Potential Diagnostic, Prognostic and Therapeutic Targets of MicroRNAs in Human Gastric Cancer. Int J Mol Sci. 2016;17:pii: E945. [PMID: 27322246 PMCID: PMC4926478 DOI: 10.3390/ijms17060945]

Graph neural network model GGDisnet for identifying genes in gastrointestinal cancer and single-cell analysis

Gastrointestinal cancer, a highly prevalent form of cancer, has been the subject of extensive research resulting in the identification of numerous pathogenic genes. However, validation and exploration of these findings often require traditional biological experiments, which are time-consuming and limit the ability to make extensive assessments promptly. To address this challenge, this paper introduces GGDisnet, a novel model for identifying genes associated with gastrointestinal cancer. GGDisnet efficiently screens human genes, providing a set of genes with a high correlation to gastrointestinal cancer for reference. Comparative analysis with other models demonstrates GGDisnet's superior performance. Furthermore, we conducted enrichment and single-cell analyses based on GGDisnet-predicted genes, offering valuable clinical insights.

Upregulation of circRNA_0023685 promotes gastric cancer progression via a circRNA-miRNA-mRNA interaction network

Circular RNAs (circRNAs) have been extensively studied for their critical roles as noncoding RNAs (ncRNAs) in gastric cancer (GC). In this study, we focused on the expression, function and molecular mechanism of circRNA_0023685 in gastric cancer (GC) to provide new ways for the diagnosis and treatment of GC. Firstly, a novel differentially expressed circRNA, circRNA_0023685, was identified, and its differential expression in GC plasma, tissue, and cell lines was further verified by RT-qPCR. Next, circRNA_0023685 was verified to promote the proliferation, migration and apoptosis of GC cells in vitro. CircRNA_0023685 was also proved to enhance the growth of GC tumors in xenograft models. Finally, for excavating the mechanism to promote GC, downstream microRNAs (miRNAs) and mRNAs were screened by bioinformatics analyses. After intersecting the target genes and genes enriched in GO analysis, a circRNA competing endogenous RNAs (ceRNAs) network was built. A protein-protein interaction (PPI) network was then constructed to find the candidate gene, APP. Our study confirmed that the highly expressed circRNA_0023685 could promote GC, which provided a new clinical diagnostic biomarker and therapeutic target for GC.

Landscape of Innovative Methods for Early Diagnosis of Gastric Cancer: A Systematic Review

From a global perspective, gastric cancer (GC) persists as a significant healthcare issue. In the Western world, the majority of cases are discovered at late stages, when the treatment is generally unsuccessful. There are no organized screening programs outside of Asia (Japan and Republic of Korea). Traditional diagnosis techniques (such as upper endoscopy), conventional tumor markers (CEA, CA19-9, and CA72-4), radiographic imaging, and CT scanning all have drawbacks. The gold standard for the earliest detection of cancer and related premalignant lesions is still endoscopy with a proper biopsy follow-up. Since there are currently no clinically approved biomarkers for the early diagnosis of GC, the identification of non-invasive biomarkers is expected to help improve the prognosis and survival rate of these patients. The search for new screening biomarkers is currently underway. These include genetic biomarkers, such as circulating tumor cells, microRNAs, and exosomes, as well as metabolic biomarkers obtained from biofluids. Meanwhile, cutting-edge high-resolution endoscopic technologies are demonstrating promising outcomes in the visual diagnosis of mucosal lesions with the aid of linked color imaging and machine learning models. Following the PRISMA guidelines, this study examined the articles in databases such as PubMed, resulting in 167 included articles. This review discusses the currently available and emerging methods for diagnosing GC early on, as well as new developments in the endoscopic detection of early lesions of the stomach.

Identification of memory B-cell-associated miRNA signature to establish a prognostic model in gastric adenocarcinoma

BACKGROUND

Memory B cells and microRNAs (miRNAs) play important roles in the progression of gastric adenocarcinoma (GAC), also known as stomach adenocarcinoma (STAD). However, few studies have investigated the use of memory B-cell-associated miRNAs in predicting the prognosis of STAD.

METHODS

We identified the marker genes of memory B cells by single-cell RNA sequencing (scRNA-seq) and identified the miRNAs associated with memory B cells by constructing an mRNA‒miRNA coexpression network. Then, univariate Cox, random survival forest (RSF), and stepwise multiple Cox regression (StepCox) algorithms were used to identify memory B-cell-associated miRNAs that were significantly related to overall survival (OS). A prognostic risk model was constructed and validated using these miRNAs, and patients were divided into a low-risk group and a high-risk group. In addition, the differences in clinicopathological features, tumour microenvironment, immune blocking therapy, and sensitivity to anticancer drugs in the two groups were analysed.

RESULTS

Four memory B-cell-associated miRNAs (hsa-mir-145, hsa-mir-125b-2, hsa-mir-100, hsa-mir-221) with significant correlations to OS were identified and used to construct a prognostic model. Time-dependent receiver operating characteristic (ROC) curve analysis confirmed the feasibility of the model. Kaplan‒Meier (K‒M) survival curve analysis showed that the prognosis was poor in the high-risk group. Comprehensive analysis showed that patients in the high-risk group had higher immune scores, matrix scores, and immune cell infiltration and a poor immune response. In terms of drug screening, we predicted eight drugs with higher sensitivity in the high-risk group, of which CGP-60474 was associated with the greatest sensitivity.

CONCLUSIONS

In summary, we identified memory B-cell-associated miRNA prognostic features and constructed a novel risk model for STAD based on scRNA-seq data and bulk RNA-seq data. Among patients in the high-risk group, STAD showed the highest sensitivity to CGP-60474. This study provides prognostic insights into individualized and precise treatment for STAD patients.

A thorough and current study of miR-214-related targets in cancer

Cancer is a complex genetic anomaly involving coding and non-coding transcript structural and expressive irregularities. A class of tiny non-coding RNAs known as microRNAs (miRNAs) regulates gene expression at the post-transcriptional level by binding only to messenger RNAs (mRNAs). Due to their capacity to target numerous genes, miRNAs have the potential to play a significant role in the development of tumors by controlling several biological processes, including angiogenesis, drug resistance, metastasis, apoptosis, proliferation, and drug resistance. According to several recent studies, miRNA-214 has been linked to the emergence and spread of tumors. The human genome's q24.3 arm contains the DNM3 gene, which is about 6 kb away and includes the microRNA-214. Its primary purpose was the induction of apoptosis in cancerous cells. The multifaceted and complex functions of miR-214 as a modulator in neoplastic conditions have been outlined in the current review.

Tumor Microenvironment Remodeling in Gastrointestinal Cancer: Role of miRNAs as Biomarkers of Tumor Invasion

Gastrointestinal (GI) cancers are the most frequent neoplasm, responsible for half of all cancer-related deaths. Metastasis is the leading cause of death from GI cancer; thus, studying the processes that regulate cancer cell migration is of paramount importance for the development of new therapeutic strategies. In this review, we summarize the mechanisms adopted by cancer cells to promote cell migration and the subsequent metastasis formation by highlighting the key role that tumor microenvironment components play in deregulating cellular pathways involved in these processes. We, therefore, provide an overview of the role of different microRNAs in promoting tumor metastasis and their role as potential biomarkers for the prognosis, monitoring, and diagnosis of GI cancer patients. Finally, we relate the possible use of nutraceuticals as a new strategy for targeting numerous microRNAs and different pathways involved in GI tumor invasiveness.

Ferroptosis-Related lncRNAs Act as Novel Prognostic Biomarkers in the Gastric Adenocarcinoma Microenvironment, Immunotherapy, and Chemotherapy

Ferroptosis, a form of programmed cell death akin to necrosis, is managed by iron and is distinguished by lipid peroxidation. Gastric cancer is a highly aggressive form of cancer, responsible for the third highest number of cancer-related deaths globally. Despite this, the potential of ferroptosis to predict the occurrence of this cancer is yet to be determined. In this research, a comprehensive examination was conducted to explore the link between long noncoding RNAs (lncRNAs) and ferroptosis, in order to uncover an lncRNA signature that can predict drug susceptibility and tumor mutational burden (TMB) in gastric adenocarcinoma. We conducted an in-depth analysis of the GC immune microenvironment and immunotherapy, with a particular focus on ferroptosis-related lncRNA prognostic biomarkers, and further explored the correlation between these factors and prognosis, immune infiltration, single nucleotide variation (SNV), and drug sensitivity for gastric adenocarcinoma patients. Through our investigations, we have discovered five lncRNA signatures related to ferroptosis that can accurately forecast the prognosis of gastric adenocarcinoma patients and also regulate the proliferation, migration, and occurrence of ferroptosis in gastric adenocarcinoma cells. In conclusion, this lncRNA signature associated with ferroptosis may be employed as a prognostic indicator for gastric adenocarcinoma, thus presenting a potential solution.

