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Purpose: Solute carrier family 1 member 3(SLC1A3), a member of the glutamate transporter family, is implicated in the progression of gastric carcinoma and the renewal of thyroid carcinoma stem cells. The purpose of this work is to use experimental validation and bioinformatics analysis to look at the possible involvement of SLC1A3 in hepatocellular carcinoma (HCC). Materials and methods: We examined the levels of SLC1A3 within HCC and its implications on immunological and epithelial–mesenchymal transition (EMT) features using the TCGA, ImmPort, and Molecular Signatures databases. The relationship between drug sensitivity and SLC1A3 expression was investigated using the GDSC database. Real-time quantitative polymerase chain reaction (qRT-PCR), Western blotting (WB), and cellular function assays were performed to assess SLC1A3 expression and its carcinogenic effects in HCC. Results: According to our research, SLC1A3 overexpression in HCC is associated with a poor prognosis. Elevated levels of SLC1A3 promote HCC cell motility and invasion and can affect the prognosis of HCC by modifying immune responses and epithelial–mesenchymal transition. SLC1A3 has emerged as a novel prognostic marker in HCC and is associated with resistance to certain antitumor drugs. Conclusion: SLC1A3 functions as a cancer-promoting factor contributing to poor HCC prognosis by affecting immune cell infiltration and regulating the EMT process. Elevated SLC1A3 expression may also serve as a predictor of treatment response to specific antitumor drugs. [ABSTRACT FROM AUTHOR]

Background: The Epithelial–Mesenchymal Transition (EMT) is a very important process involved in cancer invasion and metastasis. Additionally, the Cathepsin K (CTSK) gene is closely related to the degradation of the extracellular matrix, which is a critical component of the EMT. The purpose of this study was to determine the relationships between EMT-related genes and immune cell infiltration and their prognostic value in Thyroid carcinoma (THCA). The effect of the CTSK gene on the aggressive biological features of THCA was assessed. Methods: Within the framework of the present study, the THCA cohort was analyzed in detail based on data obtained from The TCGA database in the context of the EMT. The TCGA-THCA cohort was then divided into two groups, namely, high- and low-risk groups, based on the calculated EMT scores. Finally, based on the findings from the Weighted Gene Co-Expression Network Analysis (WGCNA) algorithm, LASSO regression analysis, and Kaplan−Meier plotter, we selected five genes (CTSK, C3ORF80, FBLN2, PRELP and SRPX2) associated with patient prognosis. Furthermore, this study examined the presence of various immune cells within the THCA samples using three distinct algorithms, namely ssGSEA, xCell, and MCPcounter. Additional studies have been conducted to establish the roles of CTSK in THCA cell proliferation and migration using various assays, such as CCK8, colony formation, EdU proliferation, Transwell migration and wound healing assays. Additionally, the involvement of CTSK in the regulation of various EMT-related markers was confirmed using Western blot analysis. Results: Based on EMT scores, TCGA-THCA patients were further divided into two groups, and the study revealed that patients in the high-risk group had a worse prognosis than those in the low-risk group. Among the five genes linked to the prognostic value of EMT (CTSK, C3ORF80, FBLN2, PRELP, and SRPX2), CTSK exhibited notably elevated expression in the high-risk cohort. This group also exhibited pronounced immune cell infiltration, with a marked correlation observed between CTSK expression and the levels of macrophages, MDSCs, and various T-cell subtypes. Furthermore, in vitro studies demonstrated that reducing CTSK expression led to significant reductions in THCA cell viability; clonogenic, proliferative, motility and migratory capacities; and the expression of key EMT-related proteins, including N-cadherin, vimentin, slug, and snail. Conclusion: Our results suggest that the expression of CTSK, a gene associated with the EMT, may be associated with THCA onset and progression and thus may serve as a promising prognostic biomarker. [ABSTRACT FROM AUTHOR]

Immunotherapy has emerged as a vital component in the contemporary landscape of cancer treatment. Recent studies have indicated that CEP55 plays an oncogenic role; however, its specific mechanisms in promoting tumor proliferation and its potential value in prognosis and immunotherapy prediction across various cancers remain to be elucidated. CEP55 was significantly overexpressed in 22 cancer types compared with their adjacent normal tissues. Elevated CEP55 expression was positively correlated with younger onset age, worse tumor stage, lower response rate to the first treatment, lower tumor-free survival rate, and poorer overall survival (OS) and disease-free survival (DFS) prognosis in most cancers. Moreover, CEP55 expression was positively correlated with its binding and related genes, such as KIF11 (R = 0.83, P < 0.001), CDK1 (R = 0.77, P < 0.001) and CCNA2 (R = 0.76, P < 0.001), and the classic proliferation markers, including MKI67 and PCNA. Enrichment analyses indicated that CEP55 was predominantly associated with cell division, cell cycle activities and proliferation. Immune cell infiltration analysis by TIMER2.0 revealed that CEP55 expression was positively correlated with many kinds of infiltrating cells, such as Th2 cells and some CD4+ T cell subsets. The CEP55 expression was positively associated with increased MSI and TMB in various cancers. Our analyzation indicated that the CEP55 expression level in patients with complete remission (CR) or partial remission (PR) to anti-PDL1 therapy was significantly higher than patients with stable disease (SD) or progressive disease (PD) based on IMvigor210 cohort. We also used Gene Set Cancer Analysis (GSCA) to predict a serious of small molecule CEP55 targeted drugs, such as AZ628, SB52334, SB590885, A-770,041, AZD7762, Elesclomol, panobinostat, BRD-A94377914, and LRRK2-IN-1. Furthermore, the patients with high level of CEP55-posivie tumor epithelial cells had inferior overall survival in ccRCC according to single-cell analysis. Finally, our wet lab experiments verified that the CEP55-positive rate in ccRCC tissues (19/30, 63.3%) was significantly higher than that in renal adjacent tissues (10/30, 33.3%). The clinicopathologic analysis revealed that CEP55 protein level was significantly associated with tumor size (P = 0.044), histology grade (P < 0.001) and stage (P = 0.034). Our study indicated that CEP55 overexpression in most caner types was associated with poor prognosis. Notably, CEP55 was closely relevant to immune cell infiltration and impacted the response to immunotherapy and small molecule drugs against cancers. [ABSTRACT FROM AUTHOR]

The Schlafen (SLFN) gene family has emerged as a critical subject of study in recent years, given its involvement in an array of cellular functions such as proliferation, differentiation, immune responses, viral infection inhibition, and DNA replication. Additionally, SLFN genes are linked to chemosensitivity, playing a pivotal role in treating malignant tumors. Human SLFNs comprise three domains: the N-terminal, middle (M), and C-terminal. The N- and C-terminal domains demonstrate nuclease and helicase/ATPase activities, respectively. Meanwhile, the M-domain likely functions as a linker that connects the enzymatic domains of the N- and C-terminals and may engage in interactions with other proteins. This paper aims to present a comprehensive overview of the SLFN family's structure and sequence, examine its significance in various tumors, and explore its connection with immune infiltrating cells and immune checkpoints. The objective is to assess the potential of SLFNs as vital targets in cancer therapy and propose novel strategies for combined treatment approaches. [ABSTRACT FROM AUTHOR]

Myocardial ischemia‐reperfusion injury (MIRI) is a significant risk factor for acute myocardial infarction and is closely associated with ferroptosis. This study aimed to identify key ferroptosis‐related genes as potential diagnostic markers for MIRI and to explore their roles in immune infiltration and therapeutic targeting in myocardial tissue. We obtained single‐cell RNA sequencing (scRNA‐seq) and RNA‐seq data on MIRI from the GEO database, applied Seurat and UMAP for data processing and clustering, and analyzed ligand‐receptor interactions using CellPhoneDB. By scoring ferroptosis in cardiomyocytes, we identified differentially expressed genes and conducted GO and KEGG pathway analyses. A protein interaction network was then constructed using the STRING database, and seven key genes (Atp5h, Vdac2, Pkm, Cycs, Hspa8, Tpi1, Ldha) were identified through Lasso regression modeling, showing significant associations with immune responses. In vivo experiments in a mouse ischemia‐reperfusion model confirmed the roles of these seven genes in MIRI via RT‐qPCR. To further investigate the role of Hspa8 in ferroptosis and MIRI, siRNA knockdown experiments were performed in H9C2 rat cardiomyocytes, and its involvement in ferroptosis was validated by JC‐1 staining and PCR analysis. This study reveals the importance of ferroptosis‐related genes in MIRI through integrated bioinformatics and experimental approaches, offering new insights into diagnostic markers and immune‐related therapeutic targets for MIRI. [ABSTRACT FROM AUTHOR]

Pancreatic ductal adenocarcinoma (PDAC), one of the most challenging cancers, is uniquely characterized by a biological barrier composed of multiple components in the extracellular matrix, preventing penetration of chemotherapeutic agents and hindering clinical drug treatment. Collagen I arrangement is critical. In this study, gemcitabine is chosen as the chemotherapeutic agent and dasatinib as the collagen‐I‐disrupting agent. When collagen I arrangement is disrupted, not only the chemotherapeutic drug enters the tumor area better, but the infiltration of CD8+ T cells into the tumor also increases. Therefore, a hypoxia‐responsive linker‐crosslinked polymer, DGD/L@GBI, is designed, which can be simultaneously loaded with two therapeutic agents, gemcitabine and dasatinib. The polymer is encapsulated by nucleic acid aptamers that target the PDAC stromal microenvironment and shield the surface. The aptamer is removed upon arrival at the PDAC hypoxic microenvironment, exposing the positively charged core to achieve charge reversal. Particle size transformation is achieved using linkers that respond to a hypoxic microenvironment. Increased intratumoral penetration is achieved using the dual transformation capabilities of the formulation. Pairing these two agents can result in a powerful efficacy in chemotherapy sensitization and immune infiltration. [ABSTRACT FROM AUTHOR]

