Differential mRNA display analysis of gene expression in Cryptosporidium parvum-infected HCT-8 cells

Expression Profiles of mRNA and lncRNA in HCT-8 Cells Infected With Cryptosporidium parvum IId Subtype

Cryptosporidium parvum is one of the most important enteric protozoan pathogens, responsible for severe diarrhea in immunocompromised human and livestock. However, few effective agents were available for controlling this parasite. Accumulating evidences suggest that long non-coding RNA (lncRNA) played key roles in many diseases through regulating the gene expression. Here, the expression profiles of lncRNAs and mRNAs were analyzed in HCT-8 cells infected with C. parvum IId subtype using microarray assay. A total of 821 lncRNAs and 1,349 mRNAs were differentially expressed in infected cells at 24 h post infection (pi). Of them, all five types of lncRNAs were identified, including 22 sense, 280 antisense, 312 intergenic, 44 divergent, 33 intronic lncRNAs, and 130 lncRNAs that were not found the relationship with mRNAs’ location. Additionally, real-time polymerase chain reactions of 10 lncRNAs and 10 mRNAs randomly selected were successfully confirmed the microarray results. The co-expression and target prediction analysis indicated that 27 mRNAs were cis-regulated by 29 lncRNAs and 109 were trans-regulated by 114 lncRNAs. These predicted targets were enriched in several pathways involved in the interaction between host and C. parvum, e.g., hedgehog signaling pathway, Wnt signaling pathway, and tight junction, suggesting that these differentially expressed lncRNAs would play important regulating roles during the infection of C. parvum IId subtype.

Cryptosporidium parvum gene discovery

Cryptosporidium parvum is a well-recognized cause of diarrhea in humans and animals throughout the world, and is associated with a substantial degree of morbidity and mortality in patients with acquired immunodeficiency syndrome (AIDS). At the present time, there is no effective therapy for treating or preventing infection with C. parvum. This is primarily due to a lack of understanding of the basic cellular and molecular biology of this pathogen in terms of virulence factors, genome structure, gene expression, and regulation. Over the past few years, large-scale sequencing of randomly selected cDNAs or fragments of genomic DNA has proven to be an efficient approach for obtaining large amount of genomic information. Recently, large-scale sporozoite expressed sequence tag (EST) and genomic sequence tag (GST) projects have been initiated for C. parvum. These projects have greatly increased the number of C. parvum genes identified and demonstrate the usefulness of large-scale sequencing for expanding our understanding of C. parvum biology. Continued characterization of the C. parvum genome will increase our basic understanding of the cellular and molecular biology of C. parvum in terms of gene and genome structure, and will identify key metabolic and pathophysiologic features of the organism for future development of safe and effective strategies for prevention and treatment of disease.

Methods to prepare RNA and to isolate developmentally regulated genes from Eimeria

Coccidians represent a large class of important intracellular parasites that traverse multiple developmental stages that are distinct and required to complete the life cycle. The biochemical details underlying the regulation of transformation from one developmental form to the next are limited and the study of such details presents unique obstacles. However, the genetic program is critical and may provide a basis for understanding the biology of these organisms in addition to the opportunity to suppress development and infection. We provide a basic overview of several strategies, including previously unpublished results, used by this laboratory to isolate stage-specific genes from Eimeria bovis. Additionally, we have included detailed discussions that summarize the associated advantages and disadvantages of each as applied to coccidia and potentially to other parasites in the phylum Apicomplexa. Given that the purification of sufficient quantities of high-quality RNA is vital, we have included detailed protocols for the isolation of RNA from various parasite stages. Also included is a detailed protocol to apply mRNA differential display to investigate stage-specific developmental regulation.