ClC-3/SGK1 regulatory axis enhances the olaparib-induced antitumor effect in human stomach adenocarcinoma

Genome-Wide DNA Methylation and Copy Number Alterations in Gastrointestinal Stromal Tumors

Gastrointestinal stromal tumors (GISTs) span a broad clinical spectrum, from indolent neoplasms to life-threatening metastatic tumors. A persistent limitation of current risk stratification systems is that a subset of GISTs is graded as low-risk but nevertheless metastasizes. Therefore, new predictive factors that improve risk stratification are needed. In this exploratory study, we investigated the potential of genome-wide DNA methylation profiling and copy number variation (CNV) analysis as additional prognostic tools for GISTs. We collected a cohort of 28 patients with GIST diagnosed between 2001 and 2022, with available follow-up and molecular data. This included 15 patients without progressive disease (seven low-risk and eight moderate- to high-risk GISTs) and 13 with progressive disease. Among those with progression, eight experienced recurrence or metastasis post-surgery (one low-risk, seven high-risk GISTs), while five had metastatic disease at initial diagnosis. Risk stratification was determined according to Miettinen's criteria. Genome-wide DNA methylation data and CNV plots were generated from imatinib-naïve primary GISTs using the Illumina Infinium MethylationEPIC BeadChip array. Unsupervised cluster analysis revealed distinct DNA methylation patterns predominantly associated with anatomical location and genotype. Differential DNA methylation analysis comparing primary gastric GISTs associated with and without progressive disease showed 8 differentially methylated regions spanning the coding and promoter areas of 6 genes. CNV analysis demonstrated that GISTs associated with progressive disease had the most CNVs, whereas low-risk, non-progressive GISTs had the fewest. Despite the limited sample size, this exploratory study indicates that genome-wide DNA methylation profiling and CNV analysis could enhance GIST risk stratification.

Construction of a prognostic risk model for Stomach adenocarcinoma based on endoplasmic reticulum stress genes

OBJECTIVE

Stomach adenocarcinoma (STAD) is caused by malignant transformation of gastric glandular cells and is characterized by a high incidence rate and a poor prognosis. This study was designed to establish a prognostic risk model for STAD according to endoplasmic reticulum (ER) stress feature genes as cancer cells are susceptible to ER stress.

METHODS

The TCGA-STAD dataset was downloaded to screen differentially expressed genes (DEGs). By intersecting DEGs with ER stress genes retrieved from GeneCards, ER stress-related DEGs in STAD were obtained. Kmeans cluster analysis of STAD subtypes and Single sample gene set enrichment analysis (ssGSEA) analysis of immune infiltration were performed. Cox regression analysis was utilized to construct a risk prognostic model. Samples were split into high-risk and low-risk groups according to the median risk score. Survival analysis and Receiver Operating Characteristic (ROC) curves were conducted to assess the validity of the model. Gene set enrichment analysis (GSEA) was performed to investigate differential pathways in the two risk groups. Cox analysis was performed to verify the independence of the risk model, and a nomogram was generated.

RESULTS

A total of 162 ER stress-related DEGs in STAD were identified by bioinformatics analysis. Kmeans cluster analysis showed that STAD was divided into 3 subgroups. The ssGSEA showed that the levels of immune infiltration in subgroups 2 and 3 were significantly higher than subgroup 1. With 12 prognostic genes (MATN3, ATP2A1, NOX4, AQP11, HP, CAV1, STARD3, FKBP10, EGF, F2, SERPINE1, CNGA3) selected from ER stress-related DEGs using Cox regression analysis, we then constructed a prognostic model. Kaplan-Meier (K‑M) survival curves and ROC curves showed good prediction performance of the model. Significant enrichment of genes in the high-risk group was found in extracellular matrix (ECM) receptor interaction. Cox regression analysis combined with clinical factors showed that the risk model could be used as an independent prognostic factor. The prediction correction curve showed that the good prediction ability of the nomogram.

