Overexpression of E2F mRNAs associated with gastric cancer progression identified by the transcription factor and miRNA co-regulatory network analysis

FASTKD1 as a diagnostic and prognostic biomarker for STAD: Insights into m6A modification and immune infiltration

Fas-activated serine/threonine kinase domain 1 (FASTKD1), a known modulator of mitochondrial-mediated cell death and survival processes, has garnered attention for its potential role in various biological contexts. However, its involvement in gastric cancer remains unclear. Thus, the present study aimed to investigate the relationship between FASTKD1 expression and key factors, including clinicopathological characteristics, immune infiltration and m6A modification in stomach adenocarcinoma (STAD). The expression of FASTKD1 was analyzed in STAD and normal adjacent tissues to assess its association with clinicopathological characteristics and survival prognosis. Data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were used in this study. Additionally, the findings were validated through immunohistochemical staining. Co-expression analysis of FASTKD1 was performed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (GO/KEGG) enrichment analysis, Gene Set Enrichment Analysis (GSEA) and LinkedOmics database analysis. An in-depth analysis was conducted using databases, such as Tumor Immune Estimation Resource (TIMER), Gene Expression Profiling Interactive Analysis (GEPIA), GEO and TCGA to explore the potential correlation between FASTKD1 expression and immune infiltration and m6A modification in STAD. The results revealed that FASTKD1 was significantly upregulated across different tumor types, including STAD. Notably, FASTKD1 was able to distinguish between tumor and normal tissue samples with accuracy. Furthermore, the expression levels of FASTKD1 were significantly associated with clinical stage and survival. Through GO/KEGG enrichment analysis and GSEA, it was revealed that the genes co-expressed with FASTKD1 were active in a variety of biological processes. Within the TIMER, GEPIA and TCGA databases, a notable inverse correlation was observed between FASTKD1 expression and the abundance of immune cell subsets. Notably, significant correlations were established between FASTKD1 and m6A modification genes, YTHDF1 and LRPPRC, in both TCGA and GEO datasets. In conclusion, FASTKD1 may serve a significant role in m6A modification and immune infiltration processes, making it a potentially valuable diagnostic and prognostic biomarker in STAD.

Aspartame carcinogenic potential revealed through network toxicology and molecular docking insights

The research employed network toxicology and molecular docking techniques to systematically examine the potential carcinogenic effects and mechanisms of aspartame (L-α-aspartyl-L-phenylalanine methyl ester). Aspartame, a commonly used synthetic sweetener, is widely applied in foods and beverages globally. In recent years, its safety issues, particularly the potential carcinogenic risk, have garnered widespread attention. The study first constructed an interaction network map of aspartame with gastric cancer targets using network toxicology methods and identified key targets and pathways. Preliminary validation was conducted through microarray data analysis and survival analysis, and molecular docking techniques were employed to further examine the binding affinity and modes of action of aspartame with key proteins. The findings suggest that aspartame has the potential to impact various cancer-related proteins, potentially raising the likelihood of cellular carcinogenesis by interfering with biomolecular function. Furthermore, the study found that the action patterns and pathways of aspartame-related targets are like the mechanisms of known carcinogenic pathways, further supporting the scientific hypothesis of its potential carcinogenicity. However, given the complexity of the in vivo environment, we also emphasize the necessity of validating these molecular-level findings in actual biological systems. The study introduces a fresh scientific method for evaluating the safety of food enhancers and provides a theoretical foundation for shaping public health regulations.

PPARδ dysregulation of CCL20/CCR6 axis promotes gastric adenocarcinoma carcinogenesis by remodeling gastric tumor microenvironment

BACKGROUND

Peroxisome proliferator-activated receptor delta (PPARδ) promotes inflammation and carcinogenesis in many organs, but the underlying mechanisms remains elusive. In stomachs, PPARδ significantly increases chemokine Ccl20 expression in gastric epithelial cells while inducing gastric adenocarcinoma (GAC). CCR6 is the sole receptor of CCL20. Here, we examine the role of PPARδ-mediated Ccl20/Ccr6 signaling in GAC carcinogenesis and investigate the underlying mechanisms.

METHODS

The effects of PPARδ inhibition by its specific antagonist GSK3787 on GAC were examined in the mice with villin-promoter-driven PPARδ overexpression (PpardTG). RNAscope Duplex Assays were used to measure Ccl20 and Ccr6 levels in stomachs and spleens. Subsets of stomach-infiltrating immune cells were measured via flow cytometry or immunostaining in PpardTG mice fed GSK3787 or control diet. A panel of 13 optimized proinflammatory chemokines in mouse sera were quantified by an enzyme-linked immunosorbent assay.

RESULTS

GSK3787 significantly suppressed GAC carcinogenesis in PpardTG mice. PPARδ increased Ccl20 level to chemoattract Ccr6+ immunosuppressive cells, including tumor-associated macrophages, myeloid-derived suppressor cells and T regulatory cells, but decreased CD8+ T cells in gastric tissues. GSK3787 suppressed PPARδ-induced gastric immunosuppression by inhibiting Ccl20/Ccr6 axis. Furthermore, Ccl20 protein levels increased in sera of PpardTG mice starting at the age preceding gastric tumor development and further increased with GAC progression as the mice aged. GSK3787 decreased the PPARδ-upregulated Ccl20 levels in sera of the mice.

CONCLUSIONS

PPARδ dysregulation of Ccl20/Ccr6 axis promotes GAC carcinogenesis by remodeling gastric tumor microenvironment. CCL20 might be a potential biomarker for the early detection and progression of GAC.

Bufalin targeting BFAR inhibits the occurrence and metastasis of gastric cancer through PI3K/AKT/mTOR signal pathway

Gastric cancer (GC) is the most common malignant tumor of digestive system. Bufalin extracted from Venenum Bufonis is one of the most effective anticancer monomers, which has been proved to play anticancer roles in a variety of cancers such as ovarian cancer, prostate cancer and neuroblastoma. However, there are few studies on bufalin in GC, and lack of clear targets. The effect of bufalin on the proliferation and migration of GC cells was detected by CCK-8, scratch wound healing assay, transwell assay and Western blotting. The potential direct interaction proteins of bufalin were screened by human proteome microarray containing 21,838 human proteins. The target protein was determined by bioinformatics, and the binding sites were predicted by molecular docking technique. Biological experiments in vitro and in vivo were conducted to verify the effect of bufalin directly interaction protein and the mechanism of bufalin targeting the protein to inhibit the development of GC. The results showed that bufalin inhibited the proliferation and migration of MKN-45 and HGC-27 GC cell lines in vitro. BFAR, a direct interaction protein of bufalin has several potential binding sites to bufalin. BFAR is highly expressed in GC and promotes the occurrence and metastasis of GC by activating PI3K/AKT/mTOR signal pathway in vitro and in vivo. Bufalin reversed the promoting effect of BFAR on the carcinogenesis and metastasis of GC by down-regulating the expression of BFAR. Our results show that bufalin targeting BFAR inhibits the occurrence and metastasis of GC through PI3K/AKT/mTOR signal pathway. These results provide a new basis for bufalin as a promising drug for the treatment of GC.

The Comprehensive Analysis of N6-Methyadenosine Writer METTL3 and METTL14 in Gastric Cancer

Methyltransferase-like 3 (METTL3) and methyltransferase-like 14 (METTL14) were two core components of the N6-methyadenosine (m6A) methyltransferase complex (MTC) and played a basic role in maintaining an appropriate m6A level of target genes. In gastric cancer (GC), previous researches on the expression and role of METTL3 and METTL14 were not consistent, and their specific function and mechanism have remained elusive. In this study, the expression of METTL3 and METTL14 was evaluated based on the TCGA database, 9 paired GEO datasets, and our 33 GC patient samples, and METTL3 was highly expressed and acted as a poor prognostic factor, whereas METTL14 showed no significant difference. Moreover, GO and GSEA analyses were performed, and the results pointed out that METTL3 and METTL14 were jointly involved in multiple biological processes, while they could also take part in different oncogenic pathways independently. And BCLAF1 was predicted and identified as a novel shared target of METTL3 and METTL14 in GC. In total, we conducted a comprehensive analysis of METTL3 and METTL14 in GC including their expression, function, and role, which could provide a novel insight into the research of m6A modification in GC.

High DAPK1 Expression Promotes Tumor Metastasis of Gastric Cancer

Gastric cancer (GC) is a common upper gastrointestinal tumor. Death-associated protein kinase (DAPK1) was found to participate in the development of various malignant tumors. However, there are few reports on DAPK1 in gastric cancer. In this study, the TCGA and GEO datasets were used to explore the expression and role of DAPK1 in gastric cancer. The functions of DAPK1 in gastric cancer were determined by proliferation, migration and invasion assays. In addition, genes co-expressed with DAPK1 in gastric cancer were estimated through the WGCNA and correlation analysis. A DAPK1-related gene prognostic model was constructed using the Cox regression and lasso analyses. The expression of DAPK1 was significantly up-regulated in gastric cancer tissues. Kaplan-Meier analysis showed that low expression of DAPK1 was a favorable prognostic factor of overall survival and disease-free survival for gastric cancer patients. Functional experiments demonstrated that DAPK1 can promote the migration and invasion of gastric cancer cells. WGCNA, correlation analysis, Cox regression, and lasso analyses were applied to construct the DAPK1-related prognostic model. The prognostic value of this prognostic model of DAPK1-related genes was further successfully validated in an independent database. Our results indicated that DAPK1 can promote gastric cancer cell migration and invasion and established four DAPK1-related signature genes for gastric cancer that could independently predict the survival of GC patients.

