Recently, liver cancer has emerged as a global health challenge, and its incidence is booming worldwide. It is estimated that more than 1 million individuals will have liver cancer by 2025 [13]. HCC serves as the major form of primary liver cancer. Integrated miRNA and mRNA microarray analysis provide a new approach to explore the mechanism of HCC. Previous researchers have conducted plenty of expression profiles about HCC to explore dysregulated genes and miRNAs. However, because of different platforms and control selection, the results are always discrepant and unsatisfying. Hence, there are a lot of unexplained mysteries between DEGs and DEMs involved in HCC owing to the lack of integrated analysis. Furthermore, the synergistic effects of TFs and miRNAs regulating genes in the network remain to be observed. We are convinced that this study is a significant trial to reveal interactions between DEGs and DEMs.
In this study, 177 common DEGs were identified, involving 34 increasing genes and 143 decreasing genes. To further understand the function of these DEGs, the GO and KEGG enrichment analyses were conducted by ClueGO. For GO enrichment analysis, most of the genes were enriched in the GO terms related to the cellular metabolic processes, which have previously been essential to cancer progression. And the KEGG analysis indicated that these identified genes were significantly enriched in the chemical carcinogenesis pathway. It is well known that the chemical carcinogens is highly relevent to the imitation and procession of cancers [14]. Various investigations have revealed that chemical carcinogenesis played a crucial role in the etiology of HCC. Ten DEGs (ADH1B, ADH1C, ADH4, ADH6, CYP1A2, CYP2C19, CYP2C9, CYP2E1, CYP3A4, NAT2) were associated with this pathway. ADH1B and ADH1C are involved in alcohol metabolism and strongly impact carcinogenic acetaldehyde accumulation [15]. ADH4 served as an essential member of the ADH family and was suggested as a potential prognostic marker for HCC patients [16]. CYP1A2, predominantly expressed in the liver tissue, could inhibit cell viability and clonogenicity and reduce cell migration and invasion in HCC [17]. CYP2C19 played a crucial role in detoxifying or inactivating potential carcinogens through activating DNA-binding metabolites. The expression of CYP2C19 has been proved to be associated with the development of various cancers such as hepatocellular carcinoma, lung cancer, and gastric cancer [18]. CYP2E1 is one of the carcinogen metabolism genes, and it is reported to activate chemical carcinogenesis [19].
Additionally, ten hub genes (CDC20, TOP2A, ASPM, NCAPG, AURKA, CYP2E1, HMMR, PRC1, TYMS, and CYP4A11) were identified by construction of the PPI network. Of these DEGs, specific genes have previously been reported to be related to the genesis and development in HCC. CDC20 is proved to be an essential cell-cycle regulator and the overexpression of CDC20 accelerates the progression of HCC [20]. TOP2A plays a critical regulatory role in cancers and is closely related to the prognosis of HCC. In hepatocarcinogenesis, the overexpressed TOP2A is correlated with early age onset, poor survival rates, and chemoresistance [21]. ASPM regulated cell proliferation and is identified as a biomarker for early recurrence and poor prognosis of HCC [22]. NCAPG is performed as an essential oncogene for HCC growth [23]. AURKA has been proved to promote cancer metastasis in HCC [24]. CYP2E1 regulate the metabolism of various toxicants and activate chemical procarcinogens. And the overexpression of CYP2E1 is proved to accelerate the procession of hepatocarcinogenesis [25]. Previous research showed that in HCC tissues, the expression of HMMR was more elevated than healthy liver tissues, which was consistent with the results of this study. And the increased expression of HMMR in liver hepatocellular carcinoma patients was identified as an adverse prognostic factor [26]. High PRC1 activity is a risk factor for early HCC recurrence and poor patient outcomes. In HCC, PRC1 perfomed as an oncogenic gene to accelerate cancer cell proliferaton, metastasis and stemness [27]. TYMS plays an essential role in the development of various malignancies, including HCC [28]. CYP4A11 has been linked to the aggravation of various cancers and affects different regulated metabolites. And for HCC patients, the CYP4A11 is a favorable prognostic factor, and its expression is positively correlated with good prognostic factors [29].
miRNAs are a kind of small RNAs that regulate gene expression via binding miRNAs to the 3' untranslated region of mRNAs, thereby inducing mRNA-silencing [30]. Mounting evidence has shown that the aberrant expression of miRNA may trigger carcinogenesis [31]. This study screened DEMs, and the potential candidate target genes of the DEMs were predicted. Then a miRNA-mRNA network was created based on the DEMs and their targets. A key DEM (hsa-miR-124-3p) was identified according to the network topology. And the miRNA-target gene-TF regulatory networks for hsa-miR-124-3p were constructed. hsa-miR-124-3p and two TFs such as GTF2A1 and POU5F1 were identified as co-regulators of EGR1 and SLITRK3. Lately, many researches have verified that aberrant expression of miR-124-3p is associated with various cancers. For triple-negative breast cancer cells, miR-124-3p can regulate cell proliferation by interaction with TNBC [32]. And in gastric cancer, miR-124-3p enhanced cell metastasis and proliferation by targeting the DNMT3B. GTF2A1, performed as a transcriptional factor, is associated with the susceptibility to gastric cancer. POU5F1 functions as a transcription factor that can activate their downstream genes through binding to the octameric sequence motif. Previous studies showed that the POU5F1 is a pan-cancer gene for various cancers and indicated that POU5F1 is functionally carcinogenic in HCC [33]. EGR1 can be rapidly and transiently induced in response to several stimuli, including growth factors, cytokines, and mechanical stresses. It has been proved that EGR1 can bind with miR-365a-3p promoted by CBX8 to exhibit oncogenic activity in HCC [34]. SLITRK3 is a prognostic molecular biomarker for gastrointestinal stromal tumors, and the expression of SLITRK3 correlates to gastrointestinal stromal tumor risk rating and prognosis [35]. However, given the complication of miRNA and TF crosstalk, these regulatory interactions need to be scanned thoroughly. In any case, these potential regulatory patterns may cast light to discover new molecular targets for HCC diagnosis and treatment.