Identification of malaria parasite-infected red blood cell surface aptamers by inertial microfluidic SELEX (I-SELEX)

Abstract

Plasmodium falciparum malaria parasites invade and remodel human red blood cells (RBCs) by trafficking parasite-synthesized proteins to the RBC surface. While these proteins mediate interactions with host cells that contribute to disease pathogenesis , the infected RBC surface proteome remains poorly characterized. Here we use a novel strategy (I-SELEX) to discover high affinity aptamers that selectively recognize distinct epitopes uniquely present on parasite-infected RBCs. Based on inertial focusing in spiral microfluidic channels , I-SELEX enables stringent partitioning of cells (efficiency≥10 6) from unbound oligonucleotides at high volume throughput (-2×10 6 cellsmin-1). Using an RBC model displaying a single , non-native antigen and live malaria parasite-infected RBCs as targets , we establish suitability of this strategy for de novo aptamer selections. We demonstrate recovery of a diverse set of aptamers that recognize distinct , surface-displayed epitopes on parasite-infected RBCs with nanomolar affinity , including an aptamer against the protein responsible for placental sequestration , var2CSA. These findings validate I-SELEX as a broadly applicable aptamer discovery platform that enables identification of new reagents for mapping the parasite-infected RBC surface proteome at higher molecular resolution to potentially contribute to malaria diagnostics , therapeutics and vaccine efforts.