Chromosomal instability (CIN) is associated with immunosuppression in the tumor microenvironment (TME), resulting in cancer progression, metastasis, and resistance to immune checkpoint blockade therapy. We previously established a tumor immune status scoring algorithm (TIMMUSCORA) in which the immune status in the TME is evaluated numerically from activation to suppression. In the present study, we clarified the relationships between structural variation-related parameters and immunological features by applying TIMMUSCORA to solid cancers. Whole genome sequencing (WGS) and gene expression profiling (GEP) data were obtained from 394 cancer patients, and CIN-related parameters, such as the tumor mutation burden (TMB), structural variant (SV), microsatellite instability (MSI) score, ploidy, homologous recombination deficiency score, and chromothripsis (CT) and whole genome duplication (WGD) scores, were assessed. The TIMMUSCORA system demonstrated that most CIN-related parameters contributed to the low TIMMUSCORA score implicating an immunosuppressive state. Comparisons of differentially expressed genes between WGD- or CT-positive and -negative tumors showed the down-regulation of B cell markers, the down-regulation of myeloid cell markers, and the up-regulation of the NKG2D gene. In addition, the following novel observations were verified; (1) TP53 and EGFR mutation events can be associated with WGD and low TIMMUSCORA scores, and (2) NK cell activation and cancer–testis antigen gene up-regulation might be associated with CT. These results suggest that TIMMUSCORA might be useful tool evaluating immune status of CIN-harboring tumors. In future, the specific mechanism for CIN-associated immunosuppression in the tumor can be explored and clarified.
Tumor-infiltrating myeloid cells occupy heterogeneous functional states that are not adequately represented by macrophage abundance or fixed polarization labels. We developed the myeloid damage response index (MDRi), a single-cell-informed framework comprising injury, resolution and antigen-presentation/interferon (APC/IFN) programs, together with a derived injury–resolution axis. MDRi was established in an immune checkpoint blockade-treated multi-cancer atlas containing 47,750 myeloid cells from 192 samples across eight cancer types and assessed separately in an independent multi-cancer myeloid dataset. The programs organized recurrent macrophage and monocyte states along related but non-identical functional dimensions. Non-overlapping antigen-presentation and interferon-response signatures provided gene-independent support for the APC/IFN dimension. Root-sensitivity analyses showed stable state connectivity but root-dependent pseudotime directionality, supporting transcriptional topology rather than a universal developmental sequence. Exploratory response analyses showed concurrent elevation of injury, resolution and APC/IFN scores in post-treatment non-responders, whereas cancer- and regimen-adjusted analyses did not support an independent predictive effect. Complementary T/NK-cell analyses indicated that response-associated immune differences were more evident in pretreatment samples. In primary-tumor TCGA cohorts summarized at the patient level, joint multivariable Cox models containing MDR injury, MDR resolution and MDR APC/IFN identified MDR injury as an adverse factor in selected cancers, whereas resolution and APC/IFN showed cancer- and endpoint-dependent associations. The derived injury–resolution axis was excluded from these joint models because it is mathematically dependent on injury and resolution. Benchmarking against immune-deconvolution and tumor-associated macrophage signatures demonstrated partial but non-uniform overlap. Nasopharyngeal carcinoma Visium and multi-cancer Xenium analyses further revealed platform- and cancer-dependent spatial distributions of MDRi-related programs. MDRi Explorer provides an open-source implementation for scoring, reference comparison and exploratory clinical analysis. MDRi therefore represents a reusable, hypothesis-generating framework for investigating context-dependent myeloid functional organization rather than a universal prognostic signature or clinically validated predictor.
