LINC00973 Induces Proliferation Arrest of Drug-Treated Cancer Cells by Preventing p21 Degradation
Abstract
:1. Introduction
2. Results
2.1. Bioinformatics Analysis of LINC00973 Expression in Cancer Cells Treated with Chemotherapeutics
2.2. LINC00973 Subcellular Localization
2.3. LINC00973 Knockdown Results in Dramatic Increase in HT-29 Cell Proliferation and 5-Fluorouracil Sensitivity, As Well As in Inhibition of Apoptosis
2.4. Analysis of Transcriptomic and Proteomic Changes in LINC00973 KD and LINC00973 Ectopically Over-Expressing Cells
3. Discussion
4. Materials and Methods
4.1. Analysis RNA-Seq Data and Data from the NCBI Sequence Read Archive
4.2. Cell Lines and Drug Treatment
4.3. RT-qPCR
4.4. LINC00973 Subcellular Localization
4.5. LINC00973 Knockdown
4.6. Viral Particle Production and Lentivirus Transduction
4.7. Analysis of Cellular Phenotypes
4.8. Determination of IC50 upon 5-FU Treatment
4.9. RNA Sequencing
4.10. Identification and Ranking of Differentially Expressed Transcripts
4.11. Western Blotting
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
LincRNA | Long intergenic non-coding RNA |
DDR | DNA damage response |
5-FU | 5-Fluorouracil |
OXP | Oxaliplatin |
CIS | Cisplatin |
CAR | Carboplatin |
CSC | Cancer stem cell |
PAC | Paclitaxel |
ETO | Etoposide |
DXR | Doxorubicin |
RT-qPCR | Reverse transcription quantitative PCR |
CPM | Counts per million |
FC | Fold change |
FDR | False discovery rate |
CRC | Colorectal cancer |
COAD | Colon adenocarcinoma |
LUAD | Lung adenocarcinoma |
NB | Neuroblastoma |
OS | Osteosarcoma |
ILF | Immortalized fetal lung fibroblasts |
GEP-NET | Gastro-entero-pancreatic neuroendocrine tumor |
LINC00973 KD | CRISPR-induced LINC00973 knockdown in PXK/HT-29 cells |
PXK | HT-29 subclone derived from a single HT-29 cell, transfected with an empty plasmid PX459 |
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Cell Line | Cell Type 1 | Drug | Log2FC | P53 | Reference |
---|---|---|---|---|---|
Status | |||||
HT-29 | COAD | 5-Fluorouracil | 7.2 | R273H | [7] |
HT-29 | COAD | Oxaliplatin | 2.7 | R273H | [7] |
HCT-116 | COAD | Oxaliplatin | 2.8 | wt | [7] |
HCT-116 | COAD | Doxorubicin | 1.7 | wt | [9] |
SK-N-SH | NB | Doxorubicin | 5.3 | wt | [10] |
SK-N-SH | NB | Cisplatin | 5.2 | wt | [10] |
IMR5/75 | NB | Doxorubicin | 4.4 | wt | [3] |
U2OS | OS | Methyl methanesulfonate | −2.7 | wt | [11] |
U2OS | OS | Etoposide | −1.5 | wt | [11] |
pC9 | LUAD | Carboplatin | 2.5 | R248Q | [12] |
A549 | LUAD | Paclitaxel | 1.1 | wt | [13] |
IMR90 | ILF | Etoposide | 5.4 | wt | [14] |
Cell Line | HCT116 | SW48 | ||
---|---|---|---|---|
p53 Status | WT | KO | WT | KO |
LINC00973 | 1.73 | −0.17 | 0.68 | −0.1 |
CDKN1A | 3.11 | 0.19 | 3.33 | −0.47 |
GDF15 | 2.5 | −0.95 | 4.02 | −0.33 |
BTG2 | 2.41 | 0.34 | 2.26 | −0.02 |
BBC3 | 1.32 | −0.71 | 1.83 | −0.61 |
PMAIP1 | 1.51 | 0.61 | 0.68 | −0.08 |
GADD45 | 1.65 | −0.16 | 1.67 | −0.05 |
Cell Line | HT-29 | SK-N-SH | IMR90 | pC9 | |||
---|---|---|---|---|---|---|---|
Cell Type | COAD | NB | ILF | LUAD | |||
Drug | 5-FU | CIS | DXR | ETO | CAR | ||
LINC00973 | LV2 | ||||||
KD vs. PXK | vs. LV1 | ||||||
LINC00973 | −5.64 | 4.51 | 7.15 | 5.24 | 5.3 | 5.39 | 2.49 |
RNF157 | 2.39 | −2.11 | −2.86 | −2.86 | −2.38 | −1.19 | −0.43 |
NEURL1B | 2.06 | 0.1 | −4.05 | −2.59 | −2.52 | −3.53 | 2.39 |
CDKN2B | −1.51 | 0.23 | 2.19 | 3.26 | 3.43 | 2.13 | 2.5 |
DCBLD2 | −2.01 | 0.1 | 1.9 | 2.29 | 2.74 | 0.18 | −0.49 |
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Karpov, D.S.; Spirin, P.V.; Zheltukhin, A.O.; Tutyaeva, V.V.; Zinovieva, O.L.; Grineva, E.N.; Matrosova, V.A.; Krasnov, G.S.; Snezhkina, A.V.; Kudryavtseva, A.V.; et al. LINC00973 Induces Proliferation Arrest of Drug-Treated Cancer Cells by Preventing p21 Degradation. Int. J. Mol. Sci. 2020, 21, 8322. https://doi.org/10.3390/ijms21218322
Karpov DS, Spirin PV, Zheltukhin AO, Tutyaeva VV, Zinovieva OL, Grineva EN, Matrosova VA, Krasnov GS, Snezhkina AV, Kudryavtseva AV, et al. LINC00973 Induces Proliferation Arrest of Drug-Treated Cancer Cells by Preventing p21 Degradation. International Journal of Molecular Sciences. 2020; 21(21):8322. https://doi.org/10.3390/ijms21218322
Chicago/Turabian StyleKarpov, Dmitry S., Pavel V. Spirin, Andrey O. Zheltukhin, Vera V. Tutyaeva, Olga L. Zinovieva, Evgenia N. Grineva, Vera A. Matrosova, George S. Krasnov, Anastasiya V. Snezhkina, Anna V. Kudryavtseva, and et al. 2020. "LINC00973 Induces Proliferation Arrest of Drug-Treated Cancer Cells by Preventing p21 Degradation" International Journal of Molecular Sciences 21, no. 21: 8322. https://doi.org/10.3390/ijms21218322