MiR-942-3p as a Potential Prognostic Marker of Gastric Cancer Associated with AR and MAPK/ERK Signaling Pathway
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data Downloading and Processing
2.2. Detection of Differentially Expressed miRNAs and mRNA Combined with Clinical Information
2.3. Construction of Sample Grouping and Prognostic Module
2.4. Independent Prognostic Ability of miRNA
2.5. miRNA Target Genes Prediction and Functions Analysis
2.6. Screening Core Target Genes and Survival Analysis
3. Results
3.1. Detection of Differentially Expressed miRNAs and Differentially Expressed mRNAs
3.2. Five miRNAs Associated with Overall Survival
3.3. Prediction and Assessment of Five miRNAs for Overall Survival in Three Groups
3.4. Independence of the Five miRNAs
3.5. Target Genes Prediction of Five miRNAs
3.6. Target Genes Functional Enrichment Analysis
3.7. Hub Genes of PPI Network and Survival Analysis of Target Genes
3.8. The Working Mechanism of AR and Its Potential Relationship with the MAPK/ERK Signaling Pathway
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Variables | miRNA Expression Profiles | mRNA Expression Profiles | |
---|---|---|---|
Case | Count | 436 | 380 |
Primary Site | Stomach | stomach | |
Program | TCGA | TCGA | |
Project | TCGA-STAD | TCGA-STAD | |
Files | Count | 491 | 407 |
Data Category | Transcriptome Profiling | Transcriptome Profiling | |
Data Type | Isoform Expression Quantification | Gene Expression Quantification | |
Workflow Type | BCGSC miRNA Profiling | HTSeq-Counts |
Variables | Case | Percentage (%) | |
---|---|---|---|
Gender | Male | 285 | 64.3 |
Female | 158 | 35.7 | |
Age (years) | Range | 30–90 | |
Median | 68 | 3.1 | |
Futime (day) | Range | 0–3720 | |
Median | 422 | ||
Fustat | 1 | 171 | 38.6 |
0 | 272 | 61.3 | |
Clinical stage | I | 59 | 13.2 |
II | 130 | 29.2 | |
III | 183 | 41.1 | |
IV | 44 | 9.9 | |
Unknown | 27 | 6 | |
T stage | T1 | 23 | 5 |
T2 | 93 | 20.8 | |
T3 | 198 | 44.6 | |
T4 | 119 | 26.7 | |
TX | 10 | 2.2 | |
Lymph node stage | N0 | 132 | 29.7 |
N1 | 119 | 26.8 | |
N2 | 85 | 19.1 | |
N3 | 88 | 19.7 | |
NX | 17 | 3.8 | |
Unknown | 2 | 0.4 | |
Metastatic | M0 | 391 | 88.2 |
M1 | 30 | 6.7 | |
MX | 22 | 4.9 |
ID | Univariate Cox Regression | Multivariate Cox Regression | |||||||
---|---|---|---|---|---|---|---|---|---|
HR | HR.95L | HR.95H | p-Value | Coef | HR | HR.95L | HR.95H | p-Value | |
hsa-miR-96-5p | 0.761 | 0.642 | 0.903 | 0.002 | |||||
hsa-miR-7-5p | 0.801 | 0.695 | 0.923 | 0.002 | |||||
hsa-let-7e-3p | 1.379 | 1.112 | 1.71 | 0.003 | |||||
hsa-miR-143-5p | 1.265 | 1.077 | 1.487 | 0.004 | 0.134 | 1.144 | 0.961 | 1.361 | 0.129 |
