Diagnostic Biomarkers For Gastric Cancer Research Articles

A novel tRNA-derived fragment tRF-17-18VBY9M works as a potential diagnostic biomarker for gastric cancer

BackgroundGastric cancer (GC) is one of the most prevalent malignant tumors worldwide. The low effectiveness of common biomarkers for the detection of early GC makes it essential to seek new biomarkers to improve diagnostic efficacy. tsRNAs (transfer RNA-derived small RNAs) are related to the growth of malignant tumors. In this article, we focused on whether tsRNAs may be employed as biomarkers for GC.MethodstRF-17-18VBY9M was screened in the tsRFun database as a research object. The methodological efficacy of tRF-17-18VBY9M was evaluated using Sanger sequencing, agarose gel electrophoresis assays, and gradient dilution. The χ2 test was applied to assess the interaction between tRF-17-18VBY9M expression and clinicopathologic characteristics. The receiver operating characteristic (ROC) curve was utilized to investigate the clinical efficiency of tRF-17-18VBY9M in GC.ResultsThe Chi-square test demonstrated that high-expressed tRF-17-18VBY9M was closely associated with the T stage, tumor node metastasis stage (TNM), lymph node metastasis, and neurological/vascular invasion. ROC curve analysis revealed that the diagnostic value of tRF-17-18VBY9M in GC was superior to carcinoembryonic antigen (CEA), carbohydrate antigen 199 (CA199), and carbohydrate antigen 724 (CA724).ConclusiontRF-17-18VBY9M is up-regulated in both GC sera and tissues. Differential tRF-17-18VBY9M expression distinguishes GC patients from healthy donors and gastritis patients, which suggests tRF-17-18VBY9M could act as a diagnostic biomarker in GC.

Downregulation of lncRNA EPB41L4A-AS1 promotes gastric cancer cell proliferation, migration and invasion.

The incidence of gastric cancer ranks the first among digestive tract tumors in China. However, there are no specific symptoms in the early stage of the tumor and the diagnosis process is complex, so more effective detection methods are very needed. In this study, a novel long noncoding RNA (lncRNA) was introduced as a diagnostic biomarker for gastric cancer, which brought new thinking to the exploration of its pathological mechanism and clinical prediction. The level of lncRNA EPB41L4A-AS1 (EPB41L4A-AS1) in gastric cancer serum and cells was verified via real-time quantitative polymerase chain reaction (RT-qPCR). Receiver operating characteristic (ROC) curve was performed based on the EPB41L4A-AS1 level, and the diagnostic possibility of EPB41L4A-AS was analyzed. The chi-square test evaluated the correlation between EPB41L4A-AS expression and clinical information. The cells were cultured and transfected in vitro, and the mediations of abnormal EPB41L4A-AS level on the viability and motility of gastric cancer cells were verified through cell counting kit-8 (CCK-8) and Transwell assay. Furthermore, luciferase activity assay was performed to confirm the sponge molecule microRNA-17-5p (miR-17-5p) of EPB41L4A-AS1. EPB41L4A-AS1 was decreased in gastric cancer, and low EPB41L4A-AS1 level indicated resultful diagnostic value. Overexpression of EPB41L4A-AS1 inhibited the activity of gastric cancer cells, while knockdown of EPB41L4A-AS1 promoted tumor deterioration. EPB41L4A-AS1 directly targeted and regulated the expression ofmiR-17-5p. This study elaborated that EPB41L4A-AS1 is lowly expressed in gastric cancer. Silencing EPB41L4A-AS1 was beneficial to cell proliferation, migration, and invasion. EPB41L4A-AS1 provides a new possibility for the diagnosis of gastric cancer patients by targeting miR-17-5p.

Validation of CDC45 as a novel biomarker for diagnosis and prognosis of gastric cancer.