Association of the TGFβ gene family with microenvironmental features of gastric cancer and prediction of response to immunotherapy

In the complex tumor microenvironment, TGFβ is a pleiotropic cytokine involved in regulating cellular processes such as cancer cell proliferation, apoptosis and metastasis. TGFβ defines three subtypes (TGFβ1, TGFβ2, and TGFβ3), of which TGFβ is highly expressed in many cancers, especially those showing high dissemination potential. In addition, increased expression of TGFβ in multiple cancers is usually positively correlated with epithelial mesenchymal transition (EMT) and coordinated with the expression of genes driving EMT-related genes. TGFβ signaling in the tumor microenvironment inhibits the antitumor function of multiple immune cell populations, including T cells and natural killer cells, and the resulting immunosuppression severely limits the efficacy of immune checkpoint inhibitors and other immunotherapeutic approaches. As a major pathway to enhance the efficacy of cancer immunotherapy effects, the role of TGFβ signaling inhibitors have been evaluated in many clinical trials. However, the potential functions and mechanisms of TGFβ1, TGFβ2 and TGFβ3 in gastric cancer progression and tumor immunology are unclear. In this study, we comprehensively analyzed TGFβ1, TGFβ2 and TGFβ3 and gastric cancer microenvironmental features, including immune cell infiltration, EMT, hypoxia, mutation, immunotherapy and drug treatment, based on HMUCH sequencing data (GSE184336) and public databases. We also validated the protein expression levels of TGFβ in gastric cancer tissues as well as the role of TGFβ factor in cytology experiments. This report reveals the important role of the TGFβ gene family in gastric cancer and provides possible relationships and potential mechanisms of TGFβ in gastric cancer.

E2F4 transcription factor is a prognostic biomarker related to immune infiltration of head and neck squamous cell carcinoma

To investigate the relationship between the transcription factor, E2F4, and head and neck squamous cell carcinoma (HNSCC), and to preliminarily explore the signaling pathways and immunological role of E2F4. The mRNA expression of E2F4 in HNSCC was evaluated by searching Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets. E2F4 protein expression was analyzed by immunohistochemistry using the CMU1h-ENT database. The association between E2F4 expression and tumor infiltration of immune cells was analyzed. Intracellular signaling by E2F4 was explored using KEGG and GO analysis. The correlation of E2F4 expression with clinical characteristics and its prognostic role were validated and analyzed in TCGA database. From the analysis of GEO and TCGA data, E2F4 expression was found to be up-regulated in HNSCC tumor tissues, and its level was associated with T, Grade, and M staging. Kaplan–Meier curve and Cox analyses indicated that the high expression of E2F4 was related to a poor prognosis. Thus, E2F4 was considered a potential prognostic factor for HNSCC. Immunohistochemical staining showed that E2F4 was mainly localized in the cell nucleus; it was highly expressed in HNSCC tissues, with a significant difference noted from that in pericancerous mucosa tissues. A correlation was observed between the differential expression of E2F4 and the immune infiltration of HNSCC. As revealed by KEGG and GO analysis, differential enrichment was found in the cell cycle, spliceosome, meiosis, microbial polysaccharide synthesis, and WNT signaling pathway, as well as in cyclic adenosine monophosphate, ERBB2, VEGF, GCNP and MYC pathways. E2F4 plays an important role in tumor progression and may be a critical biological prognostic factor for HNSCC. In addition, it functions in the nucleus as a transcription factor, regulates immune cells, and could be a promising molecular target for the diagnosis and treatment of HNSCC.

TGFβ2 is a Prognostic Biomarker for Gastric Cancer and is Associated With Methylation and Immunotherapy Responses

TGFβ signaling plays a key role in cancer progression and by shaping tumor architecture and inhibiting the anti-tumor activity of immune cells. It was reported that high expression of TGFβ can promote the invasion and metastasis of cancer cells in a variety of tumors. However, there are few studies on TGFβ2 and its methylation in gastric cancer. We analyzed the Harbin Medical University Cancer Hospital (HMUCH) sequencing data and used public data to explore the potential function and prognostic value of TGFβ2 and its methylation in gastric cancer. In this study, we used the ssGSEA algorithm to quantify 23 methylation sites related to TGFβ2. Survival analysis showed that high expression of TGFβ2 and hypomethylation levels of TGFβ2 were negative factors in the prognosis of gastric cancer. Functional enrichment analysis of methylation revealed that methylation of different TGFβ2 methylation scores was mainly involved in energy metabolism, extracellular matrix formation and cell cycle regulation. In the gastric cancer microenvironment TGFβ2 was associated with high levels of multiple immune cell infiltration and cytokine expression, and high TGFβ2 expression was significantly and positively correlated with stemness markers, stromalscore and EMT. Gene set enrichment analysis also revealed an important role of TGFβ2 in promoting EMT. In addition, we discussed the relationship between TGFβ2 and immunotherapy. The expression of PD-1, PD-L1 and CTLA-4 was elevated in the TGFβ2 high expression group. Also when TGFβ2 was highly expressed, the responsiveness of immune checkpoint blockade (ICB) was significantly enhanced. This indicates that TGFβ2 may become an indicator for predicting the efficacy of immunosuppressive agents and a potential target for immunotherapy.

High Level of Staufen1 Expression Confers Longer Recurrence Free Survival to Non-Small Cell Lung Cancer Patients by Promoting THBS1 mRNA Degradation

Stau1 is a pluripotent RNA-binding protein that is responsible for the post-transcriptional regulation of a multitude of transcripts. Here, we observed that lung cancer patients with a high Stau1 expression have a longer recurrence free survival. Strikingly, Stau1 did not impair cell proliferation in vitro, but rather cell migration and cell adhesion. In vivo, Stau1 depletion favored tumor progression and metastases development. In addition, Stau1 depletion strongly impaired vessel maturation. Among a panel of candidate genes, we specifically identified the mRNA encoding the cell adhesion molecule Thrombospondin 1 (THBS1) as a new target for Staufen-mediated mRNA decay. Altogether, our results suggest that regulation of THBS1 expression by Stau1 may be a key process involved in lung cancer progression.

GPR116 overexpression correlates with poor prognosis in gastric cancer

ABSTRACT

The G protein-coupled receptor 116 (GPR116) is an adhesion subtype of the G protein-coupled receptor family and has been reported to be involved in tumorigenesis and cancer progression. Moreover, it has been shown to predict poor prognosis in breast and colorectal cancers. However, little is known about the role of GPR116 in gastric cancer (GC). In this study, we aimed to investigate the expression and clinical prognostic significance of GPR116 in GC.The mRNA expression levels of GPR116 in GC were analyzed using Gene Expression Omnibus and UALCAN databases, and GPR116 protein expression in GC tissues was detected using immunohistochemistry. The relationship between GPR116 expression and prognosis in patients with GC was analyzed and further validated using the Kaplan-Meier Plotter database. The correlation between GPR116 and the differentially expressed genes identified was analyzed using the LinkedOmics database. Gene set enrichment analysis was performed using WebGestalt. The results revealed that GPR116 expression was significantly upregulated in GC tissues, which was positively correlated with tumor node metastasis (TNM) staging and tumor invasion. Prognostic analysis suggested that high GPR116 expression contributed to poor overall survival in GC patients. Multivariate Cox analysis indicated that GPR116 overexpression was an independent prognostic indicator in patients with GC (HR = 1.855, 95% CI 1.021-3.370, P = .043). Enrichment analysis showed that GPR116 co-expression genes were mainly involved in extracellular matrix-receptor interaction, focal adhesion, cell adhesion, PI3K-Akt signaling, DNA replication, and cell cycle pathways. In conclusion, GPR116 was highly expressed in GC tissues and associated with poor prognosis in patients with GC, Thus GPR116 may be a novel prognostic marker and a potential therapeutic target for GC treatment.

