Identification of Potential Diagnostic and Prognostic Pseudogenes in Hepatocellular Carcinoma Based on Pseudogene-miRNA-mRNA Competitive Network.

BACKGROUND It is widely known that hepatocellular carcinoma (HCC) has high rates of morbidity and mortality. A large number of studies have indicated that pseudogenes have an important effect on the carcinogenesis of HCC. Pseudogenes can play a role through the ceRNA network. There have been numerous studies on lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA networks. However, the pseudogene-miRNA-mRNA network in HCC has rarely been researched or reported on. MATERIAL AND METHODS The Cancer Genome Atlas (TCGA) database was researched and differences between selected genes were studied. A pseudogene-miRNA-mRNA network was then constructed and clustering of pseudogenes was studied. The diagnostic value of the selected pseudogenes, their functions, and pathways were investigated using available databases to understand their possible pathogenic mechanism in HCC. The protein-protein interaction network of target genes was found and the top 10 hub genes were identified. Expression of hub genes in HCC tissues was then detected by RT-qPCR. RESULTS By analyzing the gene difference and clinical data of HCC, we constructed a ceRNA network composed of 4 pseudogenes, 8 miRNAs, and 30 mRNAs. The pseudogenes AP000769.1, KRT16P1, KRT16P3, and RPLP0P2 were all correlated with the diagnosis and prognosis of HCC. Functional analyses through the Kyoto Encyclopedia of Genes and Genomes and the Gene Ontology databases indicated that pseudogenes can affect the physiological process of HCC through the p53 pathway. The top 10 hub genes identified were all highly expressed in HCC tissues and affected the patient survival rate. CONCLUSIONS In this study, 4 pseudogenes related to the diagnosis and prognosis of liver cancer were found through the construction of a ceRNA network. These 4 pseudogenes might constitute new therapeutic targets for liver cancer patients.

Prognostic Value and Molecular Regulatory Mechanism of MSTO2P in Hepatocellular Carcinoma: A Comprehensive Study Based on Bioinformatics, Clinical Analysis and in vitro Validation.

BACKGROUND: Accumulating studies have shown that pseudogenes could become key regulators in human cancers. Misato family member 2, pseudogene (MSTO2P) is overexpressed in lung and gastric cancer and affects the biological functions of tumor cells. However, the role of MSTO2P in hepatocellular carcinoma (HCC) is unreported. PURPOSE: This study aimed to examine the diagnostic and prognostic value of MSTO2P in HCC, to investigate the effects of MSTO2P on the biological functions of HCC cells, and to explore the potential mechanisms of MSTO2P in HCC. METHODS: Relevant data on HCC were downloaded from the Gene Expression Omnibus database and the Cancer Genome Atlas database and used to analyze MSTO2P expression and the role of MSTO2P in HCC prognosis. MSTO2P in HCC cell lines was knocked down by shRNA to study the effects of MSTO2P on cell proliferation, apoptosis, metastasis and invasion in HCC. Expressions of the main proteins involved in epithelial-mesenchymal transition and the PI3K/AKT/mTOR signaling pathway in HCC were examined via Western blot analysis. RESULTS: MSTO2P had significant diagnostic and prognostic value in HCC. MSTO2P was highly expressed in HCC tissues and cells, and MSTO2P increased HCC cell proliferation, invasion and metastasis. MSTO2P knockdown also increased E-cadherin expression and decreased N-cadherin and Vimentin expression. Additionally, MSTO2P increased the expressions of proteins in the PI3K/AKT/mTOR pathway, including PI3K, p-AKT and p-mTOR. CONCLUSION: MSTO2P might be used as a potential target for diagnosing and curing HCC. MSTO2P may affect HCC cell proliferation, apoptosis, metastasis and invasion through the PI3K/AKT/mTOR pathway.

The Long Non-Coding RNA SBF2-AS1 Exerts Oncogenic Functions In Gastric Cancer By Targeting The miR-302b-3p/E2F Transcription Factor 3 Axis.