Opoid dependency (OD) is associated with adverse clinical outcomes in hospitalized patients; nevertheless, the understanding of OD and its impact on cancer patients remains restricted. Alongside addressing the symptoms related to disease, hospitalized patients with OD also grapple with mental illness (MI) challenges and the risk of infectious consequences (ICs), which remain unrecognized in cancer patients. We utilized national inpatient database to examine patient and clinical characteristics among renal cell carcinomas (RCC), prostate cancers (PC) and cancers of the lip, oral cavity, and pharynx (CLOP). We used generalized linear models to evaluate the association of OD and outcome of burden of illness (BOI), specifically length of stay (LOS). We also evaluated the association between OD and emergency department (ED) referral/admission status, ICs (specifically septicemias), weight loss, fluid and electrolyte disorders (FED), status of MI screening, and anxiety and depressive disorders. Of the 88,105 RCC there were 610 OD patients; PC (209,410) with 1115 OD; CLOP (54,265) with 495 OD. PC patients with OD were associated with longer LOS (Coefficient, 1.59; 95
Cancer is increasingly recognized as a systemic disease whose biology is shaped by reciprocal interactions with its microenvironment, including the central and peripheral nervous systems. Recent evidence demonstrates that neural inputs can directly promote tumour growth through synaptic, paracrine, and neuroendocrine mechanisms, and that these inputs intersect with canonical drug-resistance pathways, creating new opportunities and challenges for precision oncology. Primary brain tumours such as gliomas form bona fide functional synapses with neurons, hijacking both excitatory (AMPA/NMDA) and inhibitory (GABA_A) inputs to sustain proliferation. Comparable mechanisms are now described in brain metastases and, remarkably, in small cell lung cancer (SCLC), where cortical and vagal neurons establish synaptic contacts with tumour cells. Beyond synaptic communication, paracrine neurotransmitter signalling, tumour innervation, autonomic balance (β-adrenergic versus vagal tone), and systemic stress responses jointly modulate tumour biology, immune surveillance, and therapeutic response. Convergent evidence further indicates that neural and stress-related signalling cooperates with classical resistance circuits—including p53–EGFR–ERK signalling, P-glycoprotein–mediated drug efflux, reactive oxygen species (ROS)–dependent redox programmes, and adipokine–Hsp90 axes—to attenuate the efficacy of chemotherapy, targeted agents, and immune checkpoint inhibitors. Neuron–tumour interactions represent a novel and clinically actionable dimension of cancer pathogenesis that extends well beyond gliomas. Targeting neuron–tumour synapses, neurotransmitter pathways, autonomic inputs, and the resistance circuits with which they intersect offers new therapeutic opportunities, but translation requires careful attention to specificity, neurological safety, and rational combination with cytotoxic, targeted, and immune therapies. Cancer is not driven solely by genetic mutations; it is also shaped by signals from the nervous system. This review synthesizes how nerves and brain activity directly influence tumour growth across multiple diseases—including gliomas, small cell lung cancer, breast cancer, pancreatic cancer, and prostate cancer—and how these neural signals converge with metabolic and drug-resistance pathways that limit the efficacy of conventional therapy. Recent discoveries show that some cancers form direct synapse-like connections with neurons and exploit neurotransmitters to fuel tumour progression and treatment escape. Understanding these interactions opens new therapeutic opportunities—such as targeting neural signalling, autonomic pathways, or neuro-modulated resistance mechanisms—and positions the nervous system as a previously underappreciated but clinically relevant driver of cancer behaviour.
Synthetic cobalt Schiff bases have recently emerged as promising metal-based anticancer candidates. In this study, we investigated the biological effects of a mononuclear octahedral cobalt(III) Schiff base complex [CoL3] (L = 2-((allylimino) methyl) − 6-methoxyphenol)) on the cell cycle progression and apoptosis of the HT-29 cells, a human colorectal cancer cell line. Cytotoxic activity of [CoL3] was evaluated using the MTT assay. Then, its impact on apoptosis was assessed via annexin V-FITC/propidium iodide (PI) staining. To elucidate the underlying mechanisms, we employed flow cytometry, real-time PCR, and Western blotting to analyze cell cycle distribution and the expression of apoptotic and cell cycle-related genes. Our results revealed that [CoL3] exhibited potent cytotoxicity with an IC50 of 3.47 µM and induced cell cycle arrest in the G1/S and G2/M transition phases in colorectal cancer cells (p < 0.001, p < 0.01). Treatment of colorectal cancer cells with [CoL3] resulted in a significant decrease in CDK4 and CDK6 expression, with mean values of 0.62 (p < 0.05) and 0.33 (p < 0.01), respectively. Additionally, the protein expression of CDK4 and CDK6 was downregulated, with mean protein intensities of 0.48 and 0.79, respectively (p < 0.001), supporting its role in G1 phase blockade. Moreover, [CoL3] downregulated BCL2 (p < 0.01), which was associated with increased early and late apoptosis in treated cells. Docking analyses further demonstrated favorable spontaneous binding of [CoL3] to CDK4 and CDK6, reinforcing its mechanistic involvement in cell cycle inhibition. Collectively, these findings indicate that [CoL3] induces cell-cycle arrest and promotes apoptosis in HT-29 colorectal cancer cells, potentially through the downregulation of CDK4/6 and BCL2.
