lncRNA Expression after Irradiation and Chemoexposure of HNSCC Cell Lines
<p>Heat map and clustering of 96 lncRNAs after irradiation of head and neck squamous cell carcinoma (HNSCC) cell lines using dose of 5 Gy, 10 Gy, and 20 Gy. Data shown as 2<sup>−</sup><sup>ΔΔ</sup><sup>Ct</sup> (compared to non-irradiated control).</p> "> Figure 2
<p>Differences in lncRNAs expression: HOTAIR, HOXA3as, SNHG5, and Zfhx2as in HNSCC cell lines after exposure to 5 Gy irradiation. Paired <span class="html-italic">t</span>-test; the graphs show relative expression, mean value with standard error of mean (SEM); * <span class="html-italic">p</span> < 0.05.</p> "> Figure 3
<p>Differences in lncRNAs expression: CAR Intergenic 10, Dio3os (family), HAR1A, Zfhx2as, and HAR1B in HNSCC cell lines after exposure to 10 Gy irradiation and in non-irradiated controls. Paired <span class="html-italic">t</span>-test; the graphs show relative expression, mean value with SEM; * <span class="html-italic">p</span> < 0.05; ** <span class="html-italic">p</span> < 0.01.</p> "> Figure 4
<p>Differences in lncRNAs expression: HOXA6as, PTENP1, and Zfhx2as in HNSCC cell lines after exposure to 20 Gy irradiation. Paired <span class="html-italic">t</span>-test; the graphs show relative expression, mean value with SEM; * <span class="html-italic">p</span> < 0.05.</p> "> Figure 5
<p>Heat map and clustering of 96 lncRNAs after cisplatin and doxorubicin exposure of HNSCC cell lines. Data shown as 2<sup>−</sup><sup>ΔΔ</sup><sup>Ct</sup> (compared to non-treated control).</p> "> Figure 6
<p>Differences in lncRNAs expression: AIR, antiPEG11, BACE1AS (family), CAR Intergenic 10, DISC2 (family), IPW, MEG3 (family), lincRNA-ROR, ncR-uPAR, PCGEM1, PRINS, PSF Inhibiting RNA, PTENP1, SNHG6, SRA, and ST7OT in HNSCC cell lines after exposure to cisplatin. Paired <span class="html-italic">t</span>-test; the graphs show relative expression, mean value with SEM; * <span class="html-italic">p</span> < 0.05, ** <span class="html-italic">p</span> < 0.01.</p> "> Figure 7
<p>Differences in lncRNAs expression: antiPEG11, BACE1AS (family), EgoA, Evf1 and EVF2, lincRNA-p21, lincRNA-SFMBT2, Malat1, Nespas, PCGEM1, UM9-5, Zfas1, and ST7OT in HNSCC cell lines after exposure to doxorubicin and controls non-treated. Paired <span class="html-italic">t</span>-test; the graphs show relative expression, mean value with SEM; * <span class="html-italic">p</span> < 0.05, ** <span class="html-italic">p</span> < 0.01, *** <span class="html-italic">p</span> < 0.001.</p> ">
Abstract
:1. Introduction
2. Materials and Methods
2.1. Cell Culture
2.2. Irradiation and Chemoexposure of Cell Lines
2.3. RNA Isolation
2.4. Reverse Transcription
2.5. Quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR)
2.6. Prediction of Molecular Interactions In Silico
2.7. Statistical Analysis
3. Results
3.1. Long Non-Coding RNAs Expression after Irradiation Depends on Radiation Dose and Type of Cell Line
3.2. Long Non-Coding RNAs Expression after Chemoexposure Depends on the Drug and Type of Cell Line
3.3. Possible Regulation of Important Biological Processes and Cellular Pathways by Dysregulated lncRNAs In Silico
4. Discussion
5. Conclusions
Author Contributions
