Fetal hemoglobin in sickle cell anemia: Molecular characterization of the unusually high fetal hemoglobin phenotype in African Americans (original) (raw)
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Blood cells, molecules & diseases, 2014
Increased levels of fetal hemoglobin (HbF, α2γ2) may reduce sickle cell anemia severity due to its ability to inhibit HbS polymerization and also reduce the mean corpuscular HbS concentration. We have investigated the influence of three known major loci on the HbF trait (HBG2, rs748214; BCL11A, rs4671393; and HBS1L-MYB, rs28384513, rs489544 and rs9399137) and HbF levels in SCA patients from the State of Pará, Northern Brazil. Our results showed that high levels of HbF were primarily influenced by alleles of BCL11A (rs4671393) and HMIP (rs4895441) loci, and to a lesser extent by rs748214 Gγ-globin (HBG2) gene promoter. The SNPs rs4671393 and rs4895441 explained 10% and 9.2%, respectively, of the variation in HbF levels, while 4.1% of trait variation was explained by rs748214. The results can be considered as in accordance with the pattern of ancestry displayed by the SCA patients: 39.6% European, 29.6% African and 30.8% Native American, and reinforce the suggestion that studies of as...
Fetal hemoglobin in sickle cell anemia: Genetic studies of the Arab-Indian haplotype
Blood Cells, Molecules, and Diseases, 2013
Most sickle cell anemia (SCA) patients indigenous to the Eastern Province of Saudi Arabia have their HbS gene on the Arab-Indian (AI) HBB gene cluster haplotype. Their fetal hemoglobin (HbF) levels are near 20% and they have milder disease compared with SCA where the HbS gene is on African origin HBB haplotypes . The AI haplotype is characterized by an Xmn1 restriction site at position 2158 5 0 to HBG2 (rs7482144), a Hinc2 site 5 0 to HBE (rs3834466) and other polymorphisms . The causal elements that modify HbF might be in linkage disequilibrium with the b S globin gene in this Saudi population. We first performed homozygosity mapping using genome-wide single nucleotide polymorphisms (SNPs) in AI HbS homozygotes and identified a single large autozygous region including the HBB cluster and surrounding genes. By next generation sequencing, we examined this region in these same individuals and identified several variants that included a SNP in the HBD promoter region at position 268 bp 5 0 to HBD (CCAAC > TCAAC). We found this SNP only when the HbS gene was on an AI haplotype and not in SCA with other haplotypes. This SNP was functional in reporter assays in K562 cells and is an AI haplotype-specific marker. summarizes the patient characteristics. Using genome-wide SNP data from a limited number of cases, a region of autozygosity was found only in AI HbS homozygotes on chromosome 11 (coordinates 5,196,450-5,323,071). The region contains HBD, HBG1, HBG2, HBE1, and the Xmn1 5 0 HBG2 restriction site (rs7482144). By targeted deep sequencing of 400 kb of chromosome 11 (coordinates 5,143,424-5,543,424; average coverage 42x) in 4 AI patients 1,195 variants were found. A homozygous C-T variant 268 bp 5 0 HBD with high genotyping and mapping quality that was not in dbSNP build 135 or 1,000 Genomes, was present. Resequencing of 15.9 kb of chr11 (coordinates 5,253,531-5,269,435) by Sanger sequencing detected three new SNPs of which one was the 268 C > T SNP. We focused on this SNP because of its location within the Corfu deletion region and its location in the HBD promoter.
2018
Sickle cell disease (SCD) is a group of inherited hemoglobinopathies produced by several mutations in the 6 th codon of the -globin (HBB) gene. However, patients with the same genetic mutation display a wide range of clinical symptoms and complications. Fetal hemoglobin (HbF) expression has been demonstrated as an important genetic modifier of SCD leading to improved long-term survival. Therefore to discover genetic factors associated with HbF expression, we performed a genome-wide association study (GWAS) using a case-control experimental design for 244 African American patients with SCD. The case group consisted of subjects with HbF >8.6% (133 samples) and control group subjects with HbF <3.2% (111 samples). Our GWAS replicated several SNPs previously identified in an erythroid-specific enhancer region located in the second intron of the BCL11A gene, highly associated with HbF expression. Moreover, we identified SNPs in SPARC, GJC1, EFTUD2 and JAZF1 as potential candidate genes associated with HbF level in sickle cell patients. To gain insights into mechanisms of globin gene regulation in the HBB locus, linkage disequilibrium (LD) and haplotype analysis was 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 surrounding the -globin gene region. A search of known HBB locus regulatory elements demonstrated SNPs 5' of -globin located in an HbF-silencing region. In particular SNP rs4910736 created a potential binding site for a known transcription repressor GFi1 as a potential gene target for further investigation. Another HbF-associated SNP rs7482144 in the cAMP response element upstream of G-globin was analyzed for functional relevance. Studies performed with siRNA-mediated knockdown of CREB binding protein (CBP) in human 3 primary erythroid cells demonstrated -globin gene activation and HbF induction supporting a repressor role for CBP. The implications of our findings are discussed.
