Walzer KA, Fradin H, Emerson LY, Corcoran DL, Chi JT. Latent transcriptional variations of individual Plasmodium falciparum uncovered by single-cell RNA-seq and fluorescence imaging.
PLoS Genet 2019;
15:e1008506. [PMID:
31856180 PMCID:
PMC6952112 DOI:
10.1371/journal.pgen.1008506]
[Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/09/2020] [Accepted: 11/03/2019] [Indexed: 02/07/2023] Open
Abstract
Malaria parasites follow a complex life cycle that consists of multiple stages that span from the human host to the mosquito vector. Among the species causing malaria, Plasmodium falciparum is the most lethal, with clinical symptoms manifesting during the intraerythrocytic developmental cycle (IDC). During the IDC, P. falciparum progresses through a synchronous and continuous cascade of transcriptional programming previously established using population analyses. While individual parasites are known to exhibit transcriptional variations to evade the host immune system or commit to a sexual fate, such rare expression heterogeneity is largely undetectable on a population level. Therefore, we combined single-cell RNA-sequencing (scRNA-seq) on a microfluidic platform and fluorescence imaging to delineate the transcriptional variations among individual parasites during late asexual and sexual stages. The comparison between asexual and sexual parasites uncovered a set of previously undefined sex-specific genes. Asexual parasites were segregated into three distinct clusters based on the differential expression of genes encoding SERAs, rhoptry proteins, and EXP2 plus transporters. Multiple pseudotime analyses revealed that these stage-specific transitions are distinct. RNA fluorescent in situ hybridization of cluster-specific genes validated distinct stage-specific expression and transitions during the IDC and defined the highly variable transcriptional pattern of EXP2. Additionally, these analyses indicated huge variations in the stage-specific transcript levels among parasites. Overall, scRNA-seq and RNA-FISH of P. falciparum revealed distinct stage transitions and unexpected degrees of heterogeneity with potential impact on transcriptional regulation during the IDC and adaptive responses to the host.
Malaria poses a significant global health problem and is responsible for nearly 445,000 deaths. It is caused by a single-celled parasite that infects a human host and propagates asexually through red blood cells. The most deadly malaria parasite, P. falciparum, follows a tightly synchronous life cycle characterized by a continuous cascade of gene expression programming. Beyond these changes in the population, individual P. falciparum parasites are known to exhibit unique and rare expression, particularly to evade the host immune system and also to commit to a sexual fate. But such rare expression is often masked in bulk-cell studies. To understand expression variations among individual parasites, we combined single-cell RNA sequencing and fluorescence imaging to study the gene expression among individual asexual and sexual parasites. We discovered previously undefined sex-specific genes as well as three distinct clusters of late stage asexual parasites largely defined by stage-specific genes. We also showed that EXP2, a marker gene of one cluster, was expressed at multiple times throughout the life cycle. Furthermore, stage-specific gene expression was greatly variable among individual parasites. Our results have great implications for individual parasite survival and adaptation, particularly in response to environmental stresses like the host immune system.
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