Ubiquitination is a prevalent post-translational modification that plays a crucial role in a wide range of pathophysiological processes, including cell proliferation, apoptosis, autophagy, immune response, and DNA damage repair. Among the enzymes involved in ubiquitination, E3 ubiquitin ligases are particularly significant, serving as key regulators of numerous diseases, including tumours. This review focuses on HECW2 (HECT, C2, and WW domain-containing E3 ubiquitin protein ligase 2, also known as NEDL2), providing a comprehensive overview of its interactors and its pathological roles in tumorous cancer and other diseases. The insights gained from this review may contribute to the development of novel treatment strategies for various diseases, particularly tumours. [ABSTRACT FROM AUTHOR]

Background: Targeting the STAT3 signaling pathway is a promising therapeutic approach for cancer patients. However, the association between STAT3 expression, the tumor immune microenvironment, and genetic variation remains unclear across human cancers, especially prostate cancer. Methods: We used R software and other tools to analyze pan-cancer and mutation data from publicly available databases statistically. A comprehensive investigation was performed to assess the genetic heterogeneity and clinical relevance of STAT3 in various malignancies, with a specific focus on its role in the immune landscape and prognostic significance in prostate cancer. The findings were validated through immunohistochemistry (IHC) and multiplex immunofluorescence (mIF). Results: STAT3 expression is abnormal in the majority of cancer tissues, which is strongly correlated with these patients' prognosis. Eight measures of tumor heterogeneity and six measures of tumor stemness of multiple tumor types showed a strong correlation with STAT3 expression. Furthermore, in individuals with prostate cancer, STAT3 expression indicated the degree of immune cell infiltration and the advancement of the disease. IHC analysis revealed that STAT3 was down-regulated in prostate tumor tissues, while mIF analysis demonstrated that STAT3 signaling (p-STAT3) was extensively active in tumor tissues and positive lymph node tissues. Conclusion: STAT3 may serve as a valuable prognostic biomarker and therapeutic target across various cancers, with particular relevance to prostate cancer. [ABSTRACT FROM AUTHOR]

Background: Lacrimal gland enlargement is a common pathological change in patients with thyroid eye disease (TED). Tear fluid has emerged as a new source of diagnostic biomarkers, but tear-based diagnostic biomarkers for TED with high efficacy are still lacking. Objective: We aim to investigate genes associated with TED-associated lacrimal gland lesions. Additionally, we seek to identify potential biomarkers for diagnosing TED in tear fluid. Methods: We obtained two expression profiling datasets related to TED lacrimal gland samples from the Gene Expression Omnibus (GEO). Subsequently, we combined the two separate datasets and conducted differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) on the obtained integrated dataset. The genes were employed for Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The genes were intersected with the secretory proteins profile to get the potential proteins in the tear fluid. Machine learning techniques were then employed to identify optimal biomarkers and develop a diagnostic nomogram for predicting TED. Finally, gene set enrichment analysis (GSEA) and immune infiltration analysis were conducted on screened hub genes to further elucidate their potential mechanisms in TED. Results: In our analysis of the integrated TED dataset, we identified 2,918 key module genes and 157 differentially expressed genes and finally obtained 84 lacrimal-associated key genes. Enrichment analysis disclosed that these 84 genes primarily pertain to endoplasmic reticulum organization. After intersecting with the secretory proteins, 13 lacrimal gland-associated secretory protein genes (LaSGs) were identified. The results from machine learning indicated the substantial diagnostic value of dyslexia associated gene (KIAA0319) and peroxiredoxin4 (PRDX4) in TED-associated lacrimal gland lesions. The two hub genes were chosen as candidate biomarkers in tear fluid and employed to establish a diagnostic nomogram. Furthermore, single-gene GSEA results and immune cell infiltration analysis unveiled immune dysregulation in the lacrimal gland of TED, with KIAA0319 and PRDX4 showing significant associations with infiltrating immune cells. Conclusions: We uncovered the distinct pathophysiology of TED-associated lacrimal gland enlargement compared to TED-associated orbital adipose tissue enlargement. We have demonstrated the endoplasmic reticulum-related pathways involved in TED-associated lacrimal gland lesions and established a diagnostic nomogram for TED utilizing KIAA0319 and PRDX4 through integrated bioinformatics analysis. This contribution offers novel insights for non-invasive, prospective diagnostic approaches in the context of TED. [ABSTRACT FROM AUTHOR]

Background: Sepsis is a serious condition that occurs when the body's response to infection becomes uncontrolled, resulting in a high risk of death. Despite improvements in healthcare, identifying sepsis early is difficult because of its diverse nature and the absence of distinct biomarkers. Recent studies suggest that 5-methylcytosine (m5C)-related genes play a significant role in immune responses, yet their diagnostic potential in sepsis remains unexplored. Methods: This research combined and examined four sepsis-related datasets (GSE95233, GSE57065, GSE100159, and GSE65682) sourced from the Gene Expression Omnibus (GEO)database to discover m5C-related genes with differential expression. Various machine learning methods, such as decision tree, random forest, and XGBoost, were utilized in identifying crucial hub genes. Receiver Operating Characteristic (ROC) curve analysis was used to assess the diagnostic accuracy of these genetic markers. Additionally, single-gene enrichment and immune infiltration analyses were conducted to investigate the underlying mechanisms involving these hub genes in sepsis. Results: Three hub genes, DNA Methyltransferase 1 (DNMT1), tumor protein P53 (TP53), and toll-like receptor 8 (TLR8), were identified and validated for their diagnostic efficacy, showing area under the curve (AUC) values above 0.7 in both test and validation sets. Enrichment analyses revealed that these genes are involved in key pathways such as p53 signaling and Toll-like receptor signaling. Immune infiltration analysis indicated significant correlations between hub genes and various immune cell types, suggesting their roles in modulating immune responses during sepsis. Conclusion: The study highlights the diagnostic potential of m5C-related genes in sepsis and their involvement in immune regulation. These findings offer new insights into sepsis pathogenesis and suggest that DNMT1 , TP53 , and TLR8 could serve as valuable biomarkers for early diagnosis. Further studies should prioritize validating these biomarkers in clinical settings and investigating their potential for therapy. [ABSTRACT FROM AUTHOR]

A pan-cancer analysis summarizing the overall changes in mRNA and protein stability of ADM9, as well as its oncogenic function on immune cell line modulation and checkpoints within the tumor microenvironment (TME), is lacking, despite the fact that ADM9 up-regulation is correlated with the progression of many cancers. Therefore, in this study, we comprehensively analyzed the role of ADAM9 expression and its prognostic value in different cancers to fill this gap. Multiple bioinformatics databases such as Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Clinical Proteomic Tumor Analysis Consortium (CPTAC) were used to evaluate the ADAM9 genetic alternation, phosphorylation, and methylation, and indicated highly positive correlated genes that might play a critical interaction with ADAM9 and their molecular function with GO analysis. We also evaluate the effect of higher ADAM9 with prominent immune modulatory genes and immune infiltration especially in liver cancer pathogenesis stimulates lower NK cell effector functions based on its role in MICA shedding and increasing the Tregs infiltration. Immunohistochemistry (IHC) staining from 90 pathologically verified samples proved the positive correlation between ADAM9 and tumor stages and proved the higher expression of ADAM9 correlated genes (SNX9, APP, TNF, CDH1, ITGAV, MAD2L2) in HCC pathogenesis. In conclusion, this pan-cancer study provides a comprehensive understanding of the prognostic value of ADAM9 in various tumors emphasizing its importance to be considered as an innovative treatment approach, especially in tumor immunity shortly. [ABSTRACT FROM AUTHOR]

ABSTRACT Objective Materials and Methods Results Conclusion Histone lysine lactylation (Kla) plays a vital role in cancer progression. However, the prognostic value of histone Kla in oral squamous cell carcinoma (OSCC) remains unclear.OSCC RNA expression data were obtained from the TCGA and GEO databases. We explored the prognostic value of histone Kla in OSCC via constructing a Cox model and determined the role of Kla in OSCC drug susceptibility and tumor microenvironment (TME). In addition, the biological roles of candidate biomarkers were identified.A total of 1223 Kla‐specific genes were obtained, with 228 DEKlaGs in OSCC. GO and KEGG enrichment analyses suggested that DEKlaGs contributed to inflammatory and cancer progression. A Cox model in accordance with BCAM, CGNL1, DGKG, and OLR1 could predict OSCC patient prognosis accurately. Subsequently, Kla‐induced prognostic genes were identified to play a crucial role in OSCC drug therapy and TME. Moreover, BCAM was identified as a biomarker that promoted OSCC invasion, angiogenesis, and chemotherapy resistance.Kla was identified to be associated with OSCC prognosis, drug therapy, and TME. Histone Kla‐induced BCAM was identified to play a crucial role during OSCC progression, suggesting that Kla is promising to be a novel therapeutic target for OSCC. [ABSTRACT FROM AUTHOR]

Background: Prostate cancer (PCa) is a prevalent malignant tumor in males, with a significant incidence of biochemical recurrence (BCR) despite advancements in treatment. Adipose tissue surrounding the prostate, known as periprostatic adipose tissue (PPAT), contributes to PCa invasion through adipocytokine production. However, the relationship between adipocytokine-related genes and PCa prognosis remains understudied. This study was conducted to provide a theoretical basis and serve as a reference for the use of adipocytokine-related genes as prognostic markers in PCa. Methods: Transcriptome and survival data of PCa patients from The Cancer Genome Atlas (TCGA) database were analyzed. Differential gene expression analysis was conducted using the DESeq2 and limma packages. Prognostic genes were identified through univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression. A prognostic model was developed and validated utilizing receiver operating characteristic (ROC) and Kaplan-Meier (K-M) curves. Assessments of immune cell infiltration and drug sensitivity were also carried out. Subsequently, the function of BNIP3L gene in PCa was verified. Results: A total of 47 adipocytokine-related differentially expressed genes (DEGs) were identified. Five genes (PPARGC1A, APOE, BNIP3L, STEAP4, and C1QTNF3) were selected as prognostic markers. The prognostic model demonstrated significant predictive accuracy in both training and validation cohorts. Patients with higher risk scores exhibited poorer survival outcomes. Immune cell infiltration analysis revealed that the high-risk group had increased immune and ESTIMATE scores, while the low-risk group had higher tumor purity. In vitro experiments confirmed the suppressive effects of BNIP3L on PCa cell proliferation, migration, and invasion. Conclusion: The prognostic model independently predicts the survival of patients with PCa, aiding in prognostic prediction and therapeutic efficacy. It expands the study of adipocytokine-related genes in PCa, presenting novel targets for treatment. [ABSTRACT FROM AUTHOR]

