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Detection of Immune Microenvironment Changes and Immune-Related Regulators in Langerhans Cell Histiocytosis Bone Metastasis.
The inflammation/immune response pathway is considered a key contributor to the development of Langerhans cell histiocytosis (LCH) bone metastasis. However, the dynamic changes in the immune microenvironment of LCH bone metastasis and critical regulators are still unclear. Expression profiling by arrays of GSE16395, GSE35340, and GSE122476 was applied to detect the immune microenvironment changes in the development of LCH bone metastasis. The single-cell high-throughput sequencing of GSE133704, involved in LCH bone lesions, was analyzed. The online database Metascape and gene set variation analysis (GSVA) algorithms were used to detect the gene function of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The protein-protein interaction (PPI) network of hub regulators was constructed by the STRING database. In these results, key immune cells, such as Tem cells, NK T cells, CD8(+) T cells, and Th1 cells, were identified in LCH bone metastasis. These genes, which include LAG3, TSPAN5, LPAR5, VEGFA, CXCL16, CD74, and MARCKS, may significantly correlate with the cellular infiltration of B cells, aDCs, pDCs, cytotoxic cells, T cells, CD8+ T cells, T helper cells, and Tcm cells. In conclusion, our study constructed an atlas of the immune microenvironment of LCH bone metastasis. Genes including LAG3, TSPAN5, LPAR5, VEGFA, CXCL16, CD74, and MARCKS may be involved in the development of LCH bone metastasis. The hub gene-immune cell interactive map may be a potential prognostic biomarker for the progression of LCH bone metastasis and synergetic targets for immunotherapy in LCH patients.
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Assessment of long non-coding RNA expression reveals novel mediators of the lung tumour immune response.
The tumour immune microenvironment is a crucial mediator of lung tumourigenesis, and characterizing the immune landscape of patient tumours may guide immunotherapy treatment regimens and uncover novel intervention points. We sought to identify the landscape of tumour-infiltrating immune cells in the context of long non-coding RNA (lncRNAs), known regulators of gene expression. We examined the lncRNA profiles of lung adenocarcinoma (LUAD) tumours by interrogating RNA sequencing data from microdissected and non-microdissected samples (BCCRC and TCGA). Subsequently, analysis of single-cell RNA sequencing data from lung tumours and flow-sorted healthy peripheral blood mononuclear cells identified lncRNAs in immune cells, highlighting their biological and prognostic relevance. We discovered lncRNA expression patterns indicative of regulatory relationships with immune-related protein-coding genes, including the relationship between AC008750.1 and NKG7 in NK cells. Activation of NK cells in vitro was sufficient to induce AC008750.1 expression. Finally, siRNA-mediated knockdown of AC008750.1 significantly impaired both the expression of NKG7 and the anti-tumour capacity of NK cells. We present an atlas of cancer-cell extrinsic immune cell-expressed lncRNAs, in vitro evidence for a functional role of lncRNAs in anti-tumour immune activity, which upon further exploration may reveal novel clinical utility as markers of immune infiltration.
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Predicting Prognosis and Immunotherapy Response in Glioblastoma (GBM) With a 5-Gene CAF-Risk Signature.
BACKGROUND: Cancer-associated fibroblasts (CAF) represent significant constituents within the extracellular matrix (ECM) across a range of cancers. Nevertheless, there exists a scarcity of direct proof concerning the function of CAF in glioblastoma (GBM). AIMS: This study endeavors to probe the participation of CAF in GBM by developing and validating a CAF-risk signature and exploring its correlation with immune infiltration and immunotherapy responsiveness. METHODS AND RESULTS: To fulfill these objectives, mRNA expression profiles of GBM samples and their corresponding clinical data were retrieved from two databases. First, stromal CAF-associated genes were identified by weighted gene co-expression network analysis (WGCNA). This method constructs co-expression networks and pinpoints gene modules with similar expression patterns to detect relevant genes. Subsequently, a CAF-risk signature was established via univariate and LASSO Cox regression analyses. Thereafter, gene set enrichment analysis (GSEA) and single-sample gene set enrichment analysis (ssGSEA) were carried out to investigate the underlying molecular mechanisms. The immune status was evaluated with several R packages, and the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm was utilized to assess the response to immunotherapy. Validation was performed using single-cell RNA sequencing (scRNA) datasets, the Cancer Cell Line Encyclopedia (CCLE), and the Human Protein Atlas (HPA). Eventually, a 5-gene (ITGA5, MMP14, FN1, COL5A1, and COL6A1) prognostic CAF model was constructed. Notably, immune infiltration analysis demonstrated a significant correlation between Treg, Macrophage, and CAF risk scores. Moreover, TIDE analysis suggested a decreased responsiveness to immunotherapy in high CAF-risk patients. In addition, GSEA showed significant enrichment of the transforming growth factor alpha (TGF-α), inflammatory response, and epithelial-mesenchymal transition (EMT) pathways in this subgroup. Finally, the validation through scRNA, CCLE, and HPA datasets confirmed these findings. CONCLUSION: The 5-gene CAF-risk signature exhibited accurate prognostic predictions and efficiently evaluated clinical immunotherapy responses among GBM patients. These results offer robust evidence regarding the implication of CAF in GBM and underscore the potential clinical value of personalized anti-CAF therapies in conjunction with immunotherapy.
