Actin cytoskeleton remodeling at the cancer cell side of the immunological synapse: good, bad, or both?

Advancing personalized, predictive, and preventive medicine in bladder cancer: a multi-omics and machine learning approach for novel prognostic modeling, immune profiling, and therapeutic target discovery

Objective

This study aimed to identify and analyze immunogenic cell death (ICD)-related multi-omics features in bladder cancer (BLCA) using single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data. By integrating these datasets, we sought to construct a prognostic signature (ICDRS) and explore its clinical and biological implications, including its association with immune cell infiltration, tumor microenvironment (TME), and drug sensitivity.

Methods

Publicly available datasets from TCGA and GEO, including scRNA-seq (GSE222315, 9 samples) and bulk RNA-seq (TCGA-BLCA, 403 samples; GSE13507, 160 samples), were analyzed. Single-cell data were processed using Seurat, and ICD scores were calculated using single-sample gene set enrichment analysis (ssGSEA). Weighted gene co-expression network analysis (WGCNA) identified ICD-related modules, and machine learning algorithms (Lasso, Ridge, CoxBoost) were employed to construct the ICDRS. Survival analysis, immune infiltration, pathway enrichment, and drug sensitivity were evaluated to validate the model.

Results

The ICDRS, based on eight key genes (IL32, AHNAK, ANXA5, FN1, GSN, CNN3, FXYD3, CTSS), effectively stratified BLCA patients into high- and low-risk groups with significant differences in overall survival (OS, P < 0.001). High ICDRS scores were associated with immune-suppressive TME, including increased infiltration of T cells CD4 memory resting (P = 0.02) and macrophages M0/M1/M2 (P = 0.01). Pathway enrichment revealed correlations with cholesterol homeostasis, epithelial-mesenchymal transition (EMT), and KRAS signaling. Drug sensitivity analysis showed high-risk groups were resistant to Cisplatin (P = 0.003), Mitomycin C (P = 0.01), and Paclitaxel (P = 0.004), with IC50 values significantly higher than low-risk groups.

Conclusion

The ICDRS serves as a robust prognostic biomarker for BLCA, offering insights into tumor immune evasion mechanisms and potential therapeutic targets. Its integration with clinical features enhances personalized treatment strategies, highlighting the importance of ICD in BLCA immunotherapy and precision medicine. The model's predictive accuracy and biological relevance were validated across multiple datasets, underscoring its potential for clinical application.

Integrating network pharmacology to investigate the mechanism of quercetin's action through AKT inhibition in co-expressed genes associated with polycystic ovary syndrome and endometrial cancer

Endometrial cancer (EC) is a common gynecological malignancy for which polycystic ovarian syndrome (PCOS) has been identified as a significant risk factor. Quercetin, a widely distributed natural flavonoid, has demonstrated potential therapeutic effects in managing both PCOS and EC. However, the specific molecular targets of quercetin in the context of PCOS comorbid with EC (PCOS-EC) remain poorly defined. This study aims to elucidate the therapeutic potential of quercetin for treating PCOS-EC using network pharmacology, molecular dynamics simulations, and in vitro assays. The intersection of 379 PCOS-EC-associated targets with 361 quercetin targets identified 47 potential therapeutic targets of quercetin for PCOS-EC. Gene Ontology enrichment analysis revealed the biological functions, while Kyoto Encyclopedia of Genes and Genomes identified the pathways potentially involved in quercetin's effects against PCOS-EC. Protein-protein interaction network analysis highlighted six overlapping targets, namely, ACTB, AKT1, EGFR, ESR1, PTGS2, and TP53. Molecular docking and molecular dynamics simulations indicated that quercetin bound with high affinity to the hub genes, with AKT1 emerging as a central target. In vitro experiments confirmed that quercetin treatment significantly downregulated AKT expression in EC cells. These findings elucidate potential targets and molecular mechanisms through which quercetin exerts its therapeutic effects.