Cell division cycle protein 45 (CDC45) has been demonstrated to play vital roles in the progression of various malignancies. However, the clinical significance of CDC45 in gastric cancer (GC) remains unreported. In this study, we employed the TCGA database and the TCGA & GTEx dataset to compare the mRNA expression levels of CDC45 between gastric cancer tissues and adjacent or normal tissues (p < 0.05 was considered statistically significant), which was further validated in multiple datasets including GSE13911, GSE29272, GSE118916, GSE66229, as well as RT-qPCR. Furthermore, we harnessed the Human Protein Atlas (HPA) to evaluate the protein expression of CDC45, which was subsequently verified through immunohistochemistry (IHC). To ascertain the diagnostic utility of CDC45, receiver operating characteristic (ROC) curves and the area under the ROC curve (AUC) were calculated in TCGA database, and further validated it in TCGA & GTEx and GSE66229 datasets. The Kaplan-Meier method was used to reveal the prognostic importance of CDC45 in The Cancer Genome Atlas (TCGA) database and authenticated through the GSE66229, GSE84433, and GSE84437 datasets. Through cBioPortal, we identified co-expressed genes of CDC45, and pursued enrichment analysis. Additionally, we availed gene set enrichment analysis (GSEA) to annotate the biological functions of CDC45. Differential expression analysis revealed that CDC45 was significantly upregulated at both the mRNA and protein levels in GC (all p < 0.05). Remarkably, CDC45 emerged as a promising prognostic indicator and a novel diagnostic biomarker for GC. In a comprehensive the drug susceptibility analysis, we found that patients with high expression of CDC45 had high sensitivity to various chemotherapeutic agents, among which 5-fluorouracil, docetaxel, cisplatin, and elesclomol were most evident. Furthermore, our findings suggested a plausible association between CDC45 and immune cell infiltration. Enrichment analysis revealed that CDC45 and its associated genes may play crucial roles in muscle biofunction, whereas GSEA demonstrated significant enrichment of gene sets pertaining to G protein-coupled receptor ligand binding and G alpha (i) signaling events. Our study elucidates that upregulation of CDC45 is intricately associated with immune cell infiltration and holds promising potential as a favorable prognostic marker and a novel diagnostic biomarker for GC.

Clinical Significance of Disulfidptosis-related Genes and Functional Analysis in Gastric Cancer.

Background: Worldwide, gastric cancer (GC) remains intractable due to its poor prognosis and high morbidity and mortality. Disulfidptosis is a novel kind of cell death mediated by abnormal accumulation of intracellular disulphides. The correlation between disulfidptosis and GC is still unknown. Therefore, it is necessary to elucidate the pathogenesis and mechanism of disulfidptosis and GC for clinical diagnosis and intervention. Methods: RNA-sequencing data from several public data portals and clinical samples were collected. We compared the expression levels of four key genes of disulfidptosis, including SLC7A11, SLC3A2, RPN1, and NCKAP1, in GC and selected prognostic genes to build a novel GC prognosis-related nomogram model. The biological functions and immune landscape of the identified prognostic genes were explored. Results: Overexpressed NCKAP1 and SLC7A11 were prognostic disulfidptosis-related genes in GC. We combined these genes and several clinicopathological factors to build a prognostic nomogram model for GC. Meanwhile, the ROC curves showed that NCKAP1 and SLC7A11 were promising biomarkers for GC screening. The biological and cellular functions were focused on actin activities, GTPase and immunoreaction. The tumour immune microenvironment and immune therapy targets were identified. Competing endogenous RNA network was built to explore the downstream regulatory mechanisms. Finally, the elevated NCKAP1 and SLC7A11 expression in GC was validated via qRT-PCR in a cell line and tissue line. Conclusion: In conclusion, NCKAP1 and SLC7A11 are promising prognostic and diagnostic biomarkers for GC that correlate with the activities of actin, energy metabolism of GTPase, immune infiltration and immunotherapy.

Cell-free Nucleic Acid as Promising Diagnostic Biomarkers for Gastric Cancer: a Systematic Review.

Background: Gastric cancer (GC) is a common malignancy with early detection being crucial for survival. Liquid biopsy analysis using cell-free nucleic acid is a preferred method for detection. Hence, we conducted a systematic review to assess the diagnostic efficacy of cell-free nucleic acid markers for GC. Methods: We searched PubMed and ISI Web of Science databases for articles that conformed to our inclusion and exclusion criteria from 2012 to 2022. The following information was abstracted: first author, year of publication, country/region, age, male proportion, tumor stage for cases, specimen type, measurement method, targeted markers and diagnostic related indicators (including sensitivity, specificity, AUC, P-value). Results: Fifty-eight studies examined cell-free RNAs (cfRNAs) with a total of 62 individual circulating markers and 7 panels in serum or plasma, while 21 studies evaluated cell-free DNAs (cfDNAs) with 29 individual circulating markers and 7 panels. For individual cfRNAs, the median (range) sensitivity and specificity were 80% (21% - 98%) and 80% (54% - 99%), respectively. The median (range) sensitivity and specificity for cfRNA panels were 86% (83% - 90%) and 75% (60% - 98%), respectively. In comparison, the median (range) sensitivity and specificity reported for individual cfDNAs were 50% (18% - 96%) and 93% (57% - 100%), respectively, while cfDNA panels had a median (range) sensitivity and specificity of 85% (41% - 92%) and 73.5% (38% - 90%), respectively. The meta results indicate that cfRNA markers exhibit high sensitivity (80%) and low specificity (80%) for detecting GC, while cfDNA markers have lower sensitivity (59%) but higher specificity (92%). Conclusions: This review has demonstrated that cell-free nucleic acids have the potential to serve as useful diagnostic markers for GC. Given that both cfRNA and cfDNA markers have shown promising diagnostic performance for GC, the combination of the two may potentially enhance diagnostic efficiency.

