4. Discussion
Symbolic progress has been accomplished in the diagnosis and treatment of EOC. However, EOC remains the fifth most common cancer worldwide [
48]. Due to the high risk of recurrence and the poor survival rates of metastatic EOC patients, high-grade ovarian epithelial cancer, normal ovarian epithelium and normal fallopian tube were used to investigate the molecular mechanisms which are associated with metastasis. In previous studies, gene expression profiling has been used to identify the biomarkers and pathways which are associated with EOC [
49], as well as genome-wide changes in EOC [
50].Based on the cutoff criteria, a total of 276 up-regulated and 276 down-regulated genes were diagnosed from E-MTAB-3706. Methylation inactivation ASS1 was linked with cisplatin resistance in EOC [
51]. Over expression of SLPI was associated with pathogenesis of EOC [
52,
53]. HS6ST2 was critical for fibroblast growth factor 2 activation [
54]. HS6ST2 was responsible for angiogenesis in colorectal cancer [
55]. HS6ST2 is associated with angiogenesis in EOC [
56]. FBLN1 was associated with invasion of EOC cells [
57,
58]. ADM (adrenomedullin) was linked with angiogenesis in EOC [
59]. ADM was responsible forpathogenesis of EOC [
60]. UCHL1 was associated with growth breast cancer [
61]. The loss of tumor suppressor UCHL1 was responsible for the inactivation of apoptosis, as well as cisplatin resistance, in EOC [
62]. Methylation inactivation of tumor suppressors such as UCHL1 [
63] and TUSC3 [
64] were diagnosed with EOC.IFI27 was responsible for the proliferation of epithelial cancer cells [
65].Li IFI27 was associated with invasion and drug resistance in EOC [
66]. The loss of tumor suppressor DKK3 was important for invasion of cervical cancer [
67]. The methylation inactivation of tumor suppressor DKK3 was linked with pathogenesis of gastric cancer [
68].The loss of DKK3 was responsible for the progression of EOC [
69].The loss of GSTT1 was responsible for the inactivation of the detoxification processes in EOC [
70]. Polymorphism in GSTT1 is important for the improvement of EOC [
71,
72].
In pathway enrichment analyses, chemical carcinogenesis, urea cycle, packaging of telomere ends, arginine and proline metabolism, genes encoding enzymes and their regulators involved in the remodeling of the extracellular, nicotine degradation, EPHA2 forward signaling, arginine and proline metabolic, and verapamil pathway were the most significant pathways from different pathway databases such as KEGG, BIOCYC, PID, Reactome, GenMAPP, MSigDB C2 BIOCARTA, PantherDB, Pathway Ontology and SMPDB for up-regulated genes.CYP1B1 was responsible for drug resistance in EOC [
73]. Polymorphisms in EPHX1 [
74] and GSTO2 [
75] were responsible for the pathogenesis of EOC. MGST1 was linked with the invasion and chemoresistance in EOC [
76].The loss of AKR1C2 was responsible for the advancement of prostate cancer [
77], but the inactivation of this gene may be associated with the development of EOC. ALDH3A1 was responsible for drug resistance in breast cancer [
78], but this gene may be associated with drug resistance in EOC. Polymorphism in UGT1A7 was an indicator of drug toxicity in colorectal cancer [
79], but this polymorphic gene may be associated with drug toxicity in EOC. Mutation in UGT2B7 was important for the growth of breast cancer [
80], but mutations in this gene may be responsible for the development of EOC. Mutations in ASS1 were involved in the development of lung cancer [
81], but mutations in this gene may be linked with pathogenesis of EOC. VAV3 was linked with metastasis of EOC [
82]. Single nucleotide polymorphism (SNP) in EFNA1 was important for the progression of gastric cancer [
83], but SNP in this gene may be associated with development of EOC. SERPINB3 was associated with invasion of EOC cells [
84,
85]. CD109 was found to be associated with the growth of small cell lung cancer [
86], but this gene may be associated with the pathogenesis of EOC. Methylation inactivation of EDNRB (endothelin receptor type B) was linked with the development ofprostate cancer [
