Integrated bioinformatics analysis of microarray data from the GEO database to identify the candidate genes linked to poor prognosis in lung adenocarcinoma

BACKGROUND

Lung adenocarcinoma (LUAD) is one of the most common cancers with high morbidity and mortality and remains a crucial factor endangering human health.

OBJECTIVE

This study aimed to elucidate the potential treatment target and prognostic biomarker in patients with LUAD through a comprehensive bioinformatics analysis.

METHODS

The three public microarray datasets of GSE118370, GSE116959, and GSE43767 were obtained from the GEO data resource. The DEGs were explored between LUAD and non-malignant samples using GEO2R online tool in GEO data resource. GO along with KEGG analysis of DEGs were examined using WebGestalt tool. The STRING web resource was employed to develop the PPI network of DEGs, whereas Cytoscape software was employed to perform module analysis. Finally, the mRNA, protein expression along with survival analysis of hub genes were explored via GEPIA, HPA along with Kaplan-Meier plotter web resource, respectively.

RESULTS

Only 82 upregulated and 105 downregulated DEGs were found among the three datasets. Further, GO analysis illustrated that 187 DEGs were primary enriched in extracellular structure organization, tube development along with cell adhesion. The KEGG enrichments showed that these DEGs were primary linked to leukocyte transendothelial migration, vascular smooth muscle contraction along with ECM-receptor interaction. Among the 187 DEGs, the 10 hub genes (P4HB, SPP1, CP, GOLM1, COL1A1, MMP9, COL10A1, APOA1, COL4A6, and TIMP1) were identified. The mRNA along with protein levels of hub genes in LUAD tissues were further verified by Oncomine, UCSC Xena, GEPIA and HPA databases. Additionally, overall survival curves illustrated that LUAD patients with the higher levels of P4HB, SPP1, COL1A1, and MMP9 were dramatically linked to shorter overall survival.

CONCLUSIONS

The current study identified DEGs candidate genes (P4HB, SPP1, COL1A1, and MMP9) and pathways in LUAD using bioinformatics analysis, which could enhance our understanding of pathogenesis along with underlying molecular events in LUAD, and these hub genes and pathways may help provide candidate treatment targets for LUAD.

Microfibril Associated Protein 5 (MFAP5) Is Related to Survival of Ovarian Cancer Patients but Not Useful as a Prognostic Biomarker

Ovarian cancer (OC) is usually diagnosed late due to its nonspecific symptoms and lack of reliable tools for early diagnostics and screening. OC studies concentrate on the search for new biomarkers and therapeutic targets. This study aimed to validate the MFAP5 gene, and its encoded protein, as a potential prognostic biomarker. In our previous study, we found that patients with high-grade serous OC who had higher MFAP5 mRNA levels had shorter survival, as compared with those with lower levels. Here, we used the Kaplan-Meier Plotter and CSIOVDB online tools to analyze possible associations of MFAP5 expression with survival and other clinico-pathological features. In these analyses, higher MFAP5 mRNA expression was observed in the more advanced FIGO stages and high-grade tumors, and was significantly associated with shorter overall and progression-free survival. Next, we analyzed the expression of the MFAP5 protein by immunohistochemistry (IHC) in 108 OC samples and tissue arrays. Stronger MFAP5 expression was associated with stronger desmoplastic reaction and serous vs. non-serous histology. We found no significant correlation between IHC results and survival, although there was a trend toward shorter survival in patients with the highest IHC scores. We searched for co-expressed genes/proteins using cBioPortal and analyzed potential MFAP5 interaction networks with the STRING tool. MFAP5 was shown to interact with many extracellular matrix proteins, and was connected to the Notch signaling pathway. Therefore, although not suitable as a prognostic biomarker for evaluation with a simple diagnostic tool like IHC, MFAP5 is worth further studies as a possible therapeutic target.

The role of complement in the clinical course of hepatocellular carcinoma

Background

The complement system, an innate immune system, may either play an antitumor role, or promote tumorigenesis and cancer progression in different kinds of cancer. The function of complement in hepatocellular carcinoma (HCC) is unclear.

Methods

The gene expressions of the complement system were based on data obtained from TCGA and GEO. We explored gene expressions, mutation, enrichment analysis, clinicopathology, patients' outcome, and immune infiltration via Gepia2, cBioPortal, Metascape, UALCAN, Kaplan–Meier Plotter, and TIMER 2.

Results

Five complement genes, including C1R, C6, C7, CFP, and CFHR3, were not only found to be significantly downregulated in HCC samples compared with normal liver samples, but also found to be significantly associated with overall survival, disease‐free survival, and progress‐free survival in HCC patients. In addition, lower mRNA expression of C1R, C6, C7, and CFHR3 were found correlated with advanced cancer stages and higher tumor grades in HCC patients. Also, the expression levels of CFP were correlated with many sets of immune markers of tumor immune cells, such as those of CD8+ T cells, CD4+ T cells, B cells, M2 macrophages, neutrophils, DCs, Th1 cells, Th2 cells, and T cell exhaustion in HCC. Based on that, we developed a prognostic model for HCC patients—Riskscore = (−0.0053)*C6+(−0.0498)*C7+(−0.1045)*CFHR3.

Conclusion

C1R, C6, C7, CFP, and CFHR3 could be prognostic biomarkers for patients with HCC.

Elevated expression of Tweety homologue 3 predicts poor clinical outcomes in ovarian cancer

Objective: To define the alteration of tweety homolog (TTYH) expression in patients with ovarian carcinoma (OC) and its correlation to prognosis.

