BACKGROUND Tropomyosin 3 (TPM3) has been implicated in the progression of several cancers; however, its specific role and underlying molecular mechanisms in gastric cancer (GC) remain unclear. The current research aimed to investigate the role of TPM3 in the onset and advancement of GC, along with the related molecular pathways. AIM To investigate TPM3’s role in enhancing GC malignancy and elucidates the underlying molecular mechanisms. METHODS TPM3 expression in GC tissues was evaluated using bioinformatics analysis. Protein expression levels were determined using western blotting, and mRNA levels were measured through quantitative real-time PCR. Cellular functional assays, including cell counting kit-8 assay, 5-ethynyl-2-deoxyuridine incorporation, colony formation, wound-healing, and transwell migration/invasion, were conducted to assess the effects of TPM3 and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein gamma (YWHAG) on GC cell proliferation, migration, invasion, and metastatic potential. Cell cycle progression and apoptosis were analyzed using flow cytometry. A subcutaneous xenograft model in nude mice was employed to assess the tumorigenic potential of GC cells, while a tail vein injection model was used to evaluate their invasive and metastatic potential in vivo . RESULTS TPM3 was significantly upregulated in GC tissues and cells, and its high expression correlated with poor patient prognosis. Silencing TPM3 markedly inhibited GC cell proliferation, invasion, and metastasis while promoting apoptosis. TPM3 interacted with YWHAG, and TPM3 knockdown reduced YWHAG expression. Notably, the inhibitory effects of TPM3 silencing on GC progression were partially reversed by overexpressing YWHAG, confirming YWHAG as a key downstream effector. Furthermore, TPM3 knockdown suppressed activation of the mitogen-activated protein kinase pathway in a YWHAG-dependent manner. In vivo experiments demonstrated that increased TPM3 expression significantly promoted GC tumor growth and metastasis, whereas silencing YWHAG effectively attenuated this effect. CONCLUSION TPM3 promotes GC progression by regulating YWHAG and activating the mitogen-activated protein kinase signaling pathway. These findings identify the TPM3/YWHAG axis as a potential therapeutic target for GC intervention.

Oxaliplatin (OXA) is widely used to treat advanced gastric cancer, but acquired resistance limits its benefit. How resistant cells avoid ferroptosis remains unclear. Quantitative proteomics identified UGT8, a glycosphingolipid biosynthetic enzyme, as an upregulated protein in OXA-resistant gastric cancer cells. UGT8 protein was also increased in tumors from clinically OXA-resistant patients treated with oxaliplatin-based chemotherapy, and high UGT8 expression was associated with shorter survival. UGT8 overexpression increased OXA tolerance, while UGT8 depletion sensitized resistant cells and patient-derived organoids (PDOs) from clinically OXA-resistant patients to OXA. UGT8 depletion increased lipid reactive oxygen species and malondialdehyde, reduced glutathione, and aggravated ferroptosis-associated mitochondrial damage. Immunoprecipitation followed by mass spectrometry identified USP10 as a UGT8-associated protein. USP10 increased UGT8 stability and limited its K48-linked polyubiquitination. K307 was identified by mutational analysis as a functionally important residue involved in USP10-regulated UGT8 ubiquitination. UGT8 increased NRF2 nuclear accumulation and maintained HO-1, SLC7A11, and GPX4 expression. Restoring UGT8 or pharmacologically enhancing NRF2-associated antioxidant signaling reduced the effects of USP10 or UGT8 depletion on OXA sensitivity and ferroptosis-associated changes. Disrupting the USP10-UGT8 pathway also improved the OXA response in xenografts. These results support a role for USP10-dependent UGT8 stabilization in sustaining NRF2-associated antioxidant signaling, suppressing ferroptosis, and promoting OXA resistance.

