| Literature DB >> 29121993 |
Shenglong Li1, Yujin Dong2, Ke Wang3, Zhe Wang4, Xiaojing Zhang5.
Abstract
BACKGROUND: Increasing evidence has indicated parathyroid hormone type 1 receptor (PTHR1) plays important roles for the development and progression of osteosarcoma (OS). However, its function mechanisms remain unclear. The goal of this study was to further illuminate the roles of PTHR1 in OS using microarray data.Entities:
Keywords: Angiogenesis; Inflammation; Osteosarcoma; PTHR1; Wnt pathway
Mesh:
Substances:
Year: 2017 PMID: 29121993 PMCID: PMC5679487 DOI: 10.1186/s13018-017-0664-2
Source DB: PubMed Journal: J Orthop Surg Res ISSN: 1749-799X Impact factor: 2.359
Top 15 upregulated and downregulated genes differentially expressed between Pth1r knockout osteosarcoma cells and control
| Expression | Gene_Symbol | LogFC | Adjusted |
|---|---|---|---|
| Upregulated | Grin2c | 2.272 | 4.27E−06 |
| Ccnb3 | 3.243 | 4.27E−06 | |
| Usp51 | 1.702 | 4.45E−06 | |
| Slc1a3 | 1.443 | 6.34E−06 | |
| Kcnk1 | 2.774 | 6.34E−06 | |
| Bmp3 | 2.764 | 9.74E−06 | |
| Rbm44 | 1.846 | 1.14E−05 | |
| Plppr5 | 2.010 | 1.85E−05 | |
| Phex | 1.977 | 1.85E−05 | |
| Nell1 | 2.368 | 2.00E−05 | |
| AI593442 | 1.477 | 2.00E−05 | |
| Ooep | 0.828 | 2.00E−05 | |
| Trpc6 | 1.628 | 2.00E−05 | |
| Dkk1 | 1.730 | 2.00E−05 | |
| Downregulated | Lef1 | − 1.677 | 2.90E−06 |
| Elf1 | − 1.300 | 4.79E−06 | |
| Jph1 | − 1.674 | 5.47E−06 | |
| Zfhx4 | − 2.183 | 6.34E−06 | |
| S1pr3 | − 1.209 | 8.30E−06 | |
| Slc20a2 | − 1.031 | 9.06E−06 | |
| Pdgfc | − 1.073 | 9.20E−06 | |
| Wbp4 | − 1.221 | 9.74E−06 | |
| Robo1 | − 1.536 | 1.12E−05 | |
| Dgkh | − 1.183 | 1.12E−05 | |
| Mpped2 | − 1.873 | 1.14E−05 | |
| Dnajc15 | − 1.661 | 1.24E−05 | |
| Atp10a | − 1.118 | 1.85E−05 | |
| Slc6a15 | − 2.051 | 1.85E−05 |
FC fold change, adjusted p value the p value was corrected with the Benjamini-Hochberg (BH) algorithm
KEGG pathway enrichment of all DEGs and modules
| DEGs | Expression | Term | Count |
| Genes |
|---|---|---|---|---|---|
| All | Upregulated | mmu05150:Staphylococcus aureus infection | 13 | 1.16E−08 | C1qa, C3ar1, C1qb, Selp, Fcgr2b, C4b, Fcgr4, H2-aa, Cfd, H2-ea.-ps… |
| mmu05152:Tuberculosis | 16 | 1.64E−04 | Mrc1, Cd209a, Tlr1, Fcgr4, Ctss, Tlr9, Fcgr3, Vdr, Fcgr2b, Mapk13… | ||
