Comprehensive analysis of prognostic genes in gastric cancer

Biomarker discovery with quantum neural networks: a case-study in CTLA4-activation pathways

BACKGROUND

Biomarker discovery is a challenging task due to the massive search space. Quantum computing and quantum Artificial Intelligence (quantum AI) can be used to address the computational problem of biomarker discovery from genetic data.

METHOD

We propose a Quantum Neural Networks architecture to discover genetic biomarkers for input activation pathways. The Maximum Relevance-Minimum Redundancy criteria score biomarker candidate sets. Our proposed model is economical since the neural solution can be delivered on constrained hardware.

RESULTS

We demonstrate the proof of concept on four activation pathways associated with CTLA4, including (1) CTLA4-activation stand-alone, (2) CTLA4-CD8A-CD8B co-activation, (3) CTLA4-CD2 co-activation, and (4) CTLA4-CD2-CD48-CD53-CD58-CD84 co-activation.

CONCLUSION

The model indicates new genetic biomarkers associated with the mutational activation of CLTA4-associated pathways, including 20 genes: CLIC4, CPE, ETS2, FAM107A, GPR116, HYOU1, LCN2, MACF1, MT1G, NAPA, NDUFS5, PAK1, PFN1, PGAP3, PPM1G, PSMD8, RNF213, SLC25A3, UBA1, and WLS. We open source the implementation at: https://github.com/namnguyen0510/Biomarker-Discovery-with-Quantum-Neural-Networks .

Prognostic mutation signature would serve as a potential prognostic predictor in patients with diffuse large B-cell lymphoma

The present study aimed to elucidate the prognostic mutation signature (PMS) associated with long-term survival in a diffuse large B-cell lymphoma (DLBCL) cohort. All data including derivation and validation cohorts were retrospectively retrieved from The Cancer Genome Atlas (TCGA) database and whole-exome sequencing (WES) data. The Lasso Cox regression analysis was used to construct the PMS based on WES data, and the PMS was determined using the area under the receiver operating curve (AUC). The predictive performance of eligible PMS was analyzed by time-dependent receiver operating curve (ROC) analyses. After the initial evaluation, a PMS composed of 94 PFS-related genes was constructed. Notably, this constructed PMS accurately predicted the 12-, 36-, and 60-month PFS, with AUC values of 0.982, 0.983, and 0.987, respectively. A higher level of PMS was closely linked to a significantly worse PFS, regardless of the molecular subtype. Further evaluation by forest plot revealed incorporation of international prognostic index or tumor mutational burden into PMS increased the prediction capability for PFS. The drug-gene interaction and pathway exploration revealed the PFS-related genes were associated with DNA damage, TP53, apoptosis, and immune cell functions. In conclusion, this study utilizing a high throughput genetic approach demonstrated that the PMS could serve as a prognostic predictor in DLBCL patients. Furthermore, the identification of the key signaling pathways for disease progression also provides information for further investigation to gain more insight into novel drug-resistant mechanisms.

Complementary biomarkers of computed tomography for diagnostic grading of gastric cancer: DSCC1 and GINS1

OBJECTIVE

Computed tomography (CT) is an important tool for grading gastric cancer. Gastric cancer typically originates from epithelial cells of gastric mucosa. However, complementary markers for gastric cancer, relationship between DSCC1, GINS1 and gastric cancer remain unclear.

METHODS

Gastric cancer data were obtained from gene expression omnibus (GEO). Differentially expressed genes (DEGs) were identified, weighted gene co-expression network analysis (WGCNA) was conducted. Protein-protein interaction (PPI) network was constructed and analyzed. Functional enrichment analysis, gene set enrichment analysis (GSEA), gene expression heatmaps, immune infiltration analysis were performed. The most relevant diseases related to core genes were identified using Comparative Toxicogenomics Database (CTD). TargetScan was used to screen miRNAs. Validation was carried out using Western blotting (WB) and reverse transcription-polymerase chain reaction (RT-PCR).

