| Literature DB >> 34689294 |
Yunyuan Zhang1, Qing Wang2, Xian Chen3, Yukun Xue4, Jiao Feng5, Qingwu Tian3.
Abstract
BACKGROUND: More than half of Neuroblastoma (NB) patients presented with distant metastases and the relapse of metastatic patients was up to 90%. It is urgent to explore a biomarker that could facilitate the prediction of metastasis in NB patients. METHODS ANDEntities:
Keywords: Bioinformatics analysis; Biomarker; Metastasis; Neuroblastoma; S100A9
Mesh:
Substances:
Year: 2021 PMID: 34689294 PMCID: PMC8604885 DOI: 10.1007/s11033-021-06783-2
Source DB: PubMed Journal: Mol Biol Rep ISSN: 0301-4851 Impact factor: 2.316
Fig. 1A Heat map for the differentially expressed genes (DEGs). B Volcano plots reflecting number, significance and reliability of differentially expressed mRNA in NB. The red dots indicate dysregulated mRNAs
The tops enriched GO terms of the differentially expressed genes
| Category | ID | Term | p-value | Gene count | Genes |
|---|---|---|---|---|---|
| BP | GO:0001558 | Regulation of cell growth | 3.13E-04 | 6 | NANOS1, NRG3, IGFBP2, AGTR1, IGFBP7, WISP1 |
| GO:0006954 | Inflammatory response | 5.07E-04 | 11 | CCL7, TRIL, C3AR1, FPR3, IL1RAP, CDO1, PTGS2, TAC1, HDAC9, S100A9, CHST2 | |
| GO:0007204 | Positive regulation of cytosolic calcium ion concentration | 0.00316801 | 6 | AGTR1, C3AR1, ADM, FPR3, LPAR3, TAC1 | |
| GO:0030335 | Positive regulation of cell migration | 0.011814659 | 6 | CCL7, GPNMB, CDH13, SEMA3E, LAMC2, FGF1 | |
| GO:0051384 | Response to glucocorticoid | 0.012309797 | 4 | IGFBP2, ADM, CDO1, PTGS2 | |
| GO:0,007,200 | Phospholipase C-activating G-protein coupled receptor signaling pathway | 0.012827699 | 4 | HTR1D, AGTR1, C3AR1, FPR3 | |
| GO:0051482 | Positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G- | 0.018038462 | 3 | GPR65, AGTR1, LPAR3 | |
| GO:0008285 | Negative regulation of cell proliferation | 0.027623627 | 8 | MYOG, KAT2B, GPNMB, CDH13, IGFBP7,ADM,PTGS2,MYO16 | |
| GO:0030819 | Positive regulation of cAMP biosynthetic process | 0.035152385 | 3 | GPR65, RLN2, ADM | |
| GO:0007267 | Cell–cell Signaling | 0.040239268 | 6 | CCL7, ADM, TAC1, PCSK5, S100A9, WISP1 | |
| CC | GO:0043005 | Neuron projection | 0.007369421 | 7 | SLC32A1, CASP5, PTPRO, STMN2,CDH13,PTGS2,POU4F1 |
| GO:0005615 | Extracellular space | 0.007817435 | 19 | GDF10, IGFBP2, SECTM1, ADM, LAMC2, SEMA3E, FGF1, PCSK5, WISP1, CCL7, NRG3, PLBD1, CDH13, IGFBP7, TAC1, S100A9, ANGPTL1, MICA, CPA4 | |
| GO:0005576 | Extracellular region | 0.011007958 | 21 | OLFML2B, IGFBP2, PSG1, ADM, LAMC2, SEMA3E, IL1RAP, FGF1, THBS2, FBLN2, APOLD1, CCL7, NRG3, RLN2, FDCSP, IGFBP7, CCDC3, VIP, TAC1, S100A9, CHGB | |
| GO:0005887 | Integral component of plasma membrane | 0.012602605 | 19 | GABRB1, VIPR1, SLC10A1, GPR65, PTPRO, HTR1D, LPAR3, FPR3, IL1RAP, HCRTR1, TSPAN13, GPNMB, NRG3, GPR183, C3AR1, AGTR1, LGR5, MICA, SLC38A4 | |
| GO:0005901 | Caveola | 0.079588673 | 3 | SDPR, CDH13, PTGS2 | |
| MF | GO:0008201 | Heparin binding | 0.007960505 | 6 | CCL7, GPNMB, LAMC2, THBS2, FGF1, WISP1 |
| GO:0003705 | Transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding | 0.014352101 | 4 | MYOG, FOXC1, POU4F1, VGLL3 | |