Methods: Kaplan-Meier (KM) plotter was used to evaluate the association between TTYHs expression and clinical outcomes of OC patients. The distribution of 20-year overall survival (OS) and progression-free survival (PFS) was estimated using KM survival plots. The mRNA expression of TTYHs in OC and normal ovarian tissues was confirmed by the Oncomine database. Then, using immunohistochemistry assay, the expression of TTYH1 and TTYH3 proteins in serous OC and normal ovarian tissues was detected. In addition, the protein and mRNA levels of TTYH1 and TTYH3 in human OC cell lines ES-2, A2780 and SKOV3 and normal ovarian epithelial cell lines IOSE80 were assessed by western blotting and real-time quantitative polymerase chain reaction (qRT-PCR).

Results: TTYH1 possessed meaningful significance in predicting better prognosis in the serous, advanced stage, and well-differentiated OC patients, while TTYH3 expression predicted worse prognosis in serous, late-stage, and poorly differentiated OC patients. High expression of TTYH1 displayed an association with favorable PFS in OC patients with TP53 mutation. However, enhanced TTYH3 was related to an adverse clinical outcome in TP53-mutated OC patients. In addition, TTYH1 was related to a better clinical outcome in OC patients with platinums-based chemotherapy, but only indicated improved overall survival in OC patients who received taxol or platin + taxol chemotherapy. The up-regulated expression of TTYH3 predicted worse survival in OC patients receiving platin, taxol, or platin + taxol chemotherapy regimen. The levels of TTYH3 mRNA and protein were higher in OC cells and tissues when compared to normal ovarian cells and tissues.

Conclusions: TTYH3 was a potential predictor for poor clinical outcome in OC patients, particularly in patients with serous, late-stage, poorly differentiated, TP53-mutation or the patients treated with chemotherapy regimens (platin, taxol, or platin + taxol).

Prognostic value of small mother against decapentaplegic expression in human gastric cancer

Gastric cancer is the fifth most common malignancy in the world with alow 5-year survival rate. To date, no study has investigated the prognostic role of the small mother against decapentaplegic (SMAD) in gastric cancer. The association of SMADs with overall survival (OS) of gastric cancer was analyzed on the online Kaplan-Meier (KM) plotter database. Clinical data such as stage, differentiation, gender, treatment, and Her2 mutation status of gastric cancer patients were analyzed. The (E)-SIS3 was used to inhibit SMAD3 expression in gastric cancer cells, and the effects of SMAD3 on gastric cancer cells were analyzed via real-time cellular analysis (RTCA), flow cytometry, colony formation, and immunofluorescence assay. The results showed that the high expression of three members of SMADs (SMAD1, SMAD2, SMAD4) was correlated with afavorable OS of gastric cancer patients. Meanwhile, SMAD3 expression level indicated highly differentiated cancer. We also observed that surgical treatment was associated with high expression level of SMAD1 and SMAD2. Besides, the effect of Her2 on gastric cancer was not noticeable. Moreover, (E)-SIS3 pharmacological assay revealed that inhibition of expression of SMAD3 suppressed the proliferation and migration ability of gastric cancer cells via inducing apoptosis. Collectively, these results demonstrate that the high expression level of three members of SMADs (SMAD1, SMAD2, and SMAD4) is significantly correlated with favorable OS of gastric cancer patients, which is opposite to SMAD3. Thus, SMADs regulate the differentiation of cancer and can be used to guide treatment decisions.

The prognostic value of the lysyl oxidase family in ovarian cancer

BACKGROUND

Our study intended to evaluate the prognostic value of lysyl oxidase (LOX) and its four relevant members, the lysyl oxidase-like genes (LOXL1-4), in ovarian cancer (OC) patients.

MATERIAL AND METHODS

The Kaplan-Meier plotter (KM plotter) database was used to investigate the prognostic power of the LOX family for OC patients. Overall survival (OS) and progression-free survival (PFS) were the clinical endpoints. The prognostic roles of the LOX family in OC patients were also analyzed according to various clinicopathological characteristics, including histological subtypes, clinical stages, pathological grades, and chemotherapeutic treatments.

RESULTS

Overexpression of LOX, LOXL1, LOXL2, and LOXL3 mRNA indicated poor OS and PFS in OC patients, particularly in serous and grade II + III OC patients. Overexpression of LOXL4 mRNA resulted in worse PFS in OC patients. Overexpression of LOX and LOXL1 mRNA showed worse OS and PFS in stage III + IV OC patients, and overexpression of LOXL3 mRNA indicated worse OS and PFS in stage I + II OC patients. Overexpression of LOX, LOXL3, and LOXL4 mRNA indicated worse OS and PFS among OC patients who received platinum, taxol, and taxol + platinum chemotherapy. Overexpression of LOXL1 and LOXL2 mRNA was related to lower OS and PFS in OC patients who received platinum chemotherapy.

CONCLUSION

LOX, LOXL1, LOXL2, and LOXL3 may become potential predictive markers for negative outcomes in OC patients. Moreover, the LOX family can serve as new molecular predictors for the efficiency of platinum-based chemotherapy in OC patients.

Comprehensive analysis of the prognosis for chromobox family in gastric cancer

Background

Chromobox (CBX) family proteins are a class of transcriptional repressors involved in epigenetic regulation and developmental processes of various tumors, including gastric cancer. However, the function and prognosis of different CBXs in gastric cancer remain unknown.

Methods

This study addresses this issue by synthesizing several mainstream databases (Oncomine, GEPIA2, cBioportal, and Kaplan-Meier plotter, among others) that currently contain many tumor samples and provide very reliable analysis results, investigating the role of CBXs in the prognosis of gastric cancer.

Results

The mRNA of CBX1/2/3/4/5/8 was highly expressed in gastric cancer, the mRNA of CBX7 was lowly expressed in gastric cancer, and the mRNA expression of CBX6 was not significantly different in CRC. Besides, high and low CBXs mRNA expression correlated with cancer stage, node metastasis status, H. pylori infection status, and tumor grade in CRC patients. We found that high mRNA expression of CBX4/5/6/7/8 was significantly associated with worse overall survival (OS), progression-free survival (FP), and post-progression survival (PPS) in a large number of CRC patients. High mRNA expression of CBX3 was significantly associated with better OS and FP. We also found that none of the eight CBXs family genes had a mutation rate of less than 5% in gastric cancer, and the highest mutation rate was in CBX3 (14%).