BACKGROUND AND AIMS: Studies show that the long non-coding RNA, SBF2-AS1, plays a critical role in cancer progression, but the role of SBF2-AS1 in gastric cancer has not been reported. Therefore, this study aimed to elucidate the mechanism of SBF2-AS1 in gastric cancer (GC). METHODS: A meta-analysis, based on the gene expression omnibus database and TCGA dataset was performed to explore the prognostic value of SBF2-AS1 in GC. RT-PCR was also conducted to investigate the clinicopathologic value of SBF2-AS1 in GC. The effect of SBF2-AS1 in GC cell lines was conducted by gain or loss-of-function assays, and the SBF2-AS1 target gene was confirmed using a luciferase reporter assay and bioinformatics. RESULTS: SBF2-AS1 was overexpressed in GC tissues and cell lines, and SBF2-AS1 overexpression indicated poor overall survival and could serve as an independent prognostic factor. Moreover, knockdown of SBF2-AS1 inhibited cell growth, invasion, and metastasis, promoted apoptosis, and caused cell cycle arrest. Luciferase reporter and gain- or loss-of-function assays indicated that SBF2-AS1 acted as a competing endogenous (ceRNA) for microRNA (miR)-302b-3p, which blocked the inhibitory effect of miR-302b-3p on the E2F transcription factor 3 (E2F3). CONCLUSION: SBF2-AS1 could be a potential diagnostic and prognostic biomarker in GC, and SBF2-AS1 accelerates tumor progression via the miR-302b-3p/E2F3 axis.

Long Noncoding RNA LINC00265 Targets EGFR and Promotes Deterioration of Colorectal Cancer: A Comprehensive Study Based on Data Mining and in vitro Validation.

BACKGROUND: LncRNAs are found to be aberrantly expressed in human cancers and could function as potential oncogenes or tumor suppressor genes. LINC00265 is a newly discovered LncRNA and its function in colorectal cancer (CRC) remains unknown. METHODS: Comprehensive bioinformatics analysis were performed to investigate the expression, clinical significance and potential biologic functions of LINC00265 in CRC based on the data from the Cancer Genome Atlas (TCGA). To further investigate the potential role of LINC00265 in CRC, we knocked down the LINC00265 expression in HT29 cells. The cell proliferation, invasion, cycle distribution, and apoptosis were evaluated in control, NC and siRNA groups. Additionally, effect of LINC00265 on the expression of EGFR was also measured. RESULTS: The expression level of LINC00265 is increased in CRC tissues. Elevated level of LINC00265 is correlated with lymph node metastases and advanced pathological stage. We obtained 269 LINC00265 related genes; the results of functional analysis of these genes revealed that LINC00265 might involve in carcinogenesis of CRC. In addition, further experiments indicated that LINC00265 knockdown impaired cell proliferation and invasion, promoted cell cycle distribution and apoptosis in HT29 cells. Moreover, Western blot analysis revealed that downregulation of LINC00265 suppressed the expression of EGFR. CONCLUSION: Our results indicate that LINC00265 induces cell proliferation, migration and inhibits CRC cells apoptosis by targeting EGFR. LINC00265 could be served as a diagnostic factor and therapeutic target for CRC patients.

SUCO as a Promising Diagnostic Biomarker of Hepatocellular Carcinoma: Integrated Analysis and Experimental Validation.

BACKGROUND Hepatocellular carcinoma (HCC) is not frequently diagnosed until the late stage due to its concealed symptoms. Therefore, the identification of biomarkers that have effective diagnostic performance and act as potential key therapeutic targets for HCC becomes urgent. MATERIAL AND METHODS Comprehensive analysis of accumulated data downloaded from the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA) databases was used to obtain more reliable potential diagnostic biomarkers of HCC and to explore related molecular mechanisms. Meta-analysis and summary receiver operating characteristic (SROC) curve analysis were performed to evaluate the differential expression of SUCO gene in HCC and identify the capability of SUCO in distinguishing HCC-tissues from normal liver-tissues. RESULTS SUCO was found to be upregulated in HCC-tissues and exhibited a favorable value in diagnosing HCC. Bioinformatics analysis showed that SUCO might play important roles in HCC progression, and was significantly related to cell cycle, cell metabolism, and proliferation. CONCLUSIONS This study was the first to demonstrate that SUCO was overexpressed in HCC-tissues, and that high expression of SUCO was significantly related to poor overall survival in HCC patients. SUCO might be a potential diagnostic biomarker for HCC patients, which promotes the tumorigenesis and progression of HCC.

Pseudogene DUXAP10 acts as a diagnostic and prognostic marker and promotes cell proliferation by activating PI3K/AKT pathway in hepatocellular carcinoma.

