Single-Cell RNA Sequencing Reveals that the Switching of the Transcriptional Profiles of Cysteine-Related Genes Alters the Virulence of Entamoeba histolytica

Entamoeba histolytica is an intestinal protozoan that causes human amoebic colitis and extraintestinal abscesses. Virulence variation is observed in the pathogenicity of E. histolytica trophozoites, but the detailed mechanism remains unclear. Here, a single trophozoite was cultured alone, and the progeny of the trophozoites of each generation were subjected to single-cell RNA sequencing (scRNA-seq) to study the transcriptional profiles of trophozoites. The scRNA-seq analysis indicated the importance of sulfur metabolism and the proteasome pathway in pathogenicity, whereas the isobaric tags for relative and absolute quantitation (iTRAQ) proteomic analysis did not identify the bulk trophozoites. The trophozoite improved the synthesis of cysteine under cysteine-deficient conditions but downregulated the expression of the intermediate subunit of the lectin of E. histolytica trophozoites and retained the expression of the heavy subunit of lectin, resulting in decreased amoebic phagocytosis and cytotoxicity. The variation in the transmembrane kinase gene family might be critical in regulating the proteasome pathway. Thus, the scRNA-seq technique provided an improved understanding of the biological characteristics and the mechanism of virulence variation of amoebic trophozoites. IMPORTANCE Studies on the trophozoite of Entamoeba histolytica suggested this organism could accumulate polyploid cells in its proliferative phase and differentiate its cell cycle from that of other eukaryotes. Therefore, a single-cell sequencing technique was used to study the switching of the RNA transcription profiles of single amoebic trophozoites. We separated individual trophozoites from axenic cultured trophozoites, CHO cell-incubated trophozoites, and in vivo trophozoites. We found important changes in the sulfur and cysteine metabolism in pathogenicity. The trophozoites strategically regulated the expression of the cysteine-rich protein-encoding genes under cysteine-deficient conditions, thereby decreasing amoebic phagocytosis and cytotoxicity. The single-cell sequencing technique shows evident advantages in comparison with the isobaric tags for relative and absolute quantitation (iTRAQ) proteomic technology (bulk trophozoite level) and reveals the regulation strategy of trophozoites in the absence of exogenous cysteine. This regulation strategy may be the mechanism of virulence variation of amoebic trophozoites.