Dynamically expressed genes provide candidate viability biomarkers in a model coccidian

Abstract

Eimeria parasites cause enteric disease in livestock and the closely related Cyclospora cayetanensis causes human disease. Oocysts of these coccidian parasites undergo maturation (sporulation) before becoming infectious. Here, we assessed transcription in maturing oocysts of Eimeria acervulina, a widespread chicken parasite, predicted gene functions, and determined which of these genes also occur in C. cayetanensis. RNA-Sequencing yielded ~2 billion paired-end reads, 92% of which mapped to the E. acervulina genome. The ~6,900 annotated genes underwent temporally-coordinated patterns of gene expression. Fifty-three genes each contributed >1,000 transcripts per million (TPM) throughout the study interval, including cation-transporting ATPases, an oocyst wall protein, a palmitoyltransferase, membrane proteins, and hypothetical proteins. These genes were enriched for 285 gene ontology (GO) terms and 13 genes were ascribed to 17 KEGG pathways, defining housekeeping processes and functions important throughout sporulation. Expression differed in mature and immature oocysts for 40% (2,928) of all genes; of these, nearly two-thirds (1,843) increased their expression over time. Eight genes expressed most in immature oocysts, encoding proteins promoting oocyst maturation and development, were assigned to 37 GO terms and 5 KEGG pathways. Fifty-six genes underwent significant upregulation in mature oocysts, each contributing at least 1,000 TPM. Of these, 40 were annotated by 215 GO assignments and 9 were associated with 18 KEGG pathways, encoding products involved in respiration, carbon fixation, energy utilization, invasion, motility, and stress and detoxification responses. Sporulation orchestrates coordinated changes in the expression of many genes, most especially those governing metabolic activity. Establishing the long-term fate of these transcripts in sporulated oocysts and in senescent and deceased oocysts will further elucidate the biology of coccidian development, and may provide tools to assay infectiousness of parasite cohorts. Moreover, because many of these genes have homologues in C. cayetanensis, they may prove useful as biomarkers for risk.

Cyclospora cayetanensis: A Perspective (2020–2023) with Emphasis on Epidemiology and Detection Methods

“…Additionally, many Eimeria species pose no risk to the health of human investigators. Thus, surrogates could speed up efforts to evaluate methods to filter parasites from irrigation water, treat food in ways that may render contaminants harmless, or treat infections when prevention fails [ 13 , 15 , 123 ]. Surrogates could also be studied in their natural hosts to evaluate whether an intervention rendered oocysts incapable of infecting their hosts.…”

Life Cycle and Transmission of Cyclospora cayetanensis: Knowns and Unknowns

“…Furthermore, Eimeria can and should be exploited as surrogates for evaluating methods requiring large numbers of C. cayetanensis oocysts. For example, maturation of oocysts of Eimeria acervulina (a common poultry parasite) entails upregulation of a suite of genes most of which have homologues in C. cayetanensis [19]. These abundant parasites, which pose no risk to the health of human investigators, can speed efforts to evaluate methods to filter parasites from irrigation water, and treat food in ways that may render such contaminants harmless, or treat infections when prevention fails.…”

“…Genome assembly and annotation for Cyclospora and for its Eimeria relatives remain far from complete, impeding efforts to understand their comparative biology. Nonetheless, a recent study of sporulation in E. acervulina suggests that similar genes in each species may be important regulators or effectors of parasite maturation [19]. Maturing cohorts of E. acervulina undergo concerted changes in the expression of many genes; most of these increase their expression over the course of sporulation.…”

Hastening Progress in Cyclospora Requires Studying Eimeria Surrogates

“…Surrogate organisms offer an abundant source of material to evaluate broader conditions, characterize oocyst responses to a variety of environmental and chemical exposures, and identify biomarkers characteristic of immature, mature, senescent, and dead parasites. Orchestrated changes in gene expression characterize maturing oocysts of E. acervulina [ 81 ] and two-thirds of the genes undergoing the greatest changes have direct homologues in C. cayetanensis . We are evaluating gene expression under a variety of environmental conditions and leveraging such data to develop assays that predict viability and infectiousness.…”

“…True risk assessment requires viability assays. We see Eimeria surrogates as key to developing such tools, leveraging candidate biomarkers we have recently identified [ 81 , 107 ]. The first tools will likely remain in the purview of reference diagnostic labs.…”