Exploring parasite heterogeneity using single-cell RNA-seq reveals a gene signature among sexual stage Plasmodium falciparum parasites

Exp Cell Res. 2018 Oct 1;371(1):130-138. doi: 10.1016/j.yexcr.2018.08.003. Epub 2018 Aug 8.

Abstract

The malaria parasite has a complex lifecycle, including several events of differentiation and stage progression, while actively evading immunity in both its mosquito and human hosts. Important parasite gene expression and regulation during these events remain hidden in rare populations of cells. Here, we combine a capillary-based platform for cell isolation with single-cell RNA-sequencing to transcriptionally profile 165 single infected red blood cells (iRBCs) during the intra-erythrocytic developmental cycle (IDC). Unbiased analyses of single-cell data grouped the cells into eight transcriptional states during IDC. Interestingly, we uncovered a gene signature from the single iRBC analyses that can successfully discriminate between developing asexual and sexual stage parasites at cellular resolution, and we verify five, previously undefined, gametocyte stage specific genes. Moreover, we show the capacity of detecting expressed genes from the variable gene families in single parasites, despite the sparse nature of data. In total, the single parasite transcriptomics holds promise for molecular dissection of rare parasite phenotypes throughout the malaria lifecycle.

Keywords: Gametocyte signature; Malaria; Parasites; Plasmodium falciparum; Single-cell RNA-seq; Single-parasite picking; Transcriptomics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Erythrocytes / parasitology*
  • Erythrocytes / pathology
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental
  • Gene Ontology
  • Genetic Heterogeneity
  • Humans
  • Life Cycle Stages / genetics*
  • Molecular Sequence Annotation
  • Plasmodium falciparum / genetics*
  • Plasmodium falciparum / growth & development
  • Plasmodium falciparum / metabolism
  • Protozoan Proteins / genetics*
  • Protozoan Proteins / metabolism
  • Sequence Analysis, RNA
  • Single-Cell Analysis
  • Transcriptome*

Substances

  • Protozoan Proteins