Aflatoxin B1 Exposure Suppresses the Migration of Dendritic Cells by Reshaping the Cytoskeleton

Exposure to Aflatoxin B1 (AFB1) is considered a significant risk factor for human diseases, including the immune function impairment of immune cells. Dendritic cells (DCs), as essential antigen-presenting cells, play a pivotal role in bridging innate and adaptive immunity. However, the impact of AFB1 exposure on DCs has not been fully elucidated. In this study, we investigated the effects of AFB1 exposure on the migration ability of DCs and its underlying action model. Initially, we observed that AFB1 exposure inhibited the survival of DCs and altered their cellular morphology. Further investigation revealed that AFB1 promotes cell adhesion and inhibits DC migration by modulating the expression of cell adhesion molecules. Additionally, our findings indicated that cytoskeletal remodeling plays a crucial role in these processes. Experimental techniques such as immunofluorescence and RNA sequencing confirmed that AFB1 exposure regulates the expression of cytoskeleton-related genes. Moreover, we found that the perturbation of the gene expression profile through AFB1 exposure is associated with cell communication. Collectively, our study findings demonstrate that AFB1 can disrupt the expression of cytoskeleton- and adhesion-related molecules in DCs, thereby altering cell morphology and migration. These insights could provide new perspectives for further understanding the immunosuppressive effects of AFB1 and developing therapeutic strategies for diseases associated with AFB1 exposure.

Actin dysregulation induces immune evasion via oxidative stress-activated PD-L1 in gastric cancer

Diffuse gastric adenocarcinoma (DGAC) is an aggressive malignancy with limited therapeutic options, poor prognosis, and poorly understood biology. CRACD, an actin polymerization regulator, is often inactivated in gastric cancer, including DGAC. We found that genetic engineering of murine gastric organoids with Cracd ablation combined with Kras mutation and Trp53 loss induced aberrant cell plasticity, hyperproliferation, and hypermucinosis, the features that recapitulate DGAC transcriptional signatures. Notably, CRACD inactivation remodeled the immune landscape for immune evasion through PD-L1 enrichment in tumor cells. Mechanistically, CRACD loss disrupted actin dynamics, generating reactive oxygen species that activated HIF1α, which transactivated PD-L1 . Pharmacologic inhibition of HIF1α or PD-L1 restored immune surveillance and suppressed tumorigenesis. These findings reveal a novel role of actin homeostasis in limiting cell plasticity and immune evasion, position CRACD as a potential biomarker for stratifying patients with DGAC, and highlight HIF1α and PD-L1 as actionable therapeutic targets.

Multi-omics analysis of overexpressed tumor-associated proteins: gene expression, immunopeptide presentation, and antibody response in oropharyngeal squamous cell carcinoma, with a focus on cancer-testis antigens

Introduction

The human leukocyte antigen complex (HLA) is essential for inducing specific immune responses to cancer by presenting tumor-associated peptides (TAP) to T cells. Overexpressed tumor associated antigens, mainly cancer-testis antigens (CTA), are outlined as essential targets for immunotherapy in oropharyngeal squamous cell carcinoma (OPSCC). This study assessed the degree to which presentation, gene expression, and antibody response (AR) of TAP, mainly CTA, are correlated in OPSCC patients to evaluate their potential as immunotherapy targets.

Materials and methods

Snap-frozen tumor (NLigand/RNA=40), healthy mucosa (NRNA=6), and healthy tonsils (NLigand=5) samples were obtained. RNA-Seq was performed using Illumina HiSeq 2500/NovaSeq 6000 and whole exome sequencing (WES) utilizing NextSeq500. HLA ligands were isolated from tumor tissue using immunoaffinity purification, UHPLC, and analyzed by tandem MS. Antibodies were measured in serum (NAb=27) utilizing the KREX™ CT262 protein array. Data analysis focused on 312 proteins (KREX™ CT262 panel + overexpressed self-proteins).

Results

183 and 94 of HLA class I and II TAP were identified by comparative profiling with healthy tonsils. Genes from 26 TAP were overexpressed in tumors compared to healthy mucosa (LFC>1; FDR<0.05). Low concordance (r=0.25; p<0.0001) was found between upregulated mRNA and class I TAP. The specific mode of correlation of TAP was found to be dependent on clinical parameters. A lack of correlation was observed both between mRNA and class II TAP, as well as between class II tumor-unique TAP (TAP-U) presentation and antibody response (AR) levels.

