An erythroid-specific ATP2B4 enhancer mediates red blood cell hydration and malaria susceptibility

J Clin Invest. 2017 Aug 1;127(8):3065-3074. doi: 10.1172/JCI94378. Epub 2017 Jul 17.


The lack of mechanistic explanations for many genotype-phenotype associations identified by GWAS precludes thorough assessment of their impact on human health. Here, we conducted an expression quantitative trait locus (eQTL) mapping analysis in erythroblasts and found erythroid-specific eQTLs for ATP2B4, the main calcium ATPase of red blood cells (rbc). The same SNPs were previously associated with mean corpuscular hemoglobin concentration (MCHC) and susceptibility to severe malaria infection. We showed that Atp2b4-/- mice demonstrate increased MCHC, confirming ATP2B4 as the causal gene at this GWAS locus. Using CRISPR-Cas9, we fine mapped the genetic signal to an erythroid-specific enhancer of ATP2B4. Erythroid cells with a deletion of the ATP2B4 enhancer had abnormally high intracellular calcium levels. These results illustrate the power of combined transcriptomic, epigenomic, and genome-editing approaches in characterizing noncoding regulatory elements in phenotype-relevant cells. Our study supports ATP2B4 as a potential target for modulating rbc hydration in erythroid disorders and malaria infection.

MeSH terms

  • Animals
  • CRISPR-Cas Systems
  • Calcium / metabolism
  • Calcium-Transporting ATPases / genetics*
  • Calcium-Transporting ATPases / metabolism
  • Chromosome Mapping
  • Enhancer Elements, Genetic
  • Epigenomics
  • Erythroblasts / metabolism
  • Erythrocytes / cytology*
  • Gene Expression Profiling
  • Gene Regulatory Networks
  • Genetic Predisposition to Disease*
  • Genome-Wide Association Study
  • HEK293 Cells
  • Humans
  • Malaria / genetics*
  • Malaria / metabolism
  • Male
  • Mice
  • Mice, Transgenic
  • Phenotype
  • Plasma Membrane Calcium-Transporting ATPases / genetics*
  • Plasma Membrane Calcium-Transporting ATPases / metabolism
  • Polymorphism, Single Nucleotide
  • Quantitative Trait Loci


  • PMCA4 protein, mouse
  • ATP2B4 protein, human
  • Plasma Membrane Calcium-Transporting ATPases
  • Calcium-Transporting ATPases
  • Calcium