Single-cell views of the Plasmodium life cycle

Single-cell transcriptomics has been used to profile the life cycle of multiple Plasmodium species, illuminating developmental trajectories and revealing rare or transient cell states, including the dormant hypnozoite typical of relapsing malaria infections. Host–parasite interactions are essential for progression through the life cycle and could provide new opportunities for antimalarial interventions, but very few single-cell studies have reported on the host side. Parallel single-cell RNA sequencing profiling of host and parasite transcriptional responses has started to shine a light on the interdependency between host and parasite states. Single-cell multi-omics technologies will be essential to map out heterogenous host-parasite interactions across the life cycle and establish how parasite cell fate decisions and overall fitness may be modulated by the host in the context of infection and vaccination. Malaria-causing Plasmodium parasites undergo multiple phenotypic transitions as they cycle between diverse niches in the mammalian and mosquito hosts. Recent applications of single-cell technologies to Plasmodium have enabled the systematic investigation of the distinct stages across the life cycle. Most single-cell data have focused on the parasite exclusively, but a few studies have started to profile both parasite and host cells to shed light on the heterogeneity of cell states that underpin host–parasite interactions. In this opinion article, we highlight how atlasing initiatives are starting to be used to infer functional interactions between parasite and host and could be a powerful tool in drug discovery and vaccine development. Malaria-causing Plasmodium parasites undergo multiple phenotypic transitions as they cycle between diverse niches in the mammalian and mosquito hosts. Recent applications of single-cell technologies to Plasmodium have enabled the systematic investigation of the distinct stages across the life cycle. Most single-cell data have focused on the parasite exclusively, but a few studies have started to profile both parasite and host cells to shed light on the heterogeneity of cell states that underpin host–parasite interactions. In this opinion article, we highlight how atlasing initiatives are starting to be used to infer functional interactions between parasite and host and could be a powerful tool in drug discovery and vaccine development. a commercial droplet-based protocol for scRNA-seq. It enables the transcriptomic profiling of thousands of single cells in a single run. a plate-based scRNA-seq method that enables early multiplexing for cost effectiveness and uses in vitro transcription instead of PCR for cDNA amplification, which reduces noise. Unlike SmartSeq2, it incorporates unique molecular identifiers (UMIs) to label individual mRNA molecules, which improves transcript quantification. cellular indexing of transcriptomes and epitopes by sequencing is a multimodal phenotyping method enabling the integration of protein and transcriptome measurements in single cells. So far, only surface proteins can be quantified using this method. a droplet-based method for high-throughput scRNA-seq. More cost-effective than 10x, but less sensitive. a low-throughput method for spatial transcriptional profiling whereby single cells from a region of interest in a tissue section are first isolated by laser capture microdissection and subsequently profiled by SmartSeq2. a plate-based protocol for massively parallel scRNA-seq that combines FACS sorting and robotics, enabling sequencing of several thousands of cells. Plate, cellular, and molecular barcodes facilitate multiplexing. Relies on in vitro transcription for linear cDNA amplification. paired-cell RNA sequencing profiles gene expression of pairs of adjacent cells. It has been applied to resolve the spatial localization of liver endothelial cells based on the known spatial transcriptome of hepatocytes in the mouse liver. variable that measures the ordering of cells along a trajectory based on single-cell gene expression profiles. single cell RNA barcoding and sequencing is a plate-based scRNA-seq protocol. Like CEL-Seq2 and MARS-seq, it uses UMIs. low-cost scRNA-seq platform in which single cells and barcoded mRNA capture beads are sealed in an array of nano-wells using a semipermeable membrane, enabling efficient cell lysis and transcript capture from thousands of cells. a collection of annotated single-cell transcriptomes from different anatomical regions and/or developmental stages of an organism. refers to a variety of methods for transcriptome-wide sequencing of single-cells. a plate-based protocol that allows the generation of full-length cDNA from single-cells, enabling high sensitivity and accuracy. The full-length coverage enables the identification of sequence variants and splice forms. Cell separation is typically achieved by FACS sorting, which limits the number of cells analyzed to 102–103. Each cell is processed individually (without early barcoding). single molecule fluorescence in situ hybridization is an in situ hybridization technique that enables the detection of mRNA transcripts with single molecule resolution. in silico reconstruction of the distribution of individual cells within tissues from in situ gene expression measurements and transcriptome-wide single-cell data. a high-throughput approach for spatial transcriptional profiling whereby transcripts are labeled in situ with spatial barcodes before sequencing. Can achieve near single-cell resolution. spatially resolved transcriptomics via epitope anchoring is a spatial mapping protocol enabling the annotation of histological data sets based on CITE-seq reference cell atlases.