Identification of potential hub genes and regulatory networks of smoking-related endothelial dysfunction in atherosclerosis using bioinformatics analysis
Restricted accessResearch articleFirst published online May, 2024
Identification of potential hub genes and regulatory networks of smoking-related endothelial dysfunction in atherosclerosis using bioinformatics analysis
Endothelial dysfunction, the earliest stage of atherosclerosis, can be caused by smoking, but its molecular mechanism requires further investigation.
OBJECTIVE:
This study aimed to use bioinformatics analysis to identify potential mechanisms involved in smoking-related atherosclerotic endothelial dysfunction.
METHODS:
The transcriptome data used for this bioinformatics analysis were obtained from the Gene Expression Omnibus (GEO) database. The GSE137578 and GSE141136 datasets were used to identify common differentially expressed genes (co-DEGs) in endothelial cells treated with oxidized low-density lipoprotein (ox-LDL) and tobacco. The co-DEGs were annotated using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomics (KEGG) databases. Additionally, a protein-protein interaction (PPI) network was constructed to visualize their interactions and screen for hub genes. GSE120521 dataset was used to verify the expression of hub genes in unstable plaques. The miRNA expression profile GSE137580 and online databases (starBase 2.0, TargetScan 8.0 and DGIdb v4.2.0) were used to predict the related non-coding RNAs and drugs.
RESULTS:
A total of 232 co-DEGs were identified, including 113 up-regulated genes and 119 down-regulated genes. These DEGs were primarily enriched in detrimental autophagy, cell death, transcription factors, and cytokines, and were implicated in ferroptosis, abnormal lipid metabolism, inflammation, and oxidative stress pathways. Ten hub genes were screened from the constructed PPI network, including up-regulated genes such as FOS, HMOX1, SQSTM1, PTGS2, ATF3, DDIT3, and down-regulated genes MCM4, KIF15, UHRF1, and CCL2. Importantly, HMOX1 was further up-regulated in unstable plaques ( 0.034). Finally, a regulatory network involving lncRNA/circRNA-miRNA-hub genes and drug-hub genes was established.
CONCLUSION:
Atherosclerotic endothelial dysfunction is associated with smoking-induced injury. Through bioinformatics analysis, we identified potential mechanisms and provided potential therapeutic targets.
XuSIlyasILittlePJLiHKamatoDZhengX, et al. Endothelial dysfunction in atherosclerotic cardiovascular diseases and beyond: From mechanism to pharmacotherapies. Pharmacol Rev.2021; 73(3): 924-67. doi: 10.1124/pharmrev.120.000096.
3.
Popa-FoteaNMFerdoschiCEMicheuMM. Molecular and cellular mechanisms of inflammation in atherosclerosis. Front Cardiovasc Med.2023; 10: 1200341. doi: 10.3389/fcvm.2023.1200341.
4.
RanaJSMoffetHHLiuJYNasirKBlanksteinRKarterAJ, et al. Smoking and risk of premature atherosclerotic cardiovascular disease. Am J Prev Med.2022; 62(3): 466-68. doi: 10.1016/j.amepre.2021.08.019.
5.
HackshawAMorrisJKBonifaceSTangJ-LMilenkovićD. Low cigarette consumption and risk of coronary heart disease and stroke: meta-analysis of 141 cohort studies in 55 study reports. Bmj. 2018. doi: 10.1136/bmj.j5855.
6.
KleinJDiaba-NuhohoPGiebeSBrunssenCMorawietzH. Regulation of endothelial function by cigarette smoke and next-generation tobacco and nicotine products. Pflugers Arch.2023; 475(7): 835-44. doi: 10.1007/s00424-023-02824-w.
7.
WangDJuonalaMViikariJSAWuFHutri-KahonenNRaitakariOT, et al. Exposure to Parental Smoking in Childhood is Associated with High C-Reactive Protein in Adulthood: The Cardiovascular Risk in Young Finns Study. J Atheroscler Thromb.2017; 24(12): 1231-41. doi: 10.5551/jat.40568.
8.
