A Deep Analysis of the Small Non-Coding RNA Population in Schistosoma japonicum Eggs

BackgroundSchistosoma japonicum is a parasitic flatworm that causes zoonotic schistosomiasis. The typical outcome of schistosomiasis is hepatic granuloma and fibrosis, which is primarily induced by soluble egg-derived antigens. Although schistosomal eggs represent an important pathogenic stage to the host, the biology of this critical stage is largely unknown. We previously investigated the expression profiles of sncRNAs during different developmental stages of this parasite. However, using small RNA extracted from egg-deposited liver tissues generated limited information about sncRNAs in eggs. Here, we characterized the complete small RNAome in this stage of the parasite after optimization of RNA purification.Methodology and Principal FindingsA library, SjE, was constructed with the small RNA extracted from S. japonicum eggs and subjected to high-throughput sequencing. The data were depicted by comprehensive bioinformatic analysis to explore the expression features of sncRNAs in the egg stage. MicroRNAs accounted for about one quarter of the total small RNA population in this stage, with a strongly biased expression pattern of certain miRNA family members. Sja-miR-71, sja-miR-71-5p, and sja-miR-36-3p were suggested to play important roles in embryo development. A panel of transfer RNA fragments (tRFs) precisely processed from the 5′ end of mature tRNAs was identified for the first time, which represented a strong egg stage-biased expression. The tRNA-Ala derived small RNAs were the most highly expressed Sj-tRFs in eggs. Further, the expression of siRNAs from 29 types of well-defined transposable elements (TEs) was observed to be relatively stable among different developmental stages.Conclusions and SignificanceIn this study, we characterized the sncRNA profile in the egg stage of S. japonicum. Featured expression of sncRNAs, especially the tRNA-derived small RNAs, was identified, which was further compared with that of other developmental stages. These novel findings would facilitate a deeper understanding of the biology of schistosomal parasites.

研究背景：日本血吸虫（Schistosoma japonicum）是一种可引发人畜共患血吸虫病的寄生扁形动物。血吸虫病的典型病变为肝肉芽肿与肝纤维化，其主要致病诱因源自虫卵可溶性抗原。尽管血吸虫虫卵是宿主的重要致病阶段，但该关键阶段的生物学特性目前仍知之甚少。此前我们曾针对该寄生虫不同发育阶段的小非编码RNA（small non-coding RNA, sncRNA）表达谱展开研究，但通过从虫卵沉积的肝脏组织中提取小RNA，所获得的虫卵sncRNA相关信息十分有限。本研究通过优化RNA纯化流程，对该寄生虫虫卵阶段的完整小RNA组（small RNAome）进行了系统表征。

实验方法与主要研究结果：本研究构建了命名为SjE的文库，该文库以日本血吸虫虫卵来源的小RNA为材料，并进行了高通量测序。通过全面的生物信息学分析对测序数据进行解析，以探究虫卵阶段sncRNA的表达特征。本阶段小RNA群体中，microRNA（miRNA）占比约四分之一，且特定miRNA家族成员呈现显著的表达偏好性。研究提示sja-miR-71、sja-miR-71-5p及sja-miR-36-3p在胚胎发育中发挥重要作用。本研究首次鉴定出一类由成熟tRNA 5'端精准剪切产生的转运RNA片段（transfer RNA fragments, tRFs），该类片段呈现显著的虫卵阶段特异性高表达，其中源自丙氨酸tRNA的小RNA是虫卵中表达量最高的日本血吸虫tRF（Sj-tRF）。此外，研究还观察到来自29种明确分类的转座因子（transposable elements, TEs）的小干扰RNA（small interfering RNA, siRNAs）在不同发育阶段的表达相对稳定。

结论与意义：本研究系统表征了日本血吸虫虫卵阶段的sncRNA表达谱，鉴定出该阶段特有的sncRNA表达特征，尤其是tRNA衍生小RNA的表达模式，并与其他发育阶段进行了对比分析。上述新发现将有助于更深入地解析血吸虫的生物学特性。