Purpose: Breast cancer (BRCA) is the most common malignant tumor among women, characterized by high incidence rates and mortality rates. Oxidative stress and immunity, particularly in relation to mitochondria, have emerged as pivotal factors in breast carcinogenesis. Nonetheless, limited research has explored the specific contribution of mitochondrial oxidative stress to the prognosis of BRCA. Method: In this study, we conducted univariate and multivariate Cox regression analyses to pinpoint independent prognostic genes associated with mitochondrial oxidative stress (MOSRGs) and their correlation with BRCA clinical outcomes. Subsequently, we developed a robust and accurate MOS scoring system for BRCA patients based on these identified independent prognostic MOSRGs. Result: Our findings were further substantiated by immune infiltration and somatic mutation analyses, providing additional evidence that the MOS scoring system holds predictive value for clinical outcomes in patients and correlates directly with three subtypes of BRCA. In vitro experiments in the MCF7 cell and breast tissue further verified the mRNA and protein expression level of independent prognostic genes, validating the consistency of the MOS prognostic signatures in BRCA. Conclusion: This research has unveiled a novel prognostic scoring system, providing valuable insights for improving patient prognosis assessment and developing individualized treatment strategies in BRCA patients. [ABSTRACT FROM AUTHOR]

Background: Mitochondrial fusion and fission are critical for the morphology and function of cells. DNM1L encodes dynamin-related protein 1 (DRP1), a key protein mediating mitochondrial fission, which is upregulated in a variety of cancers and is strongly associated with tumorigenesis. We aim to investigate the relationship between DNM1L and the prognosis of gastric cancer, as well as to explore the function and mechanism of DNM1L in gastric cancer (GC). Materials and methods: In this study, we analyzed the expression differences of DNM1L in gastric cancer tissues and paracancerous tissues using The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) database. This was followed by validation through tissue microarrays. We then utilized the cohort information from these microarrays to explore the relationship between DNM1L expression and gastric cancer prognosis. Furthermore, we conducted enrichment analysis to investigate the function and mechanisms of DNM1L in gastric cancer, and lastly, we performed immune cell infiltration analysis using the CIBERSORT algorithm. Results: We discovered that the expression of DNM1L is elevated in GC tissues. TCGA data showed that the overexpression of DNM1L was positively correlated with the T-stage of GC but not with lymph node metastasis, which was also corroborated by our immunohistochemistry experiments. Based on the Kaplan–Meier curves, the high DNM1L expression was remarkably correlated with poor overall survival in patients with GC. In addition, results of COX regression analysis indicated that high DNM1L expression was an independent prognostic factor in patients with GC. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene set enrichment analysis (GSEA) showed that DNM1L was closely associated with multiple signaling pathways and immune responses. CIBERSORT analysis indicated that increased DNM1L expression may affect the infiltration of immune cells in the tumor microenvironment. Conclusion: The results of this study indicate that DNM1L is upregulated in gastric cancer (GC) and positively correlates with the T-stage and poor prognosis of GC patients, and it plays an important role in tumor immune infiltration. [ABSTRACT FROM AUTHOR]

Background: Cuproptosis, a recently identified type of programmed cell death triggered by copper, has mechanisms in Wilms tumor (WT) that are not yet fully understood. This research focuses on examining the link between WT and Cuproptosis-related genes (CRGs), with the goal of developing a predictive model for WT. Methods: Four gene expression datasets related to WT were sourced from the GEO database. Subsequently, expression profiles of CRGs were extracted for differential analysis and immune infiltration studies. Utilizing 105 WT samples, clusters related to Cuproptosis were identified. This involved analyzing associated immune cell infiltration and conducting functional enrichment analysis. Disease-characteristic genes were pinpointed using weighted gene co-expression network analysis. Finally, the WT risk prediction model was constructed by four machine learning methods: random forest, support vector machine (SVM), generalized linear and extreme gradient strength model. The best-performing machine learning model was chosen, and a nomogram was created. The effectiveness of this predictive model was validated using methods such as the calibration curve, decision curve analysis, and by appiying it to the TARGET-GTEx dataset. Results: Thirteen differentially expressed Cuproptosis-related genes were identified. The infiltration level of CD8 + T cells in WT children was lower than that in Normal tissue (NT) children, and the level of M0 infiltration of macrophages and T follicular helper cells was higher than that in NT children. In addition, two clusters of cuproptosis-related WT were identified. Enrichment analysis results indicated that genes in cluster 2 were primarily involved in cell division, nuclear division regulation, DNA biosynthesis process, ubiquitin-mediated proteolysis. The SVM model was judged to be the optimal model using 5 genes. Its accuracy was confirmed through a calibration curve and decision curve analysis, demonstrating satisfactory performance on the TARGET-GTEx validation dataset. Additional analysis revealed that these five genes exhibited high expression in both the TARGET-GTEx validation dataset and sequencing data. Conclusion: This research established a link between WT and Cuproptosis. It developed a predictive model for assessing the risk of WT and pinpointed five key genes associated with the disease. [ABSTRACT FROM AUTHOR]

Lack of significant and durable clinical benefit from anti-cancer immunotherapies is partly due to the failure of cytotoxic immune cells to infiltrate the tumor microenvironment. Immune infiltration is predominantly dependent on the chemokine network, which is regulated in part by chemokine and atypical chemokine receptors. We investigated the impact of hypoxia in the regulation of Atypical Chemokine Receptor 2 (ACKR2), which subsequently regulates major pro-inflammatory chemokines reported to drive cytotoxic immune cells into the tumor microenvironment. Our in silico analysis showed that both murine and human ACKR2 promoters contain hypoxia response element (HRE) motifs. Murine and human colorectal, melanoma, and breast cancer cells overexpressed ACKR2 under hypoxic conditions in a HIF-1α dependent manner; as such overexpression was abrogated in melanoma cells expressing non-functional deleted HIF-1α. We also showed that decreased expression of ACKR2 in HIF-1α-deleted cells under hypoxia was associated with increased CCL5 levels. Chromatin immunoprecipitation data confirmed that ACKR2 is directly regulated by HIF-1α at its promoter in B16-F10 melanoma cells. This study provides new key elements on how hypoxia can impair immune infiltration in the tumor microenvironment. [ABSTRACT FROM AUTHOR]

Lung cancer is one of the most common malignant tumors, and patients are often diagnosed at an advanced stage, posing a substantial risk to human health, so it is crucial to establish a model to forecast the prognosis of patients with lung cancer. Recent research has indicated that proteasome 20S subunit 6 (PSMB6) may be closely associated with anti-apoptotic pathways, and proliferation transduction signals in tumor cells of different tumors. However, the precise role of PSMB6 in the immunoregulatory processes within lung adenocarcinoma (LUAD) is yet to be elucidated. By analyzing the TCGA database, we discovered a positive correlation between the expression of PSMB6 and tumor growth trends, and lung adenocarcinoma patients with elevated PSMB6 expression levels had a worse prognosis. Our findings suggest a close correlation between PSMB6 expression levels, immune cell infiltration and immune checkpoint gene expression, which suggests that PSMB6 may become a new independent prognostic indicator. In addition, we developed a prognostic model of PSMB6-regulated immune infiltration-associated genes by analyzing the link between PSMB6 and the immune microenvironment. This model can not only predict the prognosis of lung adenocarcinoma but also forecasts the patient's reaction to immunotherapy. The validity of this research outcome has been confirmed by the GSE31210 and IMvigor210 cohorts. Analysis of the Kaplan-Meier Plotter database indicates that individuals with elevated levels of PSMB6 expression exhibit a poorer prognosis. Additionally, in vitro experiments demonstrated that knockdown of PSMB6 inhibits the proliferation, migration, and invasion of lung adenocarcinoma cells while promoting their apoptosis. Overall, our findings suggest that PSMB6 could remarkably influence the management and treatment of lung adenocarcinoma, opening new avenues for targeted immunotherapeutic strategies. [ABSTRACT FROM AUTHOR]

Introduction: Thyroid cancer (THCA) is the most common endocrine tumor. Coagulation may be associated with the development of cancer, but its role in THCA patients is not yet clear. Methods: In this study, we determined the predictive value of coagulation biomarker D-dimer for THCA patient lateral lymph node metastasis (LLNM) through receiver operating characteristics (ROC) analysis and logistic regression analysis. Subsequently, this study used the TCGA database to identify coagulation-related molecular subtypes through consensus clustering analysis and compared their prognosis. We identified coagulation-related genes (CRGs) associated with prognosis in thyroid cancer through gene expression data and clinical information, and constructed a prognostic model by selecting the prognostic CRGs using LASSO regression. Patients were divided into high-risk and low-risk groups based on the median score. Subsequently, prognosis, clinical characteristics, gene mutation occurrence, immune infiltration, function, and drug sensitivity of the two groups were analyzed. We also constructed a nomogram combining the model and clinical features. Finally, the expression of the prognostic CRGs was validated by RT-qPCR. Results: D-dimers had better performance in predicting LLNM(the area under the curve was 0.656 (95% CI 0.580-0.733), with a cut-off value of 0.065 mg/l), and D-dimer>0.065mg/l was an independent predictor of LLNM. Then, we selected 8 prognostic CRGs to construct a predictive model. The prognosis of low-risk group patients was significantly better than that of high-risk group (P<0.001). The results showed significant differences in clinical characteristics, gene mutation occurrence, immune infiltration, function, and drug sensitivity between the high-risk and low-risk groups. We validated by qPCR that these 8 prognostic CRGs were overexpressed in THCA cell lines. Discussion: Overall, this study provided an in-depth exploration of the potential role of the coagulation in thyroid cancer and its clinical significance, offering a new theoretical basis and research direction for personalized therapy and prognostic evaluation. [ABSTRACT FROM AUTHOR]

