| Literature DB >> 34964707 |
Yun Yu1, Yu-Han Zhang2, Liang Liu1, Ling-Ling Yu3, Jun-Pei Li1, Jing-An Rao1, Feng Hu1, Ling-Juan Zhu1, Hui-Hui Bao1, Xiao-Shu Cheng1.
Abstract
Obesity is a complex medical condition that affects multiple organs in the body. However, the underlying mechanisms of obesity, as well as its treatment, are largely unexplored. The focus of this research was to use bioinformatics to discover possible treatment targets for obesity. To begin, the GSE133099 database was used to identify 364 differentially expressed genes (DEGs). Then, DEGs were subjected to tissue-specific analyses and enrichment analyses, followed by the creation of a protein-protein interaction (PPI) network and generation of a drug-gene interaction database to screen key genes and potential future drugs targeting obesity. Findings have illustrated that the tissue-specific expression of neurologic markers varied significantly (34.7%, 52/150). Among these genes, Lep, ApoE, Fyn, and FN1 were the key genes observed in the adipocyte samples from obese patients relative to the controls. Furthermore, nine potential therapeutic drugs (dasatinib, ocriplasmin, risperidone, gemfibrozil, ritonavir, fluvastatin, pravastatin, warfarin, atorvastatin) that target the key genes were also screened and selected. To conclude the key genes discovered (Lep, ApoE, Fyn, and FN1), as well as 9 candidate drugs, could be used as therapeutic targets in treating obesity.Entities:
Keywords: Obesity; adipocyte; bioinformatics; biomarkers; drug-gene interaction; tissue-specific gene expression
Mesh:
Substances:
Year: 2022 PMID: 34964707 PMCID: PMC8726706 DOI: 10.1080/21623945.2021.2013406
Source DB: PubMed Journal: Adipocyte ISSN: 2162-3945 Impact factor: 4.534
Figure 1.Differentially expressed genes (DEGs) between the obesity and control cohorts. Volcano plot of GSE133099 and 11 substantially expressed genes were detected. Black, green, and red dots represent unchanged, downregulated, and upregulated genes, in that order
Significantly enriched GO terms in obesity-related DEGs
| Category | Term | Genes | FDR |
|---|---|---|---|
| Extracellular matrix organization | ITGB1, EGFL6, HPSE2, ELN, FN1, MFAP5, CCDC80, COL1A2, COL5A1, LOX, COL4A4, COL6A2, COL4A3, COL6A3, ITGA5, RECK | 0.003150327 | |
| Extracellular fibril organization | MFAP5, CST3, MFAP4, COL5A1, LTBP2 | 0.033994008 | |
| Proteinaceous extracellular matrix | WNT2B, HPSE2, ELN, LTBP2, PRELP, FBLN2, ADAMTS10, GLG1, WISP2, PTPRZ1, CHL1, TIMP2, ADAMTS9, WNT3, CRTAP, FN1, MMP13, COL1A2, COL5A1, LOX, CILP, COL4A4, COL6A2, COL4A3, MGP, COL6A3, CHI3L1, MMP19, CD248, GPLD1 | 2.65E-13 | |
| Extracellular exosome | SCARB2, CLIC6, ITGB1, HSP90AB1, GALNT16, GDA, PROS1, DNHD1, PTPRJ, SLC2A5, WISP2, SCPEP1, UCHL1, ISLR, LAMP1, CHL1, GLIPR2, NCS1, TIMP2, QSOX1, PTGDS, EDIL3, CACNA2D1, IL18, RENBP, PSMA6, ALDH1A3, COL6A2, CMPK1, COL6A3, CHI3L1, DNASE2, MFGE8, GPLD1, RHOQ, ANGPTL1, PLBD2, ASAH1, SLC22A5, C1S, NPR3, SEMA3G, PRELP, LTBP2, SLC1A4, LIN7A, PDHB, SDSL, NDRG2, FBLN2, GNS, THBS4, ACACA, GLG1, CST3, CLEC3B, SCIN, PDLIM2, PSAP, SH3BP4, ST3GAL6, IGFBP6, MAP4, APOE, SIAE, WNT3, GSTM3, FN1, DSTN, CDC42BPB, TUBB4B, ASS1, RAB11A, PTPRD, MFAP4, BST1, FMNL1, COL1A2, COL5A1, TCN2, MAN2B2, GLB1, CILP, FAM151A, XPNPEP2, MGP, APOC1, CD248, NUCB2 | 9.44E-08 | |
