative variants: rs1427407 and rs6545816 in BCL11A, rs66650371 (3-bp deletion) and rs9376090 in HMIP-2A, rs9494142 and rs9494145 in HMIP-2B, and rs7482144 (Xmn1-HBG2 in the β-globin locus) to create g(HbF), a genetic quantitative variable for HbF in SCD. Only patients aged ≥5 years with complete genotype and HbF data were studied. Five hundred eighty-one patients with hemoglobin SS (HbSS) or HbSβ0 thalassemia formed the "discovery" cohort. Multiple linear regression modeling rationalized the 7 variants down to 4 markers (rs6545816, rs1427407, rs66650371, and rs7482144) each independently contributing HbF-boosting alleles, together accounting for 21.8% of HbF variability (r2) in the HbSS or HbSβ0 patients. The model was replicated with consistent r2 in 2 different cohorts: 27.5% in HbSC patients (N = 186) and 23% in 994 Tanzanian HbSS patients. g(HbF), our 4-variant model, provides a robust approach to account for the genetic component of HbF in SCD and is of potential utility in sickle genetic and clinical studies.
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22
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Li B, Zhu X, Ward CM, Starlard-Davenport A, Takezaki M, Berry A, Ward A, Wilder C, Neunert C, Kutlar A, Pace BS. MIR-144-mediated NRF2 gene silencing inhibits fetal hemoglobin expression in sickle cell disease. Exp Hematol 2018; 70:85-96.e5. [PMID: 30412705 DOI: 10.1016/j.exphem.2018.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/01/2018] [Indexed: 12/30/2022]
Abstract
Inherited genetic modifiers and pharmacologic agents that enhance fetal hemoglobin (HbF) expression reverse the clinical severity of sickle cell disease (SCD). Recent efforts to develop novel strategies of HbF induction include discovery of molecular targets that regulate γ-globin gene transcription and translation. The purpose of this study was to perform genome-wide microRNA (miRNA) analysis to identify genes associated with HbF expression in patients with SCD. We isolated RNA from purified reticulocytes for microarray-based miRNA expression profiling. Using samples from patients with contrasting HbF levels, we observed an eightfold upregulation of miR-144-3p (miR-144) and miR-144-5p in the low-HbF group compared with those with high HbF. Additional analysis by reverse transcription quantitative polymerase chain reaction confirmed individual miR-144 expression levels of subjects in the two groups. Subsequent functional studies in normal and sickle erythroid progenitors showed NRF2 gene silencing by miR-144 and concomitant repression of γ-globin transcription; by contrast, treatment with miR-144 antagomir reversed its silencing effects in a dose-dependent manner. Because NRF2 regulates reactive oxygen species levels, additional studies investigated mechanisms of HbF regulation using a hemin-induced oxidative stress model. Treatment of KU812 cells with hemin produced an increase in NRF2 expression and HbF induction that reversed with miR-144 pretreatment. Chromatin immunoprecipitation assay confirmed NRF2 binding to the γ-globin antioxidant response element, which was inhibited by miR-144 mimic treatment. The genome-wide miRNA microarray and primary erythroid progenitor data support a miR-144/NRF2-mediated mechanism of γ-globin gene regulation in SCD.
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Affiliation(s)
- Biaoru Li
- Department of Pediatrics, Augusta University, Augusta, GA, USA
| | - Xingguo Zhu
- Department of Pediatrics, Augusta University, Augusta, GA, USA
| | - Christina M Ward
- Department of Biochemistry and Molecular Biology, Boston University, Boston, MA, USA
| | - Athena Starlard-Davenport
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Mayuko Takezaki
- Department of Pediatrics, Augusta University, Augusta, GA, USA
| | - Amber Berry
- Medical College of Georgia, Augusta, GA, USA
| | - Alexander Ward
- Department of Pediatrics, Augusta University, Augusta, GA, USA
| | - Caroline Wilder
- Department of Otolaryngology, Augusta University, Augusta, GA, USA
| | - Cindy Neunert
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Abdullah Kutlar
- Department of Medicine, Augusta University, Augusta, GA, USA
| | - Betty S Pace
- Department of Pediatrics, Augusta University, Augusta, GA, USA; Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA, USA.
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23
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The Genetic Landscape of Cerebral Steno-Occlusive Arteriopathy and Stroke in Sickle Cell Anemia. J Stroke Cerebrovasc Dis 2018; 27:2897-2904. [PMID: 30076115 DOI: 10.1016/j.jstrokecerebrovasdis.2018.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/28/2018] [Accepted: 06/02/2018] [Indexed: 11/24/2022] Open
Abstract
Sickle cell disease (SCD) is one of the most common autosomal recessive diseases in humans, occurring at a frequency of 1 in 365 African-American and 1 in 50 sub-Saharan African births. Despite progress in managing complications of SCD, these remain a major health burden worldwide. Stroke is a common and serious complication of SCD, most often associated with steno-occlusive cerebral arteriopathy, but little is known about its pathogenesis. Transcranial Doppler ultrasonography is currently the only predictive test for future development of stroke in patients with sickle cell anemia and is used to guide preventative treatment. However, transcranial Doppler ultrasonography does not identify all patients at increased risk for stroke, and progressive arteriopathy may occur despite preventative treatment. While sibling studies have shown a strong genetic contribution to the development of steno-occlusive arteriopathy (SOA) in SCD, the only genome-wide association study compared a relatively small cohort of 177 patients with stroke to 335 patients with no history of stroke. This single study detected variants in only 2 genes, ENPP1 and GOLGB1, and only one of these was confirmed in a subsequent independent study. Thus, the underlying genes and pathogenesis of SOA in SCD remain poorly understood, greatly limiting the ability to develop more effective preventive therapies. Dissecting the molecular causes of stroke in SCD will provide valuable information that can be used to better prevent stroke, stratify risk of SOA, and optimize personalized medicine approaches.
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24
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Biomarker signatures of sickle cell disease severity. Blood Cells Mol Dis 2018; 72:1-9. [PMID: 29778312 DOI: 10.1016/j.bcmd.2018.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 05/10/2018] [Indexed: 12/26/2022]
Abstract
Identifying sickle cell disease patients at high risk of complications could lead to personalized treatment and better prognosis but despite many advances prediction of the clinical course of these patients remains elusive. We propose a system-type approach to discover profiles of multiple, common biomarkers that correlate with morbidity and mortality in sickle cell disease. We used cluster analysis to discover 17 signatures of 17 common circulating biomarkers in 2320 participants of the Cooperative Study of Sickle Cell Disease, and evaluated the association of these signatures with risk for stroke, pain, leg ulceration, acute chest syndrome, avascular necrosis, seizure, death, and trend of fetal hemoglobin and hemolysis using longitudinally collected data. The analysis shows that some of the signatures are associated with reduced risk for complications, while others are associated with increased risk for complications. We also show that these signatures repeat in two more contemporary studies of sickle cell disease and correlate with recently discovered biomarkers of pulmonary vascular disease. With replication and further study, these biomarker signatures could become an important and affordable precision medicine tool to aid treatment and management of the disease.