• H3K36me3, H3K4me3, H3K79me2, and H3K9ac co-regulate gene expression in HCC. • Key histone modifications in five key regions co-regulate gene expression. • CBX2 , CEBPZOS , LDHA , and UMPS are key target genes associated with prognosis. • Key target genes are associated with immune microenvironment and drug sensitivity. Hepatocellular carcinoma (HCC) is a cancer with high morbidity and mortality. Studies have shown that histone modification plays an important regulatory role in the occurrence and development of HCC. However, the specific regulatory effects of histone modifications on gene expression in HCC are still unclear. This study focuses on HepG2 cell lines and hepatocyte cell lines. First, the distribution of histone modification signals in the two cell lines was calculated and analyzed. Then, using the random forest algorithm, we analyzed the effects of different histone modifications and their modified regions on gene expression in the two cell lines, four key histone modifications (H3K36me3, H3K4me3, H3K79me2, and H3K9ac) and five key regions that co-regulate gene expression were obtained. Subsequently, target genes regulated by key histone modifications in key regions were screened. Combined with clinical data, Cox regression analysis and Kaplan-Meier survival analysis were performed on the target genes, and four key target genes (CBX2 , CEBPZOS , LDHA , and UMPS) related to prognosis were identified. Finally, through immune infiltration analysis and drug sensitivity analysis of key target genes, the potential role of key target genes in HCC was confirmed. Our results provide a theoretical basis for exploring the occurrence of HCC and propose potential biomarkers associated with histone modifications, which may be potential drug targets for the clinical treatment of HCC. [ABSTRACT FROM AUTHOR]

Purpose: This study explores the immune cells' role in anti-VEGF resistance in nAMD patients, and the potential of Zi-Yin-Jiang-Huo-Tang (ZYJHT), a Traditional Chinese Medicine formula, as complementary therapy. Methods: Aqueous humor proteomics data from 10 nAMD patients with anti-VEGF resistance and 10 nAMD patients without anti-VEGF resistance were analyzed, investigating immune cells's role in anti-VEGF resistance and its underlying mechanism. Network pharmacology methods are employed to analyze the active ingredients in ZYJHT that contribute to therapeutic effects and their mechanisms. Real-time PCR (polymerase chain reaction) was used to detect changes in the expression of SOD1 (superoxide dismutase 1) after treatment with compounds targeting SOD1 in ARPE-19 cells. Results: nAMD patients with anti-VEGF resistance showed enhancement of biological processes linked to the positive regulation of immune function, along with decreased cellular resistance to oxidative stress. Infiltration of B cells memory, plasma cells, CD8+and γδ-T cells were higher in nAMD patients with anti-VEGF resistance. SOD1 was identified as a hub gene in the occurrence of anti-VEGF resistance and a core therapeutic target of ZYJHT, negatively correlated with B and T cell infiltration. Compounds diosgenin, naringenin, and liquiritin in ZYJHT can bind to SOD1 and upregulating SOD1 expression in ARPE-19 cells. [ABSTRACT FROM AUTHOR]

High stemness index scores are associated with poor survival in patients with lung cancer. Studies on the mRNA expression-based stemness index (mRNAsi) are typically conducted using tumor tissues; however, mRNAsi-related expression signatures based on cell-free RNA (cfRNA) are yet to be comprehensively investigated. The present study aimed to elucidate the gene expression profiles of tumor stemness in lung cancer tissues and corresponding cfRNAs in blood, and to assess their links with immune infiltration. Tumor tissue, paracancerous tissue, peripheral blood and lymph node samples were collected from patients with stage I-III non-small cell lung cancer and RNA sequencing was performed. The TCGAbiolinks package was used to calculate the mRNAsi for each of these four types of sample. Weighted gene co-expression network analysis and differentially expressed gene analyses were performed to investigate mRNAsi-related genes, and pathway enrichment analysis was performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology-based annotation system. In addition, the STAR-Fusion tool was used to detect fusion variants, and CIBERSORT was used to analyze the correlations of stemness signatures in tissues and blood with immune cell infiltration. The mRNAsi values in peripheral blood and lymph nodes were found to be higher than those in cancer tissues. 'Hematopoietic cell lineage' was the only KEGG pathway enriched in mRNAsi-related genes in both lung cancer tissues and peripheral blood. In addition, the protein tyrosine phosphatase receptor type C associated protein gene was the only gene commonly associated with the mRNAsi in these two types of sample. The expression of mRNAsi-related genes was increased in the dendritic and Treg cells in tumor tissues, but was elevated in Treg and CD8 cells in the blood. In conclusion, cfRNAs in the blood exhibit unique stemness signatures that have potential for use in the diagnosis of lung cancer. [ABSTRACT FROM AUTHOR]

Liver cancer is the second leading cause of tumor-related death worldwide, and a serious threat to lives and health. Circulating tumor cells (CTCs) facilitate the progression of various cancers, including liver cancer. The relationship between CTC/circulating tumor microemboli-related genes (CRGs) and the prognosis of liver cancer is unclear. The aim of the present study was to identify CTC/circulating tumour microemboli-related genes (CRGs) in hepatocellular carcinoma and to investigate their clinical significance. Transcriptomic data from The Cancer Genome Atlas (International Cancer Genome Consortium (ICGC) and GSE117623 databases were combined, and differentially expressed CRGs were identified. These were subsequently analyzed via least absolute shrinkage and selection operator and multivariate Cox analyses, and a five-gene risk signature was constructed. The signature was validated in the ICGC and GSE14520 dataset with survival analysis and receiver operating characteristic curve analysis. Immunocyte infiltration, tumor mutation burden (TMB), tumor immune dysfunction and exclusion (TIDE), and the somatic mutation rate were also compared between high- and low-risk groups, based on the median predictive index, to further evaluate the immunotherapeutic value of the model. Molecular subtypes of liver cancer were characterized by the non-negative matrix factorization method and potential therapeutic compounds were evaluated for different subtypes. Nomograms were utilized to predict the prognosis of patients, and the signature was compared with previous literature models. Additionally, the biological function of one of the CRGs, tumor protein p53 inducible protein 3 (TP53I3), in liver cancer was further explored through in vitro experiments. Analysis of the prognostic characteristics of the five CRGs led to the identification of two liver cancer subtypes. Patients in the low-risk group had a longer survival compared with those in the high-risk group, and patients in the latter group were associated with a higher TMB, immunocyte infiltration and somatic mutation rate, and lower TIDE scores. The prognostic profile was validated in the ICGC and GSE14520 datasets and exhibited a good predictive performance. In vitro analysis showed that the knockdown of TP53I3 suppressed liver cancer cell proliferation. In summary, CRGs were used to develop a new prognostic signature to predict the prognosis of patients with liver cancer. This signature may be used to assess the prognosis of patients and may provide new insights for clinical management strategies. In addition, TP53I3 is potentially a therapeutic target for liver cancer. [ABSTRACT FROM AUTHOR]

Metastasis occurs in nearly 50% of cases of adult soft-tissue sarcoma (ASTS), leading to a dismal prognosis, with a 2-year survival rate of ~30%. Consequently, a prognostic model that incorporates metastatic characteristics may be instrumental in predicting survival time and in crafting optimal personalized therapeutic strategies for patients with ASTS. In the present study, a prognostic prediction model for ASTS was developed by examining genes that are differentially expressed between non-metastatic and metastatic patients in the Gene Expression Omnibus dataset. The prognostic model, which includes five featured genes [actin γ2 (ACTG2), apolipoprotein D, coatomer protein complex subunit γ2 imprinted transcript 1, collagen type VI α6 chain and osteomodulin], was further validated in patients with ASTS from the Cancer Genome Atlas dataset. Based on these five-gene signatures, patients were categorized into high- and low-risk groups. Functional and pathway analyses revealed disparities in stemness, extracellular matrix and cell adhesion-related pathways between the two risk groups, particularly noting the activation of the PI3K-Akt pathway in high-risk cases. Analysis of immune infiltration also revealed variations in immune microenvironment changes between the two risk groups. Immunohistochemical staining substantiated the prognostic significance of these gene signatures in a specific sarcoma subtype. Additionally, wound-healing and Transwell assays demonstrated that inhibition of ACTG2 by shRNAs curbed cell migration and invasion in a sarcoma HOS cell line, underscoring its role in sarcoma metastasis. In conclusion, the present study successfully developed and validated a metastasis-based prognosis prediction model. This model not only reliably forecasts the survival of patients with ASTS, but also may pave the way for further investigation into the processes underlying sarcoma metastasis, ultimately aiding in the design of tailored therapeutic regimens. [ABSTRACT FROM AUTHOR]

Background: To assess the distribution characteristics of immune infiltration and lymphovascular invasion in breast cancer skin recurrence patients. Methods: We retrospectively analyzed the clinicopathological data of patients who underwent radical surgery for primary breast cancer and experienced skin recurrence between January 2001 and April 2019. Immune and lymphovascular biomarkers were quantified in primary breast cancers, skin lesions and visceral metastatic lesions. Differences in biomarkers distribution between matched tissues were statistically analyzed using the Wilcoxon signed-rank test and Kruskal–Wallis one-way ANOVA. Results: A total of 71 female breast cancer patients were reviewed in this study. Our study found that the expression levels of various lymphocyte immune markers in primary tumor specimens were higher than those in skin recurrences. The expression of CD8, CD57 and CD31 in primary breast cancer was higher than those in the skin. Compared to visceral metastatic lesions, D2-40 was highly expressed in the skin, while CD8 tended to decrease. In the skin specimens, the expression of CD8 (P < 0.001), FOXP3 (P = 0.006) and CD68 (P < 0.001) in the intratumoral area was higher, while the expression of CD57 (P < 0.001) was higher in the peritumoral area. Analyzing specimens from the same patient at different time points of skin progression, it was found that the expression of peritumoral CD4 decreased (P = 0.044) as the disease progressed. The low expression of D2-40 and CD163 in the skin lesions suggested a decrease in DFS. Conclusion: The immune microenvironment of breast cancer skin recurrence may be in a state of suppression, and this suppression may intensify with disease progression. The pattern of skin recurrence may be more inclined toward lymphatic invasion. Our study provides new insights into the biological behaviors of this disease and its response to immunotherapy. [ABSTRACT FROM AUTHOR]

