A single-cell sequencing approach to understand P. vivax gene regulation at the epigenetic level

Malaria parasites employ an epigenetic bet-hedging strategy for rapid adaptation to changing host environments, based on transcriptional heterogeneity as grounds for natural selection. Plasmodium vivax, responsible for one third of the malaria cases outside of Africa, cannot be continuously cultured, and this has seriously obstructed progress in epigenetic research. We plan to submit an FWO proposal where we leverage recent advancements in single-cell techniques to for the first time investigate P. vivax blood stage regulation at the epigenetic level, and study its adaptive role. The cornerstone of this proposal will be the use of single-cell epigenome sequencing (heterochromatin profile) of P. vivax patient isolates, using the novel single-cell (sc) CUT&Tag technique. This would allow us to link epigenetic profiles to transcriptional heterogeneity, identify which genes are regulated at the epigenetic level, monitor epigenetic changes as adaptive response to different environmental conditions, and elucidate a P. vivax survival mechanism from the molecular to the phenotypic level. In this jPPP, we will work together with the Cortés-lab to apply (sc)CUT&Tag sequencing to Plasmodium for the first time. The CUT&Tag technique will be optimised using P. knowlesi, which is phylogenetically closely related to P. vivax but can be long-term cultured in the lab. Next, we will determine the input requirements for P. vivax, and ultimately provide a proof of principle by carrying out scCUT&Tag on two cryopreserved P. vivax samples.