| mmu03320:PPAR signaling pathway | 10 | 4.65E−04 | Lpl, Cd36, Cyp27a1, Pparg, Fabp4, Aqp7, Fabp7, Adipoq, Acsl6, Angptl4 | ||
| mmu04145:Phagosome | 15 | 4.89E−04 | Mrc1, H2-m9, Cd209a, Fcgr4, Ctss, Fcgr3, Cybb, Cd36, H2-m11, Fcgr2b… | ||
| mmu04610:Complement and coagulation cascades | 9 | 0.001 | C1qa, C3ar1, C1qb, C4b, Cd59a, F3, F8, Cfd, C1qc | ||
| mmu04620:Toll-like receptor signaling pathway | 10 | 0.002 | Cd86, Ccl3, Mapk13, Irf7, Tlr1, Il12a, Ticam2, Tlr7, Tlr8, Tlr9 | ||
| mmu04514:Cell adhesion molecules (CAMs) | 13 | 0.002 | Selp, H2-m9, Cadm1, Neo1, Ncam1, Siglec1, Cd86, H2-m11, H2-aa, Cd4… | ||
| mmu04614:Renin-angiotensin system | 6 | 0.003 | Ace, Agtr1a, Agt, Prcp, Cpa3, Enpep | ||
| mmu04080:Neuroactive ligand-receptor interaction | 18 | 0.004 | C3ar1, Thrb, Grik2, Lpar3, Vipr2, Ednra, P2ry13, Aplnr, P2ry6, Adrb2… | ||
| mmu04924:Renin secretion | 8 | 0.004 | Ednra, Ace, Adrb2, Agtr1a, Agt, Pde1a, Pde3b, Cacna1d | ||
| mmu05330:Allograft rejection | 7 | 0.005 | H2-m9, Cd86, H2-m11, Il12a, H2-aa, H2-t24, H2-ea.-ps | ||
| mmu04978:Mineral absorption | 6 | 0.006 | Vdr, Atp1b1, Mt2, Cybrd1, Slc40a1, Trf | ||
| mmu04940:Type I diabetes mellitus | 7 | 0.009 | H2-m9, Cd86, H2-m11, Il12a, H2-aa, H2-t24, H2-ea.-ps | ||
| mmu05142:Chagas disease (American trypanosomiasis) | 9 | 0.010 | C1qa, C1qb, Ace, Ccl3, Mapk13, Il12a, Smad3, C1qc, Tlr9 | ||
| mmu05332:Graft-versus-host disease | 6 | 0.017 | H2-m9, Cd86, H2-m11, H2-aa, H2-t24, H2-ea.-ps | ||
| mmu05133:Pertussis | 7 | 0.020 | C1qa, C1qb, C4b, Mapk13, Il12a, Ticam2, C1qc | ||
| mmu04310:Wnt signaling pathway | 10 | 0.021 | Fzd9, Dkk1, Sfrp1, Sfrp2, Fzd3, Camk2b, Fzd5, Daam2, Lrp5, Fzd6 | ||
| mmu04060:Cytokine-cytokine receptor interaction | 14 | 0.025 | Il1r2, Il1r1, Ccl3, Osmr, Ccl8, Pf4, Ccl7, Tnfsf10, Ccr5, Cxcl13… | ||
| mmu04960:Aldosterone-regulated sodium reabsorption | 5 | 0.027 | Atp1b1, Sgk1, Nr3c2, Igf1, Insr | ||
| mmu04380:Osteoclast differentiation | 9 | 0.029 | Il1r1, Cybb, Fcgr2b, Mapk13, Pparg, Fcgr4, Fhl2, Trem2, Fcgr3 | ||
| mmu04612:Antigen processing and presentation | 7 | 0.031 | H2-m9, H2-m11, H2-aa, Cd4, Ctss, H2-t24, H2-ea.-ps | ||
| mmu04640:Hematopoietic cell lineage | 7 | 0.034 | Il1r2, Il1r1, Cd36, Cd59a, Cd33, Csf3r, Cd4 | ||
| mmu05140:Leishmaniasis | 6 | 0.037 | Mapk13, Il12a, Fcgr4, H2-aa, H2-ea.-ps, Fcgr3 | ||
| mmu05144:Malaria | 5 | 0.049 | Selp, Cd36, Il12a, Thbs4, Tlr9 | ||