RESULTS

1243 DEGs were identified. Gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) analyses revealed significant enrichment in cell cycle regulation, macrophage migration control, basement membrane, extracellular regions, growth factor binding, protein complex binding, P53 signaling pathway, protein digestion and absorption, metabolic pathways. Immune infiltration analysis indicated that high expression of activated Mast cells and Neutrophils, with a strong positive correlation between them, may influence progression of gastric cancer. CTD analysis revealed associations between DSCC1, GINS1 and gastric tumors, gastrointestinal diseases, tumors, gastritis, inflammation, necrosis. WB and RT-PCR results demonstrated high expression of DSCC1 and GINS1 in gastric cancer.

CONCLUSION

The expressions of DSCC1 and GINS1 are up-regulated in gastric cancer, which can be used as supplementary markers for CT diagnostic grading of gastric cancer.

[High expression of CPNE3 correlates with poor long-term prognosis of gastric cancer by inhibiting cell apoptosis via activating PI3K/AKT signaling]

OBJECTIVE

To explore the correlation of CPNE3 expression with long-term prognosis of patients with gastric cancer (GC) and the possible mechanism.

METHODS

We retrospectively collected the data of 104 GC patients undergoing radical surgery in our hospital from February, 2013 to October, 2017. TCGA database and immunohistochemistry were used to analyze CPNE3 expression level in GC tissues and its effects on tumor progression and long-term prognosis of the patients. GO analysis was performed to predict the biological role of CPNE3 in GC. We also conducted cell experiments with MGC803 cells and observed the effects of CPNE3 knockdown, CPNE3 overexpression and LY294002 (a PI3K/AKT inhibitor) treatment on cell apoptosis and cellular expressions of apoptotic proteins using flow cytometry and Western blotting.

RESULTS

TCGA analysis and immunohistochemistry both showed high expressions of CPNE3 in GC (P < 0.05). The patients with high CPNE3 expressions had a reduced 5-year survival (P < 0.01), and a high CPNE3 expression, CEA level≥5 μg/L, CA19-9 level ≥37 kU/L, T3-T4 stage, and N2-N3 stage were all independent risk factors for a lowered 5-year survival rate after surgery. The sensitivity and specificity of CPNE3 for predicting 5-year mortality was 79.59% and 74.55%, respectively (P < 0.05). GO analysis predicted that CPNE3 negatively regulated GC cell apoptosis. In MGC803 cells, CPNE3 knockdown significantly increased cell apoptosis, enhanced Bax and Cleaved Caspase-3 expressions and decreased Bcl-2 expression, while CPNE3 overexpression produced the opposite results (P < 0.05). The cellular expressions of p-PI3K and p-AKT were significantly decreased following CPNE3 knockdown and increased following CPNE3 overexpression (P < 0.05). Treatment with LY294002 obviously attenuated the inhibitory effect of CPNE3 overexpression on apoptosis of MGC803 cells (P < 0.05).

CONCLUSION

CPNE3 is highly expressed in GC tissues and affects the long-term prognosis of the patients possibly by inhibiting GC cell apoptosis through activation of PI3K/AKT signaling.

A new strategy to identify ADAM12 and PDGFRB as a novel prognostic biomarker for matrine regulates gastric cancer via high throughput chip mining and computational verification

BACKGROUND

Gastric cancer is a life-threatening disease that poses a serious risk to human health. Although there are numerous molecular targets for gastric cancer in clinical practice, they often exhibit low specificity and sensitivity. Consequently, this can result in a low early diagnosis rate, delayed treatment, and poor prognosis for patients with gastric cancer. Hence, it remains crucial to identify more precise diagnostic markers for this disease.

METHODS

This study utilized ceRNA chips and bioinformatics methods to investigate the key genes and mechanisms involved in matrine intervention in gastric cancer cells.

RESULTS

ADAM12 and PDGFRB are the key genes that are down-regulated after matrine intervention in gastric cancer cells. By conducting bioinformatics analysis, two ceRNA regulatory axes were identified, which are associated with the prognosis of gastric cancer. These axes are lncRNA DGCR5/hsa-miR-206/ADAM12 and circRNA ITGA3/hsa-miR-24-3p/PDGFRB.

CONCLUSION

The low expression of ADAM12 may weaken the digestion of extracellular matrix (ECM) molecules, which can result in the invasion and metastasis of tumor cells. This occurs without the catalysis of ECM proteases, thereby impacting the invasion and metastasis of gastric cancer cells. Additionally, the analysis of immune infiltration suggests that ADAM12 and PDGFRB may influence changes in the tumor immune microenvironment, thereby affecting the occurrence and development of gastric cancer. This study contributes to a deeper understanding of the role of the matrine-related ceRNA network in gastric cancer, providing a reference for clinical diagnosis and treatment. It holds significant importance in discovering new drug treatment targets.

