Identification of Hub Genes in Idiopathic Pulmonary Fibrosis and Their Association with Lung Cancer by Bioinformatics Analysis
Abstract
:Highlights
- Identification of 1888 differentially expressed genes (DEGs) related to idiopathic pulmonary fibrosis (IPF), including 1105 upregulated and 783 downregulated genes.
- Discovery of 10 hub genes with high connectivity that may play a crucial role in the pathogenesis of IPF, with implications for potential diagnostic biomarkers and therapeutic targets.
- The study sheds light on the genetic landscape of IPF, uncovering potential key players in its development and progression.
- These identified hub genes have relevance beyond IPF, being expressed in lung cancer and associated with various stages of cancer progression, suggesting a link between IPF and lung cancer that could pave the way for improved diagnostics and therapies.
Abstract
1. Introduction
2. Materials and Methods
2.1. Ethical Statement
2.2. Selection and Inclusion Criteria for Gene Expression Microarray Data
2.3. Identification of DEGs
2.4. GO Enrichment and KEGG Pathway Enrichment Analyses
2.5. PPI Network Analysis
2.6. Validation of the Hub Genes
2.7. Analysis for miRNA Target Gene Prediction and miRNA-mRNA Network Construction
2.8. Analysis of Hub Gene Expression in Lung Cancer
3. Results
3.1. Processing of Microarray Datasets and Identification of DEGs in IPF
3.2. GO Enrichment and KEGG Pathway Analyses for DEGs in IPF
3.3. PPI Network and Identification of Hub Genes
3.4. GO and KEGG Pathway Enrichment Analysis for the DEGs Present in the Three Main Modules of the PPI Network
3.5. GO Enrichment and KEGG Pathway Analyses for the Top 10 Hub Genes in the PPI Network
3.6. In Silico Validation of Hub Genes
3.7. miRNA-mRNA Interaction Prediction and Network
3.8. Hub Genes in IPF Are Expressed in Lung Cancer and Are Associated with Cancer Progression
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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GEO ID | Platform | Samples | Reference | |
---|---|---|---|---|
Control | IPF | |||
GSE24206 | GPL570 | 6 | 17 | [19] |
GSE21369 | GPL570 | 6 | 11 | [20] |
GSE110147 | GLP6244 | 11 | 22 | [21] |
GSE72073 | GPL6480 | 3 | 5 | [22] |
GSE32539 | GPL6244 | 50 | 119 | [23] |
Total | 76 | 174 |
Category | Term | Count | p-Value | Genes |
---|---|---|---|---|
BP | GO:0030198~extracellular matrix organization | 5 | 2.17 × 10−6 | SPP1, TNC, FN1, CYR61, FBN1 |
BP | GO:0007155~cell adhesion | 5 | 6.23 × 10−5 | CDH2, SPP1, TNC, FN1, CYR61 |
BP | GO:0006953~acute-phase response | 3 | 1.87 × 10−4 | IL6, SERPINA1, FN1 |
BP | GO:0022617~extracellular matrix disassembly | 3 | 7.13 × 10−4 | SPP1, FN1, FBN1 |
BP | GO:0042060~wound healing | 3 | 7.90 × 10−4 | IL6, TNC, FN1 |
MF | GO:0008201~heparin binding | 4 | 6.73 × 10−5 | FN1, APOE, CYR61, FBN1 |
MF | GO:0005178~integrin binding | 3 | 0.00134085 | FN1, CYR61, FBN1 |
MF | GO:0050840~extracellular matrix binding | 2 | 0.01377989 | SPP1, CYR61 |
CC | GO:0005576~extracellular region | 9 | 3.03 × 10−8 | IL6, TF, SERPINA1, SPP1, TNC, FN1, APOE, CYR61, FBN1 |
CC | GO:0005615~extracellular space | 8 | 3.74 × 10−7 | IL6, TF, SERPINA1, SPP1, TNC, FN1, APOE, FBN1 |
CC | GO:0031012~extracellular matrix | 5 | 8.06 × 10−6 | TNC, FN1, APOE, CYR61, FBN1 |
CC | GO:0005578~proteinaceous extracellular matrix | 4 | 2.47 × 10−4 | SERPINA1, FN1, CYR61, FBN1 |
CC | GO:0070062~extracellular exosome | 7 | 7.38 × 10−4 | TF, SERPINA1, CDH2, SPP1, FN1, APOE, FBN1 |
KEGG | hsa04512: ECM–receptor interaction | 3 | 0.00318652 | SPP1, TNC, FN1 |
KEGG | hsa04151: PI3K-Akt signaling pathway | 4 | 0.00376323 | IL6, SPP1, TNC, FN1 |
KEGG | hsa04510: Focal adhesion | 3 | 0.01697039 | SPP1, TNC, FN1 |
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Velázquez-Enríquez, J.M.; Reyes-Avendaño, I.; Santos-Álvarez, J.C.; Reyes-Jiménez, E.; Vásquez-Garzón, V.R.; Baltiérrez-Hoyos, R. Identification of Hub Genes in Idiopathic Pulmonary Fibrosis and Their Association with Lung Cancer by Bioinformatics Analysis. Adv. Respir. Med. 2023, 91, 407-431. https://doi.org/10.3390/arm91050032
Velázquez-Enríquez JM, Reyes-Avendaño I, Santos-Álvarez JC, Reyes-Jiménez E, Vásquez-Garzón VR, Baltiérrez-Hoyos R. Identification of Hub Genes in Idiopathic Pulmonary Fibrosis and Their Association with Lung Cancer by Bioinformatics Analysis. Advances in Respiratory Medicine. 2023; 91(5):407-431. https://doi.org/10.3390/arm91050032
Chicago/Turabian StyleVelázquez-Enríquez, Juan Manuel, Itayetzi Reyes-Avendaño, Jovito Cesar Santos-Álvarez, Edilburga Reyes-Jiménez, Verónica Rocío Vásquez-Garzón, and Rafael Baltiérrez-Hoyos. 2023. "Identification of Hub Genes in Idiopathic Pulmonary Fibrosis and Their Association with Lung Cancer by Bioinformatics Analysis" Advances in Respiratory Medicine 91, no. 5: 407-431. https://doi.org/10.3390/arm91050032
APA StyleVelázquez-Enríquez, J. M., Reyes-Avendaño, I., Santos-Álvarez, J. C., Reyes-Jiménez, E., Vásquez-Garzón, V. R., & Baltiérrez-Hoyos, R. (2023). Identification of Hub Genes in Idiopathic Pulmonary Fibrosis and Their Association with Lung Cancer by Bioinformatics Analysis. Advances in Respiratory Medicine, 91(5), 407-431. https://doi.org/10.3390/arm91050032