CuiMCuiRLiuKDongJYImanoHHayama-TeradaM, et al. Associations of tobacco smoking with impaired endothelial function: The circulatory risk in communities study (CIRCS). J Atheroscler Thromb.2018; 25(9): 836-45. doi: 10.5551/jat.42150.
9.
JiJLiXZhuYWangRYangSPengB, et al. Screening of periodontitis-related diagnostic biomarkers based on weighted gene correlation network analysis and machine algorithms. Technol Health Care.2022; 30(5): 1209-21. doi: 10.3233/THC-THC213662.
10.
TianXZhengJLuoYWeiCMaJWangD, et al. Identification of abnormally methylated differentially expressed genes in chronic periodontitis by integrated bioinformatics analysis. Technol Health Care.2023; 31(3): 809-19. doi: 10.3233/THC-220137.
11.
LiuXLiLXieXZhuangDHuC. Integrated bioinformatics analysis of microarray data from the GEO database to identify the candidate genes linked to poor prognosis in lung adenocarcinoma. Technol Health Care.2023; 31(2): 579-92. doi: 10.3233/THC-220165.
12.
ChuPHChenGKuoDBraistedJHuangRWangY, et al. Stem cell-derived endothelial cell model that responds to tobacco smoke like primary endothelial cells. Chem Res Toxicol.2020; 33(3): 751-63. doi: 10.1021/acs.chemrestox.9b00363.
13.
MahmoudADBallantyneMDMiscianinovVPinelKHungJScanlonJP, et al. The Human-Specific and Smooth Muscle Cell-Enriched LncRNA SMILR Promotes Proliferation by Regulating Mitotic CENPF mRNA and Drives Cell-Cycle Progression Which Can Be Targeted to Limit Vascular Remodeling. Circ Res.2019; 125(5): 535-51. doi: 10.1161/CIRCRESAHA.119.314876.
14.
ZhouGSoufanOEwaldJHancockREWBasuNXiaJ. NetworkAnalyst 3.0: A visual analytics platform for comprehensive gene expression profiling and meta-analysis. Nucleic Acids Res.2019; 47(W1): W234-W41. doi: 10.1093/nar/gkz240.
15.
ZhouYZhouBPacheLChangMKhodabakhshiAHTanaseichukO, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun.2019; 10(1): 1523. doi: 10.1038/s41467-019-09234-6.
16.
SzklarczykDGableALNastouKCLyonDKirschRPyysaloS, et al. The STRING database in 2021: Customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res.2021; 49(D1): D605-D12. doi: 10.1093/nar/gkaa1074.
17.
ShannonPMarkielAOzierOBaligaNSWangJTRamageD, et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res.2003; 13(11): 2498-504. doi: 10.1101/gr.1239303.
18.
ChinCHChenSHWuHHHoCWKoMTLinCY. cytoHubba: Identifying hub objects and sub-networks from complex interactome. BMC Syst Biol.2014; 8 Suppl 4: S11. doi: 10.1186/1752-0509-8-S4-S11.
McGearySELinKSShiCYPhamTMBisariaNKelleyGM, et al. The biochemical basis of microRNA targeting efficacy. Science.2019; 366(6472). doi: 10.1126/science.aav1741.
21.
FreshourSLKiwalaSCottoKCCoffmanACMcMichaelJFSongJJ, et al. Integration of the drug-gene interaction database (DGIdb 4.0) with open crowdsource efforts. Nucleic Acids Res.2021; 49(D1): D1144-D51. doi: 10.1093/nar/gkaa1084.
22.
AyerAZarjouAAgarwalAStockerR. Heme oxygenases in cardiovascular health and disease. Physiol Rev.2016; 96(4): 1449-508. doi: 10.1152/physrev.00003.2016.
23.
WenzelPRossmannHMullerCKossmannSOelzeMSchulzA, et al. Heme oxygenase-1 suppresses a pro-inflammatory phenotype in monocytes and determines endothelial function and arterial hypertension in mice and humans. Eur Heart J.2015; 36(48): 3437-46. doi: 10.1093/eurheartj/ehv544.
24.
RyterSWChoiAM. Targeting heme oxygenase-1 and carbon monoxide for therapeutic modulation of inflammation. Transl Res.2016; 167(1): 7-34. doi: 10.1016/j.trsl.2015.06.011.