Comprehensive analysis to construct a novel immune-related prognostic panel in aging-related gastric cancer based on the lncRNA‒miRNA-mRNA ceRNA network

Introduction: Gastric cancer (GC) is the fifth frequent malignancy and is responsible for the third leading cause of cancer-related deaths. Gastric cancer is an aging-related disease, with incidence and mortality rates increasing with aging. The development of GC is affected by lncRNAs, miRNAs, and mRNAs at the transcriptional and posttranscriptional levels. This study aimed to establish a prognostic panel for GC based on competing endogenous RNA (ceRNA) networks. Methods: RNA sequences were obtained from the TCGA database. Different expressions of RNAs were scrutinized with the EdgeR package. The ceRNA network was built using the starBase database and the Cytoscape. The prognostic panel was constituted with the LASSO algorithm. We developed a nomogram comprising clinical characteristic and risk score. The receiver operating characteristic (ROC) was used to evaluate the accuracy of the nomogram prediction. Hub RNAs expressions were detected by qPCR, immunohistochemistry and western blot respectively. Clinical relevance and survival analyses were analyzed. The relationship between RNAs and immune infiltrations, as well as immune checkpoints, was analyzed and evaluated using the CIBERSORT, TIMER and TISIDB databases. Results: Four DElncRNAs, 21 DEmiRNAs and 45 DEmRNAs were included in the ceRNA network. A 3-element panel (comprising lncRNA PVT1, hsa-miR-130a-3p and RECK) with poor overall survival (OS) was established and qPCR was applied to validate the expressions of hub RNAs. Hub RNAs were firmly associated with T, M, and N stage. The CIBERSORT database showed that the high lassoScore group exhibited a significantly high ratio of resting memory CD4⁺ T cells, M2 macrophages and a significantly low ratio of activated memory CD4⁺ T cells and M1 macrophages. According to the TIMER database, this panel was linked to immune infiltrations and immune cell gene markers. TISIDB database indicated that RECK was positively correlated with immune checkpoints (including CD160, CD244, PDCD1, and TGFBR1). Discussion: A novel triple prognostic panel of GC constructed based on the ceRNA network was associated with clinical prognostic, clinicopathological features, immune infiltrations, immune checkpoints and immune gene markers. This panel might provide potential therapeutic targets for GC and more experimental verification research is needed.

A novel bimetallic MXene derivative QD-based ECL sensor for miRNA-27a-3p detection

In this work, a novel ECL biosensor has been developed based on bimetallic MXene derivative QDs (Mo₂TiC₂ QDs) and SnS₂ nanosheets/lipid bilayer to detect the gastric cancer marker miRNA-27a-3p. On the one hand, the inter-band excitation of Mo₂TiC₂ QDs can inject the additional carriers, which were less suppressed by boundary effects and made a significant contribution to the luminescence process. Semiconductor Mo₂TiC₂ further inhibited the formation of internal electric field and potential oxidation. Therefore, Mo₂TiC₂ QDs processed superior luminous intensity and better stability. On the other hand, SnS₂ nanosheets coated with phospholipid bilayer were designed as sensing interface. SnS₂ nanosheets not only enhanced the luminous intensity of Mo₂TiC₂ QDs by virtue of their large surface area and low dielectric constant, but also improved the stability of lipid bilayer. Due to the excellent properties and synergy work of Mo₂TiC₂ QDs and the lipid bilayer-modified SnS₂ nanosheets, the sensing system displayed high sensitivity and good reproducibility in the analysis application. As a result, the biosensor displayed good linear correlation between the ECL intensity and the concentration of miRNA-27a-3p over a wide range from 1 fM to 10 nM with the detection limit as low as 1 fM. The sensing system including the joint contribution of Mo₂TiC₂ QDs, SnS₂ nanosheets and lipid bilayers had great potential for clinical applications.

Gastric cancer-associated long non-coding RNA profiling and noninvasive biomarker screening based on a high-risk population cohort

BACKGROUND

Effective noninvasive biomarkers of gastric cancer (GC) are critical for early detection and improvement of prognosis. We performed genome-wide long non-coding RNA (lncRNA) microarray analysis to identify and validate novel GC biomarkers depending on a high-risk population cohort.

METHODS

LncRNA profiles were described using the Human LncRNA Microarray between GC and control plasma samples. The differential candidate lncRNAs were validated in two stages by quantitative reverse transcription polymerase chain reaction (qRT-PCR). We further evaluated the joint effect between the GC-associated lncRNA and Helicobacter pylori (H. pylori) infection on the risk of cardia and non-cardia GC, respectively.

RESULTS

Different lncRNA expression profiles were identified between GC and control plasma with a total of 1206 differential lncRNAs including 470 upregulated and 736 downregulated in GC compared with the control group. The eight significantly upregulated lncRNAs (RP11-521D12.1, AC011995.3, RP11-5P4.3, RP11-244 K5.6, RP11-422 J15.1, CTD-2306 M5.1, CTC-428G20.2, and AC009133.20) in GC cases both in the present study and a similar microarray screening study by our collaborative team were selected for a two-stage validation. After the large sample size validation, the subjects with higher expression of RP11-244 K5.6 showed a significantly increased risk of GC with an adjusted odds ratio (OR) as 2.68 and 95% confidence interval (CI) as 1.15-6.24. Joint effects between RP11-244 K5.6 expression and H. pylori infection on the risk of GC were evaluated with no statistical significance.

CONCLUSIONS

Our study found different lncRNA expression profiles between GC and control plasma and preliminarily identified RP11-244 K5.6 as a potential noninvasive biomarker for GC screening.

CDK regulators—Cell cycle progression or apoptosis—Scenarios in normal cells and cancerous cells

Serine/threonine kinases called cyclin-dependent kinases (CDKs) interact with cyclins and CDK inhibitors (CKIs) to control the catalytic activity. CDKs are essential controllers of RNA transcription and cell cycle advancement. The ubiquitous overactivity of the cell cycle CDKs is caused by a number of genetic and epigenetic processes in human cancer, and their suppression can result in both cell cycle arrest and apoptosis. This review focused on CDKs, describing their kinase activity, their role in phosphorylation inhibition, and CDK inhibitory proteins (CIP/KIP, INK 4, RPIC). We next compared the role of different CDKs, mainly p21, p27, p57, p16, p15, p18, and p19, in the cell cycle and apoptosis in cancer cells with respect to normal cells. The current work also draws attention to the use of CDKIs as therapeutics, overcoming the pharmacokinetic barriers of pan-CDK inhibitors, analyze new chemical classes that are effective at attacking the CDKs that control the cell cycle (cdk4/6 or cdk2). It also discusses CDKI's drawbacks and its combination therapy against cancer patients. These findings collectively demonstrate the complexity of cancer cell cycles and the need for targeted therapeutic intervention. In order to slow the progression of the disease or enhance clinical outcomes, new medicines may be discovered by researching the relationship between cell death and cell proliferation.

A new biomarker for the early diagnosis of gastric cancer: gastric juice- and serum-derived SNCG

Aim: To explore the possibility of gastric juice (GJ)- and serum-derived SNCG as a potential biomarker for the early diagnosis of gastric cancer (GC). Materials & methods: GJ and serum samples were collected from 87 patients with GC, 38 patients with gastric precancerous lesions and 44 healthy volunteers. The levels of SNCG in GJ and serum samples were detected by ELISA. Results: The levels of SNCG in GJ and serum were significantly higher in the GC group when compared with the GPL group or the control group. The expression of SNCG in GJ and serum was associated with tumor node metastasis stage, lymph node metastasis, tumor size and drinking, and it is important for the diagnosis and prognosis of GC (p < 0.05). Conclusion: The findings highlight the significance of SNCG in GC diagnosis and prognosis and implicate SNCG as a promising candidate for GC treatment.