Conclusions

These results suggest that CBX3/4/5/6/7/8 could be a prognostic biomarker in gastric cancer patients.

Clinical and prognostic significance of MYH11 in lung cancer

Myosin heavy chain 11 (MYH11), encoded by the MYH11 gene, is a protein that participates in muscle contraction through the hydrolysis of adenosine triphosphate. Although previous studies have demonstrated that MYH11 gene expression levels are downregulated in several types of cancer, its expression levels have rarely been investigated in lung cancer. The present study aimed to explore the clinical significance and prognostic value of MYH11 expression levels in lung cancer and to further study the underlying molecular mechanisms of the function of this gene. The Oncomine database showed that the MYH11 expression levels were decreased in lung cancer compared with those noted in the normal lung tissue (P<0.05). Kaplan-Meier plotter results revealed that the decreased MYH11 expression levels were correlated with poor prognosis in lung cancer patients. Among the lung cancer cases with gene alteration of MYH11, mutation was the most common of all alteration types. Coexpedia and Metascape analyses revealed that the target genes were primarily enriched in ‘muscle contraction’, ‘contractile fiber part’, ‘actin cytoskeleton’ and the ‘adherens junction’. These results indicated that MYH11 is a potential novel drug target and prognostic indicator of lung cancer.

Associations of sirtuins with clinicopathological variables and prognosis in human ovarian cancer

Ovarian cancer (OC) is the fifth most frequent cause of cancer-associated mortality worldwide, and is accompanied by asymptomatic progression. Sirtuins (SIRTs) are a family of nicotinamide adenine dinucleotide-dependent protein deacetylases, comprising seven members (SIRT1, SIRT2, SIRT3, SIRT4, SIRT5, SIRT6 and SIRT7). Accumulating evidence has demonstrated that SIRTs act as prognostic estimators in certain types of cancer such as lung cancer, prostate cancer, gastric cancer, breast cancer and colorectal cancer. However, it remains unknown whether individual SIRTs can serve as independent prognostic factors in OC. In the present study, the Kaplan-Meier plotter online database was utilized to examine the prognostic values of SIRT mRNA expression in patients with OC. The results demonstrated that the overexpression of SIRT3, SIRT5, SIRT6 and SIRT7 mRNAs was associated with a good prognosis in patients, whereas elevated mRNA levels of SIRT1 and SIRT4 indicated poor survival in patients with OC. In addition, among the favorable predictors, SIRT3, SIRT5, SIRT6 and SIRT7 overexpression were associated with overall survival (OS), according to clinical characteristics, such as histological classification, clinical stage, pathology grade, drug therapy and tumor protein p53 mutation status in patients with OC. Similarly, SIRT4 mRNA overexpression was associated with poor OS in pathological grade III cancer. High SIRT1 and SIRT4 expression were associated with unfavorable OS at all clinical stages. Furthermore, SIRT1 and SIRT4 were negatively associated with OS in drug-treated patients. In summary, the present study demonstrated that the SIRT family is associated with the prognosis of human OC, suggesting that individual SIRTs may also act as prognostic predictors in patients.

Transcriptional expressions of Chromobox 1/2/3/6/8 as independent indicators for survivals in hepatocellular carcinoma patients

Chromobox (CBX) proteins are important components of epigenetic regulation complexes known to play key roles in hepatocellular carcinoma (HCC). Little is known about the function of distinct CBXs in HCC. To address this issue, the study investigated the roles of CBXs in the prognosis of HCC using ONCOMINE, UALCAN, Human Protein Atlas, Kaplan-Meier Plotter, c-BioPortal databases. Over expressions of 8 CBXs members were found to be significantly associated with clinical cancer stages and pathological tumor grades in HCC patients. Besides, higher mRNA expressions of CBX1/2/3/6/8 were found to be significantly associated with shorter overall survival (OS) in HCC patients, while higher mRNA expression of CBX7 was associated with favorable OS. Multivariate analysis also showed that high mRNA expressions of CBX1/2/3/6/8 were independent prognostic factors for shorter OS of HCC patients. Moreover, high mutation rate of CBXs (51%) was also observed in HCC patients, and genetic alteration in CBXs was associated with shorter OS and disease-free survival (DFS) in HCC patients. Taken together, these results indicated that CBX1/2/3/6/8 could be prognostic biomarkers for survivals of HCC patients.

Screening of potential biomarkers and their predictive value in early stage non-small cell lung cancer: a bioinformatics analysis

Background

Non-small cell lung cancer (NSCLC) remains the first leading cause of death in malignancies worldwide. Despite the early screening of NSCLC by low-dose spiral computed tomography (CT) in high-risk individuals caused a 20% reduction in the mortality, there still exists imperative needs for the identification of novel biomarkers for the diagnosis and treatment of lung cancer.

Methods

mRNA microarray datasets GSE19188, GSE33532, and GSE44077 were searched, and the differentially expressed genes (DEGs) were obtained using GEO2R. Functional and pathway enrichment analyses were performed for the DEGs using DAVID database. Protein-protein interaction (PPI) network was plotted with STRING and visualized by Cytoscape. Module analysis of the PPI network was done through MCODE. The overall survival (OS) analysis of genes from MCODE was performed with the Kaplan Meier-plotter.

Results

A total of 221 DEGs were obtained, which were mainly enriched in the terms related to cell division, cell proliferation, and signal transduction. A PPI network was constructed, consisting of 221 nodes and 739 edges. A significant module including 27 genes was identified in the PPI network. Elevated expression of these genes was associated with poor OS of NSCLC patients, including UBE2T, UNF2, CDKN3, ANLN, CCNB2, and CKAP2L. The enriched functions and pathways included protein binding, ATP binding, cell cycle, and p53 signaling pathway.

