The Tumor Microenvironment Innately Modulates Cancer Progression

Prognostic significance of neutrophil extracellular trap-related genes in childhood acute lymphoblastic leukemia: insights from multi-omics and in vitro experiment

BACKGROUND

This study aimed to develop a prognostic model based on extracellular trap-related genes (NETRGs) for patients with cALL.

METHODS

Data from the TARGET-ALL-P2 and TARGET-ALL-P3 cohorts in the Genomic Data Commons database, the transcriptome dataset GSE26713, the single-cell transcriptome dataset GSE130116 from the Gene Expression Omnibus database and 306 NETRGs identified were analysed. Differentially expressed genes (DEGs) were identified from GSE26713 and differentially expressed NETRGs (DE-NETRGs) were obtained by overlapping DEGs with NETRGs. Functional analyses were conducted. Key feature genes were identified through univariate and least absolute shrinkage and selection operator (LASSO) regression. Prognostic genes were determined via multivariate Cox regression analysis, followed by the construction and validation of a risk model and nomogram. Additional analyses included immune profiling, drug sensitivity, functional differences, cell-type-specific expression, enrichment analysis and RT-qPCR.

RESULTS

A total of 1,270 DEGs were identified in GSE26713, of which 74 overlapped with NETRGs. Seven prognostic genes were identified using univariate, LASSO and multivariate Cox regression analyses. Survival analysis revealed lower survival rates in the high-risk group. Independent prognostic analysis identified risk scores and primary diagnosis as independent predictors of prognosis. Immune cell profiling showed significant differences in cell populations such as aDCs, eosinophils and Th2 cells between risk groups. Six cell subtypes were annotated, with prognostic genes predominantly expressed in myeloid cells. RT-qPCR revealed that PTAFR, FCGR2A, RETN and CAT were significantly downregulated, while TLR2 and S100A12 were upregulated in cALL.

CONCLUSION

TLR2, PTAFR, FCGR2A, RETN, S100A12 and CAT may serve as potential therapeutic targets.

LPAR3 and COL8A1, as matrix stiffness-related biomarkers, promote nasopharyngeal carcinoma metastasis by triggering EMT and angiogenesis

Matrix stiffness affects the progression of nasopharyngeal carcinoma, but the underlying mechanism is still unknown. Here, we demonstrated that nasopharyngeal carcinoma tissues with distant metastasis contain large collagen deposits and strong matrix stiffness. First, we performed RNA-seq analysis of nasopharyngeal carcinoma cells cultured on polyacrylamide hydrogel systems and found that LPAR3 and COL8A1 are potential matrix stiffness markers. Based on in vivo and in vitro experiments, matrix stiffness mainly affected tumor metastasis rather than proliferation. Subsequently, we found that matrix stiffness triggers the formation of epithelial-mesenchymal transition by increasing the expression of LPAR3 in nasopharyngeal carcinoma, which is related to metastasis. In addition, matrix stiffness promotes the expression of COL8A1 secreted by nasopharyngeal carcinoma and is related to tumor angiogenesis. Simultaneous inhibition of LPAR3 and COL8A1 genes significantly reduced nasopharyngeal carcinoma invasion and metastasis. Based on the investigation, we confirmed that matrix stiffness governs the progression of nasopharyngeal carcinoma and that LPAR3 and COL8A1, as matrix stiffness related biomarkers, promote nasopharyngeal carcinoma metastasis by inducing epithelial-mesenchymal transition and angiogenesis. Overall, the in-depth exploration of matrix stiffness may provide a strategy for clinical treatment intervention and provide promising targets for clinical nasopharyngeal carcinoma treatment.