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Targeting exercise-related genes and placental growth factor for therapeutic development in head and neck squamous cell carcinoma.
BACKGROUND: Human cancers, including head and neck squamous cell carcinoma (HNSCC), are complex and heterogeneous diseases driven by uncontrolled cell growth and proliferation. Post-translational modifications (PTMs) of proteins play a crucial role in cancer progression, making them a promising target for pharmacological intervention. This study aims to identify key exercise-related genes with prognostic value in HNSCC through comprehensive bioinformatics analysis, with a particular focus on the therapeutic potential of placental growth factor (PIGF). METHODS: Transcriptome data for HNSCC were obtained from The Cancer Genome Atlas (TCGA) database. Differently expressed genes (DEGs) were identified and analyzed for their prognostic significance. Exercise-related gene sets were retrieved from the Gene Set Enrichment Analysis (GSEA) database. Functional enrichment analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and GSEA, were conducted. The biological functions and clinical implications of key genes were further explored through single-gene expression analysis, immune infiltration analysis, and in vitro cellular experiments. RESULTS: The study identified exercise-related genes associated with survival prognosis in HNSCC. GO and KEGG pathway analyses highlighted the biological functions of these genes, and Kaplan-Meier survival curves confirmed their prognostic value. PIGF expression analysis using TCGA data showed its diagnostic potential, with higher expression linked to advanced tumor stages. Single-cell sequencing revealed PIGF's role in the tumor microenvironment. In vitro experiments demonstrated that PIGF plays a pivotal role in enhancing cell proliferation and colony formation in HNSCC, with PIGF knockdown significantly impairing these functions, highlighting its importance in tumor growth regulation. Additionally, PIGF's predictive performance in drug sensitivity across cancer datasets suggests its potential as a pharmacological target, offering opportunities to modulate the immune microenvironment and improve therapeutic outcomes in cancer treatment. CONCLUSION: This study provides new insights into the molecular mechanisms underlying HNSCC and identifies exercise-related genes, particularly PIGF, as promising biomarkers for clinical treatment and personalized medicine. By focusing on PTMs and their role in cancer progression, our findings suggest that targeting PIGF may offer innovative therapeutic strategies.
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Transcriptional landscape of pleural mesothelioma patients in relation to NF2 gene mutational status.
BACKGROUND: Pleural mesothelioma (PM) is an aggressive cancer with poor prognosis, often driven by asbestos exposure. Mutations in the NF2 gene, a key regulator of the Hippo signaling pathway, are frequently observed in PM. However, their impact on tumor biology, immune infiltration, cytokine signaling, and therapeutic response remains poorly understood. METHODS: Using data from The Cancer Genome Atlas, we analyzed 82 PM cases to assess the prevalence and consequences of NF2 mutations. Logistic regression was used to evaluate associations with clinical variables, while transcriptomic differences were examined through differential expression and functional enrichment analyses. Immune and stromal infiltration were inferred via the xCell algorithm, cytokine signaling analyzed with Cytosig, and chemotherapeutic sensitivity predicted using the pRRophetic R package. Single-cell RNA sequencing data provided further insights into transcriptional patterns in NF2-mutated tumors. RESULTS: NF2 mutations were present in 22% of cases, with no significant correlations to histological subtype, stage, or age. NF2-mutated tumors exhibited increased infiltration of basophils, naïve B cells, and pericytes, along with altered cytokine profiles, including NRG1, TGFB3, and reduced FGF2. Differentially expressed genes, such as MYL7 and HOXA11, were linked to poorer survival. Chemotherapy modeling indicated higher sensitivity to camptothecin and vinblastine in NF2-mutated tumors. CONCLUSIONS: NF2 mutations influence the tumor microenvironment, transcriptional landscape, and predicted therapeutic response in PM, underscoring their potential as prognostic biomarkers. These findings support tailored therapeutic strategies targeting NF2-related pathways, including Hippo signaling and cytokine modulation.
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Atlas of Metastatic Gastric Cancer Links Ferroptosis to Disease Progression and Immunotherapy Response.
