Your browser does not allow saving data (e.g. private mode): bookmarks will be lost when the tab closes.
Search PubMed
Keywords, author, journal, years — results from PubMed, abstracts with Russian translation, bookmarks in your browser.
Found: 4 945
Page 458 of 495-
INHBA: a mitochondrial-related pan-cell death gene associated with the prognosis and immunity of OSCC.
Oral squamous cell carcinoma (OSCC) is a malignant tumor characterized by both clinical and molecular heterogeneity. Its rising global incidence and mortality rates pose considerable clinical challenges. Accumulating evidence suggests that dysregulation of mitochondria-associated pan-cell death, a process integrating multiple mitochondrial-related cell death modalities, is closely linked to tumor initiation and progression. Nevertheless, the identification of key therapeutic targets among mitochondria-associated pan-cell death-related genes (MAPGs) in OSCC remains an unresolved issue, underscoring the need for further investigation. We systematically investigated the expression patterns, prognostic relevance, and immune microenvironmental features of mitochondria-associated pan-cell death-related genes (MAPGs) in OSCC by integrating data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) datasets (GSE42743, GSE41613, GSE75538, GSE164241, GSE172577, and GSM6339633), and the MitoCarta3.0 database. Using nine machine learning algorithms, we compared the importance and prognostic value of MAPGs and identified INHBA as the most pivotal MAPG. Its predictive power and functional relevance were further explored through enrichment analysis. We validated INHBA mRNA expression levels in clinical OSCC samples using quantitative real-time PCR (qRT‑PCR). Pan-cancer analysis was performed to assess the potential of INHBA as a therapeutic target across multiple cancer types. Single-cell RNA sequencing, spatial transcriptomics, and cell-cell communication analyses were integrated to elucidate the spatial distribution of INHBA in OSCC and its crosstalk with the immune microenvironment. Finally, drug sensitivity profiling was conducted using the GDSC and PRISM databases. A total of 19 MAPGs with the greatest prognostic value were screened out. Among them, INHBA emerged as the most critical MAPG, which was overexpressed in HNSCC and strongly correlated with poor prognosis in OSCC patients (p < 0.05). Meanwhile, INHBA expression was elevated in cancer-associated fibroblasts (CAFs). Spatial transcriptomic analysis further revealed strong spatial colocalization between INHBA and CAF-localized regions. These results indicated that INHBA primarily functioned within CAFs, especially myCAFs, and may promote OSCC progression through modulation of the immune microenvironment. Elevated INHBA expression served as a prognostic indicator in OSCC, a finding consistent with its prognostic relevance in broader HNSCC analyses. Selumetinib and naltrexone showed high sensitivity in INHBA-high contexts. INHBA is a crucial MAPG that is upregulated in OSCC and mainly functions in CAFs. It likely affects the poor prognosis of OSCC by regulating the immune microenvironment. Selumetinib and naltrexone hold promise as innovative therapeutic agents, potentially opening up new treatment avenues for OSCC patients.
-
Integrating tertiary lymphoid structure-associated genes into computational models to evaluate prognostication and immune infiltration in pancreatic cancer.
Pancreatic ductal adenocarcinoma (PDAC) is characterized by poor response to all therapeutic modalities and dismal prognosis. The presence of tertiary lymphoid structures (TLSs) in various solid cancers is of crucial prognostic significance, highlighting the intricate interplay between the tumor microenvironment and immune cells aggregation. However, the extent to which TLSs and immune status affect PDAC prognosis remains incompletely understood. Here, we sought to unveil the unique properties of TLSs in PDAC by leveraging both single-cell and bulk transcriptomics, culminating in a risk model that predicts clinical outcomes. We used TLS scores based on a 12-gene (CCL2, CCL3, CCL4, CCL5, CCL8, CCL18, CCL19, CCL21, CXCL9, CXCL10, CXCL11, and CXCL13) and 9-gene (PTGDS, RBP5, EIF1AY, CETP, SKAP1, LAT, CCR6, CD1D, and CD79B) signature, respectively, and examined their distribution in cell clusters of single-cell data from PDAC samples. The markers involved in these clusters were selected to develop a prognostic model using The Cancer Genome Atlas Program database as the training cohort and Gene Expression Omnibus database as the validation cohort. Further, we compared the immune infiltration, drug sensitivity, and enriched and differentially expressed genes between the high- and low-risk groups in our model. Therefore, we established a risk model that has significant implications for the prognostic assessment of PADC patients with remarkable differences in immune infiltration and chemosensitivity between the low- and high-risk groups. This paradigm established by TLS-related cell marker genes provides a prognostic prediction and a panel of novel therapeutic targets for exploring potential immunotherapy.
