MicroRNA, mRNA, and Proteomics Biomarkers and Therapeutic Targets for Improving Lung Cancer Treatment Outcomes
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Patient Samples
2.2. RNA Isolation and Quality Assessment
2.3. Microarray Analysis
2.4. Hierarchical Clustering Analysis and Heatmap
2.5. Nearest Centroid Classification
2.6. MiRNA Targeted Genes
2.7. Cancer Cell Line Encyclopedia
2.8. Drug Response
2.9. Proliferation Assays
2.10. Connectivity Map (CMap)
2.11. Statistical Analysis
3. Results
3.1. Identification of Diagnostic miRNA Markers
3.2. Comparison of miRNA Markers in Different Histology
3.3. Confirmation of miRNA Expression Patterns in Multiple Cohorts
3.4. MicroRNA Markers in Blood Samples
3.5. Identification of Prognostic miRNAs
3.6. Association between miRNA-Targeted Genes and Responses to Systemic Therapies and Radiotherapy
3.7. Identification of Prognostic miRNA-Targeted Genes
3.8. Discovery of Repositioning Drugs
4. Discussion
5. Conclusions
6. Patents
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Clinical Information | N |
---|---|
Cancer Stage | 109 |
1 | 40 |
2 | 34 |
3 | 13 |
Normal | 22 |
Age | |
<60 | 23 |
60–80 | 68 |
>80 | 2 |
Missing | 16 |
Gender | |
Male | 57 |
Female | 51 |
Missing | 1 |
Tumor Grade | |
1 | 4 |
2 | 29 |
3 | 42 |
Normal | 22 |
Missing | 12 |
Histology | |
NSCLC | |
Adenocarcinoma | 41 |
Adenosquamous carcinoma | 1 |
Large cell carcinoma | 2 |
Non-small cell carcinoma | 13 |
Sarcomatoid carcinoma | 1 |
Squamous cell carcinoma | 1 |
Small Cell Carcinoma | 1 |
Carcinoid tumor | 2 |
Normal Tissue | 22 |
Potential Tumor Suppressive miRNAs | Potential Oncogenic miRNAs |
---|---|
hsa-miR-144, hsa-miR-195, hsa-miR-223, hsa-miR-30a, hsa-miR-30b, hsa-miR-30d, hsa-miR-335, hsa-miR-363, hsa-miR-451, hsa-miR-99a | hsa-miR-21, hsa-miR-31, hsa-miR-411, hsa-miR-494 |
Drug | Pansensitive Genes | Panresistant Genes |
---|---|---|
afatinib | ADH7 | CCNT1, WDR47, TRIB1, hsa-miR-133a, hsa-miR-1280 |
alectinib | CCNT1, hsa-miR-30b, hsa-miR-30d | |
brigatinib | WDR47, hsa-miR-133a, hsa-miR-30a | |
cabozantinib | hsa-miR-133a, hsa-miR-210 | |
carboplatin | hsa-miR-210 | |
cisplatin | CDK1, hsa-miR-133a, hsa-miR-30a, hsa-miR-30b | |
crizotinib | hsa-miR-223, hsa-miR-218 | hsa-miR-30b, hsa-miR-30d |
dabrafenib | hsa-miR-218 | GLI2, CLCN5, CDKN3 |
dacomitinib | GLTP, FBXL4, hsa-miR-195, hsa-miR-30a | |
docetaxel | RAB30, NCEH1, GLTP, COPG1, hsa-miR-133a, hsa-miR-210, hsa-miR-30a | |
erlotinib | DGKE | GLTP, hsa-miR-1280 |
gefitinib | hsa-miR-195 | |
gemcitabine | CDK1, CDK16 | |
osimertinib | WDR47, hsa-miR-30a | |
paclitaxel | RAB30, hsa-miR-30a | |
pemetrexed | CDK16, hsa-miR-34b | |
trametinib | FOS, CDC42, PCBP1, TAOK2, NISCH, hsa-miR-195 | |
vemurafenib | hsa-miR-195 | |
vinorelbine | FOS, CDC42, RAB30, NCEH1, GLTP, hsa-miR-133a, hsa-miR-30a |
Drug | Sensitive Genes | Resistant Genes |
---|---|---|
BX-912 | ARSD, ATG4C, CD44, CDK6, CNST, G3BP2, GSTA5, KDM6B, LGMN, MCM9, NCOR2, NEGR1, NPC2, NT5C, PTPRG, RAB32, RPTOR, RRBP1, SF3B5, SOGA3, STAU1, TGFB2, TMCC2 | BCAS1, CD14, CGNL1, PALM3, VTCN1 |
daunorubicin | BCOR, KMT2B, NUDT8, OTUD4, SMS, SYT7 | |
midostaurin | ACBD5, APLF, ASH1L, BSCL2, CENPB, FMO5, JAK1, NRCAM, OPA3, PCGF1, SHC1, WDR53, ZHX3 |
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Share and Cite
Ye, Q.; Raese, R.; Luo, D.; Cao, S.; Wan, Y.-W.; Qian, Y.; Guo, N.L. MicroRNA, mRNA, and Proteomics Biomarkers and Therapeutic Targets for Improving Lung Cancer Treatment Outcomes. Cancers 2023, 15, 2294. https://doi.org/10.3390/cancers15082294
Ye Q, Raese R, Luo D, Cao S, Wan Y-W, Qian Y, Guo NL. MicroRNA, mRNA, and Proteomics Biomarkers and Therapeutic Targets for Improving Lung Cancer Treatment Outcomes. Cancers. 2023; 15(8):2294. https://doi.org/10.3390/cancers15082294
Chicago/Turabian StyleYe, Qing, Rebecca Raese, Dajie Luo, Shu Cao, Ying-Wooi Wan, Yong Qian, and Nancy Lan Guo. 2023. "MicroRNA, mRNA, and Proteomics Biomarkers and Therapeutic Targets for Improving Lung Cancer Treatment Outcomes" Cancers 15, no. 8: 2294. https://doi.org/10.3390/cancers15082294