Long Non-Coding RNA LOC339059 Attenuates IL-6/STAT3-Signaling-Mediated PDL1 Expression and Macrophage M2 Polarization by Interacting with c-Myc in Gastric Cancer.

Background: Long non-coding RNA (lncRNA) was identified as a novel diagnostic biomarker in gastric cancer (GC). However, the functions of lncRNAs in immuno-microenvironments have not been comprehensively explored. In this study, we explored a critical lncRNA, LOC339059, that can predict the clinical prognosis in GC related to the modulation of PD-L1 and determined its influence upon macrophage polarization via the IL-6/STAT3 pathway. Methods: To date, accumulating evidence has demonstrated that the dysregulation of LOC339059 plays an important role in the pathological processes of GC. It acts as a tumor suppressor, regulating GC cell proliferation, migration, invasion, tumorigenesis, and metastasis. A flow cytometry assay showed that the loss of LOC339059 enhanced PDL1 expression and M2 macrophage polarization. RNA sequencing, RNA pull-down, RNA immunoprecipitation, Chip-PCR, and a luciferase reporter assay revealed the pivotal role of signaling alternation between LOC339059 and c-Myc. Results: A lower level of LOC339059 RNA was found in primary GC tissues compared to adjacent tissues, and such a lower level is associated with a poorer survival period (2.5 years) after surgery in patient cohorts. Moreover, we determined important immunological molecular biomarkers. We found that LOC339059 expression was correlated with PD-L1, CTLA4, CD206, and CD204, but not with TIM3, FOXP3, CD3, C33, CD64, or CD80, in a total of 146 GC RNA samples. The gain of LOC339059 in SGC7901 and AGS inhibited biological characteristics of malignancy, such as proliferation, migration, invasion, tumorigenesis, and metastasis. Furthermore, our data gathered following the co-culture of THP-1 and U937 with genomic GC cells indicate that LOC339059 led to a reduction in the macrophage cell ratio, in terms of CD68+/CD206+, to 1/6, whereas the selective knockdown of LOC339059 promoted the abovementioned malignant cell phenotypes, suggesting that it has a tumor-suppressing role in GC. RNA-Seq analyses showed that the gain of LOC339059 repressed the expression of the interleukin family, especially IL-6/STAT3 signaling. The rescue of IL-6 in LOC339059-overexpressing cells reverted the inhibitory effects of the gain of LOC339059 on malignant cell phenotypes. Our experiments verified that the interaction between LOC339059 and c-Myc resulted in less c-Myc binding to the IL-6 promoter, leading to the inactivation of IL-6 transcription. Conclusions: Our results establish that LOC339059 acts as a tumor suppressor in GC by competitively inhibiting c-Myc, resulting in diminished IL-6/STAT3-signaling-mediated PDL1 expression and macrophage M2 polarization.

Gastric Cancer and Circulating microRNAs: An Updated Systematic Review and Diagnostic Meta-Analysis.

Circulating microRNAs (miRNAs, miRs) are now used as noninvasive diagnostic indicators in various malignancies. Our objective is to use a meta-analysis to assess the diagnostic performance of circulating miRNAs in gastric cancer. We reviewed databases and methodically obtained papers for analysis until October 15th, 2021. The random-effect meta-analysis was performed to construct pooled diagnostic parameters. To detect the causes of heterogeneity, spearman threshold effect analysis and subgroup analysis were performed. The I2 and Chi-square tests were also used to examine the heterogeneity. The subgroup analyses were conducted based on sample types (serum/plasma/blood), normalized genes (U6, miR-16, and miR-39), qPCR mastermix (SYBR and Taqman), and country. Finally, the publication bias was estimated using Egger's funnel plot asymmetry test. A total of 40 articles covering 73 studies (59 microRNAs) were included, containing 11,022 participants (6,324 cases and 4,698 controls). The overall pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under the curve (AUC) were 0.75 (95% CI: 0.74-0.77), 0.79 (95% CI: 0.78-0.80), 4.081 (95% CI: 3.43-4.85), 0.28 (95% CI: 0.25-0.32), 16.08 (95% CI: 12.34-20.95), and 0.877 (CI: 0.84-0.90), respectively. We conducted a subgroup analysis of diagnostic values, which revealed that serum type, U6 reference gene, SYBR mastermix, and East Asian Countries (China and Japan) had better diagnostic value. Circulating miRs can serve as diagnostic biomarkers for gastric cancer. However, specific miRNAs still need to be discovered in diagnosing gastric cancer, especially early screening.