Glucoside xylosyltransferase 2 as a diagnostic and prognostic marker in gastric cancer via comprehensive analysis

To investigate the potential role of GXYLT2 (glucoside xylosyltransferase 2) in gastric cancer (GC), the TCGA (The Cancer Genome Atlas) database and Gene Expression Omnibus (GEO) dataset were used to evaluate GXYLT2 mRNA expression, and the standardized mean difference and diagnostic value were comprehensively assessed. Survival analysis and univariate/multivariate cox regression analysis were performed to evaluate the prognostic value of GXYLT2 in GC patients. The correlation between GXYLT2 and tumor immune cells was identified by using the CIBERSORT algorithm. The results showed that GXYLT2 expression level was significantly increased in GC tissues. GXYLT2 expression was significantly correlated with the grade, stage, and invasion depth of gastric cancer. Overall survival was reduced in the high GXYLT2 expression group. Univariate and multivariate Cox regression analyses showed that GXYLT2 was a reliable prognostic factor. GSEA showed that GXYLT2 might participate in the development of GC through tumor-related pathways. The expression of GXYLT2 was positively correlated with 5 tumor-infiltrating immune cells (resting dendritic cells, m2 macrophages, monocytes, active NK cells and resting mast cells), and was negatively correlated with 6 tumor-infiltrating immune cells (plasma cells, activated memory CD4 T cells, resting NK cells, activated dendritic cells, and activated neutrophils and mast cells). Through cell experiment verification, GXYLT2 expression level in gastric cancer cells was found to be high, which verified the results from the bioinformatics analysis. Furthermore, immunohistochemical staining results also showed that GC tissues had positive GXYLT2 expression. In summary, GXYLT2 might be a potential diagnostic and prognostic biomarker for gastric cancer.

Effects and prognostic values of miR-30c-5p target genes in gastric cancer via a comprehensive analysis using bioinformatics

Gastric cancer (GC) is a common cancer and the leading cause of cancer-related death worldwide. To improve the diagnosis and treatment of GC, it is necessary to identify new biomarkers by investigating the cellular and molecular mechanisms. In this study, miR-30c-5p expression was significantly down-regulated in GC tissues by comprehensive analysis using multiple databases. The target genes of miR-30c-5p with up-regulated expression level in GC were identified, including ADAM12 (a disintegrin and metalloproteinase12), EDNRA (the Endothelin receptor type A), STC1 (stanniocalcin 1), and CPNE8 (the calcium-dependent protein, copine 8). The expression level of ADAM12 was significantly related to depth of invasion (p = 0.036) in GC patients. The expression level of EDNRA was significantly related to grade (P = 0.003), depth of invasion (P = 0.019), and lymphatic metastasis (P = 0.001). The expression level of CPNE8 was significantly related to grade (P = 0.043) and TNM stage (P = 0.027).Gene set enrichment analysis showed that they might participate in GC progression through cancer-related pathways. CIBERSORT algorithm analysis showed that their expressions were related to a variety of tumor-infiltrating immune cells. The higher expression of those target genes might be the independent risk factor for poor survival of GC patients, and they might be potential prognostic markers in GC patients.

Comprehensive Analysis of E2F Family Members in Human Gastric Cancer

Gastric cancer (GC) is the second most common cancer and the third most frequent cause of cancer-related deaths in China. E2Fs are a family of transcription factors reported to be involved in the tumor progression of various cancer types; however, the roles of individual E2Fs are still not known exactly in tumor progression of GC. In this study, we examined the expression of E2Fs to investigate their roles in tumor progression in GC patients using multiple databases, including ONCOMINE, GEPIA2, Kaplan-Meier plotter, cBioPortal, Metascape, LinkedOmics, GeneMANIA, STRING and UCSC Xena. We also performed real-time polymerase chain reaction (RT-PCR) to validate the expression levels of individual E2Fs in several GC cell lines. Our results demonstrated that the mRNA levels of E2F1/2/3/5/8 were significantly higher both in GC tissues and cell lines. The expression levels of E2F1 and E2F4 were correlated with poor overall survival (OS), decreased post-progression survival (PPS), and decreased progression-free survival (FP) in patients with GC. However, overexpression of E2F2, E2F5, E2F7 and E2F8 is significantly associated with disease-free survival and overall survival in patients with GC. In addition, higher E2F3 and E2F6 mRNA expression was found to increase GC patients' OS and PPS. 224 of 415 patients with STAD (54%) had gene mutations that were associated with longer disease-free survival (DFS) but not OS. Cell cycle pathway was closely associated with mRNA level of more than half of E2Fs (E2F1/2/3/7/8). There were close and complicated interactions among E2F family members. Finally, our results indicated the gene expressions of E2Fs had a positive relationship with its copy numbers. Taken together, E2F1/2/3/5/8 can serve as biomarkers for GC patients with high prognostic value for OS of GC patients or therapeutic targets for GC.

Knockdown of E2F4 suppresses the growth of ovarian cancer cells through the cell cycle pathway

Ovarian cancer remains one of the major causes of death from gynecologic cancer in developed countries. The E2F family has been shown to have a central role in the control of cell proliferation, differentiation, and cell cycle progression in various types of cancer. Despite advances in cancer research, the carcinogenic role of E2F transcription factor 4 (E2F4) in ovarian cancer remains unclear. In this study, we investigated the underlying molecular mechanism of E2F4 in human ovarian cancer cells (OCC). E2F4 expression was demonstrated by quantitative real time polymerase chain reaction (qRT-PCR) in OCC. The alterations of expression values were determined using 2^(-ΔΔCt) method. The effects of suppressing E2F4 on cell proliferation, migration, and differentiation were evaluated by cell proliferation assay, colony formation assay and wound healing assay in vitro. Overexpression of E2F4 was found at both mRNA and protein levels in OCC. Small interfering RNA was used to suppress E2F4 expression. Depletion of E2F4 inhibited cell proliferation and suppressed the cell migration and colony formation ability compared to controls. The expression of cell cycle machinery including cyclin A, cyclin D and cyclin dependent kinase 2 (CDK2) was increased after E2F4 knockdown. E2F4 modulates ovarian cancer cell proliferation and migration through cell cycle components including cyclin A, cyclin D, and CDK2. Our findings indicate that E2F4 may serve as a valuable candidate and therapeutic target for ovarian cancer treatment in regard to cell cycle control.

The Role and Clinical Implications of the Retinoblastoma (RB)-E2F Pathway in Gastric Cancer

Gastric cancer is the most common malignant tumor in the digestive tract, with very high morbidity and mortality in developing countries. The pathogenesis of gastric cancer is a complex biological process mediated by abnormal regulation of proto-oncogenes and tumor suppressor genes. Although there have been some in-depth studies on gastric cancer at the molecular level, the specific mechanism has not been fully elucidated. RB family proteins (including RB, p130, and p107) are involved in cell cycle regulation, a process that largely depends on members of the E2F gene family that encode transcriptional activators and repressors. In gastric cancer, inactivation of the RB-E2F pathway serves as a core transcriptional mechanism that drives cell cycle progression, and is regulated by cyclins, cyclin-dependent kinases, cyclin-dependent kinase inhibitors, p53, Helicobacter pylori and some other upstream molecules. The E2F proteins are encoded by eight genes (i.e. E2F1 to E2F8), each of which may play a specific role in gastric cancer. Interestingly, a single E2F such as E2F1 can activate or repress transcription, and enhance or inhibit cell proliferation, depending on the cell environment. Thus, the function of the E2F transcription factor family is very complex and needs further exploration. Importantly, the presence of H. pylori in stomach mucosa may affect the RB and p53 tumor suppressor systems, thereby promoting the occurrence of gastric cancer. This review aims to summarize recent research progress on important roles of the complex RB-E2F signaling network in the development and effective treatment of gastric cancer.

The Staufen1-dependent cell cycle regulon or how a misregulated RNA-binding protein leads to cancer

In recent years, an increasing number of reports have linked the RNA-binding protein Staufen1 (STAU1) to the control of cell decision making. In non-transformed cells, STAU1 balances the expression of messenger RNA (mRNA) regulons that regulate differentiation and well-ordered cell division. Misregulation of STAU1 expression and/or functions changes the fragile balance in the expression of pro- and anti-proliferative and apoptotic genes and favours a novel equilibrium that supports cell proliferation and cancer development. The misregulation of STAU1 functions causes multiple coordinated modest effects in the post-transcriptional regulation of many RNA targets that code for cell cycle regulators, leading to dramatic consequences at the cellular level. The new tumorigenic equilibrium in STAU1-mediated gene regulation observed in cancer cells can be further altered by a slight increase in STAU1 expression that favours expression of pro-apoptotic genes and cell death. The STAU1-dependent cell cycle regulon is a good model to study how abnormal expression of an RNA-binding protein promotes cell growth and provides an advantageous selection of malignant cells in the first step of cancer development.

Gastric cancer-associated microRNA expression signatures: integrated bioinformatics analysis, validation, and clinical significance

Background

Gastric cancer (GC) is one of the common gastrointestinal malignancy worldwide and exhibits a poor prognosis. Increasing studies have indicated that microRNAs play critical roles in the cancer progression and have shown great potential as useful biomarkers. The search for potential diagnostic and prognostic biomarkers of gastric cancer (GC) with integrated bioinformatics analyses has been undertaken in previous studies.

Methods

In this study, the robust rank aggregation (RRA) method was used to perform an integrated analysis of differentially expressed miRNAs (DEMs) from five microarray datasets in the Gene Expression Omnibus (GEO) database to find robust biomarkers for GC. Ultimately, seven miRNAs were filtered from fourteen primary miRNAs using the validation set of The Cancer Genome Atlas (TCGA) database. Based on these results, diagnostic and survival analyses were performed, and logistic regression and Cox regression were used to determine the clinicopathological characteristics of the DEM expression and overall survival.