87], but the inactivation of this gene may be responsible for the progression of EOC. GSTK1, UGT1A10, UGT1A8, HIST1H2AC, HIST1H2BC, HIST1H2BD, HIST1H2BJ, HIST1H2BK, HIST2H2AA3, HIST2H2AA4, HIST2H2BE, MAOB (monoamine oxidase B), A2M, PI3, HYAL3, KCNK1, SNTB1 and SNTB2 were novel biomarkers for pathogenesis of EOC in these pathways. Meanwhile, cell adhesion molecules, creatine biosynthesis, syndecan-4-mediated signaling event, extracellular matrix organization, glutathione metabolism, the ensemble of genes encoding core extracellular matrix, integrin signaling pathway, ubiquitin/proteasome degradation and guanidinoacetatemethyltransferase deficiency (GAMT Deficiency) were the most significant pathways from different pathway databases such as KEGG, BIOCYC, PID, Reactome, GenMAPP, MSigDB C2 BIOCARTA, PantherDB, Pathway Ontology and SMPDB for down-regulated genes.NECTIN2was linked with cell adhesion and the migration of pancreatic ductal adenocarcinomas cells [
88]. NECTIN2 was important for invasion and metastasis in colorectal carcinoma [
89]. NECTIN2 was important for the pathogenesis of EOC [
90]. VCAN was associated with the progression of prostate cancer [
91]. VCAN was responsible for invasion of EOC cells [
92]. Loss of HLA-A was found to correlated with pathogenesis of colorectal cancer, but the reduced expression of this gene may be associated with EOC [
93]. ITGB1 was involved in cell adhesion and invasion of prostate cancer cells [
94], but this gene may be associated with invasion of EOC. NECTIN3 was associated with the proliferation of colon cancer cells [
95], but this gene may be linked with the development of EOC. TNC (tenascin C) was responsible for invasion of colon cancer cells [
96] but was important for metastasis and angiogenesis in EOC [
97]. FN1 was linked with the suppression of apoptosis in renal cancer [
98], but this gene may be associated with the suppression of apoptosis in EOC. COL6A3 was responsible for the advancement of EOC [
99]. FBN1 was responsible for the pathogenesis of EOC [
100]. Polymorphism in GSTM1 was associated with cancer risk [
101,
102,
103]. CTGF (connective tissue growth factor) was involved in the growth of breast cancer [
104]. Methylation inactivation of tumor suppressor gene CTGF was responsible for the development of EOC [
105]. GAS6 was important for the migration and invasion of prostate cancer cells [
106]. GAS6 was associated with invasion of EOC cells [
107]. Low expression of tumor suppressor IGFBP7 was responsible for angiogenesis in hepatocellular carcinoma [
108]. The loss of IGFBP7 was found to be associated with angiogenesis in EOC [
109]. MFGE8 was important for pathogenesis of prostate cancer [
110]. MFGE8 was associated with the adhesion and migration of EOC cells [
111]. Metylation inactivation of tumor suppressor SLIT3 was responsible for invasion of thyroid cancer cells [
112], but silencing this gene may be associated with invasion of EOC. ECM1 was linked with angiogenesis and metastasis of breast cancer cells [
113], but this gene may be responsible for metastasis of EOC. RAC2 was diagnosed with the growth ofbrain cancer [
114], but this gene may be linked with the development of EOC. CNTNAP1, HLA-C, JAM3,NLGN2, COL16A1, COL8A1, EFEMP2, LRP4, MFAP2, P3H3, P4HA2, GSTT2, EGFLAM (EGF like, fibronectin type III and laminin G domains), PXDN (peroxidasin), ACTBL2, SNCA (synuclein alpha) and GAMT (guanidinoacetate N-methyltransferase) were novel biomarkers for pathogenesis of EOC in these pathways.
In GO enrichment analysis, cellular response to xenobiotic stimulus, nucleosome and serine-type endopeptidase inhibitor activity were the most significant GO terms, i.e., for BP, CC and MF for up-regulated genes. Polymorphism in NQO1 was associated with drug resistance in non-small cell lung cancer [
115]. Polymorphism in NQO1 was responsible for the development of EOC [
116]. Low expression of tumor suppressor SPINK13 was linked with invasion of EOC cells [
117]. Methylation inactivation of tumor suppressor SPINT2 was diagnosed with the growth of melanoma [
118], but the inactivation of this gene may be associated with the development of EOC.CES1, HIST1H1C andSPINK6 were novel biomarkers for pathogenesis of EOC in these GO terms. Meanwhile, extracellular matrix organization, extracellular matrix and cell adhesion molecule binding were the most significant GO terms for e.g. BP, CC and MF for down-regulated genes. FSCN1 was responsible for invasion of bladder cancer cells [
119]. FSCN1 was linked with invasion of EOC cells [
120]. GPC6 was involved in invasion of EOC cells [
121]. Metylation inactivation of LGALS1 was associated with angiogenesis in colorectal cancer [
122], but silencing this gene may be responsible for angiogenesis in EOC. NECTIN2 was associated with the proliferation of EOC cells [
90].WNT5B and DSP were novel biomarker for pathogenesis of EOC in these GO terms.
