Original Research: A case-control genome-wide association study identifies genetic modifiers of fetal hemoglobin in sickle cell disease

Abstract

Sickle cell disease (SCD) is a group of inherited blood disorders that have in common a mutation in the sixth codon of the b-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 0 of d-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 Gg-globin, was analyzed for functional relevance. Studies performed with siRNA-mediated CREB binding protein (CBP) knockdown in primary erythroid cells demonstrated g-globin activation and HbF induction, supporting a repressor role for CBP. This study identifies possible molecular determinants of HbF production.

Genetic modulators of fetal hemoglobin expression and ischemic stroke occurrence in African descendant children with sickle cell anemia

“…A study carried out in a group of 44 SCA patients from India and the Middle East did not replicate the previously described association between KLF1 SNPs and Hb F level [22]. In addition, studies performed on African Americans with SCA failed to detect association between KLF1 SNPs and Hb F levels [23,24]. In this regard, the lack of knowledge about the prevalence of KLF1 variants and its contribution to Hb F levels and SCA modulation is even greater when considering the African context.…”

Genetic Modifiers at the Crossroads of Personalised Medicine for Haemoglobinopathies

“…A large number of genome-wide analyses across diverse ethnic populations identified three quantitative trait loci (QTL) modulating Hb F levels: a promoter variant of the Gγ-globin gene ( Xmn I -HBG2 ), the HBS1L-MYB intergenic region (HMIP) and BCL11A , which together explain up to 50% of the genetic variation in Hb F [14,15]. Over the past few years, large-scale genome-wide association studies (GWAS) of improved power uncovered additional loci with modest effects on Hb F levels [16,17,18].…”

Genetic variants in the G gamma-globin promoter modulate fetal hemoglobin expression in the Colombian population

“…These sites are located on chromosome 2 in BCL11A (Uda et al, 2008), on chromosome 6 in the intergenic region between HBS1L and MYB (Menzel et al, 2007), and on the G gamma-globin promoter in a polymorphism located at position -158 (Gilman and Huisman, 1984). However, these three QTLs do not explain the total variability of HbF expression (Liu et al, 2016), which means that unidentified variants can influence the synthesis of HbF.…”

“…HbF is a factor that modulates the severity of sickle cell anemia, and hence, its regulation has been well studied (Basak and Sankaran, 2016;Dulmovits et al, 2016;Liu et al, 2016). Genetic variants (SNPs) have been associated with HbF expression (Li et al, 2006;Thein and Menzel, 2009).…”