Combination immunotherapy has shown encouraging activity across multiple solid tumors. We report the complete and consecutive cohort of patients with locally advanced oral squamous cell carcinoma (OSCC) treated at a single center within the prospective, multicenter, randomized phase 2 BelieveIT-201 trial (ASND0038), evaluating neoadjuvant intratumoral Toll-like receptor (TLR) 7/8 agonist (TransCon TLR7/8 Agonist) therapy combined with systemic immunotherapy. Patients with non-metastatic OSCC treated within the BelieveIT-201 trial (ASND0038) between April and December 2024 were included. Neoadjuvant therapy comprised two cycles of intratumoral TransCon TLR7/8 Agonist combined with either intravenous pembrolizumab or TransCon IL-2 β/γ according to 1:1 randomization, followed by surgical resection. The trial was terminated prematurely by the sponsor for reasons unrelated to safety or efficacy, which limited the cohort to six patients. Clinical, radiographic, pathological responses, and safety were assessed. Immunohistochemical analyses of paired pre- and post-treatment tumor samples evaluated immune cell infiltration (CD3, CD8, CD68, CD163). The individual patient was the unit of analysis, and given the small number of patients all analyses are descriptive; no inferential statistical testing was performed. Progression-free survival (PFS) and overall survival (OS) are reported as absolute event counts. Six patients were treated (median age 63 years; median follow-up 81 weeks). Three patients achieved a major clinical response, two showed partial response, and one had progressive disease. Pathologic evaluation revealed one complete response, one major response, and four non-responses. All patients underwent surgery; postoperative morbidity was substantial, with at least one grade III adverse event in every patient and one postoperative death. All three patients with a major clinical response developed sterile tumor-associated pseudoabscesses in spatial proximity to the injection site. Immunohistochemical analyses revealed remodeling of the tumor immune microenvironment, including increased T-cell infiltration, most pronounced in the tumor center. Within the first year, two of six patients experienced a progression-free survival event (n = 1 progressive disease, n = 1 death). After surgery none of the patients showed disease recurrence. Neoadjuvant intratumoral TransCon TLR7/8 Agonist-based combination immunotherapy was feasible in this small prospective cohort of patients with locally advanced OSCC and was accompanied by consistent remodeling of the tumor immune microenvironment. Because of the limited number of patients and the premature termination of the parent trial, no conclusions on efficacy or on comparative tolerability can be drawn.
T cell receptor (TCR)-like antibodies recognize intracellular antigenic peptides presented by major histocompatibility complex (MHC) class I molecules. HLA-A*02:01 (HLA-A2) is the most frequent MHC class I allele worldwide, and most TCR-like antibodies have been designed to target peptides presented by HLA-A2. However, their therapeutic applicability may be limited by allele-restricted peptide presentation and the extensive polymorphism of MHC class I molecules. In this study, we developed a TCR-like antibody specific for the preferentially expressed antigen in melanoma (PRAME) peptide presented by HLA-A*24:02 (HLA-A24), the second most frequent MHC class I allele worldwide and the most common in East Asian populations. PRAME is a cancer-testis antigen expressed in various cancers but absent from normal adult tissues except the testes, making it an attractive target for TCR-like antibodies. An anti-PRAME301–309/HLA-A24 TCR-like scFv 2F7 was identified by phage display and reformatted into a bispecific T-cell–engaging antibody. In vitro studies using human peripheral blood mononuclear cells (PBMCs) and cancer cell lines demonstrated that the 2F7 bispecific TCR-like antibody (bsTLA) specifically bound to the PRAME301–309/HLA-A24 complex and redirected PBMC-derived T cells to kill target cells presenting this peptide-HLA complex.