Results

Nine eligible miRNA datasets related to GC were selected from the GEO database for integrated analysis in this study. Diagnostic analysis implied that these miRNAs could be regarded as promising candidate diagnostic biomarkers in GC tissues, but whether the results of the tissue analysis are consistent with those of peripheral blood analysis requires further validation. The logistic regression indicated that the ectopic expression of these DEMs was relevant to the histological type, anatomical region, and pathological grade of GC. However, the survival and Cox regression analyses suggested that the poor prognosis of GC patients was not strongly dependent on the ectopic expression of the seven miRNAs, but rather, a poor prognosis was associated with age, metastasis, and histological grade.

Conclusions

Based on the results presented in this study it can be concluded that these miRNAs (miR-455-3p, miR-135b-5p, let-7a-3p, miR-195-5p, miR-204-5p, miR-149-5p, and miR-143-3p) might be potential biomarkers for the early diagnosis of GC patients, but this finding should be regarded with caution. A large-scale, prospective, and multicenter cohort study should be performed.

An integrated analysis to predict micro-RNAs targeting both stemness and metastasis in human gastric cancer

BACKGROUND AND AIM

Cancer stem cells (CSCs), a subpopulation of tumor cells, assess the capacity of self-renewal, metastasis, and therapeutic resistance. Regulation of CSCs and their epithelial to mesenchymal transition (EMT) potential is one of the promising strategies to eliminate cancer or to inhibit metastasis. Micro-RNAs (miRNAs) as regulators of several cell properties, such as self-renewal, metastasis, and resistance to the drug, could be proper targets in cancer diagnosis and therapy. The aim of the present study is to select common miRNAs targeting both self-renewal and metastasis in gastric cancer.

METHODS

Stemness-related and EMT-related genes were selected by literature mining. The common miRNAs targeting genes were chosen using different databases and r programming language. The expression pattern of selected miRNAs and genes was evaluated in gastrospheres-as a gastric CSC model-and gastric tumor biopsies.

RESULTS

Based on the integrated analysis, six miRNAs common to both stemness and metastasis were identified. miR-200c-3p and miR-520c-3p overexpressed in MKN-45 gastrospheres and grade III tumors. In AGS spheres, however, miR-520c-3p and miR-200c-3p upregulation and miR-34a-5p downregulation were similar to grade II tumors. Interestingly, miR-200c-3p and miR-520c-3p indicated a positive correlation with OCT4 and NOTCH1 expression in grade III tumors and MKN-45 spheres. Protein-protein network revealed that the EMT acquisition can be induced by stemness activation through intermediated core-regulatory genes, including CTNNB1, CTNND1, MAML1, KAT2A, and MAML3.

CONCLUSION

The upregulation of mir-200c-3p and mir-520c-3p could effect on stemness and metastasis in gastric cancer as well as gastric CSCs. Therefore, they can be used as diagnosis and prognostic factors.

Transcriptional E2F1/2/3/6 as potential prognostic biomarkers in cutaneous melanoma

Although the abnormal expression of members of the E2F family has been reported to participate in carcinogenesis in many human types of cancer, the bioinformatics role of the E2F family in melanoma is unknown. This research was designed to detect the expression, methylation, prognostic value and potential effects of the E2F family in melanoma. We investigated E2F family mRNA expression from the Oncomine and GEPIA databases and their methylation status in the MethHC database. Meanwhile, we detected the relative E2F family expression levels by qPCR and immunohistochemistry. Kaplan-Meier Plotter was used to draw survival analysis charts, and gene functional enrichment analyses were applied through cBioPortal database analysis. E2F1/2/3/4/5/6 mRNA and proteins were clearly upregulated in cutaneous melanoma patients, and high expression levels of E2F1/2/3/6 were statistically related to high methylation levels. Increased mRNA expression of E2F1/2/3/6 was related to lower overall survival rates (OS) and disease-free survival (DFS) in cutaneous melanoma cases. Meanwhile, E2F1/2/3/6 carried out these effects through regulating multiple signaling pathways, including the MAPK, PI3K-Akt and p53 signaling pathways. Taking together, our findings suggest that E2F1/2/3/6 could act as potential targets for precision therapy in cutaneous melanoma patients.

Identification of key miRNA-gene pairs in gastric cancer through integrated analysis of mRNA and miRNA microarray

Nowadays, the current bioinformatic methods have been increasingly applied in the field of oncological research. In this study, we expect a better understanding of the molecular mechanism of gastric cancer from the bioinformatic methods. By systematically addressing the differential expression of microRNAs (miRNAs) and mRNAs between gastric cancer specimens and normal gastric specimens with the application of bioinformatics tools, A total of 206 DEGs and 38 DEMs were identified. The Gene Ontology (GO) analysis of Annotation, Visualization and Integrated Discovery (DAVID) database revealed that the differentially expressed genes (DEGs) were significantly enriched in biological process, molecular function and cellular component, while Kyoto Encyclopedia of Genes and Genomes (KEGG) database showed DEGs were significantly enriched in 8 signal pathways. The miRNA-gene regulatory network was constructed based on 385 miRNA-gene (DEM-DEG) pairs, consisting of 35 miRNAs and 107 target genes. In the regulatory network, the top 5 up-regulated genes were Transmembrane Protease, Serine 11B (TMPRSS11B), regulator of G protein signaling 1 (RGS1), cysteine rich angiogenic inducer 61 (CYR61), inhibin subunit beta A (INHBA), syntrophin gamma 1 (SNTG1), and the top 5 down-regulated genes were tumor necrosis factor receptor superfamily, member 19 (TNFRSF19), pleckstrin homology domain containing B2 (PLEKHB2), Tax1 binding protein 3 (TAX1BP3), presenilin enhancer, gamma-secretase subunit (PSENEN), NME/NM23 nucleoside diphosphate kinase 3 (NME3). Based on the gastric cancer patient database from Kaplan-Meier Plotter tools, we found that 8 of 10 genes with most significant changes in the miRNA-gene regulatory network possessed a prognostic value for survival time of gastric cancer patients. Patients with higher level of RGS1, PLEKHB2, TAX1BP3 and PSENEN in gastric cancer had a longer survival time compared with the patients with lower level of these genes. On the contrary, patients with higher level of INHBA, SNTG1, TNFRSF19 and NME3 were found associated with a shorter survival time. In conclusion, our findings provided several potential targets regarding gastric cancer, which may result in a new strategy to treat gastric cancer from a system rather than a single-gene perspective.

Meta-Analysis Reveals the Prognostic Relevance of Nuclear and Membrane-Associated Bile Acid Receptors in Gastric Cancer

INTRODUCTION

Bile acids (BAs) arising from duodenogastric reflux are known to facilitate gastric cancer (GC) development. Although BAs traditionally contribute to carcinogenesis through direct cellular cytotoxicity, increasing evidence implicates nuclear and membrane BA receptors (BARs) as additional factors influencing cancer risk. Indeed, some BARs are already linked with GC, but conflicting evidence and lack of information regarding other endogenous BARs warrant further investigation. In this study, we meta-analyzed multiple data sets to identify clinically relevant relationships between BAR expression and prognosis, clinicopathology, and activity in GC.

METHODS

We collected transcriptomic data from the Gene Expression Omnibus and The Cancer Genome Atlas to analyze associations between BAR expression and GC prognosis, subtype, and clinicopathology. We also used Ingenuity Pathway Analysis to assess and predict functions, upstream regulators, and downstream mediators of membrane and nuclear BARs in GC.

RESULTS

BARs showed differential distribution in GC; membrane BARs (G protein-coupled BAR 1, sphingosine-1-phosphate receptor 2, and cholinergic receptor muscarinic 2) were enriched in diffuse-, genome-stable, and mesenchymal-type tumors, whereas nuclear BARs (pregnane-X-receptor, constitutive androstane receptor, and farnesoid-X-receptor) were enriched in chromosome instability and metabolic subtypes. High expression of all membrane but not nuclear BARs was associated with poor prognosis and unfavorable GC clinicopathologic features. Similarly, expression patterns of membrane but not nuclear BARs varied geographically, aligning with Helicobacter pylori infection and GC mortality rates. Finally, GC-related oncogenes, namely transforming growth factor β1, were associated with membrane BARs, whereas many metabolic-associated genes were associated with nuclear BARs.

DISCUSSION

Through transcriptomic meta-analysis, we identified distinct expression profiles between nuclear and membrane BARs that demonstrate prognostic relevance and warrant further investigation.