Conclusions

The DEGs in NSCLC have the potential to become useful targets for the diagnosis and treatment of NSCLC.

Expression levels and prognostic values of annexins in liver cancer

Annexins are a superfamily of calcium-dependent phospholipid-binding proteins that are implicated in a wide range of biological processes. The annexin superfamily comprises 13 members in humans (ANXAs), the majority of which are frequently dysregulated in cancer. However, the expression patterns and prognostic values of ANXAs in liver cancer are currently largely unknown. The present study aimed to analyze the expression levels of ANXAs and survival data in patients with liver cancer from the Oncomine, GEPIA, Kaplan-Meier plotter and cBioPortal for Cancer Genomics databases. The results demonstrated that ANXA1, A2, A3, A4 and A5 were upregulated, whereas ANXA10 was downregulated in liver cancer compared with normal liver tissues. The expression of ANXA10 was associated with pathological stage. High expression levels of ANXA2 and A5 were significantly associated with poor overall survival (OS) rate whereas ANXA7 and A10 were associated with increased OS. The prognostic values of ANXAs in liver cancer were determined based on sex and clinical stage, which revealed that ANXA2, A5, A7 and A10 were associated with OS in male, but not in female patients. In addition, the potential biological functions of ANXAs were identified by Gene Ontology functional annotation and Kyoto Encyclopedia of Genes Genomes pathway analysis; the results demonstrated that ANXAs may serve a role in liver cancer through the neuroactive ligand-receptor interaction pathway. In conclusion, the results of the present study suggested that ANXA1, A2, A3, A4, A5 and A10 may be potential therapeutic targets for liver cancer treatment, and that ANXA2, A5, A7 and A10 may be potential prognostic biomarkers of liver cancer.

Berzosertib (VE-822) inhibits gastric cancer cell proliferation via base excision repair system

Background

Current investigations suggest that the Base Excision Repair (BER) system may change DNA repair capacity and affect clinical gastric cancer progression such as overall survival. However, the prognostic value of BER system members in gastric cancer remains unclear.

Methods

We explored the prognostic correlation between 7 individual BER genes, including uracil-DNA glycosylase (UNG), Single-strand-selective monofunctional uracil-DNA glycosylase 1 (SMUG1), Methyl-CpG binding domain 4 (MBD4), thymine DNA glycosylase (TDG), 8-oxoguanine DNA glycosylase (OGG1), MutY DNA glycosylase (MUTYH) and Nei like DNA glycosylase 1 (NEIL1), expression and overall survival (OS) in different clinical data, such as Lauren classification, pathological stages, human epidermal growth factor receptor-2 (HER2) expression status, treatment strategy, gender and differentiation degree in gastric cancer patients, using Kaplan-Meier plotter (KM plotter) online database. Based on the bioinformatics analysis, we utilized Berzosertib (VE-822) to inhibit DNA damage repair in cancer cells compared to solvent control group via real-time cellular analysis (RTCA), flow cytometry, colony formation and migration assay. Finally, we utilized reverse transcription-polymerase chain reaction (RT-PCR) to confirm the expression of BER members between normal and two gastric cancer cells or solvent and VE-822 treated groups.

Results

Our work revealed that high UNG mRNA expression was correlated with high overall survival probability; however, high SMUG1, MBD4, TDG, OGG1, MUTYH and NEIL1 mRNA expression showed relatively low overall survival probability in all GC patients. Additionally, UNG was associated with high overall survival probability in intestinal and diffuse types, but SMUG1 and NEIL1 showed opposite results. Further, VE-822 pharmacological experiment suggested that inhibition of DNA damage repair suppressed gastric cancer cells’ proliferation and migration ability via inducing apoptosis. Further, real-time polymerase chain reaction results proposed the inhibition of gastric cancer cells by VE-822 may be through UNG, MUTYH and OGG-1 of BER system.

Conclusion

We comprehensively analyze the prognostic value of the BER system (UNG, SMUG1, MBD4, TDG, OGG1, MUTYH and NEIL1) based on bioinformatics analysis and experimental confirmation. BER members are associated with distinctive prognostic significance and maybe new valuable prognostic indicators in gastric cancer.

Distinct expression pattern and prognostic values of pituitary tumor transforming gene family genes in non-small cell lung cancer

Members of the pituitary tumor transforming gene (PTTG) family, including PTTG1, PTTG2 and PTTG3P, exhibit pivotal roles in the onset and progression of certain types of human cancer. However, to the best of our knowledge, a systematic study regarding the expression pattern and the prognostic values of PTTG family genes in non-small cell lung cancer (NSCLC) remains to be performed. The expression levels of PTTG family genes in NSCLC were successively determined using the Gene Expression Profiling Interactive Analysis, UALCAN and Oncomine databases. Subsequently, the Kaplan-Meier plotter database was used to assess the prognostic value of the PTTG family genes in patients with NSCLC, and to determine the associations between PTTG expression levels and the prognosis of patients based on different clinicopathological features, including cancer stage, grade, chemotherapy, radiotherapy, lymph node status, smoking history, and sex. PTTG1 was identified to be significantly upregulated in NSCLC in all three databases, whereas PTTG2 and PTTG3P were significantly upregulated in NSCLC in only the UALCAN database. Patients with NSCLC with higher expression levels of the three PTTG genes demonstrated shorter overall survival times. In summary, the results of the present study suggested that increased expression of PTTG family genes may serve as promising prognostic biomarkers for patients with NSCLC.