Identification of stromal cell-derived factor 4 as a liquid biopsy-based diagnostic marker in solid cancers

There is a need for serum diagnostic biomarkers to improve the prognosis of solid malignant tumors. Here, we conducted a single-institutional study to evaluate the diagnostic performance of serum stromal cell-derived factor 4 (SDF4) levels in cancer patients. Serum samples were collected from a total of 582 patients with solid cancers including gastric cancer (GC) and 80 healthy volunteers. SDF4 protein levels in sera, and conditioned media or lysates of human GC cell lines were measured by enzyme-linked immunosorbent assay, and those in GC tissue by immunohistochemistry. Serum SDF4 levels were higher in patients with cancer than the healthy control in all cancer type. Regarding GC, serum SDF4 levels distinguished healthy controls from GC patients with the area under the curve value of 0.973, sensitivity of 89%, and specificity of 99%. Serum SDF4 levels were significantly elevated in patient with early stage GC. In immunohistochemistry, the frequency of SDF4-positive GC tumors did not vary significantly between GC stages. The ability of human GC cell lines to both produce and secrete SDF4 was confirmed in vitro. In conclusion, serum SDF4 levels could be a promising candidate for a novel diagnostic biomarker for GC and other malignancies.

Extracellular vesicles in gastric cancer: role of exosomal lncRNA and microRNA as diagnostic and therapeutic targets.

Extracellular vesicles (EVs), including exosomes, play a crucial role in intercellular communication and have emerged as important mediators in the development and progression of gastric cancer. This review discusses the current understanding of the role of EVs, particularly exosomal lncRNA and microRNA, in gastric cancer and their potential as diagnostic and therapeutic targets. Exosomes are small membrane-bound particles secreted by both cancer cells and stromal cells within the tumor microenvironment. They contain various ncRNA and biomolecules, which can be transferred to recipient cells to promote tumor growth and metastasis. In this review, we highlighted the importance of exosomal lncRNA and microRNA in gastric cancer. Exosomal lncRNAs have been shown to regulate gene expression by interacting with transcription factors or chromatin-modifying enzymes, which regulate gene expression by binding to target mRNAs. We also discuss the potential use of exosomal lncRNAs and microRNAs as diagnostic biomarkers for gastric cancer. Exosomes can be isolated from various bodily fluids, including blood, urine, and saliva. They contain specific molecules that reflect the molecular characteristics of the tumor, making them promising candidates for non-invasive diagnostic tests. Finally, the potential of targeting exosomal lncRNAs and microRNAs as a therapeutic strategy for gastric cancer were reviewed as wee. Inhibition of specific molecules within exosomes has been shown to suppress tumor growth and metastasis in preclinical models. In conclusion, this review article provides an overview of the current understanding of the role of exosomal lncRNA and microRNA in gastric cancer. We suggest that further research into these molecules could lead to new diagnostic tools and therapeutic strategies for this deadly disease.

Role of serum and salivary microRNAs as diagnostic biomarkers in gastric cancer

Introduction: Incidence of Gastric cancer (GC) is increasing alarmingly in the recent past due to changing lifestyle and diet pattern. GC usually has poor prognosis due to delayed diagnosis. Salivary and serum biomarkers are a potential early diagnostic tool for GC. MicroRNAs are promising biomarkers due to their stability in these body fluids and their pivotal role in carcinogenesis. This study helps to determine the role of serum and salivary microRNAs as diagnostic biomarkers in gastric cancer. Materials and Methods: The systematic review was performed as per the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines. The population, intervention, comparison, outcomes, and study (PICOS) framework was used as a strategy for this review. The data were retrieved from online databases such as Medline (PubMed), Web of Science, Scopus, and SpringerLink. Risk of bias and applicability concerns were evaluated using the four domains of QUADAS-2: patient selection, index test, reference standard, procedure and timing. Results: Quality evaluation based on diagnostic accuracy revealed that five studies conducted by Hou et al., Jianhong et al., Kaczor-Urbanowicz et al., Saliminejad et al., and So JBY et al. had the lowest risk of bias, according to a risk of bias chart created using Revman 5.4.1 software. A serum 12-miRNA biomarker assay was validated by the low risk of bias research. Conclusion: This systematic review provides an insight into the possible role and application of an array of miRNAs from various body fluids as a biomarker for the early detection of gastric cancer. The serum 12-miRNA biomarker assay, validated by a low risk of bias research can serve as a potential diagnostic tool to detect gastric cancer. However, the validation of other salivary, serum, and plasma miRNAs as a diagnostic biomarker for gastric cancer mandates further long-term follow-up studies in diverse ethnicity of populations.

