The use of imaging flow cytometry for rapid, high-throughput and automated analysis of the Leishmania mexicana promastigote cell cycle provides new insights into cell cycle events of short duration

Promastigote Leishmania mexicana have a complex cell division cycle characterised by the ordered replication of several single-copy organelles, a prolonged S phase and rapid G2 and cytokinesis phases, accompanied by cell cycle stage-associated morphological changes. Here we exploit these morphological changes to develop a high-throughput and semi-automated imaging flow cytometry (IFC) pipeline to analyse the cell cycle of L. mexicana in live cells. Firstly, we demonstrate that, unlike several other DNA stains, Vybrant DyeCycle Orange (DCO) is non-toxic and enables quantitative DNA imaging in live L. mexicana promastigotes. Secondly, by tagging the orphan spindle kinesin, KINF, with mNeonGreen, we describe KINFs cell cycle-dependent expression and localisation. Then, by combining manual gating of DCO DNA intensity profiles with automated masking and morphological measurements of parasite images, visual determination of the number of flagella per cell, and automated masking and analysis of mNG:KINF fluorescence, we provide a newly detailed description of L. mexicana promastigote cell cycle events that, for the first time, includes the durations of individual G2, mitosis and post-mitosis phases, and identifies G1 cells within the first 12 minutes of the new cell cycle. By applying IFC in this way, we were able, in minutes, to capture tens of thousands of high-quality brightfield and fluorescent images of live L. mexicana cells in solution, and to acquire quantitative data across multiple parameters for every image captured. Our custom-developed masking and gating scheme allowed us to identify elusive G2 cells and to demonstrate that the CDK-inhibitor, flavopiridol, arrests cells in G2 phase, rather than mitosis, providing proof-of-principle of the utility of IFC for drug mechanism-of-action studies. Further, the high-throughput nature of IFC allowed the close examination of promastigote cytokinesis, revealing considerable flexibility in both the timing of cytokinesis initiation and the direction of furrowing, in contrast to the related kinetoplastid parasite, Trypanosoma brucei. Significantly, our analysis demonstrate that the cleavage furrow can ingress unidirectionally from either pole of the cell, bidirectionally from both simultaneously or even commence internally along the anterior-posterior (A-P) axis. Our new pipeline offers many advantages over traditional methods of cell cycle analysis such as fluorescence microscopy and flow cytometry and paves the way for novel high-throughput analysis of Leishmania cell division. Author SummaryLeishmania mexicana is a single-celled parasite that is spread by sand flies and causes a spectrum of diseases called the leishmaniases in humans and animals. To cause disease, L. mexicana parasites must replicate and divide, and their cell division cycle has unusual and/or complex features, including that the parasite changes shape as it replicates. To aid analysis of the L. mexicana cell cycle, we developed a new quantitative DNA staining technique and also generated a fluorescent parasite cell line that highlighted when cells were dividing their DNA (mitosis) after replicating it. We then applied a high-throughput technique called imaging flow cytometry to capture images of tens of thousands of these parasites in just a few minutes. For each image, we were able to extract data about DNA replication, cell shape, whether the cells were in mitosis or not and how they divide. This provided new insights into how the parasites replicate and how long each stage of cell division takes as well as how the parasites split in two at the end of cell division. We were also able to use our analysis method to precisely determine the cell cycle stage at which a cell cycle inhibitor acts. More importantly, the imaging pipelines we have developed offer great advantages in terms of speed and depth over more traditional analysis techniques such as microscopy and should pave the way for increasingly detailed analyses of parasite cell biology in the future.