Genetic variants of FER and SULF1 in the fibroblast-related genes are associated with non-small-cell lung cancer survival

Fibroblasts are important components in the tumor microenvironment and can affect tumor progression and metastasis. However, the roles of genetic variants of the fibroblast-related genes (FRGs) in the prognosis of non-small-cell lung cancer (NSCLC) patients have not been reported. Therefore, we investigated the associations between 26,544 single nucleotide polymorphisms (SNPs) in 291 FRGs and survival of NSCLC patients from the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial. In Cox regression multivariable analysis, we found that 661 SNPs were associated with NSCLC overall survival (OS). Then we validated these SNPs in another independent replication dataset of 984 patients from the Harvard Lung Cancer Susceptibility (HLCS) Study. Finally, we identified two independent SNPs (i.e., FER rs7716388 A>G and SULF1 rs11785839 G>C) that remained significantly associated with NSCLC survival with hazards ratios (HRs) of 0.87 (95% confidence interval [CI] = 0.77-0.98, p = 0.018) and 0.88 (95% CI = 0.79-0.99, p = 0.033), respectively. Combined analysis for these two SNPs showed that the number of protective alleles was associated with better OS and disease-specific survival. Expression quantitative trait loci analysis indicated that the FER rs7716388 G allele was associated with the up-regulation of FER mRNA expression levels in lung tissue. Our results indicated that these two functional SNPs in the FRGs may be prognostic biomarkers for the prognosis of NSCLC patients, and the possible mechanism may be through modulating the expression of their corresponding genes.

Metabolic crosstalk between platelets and cancer: Mechanisms, functions, and therapeutic potential

Platelets, traditionally regarded as passive mediators of hemostasis, are now recognized as pivotal regulators in the tumor microenvironment, establishing metabolic feedback loops with tumor and immune cells. Tumor-derived signals trigger platelet activation, which induces rapid metabolic reprogramming, particularly glycolysis, to support activation-dependent functions such as granule secretion, morphological changes, and aggregation. Beyond self-regulation, platelets influence the metabolic processes of adjacent cells. Through direct mitochondrial transfer, platelets reprogram tumor and immune cells, promoting oxidative phosphorylation. Additionally, platelet-derived cytokines, granules, and extracellular vesicles drive metabolic alterations in immune cells, fostering suppressive phenotypes that facilitate tumor progression. This review examines three critical aspects: (1) the distinctive metabolic features of platelets, particularly under tumor-induced activation; (2) the metabolic crosstalk between activated platelets and other cellular components; and (3) the therapeutic potential of targeting platelet metabolism to disrupt tumor-promoting networks. By elucidating platelet metabolism, this review highlights its essential role in tumor biology and its therapeutic implications.

Single-cell RNA sequencing highlights the role of proinflammatory fibroblasts, vascular endothelial cells, and immune cells in the keloid immune microenvironment

BACKGROUND

Keloids, characterized by an aberrant wound-healing process and a highly complex immune microenvironment, pose significant challenges for clinical management. Fibroblasts and vascular endothelial cells (VEC) were identified as the leading cells of keloid development. However, their roles in the keloid immune landscape have yet to be thoroughly elucidated.

METHODS

To explore the functional state of cells in the immune landscape of keloids, we conducted a single-cell RNA sequencing analysis on the tissue from three keloid lesions and two specimens of healthy skin. We simultaneously utilized available keloid data from the public database for external validation.

RESULTS

Specific subsets, such as proinflammatory fibroblasts (piF) and VEC, were markedly elevated in lesional skin compared to normal skin. Subsequent differential gene expression and Gene Ontology analyses indicated that these subsets may be involved in shaping the microenvironment. In keloids, there is an increased expression of immune-associated genes (P < 0.05), including TNFRSF6B, HGF, and TGFB3, alongside a decreased expression of inflammatory chemokines in the piF. Moreover, the significant upregulation of immune suppressive genes (P < 0.05), including CD39, CD73, and HIF1A, suggested the potential involvement of VEC as a conditional immune subpopulation in the keloid microenvironment. Immune cell communication analysis revealed preferential enrichment of macrophages and Tregs, highlighting intensified macrophage-centered interactions within the keloid microenvironment.

CONCLUSION

Our study highlighted the role of piF and VEC in the immune microenvironment of keloids for the first time, providing potential targets for therapeutic development.

Comprehensive characterization of T cell subtypes in lung adenocarcinoma: Prognostic, predictive, and therapeutic implications

BACKGROUND

T cells are crucial for immunosurveillance and tumor eradication, with their dysregulation or absence in the tumor microenvironment linked to immunotherapy resistance. In lung adenocarcinoma (LUAD), this resistance is a significant barrier to effective treatment, highlighting the need for robust biomarkers and therapeutic targets to improve clinical outcomes.