BACKGROUND & AIMS: Metastases from gastric adenocarcinoma (GAC) lead to high morbidity and mortality. Developing innovative and effective therapies requires a comprehensive understanding of the tumor and immune biology of advanced GAC. Yet, collecting matched specimens from advanced, treatment-naïve patients with GAC poses a significant challenge, limiting the scope of current research, which has focused predominantly on localized tumors. This gap hinders deeper insight into the metastatic dynamics of GAC. METHODS: We performed in-depth single-cell transcriptome and immune profiling on 68 paired, treatment-naïve, primary metastatic tumors to delineate alterations in cancer cells and their tumor microenvironment during metastatic progression. To validate our observations, we conducted comprehensive functional studies both in vitro and in vivo, using cell lines and multiple patient-derived xenograft and novel mouse models of GAC. RESULTS: Liver and peritoneal metastases exhibited distinct properties in cancer cells and dynamics of tumor microenvironment phenotypes, supporting the notion that cancer cells and their local tumor microenvironments co-evolve at metastatic sites. Our study also revealed differential activation of cancer meta-programs across metastases. We observed evasion of cancer cell ferroptosis via GPX4 up-regulation during GAC progression. Conditional depletion of Gpx4 or pharmacologic inhibition of ferroptosis resistance significantly attenuated tumor growth and metastatic progression. In addition, ferroptosis-resensitizing treatments augmented the efficacy of chimeric antigen receptor T-cell therapy. CONCLUSIONS: This study represents the largest single-cell dataset of metastatic GACs to date. High-resolution mapping of the molecular and cellular dynamics of GAC metastasis has revealed a rationale for targeting ferroptosis defense in combination with chimeric antigen receptor T-cell therapy as a novel therapeutic strategy with potential immense clinical implications.
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HCG18 Participates in Vascular Invasion of Hepatocellular Carcinoma by Regulating Macrophages and Tumor Stem Cells.
OBJECTIVES: To identify key genes involved in vascular invasion in hepatocellular carcinoma (HCC), to describe their regulatory mechanisms, and to explore the immune microenvironment of HCC. METHODOLOGY: In this study, the genome, transcriptome, and immune microenvironment of HCC were assessed by using multi-platform data from The Cancer Genome Atlas (n = 373) and GEO data (GSE149614). The key regulatory networks, transcription factors and core genes related to vascular invasion and prognosis were explored based on the CE mechanism. Survival analysis and gene set enrichment were used to explore pathways related to vascular invasion. Combined with single-cell transcriptome data, the distribution of core gene expression in various cells was observed. Cellular communication analysis was used to identify key cells associated with vascular invasion. Pseudo-temporal locus analysis was used to explore the regulation of core genes in key cell phenotypes. The influence of core genes on current immune checkpoint therapy was evaluated and correlations with tumor stem cell scores were explored. RESULTS: We obtained a network containing 1,249 pairs of CE regulatory relationships, including 579 differential proteins, 28 non-coding RNAs, and 37 miRNAs. Three key transcription factors, ILF2, YBX1, and HMGA1, were identified, all regulated by HCG18 lncRNA. ScRNAseq showed that HCG18 co-localized with macrophages and stem cells. CIBERSORTx assessed 22 types of immune cells in HCC and found that HCG18 was positively correlated with M0 macrophages, while being negatively correlated with M1 and M2 macrophages, monocytes, and dendritic cells. Cluster analysis based on patient prognosis suggested that regulating phenotypic transformation of macrophages could be an effective intervention for treating HCC. At the same time, higher expression of HCG18, HMGA1, ILF2, and YBX1 was associated with a higher stem cell score and less tumor differentiation. Pan cancer analysis indicated that high expression of HCG18 implies high sensitivity to immune checkpoint therapy. CONCLUSION: HCG18 participates in vascular invasion of HCC by regulating macrophages and tumor stem cells through three key transcription factors, YBX1, ILF2, and HMGA1.
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Therapeutic Targeting of Oxidative Phosphorylation in Microsatellite Instability-High Gastric Cancer.