Patients with advanced solid tumors who progress after standard therapies have limited treatment options. SDH-Combi is an autologous cellular immunotherapy integrating natural killer cells and tumor-primed T lymphocytes, designed to address tumor heterogeneity and immune escape through complementary immune mechanisms. This single-arm, phase 1 study evaluated SDH-Combi in patients with recurrent or progressive solid tumors. SDH-Combi was administered every 2 weeks for up to eight infusions. The primary endpoint was safety and tolerability in all treated patients (N = 9): Safety was assessed as treatment-emergent adverse events graded by CTCAE v5.0 with investigator-assigned causality, and tolerability as the proportion of patients completing all eight planned infusions, the relative dose intensity, and discontinuation due to toxicity. Secondary endpoints were objective response rate, disease control rate, progression-free survival, and overall survival, with tumor response evaluated according to RECIST v1.1. Quality of life (QoL), assessed with the EORTC QLQ-C30, was an exploratory endpoint. Nine patients received at least one infusion. For the primary endpoint, no grade ≥ 3 treatment-related adverse event occurred (0 of 9; 95
CD19-directed chimeric antigen receptor T cell (CAR-T) therapy is effective in relapsed or refractory B cell malignancies, but responses remain heterogeneous. Carbapenem-resistant Klebsiella pneumoniae (CRKP) colonization is common in heavily treated hematology patients. 1,5-Pentanediamine (PDA; cadaverine), a microbiota-associated metabolite produced by several Enterobacteriaceae, was detected in serum from CRKP-colonized patients. Its effects on CAR-T cells are unknown. Serum PDA was quantified by liquid chromatography–tandem mass spectrometry in 30 CRKP-colonized patients without documented bloodstream infection at sampling. Healthy-donor-derived CD19 CAR-T cells were exposed to PDA in vitro (0–12 mM; 9 mM for most functional assays). Metabolic activity, apoptosis, phenotype, target-cell killing, degranulation, cytokine secretion, and cytotoxic-molecule production were assessed. RNA sequencing, RT-qPCR, and PD-1 blockade were performed. PDA was detectable in all 30 patients. Without a non-colonized comparator cohort, these data demonstrate detectability but not CRKP-specific source attribution. At millimolar concentrations, PDA reduced CAR-T cell metabolic activity, increased apoptosis, upregulated activation and checkpoint-associated inhibitory markers, altered the CD4/CD8 distribution, and increased the regulatory T cell frequency. PDA-treated CAR-T cells showed reduced NALM-6 killing and lower cytokine, perforin, and granzyme B output despite preserved CD107a degranulation. Transcriptomic analysis showed enrichment of cell cycle, apoptosis, and stress-related pathways, suppression of immune pathways, and exhaustion-associated transcriptional features. PD-1 blockade alone did not restore function under the tested conditions. Acute millimolar PDA exposure produced a dysfunctional CAR-T cell state with impaired survival and effector output but preserved degranulation. Its physiological relevance requires validation in chronic low-dose models, controlled clinical cohorts, patient-derived CAR-T cells, and additional target-cell systems.