Prognostic values of transketolase family genes in ovarian cancer

Transketolase genes are key rate-limiting enzymes in the non-oxidative part of the pentose phosphate pathway, which is an important metabolic pathway in ribose-5-phosphate production. Three human transketolase genes have been identified: Transketolase (TKT), transketolase-like gene 1 (TKTL1) and transketolase-like gene 2 (TKTL2). Transketolase genes serve crucial roles in the tumorigenesis, metastasis and outcome of multiple types of cancer. However, the expression levels and prognostic values of transketolase family genes in patients with ovarian cancer remain unclear. The purpose of the study was to analyze the expression level and prognostic significance of transketolase family genes in ovarian cancer. In the present study, the mRNA expression levels of three transketolase genes in ovarian cancer and normal ovarian tissue were compared by Oncomine. The prognostic values of these genes were systemically assessed using the Kaplan-Meier plotter database. In addition, the associations between the mRNA levels of these transketolase genes and the clinicopathological characteristics of patients with ovarian cancer, such as histological subtype, clinical stage, grade, tumor protein p53 (TP53) mutation status and chemotherapy history were studied. The prognostic roles of transketolase genes were also evaluated in a validation dataset. The results demonstrated that TKT and TKTL1 expression in ovarian cancer tissues was elevated compared with that in normal ovarian tissues. In addition, high mRNA expression of the three transketolase genes was identified to be associated with poorer progression-free survival (PFS) in patients with serous ovarian cancer, especially in patients at an advanced stage. TKTL2 was significantly associated with poor overall survival in all patients with ovarian cancer. Additionally, transketolase family genes served a role in predicting PFS in patients with ovarian cancer treated with platinum and/or taxol. High expression of the three transketolase genes was associated with unfavorable PFS in patients with TP53-mutated ovarian cancer, but not in patients with TP53 wild-type ovarian cancer. These results suggested that transketolase family genes may serve important roles in the prognosis of patients with ovarian cancer.

Prognostic roles of mitochondrial transcription termination factors in non-small cell lung cancer

Mitochondrial transcription termination factors (MTERFs) regulate mitochondrial gene transcription and metabolism in numerous types of cells. Previous studies have indicated that MTERFs serve pivotal roles in the pathogenesis of various cancer types. However, the expression and prognostic roles of MTERFs in patients with non-small cell lung cancer (NSCLC) remain elusive. The present study investigated the gene alteration frequency and expression level using Gene Expression Omnibus datasets and reverse transcription-quantitative polymerase chain reaction, and evaluated the prognostic roles of MTERFs in patients with NSCLC using the Kaplan-Meier plotter database. In human lung cancer tissues, it was observed that the mRNA levels of MTERF1, 2, 3 and 4 were positively associated with the copy number of these genes. The mRNA expression levels of MTERF1 and 3 were significantly increased in NSCLC tissues compared with adjacent non-tumor tissues; however, the mRNA expression of MTERF2 was significantly decreased in NSCLC tissues. High mRNA expression levels of MTERF1, 2, 3 and 4 were strongly associated with an improved overall survival rate (OS) in patients with lung adenocarcinoma. Additionally, high mRNA expression levels of MTERF1, 2, 3 and 4 were also strongly associated with an improved OS of patients with NSCLC in the earlier stages of disease (stage I) or patients with negative surgical margins. These results indicate the critical prognostic values of MTERF expression levels in NSCLC. The findings of the present study may be beneficial for understanding the molecular biology mechanism of NSCLC and for generating effective therapeutic approaches for patients with NSCLC.

High WDR34 mRNA expression as a potential prognostic biomarker in patients with breast cancer as determined by integrated bioinformatics analysis

The WD-repeat domain (WDR) family is distributed in the majority of eukaryotes and has several unique biological functions. It serves important roles in signal transduction, cytoskeleton assembly, protein transport, RNA processing, chromatin modification and transcription mechanisms. WD repeat domain 34 (WDR34) has been recently identified as a member of the WDR family. Overexpression of WDR34 was accompanied by the presence of multiple centrioles in the cell, suggesting that it was associated with tumor occurrence. However, its association with breast cancer was unclear. To the best of our knowledge, it has not yet been confirmed whether WDR34 gene expression is associated with breast cancer. Therefore, the current study attempted to clarify this by performing a comprehensive study using multiple datasets in the Oncomine, Breast Cancer Gene-Expression Miner and Kaplan-Meier Plotter databases. The analysis indicated that the mRNA expression levels of WDR34 were increased in breast cancer tissues compared with normal tissues. Consistent with this result, the Broad-Novartis Cancer Cell Line Encyclopedia revealed that WDR34 mRNA expression levels were upregulated in breast cancer cell lines compared with other cancer cells. It was noted that high WDR34 mRNA expression was associated with forkhead box M1 and PTTG1 regulator of sister chromatid separation, securing in co-expression analysis. Expression profile characteristics of WDR34 mRNA were identified in different molecular subtypes of breast cancer. Furthermore, survival analysis revealed that increased expression levels of WDR34 mRNA were associated with poor overall survival in patients with breast cancer, particularly in luminal B, lymph node status-positive and estrogen receptor (ER)-negative subgroups. Additionally, Kaplan-Meier curves revealed that high WDR34 mRNA expression was associated with shorter relapse-free survival in patients with breast cancer, particularly in ER-positive, human epidermal growth factor receptor 2-negative and progesterone receptor-positive subgroups. These results suggested that WDR34 may be used as a prognosis predictor in breast cancer and may provide a novel target for the diagnosis and treatment of breast cancer.