hsa-miR-942-3p | 0.727 | 0.586 | 0.902 | 0.004 | −0.178 | 0.837 | 0.663 | 1.056 | 0.132 |
hsa-miR-183-5p | 0.806 | 0.69 | 0.942 | 0.007 | |||||
hsa-miR-196b-3p | 0.648 | 0.468 | 0.897 | 0.009 | −0.307 | 0.736 | 0.527 | 1.027 | 0.072 |
hsa-miR-125a-5p | 1.401 | 1.067 | 1.839 | 0.015 | |||||
hsa-miR-135b-3p | 0.799 | 0.665 | 0.96 | 0.017 | −0.148 | 0.862 | 0.706 | 1.052 | 0.144 |
hsa-miR-30a-3p | 1.21 | 1.024 | 1.428 | 0.025 | |||||
hsa-miR-652-5p | 0.784 | 0.623 | 0.986 | 0.037 | |||||
hsa-miR-9-3p | 1.17 | 1.008 | 1.359 | 0.039 | 0.147 | 1.159 | 0.989 | 1.358 | 0.069 |
hsa-miR-99a-3p | 1.175 | 1.007 | 1.372 | 0.040 | |||||
hsa-miR-139-5p | 1.221 | 1.007 | 1.48 | 0.042 | |||||
hsa-miR-137-3p | 1.16 | 1.000 | 1.346 | 0.049 |
Clinical Features | Univariate Cox Regression | Multivariate Cox Regression | ||||||
---|---|---|---|---|---|---|---|---|
HR | HR.95L | HR.95H | p-Value | HR | HR.95L | HE.95H | p-Value | |
Age | 1.015 | 0.999 | 1.032 | 0.062 | 1.027 | 1.010 | 1.045 | 0.002 |
Gender | 1.225 | 0.853 | 1.760 | 0.271 | 1.510 | 1.027 | 2.218 | 0.036 |
Grade | 1.278 | 0.908 | 1.800 | 0.160 | 1.115 | 0.781 | 1.591 | 0.550 |
Stage | 1.607 | 1.294 | 1.996 | <0.001 | 1.210 | 0.807 | 1.815 | 0.357 |
T | 1.288 | 1.038 | 1.599 | 0.022 | 1.215 | 0.911 | 1.621 | 0.186 |
M | 1.880 | 1.013 | 3.489 | 0.045 | 1.818 | 0.844 | 3.917 | 0.127 |
N | 1.361 | 1.170 | 1.584 | <0.001 | 1.233 | 0.987 | 1.540 | 0.065 |
riskScore | 1.726 | 1.395 | 2.136 | <0.001 | 1.971 | 1.557 | 2.494 | <0.001 |
ID | Description | p-Value | Q-Value | Count | Gene |
---|---|---|---|---|---|
hsa04024 | cAMP signaling pathway | 0.0002 | 0.0272 | 9 | TIAM1/FOS/GRIA2/MAPK10/PLN/MC2R/ATP2B4/GABBR2/RAP1A |
hsa05140 | Leishmaniasis | 0.0007 | 0.0603 | 5 | FCGR3A/FOS/STAT1/IL1A/FCGR2A |
hsa04380 | Osteoclast differentiation | 0.0011 | 0.0603 | 6 | FCGR3A/FOS/MAPK10/STAT1/IL1A/FCGR2A |
hsa05162 | Measles | 0.0017 | 0.0603 | 6 | CDK6/FOS/MAPK10/STAT1/IL1A/IL2RA |
hsa04350 | TGF-beta signaling pathway | 0.0017 | 0.0603 | 5 | CDKN2B/RGMB/LEFTY1/BAMBI/RBL1 |
hsa04080 | Neuroactive ligand-receptor interaction | 0.0039 | 0.1148 | 9 | GRIA2/GRID2/MC2R/F2/GLRA2/GABRP/GRIK3/GABBR2/OPRK1 |
hsa05152 | Tuberculosis | 0.0062 | 0.1570 | 6 | FCGR3A/MAPK10/RIPK2/STAT1/IL1A/FCGR2A |
hsa04658 | Th1 and Th2 cell differentiation | 0.0101 | 0.2256 | 4 | FOS/MAPK10/STAT1/IL2RA |
hsa04933 | AGE-RAGE signaling pathway | 0.0135 | 0.2506 | 4 | MAPK10/STAT1/IL1A/COL4A1 |
hsa04218 | Cellular senescence | 0.0159 | 0.2506 | 5 | CDK6/CDKN2B/IL1A/CCNA2/RBL1 |
hsa04978 | Mineral absorption | 0.0162 | 0.2506 | 3 | SLC6A19/CYBRD1/ATP2B4 |
