LncRNA LINC00518 Acts as an Oncogene in Uveal Melanoma by Regulating an RNA-Based Network
Abstract
:Simple Summary
Abstract
1. Introduction
2. Results
2.1. Selection of lncRNAs from the UM TCGA Dataset
2.2. Differential Expression of lncRNAs in Patient Biopsies
2.3. LINC00518 May Be Involved in Metastasis-Related Processes Rather Than Cell Proliferation
2.4. LINC00518 Transient Silencing Affects the RNA-Based Network
2.5. RNA Molecular Axes of LINC00518
2.6. RNA–RNA Interaction between LINC00518 and mRNAs
2.7. Identification of Transcription Factors Potentially Regulating LINC00518 Expression
3. Discussion
4. Materials and Methods
4.1. LncRNA Selection
4.2. Patient Recruitment and Tissue, Vitreous, and Serum Sampling
4.3. RNA Isolation from FFPE Tissues, Vitreous, and Serum Samples
4.4. Subcellular Fractionation
4.5. Computational Analysis
4.6. In Vitro Functional Assays on UM Cells
- Cell cultures
- MAPK inhibition
- Cell cycle block and activation
- EMT induction
- HIF1A activation
- LINC00518 transient silencing
- Inhibition of TFs potentially regulating LINC00518 expression
4.7. Expression Analysis through Real-Time PCR
4.8. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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92.1 | MEL270 | ||||||
---|---|---|---|---|---|---|---|
miRNAs Regulating mRNA Expression | miRNA/mRNA | 24 h | 48 h | Correlation vs. LINC00518 | 24 h | 48 h | Correlation vs. LINC00518 |
miR-143-3p | −1.08 (0.55) | 1.71 (0.61) | −0.2 (0.53) | 1.58 (0.51) | −1.63 (0.12) | −0.35 (0.26) | |
miR-145-5p | −1.19 (0.47) | 1.38 (0.46) | −0.49 (0.1) | 1.98 (0.65) | 1.08 (0.87) | 0.54 (0.06) | |
miR-199a-5p | 1.23 (0.99) | 1.46 (0.08) | −0.5 (0.09) | 1.13 (0.53) | 1.07 (0.87) | −0.16 (0.61) | |
miR-212-5p | 1 (0.63) | 1.33 (0.86) | −0.35 (0.26) | 1.6 (0.99) | −1.09 (0.51) | 0.47 (0.12) | |
miR-3191-3p | 1.94 (0.96) | 2.5 (0.08) | 0.11 (0.73) | 1.84 (0.33) | 1.21 (0.68) | 0.35 (0.26) | |
miR-497-5p | −1.12 (0.48) | 1.65 (0.48) | −0.48 (0.11) | 1.22 (0.86) | 1.19 (0.72) | 0.44 (0.15) | |
miR-212-5p, miR-3191-3p | AHCYL2 | −1.22 (0.18) | 1.82 (0.16) | −0.38 (0.22) | 1 (0.98) | 1.19 (0.21) | 0.65 (0.02) |
miR-199a-5p | CRTAP | −1.23 (0.11) | 1.11 (0.37) | 0.51 (0.09) | −1.05 (0.75) | 1.27 (0.13) | 0.64 (0.02) |
miR-3191-3p | ENTPD1 | 1.04 (0.96) | 1.59 (0.18) | 0.52 (0.08) | −1.02 (0.81) | 1.03 (0.82) | 0.74 (0.005) |
miR-145-5p | F11R | 1.33 (0.24) | 1.08 (0.12) | −0.7 (0.01) | 1.04 (0.67) | 1.07 (0.54) | 0.59 (0.04) |