25.
WuDHuQWangYJinMTaoZWanJ. Identification of HMOX1 as a critical ferroptosis-related gene in atherosclerosis. Front Cardiovasc Med.2022; 9: 833642. doi: 10.3389/fcvm.2022.833642.
26.
MengZLiangHZhaoJGaoJLiuCMaX, et al. HMOX1 upregulation promotes ferroptosis in diabetic atherosclerosis. Life Sci.2021; 284: 119935. doi: 10.1016/j.lfs.2021.119935.
27.
ZhouYZhouHHuaLHouCJiaQChenJ, et al. Verification of ferroptosis and pyroptosis and identification of PTGS2 as the hub gene in human coronary artery atherosclerosis. Free Radic Biol Med.2021; 171: 55-68. doi: 10.1016/j.freeradbiomed.2021.05.009.
28.
MiaoGZhaoXChanSLZhangLLiYZhangY, et al. Vascular smooth muscle cell c-Fos is critical for foam cell formation and atherosclerosis. Metabolism.2022; 132: 155213. doi: 10.1016/j.metabol.2022.155213.
29.
SunJJYinXWLiuHHDuWXShiLYHuangYB, et al. Rapamycin inhibits ox-LDL-induced inflammation in human endothelial cells in vitro by inhibiting the mTORC2/PKC/c-Fos pathway. Acta Pharmacol Sin.2018; 39(3): 336-44. doi: 10.1038/aps.2017.102.
30.
ChenYLiQLiQXingSLiuYLiuY, et al. p62/SQSTM1, a central but unexploited target: Advances in its physiological/pathogenic functions and small molecular modulators. J Med Chem.2020; 63(18): 10135-57. doi: 10.1021/acs.jmedchem.9b02038.
31.
HaiTHartmanMG. The molecular biology and nomenclature of the activating transcription factor/cAMP responsive element binding family of transcription factors: Activating transcription factor proteins and homeostasis. Gene.2001; 273(1): 1-11. doi: 10.1016/S0378-1119(01)00551-0.
32.
ZhouHLiNYuanYJinYGGuoHDengW, et al. Activating transcription factor 3 in cardiovascular diseases: A potential therapeutic target. Basic Res Cardiol.2018; 113(5): 37. doi: 10.1007/s00395-018-0698-6.
33.
ChiribauCBGaccioliFHuangCCYuanCLHatzoglouM. Molecular symbiosis of CHOP and C/EBP beta isoform LIP contributes to endoplasmic reticulum stress-induced apoptosis. Mol Cell Biol.2010; 30(14): 3722-31. doi: 10.1128/MCB.01507-09.
34.
GaoJIshigakiYYamadaTKondoKYamaguchiSImaiJ, et al. Involvement of endoplasmic stress protein C/EBP homologous protein in arteriosclerosis acceleration with augmented biological stress responses. Circulation.2011; 124(7): 830-9. doi: 10.1161/CIRCULATIONAHA.110.014050.
35.
QinWYangHLiuGBaiRBianYYangZ, et al. Activating transcription factor 3 is a potential target and a new biomarker for the prognosis of atherosclerosis. Hum Cell.2021; 34(1): 49-59. doi: 10.1007/s13577-020-00432-9.
36.
RenJLChenYZhangLSZhangYRLiuSMYuYR, et al. Intermedin1-53 attenuates atherosclerotic plaque vulnerability by inhibiting CHOP-mediated apoptosis and inflammasome in macrophages. Cell Death Dis.2021; 12(5): 436. doi: 10.1038/s41419-021-03712-w.
37.
HeYDuanLWuHChenSLuTLiT, et al. Integrated transcriptome analysis reveals the impact of photodynamic therapy on cerebrovascular endothelial cells. Front Oncol.2021; 11: 731414. doi: 10.3389/fonc.2021.731414.
38.
DingLLiBYuXLiZLiXDangS, et al. KIF15 facilitates gastric cancer via enhancing proliferation, inhibiting apoptosis, and predict poor prognosis. Cancer Cell Int.2020; 20: 125. doi: 10.1186/s12935-020-01199-7.
