Investigating the role of noncoding rnas in malaria parasites through targeted CAS13-mediated degradation

The National Institute of Allergy and Infectious Diseases awarded Weill Medical College of Cornell University $465,552 on June 11, 2026, under the Allergy and Infectious Diseases Research program (CFDA 93.855) to investigate the role of noncoding RNAs in malaria parasites through targeted CRISPR/Cas13-mediated degradation.

The research addresses how Plasmodium falciparum parasites evade immune destruction through antigenic variation, a process driven by expression switching among VAR genes that encode the surface protein PfEMP1. The investigator proposes to adapt the CRISPR/Cas13 system, which uses guide RNAs to target and degrade single-stranded RNA sequences, to study the hypothesized role of noncoding RNAs in regulating VAR gene expression and determining which genes activate. By degrading specific noncoding RNAs, the study will measure resulting changes in VAR gene expression to test whether noncoding RNAs control the antigenic variation mechanism that enables prolonged infections.

The award is structured as a Project Grant assistance type. Performance occurs at Weill Medical College's location in New York, New York 10065, with a period of performance running from June 11, 2026, through May 31, 2028. The obligated amount is $465,552.

Abstract

One of the most significant sources of morbidity and mortality throughout large regions of the developing world continues to be malaria caused by infection with mosquito-borne parasites of the genus plasmodium. The parasite species responsible for the most severe form of the disease is p. Falciparum. To avoid antibodies produced by their host and thereby maintain lengthy infections, these parasites undergo a process called antigenic variation by which they can extend an infection for over a year. This results from changes in expression of a protein called PFEMP1, the primary antigenic and virulence determinant expressed on the surface of infected red blood cells. A large, multicopy gene family called VAR encodes different forms of PFEMP1, and switching expression between VAR genes enables parasites to evade antibody recognition and destruction by the immune system. The process requires precise and coordinated regulation of transcription of each VAR gene, however how this is accomplished is unknown. IT was recently hypothesized that a family of noncoding rnas (ncrnas) plays a key role in controlling the expression of each VAR gene and in determining the likelihood of activation of any given gene. If correct, this would represent a significant advance in our understanding of how p. Falciparum controls antigenic variation and avoids immune clearance. To test this hypothesis, we propose to adapt the crispr/CAS13 system of targeted RNA degradation for use in p. Falciparum. Similar to the extensively used crispr/CAS9 system, crispr/CAS13 employes guide rnas to target a nuclease to a sequence-specific target, however CAS13 targets single stranded RNA rather than DNA. By applying this system to the study of VAR-related ncrnas, we will degrade specific ncrnas and determine the effect on VAR gene expression. Two classes of ncrnas previously proposed to regulate VAR gene expression will be targeted, one called RUF6 and a second encoded by the second exon of all VAR genes. This will enable US to alter ncrna expression while leaving the underlying genomic DNA untouched, thereby allowing the unambiguous attribution of any resulting phenotypes to the ncrnas. Aim 1 will optimize the CAS13 system for p. Falciparum by testing different variants of the CAS13 endonuclease for their ability to degrade mrnas encoding fluorescent reporter proteins. We will determine both the efficiency and sequence specificity of the system. Aim 2 will apply the system to VAR-associated ncrnas and quantitatively measure changes in VAR gene expression and transcriptional switching. If successful, the adaptation of the CAS13 system to p. Falciparum will provide the malaria research community with a powerful new tool for manipulating gene expression. In addition, we will gain valuable new insights into how malaria parasites regulate VAR gene expression, antigenic variation and immune evasion.