Exploring parasite heterogeneity using single-cell RNA-seq reveals a gene signature among sexual stage Plasmodium falciparum parasites.
Mtakai Ngara, Mia Palmkvist, Sven Sagasser, Daisy Hjelmqvist, Åsa K Björklund, Mats Wahlgren, Johan Ankarklev, Rickard Sandberg
Author Information
Mtakai Ngara: Ludwig Institute for Cancer Research, Karolinska Institutet, Box 240, SE-171 77 Stockholm, Sweden; Dept. of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 1, Box 285, SE-171 77 Stockholm, Sweden.
Mia Palmkvist: Department of Microbiology, Tumor and Cell Biology, Nobels väg 16, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
Sven Sagasser: Ludwig Institute for Cancer Research, Karolinska Institutet, Box 240, SE-171 77 Stockholm, Sweden.
Daisy Hjelmqvist: Dept. of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 1, Box 285, SE-171 77 Stockholm, Sweden.
Åsa K Björklund: Ludwig Institute for Cancer Research, Karolinska Institutet, Box 240, SE-171 77 Stockholm, Sweden.
Mats Wahlgren: Department of Microbiology, Tumor and Cell Biology, Nobels väg 16, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
Johan Ankarklev: Department of Microbiology, Tumor and Cell Biology, Nobels väg 16, Karolinska Institutet, SE-171 77 Stockholm, Sweden; Department of Microbiology and Immunology, Weill-Cornell Medical College of Cornell University, 1300 York Avenue, Box 62, New York, NY 10062, United States; Department of Molecular Biosciences, The Wenner Gren Institute, Stockholm University, Svante Arrhenius väg 20C, SE-106 91 Stockholm, Sweden. Electronic address: johan.ankarklev@su.se.
Rickard Sandberg: Ludwig Institute for Cancer Research, Karolinska Institutet, Box 240, SE-171 77 Stockholm, Sweden; Dept. of Cell and Molecular Biology, Karolinska Institutet, Solnavägen 1, Box 285, SE-171 77 Stockholm, Sweden. Electronic address: rickard.sandberg@ki.se.
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.
