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
Piwi-interacting RNAs(piRNAs)is a novel class of non-coding RNAs.However,changes in piRNA expression profiles in recurrent spontaneous abortion(RSA)have not yet been investigated.The aim of this study was to identify ...Piwi-interacting RNAs(piRNAs)is a novel class of non-coding RNAs.However,changes in piRNA expression profiles in recurrent spontaneous abortion(RSA)have not yet been investigated.The aim of this study was to identify differentially expressed piRNAs in deciduas of RSA patients.Decidua tissues were collected by curettage from recruited RSA patients and normal early pregnant(NEP)women with their informed consent.Small RNA sequencing was used to evaluate the differences in piRNA expression profiles between RSA and NEP.The present results demonstrated that the counts of total piRNA reads in RSA samples were increased compared with those in NEP samples(0.21%vs.0.11%).Differential expression analysis identified 29 upregulated piRNAs and 18 downregulated piRNAs in RSA samples.RT-qPCR further confirmed that the expression levels of uniq-109625,uniq-89328,uniq-50651 and uniq-4569 were decreased in 8 RSA tissues,compared with 13 NEP tissues.Otherwise,pi-22628 and uniq-173406 were increased in 8 RSA tissues.Based on GO term and KEGG pathway analysis,we speculate that these piRNAs regulate RSA by targeting extracellular matrix component pathway,cell adhesion pathway and focal adhesion pathway.PiRNAs may be involved in RSA pathogenesis by target genes function on adhesion and extracellular matrix component.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".
基金Supported by the National Natural Science Foundation of China Grants(No.81801523)the Natural Science Foundation of Guangdong Province(Nos.2017A030313789,2018A030313528,2019A1515011984)+3 种基金the Science and Technology Planning Foundation of Guangzhou City(201904010017,202102080102)Guangdong Province Medical Research Funding(No.A2021269)the Family Planning Research Institute Innovation Team of Guangdong Province grants(C-03)the Family Planning Research Institute of Guangdong Province Grants(S2018010).
文摘Piwi-interacting RNAs(piRNAs)is a novel class of non-coding RNAs.However,changes in piRNA expression profiles in recurrent spontaneous abortion(RSA)have not yet been investigated.The aim of this study was to identify differentially expressed piRNAs in deciduas of RSA patients.Decidua tissues were collected by curettage from recruited RSA patients and normal early pregnant(NEP)women with their informed consent.Small RNA sequencing was used to evaluate the differences in piRNA expression profiles between RSA and NEP.The present results demonstrated that the counts of total piRNA reads in RSA samples were increased compared with those in NEP samples(0.21%vs.0.11%).Differential expression analysis identified 29 upregulated piRNAs and 18 downregulated piRNAs in RSA samples.RT-qPCR further confirmed that the expression levels of uniq-109625,uniq-89328,uniq-50651 and uniq-4569 were decreased in 8 RSA tissues,compared with 13 NEP tissues.Otherwise,pi-22628 and uniq-173406 were increased in 8 RSA tissues.Based on GO term and KEGG pathway analysis,we speculate that these piRNAs regulate RSA by targeting extracellular matrix component pathway,cell adhesion pathway and focal adhesion pathway.PiRNAs may be involved in RSA pathogenesis by target genes function on adhesion and extracellular matrix component.