The pathogenesis of sepsis, with a high mortality rate and often poor prognosis, has not been fully elucidated. Therefore, an in-depth study on the pathogenesis of sepsis at the molecular level is essential to identify key sepsis-related genes. The aim of this study was to explore the key genes and potential molecular mechanisms of sepsis using a bioinformatics approach. In addition, key genes with miRNA network correlation analysis and immune infiltration correlation analysis were investigated. The scRNA dataset (GSE167363) and RNA-seq dataset (GSE65682, GSE134347) from GEO database were used for screening out differentially expressed genes using single-cell sequencing and transcriptome sequencing. The analysis of immune infiltration was evaluated by the CIBERSORT method. Key genes and possible mechanisms were identified by WGCNA analysis, GSVA analysis, GSEA enrichment analysis and regulatory network analysis, and miRNA networks associated with key genes were constructed. Nine key genes associated with the development of sepsis, namely IL7R, CD3D, IL32, GPR183, HLA-DPB1, CD81, PEBP1, NCL, and ETS1 were screened, and the specific signaling mechanisms associated with the key genes causing sepsis were predicted. Immune profiling showed immune heterogeneity between control and sepsis samples. A regulatory network of 82 miRNAs, 266 pairs of mRNA-miRNA relationship pairs was also constructed. These nine key genes have the potential to become biomarkers for the diagnosis of sepsis and provide new targets and research directions for the treatment of sepsis. [ABSTRACT FROM AUTHOR]

Colon adenocarcinoma (COAD) is a prevalent gastrointestinal malignant disease with a high mortality rate, and identification of novel prognostic biomarkers and therapeutic targets is urgently needed. Although NDUFA4L2 has high expressions in various tumors and affects tumor progression, its role in COAD remains unclear. The role of NDUFA4L2 in COAD was analyzed utilizing datasets available from public databases including The Cancer Genome Atlas, The Genotype-Tissue Expression (GTEx), Gene Expression Omnibus, Alabama Cancer Database (UALCAN), and The Human Protein Atlas databases. The prognostic value of NDUFA4L2 was determined using Kaplan–Meier analysis and Cox regression analysis. To investigate the possible mechanism underlying the role of NDUFA4L2 in COAD, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) were employed. The correlation between NDUFA4L2 expression and immune cell infiltration levels was examined through single-sample gene set enrichment analysis (ssGSEA). The NDUFA4L2 expression levels in COAD patients and cell lines were validated through immunohistochemistry, immunofluorescence, qRT-PCR, and Western blot. Wound healing assay was also performed to evaluate the effect of NDUFA4L2 on COAD metastasis. Furthermore, the NDUFA4L2 mediated competing endogenous RNA (ceRNA) regulatory network was predicted and constructed through a variety of databases. The comprehensive pan-cancer analysis showed that NDUFA4L2 possesses diagnostic and prognostic value in many cancers, especially in COAD. GO-KEGG and GSEA analyses indicated that NDUFA4L2 was associated with multiple biological functions including epithelial-mesenchymal transition and adaptation to hypoxia. The ssGSEA analysis showed that NDUFA4L2 expression was associated with immune infiltration. In vitro experiments confirmed upregulation of NDUFA4L2 in COAD tissues and cell lines, and NDUFA4L2 overexpression significantly promoted migration of COAD cells. In addition, the C9orf139 /miR-194-3p axis was speculated as the possible upstream regulators of NDUFA4L2 in COAD. This study demonstrated that NDUFA4L2 upregulation was correlated with tumor progression, relapsed prognosis and aggressive migration of COAD, suggesting that NDUFA4L2 can act as an effective prognostic biomarker and a promising therapeutic target for COAD treatment. [ABSTRACT FROM AUTHOR]

Cervical cancer remained among the most prevalent cancers in women. Erythropoietin-producing hepatocellular A2 (EPHA2) is overexpressed in many cancers, including cervical cancer, and the mechanism by which it regulates cervical cancer progression is not yet fully understood. Exosomes are extracellular vesicles that carry information in the form of biomolecules, deliver it to the recipient cell, and play a vital role in cellular communication. 17β-Estradiol is the natural female steroid hormone with the greatest estrogenic activity, and it induces cell death in cancer. In this study, we investigated the function of EPHA2 in cervical cancer migration and immunomodulation and the presence of EPHA2 in the cervical cancer serum-derived exosome. A knockdown of EPHA2 (KD-EPHA2) in cervical cancer reduces cancer cell migration by regulating the CD113/Ezrin pathway. Furthermore, EPHA2 exhibited significant involvement in immunomodulation by orchestrating IL-6-mediated signalling cascades, including the AKT-mTOR and JAK-STAT pathways. Immune infiltration analysis revealed a correlation between EPHA2 expression in cervical cancer and the infiltration of various immune cell populations. KD-EPHA2 enhances the 17β-Estradiol inhibitory effect on cell proliferation and migration during cancer progression. In summary, our study revealed that EPHA2 is overexpressed in cervical cancer and plays a vital role in cancer cell migration and immunomodulation, and 17β-Estradiol, along with KD-EPHA2, enhances the inhibitory effect on cancer cell migration and proliferation. [ABSTRACT FROM AUTHOR]

The impact of aging on the immune landscape of luminal breast cancer (Lum‐BC) is poorly characterized. Understanding the age‐related dynamics of immune editing in Lum‐BC is anticipated to improve the therapeutic benefit of immunotherapy in older patients. To this end, here we applied the 'multiple iterative labeling by antibody neo‐deposition' (MILAN) technique, a spatially resolved single‐cell multiplex immunohistochemistry method. We created tissue microarrays by sampling both the tumor center and invasive front of luminal breast tumors collected from a cohort of treatment‐naïve patients enrolled in the prospective monocentric IMAGE (IMmune system and AGEing) study. Patients were subdivided into three nonoverlapping age categories (35–45 = 'young', n = 12; 55–65 = 'middle', n = 15; ≥70 = 'old', n = 26). Additionally, depending on localization and amount of cytotoxic T lymphocytes, the tumor immune types 'desert' (n = 22), 'excluded' (n = 19), and 'inflamed' (n = 12) were identified. For the MILAN technique we used 58 markers comprising phenotypic and functional markers allowing in‐depth characterization of T and B lymphocytes (T&B‐lym). These were compared between age groups and tumor immune types using Wilcoxon's test and Pearson's correlation. Cytometric analysis revealed a decline of the immune cell compartment with aging. T&B‐lym were numerically less abundant in tumors from middle‐aged and old compared to young patients, regardless of the geographical tumor zone. Likewise, desert‐type tumors showed the smallest immune‐cell compartment and were not represented in the group of young patients. Analysis of immune checkpoint molecules revealed a heterogeneous geographical pattern of expression, indicating higher numbers of PD‐L1 and OX40‐positive T&B‐lym in young compared to old patients. Despite the numerical decline of immune infiltration, old patients retained higher expression levels of OX40 in T helper cells located near cancer cells, compared to middle‐aged and young patients. Aging is associated with important numerical and functional changes of the immune landscape in Lum‐BC. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland. [ABSTRACT FROM AUTHOR]

Objective: More and more studies have found that polycystic ovary syndrome (PCOS) is significantly associated with recurrent spontaneous abortion (RSA), but the specific mechanism is not yet clear. Methods: Based on the GEO database, we downloaded the PCOS (GSE10946, GSE6798 and GSE137684) and RSA (GSE165004, GSE26787 and GSE22490) datasets and performed differential analysis, weighted gene co-expression network (WGCNA), functional enrichment, and machine learning, respectively, on the datasets of the two diseases, Nomogram and integrated bioinformatics analysis such as immune infiltration analysis. Finally, the reliability of the diagnostic gene was verified by external verification and collection of human specimens. Results: In this study, PCOS and RSA datasets were obtained from Gene Expression Omnibus (GEO) database, and a total of 23 shared genes were obtained by differential analysis and WGCNA analysis. GO results showed that the shared genes were mainly enriched in the functions of lipid catabolism and cell cycle transition (G1/S). DO enrichment revealed that shared genes are mainly involved in ovarian diseases, lipid metabolism disorders and psychological disorders. KEGG analysis showed significant enrichment of Regulation of lipolysis in adipocytes, Prolactin signaling pathway, FoxO signaling pathway, Hippo signaling pathway and other pathways. A diagnostic gene FAM166 B was obtained by machine learning and Nomogram screening, which mainly played an important role in Cellular component. GSEA analysis revealed that FAM166B may be involved in the development of PCOS and RSA by regulating the cell cycle, amino acid metabolism, lipid metabolism, and carbohydrate metabolism. CIBERSORT analysis showed that the high expression of FAM166 B was closely related to the imbalance of multiple immune cells. Further verification by qPCR suggested that FAM166 B could be used as a common marker of PCOS and RSA. Conclusions: In summary, this study identified FAM166B as a common biomarker for PCOS and RSA, and conducted in-depth research and analysis of this gene, providing new data for basic experimental research and early prognosis, diagnosis and treatment of clinical diseases. [ABSTRACT FROM AUTHOR]