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25
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Kuo KH. Multiple Testing in the Context of Gene Discovery in Sickle Cell Disease Using Genome-Wide Association Studies. GENOMICS INSIGHTS 2017; 10:1178631017721178. [PMID: 28811740 PMCID: PMC5542087 DOI: 10.1177/1178631017721178] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 06/26/2017] [Indexed: 12/25/2022]
Abstract
The issue of multiple testing, also termed multiplicity, is ubiquitous in studies where multiple hypotheses are tested simultaneously. Genome-wide association study (GWAS), a type of genetic association study that has gained popularity in the past decade, is most susceptible to the issue of multiple testing. Different methodologies have been employed to address the issue of multiple testing in GWAS. The purpose of the review is to examine the methodologies employed in dealing with multiple testing in the context of gene discovery using GWAS in sickle cell disease complications.
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Affiliation(s)
- Kevin H.M. Kuo
- Departments of Medical Oncology and Hematology and Medicine, University Health Network, Toronto, ON, Canada
- Division of Hematology, Department of Medicine, University of Toronto, Toronto, ON, Canada
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26
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Serjeant GR, Vichinsky E. Variability of homozygous sickle cell disease: The role of alpha and beta globin chain variation and other factors. Blood Cells Mol Dis 2017; 70:66-77. [PMID: 28689691 DOI: 10.1016/j.bcmd.2017.06.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/10/2017] [Accepted: 06/19/2017] [Indexed: 12/11/2022]
Abstract
The single base molecular substitution characterizing sickle cell haemoglobin, β6glu→val, might be expected to result in predictable haematological and clinical features. However, the disease manifests remarkable diversity believed to reflect the interaction with other genetic and environmental factors. Some of the genetic modifiers include the beta globin haplotypes, alpha thalassaemia, factors influencing the persistence of fetal haemoglobin and the effects of the environment are addressed in this review. It is concluded that much of the genetic data present conflicting results. Environmental factors such as climate and infections, and psychological, educational and social support mechanisms also influence expression of the disease. These interactions illustrate how the expression of a 'single gene' disorder may be influenced by a variety of other genetic and environmental factors.
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Affiliation(s)
- Graham R Serjeant
- Sickle Cell Trust (Jamaica), 14 Milverton Crescent, Kingston 6, Jamaica.
| | - Elliott Vichinsky
- Hematology/Oncology, UCSF Benioff Children's Hospital Oakland, University of California San Francisco, 747 52nd Street, Oakland, CA 94609, United States.
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27
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Molecular basis of β thalassemia and potential therapeutic targets. Blood Cells Mol Dis 2017; 70:54-65. [PMID: 28651846 DOI: 10.1016/j.bcmd.2017.06.001] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 06/09/2017] [Accepted: 06/09/2017] [Indexed: 12/15/2022]
Abstract
The remarkable phenotypic diversity of β thalassemia that range from severe anemia and transfusion-dependency, to a clinically asymptomatic state exemplifies how a spectrum of disease severity can be generated in single gene disorders. While the genetic basis for β thalassemia, and how severity of the anemia could be modified at different levels of its pathophysiology have been well documented, therapy remains largely supportive with bone marrow transplant being the only cure. Identification of the genetic variants modifying fetal hemoglobin (HbF) production in combination with α globin genotype provide some prediction of disease severity for β thalassemia but generation of a personalized genetic risk score to inform prognosis and guide management requires a larger panel of genetic modifiers yet to be discovered. Nonetheless, genetic studies have been successful in characterizing the key variants and pathways involved in HbF regulation, providing new therapeutic targets for HbF reactivation. BCL11A has been established as a quantitative repressor, and progress has been made in manipulating its expression using genomic and gene-editing approaches for therapeutic benefits. Recent discoveries and understanding in the mechanisms associated with ineffective and abnormal erythropoiesis have also provided additional therapeutic targets, a couple of which are currently being tested in clinical trials.
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28
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Treadwell MJ, Makani J, Ohene-Frempong K, Ofori-Acquah S, McCurdy S, de Vries J, Bukini D, Dennis-Antwi J, Kamga KK, Mbekenga C, Wonkam ET, Tangwa G, Royal CD, Wonkam A. Stakeholder Perspectives on Public Health Genomics Applications for Sickle Cell Disease: A Methodology for a Human Heredity and Health in Africa (H3Africa) Qualitative Research Study. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 21:323-332. [PMCID: PMC5488382 DOI: 10.1089/omi.2017.0047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Advances in omics technologies alone are not a guarantee that science will translate to robust responsible innovation that is firmly grounded in societal values. This study aimed to identify best practices for Ethical, Legal, and Social Implications (ELSI) research in Africa that allows for optimal integration of community perspectives into the design and implementation of genomics research. In a large sample of 346 stakeholders in Cameroon, Ghana, and Tanzania (59% women), we used a qualitative study design with a phenomenological approach and conducted 32 group and 74 individual interviews (25% rural). We imported interview recordings into NVivo software for analysis. We created a “concept map” to organize the coded information, with Perspectives on Genomics and Sickle Cell Disease (SCD) Public Health Interventions as the central themes. We found that (1) analyses of major subthemes across and within countries revealed differential knowledge and experiences of SCD, and perspectives on various aspects of research and genomics; (2) we were able to gather empirical data efficiently from urban and rural stakeholders, to study the issues related to sample sharing, consent processes, and return of clinical and genomic study results; (3) the concept of nondirectiveness in modern genetic medicine practice can be challenged by the views of stakeholders in the context of a high-burden disease such as SCD; and (4) linking community views to current and proposed public health interventions could be understood within the context of each specific country. Our work informs future qualitative social science and technology policy research designs on genomics applications in Africa.
