Trypanosoma cruzi is a protozoan parasite of humans and animals, affecting 10 to 20 million people and innumerable animals, primarily in the Americas. Despite being the largest cause of infection-induced heart disease worldwide, even among the neglected tropical diseases (NTDs) T. cruzi is considered one of the least well understood and understudied. The genetic complexity of T. cruzi as well as the limited set of efficient techniques for genome engineering contribute significantly to the relative lack of progress in and understanding of this pathogen. Here, we adapted the CRISPR-Cas9 system for the genetic engineering of T. cruzi, demonstrating rapid and efficient knockout of multiple endogenous genes, including essential genes. We observed that in the absence of a template, repair of the Cas9-induced double-stranded breaks (DSBs) in T. cruzi occurs exclusively by microhomology-mediated end joining (MMEJ) with various-sized deletions. When a template for DNA repair is provided, DSB repair by homologous recombination is achieved at an efficiency several orders of magnitude higher than that in the absence of CRISPR-Cas9-induced DSBs. We also demonstrate the high multiplexing capacity of CRISPR-Cas9 in T. cruzi by knocking down expression of an enzyme gene family consisting of 65 members, resulting in a significant reduction of enzymatic product with no apparent off-target mutations. Lastly, we show that Cas9 can mediate disruption of its own coding sequence, rescuing a growth defect in stable Cas9-expressing parasites. These results establish a powerful new tool for the analysis of gene functions in T. cruzi, enabling the study of essential genes and their functions and analysis of the many large families of related genes that occupy a substantial portion of the T. cruzi genome.

Immunity to malaria has been linked to the availability and function of helper CD4 + T cells, cytotoxic CD8 + T cells and γδ T cells that can respond to both the asymptomatic liver-stage and the symptomatic blood-stage of Plasmodium sp. infection. These T cell responses are also thought to be modulated by regulatory T cells. However, the precise mechanisms governing the development and function of Plasmodium-specific T cells and their capacity to form tissueresident and long-lived memory populations are less well understood. The field has arrived at a point where the push for vaccines that exploit T cell-mediated immunity to malaria has made it imperative to define and reconcile the mechanisms that regulate the development and functions of Plasmodium-specific T cells. Here, we review our current understanding of the mechanisms by which T cell subsets orchestrate host resistance to Plasmodium infection, based on observational and mechanistic studies in humans, non-human primates and rodent models. We also examine the potential of new experimental strategies and human infection systems to inform a new generation of approaches to harness T cell responses against malaria.

Activated CD8+ T cells differentiate into cytotoxic effector (TEFF) cells that eliminate target cells. How TEFF cell identity is established and maintained remains less understood. Here we show Runx3 deficiency limits clonal expansion and impairs upregulation of cytotoxic molecules in TEFF cells. Runx3-deficient CD8+ TEFF cells aberrantly upregulate genes characteristic of follicular helper T (TFH) cell lineage, including Bcl6, Tcf7 and Cxcr5. Mechanistically, the Runx3-CBFβ complex deploys H3K27me3 to Bcl6 and Tcf7 genes to suppress the TFH program. Ablating Tcf7 in Runx3-deficient CD8+ TEFF cells prevents the upregulation of TFH genes and ameliorates their defective induction of cytotoxic genes. As such, Runx3-mediated Tcf7 repression coordinately enforces acquisition of cytotoxic functions and protects the cytotoxic lineage integrity by preventing TFH-lineage deviation.

Malaria, caused by the protozoan Plasmodium is a devastating mosquito-borne disease, that puts nearly half the world’s population at risk1. Despite mounting substantial T and B cell responses, humans fail to efficiently control blood-stage malaria or develop sterilizing immunity to reinfections2. Though Foxp3+ regulatory T cells (Tregs) form a part of these responses3–5, their influence remains disputed, and mode of action unknown. Here we show that Tregs, which expand in both humans and rodents during blood-stage malaria, interfere with conventional T helper (Th) cell responses and the Follicular T helper (Tfh) cell:B cell partnership in germinal centers, in a critical temporal window to impede protective immunity, through the Cytotoxic T-lymphocyte-Associated protein (CTLA)-4. Targeting Tregs or CTLA-4 with precisely timed depletion or blocking enhanced immune responses, accelerated clearance, and generated species-transcending immunity to blood-stage malaria in mice. Our study uncovers a critical mechanism of immunosuppression associated with blood-stage malaria that delays parasite clearance and prevents development of potent adaptive immunity to reinfection. These data also reveal a temporally discrete and therapeutically amenable functional role for Tregs in limiting anti-malarial immunity.

Highlights d Monocyte-derived CD11c + cells are recruited during the liver stage of malaria d Liver-infiltrating CD11c + cells acquire Plasmodium, which requires hepatocyte infection d Plasmodium-harboring CD11c + cells have distinct phenotypes and transcriptomes d These CD11c + cells prime protective CD8 + T cells in liverdraining lymph nodes