Founding
Conflicts of Interest
Ethics Approval and Consent to Participate
Consent for Publication
Availability of Data and Materials Section
References
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Cell Line | Cisplatin [μg/mL] | Doxorubicin [μg/mL] |
---|---|---|
SCC-040 | 10.67 | 1.54 |
SCC-25 | 4.49 | 2.70 |
FaDu | 5.88 | 0.23 |
Cal27 | 3.42 | 0.63 |
lncRNA | 5 Gy | Control | p Value | Regulation | ||
---|---|---|---|---|---|---|
Mean Value | SEM | Mean Value | SEM | |||
HOTAIR | 0.0007863 | 0.0001301 | 0.0003619 | 0.000062 | 0.0284 | Up |
HOXA3as | 0.003036 | 0.0003097 | 0.001569 | 0.002016 | 0.0313 | Up |
SNHG5 | 0.02683 | 0.009113 | 0.02062 | 0.008001 | 0.0444 | Down |
Zfhx2as | 0.004621 | 0.001548 | 0.007150 | 0.0008250 | 0.0415 | Down |
lncRNA | 10 Gy | Control | p Value | Regulation | ||
---|---|---|---|---|---|---|
Mean Value | SEM | Mean Value | SEM | |||
CAR Intergenic 10 | 0.003959 | 0.0006232 | 0.006326 | 0.000663 | 0.0090 | Down |
Dio3os | 0.01809 | 0.003639 | 0.02259 | 0.004096 | 0.0137 | Down |
HAR1A | 0.06480 | 0.01247 | 0.09771 | 0.01660 | 0.0486 | Down |
Zfhx2as | 0.002828 | 0.0006854 | 0.007150 | 0.0008250 | 0.0174 | Down |
HAR1B | 0.7414 | 0.1607 | 1.432 | 0.1190 | 0.0116 | Down |
lncRNA | 20 Gy | Control | p Value | Regulation | ||
---|---|---|---|---|---|---|
Mean Value | SEM | Mean Value | SEM | |||
HOXA6as | 1.402 | 0.2677 | 4.402 | 0.7998 | 0.0359 | Down |
Zfhx2as | 0.004668 | 0.0008109 | 0.007150 | 0.0008250 | 0.0399 | Down |
PTENP1 | 0.001173 | 0.00009963 | 0.0007758 | 0.0001416 | 0.0215 | Up |
lncRNA | Cisplatin | Control | p Value | Regulation | ||
---|---|---|---|---|---|---|
Mean Value | SEM | Mean Value | SEM | |||
AIR | 0.0000253 | 0.00001148 | 0.0004905 | 0.0000939 | 0.0216 | Down |
antiPEG11 | 0.000023 | 0.00002268 | 0.0007075 | 0.0001743 | 0.0346 | Down |
BACE1AS | 0.001018 | 0.0003542 | 0.005802 | 0.0004859 | 0.0101 | Down |
CAR Intergenic 10 | 0.001177 | 0.0001425 | 0.006326 | 0.0006632 | 0.0043 | Down |
DISC2 | 0.002344 | 0.0004130 | 0.003313 | 0.0006576 | 0.0383 | Down |
MEG3 | 0.0002745 | 0.00003811 | 0.0006915 | 0.0001430 | 0.0450 | Down |
ncR-uPAR | 0.03412 | 0.03412 | 0.3023 | 0.04289 | 0.0117 | Down |
PCGEM1 | 0.0004706 | 0.0004705 | 0.006559 | 0.001358 | 0.0347 | Down |
PRINS | 0.003718 | 0.0004419 | 0.009154 | 0.001596 | 0.0283 | Down |
PSF Inhibiting RNA | 0.0007353 | 0.0001013 | 0.001011 | 0.0001240 | 0.0093 | Down |
PTENP1 | 0.0002597 | 0.00004899 | 0.0007758 | 0.0001416 | 0.0326 | Down |
SNHG6 | 0.003473 | 0.001286 | 0.009557 | 0.001016 | 0.0190 | Down |
SRA | 0.001234 | 0.0004121 | 0.004215 | 0.0004109 | 0.0352 | Down |
ST7OT | 0.002699 | 0.002699 | 0.02712 | 0.003087 | 0.0018 | Down |
IPW | 0.006479 | 0.0009348 | 0.002217 | 0.0002986 | 0.0084 | Up |
lincRNA-ROR | 0.001588 | 0.0002322 | 0.000008324 | 0.000003423 | 0.0065 | Up |
lncRNA | Doxorubicin | Control | p Value | Regulation | ||
---|---|---|---|---|---|---|
Mean Value | SEM | Mean Value | SEM | |||
antiPEG11 | 0.000008542 | 0.000008388 | 0.0007075 | 0.0001743 | 0.0295 | Down |
BACE1AS | 0.001765 | 0.0008225 | 0.005802 | 0.0004859 | 0.0461 | Down |
EgoA | 0.0001311 | 0.0001299 | 8.464 | 1.256 | 0.0067 | Down |