hsa04659 | Th17 cell differentiation | 0.0169 | 0.2506 | 4 | FOS/MAPK10/STAT1/IL2RA |
hsa04010 | MAPK/ERK signaling pathway | 0.0187 | 0.2554 | 7 | CACNG8/FOS/MAPK10/IL1A/STMN1/FGF5/RAP1A |
hsa04917 | Prolactin signaling pathway | 0.0266 | 0.3244 | 3 | FOS/MAPK10/STAT1 |
hsa04110 | Cell cycle | 0.0274 | 0.3244 | 4 | CDK6/CDKN2B/CCNA2/RBL1 |
hsa04068 | FoxO signaling pathway | 0.0326 | 0.3247 | 4 | CDKN2B/MAPK10/KLF2/RAG2 |
hsa05133 | Pertussis | 0.0329 | 0.3247 | 3 | FOS/MAPK10/IL1A |
hsa05212 | Pancreatic cancer | 0.0329 | 0.3247 | 3 | CDK6/MAPK10/STAT1 |
hsa05418 | Fluid shear stress and atherosclerosis | 0.0392 | 0.3471 | 4 | FOS/MAPK10/KLF2/IL1A |
hsa04742 | Taste transduction | 0.0410 | 0.3471 | 3 | PDE1C/TAS2R5/GABBR2 |
Node_Name | MCC | DMNC | MNC | Degree | EPC | Bottle Neck | Ec Centricity | Closeness | Radiality | Betweenness | Stress | Clustering Coefficient |
---|---|---|---|---|---|---|---|---|---|---|---|---|
CCNA2 | 236 | 0.264 | 18 | 18 | 35.308 | 19 | 0.097 | 43.961 | 7.799 | 2843.324 | 5374 | 0.235 |
GRIA2 | 22 | 0.233 | 8 | 13 | 33.492 | 71 | 0.129 | 44.383 | 8.065 | 3792.232 | 8494 | 0.128 |
FOS | 17 | 0.220 | 7 | 12 | 34.894 | 84 | 0.111 | 46.076 | 8.159 | 3863.375 | 7988 | 0.091 |
AR | 33 | 0.329 | 7 | 10 | 35.226 | 18 | 0.111 | 43.369 | 7.987 | 2490.437 | 5478 | 0.200 |
RACGAP1 | 131 | 0.408 | 8 | 9 | 33.683 | 2 | 0.086 | 33.073 | 7.110 | 210.833 | 484 | 0.389 |
RBFOX1 | 12 | 0.238 | 6 | 8 | 28.267 | 4 | 0.111 | 35.586 | 7.525 | 953.058 | 2332 | 0.179 |
LIN28A | 9 | 0.309 | 3 | 8 | 28.652 | 3 | 0.097 | 36.095 | 7.517 | 790.409 | 2030 | 0.107 |
DSCC1 | 28 | 0.454 | 5 | 7 | 30.653 | 3 | 0.086 | 32.073 | 7.094 | 392.500 | 704 | 0.333 |
GRID2 | 13 | 0.285 | 6 | 7 | 28.277 | 2 | 0.111 | 34.919 | 7.525 | 366.790 | 918 | 0.286 |
OPRK1 | 10 | 0.463 | 3 | 7 | 25.901 | 13 | 0.097 | 37.251 | 7.721 | 1633.949 | 3034 | 0.143 |
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Liu, W.; Ying, N.; Rao, X.; Chen, X. MiR-942-3p as a Potential Prognostic Marker of Gastric Cancer Associated with AR and MAPK/ERK Signaling Pathway. Curr. Issues Mol. Biol. 2022, 44, 3835-3848. https://doi.org/10.3390/cimb44090263
Liu W, Ying N, Rao X, Chen X. MiR-942-3p as a Potential Prognostic Marker of Gastric Cancer Associated with AR and MAPK/ERK Signaling Pathway. Current Issues in Molecular Biology. 2022; 44(9):3835-3848. https://doi.org/10.3390/cimb44090263
Chicago/Turabian StyleLiu, Wenjia, Nanjiao Ying, Xin Rao, and Xiaodong Chen. 2022. "MiR-942-3p as a Potential Prognostic Marker of Gastric Cancer Associated with AR and MAPK/ERK Signaling Pathway" Current Issues in Molecular Biology 44, no. 9: 3835-3848. https://doi.org/10.3390/cimb44090263