Genetic variant in the BCL11A (rs1427407), but not HBS1-MYB (rs6934903) loci associate with fetal hemoglobin levels in Indian sickle cell disease patients

Abstract

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 > 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.

Introduction

Sickle cell disease [SCD] is a hemoglobinopathy that affects millions of people worldwide [1], [2]. India is estimated to be home to over 50% of the world's patients with SCD [3]. It is a debilitating monogenic disorder caused by a point mutation within the gene encoding the β-subunit of adult hemoglobin (HbA, α₂β₂). The single base pair change causes the codon to change from GAG to GTG; this gives rise to a corresponding amino acid change at the sixth position of the β-globin chain, resulting in hemoglobin that is designated as HbS or sickle hemoglobin [4].

The phenotypic manifestations of sickle cell disease show great variability. This heterogeneity is evidenced in the form of several clinical outcomes, such as stroke, vaso-occlusive episodes, acute chest syndrome, avascular necrosis, leg ulcers, priapism and retinopathy [5], [6]. These outcomes cannot be explained by the single mutation in the beta-globin gene alone but may be attributed to genetic modifiers and environmental effects [7], [8], [9].

Several studies have revealed fetal hemoglobin as a major genetic modulator in sickle cell disease [10], [11]. Fetal hemoglobin (HbF) has been shown to have an ameliorative effect as it prevents the polymerization of deoxy sickle hemoglobin [12], [13], [14].

The HbF levels are controlled by a number of genetic determinants, resulting in variable HbF concentrations, which in turn may be responsible for the phenotypic variability seen in SCD [15], [16], [17], [18]. Haplotypes of the beta-globin gene cluster are among the most extensively studied in this respect [19], [20], [21], [22], [23], [24].

Recently, genome wide association studies (GWAS) have revealed three major quantitative trait loci (QTLs) (Xmn-HBG2, HBS1L-MYB intergenic region on chromosome 6q23, and BCL11A on chromosome 2p16) that account for 20–50% of the common variation in HbF levels in patients with Sickle Cell anemia (SCA), and β-thalassemia, and in healthy adults [25], [26].

SNPs have been identified within the 14 kb intron 2 of BCL11A that correlate most strongly with the HbF expression [25]. The BCL11A genotype that is associated with high HbF is associated with reduced BCL11A expression.

Several genetic variants associated with the HBS1L-MYB intergenic (HMIP) region have also been identified that affect HbF levels. Genetic variants that show the strongest effects are concentrated in 24 kb of HMIP block 2, located 33 kb upstream of HBS1L and 65 kb upstream of MYB [27], [28].

In India, the prevalence of the sickle cell gene is high both in tribal, and non-tribal populations [2], [29], [30], [31]. Though SCD in India has a milder phenotype, which is attributable to the Arab–Indian haplotype in the beta-globin gene cluster, nevertheless it is prudent to determine the effect of other variants on the backdrop of this genetic information.

In the current study which is one of the first report from India we have attempted to determine the frequency of specific variants in the HBS1L-MYB intergenic loci (rs6934903) and BCL11a (rs1427407) in a cohort with sickle cell disease and sickle cell trait from Central India and to correlate the association of this SNP with HbF levels. This may aid in the determination and prediction of the severity of the complications in sickle cell anemia, which can in turn have important implications for genetic counseling and clinical management.