Whole Exome Sequencing Identifies Novel Genes for Fetal Hemoglobin Response to Hydroxyurea in Children with Sickle Cell Anemia

Abstract

Hydroxyurea has proven efficacy in children and adults with sickle cell anemia (SCA), but with considerable inter-individual variability in the amount of fetal hemoglobin (HbF) produced. Sibling and twin studies indicate that some of that drug response variation is heritable. To test the hypothesis that genetic modifiers influence pharmacological induction of HbF, we investigated phenotype-genotype associations using whole exome sequencing of children with SCA treated prospectively with hydroxyurea to maximum tolerated dose (MTD). We analyzed 171 unrelated patients enrolled in two prospective clinical trials, all treated with dose escalation to MTD. We examined two MTD drug response phenotypes: HbF (final %HbF minus baseline %HbF), and final %HbF. Analyzing individual genetic variants, we identified multiple low frequency and common variants associated with HbF induction by hydroxyurea. A validation cohort of 130 pediatric sickle cell patients treated to MTD with hydroxyurea was genotyped for 13 non-synonymous variants with the strongest association with HbF response to hydroxyurea in the discovery cohort. A coding variant in Spalt-like transcription factor, or SALL2, was associated with higher final HbF in this second independent replication sample and SALL2 represents an outstanding novel candidate gene for further investigation. These findings may help focus future functional studies and provide new insights into the pharmacological HbF upregulation by hydroxyurea in patients with SCA.

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

“…This effect was most evident in patients without the BCL11A SNPs but it seemed that BCL11A had a limited role in hydroxyurea induction of HbF. In these same patients, there was no association of the BCL11A SNPs with MTD HbF or delta HbF [16]. In contrast, we have found that, in our Brazilian cohort, patients with the BCL11A SNPs have an improved response to hydroxyurea.…”

Study on Hydroxyurea Response in Hemoglobinopathies Patients Using Genetic Markers and Liquid Erythroid Cultures

“…Statistically significant associations of HbF response to HU with multiple SNPs in several genes (ARG2, FLT1, HAO2, NOS1, KLF10, SALL2) have been reported. 29,30 To date the use of genetic determinants to predict the effect of HU is still not possible. For this reason human liquid erythroid culture system, an efficacious but complex and time consuming approach, at the moment remains the only method able to predict patients’ response to HU.…”

Minireview: Prognostic factors and the response to hydroxurea treatment in sickle cell disease

“…48 In other recent studies, the Bantu haplotype conferred a greater response to HU treatment, 49 a homozygous mutant state of a KLF10 SNP was associated with a poor response to HU, 50 and a coding variant in SALL2 (Spalt-like transcription factor), identified through whole exome sequencing, was associated with a higher final HbF. 51 In an ancillary analysis from the BABY HUG trial, alpha thalassemia, beta-globin haplotype, and polymorphisms known or presumed to affect HbF levels (BCL11A, HBS1L-MYB, Xmn1) were studied in 190 randomized subjects. 52 At study entry, infants with alpha thalassemia trait had lower MCV, bilirubin and reticulocyte counts; beta-globin haplotypes containing the SEN (Senegal) polymorphism were associated with higher Hb and HbF levels; and BCL11A and Xmn1 polymorphisms affected baseline HbF.…”