MicroRNA Profiling of the Tears of Children With Vernal Keratoconjunctivitis

Vernal Keratoconjunctivitis (VKC) is a chronic conjunctival inflammatory condition that typically affects children. Extracellular microRNAs (miRNAs) are small noncoding RNA molecules, the expression of which is reported to regulate cellular processes implicated in several eye diseases. The aim of this preliminary study is to identify the miRNA expression profile in the tears of children with VKC vis-à-vis controls, and to statistically evaluate these miRNAs as potential diagnostic biomarkers of VKC. The study involved a VKC group and a control group. Tear specimens were collected using Schirmer’s strips. RNA was isolated using miRNeasy Micro kit and quantification was performed using an Agilent Bioanalyzer RNA 6000 Nano kit and Small RNA kit. miRNA profiling was performed using the Agilent microarray technique. A total of 51 miRNAs (48 upregulated and three downregulated) were differentially expressed in the tears of children with VKC and controls. The three most significantly upregulated miRNAs were hsa-miR-1229-5p, hsa-miR-6821-5p, and hsa-miR-6800-5p, and the three most significantly downregulated miRNAs were hsa-miR-7975, hsa-miR-7977, and hsa-miR-1260a. All the upregulated miRNAs are potential diagnostic biomarkers of VKC pending validation due to their larger discriminatory area under the curve (AUC) values. miRNA target prediction analysis revealed multiple overlapping genes that are known to play a role in conjunctival inflammation. We identified a set of differentially expressed miRNAs in the tears of children with VKC that may play a role in VKC pathogenesis. This study serves as the platform study for future miRNA studies that will provide a deeper understanding of the pathophysiology of VKC.

Effectiveness of managing suspected metastasis using plasma D-dimer testing in gastric cancer patients

Tumor metastasis is closely related to the coagulation system. Tumor metastasis and hypercoagulability promote each other through multiple mechanisms. However, whether coagulation indicators can reflect tumor metastasis remains to be explored. Clinical characteristics of a total of 3447 patients from three tertiary referral centers were collected. Then the diagnostic efficacy of FDP, D-dimer and GC tumor markers [Carcinoembryonic antigen (CEA), Carbohydrate antigen 19-9 (CA19-9) and Carbohydrate antigen 72-4 (CA72-4)] for GC metastases was evaluated by the receiver operating characteristic curve (ROC) analyses. Then we conducted a joint ROC curve analysis. The effects of coagulation parameters and tumor markers on gastric cancer metastasis were assessed using multiple logistic regression analysis. 2049 patients were diagnosed with primary GC, 1398 patients with metastatic GC. Based on comparison of AUC, FDP (cutoff, 1.915) had significantly higher diagnostic efficacy than fibrinogen (P<0.001), CEA (P<0.001), CA199 (P<0.001) and CA724 (P<0.001). No significant difference was observed between D-dimer (cutoff, 0.905) and FDP (P=0.158). The AUC of tumor markers combined with coagulation indexes was higher than that without combination (P<0.001). In multiple logistic regression analysis, age, smoking, D-dimer, FDP, CEA, CA19-9, CA72-4 were found to be significantly associated with GC metastasis (all P<0.001, except for smoking P=0.004). We conclude that plasma FDP and D-dimer may be novel clinical biomarkers for screening metastases of GC.

Gastric cancer: An epigenetic view

Gastric cancer (GC) poses a serious threat worldwide with unfavorable prognosis mainly due to late diagnosis and limited therapies. Therefore, precise molecular classification and search for potential targets are required for diagnosis and treatment, as GC is complicated and heterogeneous in nature. Accumulating evidence indicates that epigenetics plays a vital role in gastric carcinogenesis and progression, including histone modifications, DNA methylation and non-coding RNAs. Epigenetic biomarkers and drugs are currently under intensive evaluations to ensure efficient clinical utility in GC. In this review, key epigenetic alterations and related functions and mechanisms are summarized in GC. We focus on integration of existing epigenetic findings in GC for the bench-to-bedside translation of some pivotal epigenetic alterations into clinical practice and also describe the vacant field waiting for investigation.

Survival estimation in patients with stomach and esophageal carcinoma using miRNA expression profiles

Identifying a miRNA signature associated with survival will open a new window for developing miRNA-targeted treatment strategies in stomach and esophageal cancers (STEC). Here, using data from The Cancer Genome Atlas on 516 patients with STEC, we developed a Genetic Algorithm-based Survival Estimation method, GASE, to identify a miRNA signature that could estimate survival in patients with STEC. GASE identified 27 miRNAs as a survival miRNA signature and estimated the survival time with a mean squared correlation coefficient of 0.80 ± 0.01 and a mean absolute error of 0.44 ± 0.25 years between actual and estimated survival times, and showed a good estimation capability on an independent test cohort. The miRNAs of the signature were prioritized and analyzed to explore their roles in STEC. The diagnostic ability of the identified miRNA signature was analyzed, and identified some critical miRNAs in STEC. Further, miRNA-gene target enrichment analysis revealed the involvement of these miRNAs in various pathways, including the somatotrophic axis in mammals that involves the growth hormone and transforming growth factor beta signaling pathways, and gene ontology annotations. The identified miRNA signature provides evidence for survival-related miRNAs and their involvement in STEC, which would aid in developing miRNA-target based therapeutics.

Microarray profile analysis identifies ETS1 as potential biomarker regulated by miR-23b and modulates TCF4 in gastric cancer

Background

Gastric cancer (GC), a common malignancy of the human digestive system, represents the second leading cause of cancer-related deaths worldwide. Early detection of GC has a significant impact on clinical outcomes. The aim of this study was to identify potential GC biomarkers.

Methods

In this study, we conducted a multi-step analysis of expression profiles in GC clinical samples downloaded from TCGA database to identify differentially expressed miRNAs (DEMs) and differentially expressed mRNAs (DEGs). Potential prognostic biomarkers from the available DEMs were then established using the Cox regression method. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to investigate the biological role of the predicted target genes of the miRNA biomarkers. Then, the prognostic DEM-mediated regulatory network was constructed based on transcription factor (TF)–miRNA–target interaction. Subsequently, the consensus genes were further determined based on the overlap between DEGs and these target genes of DEMs. Besides, expression profile, co-expression analysis, immunity, and prognostic values of these prognostic genes were also investigated to further explore the roles in the mechanism of GC tumorigenesis.

Results

We got five miRNAs, including miR-23b, miR-100, miR-143, miR-145, and miR-409, which are associated with the overall survival of GC patients. Subsequently, enrichment analysis of the target genes of the miRNA biomarkers shown that the GO biological process terms were mainly enriched in mRNA catabolic process, nuclear chromatin, and RNA binding. In addition, the KEGG pathways were significantly enriched in fatty acid metabolism, extracellular matrix (ECM) receptor interaction, and proteoglycans in cancer pathways. The transcriptional regulatory network consisting of 68 TFs, 4 DEMs, and 58 targets was constructed based on the interaction of TFs, miRNAs, and targets. The downstream gene ETS1 of miR-23b and TCF4 regulated by ETS1 were obtained by the regulatory network construction and co-expression analysis. High expression of ETS1 and TCF4 indicated poor prognosis in GC patients, particularly in the advanced stages. The expression of ETS1 and TCF4 was correlated with CD4⁺ T cells, CD8⁺ T cells, and B cells.

Conclusions

miR-23b, ETS1, and TCF4 were identified as the prognostic biomarkers. ETS1 and TCF4 had potential immune function in GC, which provided a theoretical basis for molecular-targeted combined immunotherapy in the future.

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.

Vitamin D modulation and microRNAs in gastric cancer: prognostic and therapeutic role

Gastric adenocarcinoma arises after a complex interaction between the host and environmental factors. Tumor location and TNM are the tools that currently guide treatment decisions. Surgery is the only curative treatment, but relapse is common. After relapse or advanced staged disease survival is poor and systemic treatment has modestly improved survival. An association between sun exposure, vitamin D status and gastric cancer (GC) incidence and mortality has been reported. The molecular differences of the histological subtypes and the new molecular classifications account for the great heterogeneity of this disease and are the basis for the discovery of new therapeutic targets. New prognostic and predictive factors are essential and microRNAs (miRNAs) are endogenous small non-coding RNA molecules with a great potential for diagnosis, prognosis and treatment of cancer. There are hundreds of miRNAs with altered expression in tumor gastric tissue when compared to normal gastric tissue. Many of these miRNAs are associated with clinicopathological variables and survival in patients with GC. Furthermore, the expression of some of these miRNAs with prognostic importance in CG is influenced by vitamin D and others are mediators of some of the actions of this vitamin. This review aims to update the evidence on several miRNAs with prognostic value and therapeutic potential in GC, whose expression may be influenced by vitamin D or may regulate vitamin D signaling.

Non-coding RNAs in Wilms' tumor: biological function, mechanism, and clinical implications

Non-coding RNAs are involved with maintenance and regulation of physiological mechanisms and are involved in pathological processes, such as cancer. Among the small ncRNAs, miRNAs are the most explored in tumorigenesis, metastasis development, and resistance to chemotherapy. These small molecules of ~ 22 nucleotides are modulated during early renal development, involved in the regulation of gene expression and Wilms' tumor progression. Wilms' tumors are embryonic tumors with few mutations and complex epigenetic dysregulation. In recent years, the small ncRNAs have been explored as potentially related both in physiological development and in the tumorigenesis of several types of cancer. Besides, genes regulated by miRNAs are related to biological pathways as PI3K, Wnt, TGF-β, and Hippo signaling pathways, among others, which may be involved with the underlying mechanisms of resistance to chemotherapy, and in this way, it has emerged as potential targets for cancer therapies, including for Wilms' tumors.