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Affiliation(s)
- Marsha J. Treadwell
- Department of Hematology/Oncology, UCSF Benioff Children's Hospital Oakland, Oakland, CA
| | - Julie Makani
- Sickle Cell Disease Programme, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | - Solomon Ofori-Acquah
- Center for Translational and International Hematology, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sheryl McCurdy
- Department of Health Promotion and Behavioral Sciences, University of Texas School of Public Health, Houston, Texas
| | - Jantina de Vries
- Bioethics Centre, University of Cape Town, Cape Town, South Africa
| | - Daima Bukini
- Sickle Cell Disease Programme, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | - Karen Kengne Kamga
- University of Yaoundé 1, Faculty of Medical and Biomedical Sciences, Yaoundé, Cameroon
| | - Columba Mbekenga
- Sickle Cell Disease Programme, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Edmond Tingang Wonkam
- University of Yaoundé 1, Faculty of Medical and Biomedical Sciences, Yaoundé, Cameroon
| | - Godfrey Tangwa
- University of Yaoundé 1, Faculty of Medical and Biomedical Sciences, Yaoundé, Cameroon
| | - Charmaine D. Royal
- Center on Genomics, Race, Identity, Difference (GRID), Duke University, Durham
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Medicine, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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29
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Gibriel AA, Adel O. Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:66-90. [PMID: 28927538 PMCID: PMC7108312 DOI: 10.1016/j.mrrev.2017.05.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/24/2017] [Accepted: 05/01/2017] [Indexed: 02/07/2023]
Abstract
Genetic variants have been reported to cause several genetic diseases. Various genotyping assays have been developed for diagnostic and screening purposes but with certain limitations in sensitivity, specificity, cost effectiveness and/or time savings. Since the discovery of ligase chain reaction (LCR) in the late nineties, it became one of the most favored platforms for detecting these variants and also for genotyping low abundant contaminants. Recent and powerful modifications with the integration of various detection strategies such as electrochemical and magnetic biosensors, nanoparticles (NPs), quantum dots, quartz crystal and leaky surface acoustic surface biosensors, DNAzyme, rolling circle amplification (RCA), strand displacement amplification (SDA), surface enhanced raman scattering (SERS), chemiluminescence and fluorescence resonance energy transfer have been introduced to both LCR and ligation based amplifications to enable high-throughput and inexpensive multiplex genotyping with improved robustness, simplicity, sensitivity and specificity. In this article, classical and up to date modifications in LCR and ligation based amplifications are critically evaluated and compared with emphasis on points of strength and weakness, sensitivity, cost, running time, equipment needed, applications and multiplexing potential. Versatile genotyping applications such as genetic diseases detection, bacterial and viral pathogens detection are also detailed. Ligation based gold NPs biosensor, ligation based RCA and ligation mediated SDA assays enhanced detection limit tremendously with a discrimination power approaching 1.5aM, 2aM and 0.1fM respectively. MLPA (multiplexed ligation dependent probe amplification) and SNPlex assays have been commercialized for multiplex detection of at least 48 SNPs at a time. MOL-PCR (multiplex oligonucleotide ligation) has high-throughput capability with multiplex detection of 50 SNPs/well in a 96 well plate. Ligase detection reaction (LDR) is one of the most widely used LCR versions that have been successfully integrated with several detection strategies with improved sensitivity down to 0.4fM.
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Affiliation(s)
- Abdullah A Gibriel
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt; Center for Drug Research & Development (CDRD), Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt.
| | - Ola Adel
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt; Center for Drug Research & Development (CDRD), Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt
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30
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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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31
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Affiliation(s)
- Frédéric B Piel
- From the Department of Epidemiology and Biostatistics, Medical Research Council-Public Health England (MRC-PHE) Centre for Environment and Health, School of Public Health, Imperial College London (F.B.P.), and the Department of Haematological Medicine, King's College Hospital, King's College London (D.C.R.), London; and the Department of Medicine, Boston University School of Medicine, Boston (M.H.S.)
| | - Martin H Steinberg
- From the Department of Epidemiology and Biostatistics, Medical Research Council-Public Health England (MRC-PHE) Centre for Environment and Health, School of Public Health, Imperial College London (F.B.P.), and the Department of Haematological Medicine, King's College Hospital, King's College London (D.C.R.), London; and the Department of Medicine, Boston University School of Medicine, Boston (M.H.S.)
| | - David C Rees
- From the Department of Epidemiology and Biostatistics, Medical Research Council-Public Health England (MRC-PHE) Centre for Environment and Health, School of Public Health, Imperial College London (F.B.P.), and the Department of Haematological Medicine, King's College Hospital, King's College London (D.C.R.), London; and the Department of Medicine, Boston University School of Medicine, Boston (M.H.S.)
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32
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Canver MC, Lessard S, Pinello L, Wu Y, Ilboudo Y, Stern EN, Needleman AJ, Galactéros F, Brugnara C, Kutlar A, McKenzie C, Reid M, Chen DD, Das PP, A Cole M, Zeng J, Kurita R, Nakamura Y, Yuan GC, Lettre G, Bauer DE, Orkin SH. Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci. Nat Genet 2017; 49:625-634. [PMID: 28218758 PMCID: PMC5374001 DOI: 10.1038/ng.3793] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/25/2017] [Indexed: 02/06/2023]
Abstract
Cas9-mediated, high-throughput, saturating in situ mutagenesis permits fine-mapping of function across genomic segments. Disease- and trait-associated variants from genome-wide association studies largely cluster in regulatory DNA. Here we demonstrate the use of multiple designer nucleases and variant-aware library design to interrogate trait-associated regulatory DNA at high resolution. We developed a computational tool for the creation of saturating mutagenesis libraries with single or combinatorial nucleases with incorporation of variants. We applied this methodology to the HBS1L-MYB intergenic region, a locus associated with red blood cell traits, including fetal hemoglobin levels. This approach identified putative regulatory elements that control MYB expression. Analysis of genomic copy number highlighted potential false positive regions, which emphasizes the importance of off-target analysis in design of saturating mutagenesis experiments. Taken together, these data establish a widely applicable high-throughput and high-resolution methodology to reliably identify minimal functional sequences within large regions of disease- and trait-associated DNA.