| GO:0005179 | Hormone activity | 0.03603451 | 4 | RLN2, ADM, VIP, CHGB |
Fig. 2A Protein-protein interaction network constructed with the dysregulated differentially expressed genes. B PPI network was visualized by Cystoscope software
Top 10 genes that evaluated by betweenness, BottleNeck, Closeness, Clustering coefficient, Degree, DMNC, EcCentricity, EPC, MCC, MNC, Radiality and Stress centrality respectively in the protein–protein interaction network
| Gene name | Clinenms centrality | MNC, Radiality and stress centrality respectively in the protein–protein interaction network | Gene name | Stress centrality | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene name | Degree centrality | Gene name | EPC centrality | Gene name | MNC centrality | Gene name | Radiality centrality | ||||
| HDAC9 | 70.66667 | 5LC22A15 | 25 | TRIM9 | 22.245 | TAC1 | 25 | TAC1 | 4.87121 | PTGS2 | 7892 |
| PTGS2 | 70.08333 | ZNF43P | 25 | GPR183 | 22.121 | STMN2 | 23 | FGF1 | 4.86344 | HDAC9 | 7010 |
| TAC1 | 69.75 | URASH3A | 23 | AK5 | 22.046 | SLC32A1 | 23 | PTGS2 | 4.84091 | TAC1 | 6490 |
| KAT2B | 64.41667 | CHST2 | 20 | CASQ1 | 19.554 | RGS7 | 18 | TAGLN | 4.79545 | FGF1 | 6136 |
| FOXC1 | 66.25 | SEMA3E | 19 | WISP1 | 19.156 | PTGS2 | 17 | CDH13 | 4.7803 | FOXC1 | 4312 |
| FGF1 | 65.83333 | HCRTR 1 | 18 | RGS7 | 19.142 | FGF1 | 17 | AGTR1 | 4.72727 | STMN2 | 4228 |
| STMN2 | 65.75 | GPR183 | 17 | NRG3 | 18.906 | CHGB | 16 | STMN2 | 4.7197 | KAT2B | 4132 |
| MYOG | 64.41667 | FPR3 | 17 | ANGPTL1 | 18.77 | IGFBP7 | 14 | MYOG | 4.69697 | CDH13 | 4034 |
| CDH13 | 63.45 | CCL7 | 17 | SEMA3E | 18.362 | THBS2 | 14 | KAT2B | 4.68939 | TAGLN | 3990 |
| TAGLN | 62.83333 | NRG3 | 16 15 | GPR65 | 17.728 | NRG3 | 13 | SLC32A1 | 4.68182 | AGTR1 | 3838 |
Fig. 3A qRT-PCR analysis for the expression of hub genes. B ELISA analysis for serum levels of S100A9 in metastatic (n=9) and non-metastatic NB (n=10) patients. C Representative IHC staining for S100A9 in tissue sections from metastatic and non-metastatic NB patients. **p < 0.01. D MTT analysis for Blank/Control/S100A9/siS100A9 SH-SY-5Y cells for sequential 5 days. *p<0.05, **p < 0.01.
Fig. 4A a. Colony formation assay for Blank/Control/S100A9/siS100A9 SH-SY-5Y cells. b. The representative images of transmembrane cells are shown in the right panel. The mean numbers of transmembrane cells ± SD per microscopic field of three independent experiments are quantified in the right panel. **p < 0.01, ***p < 0.001. B a.Transwell invasion assay for Blank/Control/S100A9/siS100A9 SH-SY-5Y cells for 24 h. b.The representative images of transmembrane cells are shown in the right panel. The mean numbers of transmembrane cells ± SD per microscopic field of three independent experiments are quantified in the right panel. Magnification, ×100, **p < 0.01, ***p < 0.001. C a.Wound healing assay for Blank/Control/S100A9/siS100A9 SH-SY-5Y cells for 72 h. b.The incision width of different sites was measured and average healing rate was calculated and shown in the right panel. *p < 0.05, **p < 0.01