Hereditary persistence of fetal hemoglobin in two patients with KLF1 haploinsufficiency due to 19p13.2–p13.12/13 deletion

Abstract

In Patient 2 no variants or deletions were found that could cause a-thalassemia or bthalassemia, and no large deletions associated with HPFH were present. In the HBG1 promoter a heterozygous 4 bp deletion HBG1:c.253-225_-53-222delAGCA (e.g. 2225_-222delAGCA) was present. This deletion is associated with relatively low expression of the HBG1 gene [6]. Finally, we genotyped SNPs in the HBS1L-MYB and BCL11A loci that are associated with variations in HbF levels in adults [1]. We observed that the SNP genotypes at the HBS1L-MYB and BCL11A loci were not particularly favorable for high HbF expression. In summary, we report hematological parameters of two unrelated patients with microdeletion of 19p13.2-p13.12/13. The commonly deleted region between the patients encompasses 728 kb and contains 33 protein-coding genes including KLF1.In the two patients reported here, the remaining KLF1 allele encodes a wildtype protein.The HbF levels of 7.1% and 16.8% can therefore not be attributed to the presence of a KLF1 variant on the remaining allele. In a Maltese pedigree in which HPFH was caused by KLF1 haploinsufficiency [2], HbF levels varied from 3.3% to 19.5% between HPFH individuals. Thus, the HbF levels of our two patients fall within this range. There is currently no explanation for this high variability in HbF levels. The two patients reported here are the first in which the entire KLF1 gene is deleted. We note that the common deleted region contains four genes (DNASE2, KLF1, LYL1, PRDX2) with known roles in erythropoiesis, and one (NFIX) that was recently linked to fetal hemoglobin levels in a population study (Supporting Information Fig. 1). It remains to be established whether haploinsufficiency for any of these genes contributes to the erythroid phenotypes of the patients. In addition, HBG1/2 promoter variants may contribute to HbF levels in the genes deleted in both patients, DNASE2, LYL1, PRDX2 and NFIX. With the advent of CRISPR/Cas9 genome editing technology for the study of human erythropoiesis, systematic analysis of the roles of these genes in human erythroid cells will be the topic of future research in our laboratories.

Investigating the Molecular Pathogenesis of Inherited Childhood Anaemia

“…Many human mutations have since been shown to cause this phenotype (Crowley et al, 2010, Garcia-Sanchez et al, 2016, Kawai et al, 2017, Ogasawara et al, 2012, Singleton et al, 2008, Wang et al, 2013, Yang et al, 2012. Haploinsufficiency of KLF1 can also lead to Hereditary Persistence of Foetal Haemoglobin (HPFH), which reflects a failure in complete globin gene switching (Borg et al, 2010, Natiq et al, 2017, Satta et al, 2011. This is consistent with previous mouse studies showing KLF1…”

Erythroid lineage chromatin accessibility maps facilitate identification and validation of NFIX as a fetal hemoglobin repressor

“…The SNP resides within a 300 kb region that includes several genes involved in erythropoiesis and erythrocyte traits, most notably KLF1, which is known to repress HbF 27 , 28 . KLF1 haploinsufficiency has also been suggested to contribute to hereditary persistence of fetal hemoglobin (HPFH) in two patients with microdeletion of chromosome 19p13.2–p13.12/13, a region that also includes NFIX 29 . Despite these data suggesting that NFIX may be involved in beta-like globin gene regulation, its direct validation as an HbF repressor had not been reported prior to our study 30 .…”

Identification of a genomic DNA sequence that quantitatively modulates KLF1 transcription factor expression in differentiating human hematopoietic cells

“…There are also benign but significant changes in mean cell volume (MCV) and mean corpuscular hemoglobin (MCH) (both lower), or in zinc protoporphyrin (ZnPP) and reticulocyte count (RTC) (higher). These changes enable identification of KLF1 mutation carriers 3 , 4 , 30 , and it is of considerable interest that allelic distribution of KLF1 mutations are dramatically higher in regions of endemic β-thalassemia 31 , where the dysregulation of γ-globin expression is of clear clinical benefit. A case report of β o /β o thalassemic twins highlights the remarkable clinical difference in anemia and transfusion dependence that follows from loss of one KLF1 allele 32 .…”