The diagnostic potential of a circRNA–miRNA network in non-small cell lung cancer

Ma, Xinyi; Lou, Chengtao; Pan, Junjie; Zhou, Chengwei; Zhao, Xiaodong; Li, Nan; Tian, Haihua; Meng, Xiaoxiao

doi:10.1007/s00109-023-02306-7

Cited by 19 publications

(7 citation statements)

References 33 publications

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“…As previously described [ 17 , 24 , 25 ], circRNA primers for qPCR were designed using Primer 3 Plus ( https://www.primer3plus.com/index.html ) [ 26 ]. All primers were synthesized by BGI (Beijing Genomics Institution, China).…”

Section: Methodsmentioning

confidence: 99%

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Exosome-transported circ_0061407 and circ_0008103 play a tumour-repressive role and show diagnostic value in non-small-cell lung cancer

Chen,

Ma,

Chen

et al. 2024

J Transl Med

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Background Circular RNAs (circRNAs), one of the major contents of exosomes, have been shown to participate in the occurrence and progression of cancers. The role and the diagnostic potential of exosome-transported circRNAs in non-small-cell lung cancer (NSCLC) remain largely unknown. Methods The NSCLC-associated exosomal circ_0061407 and circ_0008103 were screened by circRNA microarray. The role of circ_0061407 and circ_0008103 in NSCLC was examined in vitro and in vivo. The encapsulation of the two circRNAs into exosomes and the transport to recipient cells were observed by confocal microscopy. The effects of exosome-transported circ_0061407 and circ_0008103 on recipient cells were investigated using a co-culture device. Bioinformatics analyses were performed to predict the mechanisms by which circ_0061407 and circ_0008103 affected NSCLC. The quantitative polymerase chain reaction was used to quantify the exosome-containing circ_0061407 and circ_0008103 in the serum samples of healthy, pneumonia, benign lung tumours, and NSCLC. The diagnostic efficacy was evaluated using receiver operating characteristic curves. Results The levels of circ_0061407 and circ_0008103 within exosomes were down-regulated in the serum of patients with NSCLC. The up-regulation of circ_0061407 and circ_0008103 inhibited the proliferation, migration/invasion, cloning formation of NSCLC cells in vitro and inhibited lung tumour growth in vivo. Circ_0061407 and circ_0008103 were observed to be packaged in exosomes and transported to recipient cells, where they inhibited the proliferation, migration/invasion, and cloning formation abilities of the recipient cells. Moreover, circ_0061407 and circ_0008103 might be involved in the progression of NSCLC by interacting with microRNAs and proteins. Additionally, lower serum exosomal circ_0061407 and circ_0008103 levels were associated with advanced pathological staging and distant metastasis. Conclusions This study identified two novel exosome-transported circRNAs (circ_0061407 and circ_0008103) associated with NSCLC. These findings may provide additional insights into the development of NSCLC and potential diagnostic biomarkers for NSCLC.

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Section: Methodsmentioning

confidence: 99%

“…CircRNAs have diverse functions through a variety of mechanisms. They act as miRNA sponges by competitively binding to miRNAs, leading to the derepression of miRNAs on the target mRNAs [ 17 ]. Additionally, they function as transcriptional and splicing regulators through binding to RNA-binding proteins [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

Exosome-transported circ_0061407 and circ_0008103 play a tumour-repressive role and show diagnostic value in non-small-cell lung cancer

Chen,

Ma,

Chen

et al. 2024

J Transl Med

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“…Additionally, we employed the "multiMiR" package with experimental verification to screen for miRNAs that target pyroptosisassociated hub genes from miRTarBase database [25,26]. Subsequently, we estimated the target lncRNAs of the aforementioned miRNAs from the StarBase Website (http://starbase.sysu.edu.cn/) via a clipExpNum > 7-based prediction, using experimentally validated associations as a filtering criteria [25,27]. Lastly, we visualized the generated cecRNA axis in Cytoscape software.…”

Section: Generation Of Immune Infiltration and Cerna Regulatory Axesmentioning

confidence: 99%

Identification of Pyroptosis-Related Genes Regulating the Progression of Chronic Rhinosinusitis with Nasal Polyps