AGXT2L1 is downregulated in carcinomas of the digestive system

Alanine-glyoxylate aminotransferase 2-like 1 (AGXT2L1) is a modulator of phospholipid metabolism, and its role in tumor biology is obscure. Previously, significant downregulation of AGXT2L1 has been observed in hepatocellular carcinoma. The aim of the present study was to investigate AGXT2L1 expression and its association with the clinical characteristics of common carcinomas of the digestive system. In the present study, the expression levels of AGXT2L1 were detected by immunohistochemical staining in colorectal cancer (CRC), gastric cancer and pancreatic cancer tissues. The associations between AGXT2L1 expression and clinicopathological features were analyzed using public gene expression datasets. Small interfering RNA was transfected into SW480 and HCT116 cells to explore the role of AGXT2L1 in CRC cells. AGXT2L1 expression was significantly decreased in cancerous tissues compared with in normal tissues, and low AGXT2L1 expression was associated with an unfavorable prognosis in patients. Furthermore, it was revealed that AGXT2L1 may regulate phosphatidylinositol and phosphatidylserine metabolism in cancerous tissues, and that decreased AGXT2L1 expression could induce autophagy in CRC cells. Overall, the present study provides a basis for further understanding of the role of AGXT2L1 and its association with autophagy in cancer.

Novel Potential Therapeutic Target for E2F1 and Prognostic Factors of E2F1/2/3/5/7/8 in Human Gastric Cancer

E2F transcription factors (E2Fs) were found to be related with cell activities and disease progression among a variety of different tumors, including regulating cell division and cell proliferation. In the analysis, it aimed to focus on transcriptional and survival information of E2Fs in gastric cancer (GC) from Gene Expression Profiling Interactive Analysis (GEPIA), Kaplan-Meier plotter, cBioPortal, Database for Annotation, Visualization and Integrated Discovery (DAVID), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and Oncomine databases. It was found that the expression of E2F1/2/3/5/7/8 in GC tissues was obviously higher than the normal. Of interest, none of the E2Fs was related with pathological stages. Nevertheless, high expression of E2F2/3/5/7/8 was related with better survival data, except E2F6 regarding shorter first-progression (FP) survival. High expression levels of E2F2/5/7/8 have significant correlations with overall survival (OS) in patients with intestinal and diffuse GC, and this prognostic value is not affected by gender. Oppositely, the lower level of E2F1/4 illustrated superior survival data. Moreover, increased expression of E2F1 in GC tissues might play an important role in the development of GC. Collectively, E2F1 could be a potential therapeutic target for patients with GC. E2F1/2/3/5/7/8 might be original prognostic predictors of GC.

Transcriptomic analysis on the effects of melatonin in gastrointestinal carcinomas

BACKGROUND

Melatonin has been shown with anticancer property and therapeutic potential for tumors. However, there lacks a systematic study on the molecular pathways of melatonin and its antitumor effects in gastrointestinal carcinomas.

METHODS

Using the gene expression profiles of four cancer cell lines from three types of gastrointestinal carcinomas before and after melatonin treatment, including gastric carcinoma (GC), colorectal carcinoma (CRC) and hepatocellular carcinoma (HCC), differentially expressed genes (DEGs) and biological pathways influenced by melatonin were identified. The qRT-PCR analyses were performed to validate the effects of melatonin on 5-FU resistance-related genes in CRC.

RESULTS

There were 17 pathways commonly altered by melatonin in the three cancer types, including FoxO signaling pathways enriched by the upregulated DEGs and cell cycle signaling pathways enriched by the downregulated DEGs, confirmed the dual role of melatonin to tumor growth, pro-apoptosis and anti-proliferation. DEGs upregulated in the three types of cancer tissues but reversely downregulated by melatonin were commonly enriched in RNA transport, spliceosome and cell cycle signaling pathways, which indicate that melatonin might exert antitumor effects through these pathways. Our results further showed that melatonin can downregulate the expression levels of 5-FU resistance-related genes, such as thymidylate synthase in GC and ATR, CHEK1, BAX and MYC in CRC. The qRT-PCR results demonstrated that melatonin enhanced the sensitivity of CRC 5-FU resistant cells by decreasing the expression of ATR.

CONCLUSIONS

Melatonin exerts the effects of pro-apoptosis and anti-proliferation on gastrointestinal carcinomas, and might increase the sensitivity of 5-FU in GC and CRC patients.

Machine Learning-Based Ensemble Recursive Feature Selection of Circulating miRNAs for Cancer Tumor Classification

Circulating microRNAs (miRNA) are small noncoding RNA molecules that can be detected in bodily fluids without the need for major invasive procedures on patients. miRNAs have shown great promise as biomarkers for tumors to both assess their presence and to predict their type and subtype. Recently, thanks to the availability of miRNAs datasets, machine learning techniques have been successfully applied to tumor classification. The results, however, are difficult to assess and interpret by medical experts because the algorithms exploit information from thousands of miRNAs. In this work, we propose a novel technique that aims at reducing the necessary information to the smallest possible set of circulating miRNAs. The dimensionality reduction achieved reflects a very important first step in a potential, clinically actionable, circulating miRNA-based precision medicine pipeline. While it is currently under discussion whether this first step can be taken, we demonstrate here that it is possible to perform classification tasks by exploiting a recursive feature elimination procedure that integrates a heterogeneous ensemble of high-quality, state-of-the-art classifiers on circulating miRNAs. Heterogeneous ensembles can compensate inherent biases of classifiers by using different classification algorithms. Selecting features then further eliminates biases emerging from using data from different studies or batches, yielding more robust and reliable outcomes. The proposed approach is first tested on a tumor classification problem in order to separate 10 different types of cancer, with samples collected over 10 different clinical trials, and later is assessed on a cancer subtype classification task, with the aim to distinguish triple negative breast cancer from other subtypes of breast cancer. Overall, the presented methodology proves to be effective and compares favorably to other state-of-the-art feature selection methods.

Comprehensive analysis reveals CTHRC1, SERPINE1, VCAN and UPK1B as the novel prognostic markers in gastric cancer

Background

Gastric cancer (GC) is one of the most common malignant diseases worldwide, the incidence and mortality for GC is still high, thus it is urgently important to identify the effective and reliable biomarkers to evaluate GC and the underlying molecular events.

Methods

The study integrated four Gene Expression Omnibus (GEO) profile datasets and The Cancer Genome Atlas (TCGA) dataset to screen differentially expressed genes (DEGs), screened key genes by performing the Kaplan-Meier analysis, univariate and multivariate-cox analysis. Further analysis were performed to evaluate and validate the prognostic value of the key genes based on TCGA database and online websites. In addition, mechanism analysis of the key genes was performed thought biological processes and KEGG pathway analysis.

Results

In the study, 192 DEGs (92 up-regulated and 100 down-regulated) were identified from the GEO and TCGA datasets. Next, gene ontology (GO) for DEGs focused primarily on cell adhesion, extracellular region and extracellular matrix structural constituent. Then four significant key genes were screened by performed the Kaplan-Meier analysis, univariate and multivariate-cox analysis. By using Kaplan-Meier plotter and OncoLnc, the expression level was associated with a worse prognosis. In addition, the area under curve (AUC) for time-dependent receiver operating characteristic (ROC) indicated a moderate diagnostic value. Furthermore, the expression of collagen triple helix repeat containing 1 (CTHRC1), serpin family E member 1 (SERPINE1), Versican (VCAN) was associated with tumor size, Uroplakin 1B (UPK1B) expression was associated with distant metastasis. Finally, multiple biological processes and signaling pathway associated with key genes revealed the underlying mechanism in GC.

Conclusions

Taken together, CTHRC1, SERPINE1, VCAN, UPK1B were novel potential prognostic molecular markers for GC, which acted as oncogene to promote the development of GC.

Key Genes Associated with Prognosis and Tumor Infiltrating Immune Cells in Gastric Cancer Patients Identified by Cross-Database Analysis

Background: The molecular mechanisms underlying gastric cancer (GC) progression are unclear. The authors examined key genes associated with the prognosis and tumor-infiltrating immune cells in patients with GC. Materials and Methods: Gene expression omnibus (GEO) was used to filter and obtain GC-related differentially expressed genes (DEGs). The molecular functions, biological processes, and cellular components of the DEGs were subjected to enrichment analysis. Protein-protein interaction networks of proteins encoded by the DEGs were analyzed using STRING. The authors also identified hub genes of GC, as well as their expression levels in GC and their relationship with patient prognosis. The relationship between hub genes and tumor-infiltrating immune cells was analyzed by Tumor IMmune Estimation Resource. Results: Six GEO datasets were included in this study, and 265 DEGs were identified. These DEGs were enriched in different signaling pathways and had different biological functions. Six hub genes were potentially significantly related to the molecular mechanisms of GC (TOP2A, FN1, SPARC, COL3A1, COL1A1, and TIMP1). These genes are potential markers of prognosis. Five hub genes were significantly positively correlated with the number of macrophages, neutrophils, and dendritic cells. Conclusions: The authors provide a theoretical basis for exploring the molecular regulation mechanism underlying GC and identifying therapeutic targets.

