| Literature DB >> 31212858 |
Erasmia Rouka1,2, Eleftherios Beltsios3, Dimos Goundaroulis4,5, Georgios D Vavougios6, Evgeniy I Solenov7,8, Chrissi Hatzoglou9,10, Konstantinos I Gourgoulianis11, Sotirios G Zarogiannis12,13.
Abstract
Background and objectives: Malignant pleural mesothelioma (MPM) is a devastating malignancy with poor prognosis. Reliable biomarkers for MPM diagnosis, monitoring, and prognosis are needed. The aim of this study was to identify genes associated with wound healing processes whose expression could serve as a prognostic factor in MPM patients. Materials andEntities:
Keywords: in silico; malignant pleural mesothelioma; miRNA; transcriptomics; wound healing
Mesh:
Substances:
Year: 2019 PMID: 31212858 PMCID: PMC6631992 DOI: 10.3390/medicina55060267
Source DB: PubMed Journal: Medicina (Kaunas) ISSN: 1010-660X Impact factor: 2.430
The wound-healing-associated genes investigated in this study.
| Hugo Gene Nomenclature Committee Gene Name. | Gene Description |
|---|---|
|
| Integrin Subunit Alpha 3 |
|
| Integrin Subunit Alpha V |
|
| Integrin Subunit Beta 6 |
|
| Ras-Related C3 Botulinum Toxin Substrate 1 (Rho Family, Small GTP Binding Protein Rac1) |
|
| Collagen Type V Alpha 1 Chain |
|
| Collagen Type V Alpha 2 Chain |
|
| Angiopoietin 1 |
|
| Collagen Type I Alpha 1 Chain |
|
| Collagen Type III Alpha 1 Chain |
|
| Colony Stimulating Factor 3 |
|
| Heparin Binding EGF Like Growth Factor |
|
| Macrophage Migration Inhibitory Factor (Glycosylation-Inhibiting Factor) |
|
| Transforming Growth Factor Alpha |
|
| Tumor Necrosis Factor |
|
| Vitronectin |
|
| C-X-C Motif Chemokine Ligand 2 |
|
| C-X-C Motif Chemokine Ligand 5 |
|
| Interleukin 6 |
|
| Interleukin 10 |
|
| Prostaglandin-Endoperoxide Synthase 2 |
|
| Mitogen-Activated Protein Kinase 3 |
|
| Phosphatase And Tensin Homolog |
|
| Interleukin 6 Signal Transducer |
|
| Signal Transducer And Activator Of Transcription 3 |
|
| Transforming Growth Factor Beta Receptor 3 |
|
| Cathepsin G |
|
| Coagulation Factor III, Tissue Factor |
|
| Coagulation Factor XIII A Chain |
|
| Plasminogen Activator, Urokinase Receptor |
|
| Plasminogen |
|
| Serpin Family E Member 1 |
|
| IMP Metallopeptidase Inhibitor 1 |
|
| Collagen Type I Alpha 2 Chain |
|
| Integrin Subunit Beta 3 |
|
| Integrin Subunit Beta 5 |
|
| Collagen Type V Alpha 3 Chain |
|
| Vascular Endothelial Growth Factor A |
|
| Wnt Family Member 5A |
|
| WNT1 Inducible Signaling Pathway Protein 1 |
|
| Catenin Beta 1 |
|
| Mitogen-Activated Protein Kinase 1 |
|
| Epidermal Growth Factor Receptor |
|
| Transforming Growth Factor Beta 1 |
|
| Cadherin 1 |
|
| Integrin Subunit Alpha 1 |
|
| Integrin Subunit Alpha 2 |
|
| Integrin Subunit Alpha 4 |
|
| Integrin Subunit Alpha 5 |
|
| Integrin Subunit Alpha 6 |
|
| Integrin Subunit Beta 1 |
|
| Actin, Alpha 2, Smooth Muscle, Aorta |
|
| Actin, Alpha 1, Skeletal Muscle |
|
| Ras Homolog Family Member A |
|
| Transgelin |
|
| Collagen Type IV Alpha 1 Chain |
|
| Collagen Type IV Alpha 3 Chain |
|
| Collagen Type XIV Alpha 1 Chain |
|
| Cathepsin K |
|
| cathepsin L2 |
|
| Fibrinogen Alpha Chain |
|
| Matrix Metallopeptidase 1 |
|
| Matrix Metallopeptidase 2 |
|
| Matrix Metallopeptidase 7 |
|
| Matrix Metallopeptidase 9 |
|
| Plasminogen Activator, Tissue Type |
|
| Plasminogen Activator, Urokinase |
|
| Colony Stimulating Factor 2 |
|
| Connective Tissue Growth Factor |
|
| Epidermal Growth Factor |
|
| Fibroblast Growth Factor 2 |
|
| Fibroblast Growth Factor 7 |
|
| Hepatocyte Growth Factor |
|
| Insulin Like Growth Factor 1 |
|
| Platelet Derived Growth Factor Subunit A |
|
| C-C Motif Chemokine Ligand 2 |
|
| C-C Motif Chemokine Ligand 7 |
|
| CD40 Ligand |
|
| C-X-C Motif Chemokine Ligand 1 |
|
| C-X-C Motif Chemokine Ligand 11 |
|
| Interleukin 1 Beta |
|
| Interleukin 2 |
|
| Interleukin 4 |
Wound-healing-associated genes differentially expressed in malignant pleural mesothelioma (MPM) patients.