CONCLUSION

The STAD could be divided into three subgroups, and the 12-gene model constructed by ER stress signatures had a good prognostic performance for STAD patients.

Metabolic heterogeneity in tumor microenvironment - A novel landmark for immunotherapy

The surrounding non-cancer cells and tumor cells that make up the tumor microenvironment (TME) have various metabolic rhythms. TME metabolic heterogeneity is influenced by the intricate network of metabolic control within and between cells. DNA, protein, transport, and microbial levels are important regulators of TME metabolic homeostasis. The effectiveness of immunotherapy is also closely correlated with alterations in TME metabolism. The response of a tumor patient to immunotherapy is influenced by a variety of variables, including intracellular metabolic reprogramming, metabolic interaction between cells, ecological changes within and between tumors, and general dietary preferences. Although immunotherapy and targeted therapy have made great strides, their use in the accurate identification and treatment of tumors still has several limitations. The function of TME metabolic heterogeneity in tumor immunotherapy is summarized in this article. It focuses on how metabolic heterogeneity develops and is regulated as a tumor progresses, the precise molecular mechanisms and potential clinical significance of imbalances in intracellular metabolic homeostasis and intercellular metabolic coupling and interaction, as well as the benefits and drawbacks of targeted metabolism used in conjunction with immunotherapy. This offers insightful knowledge and important implications for individualized tumor patient diagnosis and treatment plans in the future.

TEAD4 Activates PCSK9 to Promote Stomach Adenocarcinoma Cell Stemness through Fatty Acid Metabolism

INTRODUCTION

This study attempted to investigate how proprotein convertase subtilisin/kexin type 9 (PCSK9) influences the stemness of stomach adenocarcinoma (STAD) cells.

METHODS

CCK-8 and sphere-formation assays were used to detect cell viability and stemness. qRT-PCR and Western blot were used to detect PCSK9 and TEAD4 expression. The binding relationship was verified by dual-luciferase and chromatin immunoprecipitation assays. The effect of TEAD4 activating PCSK9 on the stemness of STAD cells was detected by bioinformatics, BODIPY 493/503, Oil red O, Western blot, and kits. In vivo experiments verified the role of the TEAD4/PCSK9 axis in tumor formation in nude mice.

RESULTS

PCSK9 and TEAD4 were highly expressed in STAD. PCSK9 was enriched in the fatty acid metabolism (FAM) pathway. PCSK9 activated the fatty acid metabolism and promoted the proliferation and stemness of STAD cells. TEAD4 as a transcription factor upstream of PCSK9, cell experiments revealed that knockdown of PCSK9 inhibited STAD cell stemness, whereas further addition of fatty acid inhibitors could attenuate the promoting effect on STAD cell stemness brought by STAD overexpression. Rescue experiments showed overexpressed PCSK9 exerted an inhibitory effect on the stemness of STAD cells brought by TEAD4 knockdown. The hypothesis that TEAD4/PCSK9 axis can promote STAD cell growth was confirmed by in vivo experiments.

CONCLUSION

Transcription factor TEAD4 could activate PCSK9 to promote the stemness of STAD cells through FAM. These results added weight to the assumption that TEAD4/PCSK9 axis has the potential to be the therapeutic target that inhibits cancer stem cell in STAD.

A novel dopamine receptor D2 antagonist (ONC206) potentiates the effects of olaparib in endometrial cancer