Up-regulation of BOK-AS1, FAM215A and FEZF1-AS1 lncRNAs and their potency as moderate diagnostic biomarkers in gastric cancer

BackgroundGastric cancer is the fifth most frequent cancer worldwide and the fourth leading cause of death from cancer, a complex multifactorial neoplasm. LncRNAs are regulatory RNA molecules larger than 200 nucleotides, which can have profound effects on the oncogenic process of various types of cancer. Therefore, these molecules can be used as diagnostic and therapeutic biomarkers. This study aimed to determine the differences in BOK-AS1, FAM215A, and FEZF1-AS1 gene expression between tumor tissue and adjacent healthy non-tumor tissue of gastric cancer (GC) patients. MethodsIn this study one hundred pairs of cancerous and non-cancerous marginal tissues were gathered. Next, RNA extraction and cDNA synthesis were achieved for all of the samples. Then, the qRT-PCR was performed to measure the expression of BOK-AS1, FAM215A and FEZF1-AS1 genes. ResultsAll BOK-AS1, FAM215A and FEZF1-AS1 genes showed significantly increased expression in tumor tissues compared with non-tumor tissues. The outcome of the ROC analysis demonstrated that BOK-AS1, FAM215A, and FEZF1-AS1 may act as mean biomarkers with AUC of 0.7368, 0.7163 and 0.7115, specificity of 64%, 61% and 59%, and sensitivity of 74%, 70%, and 74% respectively. ConclusionBased on the increased expression of the BOK-AS1, FAM215A and FEZF1-AS1 genes in GC patients, this study suggests that these genes may function as oncogenic factors. Furthermore, the mentioned genes can be considered as intermediate biomarkers for diagnosis and treatment of gastric cancer. In addition, no association between these genes and clinicopathological features was observed.

Identification of miR-143-3p as a diagnostic biomarker in gastric cancer

BackgroundGastric cancer (GC) is among the most common types of gastrointestinal cancers and has a high incidence and mortality around the world. To suppress the progression of GC, it is essential to develop diagnostic markers. MicroRNAs regulate GC development, but a clearer insight into their role is needed before they can be applied as a molecular markers and targets.MethodsIn this study, we assessed the diagnostic value of differentially expressed microRNAs as potential diagnostic biomarkers for GC using data for 389 tissue samples from the Cancer Genome Atlas (TCGA) and 21 plasma samples from GC patients.ResultsThe expression of hsa-miR-143-3p (also known as hsa-miR-143) was significantly downregulated in GC according to the TCGA data and plasma samples. The 228 potential target genes of hsa-miR-143-3p were analyzed using a bioinformatics tool for miRNA target prediction. The target genes correlated with extracellular matrix organization, the cytoplasm, and identical protein binding. Furthermore, the pathway enrichment analysis of target genes showed that they were involved in pathways in cancer, the phosphoinositide 3-kinase (PI3K)–protein kinase B (Akt) signaling pathway, and proteoglycans in cancer. The hub genes in the protein–protein interaction (PPI) network, were matrix metallopeptidase 2 (MMP2), CD44 molecule (CD44), and SMAD family member 3 (SMAD3).ConclusionsThis study suggests that hsa-miR-143-3p may be used as a diagnostic marker for GC, contributing via the pathways involved in the development of GC.

CD93 serves as a potential biomarker of gastric cancer and correlates with the tumor microenvironment.