Prognostic value of ephrin B receptors in breast cancer: An online survival analysis using the microarray data of 3,554 patients

The roles of Ephrin B (EphB) receptors in cancer are relatively unknown as these receptors are associated with complex signaling pathways. A limited number of studies have investigated the association between EphB receptors and prognosis. Using the Kaplan-Meier plotter database, the present study investigated the associations between the mRNA expression levels of five EphB receptors and the outcomes of 3,554 patients with breast cancer who had been followed-up for 20 years. Hazard ratios (HR) and 95% confidence intervals (CI) were calculated to assess the relative risk of survival. The results demonstrated that high mRNA expression levels of EphB2 (HR, 0.74; 95% CI, 0.66-0.84; P=2.1×10-6), EphB4 (HR, 0.82; 95% CI, 0.72-0.93; P=0.0023) and EphB6 (HR, 0.69; 95% CI, 0.61-0.78; P=3×10-9) were significantly associated with improved survival, while a high mRNA expression level of EphB3 (HR, 1.14; 95% CI, 1.01-1.28; P=0.029) was associated with worse survival for patients with breast cancer. High expression levels of all EphB receptors, including EphB1 (HR, 1.4; 95% CI, 1.02-1.94; P=0.039), EphB2 (HR, 1.34; 95% CI, 1.07-1.67; P=0.011), EphB3 (HR, 1.39; 95% CI, 1.11-1.73, P=0.0038), EphB4 (HR, 1.33; 95% CI, 1.06-1.67; P=0.013) and EphB6 (HR, 1.32; 95% CI, 1.05-1.65; P=0.016), were associated with an increased risk of mortality in patients with lymph-node-positive breast cancer. High mRNA expression levels of EphB1 were not associated with survival for all patients with breast cancer (HR, 0.85; 95% CI, 0.72-1.01; P=0.058). The results of the present suggested that EphB receptors may be useful as prognostic biomarkers of breast cancer.

Prognostic value of the mRNA expression of members of the HSP90 family in non-small cell lung cancer

The aim of the present study was to investigate the potential prognostic value of members of the heat shock protein (HSP)90 family in non-small cell lung cancer (NSCLC) patients. The mRNA expression profiles of 1,926 NSCLC patients, which was available from the Kaplan-Meier plotter database, were included in the study. High expression of HSP90AA1 mRNA was significantly associated with a poorer rate of overall survival (OS) for all NSCLC patients [hazard ratio (HR), 1.21; 95% confidence interval (CI): 1.06–1.37; P=0.004], as well as for patients with adenocarcinoma (ADE; HR, 1.3; 95% CI: 1.02–1.65; P=0.034), but no significant correlation was identified for squamous cell carcinoma (SCC) patients (HR, 1.08; 95% CI: 0.85–1.38; P=0.51). High expression of HSP90AB1 and HSP90B1 mRNA was significantly associated with poorer rates of OS in lung SCC and ADE patients combined, as well as in lung ADE patients alone. By contrast, high expression of tumor necrosis factor receptor-associated protein 1 (TRAP1) mRNA was significantly associated with improved OS rates in all NSCLC patients combined (HR, 0.88; 95% CI: 0.77–0.99; P=0.041), as well as ADE patients. In stratified survival analysis, a high expression of HSP90AA1, HSP90AB1 and HSP90B1 predicted poor prognosis in stage I NSLCC patients, suggesting that these genes may serve as stage-independent prognostic indicators. As an elevated expression of HSP90AA1, HSP90AB1, HSP90B1 and TRAP1 was associated with poorer OS outcomes in patients with NSCLC, these HSP90 members may be potential prognostic biomarkers and drug targets for the treatment of NSCLC.

Prognosis Analysis of Histone Deacetylases mRNA Expression in Ovarian Cancer Patients

Histone deacetylases modulate the dynamic balance of histone acetylation and deacetylation in cells, which participate in epigenetic regulations. Accumulated evidence has demonstrated that histone deacetylases are associated with angiogenesis, cell proliferation and survival in a variety of human cancers. However, the expression and distinct prognostic value of histone deacetylases in ovarian cancer have not been well elucidated. In the present study, we collected the overall survival (OS), progress free survival (PFS), and histone deacetylases (HDAC1-11) mRNA expression in ovarian cancer from the Kaplan-Meier plotter online database. We investigated the relationship between histone deacetylases mRNA level and the clinicopathological parameters of the ovarian cancer patients, such as histology subtypes, clinical stages, grades and TP53 mutation. Our analysis data showed that over-expression of HDAC1, HDAC2, HDAC4, HDAC5 and HDAC11 were correlated to poor overall survival and unfavorable progress free survival in all ovarian cancer patients. Notably, the higher level of HDAC11 was associated with the worse OS and PFS for serous/ stage III+IV/ grade III/ TP53 mutation ovarian cancer patients. In conclusion, HDACs may play a crucial role in the prognosis of ovarian cancer, but it is worth noting that HDAC11 may be a biomarker for poor prognosis in ovarian cancer patients.

Prognostic role of miR-760 in hepatocellular carcinoma

Previous studies have demonstrated that microRNA (miR)-760 serves an important role in various cancer types. However, to the best of our knowledge, its role in hepatocellular carcinoma (HCC) has not been fully elucidated. The current study investigated the prognostic role of miR-760 in HCC by using the Kaplan-Meier plotter database. The current data indicated that low expression of miR-760 was associated with higher overall survival (OS) for all patients with HCC from both the RNA-seq [hazard ratio (HR)=2.04; 95% confidence interval (CI)=1.44–2.89; P=4.9×10⁻⁵] and the non-commercial spotted microarray (HR=1.71; CI=1.05–2.76; P=0.028). In the RNA-seq platform, a lower expression of miR-760 was strongly associated with improved OS in male patients with HCC, but not in female patients with HCC. Additionally, low expression of miR-760 was associated with improved OS in patients with stage I, II and III HCC, and was associated with improved OS in Asian and Caucasian patients. The current results indicated that miR-760 serves as an oncogene for HCC and high expression of miR-760 is significantly associated with tumor progression and poor prognosis in patients with HCC.

The prognostic values of the peroxiredoxins family in ovarian cancer

Purpose: Peroxiredoxins (PRDXs) are a family of antioxidant enzymes with six identified mammalian isoforms (PRDX1–6). PRDX expression is up-regulated in various types of solid tumors; however, individual PRDX expression, and its impact on prognostic value in ovarian cancer patients, remains unclear.