| Downregulated | mmu01130:Biosynthesis of antibiotics | 22 | 3.33E−06 | Cyp51, Ldhb, Shmt2, Msmo1, Pfkl, Hmgcr, Pafah2, Pgd, Pfkp, Fdps… | |
| mmu01100:Metabolic pathways | 63 | 2.00E−04 | Ldhb, Sgms2, Alg1, Hmgcr, Cyp2s1, Pgd, Cyp2j6, Pgam1, Lss, Hlcs… | ||
| mmu00100:Steroid biosynthesis | 6 | 2.40E−04 | Cyp51, Msmo1, Sqle, Lss, Dhcr24, Fdft1 | ||
| mmu05412:Arrhythmogenic right ventricular cardiomyopathy (ARVC) | 10 | 3.55E−04 | Itga5, Lmna, Itga11, Cacnb2, Sgcd, Actn1, Gja1, Lef1, Cacnb3, Sgcb | ||
| mmu00010:Glycolysis/Gluconeogenesis | 9 | 0.001 | Pgm2, Ldhb, Tpi1, Pfkl, Pfkp, Pgam1, Adh7, Aldh3b1, Eno1 | ||
| mmu00240:Pyrimidine metabolism | 10 | 0.005 | Pold4, Umps, Pole2, Pold1, Cda, Uck2, Dpyd, Polr3c, Nt5e, Polr2a | ||
| mmu00230:Purine metabolism | 13 | 0.011 | Ak4, Polr3c, Pfas, Polr2a, Pgm2, Pold4, Pole2, Pde1c, Pold1, Pde5a… | ||
| mmu05410:Hypertrophic cardiomyopathy (HCM) | 8 | 0.012 | Itga5, Tgfb3, Lmna, Itga11, Cacnb2, Sgcd, Cacnb3, Sgcb | ||
| mmu00030:Pentose phosphate pathway | 5 | 0.014 | Pgm2, Pfkl, Pgd, Pfkp, Dera | ||
| mmu05414:Dilated cardiomyopathy | 8 | 0.015 | Itga5, Tgfb3, Lmna, Itga11, Cacnb2, Sgcd, Cacnb3, Sgcb | ||
| mmu00670:One carbon pool by folate | 4 | 0.021 | Mthfd1, Shmt2, Aldh1l1, Mthfd1l | ||
| mmu00051:Fructose and mannose metabolism | 5 | 0.021 | Akr1b8, Tpi1, Pfkl, Pfkp, Pmm2 | ||
| mmu05217:Basal cell carcinoma | 6 | 0.029 | Wnt4, Fzd1, Lef1, Ptch2, Axin2, Gli3 | ||
| mmu01200:Carbon metabolism | 9 | 0.030 | Tpi1, Shmt2, Pfkl, Pgd, Phgdh, Pfkp, Esd, Pgam1, Eno1 | ||
| mmu00900:Terpenoid backbone biosynthesis | 4 | 0.034 | Hmgcr, Fdps, Hmgcs1, Idi1 | ||
| mmu01230:Biosynthesis of amino acids | 7 | 0.036 | Tpi1, Shmt2, Pfkl, Phgdh, Pfkp, Pgam1, Eno1 | ||
| Module | 1 | mmu04062:Chemokine signaling pathway | 6 | 1.70E−05 | CCR5, CXCL13, GNAI1, CCR3, CCR2, CCL9 |
| mmu04080:Neuroactive ligand-receptor interaction | 6 | 1.00E−04 | C3AR1, APLNR, P2RY13, S1PR3, HTR1B, LPAR3 | ||
| mmu04060:Cytokine-cytokine receptor interaction | 4 | 8.90E−03 | CCR5, CXCL13, CCR3, CCR2 | ||
| mmu04024:cAMP signaling pathway | 3 | 4.80E−02 | HTR1B, GNAI1, HCAR1 |
DEGs differentially expressed genes
Fig. 1PTH1R enriched gene ontology (GO) terms for biological processes. Cell proliferation process was enriched