MiR-455-3p inhibits gastric cancer progression by repressing Wnt/β-catenin signaling through binding to ARMC8

BACKGROUND

Globally, gastric cancer (GC) is one of the world's most widespread malignancies, with persistent high mortality and morbidity rates. Increasing evidence now suggests that microRNAs (miRNAs) participate in many biological processes, with miR-455-3p having key roles in the progression of diverse cancers. Nevertheless, miR-455-3p function and expression in GC remain unclear.

METHODS

We explored miR-455-3p expression in GC using quantitative polymerase chain reaction (qPCR). To further examine the effect of miR-455-3p in GC, after transfecting miR-455-3p mimics or inhibitors into GC cells, 5-ethynyl-2'-deoxyuridine (EdU) incorporation and colony formation assays were performed to examine cell proliferation. Flow cytometry was used to detect apoptosis, and expression levels of Bax, Bcl-2, Snail, N-cadherin, E-cadherin, and Caspase-3 were assessed by western blotting (WB). Using online databases and luciferase assays, we identified armadillo repeat-containing protein 8 (ARMC8) as a promising target of miR-455-3p. A mouse tumor model was established to investigate actions of miR-455-3p in vivo. Expression levels of C-myc, cyclinD1, and β-catenin were examined using WB and immunofluorescence.

RESULTS

MiR-455-3p expression was attenuated in GC tissue and cell lines. MiR-455-3p overexpression inhibited GC cell proliferation, epithelial-mesenchymal transition (EMT), as well as facilitated apoptosis, while suppression of miR-455-3p had the opposite effects. From luciferase assays, we confirmed that ARMC8 was a novel and direct downstream target gene of miR-455-3p, and that the tumor suppressive role of miR-455-3p was in part reversed due to ARMC8 overexpression. Moreover, miR-455-3p inhibited GC growth in vivo via ARMC8. We also observed that miR-455-3p repressed canonical Wnt pathway activation by binding to ARMC8.

CONCLUSIONS

MiR-455-3p exerted tumor inhibitory effects in GC by targeting ARMC8. Therefore, intervening in the miR-455-3p/ARMC8/Wnt/βcatenin axis could be a promising novel treatment strategy for GC.

Inhibitory role of LINC00332 in gastric cancer progression through regulating cell EMT and stemness

OBJECTIVE

Gastric cancer (GC) is one of the most common lethal malignancies worldwide. The molecular mechanisms underlying GC early detection are poorly understood. Identifying potential coding and non-coding markers and related pathways in the GC progression is essential. Some Long non-coding RNAs (lncRNAs) reportedly play vital roles during gastric GC development. However, the clinical significance and biological function of LINC00332 in GC remain largely unclear.

METHODS

The gene expression patterns of GC from an RNAseq dataset (GSE122401) were retrieved from the Gene Expression Omnibus (GEO) database to recognize differentially expressed genes (DEGs) and lncRNAs (DELs) between normal and GC samples through several bioinformatic analysis. The expression of LINC00332 and MMP-13 as a target gene was quantified in fresh frozen tissues obtained from GC patients. In addition, we investigated the potential function of LINC00332 in silico and in vitro.

RESULTS

The expressions of LINC00332 and MMP-13 were significantly downregulated and upregulated in GC tissues, respectively. A significant inverse correlation between LINC00332 and MMP-13 mRNA expression was observed in tumor samples. The mRNA expression level of mesenchymal markers, stem cell factors, and MMP genes were significantly decreased after the LINC00332 ectopic expression, while epithelial markers expression was significantly increased. The LINC00332 overexpression markedly repressed proliferation, migration, and invasion and did not induce apoptosis in AGS cells. In addition, LINC00332 overexpression notably promoted the E-cadherin protein expression. Moreover, LINC00332 significantly decreased the cisplatin resistance.

CONCLUSION

Our findings indicated that LINC00332 may be a critical anti-EMT factor and provided a new efficient therapeutic strategy for GC treatment.