The tumor microenvironment (TME) plays an important role in the growth and expansion of gastric cancer (GC). Studies have identified that CD93 is involved in abnormal tumor angiogenesis, which may be related to the regulation of the TME. To determine the role of CD93 in GC. Transcriptomic data of GC was investigated in a cohort from The Cancer Genome Atlas. Additionally, RNA-seq data sets from Gene Expression Omnibus (GSE118916, GSE52138, GSE79973, GSE19826, and GSE84433) were applied to validate the results. We performed the immune infiltration analyses using ESTIMATE, CIBERSORT, and ssGSEA. Furthermore, weighted gene co-expression network analysis (WGCNA) was conducted to identify the immune-related genes. Compared to normal tissues, CD93 significantly enriched in tumor tissues (t = 4.669, 95%CI: 0.342-0.863, P < 0.001). Higher expression of CD93 was significantly associated with shorter overall survival (hazard ratio = 1.62, 95%CI: 1.09-2.4, P = 0.017), less proportion of CD8 T and activated natural killer cells in the TME (P < 0.05), and lower tumor mutation burden (t = 4.131, 95%CI: 0.721-0.256, P < 0.001). Genes co-expressed with CD93 were mainly enriched in angiogenesis. Moreover, 11 genes were identified with a strong relationship between CD93 and the immune microenvironment using WGCNA. CD93 is a novel prognostic and diagnostic biomarker for GC, that is closely related to the immune infiltration in the TME. Although this retrospective study was a comprehensive analysis, the prospective cohort studies are preferred to further confirm these conclusions.

MicroRNA miR-1275 coordinately regulates AEA/LPA signals via targeting FAAH in lipid metabolism reprogramming of gastric cancer

Glycerophospholipid signal and fatty acid metabolism are closely related to the occurrence and progression of tumours, and metabolic reprogramming caused by hydrolytic enzymes plays an important role in gastric cancer (GC). Here, we performed whole transcriptome sequencing and combined qRT-PCR to screen out the significantly high expression of fatty acid amide hydrolase (FAAH) in GC tissues, which was further verified in both TCGA and Oncomine databases. Functional tests confirmed that FAAH played an oncogene role in GC, and silencing FAAH could delay tumour growth, inhibit tumour metastasis, and promote cell apoptosis both in vitro and in vivo. FAAH-mediated lipid metabolism reprogramming through coordinated regulation of arachidonoyl ethanolamide (AEA)/lysophosphatidic acid (LPA) signalling and activated the cyclooxygenase-2 (COX-2)/prostaglandin E2 (PGE2) axis to promote GC progression. Luciferase reporter assay and immunofluorescence-fluorescence in situ hybridization (IF-FISH) were applied to validate the interactions of miR-1275/FAAH. Overexpression and knockdown of miR-1275 in vitro could indirectly modulate the above lipid signalling by targeting FAAH, thereby affecting GC progression. Our study indicates that deregulated FAAH is a key lipid signal and the miR-1275/FAAH/AEA/LPA axis can serve as a diagnostic biomarker for GC or as a target for therapy development.

Lipid metabolism characterization in gastric cancer identifies signatures to predict prognostic and therapeutic responses.

Purpose: Increasing evidence has elucidated the significance of lipid metabolism in predicting therapeutic efficacy. Obviously, a systematic analysis of lipid metabolism characterizations of gastric cancer (GC) needs to be reported. Experimental design: Based on two proposed computational algorithms (TCGA-STAD and GSE84437), the lipid metabolism characterization of 367 GC patients and its systematic relationship with genomic characteristics, clinicopathologic features, and clinical outcomes of GC were analyzed in our study. Differentially expressed genes (DEGs) were identified based on the lipid metabolism cluster. At the same time, we applied single-factor Cox regression and random forest to screen signature genes to construct a prognostic model, namely, the lipid metabolism score (LMscore). Next, we deeply explored the predictive value of the LMscore for GC. To verify the specific changes in lipid metabolism, a total of 90 serum, 30 tumor, and non-tumor adjacent tissues from GC patients, were included for pseudotargeted metabolomics analysis via SCIEX triple quad 5500 LC-MS/MS system. Results: Five lipid metabolism signature genes were identified from a total of 3,104 DEGs. The LMscore could be a prognosticator for survival in different clinicopathological GC cohorts. As well, the LMscore was identified as a predictive biomarker for responses to immunotherapy and chemotherapeutic drugs. Additionally, significant changes in sphingolipid metabolism and sphingolipid molecules were discovered in cancer tissue from GC patients by pseudotargeted metabolomics. Conclusion: In conclusion, multivariate analysis revealed that the LMscore was an independent prognostic biomarker of patient survival and therapeutic responses in GC. Depicting a comprehensive landscape of the characteristics of lipid metabolism may help to provide insights into the pathogenesis of GC, interpret the responses of gastric tumors to therapies, and achieve a better outcome in the treatment of GC. In addition, significant alterations of sphingolipid metabolism and increased levels of sphingolipids, in particular, sphingosine (d16:1) and ceramide, were discovered in GC tissue by lipidome pseudotargeted metabolomics, and most of the sphingolipid molecules have the potential to be diagnostic biomarkers for GC.