Hepatocellular carcinoma (HCC) is a malignancy known for its unfavorable prognosis. The dysregulation of the tumor microenvironment (TME) can affect the sensitivity to immunotherapy or chemotherapy, leading to treatment failure. The elucidation of PHLDA2's involvement in HCC is imperative, and the clinical value of PHLDA2 is also underestimated. Here, bioinformatics analysis was performed in multiple cohorts to explore the phenotype and mechanism through which PHLDA2 may affect the progression of HCC. Then, the expression and function of PHLDA2 were examined via the qRT-PCR, Western Blot, and MTT assays. Our findings indicate a substantial upregulation of PHLDA2 in HCC, correlated with a poorer prognosis. The methylation levels of PHLDA2 were found to be lower in HCC tissues compared to normal liver tissues. Besides, noteworthy associations were observed between PHLDA2 expression and immune infiltration in HCC. In addition, PHLDA2 upregulation is closely associated with stemness features and immunotherapy or chemotherapy resistance in HCC. In vitro experiments showed that sorafenib or cisplatin significantly up-regulated PHLDA2 mRNA levels, and PHLDA2 knockdown markedly decreased the sensitivity of HCC cells to chemotherapy drugs. Meanwhile, we found that TGF-β induced the expression of PHLDA2 in vitro. The GSEA and in vitro experiment indicated that PHLDA2 may promote the HCC progression via activating the AKT signaling pathway. Our study revealed the novel role of PHLDA2 as an independent prognostic factor, which plays an essential role in TME remodeling and treatment resistance in HCC. [ABSTRACT FROM AUTHOR]

Recently, cellular senescence-induced unstable carotid plaques have gained increasing attention. In this study, we utilized bioinformatics and machine learning methods to investigate the correlation between cellular senescence and the pathological mechanisms of unstable carotid plaques. Our aim was to elucidate the causes of unstable carotid plaque progression and identify new therapeutic strategies. First, differential expression analysis was performed on the test set GSE43292 to identify differentially expressed genes (DEGs) between the unstable plaque group and the control group. These DEGs were intersected with cellular senescence-associated genes to obtain 40 cellular senescence-associated DEGs. Subsequently, key genes were then identified through weighted gene co-expression network analysis, random forest, Recursive Feature Elimination for Support Vector Machines algorithm and cytoHubba plugin. The intersection yielded 3 CSA-signature genes, which were validated in the external validation set GSE163154. Additionally, we assessed the relationship between these CSA-signature genes and the immune landscape of the unstable plaque group. This study suggests that cellular senescence may play an important role in the progression mechanism of unstable plaques and is closely related to the influence of the immune microenvironment. Our research lays the foundation for studying the progression mechanism of unstable carotid plaques and provides some reference for targeted therapy. [ABSTRACT FROM AUTHOR]

Background: Breast cancer, despite significant advancements in treatment, remains a major cause of cancer-related deaths among women. Immunotherapy, an emerging therapeutic strategy, offers promise for better outcomes, particularly through the modulation of immune functions. Glioma-Associated Oncogene Homolog 1 (GLI1), a transcription factor implicated in cancer biology, has shown varying roles in different cancers. However, its immunoregulatory functions in breast invasive carcinoma (BRCA) remain elusive. The current study aimed to unravel the expression patterns and immune-regulatory roles of GLI1 in BRCA. Methods: Utilizing multiple bioinformatic platforms (TIMER2.0, GEPIA2, and R packages) based on The Cancer Genome Atlas (TCGA) and/or Genotype-Tissue Expression (GTEx) databases, we analyzed the expression of GLI1 in BRCA and its pan-cancer expression profiles. We further validated these findings by conducting qPCR and immunohistochemical staining on clinical BRCA samples. Kaplan-Meier analysis and Cox proportional hazards regression were performed to assess the prognostic value of GLI1. Additionally, the association between GLI1 expression and immune infiltration within the tumor immune microenvironment (TMIE) was examined. Results: The findings reveal dysregulated expression of GLI1 in numerous cancers, with a significant decrease observed in BRCA. High GLI1 expression indicated better survival outcomes and was correlated with the age and stage of BRCA patients. GLI1 was involved in immune status, as evidenced by its strong correlations with immune and stromal scores and the infiltration levels of multiple immune cells. Meanwhile, GLI1 was co-expressed with multiple immune-related genes, and high GLI1 expression was associated with the activation of immune-related pathways, such as binding to proteasome and mismatch repair and retinol metabolism signaling pathways. Additionally, the differential expression of GLI1 may be related to the effect of immunotherapy on CTLA-4, PD-1, and other signals, and can effectively predict the immune efficacy. Conclusion: Our study underscores the critical role of GLI1 in BRCA, both as a potential tumor suppressor and an immune regulator. The association between GLI1 expression and favorable prognosis suggests its potential as a prognostic biomarker and immunotherapeutic target in BRCA. [ABSTRACT FROM AUTHOR]

Background: The aberrant expression of AEG-1 is significantly correlated with tumorigenesis, development, neurodegeneration and inflammation. However, the relationship between AEG-1 expression and immune infiltration in OSCC, as well as other tumor types, has yet to be comprehensively analyzed. Methods: The expression levels, prognostic and clinicopathological characteristics, mutation patterns and methylation landscapes of AEG-1 in various tumors were obtained from multiple databases, including TIMER, GEPIA, HPA, TCGA, UALCAN, cBioPortal, SMART and TISIDB, in addition to single-cell RNA-seq data. The integration of these datasets facilitated the elucidation of the relationships among pan-cancer cellular heterogeneity, immune infiltration and AEG-1 expression levels. In vitro experiments created AEG-1 overexpressing cell lines, and mRNA-seq analyzed AEG-1-related differential genes in OSCC. RT-PCR validated these findings in vivo using xenograft tumors. Tumor cell lines were developed to study AEG-1’s effects through H&E, Masson, and PAS staining. Immunohistochemistry examined AEG1-related gene expression patterns. Results: Our analysis demonstrated that AEG-1 is highly expressed across various cancer types and is associated with tumor grade and patient prognosis. Additionally, AEG-1 amplification was observed in multiple cancers. Notably, we identified a significant elevation of AEG-1 expression in OSCC, which strongly correlated with patient prognosis and immune infiltration. Through mRNA-seq analysis of differentially expressed genes and immune-related gene sets, we identified a strong correlation between AEG-1 and immune infiltration markers such as LCP2, CD247, HLA-DPA1, HLA-DRA, HLA-DRB1, CIITA and CD74 in OSCC. Additionally, AEG-1 was found to regulate Th1/Th2 immune homeostasis, promote glycogen accumulation, and contribute to tumor fibrosis. Conclusion: In conclusion, AEG-1 significantly correlates with prognosis and immune infiltration across various cancer types and holds potential as a novel prognostic immune biomarker for OSCC. This finding may facilitate the identification of patients who are most likely to benefit from adjuvant immunotherapy. [ABSTRACT FROM AUTHOR]

Background: Bladder urothelial carcinoma (BLCA) is one of the most prevalent tumors globally, with its incidence rising notably in developed countries, significantly affecting human health. CSE1L encodes a protein that is involved in various cellular processes and plays a critical role in cancer initiation and progression. However, its role in BLCA remains underexplored. Methods: CSE1L expression in BLCA was analyzed using TCGA data and validated by qRT-PCR and Western blot in clinical samples. Survival analysis and Cox regression models were used to evaluate its prognostic value. Functional enrichment and protein interaction analyses were performed, and immune cell infiltration was assessed using CIBERSORT. Drug sensitivity was analyzed using GDSC data. In vitro assays evaluated the effects of CSE1L knockdown on cell proliferation, migration, and invasion. Results: CSE1L was found to be significantly overexpressed in BLCA tissues compared to normal tissues. High CSE1L expression was associated with poor overall survival and unfavorable clinicopathological features. Functional enrichment analysis revealed that DEGs related to CSE1L were involved in cell cycle regulation and immune-related pathways. Immune infiltration analysis indicated a significant correlation between CSE1L expression and various immune cell types, particularly T cells and macrophages. Drug sensitivity analysis identified several chemotherapeutic agents, including MG-132, Palbociclib, and Nutlin-3a, which were more effective in the low-CSE1L expression group, while the high-CSE1L expression group showed sensitivity to drugs like S-Trityl-L-cysteine, Bleomycin, and Cisplatin. In vitro knockdown of CSE1L in BLCA cell lines inhibited cell proliferation, migration, and invasion. Conclusions: The overexpression of CSE1L is associated with the progression and poor prognosis of bladder cancer, suggesting it could be a promising target for bladder cancer in the future. [ABSTRACT FROM AUTHOR]

AbstractThe 5-methylcytosine (m5C) is a common post-transcriptional RNA methylation modification and is involved in the pathological process of many diseases. However, little is known about the role of m5C in osteoarthritis (OA). OA gene data and the corresponding information were downloaded from the Gene Expression Omnibus database. Based on 36 m5C regulators, we constructed the landscape and diagnostic model for OA. Later, two m5C modification patterns were identified, and functional analyses were performed to evaluate whether these patterns were related to endoplasmic reticulum (ER) stress and mitochondrial autophagy. We further comprehensively analyzed the immune cell infiltration characteristics in different modification patterns in OA. We also established the post-transcriptional regulatory networks and drug-gene networks. Our findings suggested that m5C regulators were differentially expressed between OA and normal samples and could serve as novel biomarkers for the diagnosis of OA. Besides, m5C regulators may be involved in regulating ER stress, mitochondrial autophagy, and immune infiltration in OA. The m5C modification can influence the sensitivity to drugs and the potential post-transcriptional regulatory mechanisms might provide promising targets. [ABSTRACT FROM AUTHOR]

