Novel Genetic Loci May Be Linked with HbF Expression in Sickle Cell Children

Anu Marahatta, PhD

A new study presented at the American Society of Hematology (ASH) 2020 Conference uncovered 2 novel gene loci that have statistical associations with fetal hemoglobin (HbF), a known ameliorator of sickle cell anemia morbidity and mortality.

A team led by Anu Marahatta, PhD, Division of Hematology, Cincinnati Children’s Hospital Medical Center, analyzed genomic DNA from children with sickle cell anemia in order to identify novel genes and variants involved in HbF expression.

“Previous genomic studies have identified three major gene loci (BCL11A, HBS1L-MYB, and HBG2) that account for ~40% of HbF variation in SCA, but additional genetic modifiers remain to be discovered,” the team wrote.

All patients (n = 1009) assessed had pre-treatment steady-state HbF levels and were enrolled in various prospective research trials from the United States, the Caribbean, and sub-Saharan Africa.

In these trials, whole blood DNA were genotyped and many samples underwent whole exome sequencing (WES) to identify over 2.2 million single nucleotide variants across the genome.

Marahatta and colleagues proceeded in 3 different phases for their genome wide association study (GWAS).

First, they performed 2 independent GWAS discovery steps using distinct African populations. They designated these steps as Discovery I (n= 211) and Discovery II (n = 223).

From both datasets, they selected for 2 independent replications steps only the single nucleotide variants that were significant (P < .05). They then designated these single nucleotide variants as either African-American (n = 157) or African (N = 269).

Finally, any single nucleotide variants that were significant in the first phase (dual discovery) and at least 1 one of the replication cohorts were then verified using an additional Caribbean cohort (N=149) with TaqMan techniques for genotyping specific variants.

Old and New Genomic Loci Are Associated with HbF Expression

From this process, the team was able to search for genomic loci with consistent HbF association across various cohorts.

“From the combined SNP and WES dataset, 8 BCL11A variants passed genome wide significance (P <10^-8) in the discovery analysis, and 1,048 additional variants were identified with nominal HbF association (P<0.001),” the investigators wrote.

However, following phase 2, they found that 173 of the novel variants had sustained association in at least of the replication cohorts (P<.05). 

After selecting 20 variants with the strongest and most consistent associations with HbF from the discovery and replication analyses, the team was able to identify and verify the HbF associations with BCL11A (rs1427407) and HBS1L-MYB (rs4895441).

Among the 18 potentially novel variants, the rs77737207 variant near the RUNX1T1 locus was strongly associated with lower HbF levels. A similar association, which approached statistical significance (P < .08) in the final verification cohort, was also noted for the coding variant rs2279587 in the ITGA1 gene.

“The RUNX1T1 gene is a broad transcriptional corepressor known to impact myeloid differentiation in hematopoiesis, while ITGA1 encodes the integrin alpha subunit of a cell-surface receptor involved in cell-cell adhesion and inflammation,” the team wrote.

They indicated that both genes may be involved in this regulation of HbF expression in the pediatric sickle cell anemia population. Marahatta and colleagues suggested that future studies should investigate them further using cellular and animal models.

The study, “Novel Genetic Loci That Influence Fetal Hemoglobin Expression in Children with Sickle Cell Anemia,” was presented at ASH 2020.