The Oncogenic and Tumor Suppressive Long Non-Coding RNA–microRNA–Messenger RNA Regulatory Axes Identified by Analyzing Multiple Platform Omics Data from Cr(VI)-Transformed Cells and Their Implications in Lung Cancer
Abstract
:1. Introduction
2. Material and Methods
2.1. Cell Culture and Microarray Analyses
2.2. Gene Set Enrichment (GSE) Analysis
2.3. Construction of the lncRNA/miRNA/mRNA Regulatory ceRNA Module Network
2.4. Cancer Stemness Signature Analysis
2.5. The ceRNA Modules and Survival Analysis Using TCGA Datasets
2.6. The Receiver Operating Characteristic (ROC) Curve Analysis
3. Results
3.1. Microarray Gene Expression Profiling and Identification of DE of lncRNAs, miRNAs, and mRNAs
3.2. Functional Annotation Analysis of DE lncRNA, miRNA, and mRNA
3.3. Oncogenic and Tumor Suppressive ceRNA Module–Protein Interactions
3.4. Identification of Oncogenic and Tumor Suppressor ceRNA Modules
3.5. Validation of the Oncogenic and Tumor Suppressor ceRNA Modules in Human Lung Cancer
3.6. Stemness Signature of ceRNA Modules
3.7. Prognostic Potential Rating of ceRNA Modules in Lung Cancer
3.8. Diagnostic Performance Assessment of Three ceRNA Modules in Lung Cancer
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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lncRNA | miRNA | mRNA | |
---|---|---|---|
Oncogenic ceRNA modules | |||
A | HOTAIRM1 | miR-182-5p | ERO1A |
B | GOLGA8B | miR-30d-5p | RUNX2 |
C | PDCD6IPP2 | miR-23a-3p | HOXA1 |
Tumor suppressor ceRNA modules | |||
D | ANXA2P1 | miR-20b-5p | FAM241A (C4orf32) |
E | MIR99AHG | miR-218-5p | GPM6A |
F | SH3RF3-AS1 | miR-34a-5p | HECW2 |
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Sweef, O.; Yang, C.; Wang, Z. The Oncogenic and Tumor Suppressive Long Non-Coding RNA–microRNA–Messenger RNA Regulatory Axes Identified by Analyzing Multiple Platform Omics Data from Cr(VI)-Transformed Cells and Their Implications in Lung Cancer. Biomedicines 2022, 10, 2334. https://doi.org/10.3390/biomedicines10102334
Sweef O, Yang C, Wang Z. The Oncogenic and Tumor Suppressive Long Non-Coding RNA–microRNA–Messenger RNA Regulatory Axes Identified by Analyzing Multiple Platform Omics Data from Cr(VI)-Transformed Cells and Their Implications in Lung Cancer. Biomedicines. 2022; 10(10):2334. https://doi.org/10.3390/biomedicines10102334
Chicago/Turabian StyleSweef, Osama, Chengfeng Yang, and Zhishan Wang. 2022. "The Oncogenic and Tumor Suppressive Long Non-Coding RNA–microRNA–Messenger RNA Regulatory Axes Identified by Analyzing Multiple Platform Omics Data from Cr(VI)-Transformed Cells and Their Implications in Lung Cancer" Biomedicines 10, no. 10: 2334. https://doi.org/10.3390/biomedicines10102334