-
Overexpression of LIMA1 Indicates Poor Prognosis and Promotes Epithelial-Mesenchymal Transition in Head and Neck Squamous Cell Carcinoma.
BACKGROUND: LIMA1 encodes LIM domain and actin binding 1, a cytoskeleton-associated protein whose loss has been linked to migration and invasion behavior of cancer cells. However, the roles of LIMA1 underlying the malignant behavior of tumors in head and neck squamous cell carcinoma (HNSC) are not fully understood. METHODS: We conducted a multi-omics study on the role of LIMA1 in HNSC based on The Cancer Genome Atlas data. Subsequent in vitro experiments were performed to validate the results of bioinformatic analysis. We first identified the correlation between LIMA1 and tumor cell functional states according to single-cell sequencing data in HNSC. The potential downstream effects of LIMA1 were explored for gene ontology and Kyoto Encyclopedia of Genes and Genomes pathways through functional enrichment analysis of the gene sets that correlated with LIMA1 in HNSC. The prognostic role of LIMA1 was assessed using the log rank test to compare difference in survival between LIMA1High and LIMA1Low patients. Univariate Cox regression and multivariate Cox regression were further carried out to identify the prognostic value of LIMA1 in HNSC. RESULTS: LIMA1 was identified as a prognostic biomarker and is associated with epithelial-mesenchymal transition (EMT) progress in HNSC. In vitro silencing of LIMA1 suppressed EMT and related pathways in HNSC. CONCLUSIONS: LIMA1 promotes EMT and further leads to tumor invasion and metastasis. Increased expression of LIMA1 indicates poor survival, identifying it as a prognostic biomarker in HNSC.
-
Regulator of G protein signaling 1 is a potential target in gastric cancer and impacts tumor-associated macrophages.
Regulator of G protein signaling 1 (RGS1) is closely associated with the tumor immune microenvironment and is highly expressed in various tumors and immune cells. The specific effects of RGS1 in the dynamic progression from chronic gastritis to gastric cancer have not been reported, and the role of tumor-associated macrophages (TAMs) is also unclear. In the present study, RGS1 was identified as an upregulated gene in different pathological stages ranging from chronic gastritis to gastric cancer by using Gene Expression Omnibus (GEO) screening together with pancancer analysis of The Cancer Genome Atlas and clinical prognostic analysis. The results indicated that RGS1 is highly expressed in gastric cancer and has potential prognostic value. We confirmed through in vivo experiments that RGS1 inhibited the proliferation of gastric cancer cells and promoted apoptosis, which was further corroborated by in vitro experiments. Additionally, RGS1 influenced cell migration and invasion. In our subsequent investigation of RGS1, we discovered its role in the immune response. Through analyses of single-cell and GEO database data, we confirmed its involvement in immune cell regulation, specifically TAM activation. Subsequently, we conducted in vivo and in vitro experiments to confirm the involvement of RGS1 in polarizing M1 macrophages while indirectly regulating M2 macrophages through tumor cells. In conclusion, RGS1 could be a potential target for the transformation of chronic gastritis into gastric cancer and has a measurable impact on TAMs, which warrants further in-depth research.