Background: Recently, the pseudogene DUXAP10 was shown to be overexpressed in various human cancers and emerged as a key cancer regulator. However, the roles of DUXAP10 in hepatocellular carcinoma (HCC) tumorigenesis and progression remain uncharacterized. Methods: Comprehensive analyses were performed to investigate DUXAP10 expression patterns, potential biologic functions, and clinical significance in HCC based on the data downloaded from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. DUXAP10 expression levels in HCC tissue sections and cells were verified using quantitative real-time PCR analysis. DUXAP10-siRNA was used to silence DUXAP10 in the Hep3B cell line to determine the roles of DUXAP10 in HCC cell proliferation. Results: DUXAP10 was significantly overexpressed in HCC, and DUXAP10 upregulation was closely associated with poor prognoses in HCC patients. DUXAP10 knockdown decreased cell proliferation and arrested HCC cells in the G1 phase of the cell cycle. Western blot analysis showed that DUXAP10 knockdown decreased p-AKT expression in HCC cells. Conclusion: Our study demonstrates that pseudogene DUXAP10 promotes HCC cell proliferation by activating PI3K/AKT pathway and could act as a potential diagnostic and prognostic biomarker for HCC patients.

Pseudogene DUXAP10 can be used as a diagnostic and prognostic biomarker in human cancers.

The pseudogene DUXAP10 is overexpressed in numerous types of human cancers. However, the diagnostic and prognostic value of DUXAP10 in cancers has yet to be characterized. PubMed, EMBASE, Web of Science, the Cancer Genome Atlas (TCGA), and Gene Expression Omnibus databases were comprehensively searched in this study. A total of 50 studies comprising 11,292 patients were collected in this integrated analysis. DUXAP10 was confirmed to be significantly overexpressed in various human cancers (p < .05). Summary receiver operating characteristic (SROC) curve analysis was implemented, which indicated that DUXAP10 was a potential diagnostic biomarker for human cancers (area under the curve [AUC] of SROC curve = 0.81 [0.77-0.84]; pooled sensitivity = 0.69 [0.62-0.75]; pooled specificity = 0.81 [0.73-0.87]). In addition, hazard ratios (HRs) with 95% confidence intervals (CIs) were obtained to evaluate the association of DUXAP10 expression with overall survival (OS) time of cancer patients. Outcomes of meta-analysis suggested that upregulation of DUXAP10 was closely associated with poor OS (pooled HR = 1.11 [1.03-1.18]). Our study revealed that the pseudogene DUXAP10 was upregulated in multiple types of cancers and could be a potential biomarker with good diagnostic and prognostic value for human cancers.

Comprehensive analysis of potential prognostic genes for the construction of a competing endogenous RNA regulatory network in hepatocellular carcinoma.

BACKGROUND: Hepatocellular carcinoma (HCC) is an extremely common malignant tumor with worldwide prevalence. The aim of this study was to identify potential prognostic genes and construct a competing endogenous RNA (ceRNA) regulatory network to explore the mechanisms underlying the development of HCC. METHODS: Integrated analysis was used to identify potential prognostic genes in HCC with R software based on the GSE14520, GSE17548, GSE19665, GSE29721, GSE60502, and the Cancer Genome Atlas databases. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway-enrichment analyses were performed to explore the molecular mechanisms of potential prognostic genes. Differentially expressed miRNAs (DEMs) and lncRNAs (DELs) were screened based on the Cancer Genome Atlas database. An lncRNA-miRNA-mRNA ceRNA regulatory network was constructed based on information about interactions derived from the miRcode, TargetScan, miRTarBase, and miRDB databases. RESULTS: A total of 152 potential prognostic genes were screened that were differentially expressed in HCC tissue and significantly associated with overall survival of HCC patients. There were 13 key potential prognostic genes in the ceRNA regulatory network: eleven upregulated genes (CCNB1, CEP55, CHEK1, EZH2, KPNA2, LRRC1, PBK, RRM2, SLC7A11, SUCO, and ZWINT) and two downregulated genes (ACSL1 and CDC37L1) whose expression might be regulated by eight DEMs and 61 DELs. Kaplan-Meier curve analysis showed that nine DELs (AL163952.1, AL359878.1, AP002478.1, C2orf48, C10orf91, CLLU1, CLRN1-AS1, ERVMER61-1, and WARS2-IT1) in the ceRNA regulatory network were significantly associated with HCC-patient prognoses. CONCLUSION: This study identified potential prognostic genes and constructed an lncRNA- miRNA-mRNA ceRNA regulatory network of HCC, which not only has important clinical significance for early diagnoses but also provides effective targets for HCC treatments and could provide new insights for HCC-interventional strategies.

