Genome-Wide Transcriptomic Analysis of Non-Tumorigenic Tissues Reveals Aging-Related Prognostic Markers and Drug Targets in Renal Cell Carcinoma
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Overview of the Proposed Approach
2.2. Materials
2.3. Data Pre-Processing
2.4. Identifying Aging-Related Genes and miRNAs
2.5. Finding DEGs in Cancer
2.6. Building Modules Using Protein–Protein Interaction Networks
2.7. Experimental Validation
2.7.1. Experimental Reagents
2.7.2. Cell Culture
2.7.3. Collection of Conditioned Media
2.7.4. siRNA-Mediated Gene Knockdown
2.7.5. Real-Time Quantitative PCR
2.7.6. Invasion Assay
2.7.7. Immunocytochemistry
2.7.8. The Enzyme-Linked Immunosorbent Assay (ELISA)
2.7.9. Animals
2.7.10. Zebrafish–Human Cancer Xenograft Model
2.7.11. Statistics for Cell-Based Analysis
3. Results
3.1. Characteristics of the Data
3.1.1. Demographics
3.1.2. Survival Analysis with Chronological Age
3.2. Tissue-Specific Aging-Related Genes and miRNAs
3.3. Association between Survival and Aging-Related Genes in BLCA, BRCA, and THCA
3.4. Analysis of KIRC
3.4.1. Association between Survival and Age-Related Genes in TCGA-KIRC
3.4.2. Module Analysis
3.4.3. Validation of Survival Significance in Kidney Renal Cells with an Independent Dataset
3.4.4. Biological Roles of Aging-Related miRNAs in the Kidney
3.4.5. Deferentially Expressed Genes (DEGs) in Kidney Cancer
3.4.6. Survival Prediction Models
- The average expression of downregulated cancer DEGs in tumor tissue;
- The average expression of upregulated cancer DEGs in tumor tissue;
- Decreasing index in normal tissue;
- Increasing index in normal tissue;
- The combination of 2 and 4.
3.5. Experimental Validation
3.5.1. Upregulated Expression of DUSP22, MAPK14, MAPKAPK3, STAT1, and VCP Genes in Aged Mouse Primary Bone Marrow-Derived Macrophages (BMDM)
3.5.2. Inhibited RCC Invasion by DUSP22 Knockdown in Macrophages Derived from Old Mice
3.5.3. DUSP22 Promotes Macrophage-Induced RCC Metastasis In Vivo
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Appendix A
Appendix A.1. Bootstrapping
- It is an aging-related gene in more than 50 bootstrap runs; and
- It is an aging-related gene in all samples
Appendix A.2. Survival Analysis
Appendix A.3. Diffusion Kernel
Appendix A.4. Association between Survival and Downregulation of Age-Related Genes in BLCA, BRCA, and THCA
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Cancer Type | Sample Size (Survival/Deceased) | Mean Age | Aging Genes | Aging microRNAs | |||||
---|---|---|---|---|---|---|---|---|---|
Gene | microRNA | Increasing | Decreasing | Total | Increasing | Decreasing | Total | ||
BLCA | 19 (8/11) | 19 (8/11) | 70.32 | 43 | 94 | 137 | 2 | 3 | 5 |
BRCA | 113 (69/44) | 104 (61/43) | 57.98 | 772 | 1678 | 2450 | 45 | 42 | 87 |
HNSC | 44 (11/33) | 44 (11/33) | 62.63 | 52 | 62 | 114 | 5 | 9 | 14 |
KICH | 24 (20/4) | 25 (21/4) | 54.55 | 202 | 139 | 341 | 5 | 10 | 15 |
KIRC | 72 (45/27) | 71 (45/26) | 62.96 | 162 | 87 | 249 | 17 | 15 | 32 |
KIRP | 32 (25/7) | 34 (26/8) | 62.40 | 137 | 215 | 352 | 9 | 20 | 29 |
LIHC | 50 (16/34) | 50 (16/34) | 61.53 | 13 | 65 | 78 | 8 | 18 | 26 |
LUAD | 59 (33/26) | 46 (33/13) | 65.83 | 339 | 289 | 628 | 12 | 11 | 23 |
LUSC | 49 (19/30) | 45 (22/23) | 69.25 | 21 | 36 | 57 | 8 | 13 | 21 |
STAD | 32 (23/9) | 45 (33/12) | 69.25 | 14 | 0 | 14 | 4 | 3 | 7 |
THCA | 58 (54/4) | 59 (55/4) | 46.03 | 386 | 205 | 591 | 34 | 36 | 70 |
UCEC | 35 (20/3, 12 Not Available) | 33 (19/3, 11 Not Available) | 59.87 | 15 | 6 | 21 | 12 | 16 | 28 |
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Oh, E.; Kim, J.-H.; Um, J.; Jung, D.-W.; Williams, D.R.; Lee, H. Genome-Wide Transcriptomic Analysis of Non-Tumorigenic Tissues Reveals Aging-Related Prognostic Markers and Drug Targets in Renal Cell Carcinoma. Cancers 2021, 13, 3045. https://doi.org/10.3390/cancers13123045
Oh E, Kim J-H, Um J, Jung D-W, Williams DR, Lee H. Genome-Wide Transcriptomic Analysis of Non-Tumorigenic Tissues Reveals Aging-Related Prognostic Markers and Drug Targets in Renal Cell Carcinoma. Cancers. 2021; 13(12):3045. https://doi.org/10.3390/cancers13123045
Chicago/Turabian StyleOh, Euiyoung, Jun-Hyeong Kim, JungIn Um, Da-Woon Jung, Darren R. Williams, and Hyunju Lee. 2021. "Genome-Wide Transcriptomic Analysis of Non-Tumorigenic Tissues Reveals Aging-Related Prognostic Markers and Drug Targets in Renal Cell Carcinoma" Cancers 13, no. 12: 3045. https://doi.org/10.3390/cancers13123045