Poly ADP-ribose polymerase (PARP) inhibitors are effective therapies for cancer patients with homologous recombination (HR) deficient tumors. The imipridone ONC206 is an orally bioavailable dopamine receptor D2 antagonist and mitochondrial protease ClpP agonist that has anti-tumorigenic effects in endometrial cancer via induction of apoptosis, activation of the integrated stress response and modulation of PI3K/AKT signaling. Both PARP inhibitors and imipridones are being evaluated in endometrial cancer clinical trials but have yet to be explored in combination. In this manuscript, we evaluated the effects of the PARP inhibitor olaparib in combination with ONC206 in human endometrioid endometrial cancer cell lines and in a genetically engineered mouse model of endometrial cancer. Our results showed that simultaneous exposure of endometrial cancer cells to olaparib and ONC206 resulted in synergistic anti-proliferative effects and increased cellular stress and apoptosis in both cell lines, compared to either drug alone. The combination treatment also decreased expression of the anti-apoptotic protein Bcl-2 and reduced phosphorylation of AKT and S6, with greater effects compared to either drug alone. In the transgenic model of endometrial cancer, the combination of olaparib and ONC206 resulted in a more significant reduction in tumor weight in obese and lean mice compared to ONC206 alone or olaparib alone, together with a considerably decreased Ki-67 and enhanced H2AX expression in obese and lean mice. These results suggest that this novel dual therapy may be worthy of further exploration in clinical trials.

Advancements and Obstacles of PARP Inhibitors in Gastric Cancer

Gastric cancer (GC) is a common and aggressive cancer of the digestive system, exhibiting high aggressiveness and significant heterogeneity. Despite advancements in improving survival rates over the past few decades, GC continues to carry a worrisome prognosis and notable mortality. As a result, there is an urgent need for novel therapeutic approaches to address GC. Recent targeted sequencing studies have revealed frequent mutations in DNA damage repair (DDR) pathway genes in many GC patients. These mutations lead to an increased reliance on poly (adenosine diphosphate-ribose) polymerase (PARP) for DNA repair, making PARP inhibitors (PARPi) a promising treatment option for GC. This article presents a comprehensive overview of the rationale and development of PARPi, highlighting its progress and challenges in both preclinical and clinical research for treating GC.

Swertia cincta Burkill alleviates LPS/D-GalN-induced acute liver failure by modulating apoptosis and oxidative stress signaling pathways

Swertia cincta Burkill is widely distributed along the southwestern region of China. It is known as "Dida" in Tibetan and "Qingyedan" in Chinese medicine. It was used in folk medicine to treat hepatitis and other liver diseases. To understand how Swertia cincta Burkill extract (ESC) protects against acute liver failure (ALF), firstly, the active ingredients of ESC were identified using liquid chromatography-mass spectrometry (LC-MS), and further screening. Next, network pharmacology analyses were performed to identify the core targets of ESC against ALF and further determine the potential mechanisms. Finally, in vivo experiments as well as in vitro experiments were conducted for further validation. The results revealed that 72 potential targets of ESC were identified using target prediction. The core targets were ALB, ERBB2, AKT1, MMP9, EGFR, PTPRC, MTOR, ESR1, VEGFA, and HIF1A. Next, KEGG pathway analysis showed that EGFR and PI3K-AKT signaling pathways could have been involved in ESC against ALF. ESC exhibits hepatic protective functions via anti-inflammatory, antioxidant, and anti-apoptotic effects. Therefore, the EGFR-ERK, PI3K-AKT, and NRF2/HO-1 signaling pathways could participate in the therapeutic effects of ESC on ALF.

Eurycomanone stimulates bone mineralization in zebrafish larvae and promotes osteogenic differentiation of mesenchymal stem cells by upregulating AKT/GSK-3β/β-catenin signaling

Background

Eurycomanone (EN) is a diterpenoid compound isolated from the roots of Eurycoma longifolia (E. longifolia). Previous studies have confirmed that E. longifolia can enhance bone regeneration and bone strength. We previously isolated and identified ten quassinoids from E. longifolia, and the result displayed that five aqueous extracts have the effects on promotion of bone formation, among whom EN showed the strongest activity. However, the molecular mechanism of EN on bone formation was unknown, and we further investigated in this study.

Methods

After the verification of purity of extracted EN, following experiments were conducted. Firstly, the pharmacologic action of EN on normal bone mineralization and the therapeutic effect of EN on Dex-induced bone loss using zebrafish larvae. The mineralization area and integral optical density (IOD) were evaluated using alizarin red staining. Then the vital signaling pathways of EN relevant to OP was identified through network pharmacology analysis. Eventually in vitro, the effect of EN on cell viability, osteogenesis activities were investigated in human bone marrow mesenchymal stem cells (hMSCs) and C3H10 cells, and the molecular mechanisms by which applying AKT inhibitor A-443654 in hMSCs.