Solid tumors such as gastric cancers exploit hypoxia-induced adaptive mechanisms to evade cell death. Here, we identify a hypoxia-triggered signaling axis in which the spliced form of XBP1s transcriptionally activates MYDGF. We demonstrate that MYDGF competitively binds the ubiquitin adaptor protein UBQLN1 at the STI1-4 domain, thereby blocking UBQLN1-mediated recognition and endoplasmic reticulum-associated degradation (ERAD) of LCN2. Stabilized LCN2 sequesters redox-active iron and inhibits iron-dependent lipid peroxidation, thereby suppressing ferroptosis. Hypoxia promotes the splicing of XBP1s, which directly binds to the MYDGF promoter, increasing its expression. Genetic disruption of this axis sensitizes gastric cancer cells to ferroptosis inducers both in vitro and in vivo. These findings reveal a previously unrecognized mechanism of hypoxia-induced ferroptosis resistance and suggest that the XBP1-MYDGF-UBQLN1-LCN2 pathway is a therapeutic target for hypoxic tumors.

Our previous work points out that methionine restriction (MR) treatment inhibits gastric cancer progression. Ferroptosis is a new form of cell death, and induction of ferroptosis has an inhibitory effect on tumors. Silencing of the ferroptosis inhibitory molecule FA complementation group D2 protein (FANCD2) has been reported to inhibit tumor growth. This investigation aims to explore whether MR treatment affects ferroptosis of gastric cancer cells by regulating FANCD2 expression, and thus affects the advancement of gastric cancer. Gastric cancer cells (AGS and HGC27) were cultured in MR condition. For ferroptosis detection, lipid ROS was examined by fluorescent staining; ACSL4 levels were estimated by western blot; malondialdehyde (MDA) and 4-hydroxy-2-nonenal (4-HNE) levels were measured via enzyme-linked immunosorbent assay. Transfection of FANCD2/METTL3 (methyltransferase-like 3) overexpression plasmids was to conduct in gain of function tests. SRAMP analysis was to predict the m6A methylation site of FANCD2, with methylated RNA immunoprecipitation detection of m6A levels of FANCD2 mRNA, and Actinomycin D experiments to evaluate its stability. Gastric cancer cells were administered through tail vein injection into BALB/c mice to conduct transplanted tumor models, and mice were given an MR diet or combined with an injection of oeFANCD2/oeMETTL3 lentivirus. The effect of FANCD2/METTL3 overexpression on tumor volume and ferroptosis was measured. The gastric cancer patient-derived organoids were also cultured and treated with MR, and the diameter was analyzed. MR treatment increased ferroptosis and reduced the volume of tumor tissue. FANCD2 levels were found to change dramatically following MR treatment, and overexpressing FANCD2 inhibited ferroptosis and promoted tumor formation. In addition, MR treatment decreased FANCD2 m6A abundance as well as FANCD2 mRNA stability. Database predictions suggested that METTL3 may be an m6A regulatory molecule influenced by MR, and our results showed that METTL3 was down-regulated under MR conditions, and METTL3 overexpression increased the m6A abundance and stability of FANCD2 mRNA. Further results showed that overexpressing METTL3 reduced ferroptosis-related indexes and increased the tumor volume, inhibiting METTL3 reversed the results. Furthermore, MR reduced the diameter of gastric cancer organoids. MR inhibits FANCD2 m6A levels and FANCD2 stability by inhibiting METTL3 expression, and then promotes ferroptosis in gastric cancer cells.

Hepatocyte nuclear factor 4A (HNF4A) is a core transcription factor that plays an important role in tumor progression. However, the regulatory mechanisms in gastric cancer remain unclear. In this study, we employed a bioinformatics-driven approach and combined it with cellular and animal experiments to investigate the regulatory mechanisms of HNF4A in gastric cancer. We identified kinesin family member 2C (KIF2C) as a novel downstream target of HNF4A and observed that both HNF4A and KIF2C were significantly upregulated in gastric cancer tissues. Knockdown of HNF4A or KIF2C inhibited the proliferation, migration, and invasion abilities of gastric cancer cells, while overexpression of KIF2C rescued these abilities of sh-HNF4A in gastric cancer cells. Mechanistically, HNF4A and KIF2C were found to colocalize in the nucleus, with HNF4A directly binding to the KIF2C promoter. Further analysis identified BS2 (−1381 −1368) and BS3 (−715 −700) as the core binding regions. In vivo experiments demonstrated that knockdown HNF4A inhibited tumor growth in BALB/c nude mice, and overexpression of KIF2C promoted tumor growth. In conclusion, HNF4A is an oncogene that promotes the proliferation, migration, and invasion of gastric cancer cells. Our study suggests that HNF4A can transcriptionally activate KIF2C and that the HNF4A-KIF2C axis may be a potential therapeutic target for gastric cancer.