lincRNA-p21 | 0.000009656 | 0.000008042 | 0.01798 | 0.001301 | 0.0008 | Down |
Malat1 | 0.002630 | 0.001737 | 0.01547 | 0.005476 | 0.0431 | Down |
PCGEM1 | 0.0000003499 | 0.0000002346 | 0.006559 | 0.001358 | 0.0169 | Down |
UM9-5 | 0.001597 | 0.0006579 | 0.007780 | 0.0007437 | 0.0019 | Down |
ST7OT | 0.00001693 | 0.00001578 | 0.02712 | 0.003087 | 0.0031 | Down |
Evf1 and EVF2 | 0.03276 | 0.008313 | 0.0003172 | 0.0001031 | 0.0290 | Up |
lincRNA-SFMBT2 | 0.04731 | 0.007573 | 0.0005287 | 0.0002873 | 0.0086 | Up |
Nespas | 0.01695 | 0.002727 | 0.01109 | 0.002470 | 0.0255 | Up |
Zfas1 | 0.2444 | 0.06615 | 0.00002017 | 0.0000069 | 0.0344 | Up |
lncRNA | Dysregulated by | Target | Biological Process/Cellular Pathway |
---|---|---|---|
HOTAIR | Radiotherapy | LPP, ABI2, NOS1 | Cell Cycle |
CFLAR, REL | Apoptosis signaling pathway | ||
FAT3 | Cadherin signaling pathway/Wnt signaling pathway | ||
PDK1 | RAS pathway/p53 pathway | ||
FZD3 | Wnt signaling pathway/angiogenesis/cadherin signaling pathway | ||
SMAD2 | TGF-beta signaling pathway | ||
FRK | Cadherin signaling pathway | ||
SRCAP | Wnt signaling pathway | ||
WNT2B | angiogenesis/Cadherin signaling pathway/Wnt signaling pathway | ||
CBL | EGFR signaling pathway | ||
SNHG5 | Radiotherapy | LPP, ABI2, HELZ, RANBP2, CEP250, CDK6, HERC1, PHC3, MYO5A | Cell Cycle |
FZD3 | Angiogenesis/Cadherin signaling pathway/Wnt signaling pathway | ||
CFLAR | Apoptosis signaling pathway | ||
FAT3, FAT1 | Cadherin signaling pathway/Wnt signaling pathway | ||
FRK | Cadherin signaling pathway | ||
SMAD2, BMPR2 | TGF-beta signaling pathway | ||
PTEN | Cell cycle/p53 pathway | ||
ZMAT3, MDM4 | p53 pathway | ||
FAT2, FER, FRK | Cadherin signaling pathway | ||
APC | Angiogenesis/Wnt signaling pathway | ||
NF1 | EGFR signaling pathway | ||
Dio3os | Radiotherapy | HELZ2, NOS1, CROCC, CEP250, LPP, ABI2, HERC2, RTEL1, SMC1A, HERC1, GAS7 | Cell Cycle |
NOTCH2 | Angiogenesis/Notch signaling pathway | ||
PKD1 | Angiogenesis/EGFR signaling pathway | ||
CFLAR | Apoptosis signaling pathway | ||
FAT3, FAT2, CELSR3 | Cadherin signaling pathway/Wnt signaling pathway | ||
CBL | EGFR signaling pathway | ||
MYH7B, SRCAP | Wnt signaling pathway | ||
NCOR2 | Notch signaling pathway | ||
HAR1A | Radiotherapy | RANBP2, LPP, ABI2, HELZ, PHC3, HERC1, MYO5A | Cell Cycle |
FZD3 | Angiogenesis | ||
CFLAR | Apoptosis signaling pathway | ||
FAT3, FZD3, CTNNA3 | Cadherin signaling pathway/Wnt signaling pathway | ||
CBL | EGFR signaling pathway | ||
BMPR2 | TGF-beta signaling pathway | ||
HAR1B | Radiotherapy | LPP, ABI2, RSF1, HERC2, HELZ | Cell Cycle |
FZD3 | Angiogenesis/Cadherin signaling pathway/Wnt signaling pathway | ||
CFLAR | Apoptosis signaling pathway | ||
FAT3 | Cadherin signaling pathway/Wnt signaling pathway | ||
FRK, FER | Cadherin signaling pathway | ||
PDK1 | RAS pathway | ||
FAT1 | Wnt signaling pathway | ||
AIR | Cisplatin | NOS1, LPP, ABI2, HELZ | Cell Cycle |
FZD3 | Angiogenesis/Cadherin signaling pathway/Wnt signaling pathway | ||
CFLAR | Apoptosis signaling pathway | ||
FAT3 | Cadherin signaling pathway/Wnt signaling pathway | ||
FRK | Cadherin signaling pathway | ||
PDK1 | RAS pathway/p53 pathway | ||
SMAD2, BMPR2 | TGF-beta signaling pathway | ||