-
Evolving Molecular Subtypes of Gastric Cancer: From Past Classifications to Present Consensus and Future Directions for Precision Therapy.
Gastric cancer is a biologically heterogeneous disease. The advent of high-throughput multi-omic technologies has revolutionized our understanding of gastric cancer by deconstructing this heterogeneous entity into distinct and more homogeneous molecular subtypes. Early classifications based on gene expression, methylation, and histology have laid the groundwork for multi-omic frameworks proposed by The Cancer Genome Atlas and Asian Cancer Research Group, which established the foundation of modern molecular taxonomy. Subsequent integrative efforts, particularly the Consensus Genomic Subtypes (Super 6) model, have unified this collected information into clinically relevant subtypes that bridge prognostic stratification with treatment strategies. Established biomarkers such as human epidermal growth factor receptor 2 amplification, microsatellite instability, and programmed death-ligand 1 expression are now used clinically to guide treatment with targeted agents and immune checkpoint inhibitors. Emerging single-cell and spatial transcriptomic analyses have further refined this landscape by deconstructing tumor microenvironments and potential evolutionary trajectories associated with disease progression. This review examines the evolution of molecular classification systems for gastric cancer, highlights current consensus frameworks, and discusses how subtype-based stratification will transform clinical trial design and enable biomarker-driven precision therapy.
-
Dissecting endothelial cell heterogeneity with new tools.
The formation of a blood vessel network is crucial for organ development and regeneration. Over the past three decades, the central molecular mechanisms governing blood vessel growth have been extensively studied. Recent evidence indicates that vascular endothelial cells-the specialized cells lining the inner surface of blood vessels-exhibit significant heterogeneity to meet the specific needs of different organs. This review focuses on the current understanding of endothelial cell heterogeneity, which includes both intra-organ and inter-organ heterogeneity. Intra-organ heterogeneity encompasses arterio-venous and tip-stalk endothelial cell specialization, while inter-organ heterogeneity refers to organ-specific transcriptomic profiles and functions. Advances in single-cell RNA sequencing (scRNA-seq) have enabled the identification of new endothelial subpopulations and the comparison of gene expression patterns across different subsets of endothelial cells. Integrating scRNA-seq with other high-throughput sequencing technologies promises to deepen our understanding of endothelial cell heterogeneity at the epigenetic level and in a spatially resolved context. To further explore human endothelial cell heterogeneity, vascular organoids offer powerful tools for studying gene function in three-dimensional culture systems and for investigating endothelial-tissue interactions using human cells. Developing organ-specific vascular organoids presents unique opportunities to unravel inter-organ endothelial cell heterogeneity and its implications for human disease. Emerging technologies, such as scRNA-seq and vascular organoids, are poised to transform our understanding of endothelial cell heterogeneity and pave the way for innovative therapeutic strategies to address human vascular diseases.
-
Construction of prognostic signature of patients with oral squamous cell carcinoma based on pyroptosis-related long non-coding RNAs.