Lung adenocarcinoma (LUAD) is the most common lung cancer, accounting for 19.4% of all cancer deaths. Our previous study discovered that INTS7 expression was upregulated in LUAD, while the precise mechanism by which INTS7 exerts pro-cancer effects remains unknown. In our study, shRNA was used to knockdown the expression of INTS7 in A549 cells. Cancer behaviors in vitro were determined by CCK8 and transwell assays. Xenograft mice models were constructed to detect the tumorigenesis in vivo. Immunofluorescence and toluidine blue staining were used to test the immune infiltration. Bioinformatics analysis was adopted to predict the potential signaling pathways and construct INTS7-derived genomic prognostic model. Western blot was utilized to confirm the molecular pathways. In total, downregulation of INTS7 suppressed proliferation, invasion and migration of A549 cells, as well as tumor growth. Bioinformatics and western blot analysis indicated that p38MAPK pathway participated in the regulatory mechanism of INTS7. Moreover, INTS7 expression was negatively correlated with infiltration of memory B cells and mast cells, while positively correlated with infiltration of macrophages M2. A nomogram, including INTS7-derived risk score, was used to estimate individual's survival probability. Generally, our findings provided comprehensive understanding of the molecular mechanisms about INTS7, and targeting INTS7 may represent a potential therapy for LUAD. [ABSTRACT FROM AUTHOR]

Head and neck squamous cell carcinoma (HNSCC) is a highly heterogeneous tumor. Commonly used tumor staging don't sufficiently and accurately assess the prognosis of HNSCC patients, resulting in a lack of guidance for clinical treatment decisions. M2 macrophage infiltration has been shown to be strongly associated with the tumor prognosis. In this study, we used the Cancer Genome Atlas (TCGA) data to screen for genes co-expressed with M2 macrophages in HNSCC. We used univariate Cox regression to screen out the genes associated with HNSCC prognosis, and constructed a HNSCC prognosis model by Lasso regression analysis. The results confirmed that the model had good predictive value and accuracy for the prognosis of HNSCC patients by survival analysis, ROC curve and nomogram. We divided the HNSCC samples into high-risk and low-risk groups according to the risk score, and the results showed that patients in the high-risk group were more prone to genetic mutations and had a higher tumor mutational burden. In addition, there were significant differences between risk groups in terms of immune cell infiltration and drug sensitivity. The HNSCC prognostic model established in this study may provide guidance for clinical therapeutic decision-making and provide a theoretical foundation for the development of new immunotherapy methods. [ABSTRACT FROM AUTHOR]

Background: The tertiary lymphoid structures (TLSs) have an immunomodulatory function and have a positive impact on the survival outcomes of patients with oral squamous cell carcinoma (OSCC). However, there is a lack of standard approaches for quantifying TLSs and prognostic models using TLS-related genes (TLSRGs). These limitations limit the widespread use of TLSs in clinical practice. Methods: A convolutional neural network was used to automatically detect and quantify TLSs in HE-stained whole slide images. By employing bioinformatics and diverse statistical methods, this research created a prognostic model using TCGA cohorts and explored the connection between this model and immune infiltration. The expression levels of three TLSRGs in clinical specimens were detected by immunohistochemistry. To facilitate the assessment of individual prognostic outcomes, we further constructed a nomogram based on the risk score and other clinical factors. Results: TLSs were found to be an independent predictor of both overall survival (OS) and disease-free survival in OSCC patients. A larger proportion of the TLS area represented a better prognosis. After analysis, we identified 69 differentially expressed TLSRGs and selected three pivotal TLSRGs to construct the risk score model. This model emerged as a standalone predictor for OS and exhibited close associations with CD4 + T cells, CD8 + T cells, and macrophages. Immunohistochemistry revealed high expression levels of CCR7 and CXCR5 in TLS + OSCC samples, while CD86 was highly expressed in TLS- OSCC samples. The nomogram demonstrates excellent predictive ability for overall survival in OSCC patients. Conclusions: This is the first prognostic nomogram based on TLSRGs, that can effectively predict survival outcomes and contribute to individual treatment strategies for OSCC patients. [ABSTRACT FROM AUTHOR]

Background: Several tetraspanin (TSPAN) proteins have been implicated in tumorigenesis and disease progression. However, the precise function of tetraspanin 6 (TSPAN6) in glioma remains unclear. Methods: Integrated raw data from the Tumor Genome Atlas (TCGA) and Gene Expression Profiling (GEO) databases were processed using R4.2.1. Bioinformatic methods were used to analyze the gene expression levels of TSPAN6 in both glioma and normal brain tissues, correlating them with clinical characteristics. Additionally, the predictive value of TSPAN6 in relation to the immune checkpoint blockade (ICB) therapy response was assessed. In vitro experiments were conducted to investigate the effects of TSPAN6 knockdown on glioma cell proliferation, migration, cell cycle regulation, and macrophage recruitment. Results: TSPAN6 expression was significantly upregulated in glioma tissues compared to normal tissues. Elevated TSPAN6 expression is strongly correlated with unfavorable clinical characteristics in gliomas. Bioinformatic analyses revealed a significant correlation between elevated TSPAN6 expression and reduced overall survival. Additionally, TSPAN6 was co-expressed with several immune checkpoint genes and revealed a prognostic value in the context of ICB therapy. Functional enrichment analysis revealed the involvement of TSPAN6 in cell-cycle regulation. Furthermore, TSPAN6 expression positively correlated with macrophage and neutrophil infiltration. In vitro experiments confirmed that the downregulation of TSPAN6 inhibited U251 cell proliferation, disrupted the cell cycle, diminished migratory capabilities, and reduced the recruitment of macrophages. Conclusion: Our findings emphasize its potential as both a diagnostic and therapeutic target as well as a predictor of immune therapy response in gliomas. [ABSTRACT FROM AUTHOR]

Objective: To investigate the prognostic significance of CXCL8 in cervical cancer and its effect on immune response based on bioinformatics method. Methods: This study employs the HPA database to investigate CXCL8 expression in normal human tissues.The TIMER2.0 database is utilized to analyze CXCL8 expression across various types of cancer.Utilizing the TCGA database, we analyze the correlation between CXCL8 and the overall survival (OS) and progression-free interval (PFI) of patients with various tumors using R 4.3.2.Additionally, its association with immune checkpoint-related genes across various types of cancer is examined.We further analyze the association between CXCL8 expression and the expression of LAG3, CTLA4, PDCD1, and CD274 in cervical cancer.The TIMER database is used to study the association between CXCL8 and the extent of Tumor-Infiltrating Immune Cells (TIICs) infiltration.Enrichment analysis of genes related to CXCL8 is conducted using the LinkedOmics database. Result: CXCL8 is found in a wide range of normal human tissues.In the majority of tumor tissues, CXCL8 expression is elevated compared to their normal counterparts.There is a significant correlation between CXCL8 expression and the overall survival (OS) and progression-free interval (PFI) of patients with various tumors.CXCL8 expression is associated with the expression of diverse immune checkpoint-related genes and the extent of Tumor-Infiltrating Immune Cells (TIICs) infiltration.Genes related to CXCL8 participate in diverse immune-related processes in cervical cancer. Conclusion: CXCL8 plays a role in modulating immune infiltration, thereby influencing the prognosis of patients with various tumors, particularly those with cervical cancer.CXCL8 could potentially act as a biomarker for forecasting the prognosis and immune response of patients with tumors. [ABSTRACT FROM AUTHOR]

Objective: Pancreatic cancer has a poor prognosis due to its high malignancy and rapid progression. The limited immunogenicity of pancreatic cancer (PAAD) contributes to its low responsiveness to immunotherapy, yet its underlying mechanism remains poorly understood. As a cancer promoting gene, Twist participates in EMT in various tumors and promotes tumor progression. The interplay between EMT and the tumor microenvironment (TME) emerges as a pivotal factor influencing tumor immunity and response to immunotherapy. Twist therefore has potential as a biomarker for gauging the outcome of tumour immunotherapy.This research aimed to assess the Twist's prognostic significance in PAAD and its relationship to immunotherapy response. Methods: In this research, transcriptional data and epigenetic alterations of Twist in pancreatic cancer, along with their impact on the prognosis of PAAD patients, were analyzed using databases. Functional enrichment analysis elucidated the biological role of Twist in PAAD. Subsequently, databases including CIBERSORT and TIDE were employed to investigate the association between Twist expression and immune cell infiltration, immune checkpoint genes, and immunotherapy sensitivity within the pancreatic cancer immune microenvironment.Paraffinized specimens from patients with pancreatic ductal adenocarcinoma confirmed by postoperative pathology were selected for Twist expression verification, and the difference was analyzed by Chi-square test; uncontaminated pancreatic cancer cell lines were used for Twist expression verification, and the differences were analyzed by Student t-test. Results: Twist mRNA expression was notably upregulated in PAAD, positively correlating with gene methylation levels. Analyses of Kaplan–Meier and Cox regression showed a correlation between better overall survival and lower Twist expression. Functional annotation indicated that Twist-associated differentially expressed genes (DEGs) were involved in EMT regulation and acute inflammation. High expression of Twist leads to a significant reduction in the infiltration of anti-tumor immune cells such as Monocytes, NKcellsactivated, and TcellsCD8, further supporting its creation of a typical immunosuppressive microenvironment in pancreatic cancer. Twist expression is positively correlated with the expression of HARVCR2, LAIR1, LGALS3 and other genes, which may be related to the treatment response to immune checkpoint inhibitors (ICIs). TIDE analysis predicts that patients with high expression of Twist will be insensitive to immunotherapy. Twist is significantly over-expressed in pancreatic cancer cell lines and tissues, and is negatively correlated with E-cadhrin expression, but positively correlated with N-cadherin,Snail, and ZEB1. Conclusion: High Twist expression in PAAD signifies a grim prognosis. Its elevated levels not only contribute to tumor progression through EMT induction but also exert regulatory control over the immune microenvironment, leading to immunosuppression and diminished effectiveness of immunotherapy. [ABSTRACT FROM AUTHOR]