MEG3 | Cisplatin | MOB3C, RANBP2, CROCC, CEP250, CDC42BPA, LPP, ABI2, HERC2. HELZ, TPR, SMC1A, HERC1, MYO5A | Cell Cycle |
TEP1 | Cell cycle/p53 pathway | ||
FZD3 | Angiogenesis/Cadherin signaling pathway/Wnt signaling pathway | ||
CFLAR, REL | Apoptosis signaling pathway | ||
FAT1, FAT2, FAT3, CELSR2 | Cadherin signaling pathway/Wnt signaling pathway | ||
FRK | Cadherin signaling pathway | ||
CBL | EGFR signaling pathway | ||
PDK1 | RAS pathway/p53 pathway | ||
SMAD2, BMPR2 | TGF-beta signaling pathway | ||
EP400, MYH3, MYH4, MYH7, MYH7B | Wnt signaling pathway | ||
ATM | p53 pathway | ||
SNHG6 | Cisplatin | LPP, ABI2, HELZ, PHC3 | Cell Cycle |
FZD3 | Angiogenesis/Cadherin signaling pathway/Wnt signaling pathway | ||
APC | Angiogenesis | ||
CFLAR, REL | Apoptosis signaling pathway | ||
FAT3 | Cadherin signaling pathway/Wnt signaling pathway | ||
FRK | Cadherin signaling pathway | ||
PDK1 | Ras pathway/p53 pathway | ||
BMPR1A | TGF-beta signaling pathway/Wnt signaling pathway | ||
SMAD2, SKIL, BMPR2 | TGF-beta signaling pathway | ||
APC | Wnt signaling pathway | ||
ATM | p53 pathway | ||
PCGEM1 | Cisplatin/Doxorubicin | LPP, ABI2, PHC3 | Cell Cycle |
FZD3 | Angiogenesis/Cadherin signaling pathway/Wnt signaling pathway | ||
CFLAR | Apoptosis signaling pathway | ||
FAT3 | Cadherin signaling pathway/Wnt signaling pathway | ||
FRK, FER | Cadherin signaling pathway | ||
PDK1 | Ras pathway/p53 pathway | ||
BMPR2 | TGF-beta signaling pathway | ||
ATM | p53 pathway | ||
EgoA | Doxorubicin | FZR1, MOB3B, NIPBL, TTC29 | Cell Cycle |
FER | Cadherin signaling pathway | ||
KRAS | Ras pathway | ||
MTA2 | p53 pathway | ||
Malat1 | Doxorubicin | LPP, ABI2, HELZ, CDK6, PHC3 | Cell Cycle |
FZD3 | Angiogenesis/Cadherin signaling pathway/Wnt signaling pathway | ||
CFLAR, REL | Apoptosis signaling pathway | ||
FAT3 | Cadherin signaling pathway/Wnt signaling pathway | ||
FRK, FER | Cadherin signaling pathway | ||
PDK1 | Ras pathway/p53 pathway | ||
SMAD2, BMPR2 | TGF-beta signaling pathway | ||
Zfas1 | Doxorubicin | LPP, ABI2, HELZ, PHC3 | Cell Cycle |
FZD3 | Angiogenesis/Cadherin signaling pathway/Wnt signaling pathway | ||
CFLAR | Apoptosis signaling pathway | ||
FRK, FER | Cadherin signaling pathway | ||
FAT3 | Cadherin signaling pathway/Wnt signaling pathway | ||
ERBB4 | Cadherin signaling pathway/EGFR signaling pathway | ||
NF1, CBL | EGFR signaling pathway |
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Guglas, K.; Kolenda, T.; Teresiak, A.; Kopczyńska, M.; Łasińska, I.; Mackiewicz, J.; Mackiewicz, A.; Lamperska, K. lncRNA Expression after Irradiation and Chemoexposure of HNSCC Cell Lines. Non-Coding RNA 2018, 4, 33. https://doi.org/10.3390/ncrna4040033
Guglas K, Kolenda T, Teresiak A, Kopczyńska M, Łasińska I, Mackiewicz J, Mackiewicz A, Lamperska K. lncRNA Expression after Irradiation and Chemoexposure of HNSCC Cell Lines. Non-Coding RNA. 2018; 4(4):33. https://doi.org/10.3390/ncrna4040033
Chicago/Turabian StyleGuglas, Kacper, Tomasz Kolenda, Anna Teresiak, Magda Kopczyńska, Izabela Łasińska, Jacek Mackiewicz, Andrzej Mackiewicz, and Katarzyna Lamperska. 2018. "lncRNA Expression after Irradiation and Chemoexposure of HNSCC Cell Lines" Non-Coding RNA 4, no. 4: 33. https://doi.org/10.3390/ncrna4040033