TASP1 Promotes Proliferation and Migration in Gastric Cancer via EMT and AKT/P-AKT Pathway

Threonine aspartase 1 (TASP1) was reported to function in the development of cancer. However, the regulatory mechanism of TASP1 in gastric cancer (GC) remains unclear. In this study, we determined the expression of TASP1 in tissues of GC patients, GC cells by qRT-PCR, and western blot and assessed the relationship between TASP1 and GC cell proliferation and migration via CCK-8 and transwell assay. It was found that the expression of TASP1 in GC tissues or GC cell lines was significantly higher than that in normal adjacent tissues or normal cells. The proliferation and migration of GC cells were inhibited upon TASP1 knockdown. Mechanism investigation revealed that TASP1 promoted GC cell proliferation and migration through upregulating the p-AKT/AKT expression. TASP1 induced GC cell migration via the epithelial -mesenchymal transition (EMT) pathway. In conclusion, TASP1 promotes GC progression through the EMT and AKT/p-AKT pathway, and it may serve as a new potential biomarker and therapeutic target for GC.

BBOX1-AS1 Accelerates Gastric Cancer Proliferation by Sponging miR-3940-3p to Upregulate BIRC5 Expression

BACKGROUND

Gastric cancer (GC) is one type of the most general malignancies in the globe. Research increasingly suggests long non-coding RNAs (lncRNAs) exert crucial roles in GC. However, the function of BBOX1-AS1 in GC has not been reported yet, it needs more explorations.

AIMS

The aim of the study is to figure out the role and related regulation mechanism of BBOX1-AS1 in GC.

METHODS

RT-qPCR assay was applied to detect genes expression. The role of BBOX1-AS1 in GC was investigated by cell counting kit-8, colony formation, tunel detection, and western blot assays. The binding ability between miR-3940-3p and BBOX1-AS1 (or BIRC5) by RIP, RNA pull-down and luciferase reporter assays.

RESULTS

The expression of BBOX1-AS1 presented significantly upregulation in GC tissues and cells. Moreover, upregulation of BBOX1-AS1 promoted GC cell proliferation, and inhibited GC cell apoptosis. However, downregulation of BBOX1-AS1 led to opposite results. Furtherly, we discovered that BBOX1-AS1 bound with miR-3940-3p and also negatively regulated miR-3940-3p. Besides, it proved that miR-3940-3p interplayed with BIRC5 and negatively regulated BIRC5. Through rescue experiments, we proved that BIRC5 reversed miR-3940-3p-mediated cell proliferation or apoptosis in BBOX1-AS1-dysregulated GC cells.

CONCLUSIONS

BBOX1-AS1 accelerates GC proliferation by sponging miR-3940-3p to upregulate BIRC5 expression, which may guide a new direction into the therapeutic strategies of GC.

Electrochemical detection of miRNA-100 in the sera of gastric cancer patients based on DSN-assisted amplification

Gastric cancer (GC) is a common malignant digestive tract tumor that leads to high mortality worldwide. Early diagnosis of GC is very important for adequate treatment. However, a rapid, specific and sensitive method for the detection of GC is currently not available. Here, a biosensor CPs/AuNP-AuE, the gold nanoparticle (AuNP)-modified Au electrode (AuE) which was coupled with DNA capture probes (CPs), was developed to detect the content of miR-100 in the sera of GC patients. The results showed that AuNPs were uniformly deposited on the surface of AuE. AuNPs enhanced the electrical conductivity and improved the effective area of AuE. CPs were successfully assembled on AuNP-AuE that could be digested by duplex-specific nuclease (DSN) from the miR-100/CPs complex on the electrode, improving the sensitivity of the biosensor by recycling miR-100. The data revealed that the biosensor was highly specific for the detection of miR-100, which had the ability to distinguish one base-pair mistake in miR-100. The detection of the biosensor for miR-100 ranged from 100 aM to 10 pM and the limit of detection (LOD) was estimated to be 100 aM. The detection results of 100 human sera samples using this biosensor indicated that the cutoff for the detection of gastric cancer was 5 fM. Therefore the biosensor developed in our study served as a rapid, specific and sensitive strategy for the detection of gastric cancer in clinic.

miR-96-5p enhances cell proliferation and invasion via targeted regulation of ZDHHC5 in gastric cancer

Objective: To explore the biological function and mechanism of miR-96-5p in gastric cancer.

Methods: The expression of differently expressed microRNAs (DEMs) related to gastric adenocarcinoma (GAC) prognosis was identified in GAC tumor samples and adjacent normal samples by qRT-PCR. A target gene miR-96-5p was selected using TargetScan, miRTarBase, miRDB databases. The combination of miR-96-5p and ZDHHC5 was verified by luciferase receptor assay. To further study the function and mechanism of miR-96-5p, we treated MGC-803 cells with miR-96-5p inhibitor and si-ZDHHC5, then detected cell viability, apoptosis, migration and invasion ability, as well as the expression of ZDHHC5, Bcl-2, Bax, cleaved caspase-3, cleaved caspase-9, and COX-2 by Western blot.

Results: Compared with adjacent normal samples, the levels of miR-96-5p, miR-222-5p, and miR-652-5p were remarkably increased, while miR-125-5p, miR-145-3p, and miR-379-3p were significantly reduced in GAC tumor samples (P<0.01), which were consistent with bioinformatics analysis. Furthermore, ZDHHC5 was defined as a direct target gene of miR-96-5p. miR-96-5p silence significantly reduced cell viability, increased cell apoptosis, and suppressed cell migration and invasion, as well as inhibited the expression of Bcl-2 and COX-2 and promoted Bax, cleaved caspase-3 and cleaved caspase-9 level in MGC-803 cells (P<0.01). Notably, ZDHHC5 silence reversed the inhibiting effects of miR-96-5p on MGC-803 cells growth and metastasis

Conclusion: Our findings identified six microRNAs (miRNAs; miR-96-5p, miR-222-5p, miR-652-5p, miR-125-5p, miR-145-3p, and miR-379-3p) related to GAC prognosis, and suggested that down-regulated miR-96-5p might inhibit tumor cell growth and metastasis via increasing ZDHHC5 expression enhance MGC-803 cell apoptosis, as well as decrease MGC-803 cell metastasis.

FOXI1 inhibits gastric cancer cell proliferation by activating miR-590/ATF3 axis via integrating ChIP-seq and RNA-seq data

FOXI1 plays a key role in the development of gastric cancer. However, the whole genome FOXI1 binding sites and its target genes are unclear. In the present study, we used ChIP-seq and RNA-seq technologies to identify the target gene of FOXI1. Firstly, ChIP-seq data showed that, 4476 unique peaks in the genome region were captured. Most of these binding peaks are located in introns or intergenic regions. We annotated all the peaks to the nearest gene and identified 404 genes as FOXI1 binding genes. KEGG and GO analysis showed that FOXI1 binding gene to be correlated with the cellular process, cell part, cell, binding, single-organism process. Further, we performed FOXI1-overexpressed RNA-seq experiment. We comprehensively analyzed the ChIP-seq and RNA-seq data and take the intersection of two databases, several genes were identified. ATF3 was selected from the intersection since ATF3 was the most enriched mRNA after FOXI1 overexpressed. ChIP-qPCR and luciferase report gene were used to validate that ATF3 was target gene of FOXI1. Intriguely, ATF3 protein was significantly downregulated after FOXI1 overexpressed. We found FOXI1 can also bind to the promoter of miR-590 and active it which directly target ATF3. The binding site between FOXI1 and miR-590 was verified by ChIP-qPCR and luciferase report gene, and the target relationship between miR-590 and ATF3 was confirmed by dual-luciferase reporter gene. In conclusion, our data identified the genome binding sites of FOXI1, and provide evidence that FOXI1 inhibits gastric cancer cell proliferation by activating miR-590/ATF3 axis.

miR-335-5p suppresses gastric cancer progression by targeting MAPK10

Background

Recent studies have established the roles of microRNAs (miRNAs) in cancer progression. The aberrant expression of miR-335-5p has been reported in many cancers, including gastric cancer (GC). In this study, the precise roles of miR-335-5p in GC as well as the molecular mechanisms underlying its effects, including the role of its target MAPK10, were evaluated.

Methods

Quantitative real-time PCR was used to evaluate miR-335-5p levels in GC cell lines and tissues. MTT and colony formation assays were used to detect cell proliferation, and Transwell and wound-healing assays were used to evaluate the invasion and migration of GC cells. The correlation between levels of miR-335-5p and the cell cycle-related target gene mitogen-activated protein kinase 10 (MAPK10) in GC was analyzed. In addition, the candidate target was evaluated by a luciferase reporter assay, qRT-PCR, and western blotting.