Fig. 2The protein–protein interaction network. The red and green nodes represent the upregulated and downregulated genes, respectively
Hub genes in the protein–protein interaction network
| Gene | Degree | Gene | Betweenness | Gene | Closeness |
|---|---|---|---|---|---|
| Agt | 39 | Agt | 13,427.92 | Agt | 2.21E−05 |
| Lpar3 | 26 | Ar | 8585.025 | Srebf1 | 2.21E−05 |
| Gnai1 | 25 | Pla2g2d | 8001.098 | Ccr2 | 2.21E−05 |
| Ccr5 | 24 | Srebf1 | 7904.877 | Ccr5 | 2.21E−05 |
| Ccl9 | 24 | Pax6 | 7664.532 | Lpar3 | 2.21E−05 |
| Ccr2 | 23 | Rhoc | 7643.579 | Gnai1 | 2.21E−05 |
| Ccr3 | 22 | Dlg4 | 6747.256 | Ptafr | 2.21E−05 |
| Igf1 | 21 | Actn1 | 6420.109 | Igf1 | 2.21E−05 |
| Entpd1 | 20 | Gnai1 | 6334.163 | Ar | 2.21E−05 |
| Rhoc | 20 | Igf1 | 5806.686 | Ccr3 | 2.20E−05 |
| Dlg4 | 19 | Racgap1 | 5675.621 | Ccl9 | 2.20E−05 |
| Entpd3 | 19 | Cyp2e1 | 5666.956 | P2ry12 | 2.20E−05 |
| C3ar1 | 19 | Lpar3 | 5255.704 | Aplnr | 2.20E−05 |
| Ar | 19 | Gpc6 | 5126.2 | C3ar1 | 2.20E−05 |
| Dlg3 | 18 | Tgfb3 | 5025.73 | Htr2a | 2.20E−05 |
| P2ry12 | 17 | H2-Aa | 4732.818 | Pparg | 2.20E−05 |
| Htr1b | 17 | Pld4 | 4646.952 | Abca1 | 2.20E−05 |
| Aplnr | 17 | Entpd1 | 4307.738 | Cd36 | 2.20E−05 |
| Srebf1 | 17 | Htr2a | 4269.31 | Pf4 | 2.20E−05 |
| Aurkb | 16 | Ctss | 4234.501 | Agtr1a | 2.20E−05 |
Degree the number of interactions per node (protein), betweenness the number of shortest paths that pass through each node, closeness centrality the average length of the shortest paths to access all other proteins in the network
Fig. 3The most significant module extracted from protein–protein interaction network. The red and green nodes represent the upregulated and downregulated genes, respectively
Module analysis
| Cluster | Score (Density × number of Nodes) | Nodes | Edges | Node IDs |
|---|---|---|---|---|
| 1 | 8 | 17 | 136 | Hcar1, Agt, Ccr2, Lpar3, Ccr5, Ccr3, Gnai1, P2ry12, P2ry13, S1pr3, C3ar1, Ccl9, Cxcl13, Aplnr, Penk, Gal, Htr1b |
| 2 | 4.75 | 20 | 95 | Cacng5, Agtr1a, Ednra, Lpar6, Gpr65, P2ry6, Ptafr, Ptgfr, Htr2a, Dlg4, Grin2c, Gria2, Grik2, Gria4, Dlg3, Cpt1c, Cacng7, Olfm1, Olfm2, Cnih2 |
| 3 | 4.667 | 12 | 56 | Rangap1, Ccnb1, Cdc20, Kif23, Racgap1, Cdca8, Aurkb, Kif2c, Cenpe, Cenph, Cenpp, Nde1 |
| 4 | 4.4 | 10 | 44 | Srebf2, Lss, Cyp51, Msmo1, Hmgcs1, Hmgcr, Sqle, Fdft1, Idi1, Fdps |
| 5 | 4 | 9 | 36 | Actn1, Igf1, Igf2, Vegfc, Tgfb3, Cfd, Pf4, Srgn, F8 |