| Extracellular region | LY6K, ADAMDEC1, CSF2, WNT2B, ELN, PROS1, ANTXR2, CHRDL1, LFNG, ISLR, GLIPR2, TMSB4X, TIMP2, QSOX1, PTGDS, IGFBP5, IL18, MR1, MMP13, LOX, COL4A4, COL6A2, COL4A3, COL6A3, HHIPL1, MMP19, MFGE8, HBEGF, ITIH5, NOTCH3, COLEC10, C1S, NXPH4, PRELP, SEMA3E, FBLN2, THBS4, SCUBE2, CST3, CLEC3B, FRZB, PSAP, PENK, FAM180A, IGFBP6, APOE, C11ORF45, PLTP, WNT3, ANGPT4, NMB, FN1, PRSS35, BMP6, MFAP5, MFAP4, COL1A2, COL5A1, TCN2, LEP, APOC1 | 1.38E-07 | |
| Extracellular matrix | FN1, PRELP, LTBP2, TUBB4B, FBLN2, ADAMTS10, THBS4, MFAP4, CLEC3B, MMP13, COL1A2, COL5A1, CILP, COL6A2, MGP, TIMP2, MMP19, COL6A3, APOE, MFGE8, EDIL3, ADAMTS9 | 1.60E-06 | |
| Extracellular vesicle | LFNG, OLFML3, COL6A2, COL6A3, PRELP, APOE, MFGE8, TUBB4B, EDIL3, FBLN2 | 6.09E-06 | |
| Extracellular space | CSF2, WNT2B, PROS1, WISP2, TIMP2, QSOX1, PTGDS, ADAMTS9, EGFL6, METRN, IL18, MMP13, LOX, COL6A2, COL6A3, CHI3L1, MFGE8, GPLD1, ANGPTL1, HBEGF, ASAH1, GCNT1, SEMA3G, PRELP, LTBP2, SEMA3E, THBS4, CST3, CLEC3B, FRZB, PSAP, IGFBP6, APOE, SIAE, PLTP, WNT3, ANGPT4, CRTAP, FN1, SULF1, BMP6, COL1A2, TCN2, GLB1, CILP, VNN3, LEP, NUCB2, CCL26 | 1.51E-05 | |
| Lysosomal lumen | SCARB2, ASAH1, TCN2, GLB1, MAN2B2, PSAP, PRELP, GNS, PLBD2 | 0.003123445 | |
| Collagen trimer | COLEC10, MMP13, COL1A2, COL5A1, LOX, COL4A4, COL6A2, COL4A3, COL6A3 | 0.00478510818157352 | |
| Endoplasmic reticulum lumen | CRTAP, STS, COL1A2, ERAP2, COL5A1, COL4A4, COL6A2, COL4A3, CERCAM, P3H2, COL6A3, WNT3 | 0.010883682 | |
| Integrin binding | ADAMDEC1, ADAM32, MMP8, MMP9, ADAM18, ADAMTS3, KEL, MMP16, FAP, MMP26, CLCA1, TLL1, CLCA4 | 4.65E-04 | |
| Extracellular matrix structural constituent | OAS1, OAS2, OAS3, OASL | 4.65E-04 |
Figure 2.Biological functions based on Gene Ontology (GO) analysis of obesity-related DEGs
Significantly enriched pathways in obesity-related DEGs
| Pathway ID | Name | Genes | P-Value |
|---|---|---|---|
| hsa04512 | ECM-receptor interaction | ITGB1, COL1A2, COL5A1, COL4A4, COL6A2, COL4A3, FN1, COL6A3, ITGA5, THBS4 | 2.86E-05 |
| hsa04510 | Focal adhesion | ITGB1, FN1, THBS4, COL1A2, CCND2, COL5A1, COL4A4, COL6A2, COL4A3, ERBB2, COL6A3, FYN, ITGA5 | 3.94E-04 |
| hsa04974 | Protein digestion and absorption | COL1A2, COL5A1, XPNPEP2, COL4A4, ELN, COL6A2, COL4A3, COL6A3 | 0.001138329 |
| hsa04151 | PI3K-Akt signalling pathway | ITGB1, ANGPT4, CSF1R, HSP90AB1, FN1, THBS4, COL1A2, CCND2, COL5A1, PPP2R2C, COL4A4, COL6A2, COL4A3, COL6A3, ITGA5 | 0.004374222 |
| hsa04142 | Lysosome | SCARB2, ASAH1, LAMP1, GLB1, PSAP, DNASE2, ABCB9, GNS | 0.00686595 |
| hsa05205 | Proteoglycans in cancer | ITGB1, WNT2B, HPSE2, ERBB2, FN1, TWIST1, ITPR3, ITGA5, WNT3, HBEGF | 0.011432848 |
| hsa05204 | Chemical carcinogenesis | SULT1A1, GSTM3, ALDH1A3, ADH4, GSTM5, SULT1A2 | 0.015821 |
| hsa04924 | Renin secretion | EDNRA, PDE3A, ITPR3, CACNA1C, KCNJ2 | 0.030065163 |
| hsa05146 | Amoebiasis | CSF2, COL1A2, COL5A1, COL4A4, COL4A3, FN1 | 0.045859559 |
