Currently, genetic and genomics related researches progress rapidly and provide new viewpoint to illuminate the molecular pathogenesis of CAD. And bioinformatics analysis also has show and devotes to search for candidate biomarkers to provide more precise screening, prompt diagnosis, sophisticated prognostic and new therapeutic targets for CAD based on massive genetic and genomics data [44]. In the present study, 1,036 DEGs were identified in the CAD group compared with normal control samples, including 525 up regulated genes and 511 down regulated gene. Genes such as PTGDS (prostaglandin D2 synthase) [45] and PDE4D [46] were responsible for development of stroke. Oncostatin M receptor (OSMR) was liable for progression of atherosclerosis [47]. Genes such as SLC19A3 [48] and RCN2 [49] were liable for progression of diabetes, but these genes may be responsible for advancement of CAD. Genes such as KLKB1 [50], PRMT5 [51], F2R [52] and IL18RAP [53] were liable for progression of CAD. AKAP5 was associated with progression of hypertension [54], but this gene may be identified with progression of CAD.
Some of the up regulated genes enriched in pathways from different pathway databases. DIO2 was linked with development of hypertension [55], but this gene may be responsible for progression CAD. Enriched genes such as CCR2 [56], CCL19 [57], CX3CL1 [58], CXCL12 [59], IL20 [60], epidermal growth factor receptor (EGFR) [61], ERBB3 [62], adrenomedullin (ADM) [63], SCUBE1 [64], LMAN1L [65] and EGFL7 [66] were responsible for pathogenesis of CAD. Enriched genes such as CXCL6 [67], BMP7 [68], RXFP2 [69], BRS3 [70], FFAR3 [71], neuropeptide B (NPB) [72], SPON2 [73], FCN3 [74], REG3A [75] and ornithine carbamoyltransferase (OTC) [76] were culpable for pathogenesis of diabetes, but these genes may be involved in development of CAD. Enriched genes such as COL18A1 [77], cortistatin (CORT) [78], guanine nucleotide binding protein (G protein) [79] and MUC2 [80] were involved in development of obesity, but these genes may be associated with pathogenesis of CAD. Enriched genes such as ADRA1A [81], corticotropin releasing hormone (CRH) [82], CRHR1 [83], GRIN1 [84], HSD3B1 [85] and nerve growth factor (beta polypeptide) (NGF) [86] were answerable for progression of hypertension, but these genes may be linked with development of CAD. ADAMTS2 was associated with progression of myocardial infarction [87], but this gene may be liable for progression of CAD. CFC1 was responsible for development of congenital cardiac disease [88], but this gene may be associated with progression of CAD. Our study found that KIT ligand (KITLG), IFNA4, IL13RA1, IL17B, thrombopoietin (THPO), nuclear factor I/B (NFIB), TFF1, OPN4, OR1J1, OR2J2, ADCY2, ADCYAP1R1, OR4C3, OR5C1, OR3A3, RASAL1, VIPR2, OR8U1, SPTBN4, OR10AD1, OR10W1, AVPR1B, RGS22, SSTR4, PTGER1, glial cell derived neurotrophic factor (GDNF), OR5H1, OR2AG1, GPR31, kalirin, RhoGEF kinase (KALRN), GPR32, OR2AG2, OR5A2, OR2T6, OR10H1, GNB4, OR52K2, GPHB5, CLEC1B, CLEC2L, SEMA5B, COL9A2, MXRA5, COL28A1, SEMA4G, COL23A1, insulin-like growth factor binding protein, acid labile subunit (IGFALS), CLEC4G, MUC22, MUC3A, MUC4, MEGF11, IL36B, ADAM21, SMOC1, FREM1, TINAGL1, SRPX2, ADAMTSL1, transforming growth factor, alpha (TGFA), eyes shut homolog (Drosophila) (EYS), INSL6, CLEC3B, tenascin XB (TNXB) and guanine nucleotide binding protein (G protein), alpha activating activity polypeptide, olfactory type (GNAL) are up regulated in CAD and has potential as a novel diagnostic and prognostic biomarker, and therapeutic target. Similarly, some of the down regulated genes enriched in pathways from different pathway data bases. Enriched genes such as HSPA8 [89], HIF1A [90], CCL4 [91], CCL20 [92], IL1B [93], NCAM1 [94], IL18R1 [95], CXCL1 [96], CXCL2 [97], oncostatin M (OSM) [98], CD80 [99], IL27 [100] and lamin A/C (LMNA) [101] were liable for progression of CAD. Enriched genes such as KIR2DL2 [102], KIR3DL1 [103], KLRC3 [104], KLRD1 [105], PIK3R1 [106] and PAK2 [107] were involved in the progression of diabetes, but these genes may be linked with progression of CAD. MAP2K4 was liable for progression of ischemic stroke [108]. Enriched genes such as S1PR1 [109] and CUL3 [110] were involved in progression of hypertension, but these genes may be associated with development of CAD. RAR-related orphan receptor A (RORA) was linked with development of obesity [111], but these genes may be involved in pathogenesis of CAD. Our study found that 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC), KIR2DS2, KIR2DL4, KIR2DS3, KIR2DS4, KIR3DL2, KLRC1, regulatory factor X-associated protein (RFXAP), PDIA3, KIR2DL5A, WIPF1, FYN oncogene related to SRC, FGR, YES (FYN), Cas-Br-M (murine) ecotropic retroviral transforming sequence b (CBLB), platelet-derived growth factor receptor, beta polypeptide (PDGFRB), CCL3L3, IL1A, PSMA1, SPTBN1, PSME4, BRWD1, IDS (iduronate 2-sulfatase), PARP4, PARP2, LMNB1, 6-pyruvoyltetrahydropterin synthase (PTS) and sarcosine dehydrogenase (SARDH) are down regulated in CAD and has potential as a novel diagnostic and prognostic biomarker, and therapeutic target.
