Long Non-Coding PROX1-AS1 Expression Correlates with Renal Cell Carcinoma Metastasis and Aggressiveness
Abstract
:1. Introduction
2. Materials and Methods
2.1. Tissues Samples
2.2. Cell Lines
2.3. RNA Isolation and Real-Time (RT)-qPCR
2.4. Methylation Analysis
2.5. In Vitro Treatment of Cultured Cells with 5-Aza-2′-Deoxycytidine
2.6. DNA Isolation, Bisulfite Modification and Sequencing PCR
Bisulfite Sequencing PCR
2.7. Statistical Analysis
3. Results
3.1. LncRNA PROX1-AS1 Expression Is Higher in RCC Specimens and Positively Correlates with Metastasis, Lymph Node Invasion, Tumor Stage, and Grade
3.2. Methylation Could Regulate PROX1-AS1 Expression in Healthy Kidney and Renal Carcinoma Cells
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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lncRNA | Expression in Renal Tumor | Role in Renal Tumor | Mechanism | Reference |
---|---|---|---|---|
FILNC1 | Downregulated | -Inhibition of energy metabolism, -Suppression of tumor development | Downregulation of tyrosine-protein kinase Met (c-Myc) protein | [14] |
TCL6 | Downregulated | -Sensitization of clear cell renal carcinoma to paclitaxel-induced apoptosis | Downregulation of miR-221 | [16] |
lnc-DILC | Downregulated | -Inhibition of proliferation, migration and invasion of clear cell renal carcinoma cells | Binding with phosphatase and tensin homolog (PTEN) and suppression of its degradation | [17] |
MRCCAT1 | Upregulated | -Promotion of proliferation, invasion and metastasis | Inhibition of natriuretic peptide receptor 3 (NPR3) and activation of p38-MAPK signaling | [15] |
URRCC | Upregulated | -Enhancement of proliferation and metastasis ofclear cell renal carcinoma cells | Positive feed-forward loop with EGF like domain multiple 7 (EGFL7)/phosphor-serine/threonine-specific protein kinase (P-AKT)/forkhead box O3 (FOXO3) signaling | [18] |
MALAT1 | Upregulated | -Promotion of proliferation and invasion, -Inhibition of apoptosis, -Adverse correlation with patient survival | Interaction with enhancer of zeste 2 polycomb repressive complex 2 subunit (Ezh2) and miR-205 | [19] |
lnc-ARSR | Upregulated | -Promotion of sunitinib-resistance | Competitive binding miR-34/miR-449, facilitation of AXL receptor tyrosine kinase and c-MET expression | [20] |
lnc-TSI | Upregulated | -Inhibitor of clear cell renal carcinoma cells metastasis | Suppression of transforming growth factor beta 1 (TGF-β) induced epithelial-mesenchymal transition | [21] |
No. | CpG-Islands (UCSC hg38) | Primers | Annealing Temperature (°C) | Fragment Length |
---|---|---|---|---|
1 | chr1:213985384–213985737 | F: GTATTTTTAGTAGGTTGAGAGGG R: CTAAATCTAACAAAAACTCCAACCC | 66 | 233 |
2 | chr1:213982658–213983508 | F: TGGTATATTGGAGGAGGTATATAGG R: TACACTTCCAAACTATAACAAAAT | 58 | 140 |
3 | chr1:213979872–213980325 | F: GAGGTTGTTAGGAGTTTGGTTTGTA R: AAAAAACTCTCCCACCCCCAAC | 65 | 239 |
Clinical and Pathological Features | Number | PROX1-AS1 Expression in Tumor | p-Value | PROX1-AS1 Expression in Non-Tumor Tissue | p-Value | ||||