Results

In zebrafish larvae, the administration in medium of EN (0.2, 1, and 5 μM) dramatically enhanced the skull mineralization area and integral optical density (IOD), and increased mRNA expressions of osteoblast formation genes (ALP, RUNX2a, SP7, OCN). Meanwhile, exposure of EN remarkably alleviated the inhibition of bone formation induced by dexamethasone (Dex), prominently improved the mineralization, up-regulated osteoblast-specific genes and down-regulated osteoclast-related genes (CTSK, RANKL, NFATc1, TRAF6) in Dex-treated bone loss zebrafish larvae. Network pharmacology outcomes showed the MAPK and PI3K-AKT signaling pathways are closely associated with 10 hub genes (especially AKT1), and AKT/GSK-3β/β-catenin was selected as the candidate analysis pathway. In hMSCs and C3H10 cells, results showed that EN at appropriate concentrations of 0.008-5 μM effectively increased the cell proliferation. In addition, EN (0.04, 0.2, and 1 μM) significantly stimulated osteogenic differentiation and mineralization as well as significantly increased the protein phosphorylation of AKT and GSK-3β, and expression of β-catenin, evidencing by the results of ALP and ARS staining, qPCR and western blotting. Whereas opposite results were presented in hMSCs when treated with AKT inhibitor A-443654, which effectively inhibited the pro-osteogenesis effect induced by EN, suggesting EN represent powerful potential in promoting osteogenesis of hMSCs, which may be closely related to the AKT/GSK-3β/β-catenin signaling pathway.

Conclusions

Altogether, our findings indicate that EN possesses remarkable effect on bone formation via activating AKT/GSK-3β/β-catenin signaling pathway in most tested concentrations.

The translational potential of this article

This study demonstrates EN is a new effective monomer in promoting bone formation, which may be a promising anabolic agent for osteoporosis (OP) treatment.

Circular RNA XRCC5 aggravates glioma progression by activating CLC3/SGK1 axis via recruiting IGF2BP2

BACKGROUND

Increasing evidences have reported the critical roles of circular RNA (circRNA) in gliomas. Whereas, the role of circXRCC5 in glioma and its underlying molecular mechanism has not been reported.

METHODS

The RNA transcripts and protein levels were detected using qRT-PCR, immunohistochemistry (IHC) and in situ hybridization (ISH) assays. Cell proliferation was characterized by CCK-8 and clone formation assays. The formation of NLRP3-inflammasomes was identified using immunofluorescence (IF) and Western blot assays. The cytokines were determined using immunosorbent assay (ELISA) and Western blot assays. The molecular interactions were validated using RIP and pull-down assays.

RESULTS

circXRCC5 was over-expressed in glioma and positively related to the shorter survival rate, advanced TNM stage and larger tumor volume. circXRCC5 knockdown inhibited cell proliferation and NLRP3-mediated inflammasome activation of glioma cells. Subsequently, we found that circXRCC5 maintained mRNA stability of CLC3 by binding to IGF2BP2. Furthermore, CLC3 accelerated SGK1 expression via PI3K/PDK1/AKT pathway. The rescue experiments showed that both overexpression of CLC3 or SGK1 dramatically alleviated circXRCC5 knockdown-induced inhibition of cell proliferation and NLRP3-mediated inflammasome activation of glioma cells. In vivo, our study proved that circXRCC5 accelerated glioma growth by regulating CLC3/SGK1 axis.

CONCLUSION

Our data concluded that circXRCC5 formed a complex with IGF2BP2 to regulate inflammasome activation and tumor growth via CLC3/SGK1 axis.

