Background
Methods
Patients and clinical tissue samples
NO. | Tumor statue | Age range (years) | Site | Clinical stage | TNM classification | Application |
---|---|---|---|---|---|---|
1 | Nonmetastatic | 40–49 | Tongue | II | T2N0M0 | Microarray assay |
2 | Nonmetastatic | 60–69 | Oral floor | III | T3N0M0 | Microarray assay |
3 | Nonmetastatic | 40–49 | Tongue | II | T2N0M0 | Microarray assay |
4 | Nonmetastatic | 60–69 | Gingiva | II | T2N0M0 | Microarray assay |
5 | Nonmetastatic | 40–49 | Tongue | IV | T4N0M0 | Microarray assay |
6 | Nonmetastatic | 50–59 | Buccal mucosa | III | T3N0M0 | Microarray assay |
7 | Metastatic | 50–59 | Tongue | III | T2N1M0 | Microarray assay |
8 | Metastatic | 60–69 | Tongue | IV | T2N2M0 | Microarray assay |
9 | Metastatic | 40–49 | Tongue | IV | T1N2M0 | Microarray assay |
10 | Metastatic | 60–69 | Tongue | IV | T2N2M0 | Microarray assay |
11 | Metastatic | 50–59 | Tongue | IV | T2N2M0 | Microarray assay |
12 | Metastatic | 50–59 | Buccal mucosa | IV | T1N2M0 | Microarray assay |
13 | Nonmetastatic | 50–59 | Tongue | II | T2N0M0 | qRT-PCR |
14 | Nonmetastatic | 40–49 | Tongue | II | T2N0M0 | qRT-PCR |
15 | Nonmetastatic | 60–69 | Buccal mucosa | II | T2N0M0 | qRT-PCR |
16 | Nonmetastatic | 40–49 | Gingiva | II | T2N0M0 | qRT-PCR |
17 | Nonmetastatic | 30–39 | Tongue | II | T2N0M0 | qRT-PCR |
18 | Nonmetastatic | 60–69 | Gingiva | III | T3N0M0 | qRT-PCR |
19 | Nonmetastatic | 70–79 | Tongue | III | T3N0M0 | qRT-PCR |
20 | Nonmetastatic | 50–59 | Tongue | IV | T4N0M0 | qRT-PCR |
21 | Metastatic | 50–59 | Buccal mucosa | IV | T1N2M0 | qRT-PCR |
22 | Metastatic | 70–79 | Tongue | IV | T2N2M0 | qRT-PCR |
23 | Metastatic | 60–69 | Tongue | IV | T2N2M0 | qRT-PCR |
24 | Metastatic | 60–69 | Tongue | IV | T2N2M0 | qRT-PCR |
25 | Metastatic | 50–59 | Oral floor | IV | T1N2M0 | qRT-PCR |
26 | Metastatic | 50–59 | Buccal mucosa | IV | T4N1M0 | qRT-PCR |
27 | Metastatic | 40–49 | Tongue | IV | T3N1M0 | qRT-PCR |
Group | nonmetastatic | metastatic | P |
---|---|---|---|
Age(y) | 55.7 | 57.9 | 0.468 |
Gender | 0.157 | ||
Man | 12 | 13 | |
Woman | 2 | 0 | |
Clinical stage | 0.012 | ||
II | 8 | 0 | |
III | 4 | 1 | |
IV | 2 | 12 | |
Tumor site | 0.163 | ||
Tongue | 8 | 9 | |
Buccal | 2 | 3 | |
Gingiva | 3 | 0 | |
Oral floor | 1 | 1 |
Total RNA isolation and microarray processing
Microarray data analysis
Gene ontology (GO) functional and pathway enrichment analysis
Quantitative real-time RT-PCR (qRT-PCR)