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Affiliation(s)
- Matthew C Canver
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Samuel Lessard
- Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Luca Pinello
- Department of Molecular Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Yuxuan Wu
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Yann Ilboudo
- Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Emily N Stern
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Austen J Needleman
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Frédéric Galactéros
- Red Cell Genetic Disease Unit, Hôpital Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), UPeC, IMRB U955 Equipe no. 2, Créteil, France
| | - Carlo Brugnara
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Abdullah Kutlar
- Department of Medicine, Sickle Cell Center, Augusta University, Augusta, Georgia, USA
| | - Colin McKenzie
- The Caribbean Institute for Health Research, University of the West Indies, Mona, Kingston, Jamaica
| | - Marvin Reid
- The Caribbean Institute for Health Research, University of the West Indies, Mona, Kingston, Jamaica
| | - Diane D Chen
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Partha Pratim Das
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Mitchel A Cole
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Japan.,Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Boston, Massachusetts, USA
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Thein SL. Genetic Basis and Genetic Modifiers of β-Thalassemia and Sickle Cell Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1013:27-57. [PMID: 29127676 DOI: 10.1007/978-1-4939-7299-9_2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
β-thalassemia and sickle cell disease (SCD) are prototypical Mendelian single gene disorders, both caused by mutations affecting the adult β-globin gene. Despite the apparent genetic simplicity, both disorders display a remarkable spectrum of phenotypic severity and share two major genetic modifiers-α-globin genotype and innate ability to produce fetal hemoglobin (HbF, α2γ2).This article provides an overview of the genetic basis for SCD and β-thalassemia, and genetic modifiers identified through phenotype correlation studies. Identification of the genetic variants modifying HbF production in combination with α-globin genotype provide some prediction of disease severity for β-thalassemia and SCD but generation of a personalized genetic risk score to inform prognosis and guide management requires a larger panel of genetic modifiers yet to be discovered.Nonetheless, genetic studies have been successful in characterizing some of the key variants and pathways involved in HbF regulation, providing new therapeutic targets for HbF reactivation.
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Affiliation(s)
- Swee Lay Thein
- Sickle Cell Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Building 10, Room 6S241 MSC 1589, 10 Center Dr., Bethesda, MD, 20892-1589, USA.
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Alapan Y, Fraiwan A, Kucukal E, Hasan MN, Ung R, Kim M, Odame I, Little JA, Gurkan UA. Emerging point-of-care technologies for sickle cell disease screening and monitoring. Expert Rev Med Devices 2016; 13:1073-1093. [PMID: 27785945 PMCID: PMC5166583 DOI: 10.1080/17434440.2016.1254038] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Sickle Cell Disease (SCD) affects 100,000 Americans and more than 14 million people globally, mostly in economically disadvantaged populations, and requires early diagnosis after birth and constant monitoring throughout the life-span of the patient. Areas covered: Early diagnosis of SCD still remains a challenge in preventing childhood mortality in the developing world due to requirements of skilled personnel and high-cost of currently available modalities. On the other hand, SCD monitoring presents insurmountable challenges due to heterogeneities among patient populations, as well as in the same individual longitudinally. Here, we describe emerging point-of-care micro/nano platform technologies for SCD screening and monitoring, and critically discuss current state of the art, potential challenges associated with these technologies, and future directions. Expert commentary: Recently developed microtechnologies offer simple, rapid, and affordable screening of SCD and have the potential to facilitate universal screening in resource-limited settings and developing countries. On the other hand, monitoring of SCD is more complicated compared to diagnosis and requires comprehensive validation of efficacy. Early use of novel microdevices for patient monitoring might come in especially handy in new clinical trial designs of emerging therapies.
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Affiliation(s)
- Yunus Alapan
- Case Biomanufacturing and Microfabrication Laboratory, Mechanical and Aerospace Engineering Department, Case Western Reserve University, Cleveland, OH, USA
| | - Arwa Fraiwan
- Case Biomanufacturing and Microfabrication Laboratory, Mechanical and Aerospace Engineering Department, Case Western Reserve University, Cleveland, OH, USA
| | - Erdem Kucukal
- Case Biomanufacturing and Microfabrication Laboratory, Mechanical and Aerospace Engineering Department, Case Western Reserve University, Cleveland, OH, USA
| | - M. Noman Hasan
- Case Biomanufacturing and Microfabrication Laboratory, Mechanical and Aerospace Engineering Department, Case Western Reserve University, Cleveland, OH, USA
| | - Ryan Ung
- Biomedical Engineering Department, Case Western Reserve University, Cleveland, OH, USA
| | - Myeongseop Kim
- Case Biomanufacturing and Microfabrication Laboratory, Mechanical and Aerospace Engineering Department, Case Western Reserve University, Cleveland, OH, USA
| | - Isaac Odame
- Division of Haematology/Oncology, The Hospital for Sick Children; Toronto, Canada
- Department of Pediatrics, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Jane A. Little
- Department of Hematology and Oncology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center at University Hospitals, Case Medical Center, Cleveland, OH, USA
| | - Umut A. Gurkan
- Case Biomanufacturing and Microfabrication Laboratory, Mechanical and Aerospace Engineering Department, Case Western Reserve University, Cleveland, OH, USA
- Biomedical Engineering Department, Case Western Reserve University, Cleveland, OH, USA
- Department of Orthopedics, Case Western Reserve University, Cleveland, OH, USA
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Friedrisch JR, Sheehan V, Flanagan JM, Baldan A, Summarell CCG, Bittar CM, Friedrisch BK, Wilke II, Ribeiro CB, Daudt LE, da Rocha Silla LM. The role of BCL11A and HMIP-2 polymorphisms on endogenous and hydroxyurea induced levels of fetal hemoglobin in sickle cell anemia patients from southern Brazil. Blood Cells Mol Dis 2016; 62:32-37. [PMID: 27838552 DOI: 10.1016/j.bcmd.2016.11.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/04/2016] [Accepted: 11/07/2016] [Indexed: 01/18/2023]
Abstract
High levels of fetal hemoglobin (HbF) reduce sickle cell anemia (SCA) morbidity and mortality. HbF levels vary considerably and there is a strong genetic component that influences HbF production. Genetic polymorphisms at three quantitative trait loci (QTL): Xmn1-HBG2, HMIP-2 and BCL11A, have been shown to influence HbF levels and disease severity in SCA. Hydroxyurea (HU) is a drug that increases HbF. We investigated the influence of single nucleotide polymorphisms (SNPs) at the Xmn1-HBG2 (rs7482144); BCL11A (rs1427407, rs4671393 and rs11886868); and HMIP-2 (rs9399137 and rs9402686) loci on baseline and HU-induced HbF levels in 111 HbSS patients. We found that both BCL11A and HMIP-2 were associated with increased endogenous levels of HbF. Interestingly, we also found that BCL11A was associated with higher induction of HbF with HU. This effect was independent of the effect of BCL11A on baseline HbF levels. Additional studies will be needed to validate these findings and explain the ample inter-individual variations in HbF levels at baseline and HU-induced in patients with SCA.