Results

The levels of miR-335-5p were downregulated in GC tissues and cell lines. Furthermore, miR-335-5p inhibited the proliferation and migration of GC cells and induced apoptosis. Additionally, miR-335-5p arrested the cell cycle at the G1/S phase in GC cells in vitro. Levels of miR-335-5p and the cell cycle-related target gene MAPK10 in GC were correlated, and MAPK10 was directly targeted by miR-335-5p.

Conclusions

These data suggest that miR-335-5p is a tumor suppressor and acts via MAPK10 to inhibit GC progression.

Polymorphisms in Pepsinogen C and miRNA Genes Associate with High Serum Pepsinogen II in Gastric Cancer Patients

Background: Pepsinogen (PG) II (PGII) is a serological marker used to estimate the risk of gastric cancer but how PGII expression is regulated is largely unknown. It has been suggested that PGII expression, from the PGC (Progastricsin) gene, is regulated by microRNAs (miRNA), but how PGII levels vary with Helicobacter pylori (H. pylori) infection and miRNAs genotype remains unclear. Methods: Serum levels of PGI and PGII were determined in 80 patients with gastric cancer and persons at risk for gastric cancer (74 first-degree relatives of patients, 62 patients with autoimmune chronic atrophic gastritis, and 2 patients with dysplasia), with and without H. pylori infection. As control from the general population, 52 blood donors were added to the analyses. Associations between PGII levels and genetic variants in PGC and miRNA genes in these groups were explored based on H. pylori seropositivity and the risk for gastric cancer. The two-dimensional difference in gel electrophoresis (2D-DIGE) and the NanoString analysis of messenger RNA (mRNAs) from gastric cancer tissue were used to determine the pathways associated with increased PGII levels. Results: PGII levels were significantly higher in patients with gastric cancer, and in those with H. pylori infection, than in other patients or controls. A PGI/PGII ratio ≤ 3 was found better than PGI < 25 ng/mL to identify patients with gastric cancer (15.0% vs. 8.8%). For two genetic variants, namely rs8111742 in miR-Let-7e and rs121224 in miR-365b, there were significant differences in PGII levels between genotype groups among patients with gastric cancer (p = 0.02 and p = 0.01, respectively), but not among other study subjects. Moreover, a strict relation between rs9471643 C-allele with H. pylori infection and gastric cancer was underlined. Fold change in gene expression of mRNA isolated from gastric cancer tissue correlated well with polymorphism, H. pylori infection, increased PGII level, and pathway for bacteria cell entry into the host. Conclusions: Serum PGII levels depend in part on an interaction between H. pylori and host miRNA genotypes, which may interfere with the cut-off of PGI/PGII ratio used to identify persons at risk of gastric cancer. Results reported new findings regarding the relation among H. pylori, PGII-related host polymorphism, and genes involved in this interaction in the gastric cancer setting.

Systematic Analysis of microRNA Biomarkers for Diagnosis, Prognosis, and Therapy in Patients With Clear Cell Renal Cell Carcinoma

The ever-increasing morbidity and mortality of clear cell renal cell carcinoma (ccRCC) urgently demands updated biomarkers. MicroRNAs (miRNAs) are involved in diverse biological processes such as cell proliferation, differentiation, apoptosis by regulating their target genes’ expression. In kidney cancers, miRNAs have been reported to be involved in tumorigenesis and to be the diagnostic, prognostic, and therapeutic response biomarkers. Here, we performed a systematic analysis for ccRCC-related miRNAs as biomarkers by searching keywords in the NCBI PubMed database and found 118 miRNAs as diagnostic biomarkers, 28 miRNAs as prognostic biomarkers, and 80 miRNAs as therapeutic biomarkers in ccRCC. miRNA-21, miRNA-155, miRNA-141, miRNA-126, and miRNA-221, as significantly differentially expressed miRNAs between cancer and normal tissues, play extensive roles in the cell proliferation, differentiation, apoptosis of ccRCC. GO and KEGG enrichment analysis of these miRNAs’ target genes through Metascape showed these target genes are enriched in Protein Domain Specific Binding (GO:0019904). In this paper, we identified highly specific miRNAs in the pathogenesis of ccRCC and explored their potential applications for diagnosis, prognosis, and treatment of ccRCC.

Screening lncRNAs with diagnostic and prognostic value for human stomach adenocarcinoma based on machine learning and mRNA-lncRNA co-expression network analysis

BACKGROUND

Stomach adenocarcinoma (STAD), is one of the most lethal malignancies around the world. The aim of this study was to find the long noncoding RNAs (lncRNAs) acting as diagnostic and prognostic biomarker of STAD.

METHODS

Base on TCGA dataset, the differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) were identified between STAD and normal tissue. The machine learning and survival analysis were performed to evaluate the potential diagnostic and prognostic value of lncRNAs for STAD. We also build the co-expression network and functional annotation. The expression of selected candidate mRNAs and lncRNAs were validated by Quantitative real-time polymerase chain reaction (qRT-PCR) and GSE27342 dataset. GSE27342 dataset were also to perform gene set enrichment analysis.

RESULTS

A total of 814 DEmRNAs and 106 DElncRNAs between STAD and normal tissue were obtained. FOXD2-AS1, LINC01235, and RP11-598F7.5 were defined as optimal diagnostic lncRNA biomarkers for STAD. The area under curve (AUC) of the decision tree model, random forests model, and support vector machine (SVM) model were 0.797, 0.981, and 0.983, and the specificity and sensitivity of the three model were 75.0% and 97.1%, 96.9% and 96%, and 96.9% and 97.1%, respectively. Among them, LINC01235 was not only an optimal diagnostic lncRNA biomarkers, but also related to survival time. The expression of three DEmRNAs (ESM1, WNT2, and COL10A1) and three optimal diagnostic lncRNAs biomarkers (FOXD2-AS1, RP11-598F7.5, and LINC01235) in qRT-PCR validation was were consistent with our integrated analysis. Except for FOXD2-AS1, ESM1, WNT2, COL10A1, and LINC01235 were upregulated in STAD, which was consistent with our integration results. Gene set enrichment analysis results indicated that DNA replication, Cell cycle, ECM-receptor interaction, and P53 signaling pathway were four significantly enriched pathways in STAD.

CONCLUSION

Our study identified three DElncRNAs as potential diagnostic biomarkers of STAD. Among them, LINC01235 also was a prognostic lncRNA biomarkers.

An insight into the roles of piRNAs and PIWI proteins in the diagnosis and pathogenesis of oral, esophageal, and gastric cancer

P-Element induced wimpy testis (PIWI)-interacting RNA (piRNA) is a member of the non-coding RNAs family. Four PIWI proteins are found to be expressed in humans. The number of studies focusing on the roles of piRNAs and PIWI proteins in the field of cancer is increasing. Oral, esophageal, and gastric cancers are considered as important causes of death. PIWI proteins and piRNAs are suggested to be involved in the pathogenesis of these diseases. Thus, studying these molecules may be beneficial for finding new therapeutics. Since it is shown that currently used biomarkers for these cancers have low sensitivity and specificity, there is a necessity for identifying novel non-invasive biomarkers which are highly sensitive and specific. This paper will provide an insight into current knowledge about the functions of PIWI proteins and piRNAs in the oral, esophageal, and gastric cancer. We discuss how PIWI proteins and piRNAs can be involved in the pathogenesis of these cancers. Moreover, we review the studies concerning with the roles of PIWI proteins and piRNAs as biomarkers which are used for diagnostic and prognostic purposes.

Inflammatory markers for predicting overall survival in gastric cancer patients: A systematic review and meta-analysis

Systemic inflammatory biomarkers have begun to be used in clinical practice to predict prognosis and survival of cancer patients, but the approach remains controversial. We conducted a meta-analysis to determine the predictive value of the c-reactive protein (CRP), neutrophil-to-lymphocyte ratio (NLR), and Glasgow prognostic score (GPS)/modified Glasgow prognostic score (mGPS) in the clinical outcome of gastric cancer (GC) patients. We searched literature databases to identify relevant studies. All articles identified in the search were independently reviewed based on predetermined selection criteria. Meta-analysis was conducted to calculate the hazard ratio (HR) and 95% confidence intervals (CI) of overall survival of the included studies. A total of 41 eligible cohort studies, involving a total of 18,348 patients meeting the inclusion criteria, were considered for meta-analysis. Increases in CRP (HR = 1.654, 95% CI: 1.272–2.151), NLR (HR = 1.605, 95% CI: 1.449–1.779), and GPS/mGPS (HR = 1.648, 95% CI: 1.351–2.011) were significantly associated with poorer survival in patients with GC. Substantial heterogeneities were noted in all three markers (I² = 86.479%, 50.799%, 69.774%, in CRP, NLR, and GPS/mGPS, respectively). Subgroup analysis revealed a significant positive correlation between each marker and poor survival, regardless of country, study quality, cancer stage, study design, or the inclusion of patients undergoing chemotherapy. This meta-analysis demonstrates that CRP, NLR, and GPS/mGPS are associated with poor survival in patients with GC. Further prospective studies using standardized measurements are warranted to conclude the prognostic value of various inflammatory markers.