Results
Identification of MMP-related DEGs and DE-miRNAs
Functional and pathway enrichment analysis
Category | GO_ID | Term | P value | Count | Genes |
---|---|---|---|---|---|
BP | GO:0030574 | collagen catabolic process | 2.583e-24 | 11 | MMP7, MMP14, MMP13, MMP1, MMP3, MMP8, MMP9, MMP12, MMP10, MMP11, MMP15 |
GO:0032963 | collagen metabolic process | 2.654e-22 | 11 | MMP7, MMP14, MMP13, MMP1, MMP3, MMP8, MMP9, MMP12, MMP10, MMP11, MMP15 | |
GO:0044259 | multicellular organismal macromolecule metabolic process | 4.247e-22 | 11 | MMP7, MMP14, MMP13, MMP1, MMP3, MMP8, MMP9, MMP12, MMP11, MMP10, MMP15 | |
GO:0022617 | extracellular matrix disassembly | 1.031e-21 | 11 | MMP7, MMP13, MMP3, MMP12, MMP10, MMP15, MMP14, MMP1, MMP8, MMP9, MMP11 | |
GO:0044236 | multicellular organismal metabolic process | 1.445e-21 | 11 | MMP7, MMP13, MMP3, MMP12, MMP10, MMP15, MMP14, MMP1, MMP8, MMP9, MMP11 | |
GO:0030198 | extracellular matrix organization | 1.668e-16 | 11 | MMP7, MMP12, MMP10, MMP15, MMP14, MMP8, MMP13, MMP3, MMP1, MMP9, MMP11 | |
GO:0043062 | extracellular structure organization | 1.720e-16 | 11 | MMP7, MMP12, MMP10, MMP15, MMP14, MMP8, MMP13, MMP3, MMP1, MMP9, MMP11 | |
GO:0006508 | proteolysis | 3.499e-11 | 12 | MMP7, MMP12, MMP10, MMP14, MMP17, MMP15, MMP13, MMP3, MMP8, MMP9, MMP11, MMP1 | |
GO:0035987 | endodermal cell differentiation | 3.661e-10 | 4 | MMP9, MMP14, MMP15, MMP8 | |
GO:0001706 | endoderm formation | 1.064e-09 | 4 | MMP9, MMP14, MMP15, MMP8 | |
CC | GO:0031012 | extracellular matrix | 1.486e-17 | 12 | MMP7, MMP12, MMP10, MMP15, MMP14, MMP8, MMP13, MMP3, MMP1, MMP17, MMP9, MMP11 |
GO:0005578 | proteinaceous extracellular matrix | 4.500e-15 | 10 | MMP7, MMP12, MMP10, MMP8, MMP13, MMP3, MMP1, MMP17, MMP9, MMP11 | |
GO:0005615 | extracellular space | 7.395e-05 | 6 | MMP7, MMP10, MMP13, MMP3, MMP8, MMP9 | |
GO:0005576 | extracellular region | 4.364e-04 | 10 | MMP10, MMP11, MMP7, MMP17, MMP8, MMP9, MMP3, MMP12, MMP13, MMP1 | |
MF | GO:0004222 | metalloendopeptidase activity | 5.214e-25 | 12 | MMP7, MMP14, MMP13, MMP1, MMP3, MMP17, MMP8, MMP9, MMP12, MMP11, MMP10, MMP15 |
GO:0008237 | metallopeptidase activity | 4.690e-22 | 12 | MMP7, MMP13, MMP3, MMP12, MMP10, MMP15, MMP14, MMP1, MMP8, MMP17, MMP9, MMP11 | |
GO:0004175 | endopeptidase activity | 7.643e-18 | 12 | MMP7, MMP12, MMP10, MMP15, MMP14, MMP8, MMP13, MMP3, MMP1, MMP17, MMP9, MMP11 | |