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Affiliation(s)
- João Ricardo Friedrisch
- Medical Sciences, Universidade Federal do Rio Grande do Sul (UFGRS); Hematology and Bone Marrow Transplantation Service of the Hospital de Clínicas de Porto Alegre (HCPA).
| | - Vivien Sheehan
- Texas Children's Hematology Center, Baylor College of Medicine, Department of Pediatrics, Houston, TX, USA.
| | - Jonathan M Flanagan
- Texas Children's Hematology Center, Baylor College of Medicine, Department of Pediatrics, Houston, TX, USA.
| | - Alessandro Baldan
- Texas Children's Hematology Center, Baylor College of Medicine, Department of Pediatrics, Houston, TX, USA.
| | - Carly C Ginter Summarell
- Texas Children's Hematology Center, Baylor College of Medicine, Department of Pediatrics, Houston, TX, USA.
| | | | | | - Ianaê Indiara Wilke
- Hematology and Bone Marrow Transplantation Service of the Hospital de Clínicas de Porto Alegre (HCPA).
| | - Camila Blos Ribeiro
- Hematology and Bone Marrow Transplantation Service of the Hospital de Clínicas de Porto Alegre (HCPA).
| | - Liane Esteves Daudt
- Hematology and Bone Marrow Transplantation Service of the Hospital de Clínicas de Porto Alegre (HCPA).
| | - Lucia Mariano da Rocha Silla
- Hematology and Bone Marrow Transplantation Service of the Hospital de Clínicas de Porto Alegre (HCPA); Medical Sciences, UFGRS, Santa Cruz do Sul, RS, Brazil.
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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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Shaikho EM, Habara AH, Alsultan A, Al-Rubaish AM, Al-Muhanna F, Naserullah Z, Alsuliman A, Qutub HO, Patra PK, Sebastiani P, Baltrusaitis K, Farrell JJ, Jiang Z, Luo HY, Chui DHK, Al-Ali AK, Steinberg MH. Variants of ZBTB7A (LRF) and its β-globin gene cluster binding motifs in sickle cell anemia. Blood Cells Mol Dis 2016; 59:49-51. [PMID: 27282567 DOI: 10.1016/j.bcmd.2016.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 04/10/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Elmutaz M Shaikho
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Alawi H Habara
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Abdulrahman Alsultan
- Sickle Cell Disease Research Center and Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - A M Al-Rubaish
- Department of Internal Medicine, College of Medicine, University of Dammam, Dammam, Saudi Arabia
| | - Fahad Al-Muhanna
- Department of Internal Medicine, College of Medicine, University of Dammam, Dammam, Saudi Arabia
| | - Z Naserullah
- Alomran Scientific Chair for Hematological Diseases, King Faisal University, Dammam, Saudi Arabia; Department of Pediatrics, Maternity & Child Hospital, Dammam, Saudi Arabia
| | - A Alsuliman
- Alomran Scientific Chair, King Faisal University, King Fahd Hospital, Hafof, Al-Ahsa, Saudi Arabia
| | - Hatem O Qutub
- Alomran Scientific Chair, King Faisal University, Al-Ahsa, Saudi Arabia
| | - P K Patra
- Department of Biochemistry, Pt. J.N.M. Medical College, Raipur, Chattisgarh, India
| | - Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Kristin Baltrusaitis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - John J Farrell
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Zhihua Jiang
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Hong-Yuan Luo
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - David H K Chui
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Amein K Al-Ali
- Prince Mohammed Center for Research & Medical Consultation, University of Dammam, Dammam, Saudi Arabia
| | - Martin H Steinberg
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
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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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Goodman SR, Pace BS, Hansen KC, D'alessandro A, Xia Y, Daescu O, Glatt SJ. Minireview: Multiomic candidate biomarkers for clinical manifestations of sickle cell severity: Early steps to precision medicine. Exp Biol Med (Maywood) 2016; 241:772-81. [PMID: 27022133 DOI: 10.1177/1535370216640150] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In this review, we provide a description of those candidate biomarkers which have been demonstrated by multiple-omics approaches to vary in correlation with specific clinical manifestations of sickle cell severity. We believe that future clinical analyses of severity phenotype will require a multiomic analysis, or an omics stack approach, which includes integrated interactomics. It will also require the analysis of big data sets. These candidate biomarkers, whether they are individual or panels of functionally linked markers, will require future validation in large prospective and retrospective clinical studies. Once validated, the hope is that informative biomarkers will be used for the identification of individuals most likely to experience severe complications, and thereby be applied for the design of patient-specific therapeutic approaches and response to treatment. This would be the beginning of precision medicine for sickle cell disease.
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Affiliation(s)
- Steven R Goodman
- Department of Pediatrics and Department of Physiology, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Betty S Pace
- Department of Pediatrics, Augusta University, Augusta, GA 30912, USA
| | - Kirk C Hansen
- Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80202, USA
| | - Angelo D'alessandro
- Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80202, USA
| | - Yang Xia
- Biochemistry and Molecular Biology Department, University of Texas at Houston, TX 77030, USA
| | - Ovidiu Daescu
- University of Texas at Dallas, Richardson, TX 75080, USA
| | - Stephen J Glatt
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY 13210, USA
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Wonkam A, Makani J, Ofori-Aquah S, Nnodu OE, Treadwell M, Royal C, Ohene-Frempong K. Sickle cell disease and H3Africa: enhancing genomic research on cardiovascular diseases in African patients. Cardiovasc J Afr 2016; 26:S50-5. [PMID: 25962948 PMCID: PMC4547555 DOI: 10.5830/cvja-2015-040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Sickle cell disease (SCD) has a high prevalence in sub-Saharan Africa. There are several cardiovascular phenotypes in SCD that contribute to its morbidity and mortality. Discussion SCD is characterised by marked clinical variability, with genetic factors playing key modulating roles. Studies in Tanzania and Cameroon have reported that singlenucleotide polymorphisms in BCL11A and HBS1L-MYB loci and co-inheritance of alpha-thalassaemia impact on foetal haemoglobin levels and clinical severity. The prevalence of overt stroke among SCD patients in Cameroon (6.7%) and Nigeria (8.7%) suggests a higher burden than in high-income countries. There is also some evidence of high burden of kidney disease and pulmonary hypertension in SCD; however, the burden and genetics of these cardiovascular conditions have seldom been investigated in Africa. Conclusions Several H3Africa projects are focused on cardiovascular diseases and present major opportunities to build genome-based research on existing SCD platforms in Africa to transform the health outcomes of patients.
