| Literature DB >> 32256724 |
Chu Chen1, Guanhua Xu1, Yuyu Sun1, Zhiming Cui1.
Abstract
Osteoarthritis is a general joint disease characterized by articular cartilage degeneration. The extracellular matrix is a principal component in articular cartilage. The dynamic remodeling of the extracellular matrix is involved in the pathological degradation of the articular cartilage. Facet joint osteoarthritis (FJOA) is a common form of osteoarthritis that occurs in the posterior aspect of the vertebral column. However, to the best of our knowledge, the current understanding of the genetic changes in FJOA is limited. The most significantly differentially expressed genes and Gene Ontology categories in FJOA were identified by transcriptome sequencing analysis. The extracellular matrix, matrix metalloproteinases (MMPs) and proteinases of the extracellular matrix were highly involved in FJOA. The canonical signaling pathway 'inhibition of matrix metalloproteinases' was further studied in detail by identifying and validating differentially expressed genes in the signaling pathway. Taken together, the present study revealed changes in MMP-related genes in FJOA and showed the importance of extracellular matrix remodeling in FJOA from a genetic aspect. Copyright: © Chen et al.Entities:
Keywords: bioinformatics analysis; extracellular matrix; facet joint osteoarthritis; matrix metalloproteinases; transcriptome sequencing
Year: 2020 PMID: 32256724 PMCID: PMC7086276 DOI: 10.3892/etm.2020.8488
Source DB: PubMed Journal: Exp Ther Med ISSN: 1792-0981 Impact factor: 2.447
Primer pairs for reverse transcription-quantitative PCR.
| Gene | Primer | Sequence (5'-3') |
|---|---|---|
| MMP7 | Forward | AGCAGCTATGCAGCTGGCCGT |
| Reverse | GCCCTGAGCCTGTTCCCACTGC | |
| ADAM12 | Forward | TCTTGCTGCCGGATTTGTGGTT |
| Reverse | AAGGGCGCACACACCTTAGTTT | |
| TIMP3 | Forward | AGGACGCCTTCTGCAAC |
| Reverse | CTCCTTTACCAGCTTCTTCC | |
| TIMP4 | Forward | ACCTGTCCTTGGTGCAGA |
| Reverse | TGTAGCAGGTGGTGATTTGG | |
| GAPDH | Forward | CCAAGGTCATCCATGACAAC |
| Reverse | TGTCATACCAGGAAATGAGC |
MMP7, matrix metalloproteinase 7; ADAM12, disintegrin and metalloproteinase domain-containing protein 12; TIMP, tissue inhibitor of metalloproteinases.
Figure 1.Expression patterns of genes in healthy and lesioned facet joint tissues. The expression levels of genes are shown in a heatmap and indicated by a color bar. Red indicates upregulated genes while blue indicates downregulated genes.
Top 10 upregulated and downregulated genes in FJOA.
| A, Upregulated | |||||
|---|---|---|---|---|---|
| GeneID | CTRL_FPKM | FJOA_FPKM | log2 (FJOA/CTRL) | q-value | Description |
| CRHR1 | 0.022303 | 0.643232 | 4.85003 | 0.00463 | Corticotropin releasing hormone receptor 1 |
| CSF3 | 0.230299 | 3.21825 | 3.80469 | 0.000259 | Colony stimulating factor 3 |
| CRLF1 | 6.24624 | 81.3432 | 3.70296 | 0.000259 | Cytokine receptor like factor 1 |
| DAW1 | 0.090234 | 1.12819 | 3.6442 | 0.022496 | Dynein assembly factor with WD repeats 1 |
| HAS1 | 2.90011 | 35.0671 | 3.59594 | 0.000259 | Hyaluronan synthase 1 |
| POSTN | 23.7872 | 265.481 | 3.48035 | 0.000259 | Periostin |
| TMEM59L | 0.181724 | 1.78416 | 3.29542 | 0.005947 | Transmembrane protein 59 like |
| PVRL4 | 0.170113 | 1.61362 | 3.24574 | 0.000259 | Poliovirus receptor-related protein 4 |