Clinical responses to immune checkpoint inhibitors (ICIs) in non-small cell lung cancer (NSCLC) remain highly heterogeneous and PD-L1 expression alone has limited predictive performance. Emerging evidence suggests that therapeutic response depends not only on immune cell abundance but also on their spatial organization within the tumor microenvironment (TME). Here, we characterized the spatial architecture of the pre-treatment NSCLC TME and evaluated its association with response to ICIs in a real-world clinical cohort. Seventeen pre-treatment specimens (10 responders and 7 non-responders) were analyzed using 13-marker tissue-based cyclic immunofluorescence (t-CyCIF) panel with single-cell phenotyping. Cell density was assessed across all samples. Spatial analyses were performed on resection specimens with preserved architecture (4 responders and 3 non-responders). Spatial analyses included assessment of lymphoid organization, cellular neighborhoods, pairwise spatial relationships and higher-order tissue architecture. Global immune and tumor cell densities did not differ between groups. TLS-related metrics showed a trend toward higher values in responders, suggesting greater immune organization within the TME. Cellular neighborhood analysis further demonstrated enrichment of cytotoxic T cell- and vasculature-associated regions in responders, whereas non-responders displayed a predominantly tumor-centered spatial architecture. Responders also exhibited shorter vessel to cytotoxic T cell distances and greater perivascular enrichment of cytotoxic and PD-1⁺ cytotoxic T cells. Higher-order spatial analysis highlighted preferential organization of PD-1⁺ cytotoxic T cells within vascular-associated niches in responder tumors. These findings demonstrate that spatial organization of immune and vascular compartments provides information beyond cellular abundance alone and may serve as a complementary biomarker framework for predicting immunotherapy response in NSCLC.
Elevated expression of tumor necrosis factor α-induced protein 8 (TIPE) is observed in colorectal cancer (CRC) and is known to regulate decoy receptor 3 (DcR3) expression while promoting M2 polarization of macrophages. However, the precise role of DcR3 in macrophage M2 polarization remains to be elucidated. We employed bioinformatic analysis alongside in vitro and in vivo experimental approaches to investigate the regulatory mechanism by which TIPE influences macrophage M2 polarization in CRC. TIPE expression in CRC tissues positively correlates with M2 macrophage markers (CD206, CD163, IL-10). Functionally, TIPE promotes M2 polarization of macrophages by upregulating DcR3. Mechanistically, DcR3 binds to heparan sulfate proteoglycan 2 (HSPG2) in a heparan sulfate (HS)-dependent manner, leading to activation of the protein kinase Bα1 (AKT1) signaling pathway. AKT1 activation not only directly drives M2 polarization but also enhances macrophage chemotaxis and recruitment toward CRC cells by upregulating the chemokine CXCL8. This study reveals a novel mechanism through which TIPE regulates M2 macrophage polarization and function via DcR3, offering new perspectives for the diagnosis and therapeutic targeting of CRC.
Glioblastoma (GBM) is largely refractory to immune checkpoint blockade (ICB), which may be attributable in part to its immunosuppressive microenvironment and systemic T-cell dysfunction. Drug repurposing provides an efficient strategy for identifying potential immunomodulatory agents. The antibiotic clofoctol (Clo) has shown antitumor activity; however, its effects on the immune landscape of GBM remain poorly understood. In this study, we evaluated the therapeutic efficacy and potential immunomodulatory mechanisms of Clo using an orthotopic GL261 GBM model. Flow cytometric analysis showed that Clo treatment increased the intratumoral representation of CD8+ T cells and enhanced the expression of cytotoxic effector molecules, consistent with a more immunologically active tumor microenvironment. Analysis of bone marrow cell composition further suggested that Clo partially alleviated tumor-associated T-cell accumulation in the bone marrow and promoted their systemic redistribution. Notably, depletion of CD8+ T cells markedly attenuated the antitumor efficacy of Clo, indicating that CD8+ T cells contribute substantially to its therapeutic effects. In vitro co-culture experiments further showed that Clo pretreatment enhanced the cytotoxic activity of CD8+ T cells, accompanied by increased expression of granzyme B (GZMB), perforin (PRF1), and IFN-γ. Mechanistically, ITSA-MS identified BCL9 as a candidate Clo-responsive protein, while subsequent western blot analyses showed that Clo treatment was associated with increased phosphorylation of VAV1, AKT, and ERK. These findings suggest the potential involvement of BCL9-associated signaling in Clo-mediated T-cell activation, although the precise regulatory relationship requires further investigation. Moreover, combined treatment with Clo and anti-PD-1 antibody increased intratumoral CD8+ T cell abundance and effector activity, achieved greater tumor control, and prolonged survival compared with either treatment alone. Collectively, these findings suggest that Clo may exert complementary immunomodulatory effects by facilitating the systemic redistribution of CD8+ T cells and enhancing their cytotoxic function, supporting its further investigation as a potential combination strategy for improving the response of GBM to ICB.