BACKGROUND AND OBJECTIVE: Oral squamous cell carcinoma (OSCC) is the most common malignant tumor in the head and neck, and its morbidity and mortality are increasing year by year. Changes in key genes are thought to be closely related to the occurrence and development of OSCC. Pyroptosis is an inflammatory form of programmed cell death that has been implicated in malignancies and inflammatory diseases. Changes in the expression of long noncoding RNAs may also affect tumorigenesis and progression. In this study, our main objective was to evaluate the association between pyroptosis-related lncRNAs and prognosis in patients with OSCC. METHODS: The RNA-seq data and clinicopathological data of OSCC patients are from The Cancer Genome Atlas database. The pyroptosis gene set is obtained from Gene Set Enrichment Analysis database. Univariate COX, Lasso and multivariate COX regression analyses were used for the construction of risk prognostic models of OSCC, eight lncRNAs were incorporated into prognostic models. The Kaplan-Meier method and log-rank test were used to evaluate the differences of overall survival between patients in high-risk and low-risk groups. The reliability of predictions across the dataset was analyzed by receiver operating characteristic (ROC) curves. The immune signature score was calculated using the single-sample gene set enrichment analysis. RESULTS: Eight pyroptosis-related lncRNAs were used to construct prognostic signature of OSCC, including AC136475.2, AC024075.2, JPX, ZFAS1, TNFRSF10A-AS1, LINC00847, AC099850.3 and IER3-AS1. According to this prognostic signature, patients with OSCC were divided into high-risk and low-risk groups. Kaplan-Meier survival analysis showed that the survival rate of the high-risk group was significantly lower than the low-risk group. ROC area for risk score was 0.716, and ROC area of the 8 lncRNAs are all between 0.5 and 1, implied that these lncRNAs had high accuracy in predicting the prognosis of OSCC patients. Immune Infiltration findings suggested that these lncRNAs affected immune responses in the microenvironment of OSCC. CONCLUSION: The prognostic signature based on pyroptosis-related lncRNAs potentially serves as an independent prognostic indicator for OSCC patients. And this signature facilitates research on targeted diagnosis and treatment of patients diagnosed with OSCC.
-
PTPN22 as a novel therapeutic target: a key intracellular checkpoint for NK cell therapy.
BACKGROUND: PTPN22, a protein tyrosine phosphatase (PTP) family member, has recently emerged as an intracellular regulator in adaptive immune cells. However, its function in natural killer (NK) cells remains unclear despite its high expression in innate immune cells. METHODS: We analyzed single-cell RNA-sequencing (scRNA-seq) datasets and The Cancer Genome Atlas (TCGA) to evaluate PTPN22 expression in NK cells and its association with clinical outcomes. We established a CRISPR-mediated PTPN22 knockout platform for NK cell gene editing and evaluated PTPN22 function using both genetic deletion and pharmacological inhibition across multiple NK cell platforms. Cytotoxicity and cytokine production were assessed against hematologic and solid tumor targets, including CD19+ and mesothelin-positive (MSLN+) cancer cells. PTPN22 knockout (PTPN22KO) anti-CD19/CAR-NK92 cells were tested in Nalm6 xenograft models. RESULTS: Published scRNA-seq datasets showed that PTPN22 was highly expressed in tumor-infiltrating NK cells. PTPN22high NK cells exhibited stress and dysfunction signatures within inflammatory and immunosuppressive tumor microenvironments (TME), with elevated PTPN22 expression in TCGA associated with poorer patient survival. Genetic deletion of PTPN22 or pharmacological inhibition enhanced NK-cell cytotoxicity and pro-inflammatory cytokine release and improved the antitumor activity of chimeric antigen receptor (CAR)-NK cells against CD19+ and MSLN+ targets. PTPN22KO preserved CAR-NK cell function under cytokine-based TME-like conditions and improved the functional persistence of primary anti-CD19 CAR-NK cells during prolonged tumor exposure. PTPN22KO NK and CAR-NK cells showed increased or preserved signal transducer and activator of transcription 3 (STAT3) phosphorylation and reduced FAS expression under inflammatory conditions. Notably, PTPN22KO anti-CD19/CAR-NK92 cells demonstrated superior anti-leukemic activity and significantly prolonged survival compared with non-knockout controls in vivo. CONCLUSIONS: These findings identify PTPN22 as a novel intracellular checkpoint that limits NK and CAR-NK cell function. Targeted deletion of PTPN22 represents a promising strategy to enhance the therapeutic efficacy and persistence of both unmodified and CAR-engineered NK cells for cancer immunotherapy.
-
CARS1 as a Prognostic Biomarker and Candidate Therapeutic Vulnerability in Hepatocellular Carcinoma: Insights Into Tumor Progression and the Immune Microenvironment.