Enhancing reproducibility of gene expression analysis with known protein functional relationships: The concept of well-associated protein

Identification of differentially expressed genes (DEGs) is well recognized to be variable across independent replications of genome-wide transcriptional studies. These are often employed to characterize disease state early in the process of discovery and prioritize novel targets aimed at addressing unmet medical need. Increasing reproducibility of biological findings from these studies could potentially positively impact the success rate of new clinical interventions. This work demonstrates that statistically sound combination of gene expression data with prior knowledge about biology in the form of large protein interaction networks can yield quantitatively more reproducible observations from studies characterizing human disease. The novel concept of Well-Associated Proteins (WAPs) introduced herein-gene products significantly associated on protein interaction networks with the differences in transcript levels between control and disease-does not require choosing a differential expression threshold and can be computed efficiently enough to enable false discovery rate estimation via permutation. Reproducibility of WAPs is shown to be on average superior to that of DEGs under easily-quantifiable conditions suggesting that they can yield a significantly more robust description of disease. Enhanced reproducibility of WAPs versus DEGs is first demonstrated with four independent data sets focused on systemic sclerosis. This finding is then validated over thousands of pairs of data sets obtained by random partitions of large studies in several other diseases. Conditions that individual data sets must satisfy to yield robust WAP scores are examined. Reproducible identification of WAPs can potentially benefit drug target selection and precision medicine studies.

[miR-449a/b negatively regulates E2F1 to suppress proliferation of gastric cancer cells]

OBJECTIVE

To investigate the possible role of miR-449a/b in the occurrence of gastric cancer.

METHODS

The expression of miR-449a/b and E2F1 mRNA in gastric cancer cells BGC-823 and gastric mucosal cells GES-1 were detected with qRT-PCR. miR-449a/b mimics or a negative control was transiently transfected into BGC-823 cells, and the changes in cell proliferation, apoptosis, and migration ability were assessed using CCK-8 assay, flow cytometry, and scratch wound healing assay, respectively. Western blotting was used to observe the effects of miR-449a/b upregulation on its target gene expression. The effects of transfection with an E2F1-over-expressing plasmid or an empty plasmid were analyzed on the expression level of miR-449a/b in BGC-823 cells using qRT-PCR and digital PCR.

RESULTS

The gastric cancer cell line BGC-823 showed significantly a lowered expression of miR-449a/b compared with the normal gastric mucosal cell line GES-1 (P < 0.01). Overexpression of miR-449a/b obviously inhibited the proliferation and migration and promoted apoptosis of BGC-823 cells (P < 0.05). Overexpression E2F1 in the cells resulted in significantly up-regulated expression of miR-449a/b (P < 0.001). Upregulation of miR-449a/b caused significant down-regulation of its direct target genes CDK4 and CDK6 and also of the expression of E2F1 protein via the CDKs-pRb-E2F1 signaling pathway.

CONCLUSIONS

The low expression of miR-449a/b and the high expression of E2F1 are both involved in the occurrence and progression of gastric cancer, and miR-449a/b negatively regulates E2F1 to inhibit the proliferation of gastric cancer cells.

Multiplex profiling of peritoneal metastases from gastric adenocarcinoma identified novel targets and molecular subtypes that predict treatment response

OBJECTIVE

Peritoneal carcinomatosis (PC) occurs frequently in patients with gastric adenocarcinoma (GAC) and confers a poor prognosis. Multiplex profiling of primary GACs has been insightful but the underpinnings of PC's development/progression remain largely unknown. We characterised exome/transcriptome/immune landscapes of PC cells from patients with GAC aiming to identify novel therapeutic targets.

DESIGN

We performed whole-exome sequencing (WES) and whole transcriptome sequencing (RNA-seq) on 44 PC specimens (43 patients with PC) including an integrative analysis of WES, RNA-seq, immune profile, clinical and pathological phenotypes to dissect the molecular pathogenesis, identifying actionable targets and/or biomarkers and comparison with TCGA primary GACs.

RESULTS

We identified distinct alterations in PC versus primary GACs, such as more frequent CDH1 and TAF1 mutations, 6q loss and chr19 gain. Alterations associated with aggressive PC phenotypes emerged with increased mutations in TP53, CDH1, TAF1 and KMT2C, higher level of 'clock-like' mutational signature, increase in whole-genome doublings, chromosomal instability (particularly, copy number losses), reprogrammed microenvironment, enriched cell cycle pathways, MYC activation and impaired immune response. Integrated analysis identified two main molecular subtypes: 'mesenchymal-like' and 'epithelial-like' with discriminating response to chemotherapy (31% vs 71%). Patients with the less responsive 'mesenchymal-like' subtype had high expression of immune checkpoint T-Cell Immunoglobulin And Mucin Domain-Containing Protein 3 (TIM-3), its ligand galectin-9, V-domain Ig suppressor of T cell activation (VISTA) and transforming growth factor-β as potential therapeutic immune targets.

CONCLUSIONS

We have uncovered the unique mutational landscape, copy number alteration and gene expression profile of PC cells and defined PC molecular subtypes, which correlated with PC therapy resistance/response. Novel targets and immune checkpoint proteins have been identified with a potential to be translated into clinics.

Identification of hub genes correlated with the pathogenesis and prognosis of gastric cancer via bioinformatics methods

BACKGROUND

Gastric cancer (GC) is the fourth most common cause of cancer-related deaths in the world and 5-year overall survival (OS) rate is less than 10%. So, it is urgent to identified novel diagnostic and prognostic biomarkers.

METHODS

Twelve GEO (gene expression omnibus) datasets were obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between GC and normal tissues were screened and integrated using limma and RobustRankAggreg (RRA) packages in R software. Protein-protein interaction (PPI) network, GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses for DEGs were conducted via STRING and DAVID, respectively. Moreover, Cox regression model was used to construct a gene prognosis signature.

RESULTS

Ten genes (COL1A1, CXCL8, COL3A1, SPP1, COL1A2, TIMP1, CXCL1, BGN, MMP3 and SERPINE1) were identified and might be highly related to GC. Further analysis showed high expression of CXCL8, COL3A1, CXCL1, MMP3 and SERPINE1, were significantly associated with late stage of GC. Lastly, we build a seven-gene prognosis signature (CYP19A1, SERPINE1, CGB5, CALCR, ASGR2, CYTL1 and ABCB5), which can give a good prediction of OS.

CONCLUSIONS

Our article screened out key genes highly associating with GC's developments and prognosis, and it is useful for researcher to further understand GC's molecular basis and direct the synthesis medicine of GC.

Gastric Cancer MicroRNAs Meta-signature

Gastric cancer (GC) is one of the most common types of cancer and the second leading cause of cancer-associated mortality. Identification of novel biomarkers is critical to prolonging patient survival. MicroRNAs (miRNAs) proved to play diverse roles in the physiological and pathological state in cancers including GC. Herein we aimed at performing a meta-analysis on miRNA profiling studies that used microarray platforms. Relevant studies were retrieved from PubMed and GEO databases. We used the robust rank aggregation to perform the meta-analysis. Moreover, for meta-signature miRNAs target genes, we performed pathway enrichment and GO molecular function enrichment analysis. A total of 19 upregulated miRNAs and seven downregulated miRNAs in GC samples were identified. However, only three upregulated and one downregulated miRNA reached statistical significance after multiple test correction. Here we showed that hsa-miR-21-5p, hsa-miR-93-5p, hsa-miR-25-3p, and hsa-miR-375 are differentially expressed in GC samples.

COL12A1, a novel potential prognostic factor and therapeutic target in gastric cancer

Dysregulation of collagen type XII α1 chain (COL12A1) has been found in several cancer types and could be involved in tumor progression. However, its clinical significance in gastric cancer (GC) remains under exploration. Online databases (Gene Expression Omnibus and UALCAN), reverse transcription-quantitative PCR and immunohistochemistry were utilized in the present study to evaluate the expression of COL12A1 in GC tissues and cell lines. It was found that COL12A1 expression was notably upregulated in GC. Clinicopathological analysis showed that elevated COL12A1 expression was positively correlated with tumor invasiveness, metastasis and advanced clinical stage. The prognostic analysis suggested that high COL12A1 expression contributed to poor overall survival. Multivariate Cox analysis indicated that COL12A1 overexpression was a powerful independent prognostic indicator in patients with GC (hazard ratio, 1.896; 95% CI, 1.267–2.837; P=0.002). The results highlighted the importance of COL12A1 in GC and suggested its potential role as a candidate for clinical outcome prediction and targeted therapy in patients with GC.

Global transcriptomic analysis identifies SERPINE1 as a prognostic biomarker associated with epithelial-to-mesenchymal transition in gastric cancer

Background

The plasminogen activation system plays a pivotal role in regulating tumorigenesis. In this work, we aim to identify key regulators of plasminogen activation associated with tumorigenesis and explore potential mechanisms in gastric cancer (GC).

Methods

Gene profiling datasets were extracted from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were screened for and obtained by the GEO2R tool. The Database for Annotation, Visualization and Integrated Discovery was used for GO and KEGG enrichment analysis. Gene set enrichment analysis (GSEA) was performed to verify molecular signatures and pathways among The Cancer Genome Atlas or GEO datasets. Correlations between SERPINE1 and markers of epithelial-to-mesenchymal transition (EMT) were analyzed using the GEPIA database and quantitative real-time PCR (qRT-PCR). Interactive networks of selected genes were built by STRING and Cytoscape software. Finally, selected genes were verified with the Kaplan–Meier (KM) plotter database.