Methods: PRDXs family protein expression profiles in normal ovarian tissues and ovarian cancer tissues were examined using the Human Protein Atlas database. Then, the prognostic roles of PRDX family members in several sets of clinical data (histology, pathological grades, clinical stages, and applied chemotherapy) in ovarian cancer patients were investigated using the Kaplan–Meier plotter.

Results: PRDXs family protein expression in ovarian cancer tissues was elevated compared with normal ovarian tissues. Meanwhile, elevated expression of PRDX3, PRDX5, and PRDX6 mRNAs showed poorer overall survival (OS); PRDX5 and PRDX6 also predicted poor progression-free survival (PFS) for ovarian cancer patients. Furthermore, PRDX3 played significant prognostic roles, particularly in poor differentiation and late-stage serous ovarian cancer patients. Additionally, PRDX5 predicted a lower PFS in all ovarian cancer patients treated with Platin, Taxol, and Taxol+Platin chemotherapy. PRDX3 and PRDX6 also showed poor PFS in patients treated with Platin chemotherapy. Furthermore, PRDX3 and PRDX5 indicated lower OS in patients treated with these three chemotherapeutic agents. PRDX6 predicted a poorer OS in patients treated with Taxol and Taxol+Platin chemotherapy.

Conclusion: These results suggest that there are distinct prognostic values of PRDX family members in patients with ovarian cancer, and that the expression of PRDX3, PRDX5, and PRDX6 mRNAs are a useful prognostic indicator in the effect of chemotherapy in ovarian cancer patients.

Identification of endothelial selectin as a potential prognostic marker in breast cancer

Endothelial selectin (ELAM1 or CD62E) has been previously reported as being associated with the prognosis of multiple types of cancer. However, its prognostic value in breast cancer (BC) remains unclear. The aim of the present study was to investigate the prognostic value of ELAM1 mRNA expression in BC tissue. The prognostic value of ELAM1 mRNA was assessed in patients with BC using the Kaplan-Meier plotter (KM-plot) database. The KM-plot generated updated ELAM1 mRNA expression data and survival analysis from a total of 3,951 patients with BC, gathered from 35 datasets. Low expression of ELAM1 mRNA was correlated with a poorer overall survival in 1,402 patients with BC followed for 20 years [hazard ratio (HR), 0.71; 95% confidence interval (CI), 0.57–0.88; log-rank P=0.0016]. Low expression of ELAM1 was also correlated with poorer relapse-free survival (HR, 0.69; 95% CI, 0.62–0.77; log-rank P=2.2e-11) in 3,951 patients and poorer distant metastasis-free survival (HR, 0.79; 95% CI, 0.65–0.96; log-rank P=0.02) in 1,746 patients with BC followed for 20 years. Results from the Metabolic gEne RApid visualizer database indicated that ELAM1 mRNA expression was elevated in normal tissue. The results of the present study suggest that ELAM1 mRNA is a potential prognostic and metastatic marker in patients with BC.

Prognostic values of the mRNA expression of natural killer receptor ligands and their association with clinicopathological features in breast cancer patients

BACKGROUND

Natural killer (NK) cells are lymphocytes of the innate immune system that have potent cytotoxic activity against tumor cells. NK cell recognition and activity towards cancer cells are regulated by an integrated interplay between numerous inhibitory and activating receptors acting in concert to eliminate tumor cells expressing cognate ligands. Despite strong evidence supporting the role of NK cells in breast cancer (BC) control, BC still develops and progresses to form large tumors and metastases. A major mechanism of BC escape from NK immunity is the alteration of the expression of NK receptor ligands. The aim of this study was to determine whether NK receptor ligands' mRNA expression might influence prognosis in BC patients and whether these effects differ by molecular subtypes and clinicopathological features.

METHODS

We used the KM plotter platform to analyze the correlation between mRNA expression of 32 NK receptor ligands and relapse-free survival (RFS) and overall survival (OS) in 3951 and 1402 BC patients, respectively. The association with tumor subtypes and clinicopathological features was determined. BC samples were split into high and low expression groups according to the best cutoff value and the two patient cohorts were compared by Kaplan-Meier survival plots. The hazard ratios with 95% confidence intervals and log rank P values were calculated and FDR-adjusted for multiple testing correction. The data was considered to be statistically significant when FDR-adjusted P value < 0.05.

RESULTS

High mRNA expression of around 80% of ligands for NK activating and inhibitory receptors associated with better RFS, which correlated with longer OS for only about half of the NK-activating ligands but for most NK-inhibitory ligands. Also, five NK-activating ligands correlated with worse prognosis. These prognostic values were differentially associated with the BC clinical criteria. In addition, the favorable prognostic influence of NK-activating ligands' upregulation, as a whole, was mainly significantly associated with HER2-positive and basal-like subtypes, lymph node positive phenotype, and high-grade tumors.

CONCLUSIONS

NK receptor ligands appear to play an important role in defining BC patient prognosis. Identification of a group of patients with worse prognosis expressing high levels of NK-activating ligands and low levels of NK-inhibitory ligands makes them ideal potential candidates for NK-based immunotherapy to eliminate residual tumor cells, prevent relapse and improve patient survival.

Expression patterns of E2F transcription factors and their potential prognostic roles in breast cancer

E2Fs, as a family of pivotal transcription factors, have been implicated in multiple biological functions in human cancer; however, the expression and prognostic significance of E2Fs in breast cancer remains unknown. In the present study, the mRNA expression patterns of E2Fs in breast cancer were investigated with Oncomine and The Cancer Genome Atlas data. Prognostic values of E2Fs for patients with breast cancer were determined using the Kaplan-Meier plotter database. The results strongly indicated that E2F1, E2F2, E2F3, E2F5, E2F7 and E2F8 were overexpressed in patients with breast cancer, whereas E2F4 and E2F6 exhibited no expression difference between patients with cancer and healthy controls. In survival analyses, elevated E2F1, E2F3, E2F5, E2F7 and E2F8 expression levels were significantly associated with lower overall survival, relapse-free survival (RFS), distant metastasis-free survival (DMFS) or post-progression survival for patients with breast cancer. Furthermore, high expression of E2F4 indicated improved RFS but reduced DMFS. Subgroup analyses based on four clinicopathological factors further revealed that E2Fs were associated with the prognosis of patients with breast cancer in an estrogen receptor-, progesterone receptor-, human epidermal growth factor 2- and lymph node status-specific manner. These data indicated that E2Fs may serve as promising biomarkers and therapeutic targets for breast cancer.