BACKGROUND: Cysteinyl-tRNA synthetase 1 (CARS1) has been included in ferroptosis-related prognostic signatures, but its clinicopathological relevance, cellular functions, and relationship with the immune microenvironment in hepatocellular carcinoma (HCC) remain incompletely characterized. METHODS: Transcriptomic and clinical data from The Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) dataset were integrated with corresponding data from an institutional HCC tissue cohort of 60 patients. CARS1 expression was evaluated by immunohistochemistry, and immune infiltration was examined using single-sample gene-set enrichment analysis (ssGSEA) and multiplex immunofluorescence, as well as by analyzing public single-cell datasets. The effects of CARS1 depletion were evaluated in MHCC97H and Hep3B cells using Cell Counting Kit-8 (CCK-8) assays, cell-cycle profiling, wound-healing assays, Transwell migration assays, western blotting, and erlotinib-sensitivity assays. RESULTS: CARS1 expression was elevated in HCC and was associated with adverse clinicopathological features and poor overall survival. Quantitative immunohistochemistry confirmed elevated CARS1 protein expression in tumor tissues. CARS1 depletion inhibited cell proliferation, altered cell-cycle distribution, impaired migration, and enhanced in vitro sensitivity to erlotinib. High CARS1 expression was also associated with increased infiltration of Th2-like immune cells. CONCLUSIONS: Elevated CARS1 expression is associated with an adverse biological and immune phenotype in HCC. These clinical, histopathological, and loss-of-function findings support further investigation of CARS1 as a prognostic marker and candidate therapeutic target in HCC, although additional mechanistic and in vivo validation is required.
-
Lipophagy-related gene RAB7A is involved in immune regulation and malignant progression in hepatocellular carcinoma.
BACKGROUND: RAB7A (RAS-related in Brain 7A) is an important member of the RAS oncogene family. However, the correlation between RAB7A and the development and immune infiltration of hepatocellular carcinoma (HCC) has rarely been studied. Here, we studied the role of RAB7A in HCC through bioinformatics analysis, real-world cohort validation, and in vitro experimental exploration. MATERIALS AND METHODS: The RAB7A expression level was analyzed through TCGA, HPA and TISIDB databases. TIMER and TISCH were used to analyze the correlation between RAB7A and tumor immune microenvironment. The expression of RAB7A was detected through real-time PCR and western blotting. The cell proliferation was detected by EdU and CCK8. Wound-healing and transwell assays were used to test the invasion and migration ability. Cell cycle distribution and reactive oxygen species (ROS) content were analyzed by flow cytometry. Identification of epithelial-mesenchymal transition (EMT) was performed by immunofluorescence double staining. Immunohistochemistry (IHC) was used to evaluate the correlation between RAB7A and immune checkpoints. RESULTS: RAB7A is upregulated in most of the tumor types, and the upregulation of RAB7A is associated with a poorer prognosis in many cancers. The results showed that RAB7A was significantly positively correlated with the infiltration of macrophages and cancer-associated fibroblasts (CAFs), but negatively correlated with M2-type macrophages in most tumors. The single-cell atlas also revealed the distribution and proportion of RAB7A in immune cells of HCC. The in vitro experiments suggested that RAB7A was increased in HCC tissue and cell lines. The knockdown of RAB7A inhibited the activation of the PIK3CA-AKT pathway and suppressed the expression of CDK4, CDK6 and CCNA2. Knockdown of RAB7A induced G0/G1 arrest and ROS accumulation in HCC. In addition, overexpression of RAB7A enhanced migration and invasion by inducing EMT. The real-world cohort showed that the expression level of RAB7A was positively correlated with the expression levels of TGFBR1 and PD-L1. CONCLUSIONS: RAB7A may serve as a potential tumor prognostic and immune infiltration-related biomarker, predicting immunotherapy efficacy in certain cancer types, especially in HCC. Besides, RAB7A was a multi-pathway target involved in the malignant progression of HCC.