The most common type of non-small cell lung cancer is lung adenocarcinoma (LUAD), which is characterized by high morbidity and poor survival. Up-regulation of SASS6 expression can lead to the progression of various malignant tumors. However, there are no relevant studies on the role of SASS6 in LUAD. SASS6 was highly expressed in most tumors, reflecting a good diagnostic value, and its overexpression in LUAD indicated discouraging overall prognosis. Functional enrichment analysis suggested that SASS6 was associated with cell cycle in LUAD. In addition, patients with high SASS6 expression had worse immune infiltration, but higher TMB and immune checkpoint, and higher sensitivity to multiple targeted drugs such as osimertinib. Cell experiments confirmed that knockdown of SASS6 could inhibit the viability of tumor cells.SASS6 has important value in the diagnosis of cancer. In particular, SASS6 is a crucial factor in the progression of LUAD, and has important clinical value, especially in the diagnosis, prognosis and treatment [ABSTRACT FROM AUTHOR]

Formyl peptide receptor 3 (FPR3) is known to have implications in the progression of various cancer types. Despite this, its biological significance within pan-cancer datasets has yet to be investigated. In this investigation, we scrutinized FPR3's expression profiles, genetic alterations, prognostic significance, immune-related characteristics, methylation status, tumor mutation burden (TMB), and microsatellite instability (MSI) across different types of cancer. We utilized TISCH's single-cell data to identify immune cells closely associated with FPR3. The predictive significance of FPR3 was evaluated independently in gliomas using data from TCGA and CGGA datasets, leading to the development of a prognostic nomogram. Immunohistochemistry and Western blot analysis confirmed FPR3 expression in gliomas. Lastly, the CCK-8 and wound-healing assays were employed to assess the impact of FPR3 on the proliferation and metastasis of GBM cell lines. In numerous cancer types, heightened FPR3 expression correlated with adverse outcomes, immune cell infiltration, immune checkpoints, TMB, and MSI. In glioma, FPR3 emerged as a notable risk factor, with the prognostic model effectively forecasting patient results. The potential biological relevance of FPR3 was confirmed in glioma, and it was shown to have significant involvement in the processes of glioma growth, immune infiltration, and metastasis. Our results imply a potential association of FPR3 with tumor immunity, indicating its viability as a prognostic indicator in glioma. [ABSTRACT FROM AUTHOR]

Background: Barrier-to-autointegration factor 1 (BANF1) is an abundant and ubiquitously expressed postnatal mammalian protein that is overexpressed in numerous human cancers and can promote cancer cell proliferation. However, the role of BANF1 in prognosis remains unclear in head and neck squamous cell carcinoma (HNSCC). Methods: BANF1 expression data were obtained from the GEO and TCGA databases. We used Cox regression and Kaplan-Meier curves to assess the prognostic potential of BANF1. The role of BANF1-related genes was investigated using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses. In addition, we explored the link between BANF1, drug sensitivity, and the tumor immune microenvironment. Finally, functional in vitro and in vivo assays were used to explore the effects of BANF1 on tumor growth and metastasis of HNSCC. Results: BANF1 was markedly overexpressed in HNSCC and was correlated with clinicopathological characteristics. According to survival analysis, BANF1 can be inversely correlated with patient survival and can act as a prognostic risk indicator. IC50 values for chemotherapeutic treatments indicated that the group with high BANF1 expression was more responsive to most antitumor treatments. Furthermore, higher TIDE scores were observed in the low BANF1 expression group, indicating a decline in the efficacy of immune checkpoint inhibitor therapy. Functionally, the malignant biological behavior of HNSCC cell lines was inhibited when BANF1 expression was knocked down. Conclusion: BANF1 can promote tumor progression in patients with HNSCC. BANF1 shows great promise as a potential biomarker to assess the prognosis. [ABSTRACT FROM AUTHOR]

Background: Few studies have explored the expression profile of RPL3 in breast cancer (BRCA). Our research provided an in-depth analysis of RPL3 expression patterns in BRCA, highlighting its significance for therapy prediction and prognosis. Methods: RPL3 was notably elevated in malignant cells, and its expression level was closely associated with tumor size and overall survival outcomes. Our study also identified RPL3-related terms and pathways and revealed a strong correlation between RPL3 expression and breast carcinoma immunity, demonstrating inconsistent expression levels in various immune cell lines. In addition, we examined the relationship between RPL3 expression and tumor mutational burden (TMB) in BRCA. To assess the clinical implications of BRCA chemotherapy, we investigated the correlation between RPL3 expression levels and drug sensitivity. Results: Our findings suggest that RPL3 plays a critical role in the BRCA process and is associated with immune infiltration, indicating its potential as a novel immunotherapy target in BRCA treatment. Conclusions: In summary, our research underscores the importance of RPL3 expression levels in tumorigenesis and its potential for guiding BRCA immunotherapy. [ABSTRACT FROM AUTHOR]

Background We aimed to pinpoint biomarkers, create a diagnostic model for ulcerative colitis (UC), and delve into its immune features to better understand this autoimmune condition. Methods The sequencing data for both the UC and the control groups were obtained from GEO, including both bulk and single-cell data. Using GSE87466 as training group, we applied differential analysis, WGCNA, PPI, LASSO, RF, and SVM-RFE for biomarker selection. A neural network shaped our diagnostic model, corroborated by GSE92415 as the validation cohort with ROC assessment. Immune cell profiling was conducted using CIBERSORT. Results 53 disease-associated genes were screened. Enrichment analysis highlighted roles in complement cascades and cell adhesion. Eight biomarkers were finally identified through multiple machine learning and PPI: B4GALNT2, PDZK1IP1, FAM195A, REG4, MTMR11, FLJ35024, CD55, and CD44. The diagnostic model had AUCs of 0.984 (training group) and 0.957 (validation group). UC tissues revealed heightened plasma cells, CD8 T cells, and other immune cells. Two unique UC immune patterns emerged, with certain T and NK cells central to immune modulation. Conclusion We identified eight biomarkers of UC by various methods, constructed a diagnostic model through neural networks, and explored the immune complexity of the disease, which contributes to the diagnosis and treatment of UC. [ABSTRACT FROM AUTHOR]

Percutaneous coronary intervention (PCI) combined with stent implantation is currently one of the most effective treatments for coronary artery disease (CAD). However, in-stent restenosis (ISR) significantly compromises its long-term efficacy. Mitophagy plays a crucial role in vascular homeostasis, yet its role in ISR remains unclear. This study aims to identify mitophagy-related biomarkers for ISR and explore their underlying molecular mechanisms. Through differential gene expression analysis between ISR and Control samples in the combined dataset, 169 differentially expressed genes (DEGs) were identified. Twenty-three differentially expressed mitophagy-related genes (DEMRGs) were identified by intersecting with mitophagy-related genes (MRGs) from the GeneCards, and functional enrichment analysis indicated their significant involvement in mitophagy-related biological processes. Using Weighted Gene Co-expression Network Analysis (WGCNA) and three machine learning algorithms (Logistic-LASSO, RF, and SVM-RFE), LRRK2, and ANKRD13A were identified as mitophagy-related biomarkers for ISR. The nomogram based on these two genes also exhibited promising diagnostic performance for ISR. Gene Set Enrichment Analysis (GSEA) as well as immune infiltration analyses showed that these two genes were closely associated with immune and inflammatory responses in ISR. Furthermore, potential small molecule compounds with therapeutic implications for ISR were predicted using the connectivity Map (cMAP) database. This study systematically investigated mitophagy-related biomarkers for ISR and their potential biological functions, providing new insights into early diagnosis and precision treatment strategies for ISR. [ABSTRACT FROM AUTHOR]

Macrophage polarization plays an essential role in tumour immune cell infiltration and tumour growth. In this study, we selected a series of genes distinguishing between M1 and M2 macrophages and explored their prognostic value in gliomas. A total of 170 genes were included in our study. The CGGA database was used as the training cohort and the TCGA database as the validation cohort. The biological processes and functions were identified by GO and KEGG analysis. Kaplan–Meier analysis was used to compare survival differences between groups. Importantly, we built a risk score model using Cox regression analysis based on the CGGA and verified it in the TCGA database and our sequencing data. Patients with gliomas in the high‐risk group were associated with high pathologic grade, IDH WT status, MGMT promoter unmethylation, 1p19q non‐codeletion and prone to have a poor outcome. GEPIA results revealed that CD300C, CNRIP1 and MYO1F are the most related genes of immune infiltrations. The differential expression of these genes between low‐grade gliomas and glioblastomas was confirmed by q‐RT‐PCR. Macrophage polarization‐related gene signatures can predict the malignancy and outcome of patients with gliomas and might act as a promising target for glioma immunotherapy in the future. [ABSTRACT FROM AUTHOR]

Oncolytic viral immunotherapy is a cancer treatment that uses native or genetically modified viruses that selectively replicate and destroy tumor cells. In this study, we aimed to construct a virus-based prognostic model for risk assessment and prognosis prediction in patients with hepatocellular carcinoma (HCC) and determine the most appropriate virus as a candidate vector for oncolytic virus immunotherapy. Microbiome and RNA sequencing data and clinical information were obtained from The Cancer Genome Atlas, and viruses with prognostic value were identified (Deltabaculovirus, Sicinivirus, and Cytomegalovirus) to construct the prognostic model. Correlation analyses were performed to evaluate the predictive function of the viral signature. Bioinformatics analyses were conducted to explore the functional enrichment of viral expression in HCC. The risk score generated by this model could distinguish patients with different survival outcomes, have excellent reliability and accuracy, and could be used as an independent prognostic indicator. The high-risk score group showed significantly lower overall survival, and this trend was also observed in subgroups with different clinicopathological features. Furthermore, Deltabaculovirus positively correlated with amino acid metabolism, energy metabolism signaling pathways, peroxisomes, and complement coagulation cascades. In addition, Deltabaculovirus was significantly related to immune cell infiltration; therefore, patients with high Delta-baculovirus expression might respond better to HCC immunotherapy. Our study identified a promising predictive viral signature for assessing clinical prognosis and guiding immunotherapy in HCC. Deltabaculovirus might be a suitable viral vector for oncolytic virus immunotherapy. [ABSTRACT FROM AUTHOR]