DUXAP8 a Pan-Cancer Prognostic Marker Involved in the Molecular Regulatory Mechanism in Hepatocellular Carcinoma: A Comprehensive Study Based on Data Mining, Bioinformatics, and in vitro Validation.

BACKGROUND: Double homeobox A pseudogene 8 (DUXAP8) has been identified as a key regulator at the posttranscriptional level in various types of cancers. However, whether DUXAP8 has a role in hepatocellular carcinoma (HCC) progression remains to be determined. Here, we aimed to investigate the potential clinical value of DUXAP8 as a pan-cancer marker, and its role in HCC development through an integrated analysis strategy and in vitro experimental validation. METHODS: Comprehensive analysis was performed using data mined from public databases to evaluate the expression patterns and clinical value of DUXAP8 in human pan-cancers. Bioinformatics analysis was performed to investigate the potential biological functions of DUXAP8 in HCC based on TCGA database. Real-time qPCR analysis was used to examine the expression levels of DUXAP8 in HCC tissue samples and cell lines. DUXAP8-siRNA was used to silence DUXAP8 in the Hep-G2 cell line to examine the role of DUXAP8 in HCC cell proliferation and invasion. RESULTS: DUXAP8 was significantly upregulated in various types of human cancers and could serve as a potential pan-cancer diagnostic and prognostic biomarker. Bioinformatics analysis suggested that DUXAP8 might be involved in the regulation of the biological processes of HCC cell cycle, cell division and cell proliferation. Additionally, downregulation of DUXAP8 inhibited HCC cell proliferation and invasion in vitro. CONCLUSION: This study revealed that DUXAP8 may serve as a potential pan-cancer prognostic and diagnostic marker in humans. In addition, DUXAP8 promoted HCC cell proliferation and invasion, suggesting that it may represent a novel therapeutic target for HCC.

Long non-coding RNA CASC2 in solid tumors: A meta-analysis.

BACKGROUND AND AIM: Recently, several studies have reported that the long non-coding RNA cancer susceptibility 2 (CASC2) is downregulated in human solid tumors. However, as the sample size in those studies was limited, the role of CASC2 in cancer remains unknown. Accordingly, we conducted this meta-analysis to explore the role of CASC2 in solid tumors. METHODS: We systematically searched the PubMed, Medline, Cochrane Library, Web of Science, EMBASE, Ovid, Chinese CNKI, and Chinese WanFang databases. Pooled odds ratios (ORs) and hazard ratios (HRs) with 95% confidence interval (CI) were used to evaluate the relation between CASC2 and the clinicopathological characteristics and prognosis of patients with cancer. Additionally, we also use The Cancer Genome Atlas (TCGA) dataset to analyze CASC2 expression. RESULTS: A total of 15 studies with 1158 patients were included in this meta-analysis. The pooled results demonstrated that the expression of CASC2 was related to tumor size (large vs. small: OR = 0.40, 95% CI = [0.30, 0.52]), differentiation (low vs. high+ moderate: OR = 0.42, 95% CI = [0.29, 0.62]) and TNM stage (I + II vs. III + IV: OR = 2.74, 95% CI = [2.08, 3.60]), but not to age, gender and differentiation. High CASC2 expression indicated better overall survival (OS) (HR = 0.41, 95% CI = [0.32, 0.50]) and disease-free survival (DFS) (HR = 0.48, 95% CI = [0.26, 0.66]). Additionally, similar results were obtained through analysis of the TCGA data set. Moreover, it was determined that CASC2 could be an independent predictive factor for OS (HR = 0.38, 95% CI = [0.22, 0.54]) in patients with cancer. CONCLUSION: This analysis revealed that low CASC2 expression was correlated with advanced clinicopathological characteristics of cancer tumors, and CASC2 may thus be a potential prognostic biomarker in human cancer. However, more studies are needed to further corroborate these findings.

DcR3 induces proliferation, migration, invasion, and EMT in gastric cancer cells via the PI3K/AKT/GSK-3ß/ß-catenin signaling pathway.