Li,

Zhang,

Wang

et al. 2024

Int Arch Allergy Immunol

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Introduction: Chronic rhinosinusitis with nasal polyps (CRSwNP) is an immunologic disease, and pyroptosis, an inflammation-based cellular death, strictly modulates CRSwNP pathology, whereas the pyroptosis genes and mechanisms involved in CRSwNP remain unclear. Herein, we explored disease biomarkers and potential therapeutic targets for pyroptosis and immune regulation in CRSwNP using bioinformatics analysis and tissue-based verification. Methods: We retrieved the transcriptional profiles of the high-throughput dataset GSE136825 from the Gene Expression Omnibus database, as well as 170 pyroptosis-related gene expressions from GeneCards. Using R, we identified differentially expressed pyroptosis-related genes and examined the potential biological functions of the aforementioned genes using Gene Ontology, Kyoto Encyclopedia of the Genome pathway, immune infiltration, and protein-protein interaction (PPI) network analyses, thereby generating a list of hub genes. The hub genes were, in turn, verified using real-time quantitative polymerase chain reaction (qRT-PCR), immunohistochemistry (IHC), and Western blotting (WB). Ultimately, using the StarBase and miRTarBase databases, we estimated the targeting microRNAs and long chain non-coding RNAs. Results: We demonstrated that the identified pyroptosis-related genes primarily modulated bacterial defense activities, as well as inflammasome immune response and assembly. Moreover, they were intricately linked to neutrophil and macrophage infiltration. Furthermore, we validated the tissue contents of hub genes AIM2, NLPR6, and CASP5 and examined potential associations with clinical variables. We also developed a competitive endogenous RNA (ceRNA) modulatory axis to examine possible underlying molecular mechanisms. Conclusion: We found AIM2, CASP5, and NLRP6, three hub genes for pyroptosis in chronic rhinosinusitis with nasal polyps, by biological analysis, experimental validation, and clinical variable validation.

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“…2.10 Construction of the circRNA-miRNA-mRNA network miRanda database (version 1.0, analysis parameters: score ≥150, and energy threshold ≤ −10) was used to predict miRNAs that interacted with CO-DE circRNAs (Enright et al, 2003). The intersection of RNAhybrid (analysis parameters: energy threshold ≤ −10 and p ≤ 0.05), TargetScan (http://www.targetscan.org, default parameters), and miRanda database was used to predict miRNAs that interacted with CO-DE mRNAs in the embryonic period (Enright et al, 2003;Krüger and Rehmsmeier, 2006;Ma et al, 2023). Finally, an endogenous competitive ceRNA (circRNA-miRNA-mRNA) network was visualized using Cytoscape software (version 3.5.1).…”

Section: Construction Of the Mrna-lncrna Coexpression Networkmentioning

confidence: 99%

Integrative transcriptomic profiling of ncRNAs and mRNAs in developing mouse lens

Zhang,

Liu,

et al. 2024

Front. Genet.

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In recent years, burgeoning research has underscored the pivotal role of non-coding RNA in orchestrating the growth, development, and pathogenesis of various diseases across organisms. However, despite these advances, our understanding of the specific contributions of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) to lens development remains notably limited. Clarifying the intricate gene regulatory networks is imperative for unraveling the molecular underpinnings of lens-related disorders. In this study, we aimed to address this gap by conducting a comprehensive analysis of the expression profiles of messenger RNAs (mRNAs), lncRNAs, and circRNAs at critical developmental time points of the mouse lens, encompassing both embryonic (E10.5, E12.5, and E16.5) and postnatal stages (P0.5, P10.5, and P60). Leveraging RNA-sequencing technology, we identified key transcripts pivotal to lens development. Our analysis revealed differentially expressed (DE) mRNAs, lncRNAs, and circRNAs across various developmental stages. Particularly noteworthy, there were 1831 co-differentially expressed (CO-DE) mRNAs, 150 CO-DE lncRNAs, and 13 CO-DE circRNAs identified during embryonic stages. Gene Ontology (GO) enrichment analysis unveiled associations primarily related to lens development, DNA conformational changes, and angiogenesis among DE mRNAs and lncRNAs. Furthermore, employing protein–protein interaction networks, mRNA–lncRNA co-expression networks, and circRNA–microRNA–mRNA networks, we predicted candidate key molecules implicated in lens development. Our findings underscore the pivotal roles of lncRNAs and circRNAs in this process, offering fresh insights into the pathogenesis of lens-related disorders and paving the way for future exploration in this field.

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The diagnostic potential of a circRNA–miRNA network in non-small cell lung cancer

Cited by 19 publications

References 33 publications

Exosome-transported circ_0061407 and circ_0008103 play a tumour-repressive role and show diagnostic value in non-small-cell lung cancer

Exosome-transported circ_0061407 and circ_0008103 play a tumour-repressive role and show diagnostic value in non-small-cell lung cancer

Identification of Pyroptosis-Related Genes Regulating the Progression of Chronic Rhinosinusitis with Nasal Polyps

Integrative transcriptomic profiling of ncRNAs and mRNAs in developing mouse lens

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