Genetics of fetal hemoglobin in tribal Indian patients with sickle cell anemia
Translational Research, 2015
India tops the list of countries with sickle cell disease (SCD) with an estimated 44,000 live births in 2010 and a prevalence of 10%-33%. In the present study, the first from India, we have investigated the effect of genetic variants in the BCL11A, the HMIP (HBS1L-MYB intergenic polymorphism) locus, in addition to the HBB locus, which are known to be associated with fetal hemoglobin (HbF) levels, a major modulator of the disease phenotype. The present study was conducted on 240 individuals with SCD and 60 with sickle cell trait. Genotyping was performed for the BCL11A rs11886868 and rs34211119; HMIP rs9399137, rs189600565, rs7776196, rs34778774, and rs53293029; HBG2 Xmn1 polymorphism rs7482144; and 268C. T HBD promoter polymorphism. All the 3 quantitative trait loci were associated with HbF levels in Indian patients with SCD. The highest difference was seen in the Xmn1 singlenucleotide polymorphism, which accounted for 11% of the trait variance, the BCL11A rs11886868 for 3.65%, whereas the HMIP rs9399137 for 3.8%. The present study indicates the BCL11A, HMIP, and b-globin region to be associated with increased HbF levels in Indian patient. Further interrogation of these genotypes with respect to pain crisis is warranted in this population, which may help in prognostication, as also a genome-wide association study, which may help uncover new loci controlling HbF levels. (Translational Research 2015;-:1-8) Abbreviations: AI haplotype ¼ Arab-Indian haplotype; ANOVA ¼ Analysis of variance; ARMS-PCR ¼ Amplification refractory mutation system-polymerase chain reaction; BCL11A ¼ B-cell lymphoma/leukemia 11A; CSSCD ¼ Cooperative study of sickle cell disease; DNA ¼ Deoxyribonucleic acid; EDTA ¼ Ethylenediaminetetraacetic acid; GWAS ¼ Genome wide association studies; HbA2 ¼ a-globin gene; HBB ¼ b-globin gene; HBD ¼ d-globin gene; HbF ¼ Fetal hemoglobin; HbG2 ¼ g-globin gene; HBS ¼ Sickle hemoglobin; HBS1L ¼ HBS1-like translational GTPase; HMIP ¼ HBS1L-MYB intergenic region; HPLC ¼ High Performance Liquid Chromatography; HWE ¼ Hardy-Weinberg Equilibrium; LD ¼ Linkage disequilibrium; MYB ¼ oncogene; OBC ¼ Other backward class; PCR ¼ Polymerase chain reaction; QTL ¼ Quantitative trait loci; SC ¼ Scheduled caste; SCD ¼ Sickle cell disease; SNP ¼ Single nucleotide polymorphism; SS ¼ Sickle cell disease patients; ST ¼ Scheduled tribe
elsvier, 2015
India along with Nigeria and DRC contribute to 57% of the world sickle cell anemia population. The annual number of newborns in India with SCA was estimated at 44,000 in 2010. Even with this high prevalence there is minimal information about genetic factors that influence the disease course in Indian patients. The current study was conducted on 240 patients with SCD and 60 with sickle cell trait, to determine the association of genetic variants at the BCL11A (rs1427407) and HBS1-MYB (rs6934903) loci with fetal hemoglobin levels (HbF). Both these loci have been implicated with influencing HbF levels, a powerful modulator of the clinical and hematologic features of SCD. Our results indicate the BCL11A rs1427407 G N T variant to be significantly associated with HbF levels {19.12 ± 6.61 (GG), 20.27 ± 6.92 (GT) and 24.83 ± 2.92 (TT) respectively} contributing to~23% of the trait variance. Interestingly no association of the HBS1L-MYB rs6934903 with the HbF levels was seen. The present study indicates the BCL11A (rs1427407) but not HMIP (rs6934903) to be associated with elevated HbF levels in Indian patient. Further interrogation of additional variants at both the loci; as also a GWAS which may help uncover new loci controlling HbF levels.