Circular RNAs as diagnostic biomarkers for gastric cancer: A comprehensive update from emerging functions to clinical significances.

The incidence and mortality of gastric cancer ranks as a fouth leading cause of cancer death worldwide, especially in East Asia. Due to the lack of specific early-stage symptoms, the majority of patients in most developing nations are diagnosed at an advanced stage. Therefore, it is urgent to find more sensitive and reliable biomarkers for gastric cancer screening and diagnosis. Circular RNAs (circRNAs), a novel type of RNAs with covalently closed loops, are becoming a latest hot spot in the field of. In recent years, a great deal of research has demonstrated that abnormal expression of circRNAs was associated with the development of gastric cancer, and suggested that circRNA might serve as a potential biomarker for gastric cancer diagnosis. In this review, we summarize the structural characteristics, formation mechanism and biological function of circRNAs, and elucidate research progress and existing problems in early screening of gastric cancer.

Serum amyloid A (SAA) and Interleukin-6 (IL-6) as the potential biomarkers for gastric cancer.

To explore serum amyloid A (SAA) and interleukin-6 (IL-6) as potential diagnostic biomarkers for gastric cancer (GCa) and the application value of the combined diagnosis of SAA, IL6, and Cancer embryonic antigen. Serum samples were collected before the initial surgery from 159 patients comprising samples from 122 patients with GCa and 37 patients with benign gastric disease. All patients were hospitalized at Beijing Aerospace General Hospital in China between 2018 and 2020. The IL-6 and SAA levels were assessed using standard laboratory protocols. The levels of SAA and IL-6 were significantly higher in patients with GCa than in controls. Compared with the healthy group, the concentration of SAA and IL-6 in FIGO III-IV group were significantly higher and the difference were statistically significant. In addition, significant differences were observed between the FIGO III-IV group and FIGO I-II groups. The Receiver operating characteristic (ROC) curve for the combined detection of SAA, IL-6, and Cancer embryonic antigen showed an area under the curve (AUC) of 0.948, sensitivity of 91.0%, and specificity of 89.2%. Spearman's correlation analysis indicated obvious correlations among the levels of serum SAA, IL-6, advanced FIGO stage, lymphatic invasion, and distant metastasis. AA and IL-6 may serve as useful biomarkers for poor prognosis of GCa. Clinical diagnosis combined with SAA and IL-6 may help assess therapeutic outcomes.

Salivary Fusobacterium nucleatum serves as a potential diagnostic biomarker for gastric cancer.

BACKGROUNDAs one of the most common tumors, gastric cancer (GC) has a high mortality rate, since current examination approaches cannot achieve early diagnosis. Fusobacterium nucleatum (Fn) primarily colonized in the oral cavity, has been reported to be involved in the development of gastrointestinal tumor. Until now, little is known about the relationship between salivary Fn and GC.AIMTo determine whether salivary Fn could be a biomarker to diagnose GC and explore the influence of Fn on GC cells.METHODSThe abundance of Fn in saliva was quantified by droplet digital polymerase chain reaction in 120 GC patients, 31 atrophic gastritis (AG) patients, 35 non-AG (NAG) patients, 26 gastric polyp (GP) patients, and 20 normal controls (NC) from Qilu Hospital of Shandong University from January 2019 to December 2020. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnostic value of Fn as well as traditional serum tumor markers, including carcinoembryonic antigen (CEA), carbohydrate antigen (CA) 19-9, and CA72-4. Transwell assay and wound-healing assay were conducted to assess the influence of Fn infection on GC cells. The expression of epithelial-mesenchymal transition (EMT) markers was detected using western blot assay.RESULTSWe found that the level of salivary Fn in GC patients was significantly increased compared with those in AG, NAG, and GP patients and NC (P < 0.001). ROC curve analysis showed a favorable capability of Fn (73.33% sensitivity; 82.14% specificity; area under the curve: 0.813) in GC diagnosis, which was superior to that of CEA, CA19-9, CA72-4, ferritin, and sialic acid. The Fn level in saliva of GC patients was increased as the TNM stage increased. GC patients with lymph node metastasis had higher Fn levels than those without metastasis. Both transwell and wound-healing assays indicated that Fn infection promoted the migration and invasion of GC cells. Western blot analysis showed that Fn infection decreased the expression of E-cadherin and increased the expressions of N-cadherin, vimentin, and snail.CONCLUSIONFn abundance in saliva could be used as a promising biomarker to diagnose GC, and Fn infection could promote GC metastasis by accelerating the EMT process.