GO:0008233 | peptidase activity | 1.534e-15 | 12 | MMP7, MMP12, MMP10, MMP14, MMP8, MMP17, MMP9, MMP11, MMP15, MMP13, MMP3, MMP1 | |
GO:0005509 | calcium ion binding | 4.088e-12 | 10 | MMP12, MMP10, MMP14, MMP8, MMP17, MMP11, MMP15, MMP13, MMP3, MMP1 | |
GO:0008270 | zinc ion binding | 4.449e-12 | 12 | MMP7, MMP12, MMP10, MMP14, MMP17, MMP15, MMP13, MMP3, MMP8, MMP9, MMP11, MMP1 | |
GO:0046914 | transition metal ion binding | 4.452e-11 | 12 | MMP7, MMP12, MMP10, MMP14, MMP17, MMP15, MMP13, MMP3, MMP8, MMP9, MMP11, MMP1 | |
GO:0016787 | hydrolase activity | 2.326e-08 | 12 | MMP10, MMP14, MMP15, MMP3, MMP11, MMP7, MMP12, MMP17, MMP13, MMP8, MMP9, MMP1 | |
GO:0046872 | metal ion binding | 7.714e-06 | 12 | MMP10, MMP14, MMP15, MMP3, MMP11, MMP7, MMP12, MMP17, MMP13, MMP8, MMP9, MMP1 | |
GO:0043169 | cation binding | 9.747e-06 | 12 | MMP10, MMP11, MMP7, MMP17, MMP8, MMP9, MMP14, MMP15, MMP3, MMP12, MMP13, MMP1 | |
GO:0003824 | catalytic activity | 1.878e-04 | 12 | MMP10, MMP11, MMP7, MMP17, MMP8, MMP9, MMP14, MMP15, MMP3, MMP12, MMP13, MMP1 |
Pathway ID | Description | Count | Genes | P Value |
---|---|---|---|---|
hsa05219 | Bladder cancer | 2 | MMP1, MMP9 | 3.863e-05 |
hsa05323 | Rheumatoid arthritis | 2 | MMP3, MMP1 | 3.837e-04 |
Construction of the MMP-related regulatory network
MMP-related DEGs | Degree | DE-miRNAs |
---|---|---|
MMP12 | 1 | miR-6090 |
MMP10 | 2 | miR-20b-5p, miR-6768-5p |
MMP7 | 2 | miR-4697-5p, miR-7109-5p |
MMP17 | 3 | miR-3198, miR-6741-5p, miR-6753-3p |
MMP1 | 5 | miR-21-3p, miR-6759-3p, miR-185-5p, miR-331-3p, miR-3651 |
MMP9 | 5 | miR-619-5p, miR-3646, miR-4750-3p, miR-4516, miR-7114-3p |
MMP3 | 7 | miR-20a-5p, miR-31-5p, miR-17-5, miR-18b-5p, miR-572, miR-6768-5p, miR-548q |
MMP11 | 8 | miR-20a-5p, miR-17-5p, miR-103a-3p, miR-4728-3p, miR-20b-5p, miR-7845-5p, miR-129-1-3p, miR-4476 |
MMP13 | 10 | miR-4697-5p, miR-6826-5p, miR-6741-5p, miR-6793-5p, miR-34b-5p, miR-6759-3p, miR-503-5p, miR-6753-3p, miR-7111-3p, miR-129-1-3p |
MMP15 | 11 | miR-619-5p, miR-3198, miR-3180-3p, miR-15b-5p, miR-7109-5p, miR-10b-5p, miR-199b-5p, miR-1227-5p, miR-6076, miR-548q, miR-7114-3p |
MMP14 | 14 | miR-6132, miR-4485-5pmiR-103a-3pmiR-6741-5p, miR-6793-5p, miR-4253, miR-154-5p, miR-1227-5p, miR-6753-3p, miR-4324, miR-6076, miR-4516, miR-7114-3p, miR-4687-3p |
MMP8 | 15 | miR-3652, miR-3663-5p, miR-142-3p, miR-486-5p, miR-6746-5p, miR-99a-5p, miR-331-3p, miR-154-5p, miR-99b-3p, miR-299-5p, miR-1227-5p, miR-7111-3p, miR-129-1-3p, miR-4687-3p, miR-100-5p |