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While Entamoeba histolytica remains a globally important pathogen, it is dramatically understudied. The tractability of E. histolytica has historically been limited, which is largely due to challenging features of its genome. To enable forward genetics, we constructed and validated the first genome-wide E. histolytica RNAi knockdown mutant library. This library allows for Illumina deep sequencing analysis for quantitative identification of mutants that are enriched or depleted after selection. We developed a novel analysis pipeline to precisely define and quantify gene fragments. We used the library to perform the first RNAi screen in E. histolytica and identified slow growth (SG) mutants. Among genes targeted in SG mutants, many had annotated functions consistent with roles in cellular growth or metabolic pathways. Some targeted genes were annotated as hypothetical or lacked annotated domains, supporting the power of forward genetics in uncovering functional information that cannot be gleaned from databases. While the localization of neither of the proteins targeted in SG1 nor SG2 mutants could be predicted by sequence analysis, we showed experimentally that SG1 localized to the cytoplasm and cell surface, while SG2 localized to the cytoplasm. Overexpression of SG1 led to increased growth, while expression of a truncation mutant did not lead to increased growth, and thus aided in defining functional domains in this protein. Finally, in addition to establishing forward genetics, we uncovered new details of the unusual E. histolytica RNAi pathway. These studies dramatically improve the tractability of E. histolytica and open up the possibility of applying genetics to improve understanding of this important pathogen., Author summary Entamoeba histolytica is a globally important pathogen that is dramatically understudied. One of the major limitations of this organism is its challenging genome. RNAi is the state-of-the-art tool for genetic manipulation in E. histolytica, though the RNAi pathway has several noncanonical features. Here, we harnessed the RNAi pathway to enable RNAi-based forward genetics for the first time in this organism. We validated the RNAi library by performing the first E. histolytica RNAi screen and identified slow growth mutants. We showed that independently-generated mutants also exhibited slow growth phenotypes, and we characterized protein localization and domains for some of the identified slow growth genes. The RNAi library that we constructed enables modern, quantitative Illumina deep sequencing analysis to identify mutants that are enriched or depleted after selection. We developed a novel analysis pipeline to precisely define and quantify full-length gene fragments inferred from read mapping. Our approach differs from previous approaches for analysis of RNAi screens, and it better represents the actual DNA fragments and their quantities. This study dramatically improves the tractability of this important pathogen. Moreover, the strategies behind this RNAi library, and its analysis, are novel, and can be applied to other organisms.