A 5`-tRNA Derived Fragment NamedtiRNA-Val-CAC-001 Works as a Suppressor in Gastric Cancer.

BackgroundGastric cancer (GC) is a common type of gastrointestinal tumor in the world. Transfer RNA (tRNA) derived fragments (tsRNAs) implicate various cancers, but their roles in GC remain unclear. Our study aimed to investigate the potential biological functions and molecular mechanisms of tsRNAs in GC.MethodsDifferentially expressed tsRNAs were identified using high-throughput sequencing. The expression levels of tsRNAs were validated in 62 paired GC tissues and adjacent normal tissues using RT-qPCR. In vitro functional assays were used to evaluate the influences of tsRNAs on GC cells. The potential mechanisms underlying tsRNAs were explored using bioinformatics analysis,RT-qPCR, RNA immunoprecipitation assays and Western blot.ResultsWe found that tiRNA-Val-CAC-001 was downregulated in GC tissues and cells, and demonstrated that tiRNA-Val-CAC-001 was a tsRNA sheared from mature tRNA-Val and mainly localized in the cytoplasm. tiRNA-Val-CAC-001 overexpression inhibited metastasis and proliferation but promoted apoptosis of GC cells; nevertheless, tiRNA-Val-CAC-001 knockdown increased metastasis and proliferation and reduced apoptosis (P<0.05). GO and KEGG analyses indicated tiRNA-Val-CAC-001 may exert its effects via Wnt/β-catenin signaling pathway by targeting LRP6. Following experiments showed that tiRNA-Val-CAC-001 could downregulated the protein levels of LRP6 and β-catenin, but up-regulated p-β-catenin, which confirmed the findings in bioinformatics analysis.ConclusionIn conclusion, tiRNA-Val-CAC-001 works as a cancer suppressor in GC by targeting LRP6 via Wnt/β-catenin signaling pathway. tiRNA-Val-CAC-001 may serve as a therapy target and a biomarker of GC in the future.Key PointstiRNA-Val-CAC-001 is downregulated in gastric cancer tissues and cell lines, tiRNA-Val-CAC-001 has potential to become a novel diagnostic biomarker in gastric cancer, and tiRNA-Val-CAC-001 regulates gastric cancer cells by targeting LRP6.

ESRRG, ATP4A, and ATP4B as Diagnostic Biomarkers for Gastric Cancer: A Bioinformatic Analysis Based on Machine Learning.

Based on multiple bioinformatics methods and machine learning techniques, this study was designed to explore potential hub genes of gastric cancer with a diagnostic value. The novel biomarkers were detected through multiple databases of gastric cancer–related genes. The NCBI Gene Expression Omnibus (GEO) database was used to obtain gene expression files. Three hub genes (ESRRG, ATP4A, and ATP4B) were detected through a combination of weighted gene co-expression network analysis (WGCNA), gene–gene interaction network analysis, and supervised feature selection method. GEPIA2 was used to verify the differences in the expression levels of the hub genes in normal and cancer tissues in the RNA-seq levels of Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) databases. The objectivity of potential hub genes was also verified by immunohistochemistry in the Human Protein Atlas (HPA) database and transcription factor–hub gene regulatory network. Machine learning (ML) methods including data pre-processing, model selection and cross-validation, and performance evaluation were examined on the hub-gene expression profiles in five Gene Expression Omnibus datasets and verified on a GEO external validation (EV) dataset. Six supervised learning models (support vector machine, random forest, k-nearest neighbors, neural network, decision tree, and eXtreme Gradient Boosting) and one semi-supervised learning model (label spreading) were established to evaluate the diagnostic value of biomarkers. Among the six supervised models, the support vector machine (SVM) algorithm was the most effective one according to calculated performance metrics, including 0.93 and 0.99 area under the curve (AUC) scores on the test and external validation datasets, respectively. Furthermore, the semi-supervised model could also successfully learn and predict sample types, achieving a 0.986 AUC score on the EV dataset, even when 10% samples in the five GEO datasets were labeled. In conclusion, three hub genes (ATP4A, ATP4B, and ESRRG) closely related to gastric cancer were mined, based on which the ML diagnostic model of gastric cancer was conducted.