MZF1 Transcriptionally Activated MicroRNA-328-3p Suppresses the Malignancy of Stomach Adenocarcinoma via Inhibiting CD44

MicroRNA-328-3p (miR-328-3p) plays a critical role in mediating the progression of multiple types of cancers. To date, no study has concentrated on the molecular mechanism of miR-328-3p in mediating stomach adenocarcinoma (STAD). In this study, it was found that miR-328-3p was downregulated in STAD, and inhibition of miR-328-3p significantly promoted the growth, migration, invasion, and stemness of STAD cells, while miR-328-3p overexpression exerted reverse effects. Through bioinformatics analysis, it was uncovered that a cluster of differentiation 44 (CD44) was upregulated in STAD and closely associated with the prognosis of STAD patients. Mechanistically, we identified CD44 as the target gene of miR-328-3p. Notably, knockdown of CD44 abolished the promoting function of miR-328-3p inhibitor in the development of STAD. Moreover, myeloid zinc finger protein 1 (MZF1) was confirmed as an upstream transcription factor for miR-328-3p, which is involved in enhancing miR-328-3p expression. In addition, the role of MZF1 downregulation in the malignant traits of STAD cells was blocked by miR-328-3p overexpression. More importantly, upregulation of miR-328-3p efficiently suppressed STAD tumor growth in vivo. Collectively, our findings illustrated that MZF1-mediated miR-328-3p acted as a cancer suppressor in STAD progression via regulation of CD44, which suggested the possibility of the MZF1/miR-328-3p/CD44 axis as a novel promising therapeutic candidate for STAD.

Identification and Validation of Biglycan as Prognosis and Therapy Markers for Patients with Stomach Adenocarcinoma

OBJECTIVE

Previous studies have confirmed the biglycan (BGN) as a core gene in stomach adenocarcinoma (STAD). Present study aimed at conducting further investigations to reveal the potential function of BGN in STAD.

METHODS

The mRNA and protein expressions of BGN in STAD were firstly evaluated, followed by immune infiltration analyses. The influence of BGN expression on the overall survival of STAD patients was subsequently analyzed, and a restrict survival analysis was performed as well. The protein-protein interaction (PPI) network analysis on the co-expressed genes with BGN was finally adopted to obtain the most important module in the whole network, and significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway associated with hub genes within the main module was further predicted.

RESULTS

(1) We verified the mRNA high expression of BGN in STAD (all P<0.05), and higher expression was observed in patients with stage 4 (P<0.001) and grade 3 (P<0.001). The BGN protein was mainly localized to the golgi apparatus, and protein expression displayed an individual difference. (2) Immune infiltration analysis showed the strongest correlation between BGN expression and abundance of natural killer cell (P<0.001), Transforming Growth Factor beta 1 (TGFB1) (P<0.001), TNF Receptor Superfamily Member 4 (TNFRSF4) (P<0.001) and C-X-C Motif Chemokine Ligand 12 (CXCL12) (P<0.001) in STAD. BGN expression was also correlated to immune subtypes (P=0.0347) and molecular subtypes (P=0.0263) in STAD. (3) High expression of BGN shortened the overall survival time of STAD patients (all P<0.01). The influence of BGN expression on the prognosis was statistically affected by several clinical phenotypes and cohorts of patients. Cox regression showed that BGN can be considered as a prognostic predictor of STAD (P<0.05). (4) Pathway analysis indicated that BGN possibly participated in ECM-receptor interaction, focal adhesion, human papillomavirus infection and PI3K-Akt signaling pathway (all P<0.001).

CONCLUSION

BGN was highly expressed in STAD, implying a poor prognosis of patients. Relevant signal pathways associated with BGN were distinguished as well. BGN could be used as a potential therapeutic biomarker for STAD.

