piwi-interactingRNAs(piRNAs) are valuable biomarkers, but functional studies are still very limited.Recent research shows that piRNA-mediated cleavage acts on Transposable Elements(TEs), messengerRNAs(mRNAs), and long...piwi-interactingRNAs(piRNAs) are valuable biomarkers, but functional studies are still very limited.Recent research shows that piRNA-mediated cleavage acts on Transposable Elements(TEs), messengerRNAs(mRNAs), and long non-codingRNAs(lncRNAs). This study aimed to predict cancer-associated piRNA-mRNA and piRNA-lncRNA interactions as well as piRNA regulatory functions. Four cancer types(BRCA, HNSC, KIRC,and LUAD) were investigated. Interactions were identified by integrated analysis of the expression and sequence data. For the expression analysis, only piRNA–mRNA and piRNA–lncRNA pairs with expression profiles that were significantly inversely correlated were retained to reduce false-positive rates during the prediction. For the sequence analysis, miRanda was used for the target prediction. We identified 198 piRNA–mRNA and 10 piRNA–lncRNA pairs. Unlike mRNA and lncRNA expressions, the piRNA expression was relatively consistent across the cancer types. Furthermore, the identified piRNAs were consistent with previously published cancer biomarkers, such as piRNA-36741, piR-21032, and piRNA-57125. More importantly, predicted piRNA functions were determined by constructing an interaction network, and piRNA targets were placed in gene ontology categories related to the cancer hallmarks "activating invasion and metastasis" and "sustained angiogenesis".展开更多
基金supported by the National Natural Science Foundation of China (Nos. 91530113, 61571341, and 61201312)the Research Fund for the Doctoral Program of Higher Education of China (No. 20130203110017)+1 种基金the Fundamental Research Funds for the Central Universities of China (Nos. BDY171416, JBZ170301, 20101164977, and JB140306)the Natural Science Foundation of Shaanxi Province in China (Nos. 2015JM6275 and 207JM6024)
文摘piwi-interactingRNAs(piRNAs) are valuable biomarkers, but functional studies are still very limited.Recent research shows that piRNA-mediated cleavage acts on Transposable Elements(TEs), messengerRNAs(mRNAs), and long non-codingRNAs(lncRNAs). This study aimed to predict cancer-associated piRNA-mRNA and piRNA-lncRNA interactions as well as piRNA regulatory functions. Four cancer types(BRCA, HNSC, KIRC,and LUAD) were investigated. Interactions were identified by integrated analysis of the expression and sequence data. For the expression analysis, only piRNA–mRNA and piRNA–lncRNA pairs with expression profiles that were significantly inversely correlated were retained to reduce false-positive rates during the prediction. For the sequence analysis, miRanda was used for the target prediction. We identified 198 piRNA–mRNA and 10 piRNA–lncRNA pairs. Unlike mRNA and lncRNA expressions, the piRNA expression was relatively consistent across the cancer types. Furthermore, the identified piRNAs were consistent with previously published cancer biomarkers, such as piRNA-36741, piR-21032, and piRNA-57125. More importantly, predicted piRNA functions were determined by constructing an interaction network, and piRNA targets were placed in gene ontology categories related to the cancer hallmarks "activating invasion and metastasis" and "sustained angiogenesis".