AIMS:To investigate the role of transcription factor activating enhancer-binding protein 4 (TFAP4) in gastric cancer (GC) progression and elucidate its mechanism in promoting metastasis and invasion through the PI3K/AKT signaling pathway. METHODS:Bioinformatics analysis was performed to assess TFAP4 expression in GC tissues. Clinical specimens were collected and validated for TFAP4 expression. Functional assays were conducted to evaluate the effects of TFAP4 overexpression and inhibition on GC cell proliferation, invasion, and metastasis. In vivo studies with HGC27 cells in BALB/c nude mice were used to assess tumor growth and metastasis. Mechanistic analysis included the measurement of MCM5 expression and activation of the PI3K/AKT signaling pathway, with PI3K inhibitor LY294002 and MCM5 knockdown applied to confirm the pathways involved. RESULTS:Elevated TFAP4 expression was observed in GC tissues, and its overexpression promoted GC cell proliferation, invasion, and metastasis. Conversely, TFAP4 inhibition suppressed these behaviors. In vivo studies confirmed that TFAP4 knockdown reduced tumor growth and metastasis in nude mice. Mechanistically, TFAP4 was found to activate MCM5, which in turn facilitated GC cell invasion and metastasis. Furthermore, TFAP4 and MCM5 activated the PI3K/AKT signaling pathway, as evidenced by increased p-PI3K and p-AKT expression. The effects of TFAP4 overexpression were reversed by MCM5 knockdown or treatment with the PI3K inhibitor LY294002. CONCLUSION:The TFAP4-MCM5 signaling axis promotes GC progression through the PI3K/AKT pathway, suggesting that targeting this axis could provide a potential therapeutic strategy for managing gastric cancer.

BACKGROUND:Methionine restriction (MR) exerts an anti-tumor immunomodulatory role. Th1 cells facilitate CD8+ cytotoxic T cell activation and targeted tumor cell killing. Our previous work shows that MR enhances the immunotherapy effect of PD-L1/PD-1 blockade on gastric cancer, MR can simultaneously inhibit Th1 cell differentiation, which may affect their synergistic therapeutic outcome. We aim to elucidate the molecular mechanism of MR regulating Th1 cell activation in gastric cancer. METHODS:Murine Foregastric Carcinoma (MFC) cells were injected into 615 mice to establish transplanted tumor models, which were then treated with an MR diet or combined with 2-bromopalmitate (2-BP). CD4+T cells were cultured with deficient methionine. The acyl-biotinyl exchange (ABE) method was to detect T-bet palmitoylation and cycloheximide experiments to detect protein stability. GPS-Palm tool was employed to screen palmitoyltransferases. The impact of T-bet palmitoylation on the pro-tumor-killing effect of Th1 cells was examined. RESULTS:MR enhanced anti-PD-1's inhibition of tumor growth, while concurrently suppressing the increased Th1 cells. Combined with 2-BP further inhibited tumor and increased Th1 cells. Suppressing Th1 activity attenuated 2-BP's synergistic therapeutic effect and reduced CD8+ GZMB+ T cells. MR inhibited Th1 differentiation by reducing T-bet expression, 2-BP treatment restored, while T-bet interference reversed 2-BP's effect. MR increased palmitoylation and T-bet underwent palmitoylation modification. ZDHHC23 mediated T-bet palmitoylation and promoted T-bet degradation. MR promoted T-bet degradation, thereby decreasing T-bet content, inhibiting Th1 cell polarization and CD8+ T cell killing effect. CONCLUSIONS:MR combined with T-bet palmitoylation intervention promotes Th1 polarization and CD8+ T cell toxicity, thereby enhancing anti-tumor immunity in gastric cancer.