| LINC00702 | 0.924058 | 8.50754 | 3.20269 | 0.002128 | Long intergenic non-protein coding RNA 702 |
| HMCN2 | 0.158359 | 1.36891 | 3.11176 | 0.000259 | Hemicentin 2 |
| B, Downregulated | |||||
| GeneID | CTRL_FPKM | FJOA_FPKM | log2 (FJOA/CTRL) | q-value | Description |
| MMP12 | 1.5777 | 0.10857 | -3.86112 | 0.013616 | Matrix metallopeptidase 12 |
| HBG1 | 57.9551 | 4.16107 | -3.79991 | 0.000259 | Hemoglobin subunit γ1 |
| SPIC | 2.63717 | 0.231806 | -3.508 | 0.00394 | Spi-c transcription factor |
| TPSB2 | 8.40967 | 0.772965 | -3.44357 | 0.000259 | Tryptase β2 (gene/pseudogene) |
| SEC14L3 | 0.596955 | 0.059692 | -3.32201 | 0.007555 | Sec14 like lipid binding 3 |
| PYHIN1 | 2.77976 | 0.280398 | -3.30942 | 0.000259 | Pyrin and hin domain family member 1 |
| CHI3L1 | 1078.35 | 114.902 | -3.23036 | 0.000259 | Chitinase 3 like 1 |
| CD19 | 1.2214 | 0.131175 | -3.21897 | 0.004793 | Cd19 molecule |
| GP5 | 3.14407 | 0.360364 | -3.12511 | 0.000259 | Glycoprotein v platelet |
| GPR15 | 1.43198 | 0.166889 | -3.10106 | 0.033956 | G protein-coupled receptor 15 |
FPKM, fragments per kilobase of transcript per million mapped reads; FJOA, facet joint osteoarthritis; CTRL, control.
Figure 2.Top enriched GO categories in facet joint osteoarthritis. The ten most enriched GO biological processes, molecular functions and cellular components. Red represents GO biological processes, blue represents GO molecular functions and green represents GO cellular components. GO, gene ontology.
Figure 3.Schematic diagram of the canonical signaling pathway ‘inhibition of matrix metalloproteinases’. Differentially expressed genes in the canonical signaling pathway ‘inhibition of matrix metalloproteinases’ are represented in red and green. Red indicates upregulated genes while green indicates downregulated genes. TIMP, tissue inhibitor of metalloproteinases; MMP, matrix metalloproteinase; RECK, reversion-inducing cysteine-rich protein with Kazal motifs; HSPG, basement membrane-specific heparan sulfate proteoglycan core protein; ADAM, disintegrin and metalloproteinase domain-containing protein; TSP2, thrombospondin-2; A2M, α-2-macroglobulin; TFPI2, tissue factor pathway inhibitor 2; LRP1, prolow-density lipoprotein receptor-related protein 1; MT1-MMP, matrix metallopeptidase 14 (membrane-inserted).
Expression levels of differentially expressed genes in the canonical signaling pathway ‘inhibition of matrix metalloproteinases’.
| GeneID | CTRL_FPKM | FJOA_FPKM | log2 (FJOA/CTRL) | q-value | Description |
|---|---|---|---|---|---|
| A2M | 152.6 | 144.685 | -0.07684 | 0.580386 | α-2-macroglobulin |
| ADAM10 | 23.1911 | 18.2402 | -0.34645 | 0.00269 | Disintegrin and metalloproteinase domain-containing protein 10 |
| ADAM12 | 5.90052 | 19.1302 | 1.69694 | 0.000259 | Disintegrin and metalloproteinase domain-containing protein 12 |
| ADAM17 | 12.845 | 12.1117 | -0.08481 | 0.581591 | Disintegrin and metalloproteinase domain-containing protein 17 |
| HSPG2 | 79.3027 | 132.242 | 0.737738 | 0.000259 | Basement membrane-specific heparan sulfate proteoglycan core protein |
| LRP1 | 251.144 | 326.912 | 0.38039 | 0.012286 | Prolow-density lipoprotein receptor-related protein 1 |
| MMP2 | 108.741 | 175.485 | 0.690452 | 0.000259 | Matrix metalloproteinase 2 |
| MMP9 | 314.457 | 91.4777 | -1.78137 | 0.000259 | Matrix metalloproteinase 9 |