BACKGROUND: Gastric cancer is the third leading cause of cancer-related mortality worldwide. According to The Cancer Genome Atlas (TCGA), it can be classified into four molecular subtypes, including microsatellite instability (MSI) and genomically stable (GS) subtypes, which display distinct clinical and pathological features. However, differences in their tumor microenvironment, particularly metabolic reprogramming, remain poorly understood. METHODS: Single-cell RNA sequencing data from gastric cancer patients classified as GS or MSI were enrolled. Cell clusters were identified and annotated to compare cellular landscapes between subtypes. Differential gene expression and pathway analyses were performed among malignant epithelial cells. Key genes related to oxidative phosphorylation were identified using LASSO regression, and their expression was further validated in the TCGA dataset. Patient-derived xenograft models were used to compare tumor growth rates, ATP levels, and expression of oxidative phosphorylation -related genes. RESULTS: Single-cell transcriptomic analysis revealed eight major cell types in MSI tumors. Compared to the GS subtype, MSI samples showed significantly greater infiltration of T cells and a lower proportion of epithelial cells. Malignant cells from MSI samples exhibited increased activity of oxidative phosphorylation pathways. LASSO regression identified five oxidative phosphorylation-related genes that were consistently overexpressed in MSI tumors in both single-cell and TCGA datasets. In Patient-derived xenograft models, MSI tumors grew more rapidly and demonstrated higher ATP levels and elevated expression of the five oxidative phosphorylation-related genes compared to MSS tumors. CONCLUSION: Our study reveals enhanced oxidative phosphorylation metabolism in MSI gastric cancer at single-cell resolution and identifies five oxidative phosphorylation-related genes that may serve as potential therapeutic targets for this subtype.
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Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators.
Alternative splicing (AS) dramatically expands the complexity of the mammalian brain transcriptome, but its atlas remains incomplete. Here we performed deep mRNA sequencing of mouse cortex to discover and characterize alternative exons with potential functional significance. Our analysis expands the list of AS events over 10-fold compared with previous annotations, demonstrating that 72% of multiexon genes express multiple splice variants in this single tissue. To evaluate functionality of the newly discovered AS events, we conducted comprehensive analyses on central nervous system (CNS) cell type-specific splicing, targets of tissue- or cell type-specific RNA binding proteins (RBPs), evolutionary selection pressure, and coupling of AS with nonsense-mediated decay (AS-NMD). We show that newly discovered events account for 23-42% of all cassette exons under tissue- or cell type-specific regulation. Furthermore, over 7,000 cassette exons are under evolutionary selection for regulated AS in mammals, 70% of which are new. Among these are 3,058 highly conserved cassette exons, including 1,014 NMD exons that may function directly to control gene expression levels. These NMD exons are particularly enriched in RBPs including splicing factors and interestingly also regulators for other steps of RNA metabolism. Unexpectedly, a second group of NMD exons reside in genes encoding chromatin regulators. Although the conservation of NMD exons in RBPs frequently extends into lower vertebrates, NMD exons in chromatin regulators are introduced later into the mammalian lineage, implying the emergence of a novel mechanism coupling AS and epigenetics. Our results highlight previously uncharacterized complexity and evolution in the mammalian brain transcriptome.
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Magnesium sulfate attenuates sepsis-induced myocardial injury through macrophage Fxyd2/NF-κB signaling: Integrated evidence from a propensity-matched cohort, single-cell atlas, and mechanistic validation.
BACKGROUND: Sepsis-induced myocardial injury (SIMI) affects approximately 20%-55% of septic patients, with associated mortality ranging from 37% to 70%; however, evidence for magnesium sulfate (MgSO₄) as a targeted SIMI intervention and its molecular basis remain poorly defined. METHODS: We integrated three evidentiary levels. A retrospective cohort of 2219 SIMI patients from the MIMIC-IV database underwent 1:1 propensity score matching (PSM; n = 992) and piecewise Cox regression (Day 10 landmark) to evaluate 28-day mortality. Single-cell RNA sequencing (scRNA-seq) of murine septic cardiac tissue characterized immune dynamics and identified MgSO₄-responsive targets. A macrophage-cardiomyocyte conditioned-medium transfer model, supplemented by Western blotting, RT-qPCR, and pyroptosis assays, validated the Fxyd2/NF-κB axis. RESULTS: MgSO₄ conferred robust survival benefit during the acute phase (Days 0-10; aHR = 0.402, 95% CI: 0.302-0.536, P < 0.001), representing a 59.8% relative risk reduction. The benefit was independent of baseline serum magnesium, indicating a pharmacological rather than nutritional effect. scRNA-seq revealed MgSO₄ enriched reparative macrophage subsets via mineral absorption pathways, identifying Fxyd2 as a key responsive gene. In vitro, MgSO₄ pretreatment remodeled the macrophage secretome-suppressing TNF-α, IL-6, and MCP-1-thereby abrogating paracrine NLRP3-caspase-1-GSDMD pyroptosis in H9c2 cardiomyocytes. Mechanistically, MgSO₄ preserved Fxyd2 expression in LPS-stimulated macrophages, inhibiting NF-κB phosphorylation and downstream pro-inflammatory transcription. CONCLUSIONS: MgSO₄ provides time-dependent cardioprotection in SIMI by reprogramming the macrophage secretome via the Fxyd2/NF-κB axis, repositioning it as a targeted immunomodulatory agent and providing rationale for early administration in future randomized trials.