ABSTRACT Oral squamous cell carcinoma (OSCC) is a prevalent malignancy in the oral-maxillofacial region with a poor prognosis. Oral microbiomes play a potential role in the pathogenesis of this disease. However, findings from individual studies have been inconsistent, and a comprehensive understanding of OSCC-associated microbiome dysbiosis remains elusive. Here, we conducted a large-scale meta-analysis by integrating 11 publicly available data sets comprising salivary microbiome profiles of OSCC patients and healthy controls. After correcting for batch effects, we observed significantly elevated alpha diversity and distinct beta-diversity patterns in the OSCC salivary microbiome compared to healthy controls. Leveraging random effects models, we identified robust microbial signatures associated with OSCC across data sets, including enrichment of taxa such as Streptococcus , Lactobacillus , Prevotella , Bulleidia moorei , and Haemophilus in OSCC samples. The machine learning models constructed from these microbial markers accurately predicted OSCC status, highlighting their potential as non-invasive diagnostic biomarkers. Intriguingly, our analyses revealed that the age- and gender-associated signatures in normal saliva microbiome were disrupted in the OSCC, suggesting perturbations in the intricate host-microbe interactions. Collectively, our findings uncovered complex alterations in the oral microbiome in OSCC, providing novel insights into disease etiology and paving the way for microbiome-based diagnostic and therapeutic strategies. Given that the salivary microbiome can reflect the overall health status of the host and that saliva sampling is a safe, non-invasive approach, it may be worthwhile to conduct broader screening of the salivary microbiome in high-risk OSCC populations as implications for early detection. IMPORTANCE The oral cavity hosts a diverse microbial community that plays a crucial role in systemic and oral health. Accumulated research has investigated significant differences in the saliva microbiota associated with oral cancer, suggesting that microbiome dysbiosis may contribute to the pathogenesis of oral squamous cell carcinoma (OSCC). However, the specific microbial alterations linked to OSCC remain controversial. This meta-analysis reveals robust salivary microbiome alterations. Machine learning models using differential operational taxonomic units accurately predicted OSCC status, highlighting the potential of the salivary microbiome as a non-invasive diagnostic biomarker. Interestingly, age- and gender-associated signatures in the normal salivary microbiome were disrupted in OSCC, suggesting perturbations in host-microbe interactions.

This study aims to explore the mechanism by which KAL inhibits the proliferation and migration of cholangiocarcinoma (CCA) cells through the downregulation of miR-21, thereby modulating the PTEN/AKT signaling pathway. Cholangiocarcinoma cell lines HUCCT1 and RBE were cultured and transfected with KAL overexpression plasmids or miR-21 mimics. Transfection efficiency was validated by Western blot. Cell viability was assessed using the CCK8 assay, apoptosis levels were analyzed via flow cytometry, and cell invasion capability was evaluated through Transwell assays. PIP3 levels were measured using ELISA. Western blot was used to detect the expression levels of PTEN, AKT/mTOR signaling pathway proteins, and apoptosis-related proteins, including BCL-2 and Cleaved-Caspase3. Dual-luciferase reporter assays were performed to confirm the interaction between PTEN and miR-21-5p. Based on in vitro experimental results, HUCCT1 cells were selected for in vivo tumorigenicity experiments to assess the effects of KAL overexpression lentivirus on CCA tumor growth. Tumor size, volume, and weight were measured, and immunohistochemistry was used to detect the positive expression levels of KI67, PTEN, BCL-2, and Cleaved-Caspase3 in tumor tissues. PCR and Western blot analyses confirmed the effective transfection of KAL overexpression into HUCCT1 and RBE cells. Overexpression of KAL significantly inhibited CCA cell proliferation and invasion, reduced PIP3 production, suppressed the AKT/mTOR signaling pathway, and promoted apoptosis. PCR results demonstrated that miR-21 mimic transfection into HUCCT1 and RBE cells was successful. Overexpression of miR-21 reversed the inhibitory effects of KAL on CCA cell proliferation and migration, as well as the pro-apoptotic effects of KAL. Additionally, miR-21 suppressed the KAL-induced upregulation of PTEN and Cleaved-Caspase3 and promoted BCL-2 expression. Dual-luciferase reporter assays confirmed a targeted interaction between PTEN and miR-21-5p. In vivo tumorigenicity experiments showed that KAL overexpression significantly inhibited tumorigenesis in CCA cells. Tumor tissues from the KAL overexpression group exhibited significantly increased expression levels of Cleaved-Caspase3 and PTEN and decreased positive expression levels of KI67 and BCL-2, indicating suppressed proliferation and enhanced apoptosis in CCA cells. Overexpression of KAL inhibits CCA cell proliferation and promotes apoptosis. Overexpression of miR-21 reverses the effects of KAL on CCA cells, suggesting that KAL suppresses CCA growth through miR-21-mediated modulation of the PTEN/AKT signaling pathway.

