Epigenomic analysis of KLF1 haploinsufficiency in primary human erythroblasts

Steven Heshusius,Laura Grech,Thamar B Van Dijk,Wilfred F J Van Ijcken,Xander T Den Dekker,Alex E Felice,Emile Van Den Akker,Joseph Borg,Benjamin Nota,Nynke Gillemans,Marieke Von Lindern,Rutger W W Brouwer,Sjaak Philipsen

doi:10.1038/s41598-021-04126-6

Abstract

Haploinsufficiency for the erythroid-specific transcription factor KLF1 is associated with hereditary persistence of fetal hemoglobin (HPFH). Increased HbF ameliorates the symptoms of β-hemoglobinopathies and downregulation of KLF1 activity has been proposed as a potential therapeutic strategy. However, the feasibility of this approach has been challenged by the observation that KLF1 haploinsufficient individuals with the same KLF1 variant, within the same family, display a wide range of HbF levels. This phenotypic variability is not readily explained by co-inheritance of known HbF-modulating variants in the HBB, HBS1L-MYB and/or BCL11A loci. We studied cultured erythroid progenitors obtained from Maltese individuals in which KLF1 p.K288X carriers display HbF levels ranging between 1.3 and 12.3% of total Hb. Using a combination of gene expression analysis, chromatin accessibility assays and promoter activity tests we find that variation in expression of the wildtype KLF1 allele may explain a significant part of the variability in HbF levels observed in KLF1 haploinsufficiency. Our results have general bearing on the variable penetrance of haploinsufficiency phenotypes and on conflicting interpretations of pathogenicity of variants in other transcriptional regulators such as EP300, GATA2 and RUNX1.

Highlights

Haploinsufficiency for the erythroid-specific transcription factor Krüppel-like factor 1 (KLF1) is associated with hereditary persistence of fetal hemoglobin (HPFH)
There are, considerable differences in HbF levels between carriers of the KLF1 p.K288X haploinsufficiency allele, prompting us to find an explanation for this variability
We found that a SNP in the promoter of the remaining wildtype KLF1 allele, which reduces KLF1 promoter activity in luciferase assays, correlated with high HbF levels in cultured erythroid progenitors derived from Maltese KLF1 p.K288X carriers

Summary

Introduction

Haploinsufficiency for the erythroid-specific transcription factor KLF1 is associated with hereditary persistence of fetal hemoglobin (HPFH). The feasibility of this approach has been challenged by the observation that KLF1 haploinsufficient individuals with the same KLF1 variant, within the same family, display a wide range of HbF levels This phenotypic variability is not readily explained by co-inheritance of known HbF-modulating variants in the HBB, HBS1L-MYB and/or BCL11A loci. Haploinsufficiency for KLF1 results in hereditary persistence of fetal hemoglobin (HPFH) through a mechanism that involves reduced expression of B CL11A4, 6 and LRF5 Modulation of this regulatory network has been proposed as an approach to increase HbF levels[1,2,3,4,5,6,7,8,9,10], a notion that has been confirmed in animal m odels[11,12,13,14,15]. We suggest that allelic variation affecting wildtype KLF1 expression explains a significant part of the HbF variability observed within this cohort of Maltese HPFH individuals

Methods

Results

Conclusion