Results

A total of 104 overlapped upregulated and 61 downregulated DEGs were obtained. Multiple GO and KEGG terms associated with the extracellular matrix were enriched among the DEGs. SERPINE1 was identified as the only regulator of angiogenesis and the plasminogen activator system among the DEGs. A high level of SERPINE1 was associated with a poor prognosis in GC. GSEA analysis showed a strong correlation between SERPINE1 and EMT, which was also confirmed with the GEPIA database and qRT-PCR validation. FN1, TIMP1, MMP2, and SPARC were correlated with SERPINE1.The KM plotter database showed that an overexpression of these genes correlated with a shorter survival time in GC patients.

Conclusions

In conclusion, SERPINE1 is a potent biomarker associated with EMT and a poor prognosis in GC. Furthermore, FN1, TIMP1, MMP2, and SPARC are correlated with SERPINE1 and may serve as therapeutic targets in reversing EMT in GC.

Identification of discrepancy between CTLA4 expression and CTLA4 activation in gastric cancer

Objective: Recently, immune checkpoints blockers showed higher anti-tumor activity for advanced gastric cancer (GC). The purpose of the study is to find out predictive biomarkers related to anti-cytotoxic lymphocyte antigen 4 (CTLA4) therapy. Materials and methods: Datasets of gene expression omnibus (GEO), the cancer genome atlas (TCGA), and gene set enrichment analysis (GESA) were extracted. Differential expression of CTLA4 between cancer tissues and normal mucosa, enrichment of WT (wild type) vs. CTLA4_KO (knockout) upregulated gene set and clinical significance were analyzed. The expression of CTLA4, CD3, and granzyme A (GZMA) were validated on 30 cases of Chinese GC. Microsatellite instability (MSI) marker MLH1 and Epstein-Barr virus (EBV) marker EBER were examined on 30 cases of Chinese GC by immunohistochemistry and in situ hybridization. Results: CTLA4 was upregulated in GC tissue relative to normal mucosa in datasets of GSE27342 (fold change = 1.586, p < .001) and GSE63089 (fold change = 1.365, p < .001). Increased CTLA4 expression was positively related to CTLA4 activation. EBV-associated GC (EBVaGC) and microsatellite instability GC (MSIGC) disclosed higher CTLA4 levels than other GCs. Genomic stability GC (GSGC) also showed higher enrichment score of CTLA4 activation. CTLA4 activation resulted in shorter overall survival in GC. The expression level of CTLA4 was well correlated to expression levels of GZMA (R = 0.701, p < .001) and CD3 (R = 0.750, p < .001). Conclusions: Based on bioinformatics analysis, GSGC should be worth noticed as a potential GC subtypes responsive to anti-CTLA4 treatment.

E2F1 induces LSINCT5 transcriptional activity and promotes gastric cancer progression by affecting the epithelial-mesenchymal transition

Background

Long noncoding RNAs (lncRNAs) have been shown to play important regulatory roles in human cancer. We previously verified that the lncRNA long stress-induced noncoding transcript 5 (LSINCT5) is overexpressed in gastric cancer (GC) cells and closely correlated with cell proliferation and patient prognosis. However, whether aberrant LSINCT5 expression has an important effect on GC progression is unclear, and the potential mechanisms remain unknown. In GC, E2F1 expression is also aberrant, but the biological functions of E2F1 are controversial, and the correlation between E2F1 and lncRNAs remains unknown.

Materials and methods

Expression of LSINCT5 was analyzed in metastatic GC tissues compared with nonmetastatic tissues using quantitative real-time PCR (qRT-PCR) assays. Gain and loss of function approaches were used to investigate the biological role of LSINCT5 in GC cell migration and invasion. A computational screen of LSINCT5 promoter was conducted to search for transcription factor-binding sites. LSINCT5 promoter activities were examined by ChIP and luciferase reporter assays. qRT-PCR and western blotting assays were performed to detect the expression of multiple EMT markers in cells in which LSINCT5 was overexpressed or knocked down.

Results

An integrated quantitative analysis revealed that LSINCT5 was significantly over-expressed in metastatic GC tissues. Forced LSINCT5 expression promoted cell migration and invasion, whereas loss of LSINCT5 function decreased cell migration and invasion. Mechanistic investigations showed that LSINCT5 is a direct transcriptional target of E2F1. Moreover, LSINCT5 overexpression was found to play an important role in the epithelial-to-mesenchymal transition by regulating the expression of E-cadherin, N-cadherin, vimentin, and matrix metalloproteinase-2.

Conclusion

These data suggest that E2F1-mediated activation of LSINCT5, a regulator of cell migration and invasion, constitute the mechanistic link between the E2F1-mediated pathway and lncRNA that regulates cell migration and invasion. Thus, LSINCT5 may be a target for new GC therapies.

Advances of circular RNAs in carcinoma

Circular RNAs (circRNAs) are a type of non-coding RNAs with single-stranded closed structure. The rapid development of high-throughput sequencing technology has allowed for the widespread presence of circRNAs in transcriptomes. Moreover, increasing studies have identified a correlation between circRNAs and different cancers. In addition, most circRNAs are dysregulated in various cancers, and some of them have been reported be vital in the occurrence and development of tumors. For example, ciRS-7 plays a role in tumor promotion and circ-ITCH acts as a tumor suppressor. This review summarizes the latest progressions in the field regarding the functions of circRNAs in relation with cancers, and anticipates the emerging roles of circRNAs and future challenges in cancer research.

Pathway Network Analysis of Complex Diseases Based on Multiple Biological Networks

Biological pathways play important roles in the development of complex diseases, such as cancers, which are multifactorial complex diseases that are usually caused by multiple disorders gene mutations or pathway. It has become one of the most important issues to analyze pathways combining multiple types of high-throughput data, such as genomics and proteomics, to understand the mechanisms of complex diseases. In this paper, we propose a method for constructing the pathway network of gene phenotype and find out disease pathogenesis pathways through the analysis of the constructed network. The specific process of constructing the network includes, firstly, similarity calculation between genes expressing data combined with phenotypic mutual information and GO ontology information, secondly, calculating the correlation between pathways based on the similarity between differential genes and constructing the pathway network, and, finally, mining critical pathways to identify diseases. Experimental results on Breast Cancer Dataset using this method show that our method is better. In addition, testing on an alternative dataset proved that the key pathways we found were more accurate and reliable as biological markers of disease. These results show that our proposed method is effective.

Identification of Potential Key Genes Associated With the Pathogenesis and Prognosis of Gastric Cancer Based on Integrated Bioinformatics Analysis

Background and Objective: Despite striking advances in multimodality management, gastric cancer (GC) remains the third cause of cancer mortality globally and identifying novel diagnostic and prognostic biomarkers is urgently demanded. The study aimed to identify potential key genes associated with the pathogenesis and prognosis of GC.

Methods: Differentially expressed genes between GC and normal gastric tissue samples were screened by an integrated analysis of multiple gene expression profile datasets. Key genes related to the pathogenesis and prognosis of GC were identified by employing protein–protein interaction network and Cox proportional hazards model analyses.

Results: We identified nine hub genes (TOP2A, COL1A1, COL1A2, NDC80, COL3A1, CDKN3, CEP55, TPX2, and TIMP1) which might be tightly correlated with the pathogenesis of GC. A prognostic gene signature consisted of CST2, AADAC, SERPINE1, COL8A1, SMPD3, ASPN, ITGBL1, MAP7D2, and PLEKHS1 was constructed with a good performance in predicting overall survivals.

Conclusion: The findings of this study would provide some directive significance for further investigating the diagnostic and prognostic biomarkers to facilitate the molecular targeting therapy of GC.

Downregulation and DNA methylation of ECRG4 in gastric cancer

Background

Esophageal cancer-related gene 4 (ECRG4) is a novel candidate tumor suppressor gene. Our study investigated the expression and function of ECRG4 in gastric cancer and highlighted the role of DNA hypermethylation at the promoter in silencing the ECRG4 expression.

Methods

The GSE63089 data set was obtained from the Gene Expression Omnibus and analyzed for differentially expressed genes. Carcinoma and para-carcinoma tissues of 102 patients with gastric cancer were collected from January 2010 to July 2011. Immunohistochemistry, real-time polymerase chain reaction (PCR), and western blot analyses were performed to evaluate the expression of ECRG4. After measuring the change in the level of ECRG4 expression, CCK-8, Transwell, and flow cytometric cell cycle assays were performed. In addition, methylation-specific PCR was performed to detect the methylation state of ECRG4, and 5-aza-2′-deoxycytidine was used for demethylation of ECRG4. All statistical analyses were performed using the SPSS 17.0 software.

Results

We found that ECRG4 expression was downregulated in gastric cancer, and this was closely related to lymph node metastasis. After ECRG4 was silenced using a specific small interfering RNA, the BGC-823 cell line became highly aggressive and proliferative. In addition, we verified whether downregulation of ECRG4 was highly correlated with DNA methylation of the ECRG4 promoter and found that the demethylating agent 5-aza-2′-deoxycytidine could effectively enhance ECRG4 expression.