Breast cancer (BC) remains one of the leading causes of cancer-related mortality among women worldwide, with distant metastasis being the primary contributor to poor prognosis. However, the molecular mechanisms driving BC metastasis are not yet fully understood. We integrated three public microarray datasets (GSE14776, GSE103357, and GSE32489) to identify the differentially expressed genes (DEGs) associated with breast cancer metastasis. Functional enrichment analysis, protein-protein interaction (PPI) network construction, and hub gene identification were performed using bioinformatics tools including DAVID, STRING, Cytoscape, and R. The prognostic significance of hub genes was assessed using Kaplan-Meier plotter and GEPIA. Expression validation was conducted through UALCAN, immunohistochemistry (IHC), and single-cell RNA sequencing (scRNA-seq) analysis from the GSE180286 dataset. A total of 295 co-DEGs were identified across the three datasets, enriched in pathways such as MAPK signaling, Rap1 signaling, and cell adhesion molecules. Twenty hub genes were identified from the PPI network, with eight showing strong prognostic value. Among them, PRC1 and POLR3H emerged as potential novel biomarkers. IHC confirmed the differential protein expression of PRC1, CDCA8, KIF14, and POLR3H. scRNA-seq analysis revealed that these hub genes were predominantly expressed in malignant epithelial and EMT (epithelial-mesenchymal transition) cells, particularly those from metastatic lymph node sites. This integrative analysis combining bulk and single-cell transcriptomic data identified key metastasis-associated genes in breast cancer. PRC1 and POLR3H, in particular, may serve as novel prognostic biomarkers and potential therapeutic targets.

Gastric cancer metastasis is a major cause of poor prognosis. Our previous research showed that methionine restriction (MR) lowers the invasiveness and motility of gastric carcinoma. In this study, we investigated the particular mechanisms of MR on gastric carcinoma metastasis. In vitro, gastric carcinoma cells (AGS, SNU-5, MKN7, KATO III, SNU-1, and MKN45) were grown in an MR medium for 24 h. In vivo, BALB/c mice were given a methionine-free (Met−) diet. Transwell assays were used to investigate cell invasion and migration. The amounts of Krüppel like factor 10 (KLF10) and cystathionine β-synthase (CBS) were determined using quantitative real-time PCR and western blot. To determine the relationship between KLF10 and CBS, chromatin immunoprecipitation and a dual-luciferase reporter experiment were used. Hematoxylin–eosin staining was used to detect lung metastasis. Liquid chromatography–mass spectrometry was used to determine cystathionine content. MR therapy had varying effects on the invasion and migration of gastric carcinoma cells AGS, SNU-5, MKN7, KATO III, SNU-1, and MKN45. KLF10 was highly expressed in AGS cells but poorly expressed in KATO III cells. KLF10 improved MR's ability to prevent gastric carcinoma cell invasion and migration. In addition, KLF10 may interact with CBS, facilitating transcription. Further detection revealed that inhibiting the KLF10/CBS-mediated trans-sulfur pathway lowered Met−‘s inhibitory effect on lung metastasis development. KLF10 transcription activated CBS, accelerated the trans-sulfur pathway, and increased gastric carcinoma cells' susceptibility to MR.