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Affiliation(s)
- Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, South Africa.
| | - Julie Makani
- Muhimbili University of Health and Allied Sciences, Dar-Es-Salaam, Tanzania
| | - Solomon Ofori-Aquah
- Center for Translational and International Hematology, University of Pittsburgh, Pittsburgh, USA
| | - Obiageli E Nnodu
- Department of Haematology and Blood Transfusion, College of Health Sciences, University of Abuja, Abuja, Nigeria/Department of Haematology and Blood Transfusion, University of Abuja Teaching Hospital, Gwagwalada, Abuja, Nigeria
| | - Marsha Treadwell
- Hematology/Oncology Department, UCSF Benioff Children's Hospital, Oakland, USA
| | - Charmaine Royal
- Department of African and African American Studies, Duke University, Durham, USA
| | - Kwaku Ohene-Frempong
- Children's Hospital of Philadelphia, Comprehensive Sickle Cell Centre, Philadelphia, USA
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de Dreuzy E, Bhukhai K, Leboulch P, Payen E. Current and future alternative therapies for beta-thalassemia major. Biomed J 2016; 39:24-38. [PMID: 27105596 PMCID: PMC6138429 DOI: 10.1016/j.bj.2015.10.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 10/12/2015] [Indexed: 11/15/2022] Open
Abstract
Beta-thalassemia is a group of frequent genetic disorders resulting in the synthesis of little or no β-globin chains. Novel approaches are being developed to correct the resulting α/β-globin chain imbalance, in an effort to move beyond the palliative management of this disease and the complications of its treatment (e.g. life-long red blood cell transfusion, iron chelation, splenectomy), which impose high costs on healthcare systems. Three approaches are envisaged: fetal globin gene reactivation by pharmacological compounds injected into patients throughout their lives, allogeneic hematopoietic stem cell transplantation (HSCT), and gene therapy. HSCT is currently the only treatment shown to provide an effective, definitive cure for β-thalassemia. However, this procedure remains risky and histocompatible donors are identified for only a small fraction of patients. New pharmacological compounds are being tested, but none has yet made it into common clinical practice for the treatment of beta-thalassemia major. Gene therapy is in the experimental phase. It is emerging as a powerful approach without the immunological complications of HSCT, but with other possible drawbacks. Rapid progress is being made in this field, and long-term efficacy and safety studies are underway.
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Affiliation(s)
- Edouard de Dreuzy
- CEA, Institute of Emerging Diseases and Innovative Therapies, Fontenay aux Roses, France; University of Paris 11, CEA-iMETI, 92260 Fontenay aux Roses, France
| | - Kanit Bhukhai
- CEA, Institute of Emerging Diseases and Innovative Therapies, Fontenay aux Roses, France; University of Paris 11, CEA-iMETI, 92260 Fontenay aux Roses, France
| | - Philippe Leboulch
- CEA, Institute of Emerging Diseases and Innovative Therapies, Fontenay aux Roses, France; University of Paris 11, CEA-iMETI, 92260 Fontenay aux Roses, France; Department of Medicine, Harvard Medical School and Genetics Division, Brigham and Women's Hospital, Boston MA, USA; Mahidol University and Ramathibodi Hospital, Bangkok, Thailand
| | - Emmanuel Payen
- CEA, Institute of Emerging Diseases and Innovative Therapies, Fontenay aux Roses, France; University of Paris 11, CEA-iMETI, 92260 Fontenay aux Roses, France; INSERM, Paris, France.
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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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Genome-wide association analyses based on whole-genome sequencing in Sardinia provide insights into regulation of hemoglobin levels. Nat Genet 2015; 47:1264-71. [PMID: 26366553 PMCID: PMC4627580 DOI: 10.1038/ng.3307] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 04/23/2015] [Indexed: 12/20/2022]
Abstract
We report genome-wide association study results for the levels of A1, A2 and fetal hemoglobins, analyzed for the first time concurrently. Integrating high-density array genotyping and whole-genome sequencing in a large general population cohort from Sardinia, we detected 23 associations at 10 loci. Five signals are due to variants at previously undetected loci: MPHOSPH9, PLTP-PCIF1, ZFPM1 (FOG1), NFIX and CCND3. Among the signals at known loci, ten are new lead variants and four are new independent signals. Half of all variants also showed pleiotropic associations with different hemoglobins, which further corroborated some of the detected associations and identified features of coordinated hemoglobin species production.
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44
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Zhang X, Zhang W, Saraf SL, Nouraie M, Han J, Gowhari M, Hassan J, Miasnikova G, Sergueeva A, Nekhai S, Kittles R, Machado RF, Garcia JGN, Gladwin MT, Steinberg MH, Sebastiani P, McClain DA, Gordeuk VR. Genetic polymorphism of APOB is associated with diabetes mellitus in sickle cell disease. Hum Genet 2015; 134:895-904. [PMID: 26025476 PMCID: PMC4607040 DOI: 10.1007/s00439-015-1572-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/22/2015] [Indexed: 02/02/2023]
Abstract
Environmental variations have strong influences in the etiology of type 2 diabetes mellitus. In this study, we investigated the genetic basis of diabetes in patients with sickle cell disease (SCD), a Mendelian disorder accompanied by distinct physiological conditions of hypoxia and hyperactive erythropoiesis. Compared to the general African American population, the prevalence of diabetes as assessed in two SCD cohorts of 856 adults was low, but it markedly increased with older age and overweight. Meta-analyses of over 5 million single-nucleotide polymorphisms (SNPs) in the two SCD cohorts identified a SNP, rs59014890, the C allele of which associated with diabetes risk at P = 3.2 × 10(-8) and, surprisingly, associated with decreased APOB expression in peripheral blood mononuclear cells (PBMCs). The risk allele of the APOB polymorphism was associated with overweight in 181 SCD adolescents, with diabetes risk in 592 overweight, non-SCD African Americans ≥ 45 years of age, and with elevated plasma lipid concentrations in general populations. In addition, lower expression level of APOB in PBMCs was associated with higher values for percent hemoglobin A1C and serum total cholesterol and triglyceride concentrations in patients with Chuvash polycythemia, a congenital disease with elevated hypoxic responses and increased erythropoiesis at normoxia. Our study reveals a novel, environment-specific genetic polymorphism that may affect key metabolic pathways contributing to diabetes in SCD.