Conclusion

The aberrant expression of ECRG4 is associated with hypermethylation in the promoter region and plays an important role in the malignancy of gastric cancer. Therefore, ECRG4 may be a potential biomarker for molecular diagnosis of gastric cancer, and the use of 5-Aza-dC to reverse the hypermethylation of ECRG4 may be a new approach to the treatment of gastric cancer.

microRNA-340 influences cell proliferation, apoptosis and invasion by targeting NF-κB1 in gastric cancer

Gastric cancer is a serious threat to human health, and its pathogenesis may be regulated by a variety of mRNAs. Abnormal expression of microRNA-340 has been frequently reported in many malignant neoplasms, while the molecular mechanism of miR-340 has not been explored in gastric cancer. In this study, the mRNA level of miR-340 was determined by real-time PCR in GC cell lines. The miR-340 mimic was transiently transfected into GC cells by using Lipofectamine™ 2000 reagent. The BrdU-ELISA results showed that introduction of miR-340 inhibited cell proliferation. It was demonstrated that miR-340 mimic arrested cell cycle progression and promoted apoptosis of MKN-45 and BGC-823 cells. In addition, the overexpression of miR-340 could inhibit invasion and EMT of MKN-45 and BGC-823 cells. The expression of NF-κB1 was evidently reduced by up-regulation of miR-340. Luciferase reporter assay further confirmed that miR-340 could directly target the 3'UTR of NF-κB1. Moreover, overexpression of NF-κB1 transfected with miR-340 mimic partially reversed the inhibitory of miR-340 mimic in MKN-45 and BGC-823 cells. In conclusion, miR-340 induced cell apoptosis and inhibited invasion by down-regulation of NF-κB1, which might be a potential target in treatment and prevention of gastric cancer.

Optimizing miRNA-module diagnostic biomarkers of gastric carcinoma via integrated network analysis

Several microRNAs (miRNAs) have been suggested as novel biomarkers for diagnosing gastric cancer (GC) at an early stage, but the single-marker strategy may ignore the co-regulatory relationships and lead to low diagnostic specificity. Thus, multi-target modular diagnostic biomarkers are urgently needed. In this study, a Z_summary and NetSVM-based method was used to identify GC-related hub miRNAs and activated modules from clinical miRNA co-expression networks. The NetSVM-based sub-network consisting of the top 20 hub miRNAs reached a high sensitivity and specificity of 0.94 and 0.82. The Z_summary algorithm identified an activated module (miR-486, miR-451, miR-185, and miR-600) which might serve as diagnostic biomarker of GC. Three members of this module were previously suggested as biomarkers of GC and its 24 target genes were significantly enriched in pathways directly related to cancer. The weighted diagnostic ROC AUC of this module was 0.838, and an optimized module unit (miR-451 and miR-185) obtained a higher value of 0.904, both of which were higher than that of individual miRNAs. These hub miRNAs and module have the potential to become robust biomarkers for early diagnosis of GC with further validations. Moreover, such modular analysis may offer valuable insights into multi-target approaches to cancer diagnosis and treatment.

Development of a computational promoter with highly efficient expression in tumors

Background

Gene therapy is a potent method to increase the therapeutic efficacy against cancer. However, a gene that is specifically expressed in the tumor area has not been identified. In addition, nonspecific expression of therapeutic genes in normal tissues may cause side effects that can harm the patients’ health. Certain promoters have been reported to drive therapeutic gene expression specifically in cancer cells; however, low expression levels of the target gene are a problem for providing good therapeutic efficacy. Therefore, a specific and highly expressive promoter is needed for cancer gene therapy.

Methods

Bioinformatics approaches were utilized to analyze transcription factors (TFs) from high-throughput data. Reverse transcription polymerase chain reaction, western blotting and cell transfection were applied for the measurement of mRNA, protein expression and activity. C57BL/6JNarl mice were injected with pD5-hrGFP to evaluate the expression of TFs.

Results

We analyzed bioinformatics data and identified three TFs, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), cyclic AMP response element binding protein (CREB), and hypoxia-inducible factor-1α (HIF-1α), that are highly active in tumor cells. Here, we constructed a novel mini-promoter, D5, that is composed of the binding sites of the three TFs. The results show that the D5 promoter specifically drives therapeutic gene expression in tumor tissues and that the strength of the D5 promoter is directly proportional to tumor size.

Conclusions

Our results show that bioinformatics may be a good tool for the selection of appropriate TFs and for the design of specific mini-promoters to improve cancer gene therapy.

Electronic supplementary material

The online version of this article (10.1186/s12885-018-4421-7) contains supplementary material, which is available to authorized users.

Aberrant promoter methylation status is associated with upregulation of the E2F4 gene in breast cancer

E2F4 is an important basal transcription factor with the potential to promote tumor growth. Its upregulation in various types of cancer has been linked to numerous genetic factors; however, the nature of the involvement of epigenetic mechanisms, including DNA methylation, remains elusive. In the present study, E2F4 expression profiles were determined in 100 paired breast tumor and control samples, through RT-qPCR using the SYBR^® green method. Furthermore, the E2F4 promoter methylation status in each of these samples was assessed using methylation specific PCR, in order to evaluate its impact on gene expression. A two-fold increase in E2F4 gene expression was observed in the breast tumors compared with in their respective controls (P=0.022); of these tumors, ~72% were under-methylated. The change in methylation status was also significantly higher (P<0.001) in the tumor samples. Methylation status was negatively correlated (r=-30) with E2F4 expression profiles, indicating that a decrease in methylation may promote higher expression of E2F4. The two study cohorts (>45 and ≤45 years) had comparable methylation profiles, though they had significantly decreased methylation status compared with controls. Various histo-pathological types also have different methylation profiles, indicating the presence of a tissue specific methylation signature. The results of the present study demonstrated that E2F4 methylation status can have a notable influence on its expression, and that it may have prognostic value in breast carcinogenesis.

TEAD1/4 exerts oncogenic role and is negatively regulated by miR-4269 in gastric tumorigenesis

TEA domain (TEAD) transcription factors are key components of the Hippo–YAP1 signaling pathway, but their functional role and regulatory mechanisms remain unclear. This study aims to comprehensively explore the expression pattern and functional role of TEAD family in gastric carcinogenesis and investigate its regulation by microRNAs (miRNAs). The mRNA and protein expression of TEAD family were examined by quantitative reverse transcription–PCR (qRT–PCR) and western blot. Their functional roles were determined by in vitro and in vivo studies. The clinicopathological association of TEAD4 in gastric cancer (GC) was studied using immunohistochemistry on tissue microarray. The prediction of miRNAs, which potentially target TEAD1/4, was performed by TargetScan and miRDB. The regulation of TEAD1/4 by miRNAs was confirmed by qRT–PCR, western blot and luciferase assays. TEAD1/4 were overexpressed in GC cell lines and primary GC tissues. Knockdown of TEAD1/4 induced a significant anticancer effect in vitro and in vivo. TEAD1 was confirmed to be a direct target of miR-377-3p and miR-4269, while TEAD4 was negatively regulated by miR-1343-3p and miR-4269. Among them, miR-4269 was the most effective inhibitor of TEAD1/4. Ectopic expression of these miRNAs substantiated their tumor-suppressive effects. In primary GC tumors, downregulation of miR-4269 was associated with poor disease-specific survival and showed a negative correlation with TEAD4. TEAD1 and TEAD4 are oncogenic factors, whose aberrant activation are, in part, mediated by the silence of miR-377-3p, miR-1343-3p and miR-4269. For the first time, the nuclear accumulated TEAD4 and downregulated miR-4269 are proposed to serve as novel prognostic biomarkers in GC.

Microarray Analysis of Circular RNA Expression Profile Associated with 5-Fluorouracil-Based Chemoradiation Resistance in Colorectal Cancer Cells

Preoperative 5-fluorouracil- (5-FU-) based chemoradiotherapy is a standard treatment for locally advanced colorectal cancer (CRC). However, the effect of 5-FU-based chemoradiotherapy on CRC is limited due to the development of chemoradiation resistance (CRR), and the molecular mechanisms underlying this resistance are yet to be investigated. Recently, circular RNAs (circRNAs), which can function as microRNA sponges, were found to be involved in the development of several cancers. In this study, we focused on clarifying the modulation of the expression profiles of circRNAs in CRR. Microarray analysis identified 71 circRNAs differentially expressed in chemoradiation-resistant CRC cells. Among them, 47 were upregulated and 24 were downregulated by more than twofold. Furthermore, expression modulation of five representative circRNAs was validated by quantitative reverse transcription PCR (qRT-PCR). Moreover, these modulated circRNAs were predicted to interact with 355 miRNAs. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the most modulated circRNAs regulate several cancers and cancer-related pathways, and the possible mechanism underlying CRR was discussed. This is the first report revealing the circRNA modulations in 5-FU chemoradiation-resistant CRC cells by microarray. The study provided a useful database for further understanding CRR and presents potential targets to overcome CRR in CRC.