Role of Mean Platelet Volume in the Prognosis of Locally Advanced Gastric Cancer: A Tertiary Cancer Center Experience

Introduction

Mean platelet volume (MPV) is an inflammatory marker suggesting the activation of platelets. Many studies observed an association between MPV and cancer spread and metastasis. Hence, we have conducted a retrospective study to find the role of MPV as a prognostic marker in locally advanced gastric cancer.

Materials and methods

The present study included a retrospective review of 149 patients with gastric cancer who had neoadjuvant chemotherapy followed by surgery. MPV was obtained and then statistically analyzed to find an association between tumor (T), node (N), and overall stage as per the American Joint Committee on Cancer (AJCC) staging system, using Statistical Package for the Social Sciences (SPSS) software (IBM Corp., Armonk, NY).

Results

In our study, we observed that MPV values were significantly high in N+ disease (OR 3.794 (95% CI 1.903 - 7.563); p-value 0.0001), higher T stage (OR for >T2 3.692 (95% CI 1.876 - 7.266); p-value 0.0001), and advanced stage (OR 7.708 (95% CI 3.258 - 18.237); p-value 0.0001) of gastric cancer.

Conclusions

MPV is an inflammatory marker that correlates with nodal disease and aids in the staging and prognostication of locally advanced gastric cancer. This inexpensive, convenient marker can aid in the risk stratification of locally advanced gastric cancer.

Evaluation of the value of multiparameter combined analysis of serum markers in the early diagnosis of gastric cancer

BACKGROUND

In early gastric cancer (GC), tumor markers are increased in the blood. The levels of these markers have been used as important indexes for GC screening, early diagnosis and prognostic evaluation. However, specific tumor markers have not yet been discovered. Diagnosis based on a single tumor marker has limited significance. The detection rate of GC is still very low.

AIM

To improve the diagnostic value of blood markers for GC.

METHODS

We used a multiparameter joint analysis of 77 indexes of malignant GC and gastric polyp (GP), 64 indexes of GC and healthy controls (Ctrls).

RESULTS

By analyzing the data, there are 27 indexes in the final Ctrls vs GC with P values < 0.01, the area under the curve (AUC) of albumin is the largest in Ctrls vs GC, and the AUC was 0.907. 30 indexes in GP vs GC have P values < 0.01. Among them, the D-dimer showed an AUC of 0.729. The 27 indexes in Ctrls vs GC and 30 indexes in GP vs GC were used for binary logistic regression, discriminant analysis, classification tree analysis and artificial neural network analysis model. For the ability to distinguish between Ctrls vs GC, GP vs GC, artificial neural networks had better diagnostic value when compared with classification tree, binary logistic regression, and discriminant analysis. When compared Ctrl and GC, the overall prediction accuracy was 92.9%, and the AUC was 0.992 (0.980, 1.000). When compared GP and GC, the overall prediction accuracy was 77.9%, and the AUC was 0.969 (0.948, 0.990).

CONCLUSION

The diagnostic effect of multi-parameter joint artificial neural networks analysis is significantly better than the single-index test diagnosis, and it may provide an assistant method for the detection of GC.

Saliva as a diagnostic tool for dental caries, periodontal disease and cancer: is there a need for more biomarkers?

Introduction: A biomarker is a biological indicator of normal or pathogenic processes. Identification of biomarkers is useful for the prevention, diagnosis and prognosis of diseases as well as for monitoring the progression of pathological disorders. Several types of molecules present in biological fluids can act as biomarkers such as DNA, coding and non-coding RNA, lipids, metabolites, proteins and even microbes. In this context, saliva emerges as a useful diagnostic tool for the detection of biomarkers involved with oral and systemic diseases, since it reflects the pathophysiological conditions of the organism and allows early, rapid, practical and noninvasive detection of biomarkers.Areas covered: This review discusses the properties of saliva as a diagnostic tool and addresses the main identified biomarkers related to dental caries, periodontal disease, head and neck cancer and other types of cancer of considerable incidence among the world population.Expert commentary: Despite extensive efforts which have been directed toward the identification of one or a combination of biomarkers with good predictive values for the early detection of dental caries, periodontal disease and cancer, these biomarkers still need validation before chairside point-of-care devices can be widely used in the clinic.

KIF2A promotes the progression via AKT signaling pathway and is upregulated by transcription factor ETV4 in human gastric cancer

Kinesin family protein 2A (KIF2A), an M-type nonmotile microtubule depolymerase, plays essential roles in development and progression of various human cancers. However, its exact function and the underlying mechanism in tumorigenesis of gastric cancer (GC) haven't been fully elucidated. In the present study, KIF2A was overexpressed in human GC and predicted poor prognosis according to the results of GEPIA analysis. KIF2A was also observed to be upregulated in 82 GC samples compared with paired pericarcinoma tissues. Its overexpression was associated with tumor metastasis (P = 0.047) and Ⅲ stage GC (P = 0.0267). The mRNA and protein expression levels of KIF2A were significantly suppressed in KIF2A specific siRNA transfected GC cells compared with the wild-type and negative control (NC) siRNA transfected cells. Furthermore, the effects of KIF2A on the growth, migration, invasion, and apoptosis of GC cell were evaluated in vitro and the underlying mechanisms were explored. It was found that silencing KIF2A effectively induced the apoptosis, and inhibited the proliferation, migration and invasion capacities of GC cells. Western blot analysis demonstrated that silencing of KIF2A significantly decreased the expression levels of AKT, Cyclin D1 and S6K. Moreover, bioinformatics analysis showed that the promoter (from -414 to -407bp) of KIF2A has the ability to bind to transcription factor ETV4, which was confirmed by bi-luciferase reporter assay using 293T cells. The level of ETV4 was upregulated and positively correlated with KIF2A in human GC tissues. Our results also proved that ETV4 upregulated the expression of KIF2A and blocked the decline of proliferation induced by KIF2A knockdown in MKN-45 and AGS cells. In summary, KIF2A is upregulated by transcription factor ETV4, and its knockdown can effectively inhibit the proliferation and induce the apoptosis of GC cells through the AKT signaling pathway in GC cells, implying that the inhibition of KIF2A expression is a potential target for GC therapy.

DNA hypomethylation promotes invasion and metastasis of gastric cancer cells by regulating the binding of SP1 to the CDCA3 promoter

BACKGROUND

Cell division cycle associated protein-3 (CDCA3) has been reported frequently upregulated in various cancers. It has been progressively realized that changed DNA methylations occur in diverse carcinomas. However, the concrete involvement of CDCA3 and DNA methylation in gastric cancer (GC) still needs to be further elucidated.

METHODS

In this study, quantitative reverse-transcription polymerase chain reaction (PCR) was utilized to determine the relative expressions of CDCA3 in GC and normal tissue samples. The methylation condition of CDCA3 was determined by bisulfite-sequencing PCR (BSP) and methylation-specific PCR (MSP). A chromatin immunoprecipitation (ChIP) assay and luciferase activity assay was used for the interaction between transcription factors and promoters and binding site determination, respectively. The effects of knockdown or overexpression of specificity protein 1 (SP1) or CDCA3 on GC cells in vitro were further assessed via wound healing assay, colony formation assay, and matrigel invasion assay.

RESULTS

In comparison to paired normal tissues, CDCA3 expressions were significantly increased in the GC tissues. The CDCA3 expression was regulated by DNA methylation, with the CpG island hypomethylation responsible for CDCA3 upregulation of GC. ChIP assays verified that the activity of SP1 binding to the CDCA3 promoter was dramatically increased. When the CDCA3 expression was downregulated in MKN45 cells by knockdown SP1, the proliferation ability, healing ability, and invasive ability were significantly suppressed.

CONCLUSION

The process by which SP1 bound to the nearest promoter region was expedited in GC cells, by which DNA was hypomethylated and CDCA3 expression was promoted. The effect on cell proliferation and invasion by CDCA3 was under the regulation of SP1 and also affected by hypomethylation of DNA.