Invasion and metastasis are the leading causes of death in individuals with malignant tumors, including gastric cancer. In this study, we aim to explore the effect and related mechanisms of methionine restriction (MR) on gastric carcinoma metastasis. In the MR cell model, gastric carcinoma cells are cultured in the MR medium, and in the animal model, BALB/c nude rodents are administered with a methionine-free diet after receiving injections of MKN45 cells into the caudal vein. Transwell assay is used to detect cell invasion and migration. Chromatin immunoprecipitation is performed to investigate the levels of H3K9me2, H3K27Ac, and H3K27me3 in the E-cadherin promoter. The results show that MR inhibits gastric carcinoma cell migration, invasion, and lung metastasis. MR increases E-cadherin while reducing the H3K27me3 level in the E-cadherin promoter. E-cadherin expression in gastric carcinoma cells is adversely regulated by HDAC2. Overexpressing HDAC2 reduces the H3K27Ac level in the E-cadherin promoter, while interfering with HDAC2 increases the H3K27Ac level. HDAC2 interference under MR conditions further upregulates E-cadherin expression and inhibits gastric carcinoma cell migration, invasion, and lung metastasis. MR combined with HDAC2 interference promotes E-cadherin expression by mediating the methylation and acetylation of E-cadherin, thus inhibiting the invasion, migration, and lung metastasis of gastric carcinoma cells. Our study provides a new theoretical basis for the inhibitory effect of MR on gastric cancer.

Gastric cancer is ranked as the fifth most prevalent cancer globally and has long been a topic of passionate discussion among numerous individuals. However, the incidence of gastric cancer in society has not decreased, but instead has shown a gradual increase in recent years. For more than a decade, the treatment effect of gastric cancer has not been significantly improved. This is attributed to the heterogeneity of cancer, which makes popular targeted therapies ineffective. Methionine is an essential amino acid, and many studies have shown that it is involved in the development of gastric cancer. Our study aimed to review the literature on methionine and gastric cancer, describing its mechanism of action to show that tumor heterogeneity in gastric cancer does not hinder the effectiveness of methionine-restricted therapies. This research also aimed to provide insight into the inhibition of gastric cancer through metabolic reprogramming with methionine-restricted therapies, thereby demonstrating their potential as adjuvant treatments for gastric cancer.

BACKGROUND:Methionine restriction (MR) is a research direction in the treatment of gastric cancer (GC). The aim of this study was to investigate the molecular mechanism of MR on enhancing cisplatin (DDP) sensitivity of drug-resistant GC cells. METHODS:Twenty pairs of GC tissues and adjacent normal gastric mucosa tissues were collected. DDP-resistant cell lines (KATO/DDP and MKN45/DDP), mouse model of GC and GC patient-derived organoid (PDO) models were established. Lentivirus-mediated METase overexpression was used for MR. Cell viability and apoptosis were detected by MTT assay and flow cytometry. Western blotting was used to detect multi-drug resistance-1 (MDR1), MDR-associated protein 1 (MRP1) eukaryotic initiation factor 4A-Ⅲ (EIF4A3), and METase protein expressions. The levels of circRNAs were detected by qRT-PCR. Tumor volume and weight were measured. The proliferation of tumor cells was detected by immunohistochemical staining. RESULTS:The differentially expressed circRNAs of GC were screened in Gene Expression Omnibus database. MR in KATO/DDP and MKN45/DDP cells significantly down-regulated circ-CDK13 level. Overexpression of circ-CDK13 significantly inhibited apoptosis of sensitive cells (KATO III and MKN45). Interference with circ-CDK13 significantly promoted apoptosis of drug-resistant cells (KATO/DDP and MKN45/DDP). MR enhanced the DDP sensitivity of GC resistant cells, GC PDO and GC mice by down-regulating circ-CDK13. EIF4A3 binds to the downstream flanking sequence of circ-CDK13, and interference with EIF4A3 reduces circ-CDK13 levels, but does not affect CDK13. The expressions of circ-CDK13 and EIF4A3 in GC clinical samples were increased and positively correlated. Simultaneously overexpression of METase and EIF4A3 in resistant cells inhibited apoptosis, and further interference with circ-CDK13 reversed this effect. CONCLUSION:MR inhibits circ-CDK13 level by down-regulating EIF4A3, thereby increasing the sensitivity of GC drug-resistant cells to DDP.