Some of the up regulated genes enriched in GO terms. Enriched genes such as noggin (NOG) [112], very low density lipoprotein receptor (VLDLR) [113] and AQP10 [114] were responsible for progression of obesity, but these genes may be involved in development of CAD. Enriched genes such as TRPM5 [115], crystallin, alpha A (CRYAA) [116], PAX6 [117], SORBS1 [118], SLC38A1 [119], complement component 7 (C7) [120] and PAX8 [121] were linked with advancement of diabetes, but these genes may be associated with pathogenesis of CAD. Enriched genes such as KCNJ11 [122], PKD2L1 [123], CSMD1 [124], SLC6A2 [125] and ATP2B3 [126] were liable for advancement of hypertension, but these genes may be involved in progression CAD. ASGR1 was linked with advancement of CAD [127]. Our study found that SHROOM4, SHISA6, amphiphysin (AMPH), TMPRSS11E, CRYBB3, crystallin, gamma A (CRYGA), BARHL1, IGSF9B, LYNX1, LRRN4, SHANK1, GRIK5, LCN1, GRK1, GRIP2, LY6H, B3GNT3, KCNK9, PROM2, TRPV6, FXYD1, FXYD3, SYT3, AQP8, SLC4A1, ATP1A4, CALHM3, TSPAN9, PROM1, protein tyrosine phosphatase, receptor type, S (PTPRS), KCNJ16, PCDHB8, TM4SF5, SLC17A5, trehalase (brush-border membrane glycoprotein) (TREH), basal cell adhesion molecule (Lutheran blood group) (BCAM), SLC4A11, EPHA8, ANTXR1, PLA2R1 and IL17REL are up regulated in CAD and has potential as a novel diagnostic and prognostic biomarker, and therapeutic target. Similarly, some of the down regulated genes enriched in GO terms. Enriched genes such as CDKN1C [128], NR4A1 [129] and ZNF627 [130] were responsible for progression of myocardial infarction, but these genes may be associated with development of CAD. Enriched genes such as PPP1R15A [131], protein kinase C, theta (PRKCQ) [132], LPIN1 [133], NOTCH2 [134], Shwachman-Bodian-Diamond syndrome (SBDS) [135], SOX13 [136] and FOXP4 [137] were culpable for advancement of diabetes, but these genes may be linked with progression of CAD. Enriched genes such as ABCB1 [138], CAMK2N1 [139], HES1 [140], TNFAIP3 [141], proliferating cell nuclear antigen (PCNA) [142], IKZF2 [143], ZNF208 [144], NRF1 [145], EGR3 [146] and SMAD7 [147] were important for progression of CAD. Filamin A (FLNA) was involved in development of hypertension [148], but this gene may be responsible for progression of CAD. Enriched genes such as PHLDA1 [149], PLK2 [150], IER3 [151] and thymopoietin (TMPO) [152] were identified with development of ischemic cardiomyopathy, but these genes may be involved in progression of CAD. TOR1AIP1 was associated with heart failure [153]. Enriched genes such as CERS6 [154], KLF3 [155] and NUCKS1 [156] were responsible for advancement of obesity, but these genes may be involved in progression of CAD. cAMP responsive element modulator (CREM) was linked with progression of cardiac arrhythmia [157], but this gene may be important for development CAD. Our study found that CHAF1B, CCNDBP1, STAG1, RPS6, TFDP3, NCAPH2, HIR histone cell cycle regulation defective homolog A (S. cerevisiae) (HIRA), BOD1, CEP78, HACE1, SERTAD1, farnesyltransferase, CAAX box, alpha (FNTA), WEE1, TRIAP1, PKP4, ZNF365, Wilms tumor 1 associated protein (WTAP), CCCTC-binding factor (zinc finger protein) (CTCF), CSNK1A1, PRIM2, PRKAA1, SENP6, CDK5RAP1, tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase (TNKS), RIOK2, MYBL1, TJP3, ZNF268, ZNF207, SMARCAD1, SMC5, junction mediating and regulatory protein, p53 cofactor (JMY), CEP120, ANGEL2, CAB39L, NCAPD3, destrin (actin depolymerizing factor) (DSTN), CLASP1, CHMP1B, KIF3A, RNF2, KLHDC2, OSBPL8, ZBTB1, FAM169A, suppressor of cancer cell invasion (SCAI), ITPR3, YBX1, SYNE1, ZNF671, recombination signal binding protein for immunoglobulin kappa J region-like (RBPJL), ZNF595, TXK tyrosine kinase (TXK), MLLT1, ZNF548, THAP6, ZNF567, ZNF680, ZFP37, zinc finger protein, X-linked (ZFX), ZNF430, ZNF26, ZFP1, ZNF83, ZBTB11, ligand dependent nuclear receptor corepressor (LCOR), BNC2, SP2, ZNF148, thymocyte selection-associated high mobility group box (TOX), HOP homeobox (HOPX), ZNF25, ZNF730, ZFP82, NR1D2, retinoic acid receptor, beta (RARB), ZNF354A, IKZF5, ZBED6, ZNF197 and RAR-related orphan receptor B (RORB) are down regulated in CAD and has potential as a novel diagnostic and prognostic biomarker, and therapeutic target.