MiR-96-5p inhibition induces cell apoptosis in gastric adenocarcinoma

BACKGROUND

Gastric adenocarcinoma (GAC) mortality rates have remained relatively changed over the past 30 years, and it continues to be one of the leading causes of cancer-related death.

AIM

To search for novel miRNAs related to GAC prognosis and further investigate the effect of miR-96-5p on MGC-803 cells.

METHODS

The miRNA expression profile data of GAC based on The Cancer Genome Atlas were obtained and used to screen differently expressed miRNAs (DEMs) and DEMs related to GAC prognosis. Then, the expression of DEMs related to GAC prognosis was identified in GAC tumor samples and adjacent normal samples by qRT-PCR. The target gene, ZDHHC5, of miR-96-5p was predicted using TargetScan, miRTarBase, and miRDB databases and confirmed by luciferase reporter assay. Furthermore, MGC-803 cells were transfected with inhibitor NC, miR-96-5p inhibitor, si-ZDHHC5, or miR-96-5p inhibitor + si-ZDHHC5, and then cell apoptosis was detected by flow cytometry. The expression of ZDHHC5, Bcl-2, and COX-2 was detected using western blotting.

RESULTS

A total of 299 DEMs and 35 DEMs related to GAC prognosis were screened based on The Cancer Genome Atlas. Then compared with adjacent normal samples, the levels of miR-96-5p, miR-222-5p, and miR-652-5p were remarkably increased, while miR-125-5p, miR-145-3p, and miR-379-3p levels were reduced in GAC tumor samples (P < 0.01), which were consistent with bioinformatics analysis. Furthermore, ZDHHC5 was defined as a direct target gene of miR-96-5p. miR-96-5p inhibition increased the number of apoptotic cells as well as promoted the expression of ZDHHC5, Bcl-2, and COX-2 in MGC-803 cells (P < 0.01). After ZDHHC5 inhibition, the number of apoptotic cells and the expression of ZDHHC5, Bcl-2, and COX-2 were reduced. The addition of an miR-96-5p inhibitor partly reversed these effects (P < 0.01).

CONCLUSION

Our findings identified six miRNAs related to GAC prognosis and suggested that downregulated miR-96-5p might induce cell apoptosis via upregulating ZDHHC5 expression in MGC-803 cells.

Validation of miR-1228-3p as Housekeeping for MicroRNA Analysis in Liquid Biopsies from Colorectal Cancer Patients

Background: Circulating microRNA (miRNA) analysis is a growing research field. However, it usually requires an endogenous control or housekeeping (HK) in order to normalize expression of specific miRNAs throughout different samples. Unfortunately, no adequate HK for circulating miRNA analysis is still known in the colorectal cancer (CRC) context whereas several have been suggested. Hence, our aims were to validate the previously suggested miR-1228-3p as HK for CRC studies, to compare its suitability with the widely used miR-16-5p, and to evaluate the influence of hemolysis on both miRNAs. Methods: We analyzed by quantitative reverse-transcription polymerase chain reaction (qRT-PCR) the expression of miR-1228-3p, miR-16-5p and the spike-in cel-miR-39 in a set of 297 plasmas (92 CRC, 101 advanced adenomas -AA-, and 100 controls) and 213 serum samples (59 CRC, 74 AA and 80 controls). We also analyzed both miRNAs depending on the hemolysis degree in 7 plasmas and 31 serums. Results: Levels of miR-1228-3p and miR-16-5p did not show significant differences between groups although miR-16-5p exhibited more variability in plasma and serum samples. Importantly, the combination of cel-miR-39 and miR-1228-3p was the most stable one. Moreover, we observed that miR-16-5p was significantly influenced by hemolysis in contrast with miR-1228-3p that exhibited no correlation with this confounding factor in both biofluids. Conclusion: MiR-1228-3p has been validated as an adequate endogenous control for circulating miRNA analysis in CRC and AA liquid biopsies.

miRNAs in gastrointestinal diseases: can we effectively deliver RNA-based therapeutics orally?

Nucleic acid-based therapeutics are evaluated for their potential of treating a plethora of diseases, including cancer and inflammation. Short nucleic acids, such as miRNAs, have emerged as versatile regulators for gene expression and are studied for therapeutic purposes. However, their inherent instability in vivo following enteral and parenteral administration has prompted the development of novel methodologies for their delivery. Although research on the oral delivery of siRNAs is progressing, with the development and utilization of promising carrier-based methodologies for the treatment of a plethora of gastrointestinal diseases, research on miRNA-based oral therapeutics is lagging behind. In this review, we present the potential role of miRNAs in diseases of the GI tract, and analyze current research and the cardinal features of the novel carrier systems used for nucleic acid oral delivery that can be expanded for oral miRNA administration.

Identification of ncRNA-Mediated Functions of Nucleus-Localized miR-320 in Cardiomyocytes

In recent years, systematic analyses of the subcellular distribution of microRNAs (miRNAs) suggest that the majority of miRNAs are present in both nuclear and cytoplasmic compartments. However, the full extent of nuclear miRNA function in cardiomyocytes is currently unknown. Here, subcellular fractionation, followed by the miRNA microarray, revealed that most miRNAs were detectable in both nuclear and cytoplasmic fractions of cardiomyocytes. We employed miR-320 as an example to explore the function of nucleus-localized miRNAs, finding that CRISPR-Cas9-mediated Ago2 knockdown abolished miR-320-induced transcriptional remodeling. Furthermore, nuclear Ago2 re-expression restored the effects of miR-320 in the nucleus. Moreover, liquid chromatography-mass spectrometry (LC-MS) analysis revealed the association of nuclear Ago2 with transcription factors YLP motif-containing protein 1 (Ylpm1) and single-stranded DNA binding protein 1 (Ssbp1). Intersection of the data of transcriptome-sequencing (seq) with Ago2-chromatin immunoprecipitation (ChIP)-seq revealed that the binding of Ago2 with the target promoter DNA may require promoter RNAs. Specifically, Cep57 was upregulated, whereas Fscn2 was downregulated by miR-320, and a similar effect was also observed by knockdown of their promoter RNA, respectively. Chromatin isolation by RNA purification (ChIRP) analysis showed decreased binding of the Cep57 and Fscn2 promoter RNA on their promoter DNA by miR-320 overexpression.Our work provided a preliminary idea that promoter RNA transcripts act as “pioneers” to disrupt chromatin that permits Ago2/miR-320 complexes to target Cep57 or Fscn2 promoter DNA for transcriptional regulation. miRNAs are naturally located in both cytoplasm and nucleus; however, their pathophysiological functions are largely unknown. Our work provided a theoretical basis for developing nuclear miRNA-based therapeutics against various diseases in the future.

Genomewide Expression Profiling Identifies a Novel miRNA-Based Signature for the Detection of Peritoneal Metastasis in Patients With Gastric Cancer

OBJECTIVE

This study aimed to conduct a genomewide transcriptomic profiling to develop a microRNA (miRNA)-based signature for the identification of peritoneal metastasis (PM) in patients with gastric cancer (GC).

SUMMARY BACKGROUND DATA

Even though PM in patients with GC has long been recognized to associate with poor prognosis, currently there is lack of availability of molecular biomarkers for its robust diagnosis.

METHODS

We performed a systematic biomarker discovery by analyzing miRNA expression profiles in primary tumors from GC patients with and without PM, and subsequently validated the expression of candidate miRNA biomarkers in 3 independent clinical cohorts of 354 patients with advanced GC.

RESULTS

Five miRNAs (miR-30a-5p, -134-5p, -337-3p, -659-3p, and -3917) were identified during the initial discovery phase; three of which (miR-30a-5p, -659-3p, and -3917) were significantly overexpressed in the primary tumors from PM-positive patients in the testing cohort (P = 0.002, 0.04, and 0.007, respectively), and distinguished patients with versus without peritoneal metastasis with the value of area under the curve (AUC) of 0.82. Furthermore, high expression of these miRNAs also associated with poor prognosis (hazard ratio = 2.18, P = 0.04). The efficacy of the combination miRNA signature was subsequently validated in an independent validation cohort (AUC = 0.74). Finally, our miRNA signature when combined together with the macroscopic Borrmann's type score offered a much superior diagnostic in all 3 cohorts (AUC = 0.87, 0.76, and 0.79, respectively).

CONCLUSIONS

We have established an miRNA-based signature that have a potential to identify peritoneal metastasis in GC patients.