miR-145-5p, miR-212-5p | IFFO2 | 1.01 (0.99) | 1.42 (0.26) | 0.13 (0.68) | 1.01 (0.87) | 1.2 (0.29) | 0.73 (0.007) |
miR-145-5p, miR-3191-3p | IP6K1 | 1.13 (0.62) | 2.41 (0.25) | −0.22 (0.49) | 1.15 (0.61) | 1.05 (0.71) | 0.74 (0.005) |
miR-3191-3p | KCTD15 | 1.02 (0.87) | −1.15 (0.1) | 0.22 (0.49) | 1.05 (0.72) | 1.05 (0.93) | 0.18 (0.57) |
miR-143-3p | KLF8 | −1.68 (0.07) | −1.12 (0.26) | 0.48 (0.11) | −1.39 (0.04) | 1.28 (0.46) | 0.15 (0.64) |
miR-497-5p | LINGO2 | −1.68 (0.09) | −1.57 (0.15) | 0.59 (0.04) | −1.47 (0.04) | −1.14 (0.18) | 0.42 (0.17) |
miR-143-3p | NFIA | −1.47 (0.13) | 1.56 (0.25) | 0.58 (0.04) | −1.48 (0.04) | 1.12 (0.48) | 0.34 (0.27) |
miR-145-5p, miR-497-5p | OTUD7B | −1.4 (0.03) | 1.26 (0.54) | 0.45 (0.14) | −1.23 (0.04) | 1 (0.59) | 0.75 (0.004) |
miR-3191-3p | RAB43 | −1.52 (0.11) | 1.27 (0.43) | 0.43 (0.16) | −1.06 (0.65) | −1.11 (0.75) | 0.72 (0.008) |
miR-212-5p | RABGAP1L | 1 (0.76) | 1.55 (0.06) | −0.29 (0.36) | 1.24 (0.12) | 1.13 (0.25) | 0.31 (0.32) |
miR-199a-5p, miR-212-5p | SEC22C | −1.31 (0.001) | 1.36 (0.16) | −0.11 (0.73) | −1.11 (0.03) | −1.07 (0.01) | 0.71 (0.009) |
miR-497-5p | SEMA6A | 1.38 (0.17) | 1.38 (0.34) | −0.58 (0.04) | −1.03 (0.99) | −1.06 (0.04) | 0.41 (0.18) |
miR-3191-3p | VAMP3 | −1.37 (0.02) | 1.31 (0.25) | 0.58 (0.04) | −1.05 (0.26) | 1.36 (0.18) | 0.58 (0.04) |
miR-199a-5p | ZBTB20 | −1.03 (0.75) | −1.1 (0.17) | −0.31 (0.32) | 1.22 (0.19) | 1.21 (0.35) | 0.04 (0.9) |
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Barbagallo, C.; Caltabiano, R.; Broggi, G.; Russo, A.; Puzzo, L.; Avitabile, T.; Longo, A.; Reibaldi, M.; Barbagallo, D.; Di Pietro, C.; et al. LncRNA LINC00518 Acts as an Oncogene in Uveal Melanoma by Regulating an RNA-Based Network. Cancers 2020, 12, 3867. https://doi.org/10.3390/cancers12123867
Barbagallo C, Caltabiano R, Broggi G, Russo A, Puzzo L, Avitabile T, Longo A, Reibaldi M, Barbagallo D, Di Pietro C, et al. LncRNA LINC00518 Acts as an Oncogene in Uveal Melanoma by Regulating an RNA-Based Network. Cancers. 2020; 12(12):3867. https://doi.org/10.3390/cancers12123867
Chicago/Turabian StyleBarbagallo, Cristina, Rosario Caltabiano, Giuseppe Broggi, Andrea Russo, Lidia Puzzo, Teresio Avitabile, Antonio Longo, Michele Reibaldi, Davide Barbagallo, Cinzia Di Pietro, and et al. 2020. "LncRNA LINC00518 Acts as an Oncogene in Uveal Melanoma by Regulating an RNA-Based Network" Cancers 12, no. 12: 3867. https://doi.org/10.3390/cancers12123867