| MMP17 | 1.17006 | 1.48701 | 0.345823 | 0.353116 | Matrix metalloproteinase 17 |
| MMP11 | 5.50944 | 8.16829 | 0.568128 | 0.001552 | Matrix metalloproteinase 11 |
| MMP3 | 373.253 | 167.156 | -1.15896 | 0.000259 | Matrix metalloproteinase 3 |
| MMP19 | 6.38089 | 10.853 | 0.766262 | 0.000497 | Matrix metalloproteinase 19 |
| MMP13 | 125.361 | 75.5355 | -0.73086 | 0.000259 | Matrix metalloproteinase 13 |
| MMP28 | 2.48386 | 4.40147 | 0.825399 | 0.026506 | Matrix metalloproteinase 28 |
| MMP23B | 0.04404 | 0.828743 | 4.23405 | 0.247905 | Matrix metalloproteinase 23B |
| MMP14 | 74.0875 | 118.202 | 0.673953 | 0.000259 | Matrix metalloproteinase 14 |
| MMP24 | 1.21904 | 1.34362 | 0.14038 | 0.778023 | Matrix metalloproteinase 24 |
| MMP8 | 37.9945 | 14.832 | -1.35708 | 0.000259 | Matrix metalloproteinase 8 |
| MMP1 | 6.78886 | 4.20773 | -0.69013 | 0.493474 | Matrix metalloproteinase 1 |
| MMP12 | 1.5777 | 0.10857 | -3.86112 | 0.013616 | Matrix metalloproteinase 12 |
| MMP15 | 1.65603 | 2.41486 | 0.54421 | 0.016667 | Matrix metalloproteinase 15 |
| MMP16 | 9.42333 | 4.70063 | -1.00338 | 0.000259 | Matrix metalloproteinase 16 |
| MMP7 | 2.13341 | 1.03658 | -1.04133 | 0.028971 | Matrix metalloproteinase 7 |
| MMP25 | 6.06705 | 2.5246 | -1.26494 | 0.000259 | Matrix metalloproteinase 25 |
| RECK | 9.33448 | 14.4833 | 0.633749 | 0.000259 | Reversion-inducing cysteine-rich protein with Kazal motifs |
| TFPI2 | 0.973482 | 0.789919 | -0.30145 | 0.53558 | Tissue factor pathway inhibitor 2 |
| TIMP1 | 322.419 | 227.107 | -0.50557 | 0.000259 | Tissue inhibitor of metalloproteinases 1 |
| TIMP2 | 216.411 | 377.86 | 0.804078 | 0.000259 | Tissue inhibitor of metalloproteinases 2 |
| TIMP3 | 91.4082 | 261.077 | 1.51408 | 0.000259 | Tissue inhibitor of metalloproteinases 3 |
| TIMP4 | 27.8848 | 57.9526 | 1.05539 | 0.000259 | Tissue inhibitor of metalloproteinases 4 |
| TSP2 | 37.7629 | 73.7939 | 0.966534 | 0.000259 | Thrombospondin-2 |
FPKM, fragments per kilobase of transcript per million mapped reads; FJOA, facet joint osteoarthritis; CTRL, control.
Figure 4.Heatmap of differentially expressed genes in the canonical signaling pathway ‘inhibition of matrix metalloproteinases’. Red indicates upregulated genes while green indicates downregulated genes. CTRL, control group; FJOA, facet joint osteoarthritis; TIMP, tissue inhibitor of metalloproteinases; MMP, matrix metalloproteinase; RECK, reversion-inducing cysteine-rich protein with Kazal motifs; HSPG, basement membrane-specific heparan sulfate proteoglycan core protein; ADAM, disintegrin and metalloproteinase domain-containing protein; TSP2, thrombospondin-2; A2M, α-2-macroglobulin; TFPI2, tissue factor pathway inhibitor 2; LRP1, prolow-density lipoprotein receptor-related protein 1.
Figure 5.Reverse transcription-quantitative PCR analysis of differentially expressed genes in the canonical signaling pathway ‘inhibition of matrix metalloproteinases’. The relative expression levels of MMP7, ADAM12, TIMP3 and TIMP4 were calculated. The red arrows indicate the expression trends of genes, as revealed by sequencing. Data were summarized from three independent experiments. *P<0.05 vs. control. FJOA, facet joint osteoarthritis; MMP7, matrix metalloproteinase 7; ADAM12, disintegrin and metalloproteinase domain-containing protein 12; TIMP, tissue inhibitor of metalloproteinases.