BMC Medical Genetics
Background: Sickle cell disease (SCD) is a blood disorder caused by a point mutation on the beta globin gene resulting in the synthesis of abnormal hemoglobin. Fetal hemoglobin (HbF) reduces disease severity, but the levels vary from one individual to another. Most research has focused on common genetic variants which differ across populations and hence do not fully account for HbF variation. Methods: We investigated rare and common genetic variants that influence HbF levels in 14 SCD patients to elucidate variants and pathways in SCD patients with extreme HbF levels (≥7.7% for high HbF) and (≤2.5% for low HbF) in Tanzania. We performed targeted next generation sequencing (Illumina_Miseq) covering exonic and other significant fetal hemoglobin-associated loci, including BCL11A, MYB, HOXA9, HBB, HBG1, HBG2, CHD4, KLF1, MBD3, ZBTB7A and PGLYRP1. Results: Results revealed a range of genetic variants, including bi-allelic and multi-allelic SNPs, frameshift insertions and deletions, some of which have functional importance. Notably, there were significantly more deletions in individuals with high HbF levels (11% vs 0.9%). We identified frameshift deletions in individuals with high HbF levels and frameshift insertions in individuals with low HbF. CHD4 and MBD3 genes, interacting in the same sub-network, were identified to have a significant number of pathogenic or non-synonymous mutations in individuals with low HbF levels, suggesting an important role of epigenetic pathways in the regulation of HbF synthesis. Conclusions: This study provides new insights in selecting essential variants and identifying potential biological pathways associated with extreme HbF levels in SCD interrogating multiple genomic variants associated with HbF in SCD.
The genetic dissection of fetal haemoglobin persistence in sickle cell disease in Nigeria
BackgroundThe clinical severity of sickle cell disease (SCD) is strongly influenced by the level of fetal haemoglobin (HbF) persistent in each patient. Three major HbF loci (BCL11A,HBS1L-MYB, andXmn1-HBG2) have been reported, but a considerable hidden heritability remains.AimBuilding on the power of a large and genetically diverse patient pool present in Nigeria, we conducted a genome-wide association study for HbF levels in patients from three regions of the country with a diverse ethnic make-up.MethodsWe analysed genome-wide trait association in 1006 Nigerian patients with SCD (HbSS/HbSβ0), followed by a replication and meta-analysis exercise in four independent SCD cohorts (3,582 patients). To dissect association signals at the major loci, we performed stepwise conditional analysis, haplotype association analysis and included public functional annotation data (fGCTA).ResultsAssociation signals were detected forBCL11A(lead SNP rs6706648, β=- 0.39,P=4.96 x 10-34) andHBS1L-MYB(lead ...
Indian Journal of Hematology and Blood Transfusion, 2015
Fetal hemoglobin (HbF) plays a dominant role in ameliorating morbidity and mortality of hemoglobinopathies. We evaluated the effects of polymorphic markers within the b-globin gene cluster to identify the genetic mechanics that influence HbF on Tunisian sickling patients (n = 242). Haplotype analysis was carried out by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and the framework polymorphism was established by PCR-sequencing, four independent regions of interest were identified: the 5 0 region of b-LCR-HS2 site, the intervening sequence II (IVSII) region of two fetal (Gc and Ac) genes and the 5 0 region of b-globin gene. The correlation of these various Haplotypes and SNPs with HbF expression and clinical data was studied. Our data showed that among the various polymorphic markers analyzed, only the sequence (AT)xN12(AT)y in LCR HS2 region was significantly associated (p \ 0.05) with increased HbF levels, suggesting that the b-globin gene cluster exerts a significant effect on HbF in sickle cell patients. This study can improve understanding of the physiopathology of the disease and aid to increase our ability to predict clinical severity.
Genetic modifiers of HbF and response to hydroxyurea in sickle cell disease
Pediatric Blood & Cancer, 2010
Fetal hemoglobin (HbF) levels are generally inversely proportional to severity of sickle cell disease (SCD) for given sickle phenotypes. Molecular regulation of HbF occurs through complex interactions cis and trans to the beta globin gene locus. Novel insights made through populationbased genetic epidemiologic studies of non-anemic populations were replicated in SCD groups, despite large differences in HbF levels. Identification of the lymphoid transcription factor BCL11A as a key suppressor of HbF expression validates approaches using population genetics to study HbF expression. We review these methods and findings, and speculate on applying pharmaco-genetics to optimize hydroxyurea therapy aimed at increasing HbF.