Bioinformatics Analysis for Identifying Differentially Expressed MicroRNAs Derived from Plasma Exosomes Associated with Radiotherapy Resistance in Non-Small-Cell Lung Cancer

Abstract

Objective. To explore the differentially expressed microRNAs (DEmiRs) derived from plasma exosomes related to radiotherapy resistance and their corresponding pathways in non-small-cell lung cancer (NSCLC). Methods. Plasma samples from NSCLC patients were retrieved and analyzed. The patients were divided into 3 groups based on the tumor regression grade criteria, assessed by radiological imaging after radiotherapy. TRG1 referred to tumor shrinkage of ≤30% after radiotherapy, TRG2 as 30 % < TRG < 50 % , and TRG3 as TRG ≥ 50 %. High-throughput sequencing and bioinformatics analysis were used to compare the DEmiRs between the three groups. The miRanda, PITA, and RNAhybrid software were used to identify potential target genes of the DEmiRs. GO function enrichment and KEGG pathway enrichment analyses were performed on the target gene set. Results. There were 24 DEmiRs (12 were upregulated and 12 downregulated) between the TRG1 and TRG2 groups, 11 between the TRG1 and TRG3 groups (6 upregulated and 5 downregulated), and 35 between the TRG2 and TRG3 groups. The common DEmiRs between the three groups were miR-92a-3p. GO analysis showed that the target genes of the DEmiRs were mainly enriched in unicellular organism processes, cell transformation, cell localization, and their establishment. KEGG enrichment analysis showed that target genes were significantly enriched in the Ras signaling pathway and associated with endocytosis. Among the 135 identified target genes of miR-92a-3p, 4 were involved in the PI3K-Akt signaling pathway (the downstream pathway of the Ras gene) and 3 in the cAMP signaling pathway (the upstream pathway of the Ras gene). Further, 2 other target genes were involved in the Rap1 signaling pathway (the upstream pathway of PI3K-Akt). Conclusion. By assessing the expression and functional profile of DEmiRs in the plasma exosomes of NSCLC patients after radiotherapy, miR-92a-3p was identified as a promising target affecting radiotherapy outcomes through the Ras signaling pathway.

miR-92a-3p regulates cisplatin-induced cancer cell death

“…For example, miR-92a-3p has been shown to inhibit apoptosis and tumor growth in many distinct malignancies by targeting the BH3-only protein BIM and PTEN respectively [ 23 , 27 ], while promoting cell proliferation by cancer-type specific mechanisms involving targeting of genes such as BTG2 in breast cancer or FBXW7 in renal cancer [ 39 , 45 ]. In lung cancer, previous reports have notably shown the diagnostic/prognostic value of miR-92a-3p as well as a significant association between expression of this miRNA and response to radiotherapy [ 46 – 49 ]. Nevertheless, although several in vitro evidence support an oncogenic role of miR-92a-3p in lung cancer cells [ 50 ], its precise molecular function remains unclear and little is known about the role played by miR-92a-3p in chemoresistance.…”

Multi-omics of extracellular vesicles: An integrative representation of functional mediators and perspectives on lung disease study

“…Using plasma samples retrieved and analyzed from lung cancer patients, differentially expressed microRNAs were screened by bioinformatic analysis, and their target gene sets were identified by the miRanda, PITA, and RNAhybrid programs and evaluated by function and KEGG pathway enrichment analyses. The results finally determined a promising plasma EVs-derived miRNA target that had an impact on radiotherapy outcomes of NSCLC patients through the Ras signaling pathway ( Zeng et al, 2022 ). Similarly, based on serum-derived Piwi-interacting RNA (piRNA) of EVs from healthy and diseased individuals, a candidate signature piRNA has been screened by differential expression analysis and validated by quantitative real-time PCR, with an assessment by the area under the curve value and associated analysis as to age and the TNM stage of patients.…”

“…There are web-based resources for elucidating molecular mechanisms and pathophysiology of EVs isolated from different disease conditions, including ExoCarta, EVpedia, and Vesiclepedia ( Keerthikumar et al, 2017 ). The miRanda, PITA, and RNAhybrid programs can be used to identify differentially expressed microRNAs derived from exosomes and their potential target genes ( Zeng et al, 2022 ). There are many bioinformatics tools available for evaluating various parameters relevant to EVs, and these analyses can help to identify the functional ability of EVs by analyzing host-pathogen interactions, toxicity, omics, and pathogenesis ( Saravanakumar et al, 2022 ).…”

Sequencing and validation of exosomal miRNAs panel as novel plasma biomarkers for early diagnosis and prognosis prediction in laryngeal cancer

“…Bene ting from the non-invasive, convenient, and e cient features, plasma exosome detection is increasingly explored in the early diagnosis of cancer, among which, miRNAs are more stable because of the speci c sorting mechanism [7], may offer an e cient, non-invasive or minimally invasive marker alternative. Recently plasma exosomal miRNAs have been shown to be early diagnostic markers for gastric cancer [8,9], epithelial ovarian cancer [9], pancreatic cancer [10], lung adenocarcinoma [11], and can be used to assess treatment response and prognosis in esophageal squamous cell carcinoma [12], non-small cell lung cancer [13], breast cancer [14], etc. In LSCC, serum exosomal hsa-miR-941 has been identi ed as a promising oncogenic marker, up-regulated level of hsa-miR-941 promotes cell proliferation and invasion [15].…”