WhileEntamoeba histolyticaremains a globally important pathogen, it is dramatically understudied. The tractability ofE. histolyticahas historically been limited, which is largely due to challenging features of its genome. To enable forward genetics, we constructed and validated the first genome-wideE. histolyticaRNAi knockdown mutant library. This library allows for Illumina deep sequencing analysis for quantitative identification of mutants that are enriched or depleted after selection. We developed a novel analysis pipeline to precisely define and quantify gene fragments. We used the library to perform the first RNAi screen inE. histolyticaand identified slow growth (SG) mutants. Among genes targeted in SG mutants, many had annotated functions consistent with roles in cellular growth or metabolic pathways. Some targeted genes were annotated as hypothetical or lacked annotated domains, supporting the power of forward genetics in uncovering functional information that cannot be gleaned from databases. While the localization of neither of the proteins targeted in SG1 nor SG2 mutants could be predicted by sequence analysis, we showed experimentally that SG1 localized to the cytoplasm and cell surface, while SG2 localized to the cytoplasm. Overexpression of SG1 led to increased growth, while expression of a truncation mutant did not lead to increased growth, and thus aided in defining functional domains in this protein. Finally, in addition to establishing forward genetics, we uncovered new details of the unusualE. histolyticaRNAi pathway. These studies dramatically improve the tractability ofE. histolyticaand open up the possibility of applying genetics to improve understanding of this important pathogen.Author SummaryEntamoeba histolyticais a globally important pathogen that is dramatically understudied. One of the major limitations of this organism is its challenging genome. RNAi is the state-of-the-art tool for genetic manipulation inE. histolytica,though the RNAi pathway has several noncanonical features. Here, we harnessed the RNAi pathway to enable RNAi-based forward genetics for the first time in this organism. We validated the RNAi library by performing the firstE. histolyticaRNAi screen and identified slow growth mutants. We showed that independently-generated mutants also exhibited slow growth phenotypes, and we characterized protein localization and domains for some of the identified slow growth genes. The RNAi library that we constructed enables modern, quantitative Illumina deep sequencing analysis to identify mutants that are enriched or depleted after selection. We developed a novel analysis pipeline to precisely define and quantify full-length gene fragments inferred from read mapping. Our approach differs from previous approaches for analysis of RNAi screens, and it better represents the actual DNA fragments and their quantities. This study dramatically improves the tractability of this important pathogen. Moreover, the strategies behind this RNAi library, and its analysis, are novel, and can be applied to other organisms.Author ContributionsA.B. designed and performed the experiments, except fragmentation of gDNA, immunofluorescence, and growth curves with expression of full-length or truncated proteins. R.L.S. performed SG1 and SG2 immunofluorescence experiments. M.C.R. performed growth curves with expression of full-length or truncated proteins. W.H. generated transfectants expressing full-length SG2. C.G.B. fragmented gDNA and processed the fragments to enable subsequent plasmid library construction. T.S.Y.T. and H.W.M. performed Gal/GalNAc lectin immunofluorescence experiments. S.S.H. designed the analysis strategy for Illumina sequencing data, and analyzed all Illumina sequencing data. M.L.S. oversaw the Illumina analysis approach. K.S.R. performed growth curves, conceived of the overall approach and oversaw the design and analysis of the experiments. A.B., S.S.H., and K.S.R. wrote the manuscript.

Eosinophils are versatile cells that regulate innate and adaptive immunity, influence metabolism and tissue repair, and contribute to allergic lung disease. Within the context of immunity to parasitic worm infections, eosinophils are prominent yet highly varied in function. We have shown previously that when mice undergo primary infection with the parasitic nematode Trichinella spiralis, eosinophils play an important immune regulatory role that promotes larval growth and survival in skeletal muscle. In this study, we aimed to address the function of eosinophils in secondary infection with T. spiralis. By infecting eosinophil-ablated mice, we found that eosinophils are dispensable for immunity that clears adult worms or controls fecundity in secondary infection. In contrast, eosinophil ablation had a pronounced effect on secondary infection of skeletal muscle by migratory newborn larvae. Restoring eosinophils to previously infected, ablated mice caused them to limit muscle larvae burdens. Passive immunization of naive, ablated mice with sera or Ig from infected donors, together with transfer of eosinophils, served to limit the number of newborn larvae that migrated in tissue and colonized skeletal muscle. Results from these in vivo studies are consistent with earlier findings that eosinophils bind to larvae in the presence of Abs in vitro. Although our previous findings showed that eosinophils protect the parasite in primary infection, these new data show that eosinophils protect the host in secondary infection.

Eosinophilia is a feature of the host immune response that distinguishes parasitic worms from other pathogens, yet a discrete function for eosinophils in worm infection has been elusive. The aim of this study was to clarify the mechanism(s) underlying the striking and unexpected observation that eosinophils protect intracellular, muscle-stage Trichinella spiralis larvae against NO-mediated killing. Our findings indicate that eosinophils are specifically recruited to sites of infection at the earliest stage of muscle infection, consistent with a local response to injury. Early recruitment is essential for larval survival. By producing IL-10 at the initiation of infection, eosinophils expand IL-10+ myeloid dendritic cells and CD4+ IL-10+ T lymphocytes that inhibit inducible NO synthase (iNOS) expression and protect intracellular larvae. The results document a novel immunoregulatory function of eosinophils in helminth infection, in which eosinophil-derived IL-10 drives immune responses that eventually limit local NO production. In this way, the parasite co-opts an immune response in a way that enhances its own survival.