ClC-3: A Novel Promising Therapeutic Target for Atherosclerosis

Chloride channel 3 (ClC-3), a Cl^-/H⁺ antiporter, has been well established as a member of volume-regulated chloride channels (VRCCs). ClC-3 may be a crucial mediator for activating inflammation-associated signaling pathways by regulating protein phosphorylation. A growing number of studies have indicated that ClC-3 overexpression plays a crucial role in mediating increased plasma low-density lipoprotein levels, vascular endothelium dysfunction, pro-inflammatory activation of macrophages, hyper-proliferation and hyper-migration of vascular smooth muscle cells (VSMCs), as well as oxidative stress and foam cell formation, which are the main factors responsible for atherosclerotic plaque formation in the arterial wall. In the present review, we summarize the molecular structures and classical functions of ClC-3. We further discuss its emerging role in the atherosclerotic process. In conclusion, we explore the potential role of ClC-3 as a therapeutic target for atherosclerosis.

miR-27-3p Enhances the Sensitivity of Triple-Negative Breast Cancer Cells to the Antitumor Agent Olaparib by Targeting PSEN-1, the Catalytic Subunit of Γ-Secretase

Olaparib has been used in the treatment of triple-negative breast cancer (TNBC) with BRCA mutations. In the present study, we demonstrated the effect of miR-27-3p on the γ-secretase pathway by regulating the sensitivity of TNBC cells to olaparib. miR-27-3p, a microRNA with the potential to target PSEN-1, the catalytic subunit of γ-secretase mediating the second step of the cleavage of the Notch protein, was identified by the online tool miRDB and found to inhibit the expression of PSEN-1 by directly targeting the 3'-untranslated region (3'-UTR) of PSEN-1. The overexpression of miR-27-3p inhibited the activation of the Notch pathway via the inhibition of the cleavage of the Notch protein, mediated by γ-secretase, and, in turn, enhanced the sensitivity of TNBC cells to the antitumor agent olaparib. Transfection with PSEN-1 containing mutated targeting sites for miR-27-3p or the expression vector of the Notch protein intracellular domain (NICD) almost completely blocked the effect of miR-27-3p on the Notch pathway or the sensitivity of TNBC cells to olaparib, respectively. Therefore, our results suggest that the miR-27-3p/γ-secretase axis participates in the regulation of TNBC and that the overexpression of miR-27-3p represents a potential approach to enhancing the sensitivity of TNBC to olaparib.

Identification and Construction of a Long Noncoding RNA Prognostic Risk Model for Stomach Adenocarcinoma Patients

Background

Long noncoding RNA-based prognostic biomarkers have demonstrated great potential in the diagnosis and prognosis of cancer patients. However, systematic assessment of a multiple lncRNA-composed prognostic risk model is lacking in stomach adenocarcinoma (STAD). This study is aimed at constructing a lncRNA-based prognostic risk model for STAD patients.

Methods

RNA sequencing data and clinical information of STAD patients were retrieved from The Cancer Genome Atlas (TCGA) database. Differentially expressed lncRNAs (DElncRNAs) were identified using the R software. Univariate and multivariate Cox regression analyses were performed to construct a prognostic risk model. The survival analysis, C-index, and receiver operating characteristic (ROC) curve were employed to assess the sensitivity and specificity of the model. The results were verified using the GEPIA online tool and our clinical samples. Pearson correlation coefficient analysis, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were performed to indicate the potential biological functions of the selected lncRNA.

Results

A total of 1917 DElncRNAs were identified from 343 cases of STAD tissues and 30 cases of noncancerous tissues. According to univariate and multivariable Cox regression analyses, four DElncRNAs (AC129507.1, LINC02407, AL022316.1, and AP000695.2) were selected to establish a prognostic risk model. There was a significant difference in the overall survival between high-risk patients and low-risk patients based on this risk model. The C-index of the model was 0.652. The area under the curve (AUC) for the ROC curve was 0.769. GEPIA results confirmed the expression and prognostic significance of AP000695.2 in STAD. Our clinical data confirmed that upregulated expression of AP000695.2 was correlated with the T stage, distant metastasis, and TNM stage in STAD. GO and KEGG analyses demonstrated that AP000695.2 was closely related to the tumorigenesis process.

Conclusions

In this study, we constructed a lncRNA-based prognostic risk model for STAD patients. Our study will provide novel insight into the diagnosis and prognosis of STAD patients.