BACKGROUND: Decoy receptor 3 (DcR3) has been reported to be overexpressed in a wide variety of malignancies and is correlated with tumorigenesis and progression. In gastric cancer (GC), DcR3 overexpression is associated with lymph node and distant metastasis, as well as poor prognosis. However, the functional role of DcR3 expression in GC remains elusive. PURPOSE: The aim of this study is to elucidate the direct role of DcR3 in regulating GC progression and metastasis and identify the potential mechanism. METHODS: DcR3 expression was stably knocked down in HGC27 and MKN28 cells by transfecting the cells with DcR3 shRNA using lentiviral vector system. After the knockdown of DcR3 was confirmed, cell proliferation, colony formation, cell cycle distribution, apoptosis, cell invasion and migration were assessed in vitro. In addition, Western blot analysis was performed to evaluate the expression of downstream mediators of DcR3. Comparisons between multiple groups were performed using one-way analysis of variance (ANOVA) or unpaired Student's t-test. Differences were considered significant at P<0.05. RESULTS: Our findings demonstrate that DcR3 induces proliferation, migration, invasion, and promotes epithelial-mesenchymal transition (EMT) of GC cells. In addition, DcR3 increases the expression levels of several components of the PI3K/AKT/GSK-3ß/ß-catenin signaling pathway, such as p-AKT, GSK-3ß, p-GSK-3ß and ß-catenin. Additionally, DcR3 also enhances the expression of N-cadherin and Vimentin and decreases the expression of E-cadherin. CONCLUSION: In summary, the findings of this study indicate that during GC progression, DcR3 plays a key role in cell proliferation and invasion via the PI3K/AKT/GSK-3ß/ß-catenin signaling pathway. Thus, targeting DcR3 might be a potential therapeutic approach for the treatment of GC.

The clinicopathological and prognostic value of Nanog in human gastrointestinal luminal cancer: A meta-analysis.

BACKGROUND: Recent studies have demonstrated that the over-expression of Nanog contributes to the progression of various malignant tumors. However, the clinicopathological and prognostic role of Nanog in gastrointestinal luminal cancer remains controversial. Therefore, we conducted a meta-analysis to assess the role of Nanog in gastrointestinal luminal cancer. METHODS: An electronic search for relevant literature was performed in PubMed, Cochrane Library, Web of Science, and EMBASE databases. The relationships between Nanog expression and clinicopathological features and survival outcomes were analyzed. Pooled odds ratios (ORs) and hazard ratios (HRs) with 95% confidence intervals (CIs) were calculated by STATA14.2 and RevMan 5.3 software. RESULTS: A total of 9 studies with 1526 patients were included in this meta-analysis. The positive expression of Nanog was related to gender, depth of infiltration, differentiation, and TNM stage; however, it was not associated with age, tumor size, or lymph node metastasis. Moreover, positive Nanog expression was correlated with a poor overall survival (OS) and poor disease-free survival (DFS) in gastrointestinal luminal cancer. CONCLUSION: The pooled results suggested that Nanog expression was associated with gender, depth of infiltration, differentiation, and TNM stage, and Nanog may be a potential biomarker to predict the prognosis of gastrointestinal luminal cancer.

Prognostic value of DcR3 in solid tumors: A meta-analysis.

BACKGROUND: Decoy receptor 3 (DcR3) has been reported to be overexpressed in a wide range of solid tumors, suggesting that DcR3 plays a crucial role in the development and progression of cancer. The present meta-analysis assesses the association between DcR3 expression and prognosis in patients with solid tumors. METHODS: Eligible studies were identified by searching the PubMed, Web of Science, Cochrane Library, EMBASE, Chinese CNKI, and Wan Fang databases. The pooled hazard ratios (HRs) for overall survival (OS) and recurrence-free survival (RFS) were calculated using fixed effects models and random effects models, respectively. RESULTS: Data from the 16 included studies, with 2209 patients, were reviewed and analyzed. DcR3 overexpression was significantly associated with worse OS in patients with solid tumors, but its expression might not be related to RFS in malignancies. CONCLUSIONS: Current evidence demonstrates that increased DcR3 expression correlates with a poor prognosis in cancer patients, which suggests that the expression status of DcR3 is a useful biomarker for the prediction of prognosis in patients with solid tumors.