39.
EliaLCondorelliG. The involvement of epigenetics in vascular disease development. Int J Biochem Cell Biol.2019; 107: 27-31. doi: 10.1016/j.biocel.2018.12.005.
40.
LiuDZhangXLYanCHLiYTianXXZhuN, et al. MicroRNA-495 regulates the proliferation and apoptosis of human umbilical vein endothelial cells by targeting chemokine CCL2. Thromb Res.2015; 135(1): 146-54. doi: 10.1016/j.thromres.2014.10.027.
41.
GiebeSHofmannABruxMLoweFBrehenyDMorawietzH, et al. Comparative study of the effects of cigarette smoke versus next generation tobacco and nicotine product extracts on endothelial function. Redox Biol.2021; 47: 102150. doi: 10.1016/j.redox.2021.102150.
42.
LinXOuyangSZhiCLiPTanXMaW, et al. Focus on ferroptosis, pyroptosis, apoptosis and autophagy of vascular endothelial cells to the strategic targets for the treatment of atherosclerosis. Arch Biochem Biophys.2022; 715: 109098. doi: 10.1016/j.abb.2021.109098.
43.
TorisuKSinghKKTorisuTLovrenFLiuJPanY, et al. Intact endothelial autophagy is required to maintain vascular lipid homeostasis. Aging Cell.2016; 15(1): 187-91. doi: 10.1111/acel.12423.
44.
CsordasAKreutmayerSPlonerCBraunPRKarlasABackovicA, et al. Cigarette smoke extract induces prolonged endoplasmic reticulum stress and autophagic cell death in human umbilical vein endothelial cells. Cardiovasc Res.2011; 92(1): 141-8. doi: 10.1093/cvr/cvr165.
45.
UngTTNguyenTTLianSLiSXiaYKimNH, et al. Nicotine stimulates IL-6 expression by activating the AP-1 and STAT-3 pathways in human endothelial EA.hy926 cells.J Cell Biochem.2019; 120(4): 5531-41. doi: 10.1002/jcb.27837.
FriedmanHMMacarakEJMacGregorRRWolfeJKefalidesNA. Virus infection of endothelial cells. J Infect Dis.1981; 143(2): 266-73. doi: 10.1093/infdis/143.2.266 %J The Journal of Infectious Diseases.
48.
SuzukiSSatoKWatanabeHNezuYNishimutaT. Environmental tobacco exposure is associated with vaccine modified measles in junior high school students. J Med Virol.2015; 87(11): 1853-9. doi: 10.1002/jmv.24252.
WuXZhangHQiWZhangYLiJLiZ, et al. Nicotine promotes atherosclerosis via ROS-NLRP3-mediated endothelial cell pyroptosis. Cell Death Dis.2018; 9(2): 171. doi: 10.1038/s41419-017-0257-3.
51.
LiuXWangCNQiuCYSongWWangLFLiuB. Adipocytes promote nicotine-induced injury of endothelial cells via the NF-κB pathway. Exp Cell Res.2017; 359(1): 251-6. doi: 10.1016/j.yexcr.2017.07.022.
52.
BatistaPJCellHYCJ. Long noncoding RNAs: Cellular address codes in development and disease. Cell.2013; 152(6): 1298-307. doi: 10.1016/j.cell.2013.02.012.
53.
DongYHeDPengZPengWShiWWangJ, et al. Circular RNAs in cancer: An emerging key player. J Hematol Oncol.2017; 10(1): 2. doi: 10.1186/s13045-016-0370-2.
54.
GaoFWangXCLuoZDHuGQMaMQLiangY, et al. LncRNA HOXA11-AS promotes vascular endothelial cell injury in atherosclerosis by regulating the miR-515-5p/ROCK1 axis. ESC Heart Fail.2022; 9(4): 2259-71. doi: 10.1002/ehf2.13815.
55.
SongJWangQZongL. LncRNA MIR155HG contributes to smoke-related chronic obstructive pulmonary disease by targeting miR-128-5p/BRD4 axis. Biosci Rep.2020; 40(3). doi: 10.1042/BSR20192567.