Tertiary lymphoid structures (TLS) are pivotal modulators of anti-tumor immunity in solid tumors; however, their clinical significance in glioblastoma (GBM) remains under-characterized. This study aimed to evaluate the correlation between TLS spatial-quantitative characteristics and survival outcomes in GBM patients to refine prognostic stratification and immunotherapy optimization. A retrospective analysis was conducted on 62 patients with isocitrate dehydrogenase (IDH)-wildtype GBM treated at our institution (2016 – 2023). TLSs were identified via H E and CD3 / CD20 immunohistochemical (IHC) staining. A grading system was established based on the quantity and spatial distribution (intratumoral vs. peritumoral) of TLS. Survival outcomes were assessed using Kaplan–Meier curves and multivariate Cox regression models to identify independent prognostic factors. TLSs were present in 58.1
Glioblastoma remains one of the most lethal primary malignant brain tumors, and immunotherapy has produced limited clinical benefit despite major success in other cancers. This resistance reflects spatial and molecular heterogeneity, myeloid-dominant immune suppression, restricted lymphocyte infiltration, antigenic instability, blood–brain barrier-related constraints, corticosteroid exposure, and treatment-induced immune remodeling. Conventional preclinical models only partially reproduce these features, limiting their ability to predict patient-specific immunotherapy responses. Patient-derived glioblastoma organoids (GBOs) have emerged as experimentally tractable platforms that can preserve key features of parental tumors while enabling functional therapeutic testing. In this review, we discuss the rationale, technical evolution, applications, and translational challenges of GBOs in immuno-oncology, including tumor-immune modeling, checkpoint blockade, cellular therapies, myeloid modulation, vaccines, oncolytic virotherapy, multi-omic readouts, and artificial intelligence-assisted analysis. We place particular emphasis on oncolytic herpes simplex virus-based strategies and on the ability of GBOs to evaluate viral entry, replication, spatial spread, innate antiviral restriction, immunogenic cell death, and rational combinations. Finally, we outline staged, clinically integrated workflows while emphasizing immune-cell attrition, incomplete microenvironmental fidelity, resource requirements, and the need for prospective validation in small exploratory trials.
Background Whole-exome sequencing is a widely used technology to identify pathogenic variants in cancer. Although sequencing itself has become increasingly accessible, downstream analysis remains computationally complex, presenting a challenge for many researchers. Existing pipelines lack integrated support for somatic and germline variant detection and still require significant computational resources. Methods We developed GATES (GATK Automated Tool for Exome Sequencing), a lightweight pipeline that automates data preprocessing, variant calling, and variant annotation directly from raw paired-end FASTQ files through a simplified command-line interface. GATES implements the GATK Best Practices for somatic and germline variant detection and leverages Ensembl’s Variant Effect Predictor for functional annotation, outputting the results in a human-readable tab-separated values (TSV) file. We evaluated the pipeline’s performance using the SEQC-II benchmarking dataset and demonstrated its application using a clinical sample harboring known pathogenic germline and somatic variants. Results GATES was run on a standard laptop and performed end-to-end variant analysis for each sample within a few hours. In benchmarking with SEQC-II samples, germline and tumor-normal somatic variant calling modes demonstrated high concordance with their respective truth sets. Tumor-only somatic mode showed decreased accuracy, consistent with expected germline contamination. GATES demonstrated high performance across various hardware configurations and compared to the established nf-core/sarek pipeline. GATES further successfully performed somatic and germline analysis of a >100X clinical sample in under 7 hours. Importantly, the pipeline accurately distinguished the known KRAS p.G12V and KEAP1 p.S338L as somatic and germline, respectively. Conclusion By lowering the technical barriers to exome sequencing analysis, GATES provides a practical solution for pathogenic variant discovery for researchers both with and without computational expertise.