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Affiliation(s)
- Xu Zhang
- Comprehensive Sickle Cell Center, Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Santosh L. Saraf
- Comprehensive Sickle Cell Center, Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL
| | - Mehdi Nouraie
- Center for Sickle Cell Disease, Howard University, Washington, DC
| | - Jin Han
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, Chicago, IL
| | - Michel Gowhari
- Comprehensive Sickle Cell Center, Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL
| | - Johara Hassan
- Comprehensive Sickle Cell Center, Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL
| | | | | | - Sergei Nekhai
- Center for Sickle Cell Disease, Howard University, Washington, DC
| | - Rick Kittles
- University of Arizona, College of Medicine, Tucson, AZ
| | - Roberto F. Machado
- Department of Medicine, Pulmonary and Critical Care Medicine, University of Illinois at Chicago, Chicago, IL
| | | | - Mark T. Gladwin
- Division of Pulmonary, Allergy, and Critical Care Medicine, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA
| | | | - Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Donald A. McClain
- Department of Internal Medicine, Wake Forest University School of Medicine and VA Medical Center, Winston Salem, NC
| | - Victor R. Gordeuk
- Comprehensive Sickle Cell Center, Section of Hematology/Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL
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45
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Saraf SL, Zhang X, Shah B, Kanias T, Gudehithlu KP, Kittles R, Machado RF, Arruda JAL, Gladwin MT, Singh AK, Gordeuk VR. Genetic variants and cell-free hemoglobin processing in sickle cell nephropathy. Haematologica 2015. [PMID: 26206798 DOI: 10.3324/haematol.2015.124875] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Intravascular hemolysis and hemoglobinuria are associated with sickle cell nephropathy. ApoL1 is involved in cell-free hemoglobin scavenging through association with haptoglobin-related protein. APOL1 G1/G2 variants are the strongest genetic predictors of kidney disease in the general African-American population. A single report associated APOL1 G1/G2 with sickle cell nephropathy. In 221 patients with sickle cell disease at the University of Illinois at Chicago, we replicated the finding of an association of APOL1 G1/G2 with proteinuria, specifically with urine albumin concentration (β=1.1, P=0.003), observed an even stronger association with hemoglobinuria (OR=2.5, P=4.3×10(-6)), and also replicated the finding of an association with hemoglobinuria in 487 patients from the Walk-Treatment of Pulmonary Hypertension and Sickle cell Disease with Sildenafil Therapy study (OR=2.6, P=0.003). In 25 University of Illinois sickle cell disease patients, concentrations of urine kidney injury molecule-1 correlated with urine cell-free hemoglobin concentrations (r=0.59, P=0.002). Exposing human proximal tubular cells to increasing cell-free hemoglobin led to increasing concentrations of supernatant kidney injury molecule-1 (P=0.01), reduced viability (P=0.01) and induction of HMOX1 and SOD2. HMOX1 rs743811 associated with chronic kidney disease stage (OR=3.0, P=0.0001) in the University of Illinois cohort and end-stage renal disease (OR=10.0, P=0.0003) in the Walk-Treatment of Pulmonary Hypertension and Sickle cell Disease with Sildenafil Therapy cohort. Longer HMOX1 GT-tandem repeats (>25) were associated with lower estimated glomerular filtration rate in the University of Illinois cohort (P=0.01). Our findings point to an association of APOL1 G1/G2 with kidney disease in sickle cell disease, possibly through increased risk of hemoglobinuria, and associations of HMOX1 variants with kidney disease, possibly through reduced protection of the kidney from hemoglobin-mediated toxicity.
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Affiliation(s)
- Santosh L Saraf
- Division of Hematology & Oncology, Department of Medicine, Comprehensive Sickle Cell Center, University of Illinois at Chicago, IL
| | - Xu Zhang
- Division of Hematology & Oncology, Department of Medicine, Comprehensive Sickle Cell Center, University of Illinois at Chicago, IL
| | - Binal Shah
- Division of Hematology & Oncology, Department of Medicine, Comprehensive Sickle Cell Center, University of Illinois at Chicago, IL
| | - Tamir Kanias
- Division of Pulmonary, Allergy, and Critical Care Medicine, Vascular Medicine Institute, University of Pittsburgh, PA
| | - Krishnamurthy P Gudehithlu
- Division of Nephrology, Department of Medicine, John H. Stroger, Jr Hospital of Cook County, Chicago, IL
| | - Rick Kittles
- Department of Surgery, University of Arizona, Tucson, AZ
| | - Roberto F Machado
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Illinois at Chicago, IL
| | - Jose A L Arruda
- Division of Nephrology, Department of Medicine, University of Illinois at Chicago, IL, USA
| | - Mark T Gladwin
- Division of Pulmonary, Allergy, and Critical Care Medicine, Vascular Medicine Institute, University of Pittsburgh, PA
| | - Ashok K Singh
- Division of Nephrology, Department of Medicine, John H. Stroger, Jr Hospital of Cook County, Chicago, IL
| | - Victor R Gordeuk
- Division of Hematology & Oncology, Department of Medicine, Comprehensive Sickle Cell Center, University of Illinois at Chicago, IL
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46
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Bae H, Perls T, Steinberg M, Sebastiani P. Bayesian Polynomial Regression Models to Fit Multiple Genetic Models for Quantitative Traits. BAYESIAN ANALYSIS 2015; 10:53-74. [PMID: 26029316 PMCID: PMC4446790 DOI: 10.1214/14-ba880] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present a coherent Bayesian framework for selection of the most likely model from the five genetic models (genotypic, additive, dominant, co-dominant, and recessive) commonly used in genetic association studies. The approach uses a polynomial parameterization of genetic data to simultaneously fit the five models and save computations. We provide a closed-form expression of the marginal likelihood for normally distributed data, and evaluate the performance of the proposed method and existing method through simulated and real genome-wide data sets.
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Affiliation(s)
- Harold Bae
- Department of Biostatistics, Boston University School of Public Health
| | - Thomas Perls
- New England Centenarian Study, Section of Geriatrics, Department of Medicine, Boston University School of Medicine
| | - Martin Steinberg
- Center of Excellence in Sickle Cell Disease Boston Medical Center, Pediatrics, Pathology and Laboratory Medicine
| | - Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health
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47
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Sebastiani P, Farrell JJ, Alsultan A, Wang S, Edward HL, Shappell H, Bae H, Milton JN, Baldwin CT, Al-Rubaish AM, Naserullah Z, Al-Muhanna F, Alsuliman A, Patra PK, Farrer LA, Ngo D, Vathipadiekal V, Chui DHK, Al-Ali AK, Steinberg MH. BCL11A enhancer haplotypes and fetal hemoglobin in sickle cell anemia. Blood Cells Mol Dis 2015; 54:224-30. [PMID: 25703683 DOI: 10.1016/j.bcmd.2015.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 01/07/2015] [Indexed: 02/04/2023]
Abstract
BACKGROUND Fetal hemoglobin (HbF) levels in sickle cell anemia patients vary. We genotyped polymorphisms in the erythroid-specific enhancer of BCL11A to see if they might account for the very high HbF associated with the Arab-Indian (AI) haplotype and Benin haplotype of sickle cell anemia. METHODS AND RESULTS Six BCL112A enhancer SNPs and their haplotypes were studied in Saudi Arabs from the Eastern Province and Indian patients with AI haplotype (HbF ~20%), African Americans (HbF ~7%), and Saudi Arabs from the Southwestern Province (HbF ~12%). Four SNPs (rs1427407, rs6706648, rs6738440, and rs7606173) and their haplotypes were consistently associated with HbF levels. The distributions of haplotypes differ in the 3 cohorts but not their genetic effects: the haplotype TCAG was associated with the lowest HbF level and the haplotype GTAC was associated with the highest HbF level and differences in HbF levels between carriers of these haplotypes in all cohorts were approximately 6%. CONCLUSIONS Common HbF BCL11A enhancer haplotypes in patients with African origin and AI sickle cell anemia have similar effects on HbF but they do not explain their differences in HbF.
