Novel LRF/ZBTB7A variants and known HbF-modulating SNPs in transfusion-dependent β-thalassemia

β-Thalassemia is a hereditary blood disorder with a highly variable clinical presentation that is partly influenced by genetic modifiers that regulate fetal hemoglobin levels. Elevated HbF can ameliorate the clinical symptoms of β-thalassemia, making the identification of HbF-modifying loci crucial for understanding disease variability and developing potential therapeutic strategies.

In this study, we evaluated the distribution and effect of known HbF-associated single nucleotide polymorphisms within the BCL11A, HMIP, and XmnI-HBG2 loci in β-thalassemia patients. Our investigation was initiated by a hypothesis based on genomic data from the K562 cell line, which indicated the presence of a specific LRF/ZBTB7A variant. In addition, we explored the role of LRF/ZBTB7A, a transcription factor implicated in globin gene regulation, through Sanger sequencing and in silico analyses. A hypothetical Genetic Modifier Score was devised to quantify the cumulative effect of the five major HbF-associated QTLs.

While we confirmed the previously reported associations of the common SNPs with HbF levels, we also identified novel rare variants in LRF/ZBTB7A (p.Pro241Leu, p.Asp344Asp, p.Glu277del) that may influence HbF expression. XmnI-HBG2 accounted for a small yet significant proportion (7%) of HbF variability. A significant positive correlation was found between the Genetic Modifier Score and HbF levels, yet the model explained only ~ 14% of the variance, highlighting a substantial role for other modifiers such as the novel LRF/ZBTB7A variants identified here.

These results suggest LRF/ZBTB7A is a novel modifier of HbF. The discovery of the variants, against a backdrop of modest QTL effects, underscores its potential and warrants further functional investigation.