Glioblastoma multiforme (GBM) is a highly aggressive brain tumor characterized by pervasive tumor recurrence and very poor patient survival. While αβ T cell-based chimeric antigen receptor (CAR) immunotherapies show efficacy in hematologic malignancies, manufacturing delays and potential fatal immune overactivation have prompted the exploration of alternative cell sources, including natural killer (NK) cells. NK cells represent an emerging cell source due to their potent antigen-independent intrinsic cytotoxicity, self-regulating inhibitory mechanisms, and low risk of graft-versus-host disease. In this study, we expanded peripheral blood NK cells using K562 feeder cells expressing membrane-bound IL-21 (K562-mb-IL-21) to produce highly activated and metabolically robust cells targeting both cell lines and patient-derived GBM tumor cells. Furthermore, our in vitro results demonstrate the broad targeting potential of our expanded NK cells, as they exhibit cytotoxicity against a cell line and patient-derived sample of another aggressive brain tumor, medulloblastoma (MB). To enhance tumor-directed cytotoxicity, we utilized CRISPR/Cas9 and adeno-associated virus-based gene delivery to generate stable anti-CD70 CAR-NK cells. CD70 is a promising target due to its minimal expression in healthy tissues and overexpression in recurrent GBM. However, NK cells gain CD70 surface expression upon expansion, causing anti-CD70 CAR-NK cell fratricide. Subsequently, knocking out the CD70 gene enabled large-scale expansion of anti-CD70 CAR-NK cells that were functional against both in vitro and in vivo GBM models.
In lung adenocarcinoma (LUAD), DNA methylation-mediated gene silencing may contribute to tumor initiation, progression, and heterogeneity in treatment response. However, the key methyltransferases involved and their therapeutic potential have not been systematically characterized. This study aimed to address three major questions: which methylation-associated gene silencing events occur in LUAD, which upstream methyltransferase predominantly drives these events, and whether targeted inhibition of this enzyme can mitigate drug-resistant phenotypes and enhance chemosensitivity. Differential expression analysis was initially performed using the GSE75037 dataset to screen candidate genes. Expression quantitative trait locus (eQTL) and protein quantitative trait locus (pQTL) data were then integrated, and key candidate genes were prioritized according to the concordance in the directions of genetic effects. Subsequently, mediation Mendelian randomization analysis was conducted to determine whether the effect of locus-specific methylation on LUAD was mediated by QDPR expression, thereby providing genetic causal evidence that methylation contributes to transcriptional repression. In addition, the associations between DNA methylation-related enzymes and QDPR expression were analyzed in the GSE33532, GSE43458, and GSE75037 datasets, followed by cross-dataset validation to identify potential key upstream regulators. Finally, cell-based experiments were performed to verify the functional effects of DNMT1 inhibition. Changes in QDPR expression were assessed by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting, and the potential chemosensitizing effect of DNMT1 inhibition in combination with platinum-based chemotherapy was further evaluated in patient-derived organoids. This study provided genetic causal evidence that locus-specific methylation influences LUAD risk, with part of this effect mediated by QDPR expression. Analyses across multiple independent datasets consistently suggested that DNMT1 may act as a key upstream epigenetic regulator contributing to the reduced expression of QDPR. Functional experiments demonstrated that DNMT1 inhibition increased QDPR expression and suppressed the proliferation and migration of LUAD cells. Drug sensitivity assays using patient-derived organoids further showed that DNMT1 inhibition exerted a significant chemosensitizing effect in the platinum low-sensitivity group. This study suggests that DNMT1 may contribute to the reduced expression of QDPR and related malignant phenotypes through epigenetic regulation. Functional and drug sensitivity experiments further support the potential of DNMT1 as a therapeutic target for improving the response to platinum-based chemotherapy in a subset of patients with LUAD. These findings provide a potential therapeutic target and offer mechanistic insights into treatment response heterogeneity and chemoresistance in LUAD.