Discussion

This study demonstrates that focusing exclusively on gene transcript levels fails to capture the full extent of TAP presentation in OPSCC. Furthermore, our findings reveal that although CTA are presented at relatively low levels, a few CTA TAP-U show potential as targets for immunotherapy.

Pericytes Are Immunoregulatory Cells in Glioma Genesis and Progression

Vascular co-option is a consequence of the direct interaction between perivascular cells, known as pericytes (PCs), and glioblastoma multiforme (GBM) cells (GBMcs). This process is essential for inducing changes in the pericytes' anti-tumoral and immunoreactive phenotypes. Starting from the initial stages of carcinogenesis in GBM, PCs conditioned by GBMcs undergo proliferation, acquire a pro-tumoral and immunosuppressive phenotype by expressing and secreting immunosuppressive molecules, and significantly hinder the activation of T cells, thereby facilitating tumor growth. Inhibiting the pericyte (PC) conditioning mechanisms in the GBM tumor microenvironment (TME) results in immunological activation and tumor disappearance. This underscores the pivotal role of PCs as a key cell in the TME, responsible for tumor-induced immunosuppression and enabling GBM cells to evade the immune system. Other cells within the TME, such as tumor-associated macrophages (TAMs) and microglia, have also been identified as contributors to this immunomodulation. In this paper, we will review the role of these three cell types in the immunosuppressive properties of the TME. Our conclusion is that the cellular heterogeneity of immunocompetent cells within the TME may lead to the misinterpretation of cellular lineage identification due to different reactive stages and the identification of PCs as TAMs. Consequently, novel therapies could be developed to disrupt GBM-PC interactions and/or PC conditioning through vascular co-option, thereby exposing GBMcs to the immune system.

A comprehensive guide to study the immunological synapse using imaging flow cytometry

Cytotoxic lymphocytes, such as cytotoxic T cells and natural killer (NK) cells, are instrumental in the recognition and eradication of pathogenic cells, notably those undergoing malignant transformation. Cytotoxic lymphocytes establish direct contact with cancer cells via the formation of a specialized cell-cell junction known as the lytic immunological synapse. This structure serves as a critical platform for lymphocytes to integrate surface signals from potential cancer cells and to direct their cytolytic apparatus toward the confirmed targets. Conversely, cancer cells evolve synaptic defense strategies to evade lymphocyte cytotoxicity. This chapter delineates protocols using imaging flow cytometry to examine and quantify important subcellular processes occurring within cytotoxic lymphocytes and cancer cells engaged into an immunological synapse. These processes encompass the spatial redistribution of cytoskeletal components, vesicles, organelles and cell surface molecules. We specifically describe methods to generate and select conjugates between MDA-MB-231 breast cancer cells or K-562 leukemic cells and either the NK-92MI cell line or primary human NK cells. In addition, we detail procedures to evaluate the synaptic polarization of the actin cytoskeleton, CD63-positive vesicular compartments, MHC class I molecules, as well as the microtubule-organizing center in effector cells.

Extracellular vesicles and microvilli in the immune synapse

T cell receptor (TCR) binding to cognate antigen on the plasma membrane of an antigen-presenting cell (APC) triggers the immune synapse (IS) formation. The IS constitutes a dedicated contact region between different cells that comprises a signaling platform where several cues evoked by TCR and accessory molecules are integrated, ultimately leading to an effective TCR signal transmission that guarantees intercellular message communication. This eventually leads to T lymphocyte activation and the efficient execution of different T lymphocyte effector tasks, including cytotoxicity and subsequent target cell death. Recent evidence demonstrates that the transmission of information between immune cells forming synapses is produced, to a significant extent, by the generation and secretion of distinct extracellular vesicles (EV) from both the effector T lymphocyte and the APC. These EV carry biologically active molecules that transfer cues among immune cells leading to a broad range of biological responses in the recipient cells. Included among these bioactive molecules are regulatory miRNAs, pro-apoptotic molecules implicated in target cell apoptosis, or molecules triggering cell activation. In this study we deal with the different EV classes detected at the IS, placing emphasis on the most recent findings on microvilli/lamellipodium-produced EV. The signals leading to polarized secretion of EV at the synaptic cleft will be discussed, showing that the IS architecture fulfills a fundamental task during this route.