Gastric Cancer (GC) is a prevalent malignancy within the digestive tract, ranking as the fifth most common malignant tumor worldwide. It is characterized by clinical features such as a tendency for metastasis and an unfavorable prognosis. Ferroptosis, a recently identified form of cell death, represents a novel mode of cellular demise that diverges from the traditional concepts of necrosis and apoptosis. Numerous studies have found that ferroptosis plays a significant role in the proliferation, metastasis, drug resistance, and microenvironment regulation within GC. This review summarizes the mechanism of ferroptosis and its role in the occurrence and development of GC cells. It provides examples demonstrating how various anti-tumor drugs can induce ferroptosis in GC cells. Additionally, it summarizes the potential application value of ferroptosis in the future treatment of GC.

Abstract The prevention and treatment of gastric cancer has been the focus and difficulty of medical research. We aimed to explore the mechanism of inhibiting migration and invasion of gastric cancer cells by methionine restriction (MR). The human gastric cancer cell lines AGS and MKN45 cultured with complete medium (CM) or medium without methionine were used for in vitro experiments. MKN45 cells were injected tail vein into BALB/c nude mice and then fed with normal diet or methionine diet for in vivo experiments. MR treatment decreased cell migration and invasion, increased E-cadherin expression, decreased N-cadherin and p-p65 expressions, and inhibited nuclear p65 translocation of AGS and MKN45 cells when compared with CM group. MR treatment increased IκBα protein expression and protein stability, and decreased IκBα protein ubiquitination level and TRIM47 expression. TRIM47 interacted with IκBα protein, and overexpression of TRIM47 reversed the regulatory effects of MR. TRIM47 promoted lung metastasis formation and partially attenuated the effect of MR on metastasis formation in vivo compared to normal diet group mice. MR reduces TRIM47 expression, leads to the degradation of IκBα, and then inhibits the translocation of nuclear p65 and the migration and invasion of gastric cancer cells.

The spatial transcriptome has enabled researchers to resolve transcriptome expression profiles while preserving information about cell location to better understand the complex biological processes that occur in organisms. Due to technical limitations, the current high-throughput spatial transcriptome sequencing methods (known as next-generation sequencing with spatial barcoding methods or spot-based methods) cannot achieve single-cell resolution. A single measurement site, called a spot, in these technologies frequently contains multiple cells of various types. Computational tools for determining the cellular composition of a spot have emerged as a way to break through these limitations. These tools are known as deconvolution tools. Recently, a couple of deconvolution tools based on different strategies have been developed and have shown promise in different aspects. The resulting single-cell resolution expression profiles and/or single-cell composition of spots will significantly affect downstream data mining; thus, it is crucial to choose a suitable deconvolution tool. In this review, we present a list of currently available tools for spatial transcriptome deconvolution, categorize them based on the strategies they employ, and explain their advantages and limitations in detail in order to guide the selection of these tools in future studies.

BackgroundThe treatment of gastric cancer remains a challenge.MethodsWe divided gastric cancer into three subtypes based on 14 cancer functional states. We investigated differences between subtypes through multi-omics data, especially at the single-cell level, which allowed us to analyze differences from the perspective of each type of cell rather than the whole.ResultsThe cluster 1 is characterized by high levels of tumor progression-related cancer functional status, worst survival outcomes, low metabolic level, high infiltration of immunosuppressive cells, high copy number variations (CNV), and low tumor mutational burden (TMB). The cluster 2 is characterized by low levels of tumor progression-related cancer functional status, favorable prognosis, moderate metabolic level, low immune cell infiltration, high CNV, and moderate TMB. Then, the cluster 3 is characterized by the high level of all cancer functional status, high metabolic level, low CNV, high TMB, high infiltration of immune cells with high cytotoxicity, and better response to immunotherapy. We also established a prognostic model based on cancer functional status and validated its robustness.ConclusionsCollectively, our study identified gastric cancer subtypes and provided new insights into the clinical treatment of gastric cancer.