Schisantherin A induces cell apoptosis through ROS/JNK signaling pathway in human gastric cancer cells

Gastric cancer is one of the most lethal cancers with unmet clinical treatment and low 5-year survival rate. Schisantherin A is a major compound derived from Fructusschisandrae while its anti-tumor role remains nearly unknown. Here, we reported that schisantherin A had an anti-proliferation effect on gastric cancer cell lines MKN45 and SGC-7901. Schisantherin A induced cell cycle arrest at G2/M phase and cell apoptosis, and inhibited cell migration in gastric cancer MKN45 and SGC7901 cells. Meanwhile, upregulation of cleaved caspase-9, cleaved caspase-3 and cleaved PARP were accompanied with the loss of mitochondrial membrane potential (MMP). Moreover, schisantherin A induced ROS-dependent JNK phosphorylation with higher ROS production. The JNK inhibitor and ROS scavenger NAC rescued the cell apoptosis and cycle inhibition elicited by schisantherin A. Furthermore, the expression level of antioxidant factor Nrf2 was suppressed by schisantherin A. These findings suggest that schisantherin A possesses an anti-tumor activity via activation of ROS/JNK with Nrf2 inhibition, indicating that schisantherin A is a promising chemotherapeutic candidate for gastric cancer.

miR-9-5p Suppresses Malignant Biological Behaviors of Human Gastric Cancer Cells by Negative Regulation of TNFAIP8L3

BACKGROUND

MicroRNA is essential for the malignant progression of human gastric cancer (GC), which is a leading cause of cancer deaths. However, the mechanism is still not so clear.

AIMS

In our present research, we investigated the effect of miR-9-5p in GC.

METHODS

We detected miR-9-5p expression in human gastric epithelial cell (GES-1) and GC cells (AGS, BGC-823, MKN-45, and MGC-803), plasma of normal or GC patients, as well as orthotopic xenograft mouse models by real-time PCR. The migration ability was detected by Transwell assays after miR-9-5p mimic or inhibitor transfection in GC cells.

RESULTS

Our results showed that miR-9-5p expression in GC cells and plasma was significantly decreased. miR-9-5p inhibited migration of GC cells by regulating TNFAIP8L3 directly. Low expression of miR-9-5p in GC patients hardly suppressed the migration mediated by TNFAIP8L3.

CONCLUSIONS

miR-9-5p, as a potential tumor suppressor gene, is closely related to the malignant progression of GC. Exploring the regulation between miR-9-5p and TNFAIP8L3 may provide a novel strategy for GC treatment.

Current and future molecular diagnostics of gastric cancer

Introduction: Gastric cancer (GC) is the fifth most common cancer and confers the second-highest mortality among other cancers. Improving the survival rates of GC patients requires prompt and accurate diagnosis and effective treatment which is often preceded by the poorly understood pathogenic mechanisms. Area covered: This literature review aims to summarize current understanding of genetic and molecular alterations that promote carcinogenesis including (1) activation of oncogenes, (2) overexpression of growth factors, receptors and matrix metalloproteinases, (3) inactivation of tumor suppressor genes, DNA repair genes, and cell adhesion molecules and (4) alterations of cell-cycle regulators that regulate biological characteristics of cancer cells. Moreover, the significance of molecular biomarkers such as micro-RNAs (miRNAs) and long non-coding RNAs (lncRNAs) and advanced molecular techniques including droplet digital polymerase chain reaction (ddPCR), quantitative PCR (qPCR) and next-generation sequencing (NGS) are also discussed. Expert opinion: A GC-specific panel of biomarkers based on the NGS or ddPCR has the potential for diagnosis, prognosis, and monitoring treatment response in GC patients. Despite the requirements for validation in larger population in clinical studies, race-specific differences in the gene panel have also to be examined by performing the clinical trials in subjects with different races.

Protein expression profiles and clinicopathologic characteristics associate with gastric cancer survival

BACKGROUND

Prognosis remains one of most crucial determinants of gastric cancer (GC) treatment, but current methods do not predict prognosis accurately. Identification of additional biomarkers is urgently required to identify patients at risk of poor prognoses.

METHODS

Tissue microarrays were used to measure expression of nine GC-associated proteins in GC tissue and normal gastric tissue samples. Hierarchical cluster analysis of microarray data and feature selection for factors associated with survival were performed. Based on these data, prognostic scoring models were established to predict clinical outcomes. Finally, ingenuity pathway analysis (IPA) was used to identify a biological GC network.

RESULTS

Eight proteins were upregulated in GC tissues versus normal gastric tissues. Hierarchical cluster analysis and feature selection showed that overall survival was worse in cyclin dependent kinase (CDK)2, Akt1, X-linked inhibitor of apoptosis protein (XIAP), Notch4, and phosphorylated (p)-protein kinase C (PKC) α/β2 immunopositive patients than in patients that were immunonegative for these proteins. Risk score models based on these five proteins and clinicopathological characteristics were established to determine prognoses of GC patients. These proteins were found to be involved in cancer related-signaling pathways and upstream regulators were identified.

CONCLUSION

This study identified proteins that can be used as clinical biomarkers and established a risk score model based on these proteins and clinicopathological characteristics to assess GC prognosis.

Long noncoding RNA SNHG16 silencing inhibits the aggressiveness of gastric cancer via upregulation of microRNA-628-3p and consequent decrease of NRP1

Background

MicroRNA-628-3p (miR-628) has been reported to play important roles in the progression of multiple human cancer types. Nonetheless, whether the expression profile of miR-628 is altered in gastric cancer remains unclear and whether its aberrant expression plays a crucial part in the aggressiveness of gastric cancer is yet to be determined. Therefore, in this study, we systematically investigated the involvement of miR-628 in gastric cancer progression.

Materials and methods

MiR-628 expression in gastric cancer tissues and cell lines were determined via reverse transcription-quantitative polymerase chain reaction (RT-qPCR). A CCK-8 assay, flow-cytometric analysis, Transwell assays, and a xenograft model experiment were performed to evaluate the influence of miR-628 overexpression on gastric cancer cells. Notably, the mechanisms underlying the tumor-suppressive activity of miR-628 in gastric cancer cells were explored by bioinformatics analysis, a luciferase reporter assay, RT-qPCR, and Western blotting.

Results

MiR-628 expression was low in gastric cancer tissue samples and cell lines. The low expression of miR-628 was closely associated with the lymph node metastasis, invasive depth and TNM stage among patients with gastric cancer. Further clinical analysis indicated that patients with gastric cancer underexpressing miR-628 had a worse prognosis than did the patients with high miR-628 expression in the tumor. Overexpressed miR-628 restrained proliferation, migration, and invasion; induced apoptosis; and impaired tumor growth of gastric cancer cells. In addition, neuropilin 1 (NRP1) mRNA was validated as the direct target of miR-628 in gastric cancer. Long noncoding RNA small nucleolar RNA host gene 16 (SNHG16) was demonstrated to sponge miR-628 in gastric cancer. Moreover, miR-628 knockdown abrogated the influence of SNHG16 silencing on gastric cancer cells.

Conclusion

Our findings elucidate how the SNHG16–miR-628–NRP1 pathway serves as a regulatory network playing crucial roles in gastric cancer progression, suggesting that this pathway may be a novel target of anticancer therapy.

MicroRNA-150-5p and SRC kinase signaling inhibitor 1 involvement in the pathological development of gastric cancer

The current study aimed to assess the regulatory mechanism of microRNA-150-5p (miR-150-5p) in the pathogenesis of gastric cancer. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was performed to verify the expression of miR-150-5p in gastric cancer tissues and cell lines, which was revealed to be highly expressed in each. In addition, the expression of miR-150-5p was associated with advanced gastric cancer and lymph node metastasis. The current study then hypothesized that SRC kinase signaling inhibitor 1 (SRCIN1) was the target gene of miR-150-5p, a theory that was confirmed via a dual luciferase reporter gene assay. RT-qPCR and western blotting were then performed to verify the expression of SRCIN1 in gastric cancer tissues and cell lines. The results demonstrated that SRCIN1 was lowly expressed in gastric cancer tissues and cells. To assess the effect of miR-150-5p on gastric cancer cells, experiments were conducted with BGC-823 cells transfected with a miR-150-5p inhibitor or a miR-150-5p inhibitor+SRCIN1-small interfering (si)RNA respectively. A cell counting kit-8 assay and flow cytometry were also used to assess cell viability and apoptosis, respectively. Western blotting and RT-qPCR were further used to measure the expression of specific markers of epithelial mesenchymal transition (EMT), including epithelial cell markers (E-cadherin and zona occluding-1) and interstitial cell markers (vimentin, N-cadherin and β-catenin). The results revealed that the miR-150-5p inhibitor attenuated cell viability, induced apoptosis, decreased the expression of interstitial cell markers and increased epithelial cell marker expression. However, all effects of the miR-150-5p inhibitor were reversed following SRCIN1-siRNA treatment. In summary, the current study indicated that the miR-150-5p inhibitor attenuated cell viability, induced apoptosis and inhibited gastric cancer cell EMT by targeting SRCIN1.