Prostate cancer is a worldwide leading malignancy, and the exploration of initiation mechanisms and therapeutic targets remains an important challenge. In this study, transcriptomic and clinical data from wide-used prostate cancer cohorts were integrated to establish a novel prognostic model and explore the biological significance of its core genes. Differential expression analysis combined with LASSO-Cox regression identified a three-gene prognostic model consisting of MECR, HVCN1, and NGFR. This model could independently predict patient outcomes and demonstrated superior predictive performance compared with conventional clinicopathological variables. Among these genes, MECR was the only one associated with poor prognosis. Functional studies revealed that MECR could promote proliferation, migration, and reduce apoptosis-related nuclear morphological changes in prostate cancer cell. Mechanistically, MECR could regulate PI3K/AKT pathway activity and immune-related cell mechanisms. In immunocompetent syngeneic tumor models, MECR knockdown significantly inhibited tumor progression and was associated with increased CD8+ T-cell activation. We found that CD8+ T-cell depletion could partially rescue the antitumor effects of MECR silencing, indicating that CD8+ T-cell-mediated immunity contributes to the antitumor effects of MECR silencing. Collectively, our findings identify MECR as a potential regulator linking tumor progression, apoptosis-related cellular phenotype, and immune microenvironment remodeling in prostate cancer. By integrating tumor-intrinsic and immune-associated mechanisms, our results provide new insights into molecular pathways in prostate cancer development and immune evasion related therapeutic resistance.
Tertiary lymphoid structures (TLS) support local antitumor immunity and are associated with favorable clinical outcomes in most cancers; however, many questions remain about how signaling and cell state changes are coordinated spatially within these structures. Using spatial transcriptomics data from TLS-containing tumors, we computationally inferred 71 cell states with EcoTyper across all major immune lineages and profiled their spatial organization with respect to the TLS-centric abundance gradient and weighted chemokine networks (CXCL13, CXCL12, and CCL19/21). Both of these strategies indicate that specific aspects of core-periphery organization only become apparent at the cell state level of resolution. Cell states of the same lineages were observed to diverge in their relationship to TLS, with some encompassing both TLS-enriched and depleted states. Of particular note, two inferred TLS-enriched CD4 T cell states had distinct marker gene programs, and CD4.T_S02 was more abundant toward the geometric TLS core. Likewise, chemokine network analysis further supported these findings and indicated two recurrent cell state communities: a lymphocyte activation one confined to TLS, and an effector-focused one that extended into the surrounding tissue, with a neutrophil cell state of tentative identity recurring as a hub across all three axes. Taken together, these results indicate that TLS are spatially zoned structures, with an active core and more diffuse effector periphery that are organized through a shared key set of chemokine signaling pathways.
Objective Oral squamous cell carcinoma (OSCC) is characterized by high recurrence rates and an unclear underlying molecular basis, highlighting the need for improved early diagnostic strategies to enhance treatment outcomes and reduce healthcare burden. Given the regulatory role of microRNAs (miRNAs) in oral cancer progression through post-transcriptional control of target genes, this study aimed to investigate the diagnostic potential of miR-4303 and miR-4291 in OSCC. Methods Using TargetScan, MAPK1 was predicted as a common target of both miR-4303 and miR-4291. Expression levels of miR-4303, miR-4291, and MAPK1 were quantified by qRT-PCR in 30 paired OSCC and adjacent normal tissue samples. Diagnostic performance was evaluated using receiver operating characteristic (ROC) curve analysis. Results MAPK1 and both miRNAs (miR-4303 and miR-4291) were significantly upregulated in OSCC tissues compared to adjacent normal tissues (P < 0.0001). MAPK1 expression showed a significant association with higher tumor grade (P = 0.003) and advanced clinical stage (P = 0.005). ROC curve analysis demonstrated strong diagnostic performance, with AUC values of 0.92 for MAPK1, 0.731 for miR-4303 (P = 0.0001), and 0.707 for miR-4291 (P < 0.0001), indicating their potential utility in distinguishing OSCC from normal tissue. Conclusion These findings suggest that miR-4303 and miR-4291, together with MAPK1, may serve as promising diagnostic biomarkers in OSCC. However, further validation in larger, independent cohorts and functional studies is required to confirm their clinical applicability.