| hsa00531 | Glycosaminoglycan degradation | HPSE2, GLB1, GNS | 0.047121568 |
Figure 3.KEGG pathway analysis of obesity-related DEGs
Tissue-specific genes identified using BioGPS
| System | Genes |
|---|---|
| Neurologic | EGFL6, ALDH1A3, MFAP4, IGFBP6, TSPAN13, GALNT17, PTGDS, CERCAM, MEF2C, SLC4A3, NDRG4, LTBP2, LTBP3, LMOD1, PENK, CHRDL1, UCHL1, PEG10, PPP2R2C, OLFML3, ITPR3, SGCE, CLIC6, PLTP, PURA, NPTX1, CHI3L1, CLIP2, TAGLN, CDR2L, SCRN1, CDC42BPB, THBS4, FBLN2, METRN, NDRG2, SCARB2, PEA15, SASH1, RBP1, FEZ1, C1S, PTPRD, PSD3, FN1, DYNC1LI2, UBE2QL1, PROS1, CD99L2, PTPRZ1, CHL1, PDE4D |
| Immune | TSPAN13, MEF2C, OSTM1, LTBP3, P3H2, ADCY7, ERAP2, CHRDL1, UCHL1, GYPC, ITPR3, SAMHD1, CLIC6, MCUB, GLB1, PDLIM1, CSF1R, APOC1, ELOVL6, CLIP2, RASSF5, SH3TC1, COL6A3, RAB6B, UNC13C, BST1, NUCB2, MZF1, NPR3, SFT2D1, SCRN1, GNS, NLRP1, NDRG2, SCARB2, SULT1A1, BCL7A, MAFB, CCND2, PBXIP1, CCNL1, MCM2, NKTR, SCPEP1, PDLIM2, MYL4, FYN, RGS2, REXO2, DDX39B, SMURF2 |
| Genital | EGFL6, MFAP5, MFAP4, PALLD, CD248, LMOD1, PENK, CHRDL1, PEG10, CALD1, TEX26, OLFML3, ITPR3, PLTP, CSF1R, SLC2A5, CHI3L1, FRZB, TAGLN, CLEC3B, EMX2, COL6A3, LEP, PAEP, COL5A1, FBLN2, NOTCH3, TIMP2, RBP1, CCIN, C15orf48, C1S, PDLIM2, GSTM3, EDNRA, RGS2, GPNMB, TWIST1 |
| Respiratory | EGFL6, ALDH1A3, MFAP4, TSPAN13, COL6A2, CCN5, ELN, SFTPA2, SFTPA1, LTBP3, ITPR3, PDLIM1, APOC1, ELOVL6, FRZB, BNC1, CLEC3B, NPR3, TCEAL9, COL5A1, TIMP2, FEZ1, C1, PDLIM2, PRELP, EDNRA, GPNMB, SMURF2 |
| Digestive | ALDH1A3, IGFBP6, TSPAN13, PALLD, LTBP3, LMOD1, CILP, PEG10, SLC2A5, APOC1, SH3BP4, PNKD, COL6A3, APOE, ADAMDEC1, SULT1A1, RBP1, C15orf48, CASQ2, C1S, MYL4, RAB11A, FN1, PROS1, XPNPEP2, ADH7, ASS1 |
| Circulatory | CCDC80, MFAP5, MFAP4, IGFBP6, PTGDS, LOX, SLC4A3, NDRG4, LTBP2, UCHL1, APOC1, TAGLN, SH3TC1, CLEC3B, MGP, ID3, COL1A2, SULF1, NEK7, COL5A1, FBLN2, MAFB, CASQ2, MYL4, FN1, GPNMB |
| Skeletal muscle | MFGE8, ALDH1A3, CCDC80, MFAP5, IGFBP6, FKBP9, CCN5, ITGB1, CD248, LOX, ELN, LTBP2, CILP, CHRDL1, OLFML3, SGCE, ELOVL6, SH3BP4, TAGLN, RECK, NPR3, COL1A2, SULF1, PTGFRN, MEDAG |
| Endocrine | TSPAN13, LTBP3, CA3, CHRDL1, UCHL1, ITPR3, CLIC6, PDLIM1, ASAH1, CLEC3B, COL6A3, MGP, NUCB2, ID3, CDC42BPB, TCEAL9, COL1A2, COL5A1, METRN, RBP1, MAFB, MCM2, SCPEP1, ISLR |
| Urinary | PALLD, ALDH1A3, PTGDS, NDRG4, LTBP3, LMOD1, P3H2, NOX4, TAGLN, PGAP1, GNS, SYT17, XPNPEP2, ASS1 |
| Haematological | MFAP4, OSTM1, UCHL1, ITPR3, MCUB, SLC2A5, CHI3L1, CLIP2, PNKD, SFT2D1, MCM2, KCNJ2 |
Figure 4.Common hub genes based on Degree, Stress, and EcCentricity algorithm
Figure 5.Venn diagram showing the key genes involved in obese adipocyte samples
Nine FDA-approved drugs potentially targeting the four key genes
| Target Gene | Drug | Interaction Types | *Score |
|---|---|---|---|
| FYN | dasatinib | inhibitor|multitarget | 8 |
| FN1 | ocriplasmin | cleavage | 3 |
| LEP | risperidone | NA | 7 |
| LEP | gemfibrozil | NA | 3 |
| APOE | ritonavir | NA | 3 |
| APOE | fluvastatin | NA | 3 |
| APOE | pravastatin | NA | 3 |
| APOE | warfarin | NA | 3 |
| APOE | atorvastatin | NA | 5 |
*Score: The number of database sources and/or PubMed references supporting the drug-gene interaction.