Table1_In silico identification of human microRNAs pointing centrin genes in Leishmania donovani: Considering the RNAi-mediated gene control.xlsx

Leishmaniasis, a parasitic disease caused by different species of the protozoa parasite Leishmania, is a neglected tropical human disease that is endemic in about a hundred countries worldwide. According to the World Health Organization (WHO), the annual incidence of cutaneous leishmaniasis (CL) is estimated to be 0.7–1.2 million cases globally, whereas the annual incidence of visceral leishmaniasis is estimated to be 0.2–0.4 million cases. In many eukaryotic organisms, including human beings and protozoan parasites, centrin genes encode proteins that play essential roles within the centrosome or basal body. Human microRNAs (miRNAs) have been linked to several infectious and non-infectious diseases associated with pathogen–host interactions, and they play the emphatic roles as gene expression regulators. In this study, we used the MirTarget bioinformatics tool, which is a machine learning-based approach implemented in miRDB, to predict the target of human miRNAs in Leishmania donovani centrin genes. For cross-validation, we utilized additional prediction algorithms, namely, RNA22 and RNAhybrid, targeting all five centrin isotypes. The centrin-3 (LDBPK_342160) and putative centrin-5 (NC_018236.1) genes in L. donovani were targeted by eight and twelve human miRNAs, respectively, among 2,635 known miRNAs (miRBase). hsa-miR-5193 consistently targeted both genes. Using TargetScan, TarBase, miRecords, and miRTarBase, we identified miRNA targets and off-targets in human homologs of centrin, inflammation, and immune-responsive genes. Significant targets were screened based on GO terminologies and KEGG pathway-enrichment analysis (Log10 p-value >0.0001). In silico tools that predict the biological roles of human miRNAs as primary gene regulators in pathogen–host interactions help unravel the regulatory patterns of these miRNAs, particularly in the early stages of inflammatory responses. It is also noted that these miRNAs played an important role in the late phase of adaptive immune response, inclusively their impacts on the immune system’s response to L. donovani.

利什曼病（Leishmaniasis）是由不同种类的利什曼原虫（Leishmania，原生动物寄生虫）引发的寄生虫病，属于被忽视的热带人类疾病，在全球约100个国家呈地方性流行。据世界卫生组织（World Health Organization，WHO）统计，全球皮肤利什曼病（cutaneous leishmaniasis，简称CL）年发病例数估计为70万至120万例，而内脏利什曼病年发病例数估计为20万至40万例。在包括人类与原生动物寄生虫在内的诸多真核生物中，中心蛋白（centrin）基因编码的蛋白质在中心体或基体中发挥关键作用。人类微小RNA（microRNAs，简称miRNAs）已被证实与多种涉及病原体-宿主互作的感染性及非感染性疾病相关，其作为基因表达调控因子发挥核心调控功能。本研究借助miRDB平台中基于机器学习开发的MirTarget生物信息学工具，预测人类微小RNA在杜氏利什曼原虫（Leishmania donovani）中心蛋白基因中的靶向结合位点。为开展交叉验证，我们额外采用了RNA22与RNAhybrid两款预测算法，对全部5种中心蛋白亚型进行靶向预测。在miRBase数据库收录的2635种已知人类微小RNA中，杜氏利什曼原虫的中心蛋白-3（LDBPK_342160）与推定中心蛋白-5（NC_018236.1）基因分别被8种和12种人类微小RNA靶向结合，其中hsa-miR-5193可同时靶向这两个基因。我们还通过TargetScan、TarBase、miRecords与miRTarBase数据库，鉴定了人类中心蛋白、炎症相关及免疫应答基因同源物中的微小RNA靶向与非靶向结合位点。基于基因本体（Gene Ontology，GO）术语与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes，KEGG）通路富集分析（Log10 P值>0.0001）筛选得到具有显著统计学意义的靶向位点。用于预测人类微小RNA作为病原体-宿主互作中核心基因调控因子生物学功能的计算机工具，有助于阐明此类微小RNA的调控模式，尤其在炎症反应的早期阶段。此外，此类微小RNA在适应性免疫应答的晚期阶段同样发挥重要作用，包括其对杜氏利什曼原虫感染的免疫系统应答的影响。