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Affiliation(s)
- P Sebastiani
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States.
| | - J J Farrell
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - A Alsultan
- Sickle Cell Disease Research Center and Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - S Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States
| | - H L Edward
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - H Shappell
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States
| | - H Bae
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, United States
| | - J N Milton
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States
| | - C T Baldwin
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - A M Al-Rubaish
- Department of Internal Medicine, College of Medicine, University of Dammam, Dammam, Saudi Arabia
| | - Z Naserullah
- Department of Pediatrics, Maternity & Child Hospital, Dammam, Saudi Arabia
| | - F Al-Muhanna
- Department of Internal Medicine, College of Medicine, University of Dammam, Dammam, Saudi Arabia
| | - A Alsuliman
- Department of Hematology, King Fahd Hospital, Hafof, Al-Ahsa, Saudi Arabia
| | - P K Patra
- Deptartment of Biochemistry, Pt. J.N.M. Medical College, Raipur, Chattisgarh, India
| | - L A Farrer
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - D Ngo
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - V Vathipadiekal
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - D H K Chui
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - A K Al-Ali
- Prince Mohammed Center for Research & Consultation Studies, University of Dammam, Dammam, Saudi Arabia
| | - M H Steinberg
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
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48
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Griffin PJ, Sebastiani P, Edward H, Baldwin CT, Gladwin M, Gordeuk V, Chui DH, Steinberg MH. The genetics of hemoglobin A2 regulation in sickle cell anemia. Am J Hematol 2014; 89:1019-23. [PMID: 25042611 PMCID: PMC4298130 DOI: 10.1002/ajh.23811] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 07/15/2014] [Accepted: 07/16/2014] [Indexed: 02/02/2023]
Abstract
Hemoglobin A2 , a tetramer of α- and δ-globin chains, comprises less than 3% of total hemoglobin in normal adults. In northern Europeans, single nucleotide polymorphisms (SNPs) in the HBS1L-MYB locus on chromosome 6q and the HBB cluster on chromosome 11p were associated with HbA2 levels. We examined the genetic basis of HbA2 variability in sickle cell anemia using genome-wide association studies. HbA2 levels were associated with SNPs in the HBS1L-MYB interval and SNPs in BCL11A. These effects are mediated by the association of these loci with γ-globin gene expression and fetal hemoglobin (HbF) levels. The association of polymorphisms downstream of the β-globin gene (HBB) cluster on chromosome 11 with HbA2 was not mediated by HbF. In sickle cell anemia, levels of HbA2 appear to be modulated by trans-acting genes that affect HBG expression and perhaps also elements within the β-globin gene cluster. HbA2 is expressed pancellularly and can inhibit HbS polymerization. It remains to be seen if genetic regulators of HbA2 can be exploited for therapeutic purposes.
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Affiliation(s)
- Paula J. Griffin
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Heather Edward
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Clinton T. Baldwin
- Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Mark Gladwin
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Victor Gordeuk
- Department of Medicine and Comprehensive Sickle Cell Center, University of Illinois, Chicago, IL
| | - David H.K. Chui
- Department of Medicine, Boston University School of Medicine, Boston, MA
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49
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Comment on "Molecular analysis and association with clinical and laboratory manifestations in children with sickle cell anemia". Rev Bras Hematol Hemoter 2014; 36:315-8. [PMID: 25305161 PMCID: PMC4318385 DOI: 10.1016/j.bjhh.2014.07.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 07/01/2014] [Indexed: 12/30/2022] Open
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50
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Menzel S, Rooks H, Zelenika D, Mtatiro SN, Gnanakulasekaran A, Drasar E, Cox S, Liu L, Masood M, Silver N, Garner C, Vasavda N, Howard J, Makani J, Adekile A, Pace B, Spector T, Farrall M, Lathrop M, Thein SL. Global genetic architecture of an erythroid quantitative trait locus, HMIP-2. Ann Hum Genet 2014; 78:434-51. [PMID: 25069958 PMCID: PMC4303951 DOI: 10.1111/ahg.12077] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/20/2014] [Indexed: 12/16/2022]
Abstract
HMIP-2 is a human quantitative trait locus affecting peripheral numbers, size and hemoglobin composition of red blood cells, with a marked effect on the persistence of the fetal form of hemoglobin, HbF, in adults. The locus consists of multiple common variants in an enhancer region for MYB (chr 6q23.3), which encodes the hematopoietic transcription factor cMYB. Studying a European population cohort and four African-descended groups of patients with sickle cell anemia, we found that all share a set of two spatially separate HbF-promoting alleles at HMIP-2, termed “A” and “B.” These typically occurred together (“A–B”) on European chromosomes, but existed on separate homologous chromosomes in Africans. Using haplotype signatures for “A” and “B,” we interrogated public population datasets. Haplotypes carrying only “A” or “B” were typical for populations in Sub-Saharan Africa. The “A–B” combination was frequent in European, Asian, and Amerindian populations. Both alleles were infrequent in tropical regions, possibly undergoing negative selection by geographical factors, as has been reported for malaria with other hematological traits. We propose that the ascertainment of worldwide distribution patterns for common, HbF-promoting alleles can aid their further genetic characterization, including the investigation of gene–environment interaction during human migration and adaptation.
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Affiliation(s)
| | | | | | - Siana N Mtatiro
- King's College London, London, UK.,Muhimbili University, Dar es Salaam, Tanzania
| | | | - Emma Drasar
- King's College London, London, UK.,King's College Hospital NHS Foundation Trust, London, UK
| | - Sharon Cox
- Muhimbili University, Dar es Salaam, Tanzania
| | - Li Liu
- University of Texas at Dallas, Richardson, TX, USA
| | | | | | - Chad Garner
- University of California Irvine School of Medicine, Irvine, CA, USA
| | | | - Jo Howard
- King's College London, London, UK.,Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | | | | | - Betty Pace
- Georgia Regents University, Augusta, GA, USA
| | | | - Martin Farrall
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Swee Lay Thein
- King's College London, London, UK.,King's College Hospital NHS Foundation Trust, London, UK
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