In the PPI network, hub genes with a high node degree distribution, betweenness centrality, stress centrality, closeness centrality and low clustring coefficient were selected. GATA4 was important for progression of CAD [158]. Genes such as MAGEL2 [159], ADHFE1 [160] and neuromedin B (NMB) [161] were associated with development of obesity, but these genes may be liable for progression of CAD. SMURF1 was liable for advancement of hypertension [162], but this may be involved in pathogenesis of CAD. . In addition, modules were extracted from PPI network, which involved 17 up regulated genes and 20 down regulated genes. TBX2 was involved in the progression of hypertension [163], but this gene may be associated with development of CAD. Genes such as podocan (PODN) [164] and PAS domain containing serine/threonine kinase (PASK) [165] were liable for progression of diabetes, but these genes may be linked with progression of CAD. In the target gene - miRNA regulatory network, 5 up regulated genes and 5 down regulated genes with a high node degree was chosen as target gene. TRIM72 was associates with development of cardiac fibrosis [166], but this gene may be liable for development of CAD. TET3 was responsible for progression of CAD [167]. PPP1R15B was important for progression of diabetes [168], but this gene may be involved in advancement of CAD. CAPN13, ACTBL2, ACTL8, ras homolog gene family, member V (RHOV), CHD5, THNSL2, SLC38A8, serine palmitoyltransferase, small subunit B (SPTSSB), SPATA21, DLG3, SLC25A36, ACTG2, ACTL6B and RAS, EF-hand domain containing (RASEF), LHX9, FOXJ1, TP73, CDK5R2, EIF1AX, HNRNPA0, RPS27, LGR6, granzyme B (GZMB), RPRD2 and SAR1A are the novel biomarkers for CAD.
In the target gene - TF regulatory network, 5 up regulated genes and 5 down regulated genes with a high node degree was chosen as target gene. GLI2 was linked with progression of obesity [169], but this gene may be responsible for advancement of CAD. Our study found that LHFPL3 is up regulated in CAD and has potential as a novel diagnostic and prognostic biomarker, similarly, our study found that EXOSC10, GDP-mannose 4,6-dehydratase (GMDS), C5ORF58 and C10orf88 are down regulated in CAD and has potential as a novel diagnostic and prognostic biomarker, and therapeutic target.
We used immune histochemical (IHC) analysis, receiver operating characteristic (ROC) curve and RT-PCR to analyze the association of 5 up and 5 down regulated hub genes expression in CAD. The results showed that only 5 up (CAPN13, ACTBL2, ERBB3, GATA4 and GNB4) and 5 down (NOTCH2, EXOSC10, RNF2, PSMA1 and PRKAA1) regulated hub genes were related to the CAD. We then evaluated the prognostic value of these only 5 up (CAPN13, ACTBL2, ERBB3, GATA4 and GNB4) and 5 down (NOTCH2, EXOSC10, RNF2, PSMA1 and PRKAA1) regulated hub genes using the ROC curve, indicating that they have potential diagnostic value for CAD.
In conclusion, 1,036 DEGs (525 up rand 511 down regulated gene) were screened out from the GSE113079 dataset, which may contain hub genes contributing to the pathogenesis of CAD. Through our bioinformatics analysis, hub genes including CAPN13, ACTBL2, ERBB3, GATA4, GNB4, NOTCH2, EXOSC10, RNF2, PSMA1 and PRKAA1 might contribute to the progression of CAD, which could serve as novel diagnostic and prognostic biomarkers and therapeutic targets for CAD.