---|---|---|---|---|---|---|---|---|---|
Mean RQ | SD | Mean RQ | SD | ||||||
Entire Group | 42 | 51.9 | 95.6 | p = 0.6 | 47.4 | 86.3 | p = 0.6 | ||
Gender | Women | 20 | 77.3 | 120.4 | p = 0.88 | 37.4 | 79.5 | p = 0.57 | |
Men | 22 | 28.9 | 59.6 | 56.4 | 93.0 | ||||
Age Group | <45 yrs | 5 | 37.8 | 77.3 | p = 0.43 | 27.6 | 45.8 | p = 0.9779 | |
≤45–65 yrs | 22 | 73.3 | 115.3 | 45.1 | 81.9 | ||||
≥65 yrs | 15 | 25.6 | 59.8 | 57.1 | 104.5 | ||||
Histopathological Type | KIRC | 33 | 54.3 | 93.4 | p = 0.64 | 42.0 | 74.9 | p = 0.1910 | |
KIRP | 3 | 7.1 | 11.9 | 12.3 | 15.2 | ||||
KICH | 3 | 111.6 | 190.8 | 1.4 | 0.3 | ||||
AML | 3 | 11.0 | 10.6 | 187.1 | 166.7 | ||||
* pTNM | Tumor Stage | pT1 | 23 | 18.0 | 37.0 | p = 0.07; (pT1 vs. pT2 p = 0.03) | 44.8 | 84.8 | p = 0.820 |
pT2 | 5 | 167.1 | 156.1 | 28.1 | 45.7 | ||||
pT3–pT4 | 14 | 66.6 | 107.9 | 58.4 | 101.9 | ||||
Lymph Node Invasion | pN0 | 37 | 38.3 | 79.5 | p = 0.04 | 50.6 | 90.2 | p = 0.734 | |
pN1 | 2 | 215.6 | 55.9 | 57.0 | 73.1 | ||||
Metastasis | pM0 | 32 | 32.1 | 64.5 | p = 0.04 | 44.3 | 80.1 | p = 0.578 | |
pM1 | 7 | 117.2 | 141.2 | 81.1 | 123.7 | ||||
** Grade | G1-G2 | 34 | 40.6 | 82.6 | p = 0.05 | 46.4 | 88.3 | p = 0.081 | |
G3-G4 | 5 | 93.3 | 115.3 | 81.6 | 94.5 |
CpG Island-1 | CpG Island-2 | CpG Island-3 | |
---|---|---|---|
Position (hg38): | chr1:213985384 | chr1:213982658 | chr1:213979872 |
–213985737 | –213983508 | –213980325 | |
Band: | 1q32.3 | 1q32.3 | 1q32.3 |
Size (bp): | 354 | 851 | 454 |
CpG count: | 40 | 84 | 42 |
Percentage CpG: | 22.6% | 19.7% | 18.5% |
Percentage C or G | 66.7% | 71.7% | 70.0% |
CpG PROX1-AS1 | 1 | 2 | 3 | |||
---|---|---|---|---|---|---|
methC | demethC | methC | demethC | methC | demethC | |
contr | 5-AZA | contr | 5-AZA | contr | 5-AZA | |
HEK293 | + | + | + | − | + | + |
786-P | + | − | + | − | + | − |
A498 | + | − | + | − | + | − |
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Rudzinska, M.; Czarnecka-Chrebelska, K.H.; Kuznetsova, E.B.; Maryanchik, S.V.; Parodi, A.; Korolev, D.O.; Potoldykova, N.; Svetikova, Y.; Vinarov, A.Z.; Nemtsova, M.V.; et al. Long Non-Coding PROX1-AS1 Expression Correlates with Renal Cell Carcinoma Metastasis and Aggressiveness. Non-Coding RNA 2021, 7, 25. https://doi.org/10.3390/ncrna7020025
Rudzinska M, Czarnecka-Chrebelska KH, Kuznetsova EB, Maryanchik SV, Parodi A, Korolev DO, Potoldykova N, Svetikova Y, Vinarov AZ, Nemtsova MV, et al. Long Non-Coding PROX1-AS1 Expression Correlates with Renal Cell Carcinoma Metastasis and Aggressiveness. Non-Coding RNA. 2021; 7(2):25. https://doi.org/10.3390/ncrna7020025
Chicago/Turabian StyleRudzinska, Magdalena, Karolina H. Czarnecka-Chrebelska, Ekaterina B. Kuznetsova, Sofya V. Maryanchik, Alessandro Parodi, Dmitry O. Korolev, Nataliya Potoldykova, Yulia Svetikova, Andrey Z. Vinarov, Marina V. Nemtsova, and et al. 2021. "Long Non-Coding PROX1-AS1 Expression Correlates with Renal Cell Carcinoma Metastasis and Aggressiveness" Non-Coding RNA 7, no. 2: 25. https://doi.org/10.3390/ncrna7020025