Background Hepatocellular carcinoma (HCC) is a malignant tumor with a poor prognosis. The progression of numerous malignancies has been linked to abnormal vesicle-mediated transport-related gene (VMTRG) expression. The prognostic importance of VMTRGs in HCC is uncertain nonetheless. Methods Utilizing HCC data from TCGA and ICGC, we employed univariate cox analysis, unsupervised clustering, and lasso analysis to construct molecular subtypes and prognostic signature of HCC based on the prognostic-associated VMTRGs expression levels. Subsequently, we validated the expression levels of the signature genes. We investigated the probable pathways using gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA). Six methods were utilized to compare immune cell infiltration between two risk groups. Moreover, the “pRRophetic” algorithm was utilized to test the drug sensitivity of both groups. Results We identified two distinct subtypes with divergent biological behaviors and immune functionality through unsupervised clustering. Subtype C1 demonstrated a poorer prognosis. A prognostic signature incorporating two VMTRGs (KIF2C and RAC1) was formulated. Immunohistochemistry and qRT-PCR analyses unveiled a significant upregulation of these pivotal genes within HCC tissues. The prognosis was worse for the high-risk group, which also had a higher clinicopathological grade, higher levels of tumor mutation burden (TMB), a higher immunological infiltration of CD8 + T cells, a higher expression of immune checkpoints, and enhanced immunotherapy efficacy. These two risk groups also have varied chemotherapy drug sensitivities. Conclusions Based on VMTRGs, we have developed a signature that assists in accurate prognosis prediction and formulating personalized treatment strategies for HCC patients.

BackgroundWe developed a novel system for quantifying DNA damage response (DDR) to help diagnose and predict the risk of Alzheimer's disease (AD). MethodsWe thoroughly estimated the DDR patterns in AD patients Using 179 DDR regulators. Single-cell techniques were conducted to validate the DDR levels and intercellular communications in cognitively impaired patients. The consensus clustering algorithm was utilized to group 167 AD patients into diverse subgroups after a WGCNA approach was employed to discover DDR-related lncRNAs. The distinctions between the categories in terms of clinical characteristics, DDR levels, biological behaviors, and immunological characteristics were evaluated. For the purpose of choosing distinctive lncRNAs associated with DDR, four machine learning algorithms, including LASSO, SVM-RFE, RF, and XGBoost, were utilized. A risk model was established based on the characteristic lncRNAs. ResultsThe progression of AD was highly correlated with DDR levels. Single-cell studies confirmed that DDR activity was lower in cognitively impaired patients and was mainly enriched in T cells and B cells. DDR-related lncRNAs were discovered based on gene expression, and two different heterogeneous subtypes (C1 and C2) were identified. DDR C1 belonged to the non-immune phenotype, while DDR C2 was regarded as the immune phenotype. Based on various machine learning techniques, four distinctive lncRNAs associated with DDR, including FBXO30-DT, TBX2-AS1, ADAMTS9-AS2, and MEG3 were discovered. The 4-lncRNA based riskScore demonstrated acceptable efficacy in the diagnosis of AD and offered significant clinical advantages to AD patients. The riskScore ultimately divided AD patients into low- and high-risk categories. In comparison to the low-risk group, high-risk patients showed lower DDR activity, accompanied by higher levels of immune infiltration and immunological score. The prospective medications for the treatment of AD patients with low and high risk also included arachidonyltrifluoromethane and TTNPB, respectively, ConclusionsIn conclusion, immunological microenvironment and disease progression in AD patients were significantly predicted by DDR-associated genes and lncRNAs. A theoretical underpinning for the individualized treatment of AD patients was provided by the suggested genetic subtypes and risk model based on DDR.