Single Cell RNA-Seq Reveals Up-Regulation of Specific Epigenetic Regulators During Sexual Commitment of Malaria
Asaf Poran1, Christopher Nötzel2, Omar Aly1, Olivier Elemento1,#, Björn F.C. Kafsack2,#
1Department of Physiology and Biophysics, 2Department of Microbiology & Immunology, Weill Cornell Medicine, New York, NY, USA
Malaria is the most important vector-borne disease. Following infectious mosquito bites, Plasmodium falciparum, the most widespread and virulent human malaria, eukaryotic parasites infect red blood cells (iRBCs) where asexual replication occurs. However, transmission is dependent on the parasite’s ability to differentiate into male and female gametocytes, which could be taken up by a mosquito. Therefore, a subset of asexually replicating parasites (<1-30%) trigger a genetic program that poises them for differentiation into non-replicating sexual gametocytes upon re-invasion in the following cycle. Since sexually-committed parasites comprise only a small sub-population and are morphologically indistinguishable from asexually-committed ones, defining their transcriptional state has been difficult using traditional, bulk transcriptome profiling.
Here, we use highly-parallel, single-cell RNA sequencing to define the transcriptional profiles of over 16,000 parasites at multiple stages of development to define for the first time the transcriptional state of sexually-committed parasites. This first application of scRNA-seq to malaria parasites allowed us to place the parasites along the parasitic cell cycle, identify the sexually-committing subset, and to reveal a novel set of genes upregulated in committing parasites, including transcription factors, epigenetic modifiers and chromatin regulators. In sexually committed progeny, these regulators act in concert to poise genes necessary for gametocyte differentiation for expression in the subsequent cell cycle.
The ability to resolve gene expression profiles of thousands of individual parasites infecting single target cells now enables us to address key questions involving small sub-populations necessary for the human-mosquito-human transmission.