In the PPI network (up regulated), hub genes such as E2F4, SRPK2, A2M, CDH1 and MAP1LC3A were identified with high node degrees. E2F4was linked with the proliferation of breast cancer cells [
123], but this gene may be responsible for the proliferation of EOC cells. CDH1 was responsible for metastasis of gastric cancer and colorectal cancer [
124]. Mutation in CDH1 was responsible for metastasis of EOC [
125]. Hub genes with highest betweenness centralities such as E2F4, CEBPD, CCT5, ATP6V1B1 and MCM4. MCM4 was identified with the proliferation of non small cell lung cancer cells [
126], but this gene may be responsible for the proliferation of EOC cells. Hub genes with highest stress centralities such as SRPK2, E2F4, CDH1, CCT5 and HIST2H2BE.Hub genes with highest closeness centrality such as IL20RB, HNRNPA3, HIST1H1C, MCM4 and SRPK2. Hub genes with lowest clustering coefficient such as NPTX1, KLHL35, NEFH, SLPI and TYMP. SRPK2, MAP1LC3A, CEBPD, CCT5, ATP6V1B1 and IL20RB were novel biomarkers for pathogenesis of EOC in this PPI network. Meanwhile, PPI network (down-regulated), hub genes such as UCHL1, HLA-C, VAT1, ECM1 and SNRPN were identified with high node degree. Hub genes with high betweenness such as UCHL1, HLA-C, VAT1, ECM1 and SNRPN. Hub genes with high stress such as FN1, TCF3, RPS6, EFEMP2 and MECOM. TCF3 was linked with drug resistance in gastric cancer [
127], but this gene may be responsible for drug resistance in EOC. TCF3 was found to be associated with the growth of EOC [
128]. MECOM was associated with the proliferation of glioblastoma multiforme cells [
129]. MECOM was responsible for pathogenesis of EOC [
130]. RPS6 was associated with drug resistance in colorectal cancer [
131], but this gene may be responsible for drug resistance in EOC. Hub genes with high closeness such as FN1, VIM, RPS6, RPL26 and LGALS1. Hub genes with low clustering coefficient such as FAM69B, COL6A3, SNURF, SCARA3 and TMEM107. SCARA3 was associated with metastasis in EOC [
132]. SNRPN, VIM, RPL26 and LGALS1 were novel biomarkers for pathogenesis of EOC in this PPI network.
In a module analysis for PPI network (up-regulated), hub genes such as HIST1H2BD, HIST1H1C, KRT17, PYCARD, CASP1, TFAP2C, CCT5, HNRNPA3 and HIST2H2BE were in all four modules. KRT17, KIF7, SLC7A5 and SLC3A2 were novel biomarkers for EOC in these modules. Meanwhile, in a module analysis for the PPI network (down-regulated), hub genes such as FN1, FSCN1, RPL10, VIM, RPS6, LGALS1,RPL26, ITGB1, PTPRB, LGALS1, CTGF, PELI2, ACOT13, FBN1, TNC, EEF1A2, ACTBL2and DSP were found to be in all four modules. EEF1A2 was associated with angiogenesis in breast cancer [
133]. EEF1A2 was linked with pathogenesis of EOC [
134]. RPL10, PTPRB, PELI2 and DSP were novel biomarkers for pathogenesis of EOC in these modules.
In the miRNA-target gene regulatory network (up-regulated), hub genes such as MBNL3, KIAA1644, HNRNPA3, NPTX1 and FAM46A. MBNL3, KIAA1644 and FAM46A were novel biomarkers for pathogenesis of EOC in this network. Meanwhile, in the miRNA-target gene regulatory network (down-regulated), hub genes such as RIMKLB, GPC6, MPRIP, KLF6 and TMEM47. The modification in tumor suppressor KLF6 was responsible for the advancement of prostate cancer [
135]. The loss of tumor suppressor KLF6 was responsible for pathogenesis of EOC [
136]. RIMKLB, MPRIP and TMEM47 were novel biomarkers for pathogenesis of EOC in this network.
In TF-target gene regulatory network (up-regulated), hub genes such as KRT6A, MRPS30, FAM217B, MFSD3 and KIAA1644. SNP in tumor suppressor MRPS30 was associated with advancement of breast cancer [
137], but SNP in this gene may be responsible for pathogenesis of EOC. KRT6A, FAM217B and MFSD3 were novel biomarkers for pathogenesis of EOC in this network. In the TF-target gene regulatory network (down-regulated), hub genes such as TMSB15A, ZNF280B, BRSK1, IFI27L2 and RIMKLB. TMSB15A, ZNF280B, BRSK1 and IFI27L2 were novel biomarkers for pathogenesis of EOC in this network.
Survival analysis revealed that hub genes with high expression, such as FBLN1, VAV3, HLA-A and SACS were associated with improved survival in EOC, while hub genes with high expression such as CEBPD, MID2, KRT6A, VACAN, KLF6 and FBN1 showed the opposite tendency. Expression levels revealed that hub genes such as CEBPD, MID2, FBLN1, KRT6A, VAV3, VACAN and FBN1were highly expressed in EOC (stages 3 and 4), meanwhile those such as HLA-A, KLF6 and SACS were highly expressed in EOC (stages 2 and 4).