| Q Value | FC | |
|---|---|---|
|
| ||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| ||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Figure 1(A) Violin plot of the ITGAV gene expression shows that it is significantly overexpressed in MPM patients compared to controls. (B) Low ITGAV gene expression in MPM patients favors their survival (shown in months).
Figure 2Results of Kaplan–Meier survival analysis from The Cancer Genome Atlas (TCGA) mesothelioma dataset derived from PROGgeneV2 database, shows that low ITGAV gene expression favors survival (shown in days) in MPM patients.
Statistical modeling of the correlation of ITGAV and COL5A1 gene expressions.
| Coefficients | Estimate | Std. Error | T Value | Pr (>|t|) |
|---|---|---|---|---|
| (Intercept) | 1.89725 | 0.20885 | 9.084 | 4.59 × 10−11 *** |
| COL5A1 | 0.41537 | 0.07451 | 5.574 | 2.18 × 10−6 *** |
Functional enrichment analysis relative to Biological Functions of the wound-healing-associated genes differentially expressed in MPM patients *.
| ID | Name | P-Value | FDR B&H | FDR | Bonferroni | Genes From Input | Genes in Annotation | |
|---|---|---|---|---|---|---|---|---|
| 1 | GO:0040011 | locomotion | 2.531 × 10−23 | 7.177 × 10−20 | 6.120 × 10−19 | 7.177 × 10−20 | 26 | 1735 |
| 2 | GO:0016477 | cell migration | 5.798 × 10−23 | 1.644 × 10−19 | 24 | 1300 | ||
| 3 | GO:0051674 | localization of cell | 5.395 × 10−22 | 3.825 × 10−19 | 3.262 × 10−18 | 1.530 × 10−18 | 24 | 1428 |
| 4 | GO:0048870 | cell motility | 5.395 × 10−22 | 3.825 × 10−19 | 3.262 × 10−18 | 1.530 × 10−18 | 24 | 1428 |
| 5 | GO:0030334 | regulation of cell migration | 1.635 × 10−21 | 9.274 × 10−19 | 7.909 × 10−18 | 4.637 × 10−18 | 20 | 742 |
* Results were obtained through ToppFun, an application of the ToppGene suite (https://toppgene.cchmc.org/). FDR: False discovery rate; B&H: Benjamini–Hochberg; B&Y: Benjamini–Yekutieli. Only the top five results are presented.
Functional enrichment analysis relative to miRNAs of the wound-healing-associated genes differentially expressed in MPM patients *.
| ID | Name | Source | P-Value | FDR B&H | FDR | Bonferroni | Genes From Input | Genes in Annotation | |
|---|---|---|---|---|---|---|---|---|---|
| 1 | hsa-miR-143-3p:Functional MTI | Functional MTI | miRTarbase | 5.442 × 10−12 | 1.459 × 10−8 | 1.236 × 10−7 | 1.459 × 10−8 | 7 | 228 |
| 2 | hsa-miR-223-3p:Functional MTI | Functional MTI | miRTarbase | 5.747 × 10−10 | 7.704 × 10−7 | 6.526 × 10−6 | 1.541 × 10−6 | 5 | 98 |
| 3 | hsa-miR-29b-3p:Functional MTI | Functional MTI | miRTarbase | 1.159 × 10−9 | 1.036 × 10−6 | 8.776 × 10−6 | 3.108 × 10−6 | 6 | 261 |
| 4 | hsa-miR-29a:PITA | hsa-miR-29a:PITA TOP | PITA | 3.728 × 10−9 | 1.666 × 10−6 | 1.411 × 10−5 | 9.995 × 10−6 | 7 | 583 |
| 5 | hsa-miR-29c:PITA | hsa-miR-29c:PITA TOP | PITA | 3.728 × 10−9 | 1.666 × 10−6 | 1.411 × 10−5 | 9.995 × 10−6 | 7 | 583 |
* Results were obtained through ToppFun, an application of the ToppGene suite (https://toppgene.cchmc.org/). FDR: False discovery rate; B&H: Benjamini–Hochberg; B&Y: Benjamini–Yekutieli. Only the top five results are presented.