The transcription levels and prognostic values of seven proteasome alpha subunits in human cancers

Proteasome alpha subunits (PSMAs) have been shown to participate in the malignant progression of human cancers. However, the expression patterns and prognostic values of individual PSMAs remain elusive in most cancers. In the present study, we investigated the mRNA expression levels of seven PSMAs in different kinds of cancers using Oncomine and The Cancer Genome Atlas (TCGA) databases. The prognostic significance of PSMAs was also determined by Kaplan-Meier Plotter and PrognScan databases. Combined with Oncomine and TCGA, the mRNA expression levels of PSMA1-7 were significantly upregulated in breast, lung, gastric, bladder and head and neck cancer compared with normal tissues. Moreover, only PSMA6 and PSMA5 were not overexpressed in colorectal and kidney cancer, respectively. In survival analyses based on Kaplan-Meier Plotter, PSMA1-7 showed significant prognostic values in breast, lung and gastric cancer. Furthermore, potential correlations between PSMAs and survival outcomes were also observed in ovarian cancer, colorectal cancer and melanoma by Kaplan-Meier Plotter and PrognScan. These data indicated that PSMAs might serve as novel biomarkers and potential therapeutic targets for multiple human cancers. However, further studies are needed to explore the detailed biological functions and molecular mechanisms involved in tumor progression.

Prognostic value of alcohol dehydrogenase mRNA expression in gastric cancer

Previous studies have reported that alcohol dehydrogenase (ADH) isoenzymes possess diagnostic value in gastric cancer (GC). However, the prognostic value of ADH isoenzymes in GC remains unclear. The aim of the present study was to identify the prognostic value of ADH genes in patients with GC. The prognostic value of ADH genes was investigated in patients with GC using the Kaplan-Meier plotter tool. Kaplan-Meier plots were used to assess the difference between groups of patients with GC with different prognoses. Hazard ratios (HR) and 95% confidence intervals (CI) were used to assess the relative risk of GC survival. Overall, 593 patients with GC and 7 ADH genes were included in the survival analysis. High expression of ADH 1A (class 1), α polypeptide (ADH1A; log-rank P=0.043; HR=0.79; 95% CI: 0.64–0.99), ADH 1B (class 1), β polypeptide (ADH1B; log-rank P=1.9×10⁻⁰⁵; HR=0.65; 95% CI: 0.53–0.79) and ADH 5 (class III), χ polypeptide (ADH5; log-rank P=0.0011; HR=0.73; 95% CI: 0.6–0.88) resulted in a significantly decreased risk of mortality in all patients with GC compared with patients with low expression of those genes. Furthermore, protective effects may additionally be observed in patients with intestinal-type GC with high expression of ADH1B (log-rank P=0.031; HR=0.64; 95% CI: 0.43–0.96) and patients with diffuse-type GC with high expression of ADH1A (log-rank P=0.014; HR=0.51; 95% CI: 0.3–0.88), ADH1B (log-rank P=0.04; HR=0.53; 95% CI: 0.29–0.98), ADH 4 (class II), π polypeptide (log-rank P=0.033; HR=0.58; 95% CI: 0.35–0.96) and ADH 6 (class V) (log-rank P=0.037; HR=0.59; 95% CI: 0.35–0.97) resulting in a significantly decreased risk of mortality compared with patients with low expression of those genes. In contrast, patients with diffuse-type GC with high expression of ADH5 (log-rank P=0.044; HR=1.66; 95% CI: 1.01–2.74) were significantly correlated with a poor prognosis. The results of the present study suggest that ADH1A and ADH1B may be potential prognostic biomarkers of GC, whereas the prognostic value of other ADH genes requires further investigation.

Decreased expression of ALDH5A1 predicts prognosis in patients with ovarian cancer

Aldehyde dehydrogenase 5 family, member A1 (ALDH5A1) belongs to the superfamily of aldehyde dehydrogenases (ALDHs). However, the prognostic value of ALDH5A1 in ovarian cancer remains unclear. The aim of this study was to explore the relationship between ALDH5A1 and the prognosis of patients with ovarian cancer (OC). We compared the expression of ALDH5A1 in OC to that innormal controls, using GSE40595 profiling data. Tissue microarray analysis was conducted for192 OC patients, 14 adjacent normal ovary tissues, and 2 normal ovary tissues. Using the "Kaplan-Meier plotter" (KM plotter) database, updated gene expression data and survival information of a total of 1583 OC patients were used to evaluate the prognostic value of ALDH5A1 in OC patients. We found that ALDH5A1 mRNA expression was downregulated in OC patients compared with that innormal tissues. In survival analyses, we found that ALDH5A1 was positively linked to prognosis in patients with OC, particularly in those with serous ovarian cancer (SOC). In addition, high Ctranscription activity of ALDH5A1 was correlated with better overall survival in SOC patients expressing mutatedTP53, but not in those expressing wild-type TP53. In pathological grades II/III, a high mRNA level of ALDH5A1 was associated with improved overall survival. The positive association between ALDH5A1 and prognosis was found not only in early stages(I and II), but also in advanced stages (III and IV) of SOC patients. results indicate that ALDH5A1 is an excellent predictive factor of OC and may play crucial roles in OC progression.