METHODS

T cell-related markers were identified through single-cell RNA sequencing analysis. The TCGA dataset was used for consensus clustering to define molecular subtypes associated with distinct survival outcomes and immune profiles. A T cell-related prognostic signature was developed by integrating LUAD datasets from TCGA, GSE31210, GSE50081, and GSE68465 using 10 machine learning algorithms. Further analysis linked risk scores to immune infiltration and drug sensitivity. The role of a hub gene in CD4+ T cell function and its involvement in tumor immunity was explored through in vitro experiments and molecular biology techniques.

RESULTS

Cluster analysis identified three LUAD subtypes, with cluster1 showing the best prognosis and immune characteristics. A Lasso + PLSRcox-based signature was a significant risk factor for predicting LUAD patient outcomes, outperforming traditional clinicopathological factors. The risk score correlated with immune microenvironment features, immune cell infiltration, and sensitivity to immunotherapy and chemotherapy. CPA3 expression was elevated in activated CD4+ T cells, particularly in Th1 cells, promoting differentiation and IFN-γ secretion. Overexpression of CPA3 enhanced tumor cell apoptosis and increased Granzyme B and IFN-γ levels, highlighting its role in immune responses.

CONCLUSION

We developed a powerful prognostic signature in LUAD that accurately predicts clinical outcomes and can guide immunotherapy and chemotherapy responses.

Nociceptor neurons promote PDAC progression and cancer pain by interaction with cancer-associated fibroblasts and suppression of natural killer cells

The emerging field of cancer neuroscience has demonstrated great progress in revealing the crucial role of the nervous system in cancer initiation and progression. Pancreatic ductal adenocarcinoma (PDAC) is characterized by perineural invasion and modulated by autonomic (sympathetic and parasympathetic) and sensory innervations. Here, we further demonstrated that within the tumor microenvironment of PDAC, nociceptor neurons interacted with cancer-associated fibroblasts (CAFs) through calcitonin gene-related peptide (CGRP) and nerve growth factor (NGF). This interaction led to the inhibition of interleukin-15 expression in CAFs, suppressing the infiltration and cytotoxic function of natural killer (NK) cells and thereby promoting PDAC progression and cancer pain. In PDAC patients, nociceptive innervation of tumor tissue is negatively correlated with the infiltration of NK cells while positively correlated with pain intensity. This association serves as an independent prognostic factor for both overall survival and relapse-free survival for PDAC patients. Our findings highlight the crucial regulation of NK cells by nociceptor neurons through interaction with CAFs in the development of PDAC. We also propose that targeting nociceptor neurons or CGRP signaling may offer a promising therapy for PDAC and cancer pain.

Emerging Trends in Neuroblastoma Diagnosis, Therapeutics, and Research

This review explores the current understanding and recent advancements in neuroblastoma, one of the most common extracranial solid pediatric cancers, accounting for ~ 15% of childhood cancer-related mortality. The hallmarks of NBL, including angiogenesis, metastasis, apoptosis resistance, cell cycle dysregulation, drug resistance, and responses to hypoxia and ROS, underscore its complex biology. The tumor microenvironment's significance in disease progression is acknowledged in this study, along with the pivotal role of cancer stem cells in sustaining tumor growth and heterogeneity. A number of molecular signatures are being studied in order to better understand the disease, with many of them serving as targets for the development of new therapeutics. This includes inhibitor therapies for NBL patients, which notably concentrate on ALK signaling, MDM2, PI3K/Akt/mTOR, Wnt, and RAS-MAPK pathways, along with regulators of epigenetic mechanisms. Additionally, this study offers an extensive understanding of the molecular therapies used, such as monoclonal antibodies and CAR-T therapy, focused on both preclinical and clinical studies. Radiation therapy's evolving role and the promise of stem cell transplantation-mediated interventions underscore the dynamic landscape of NBL treatment. This study has also emphasized the recent progress in the field of diagnosis, encompassing the adoption of artificial intelligence and liquid biopsy as a non-intrusive approach for early detection and ongoing monitoring of NBL. Furthermore, the integration of innovative treatment approaches such as CRISPR-Cas9, and cancer stem cell therapy has also been emphasized in this review.

Pan-cancer analysis and validation show GTF2E2's diagnostic, prognostic, and immunological roles in regulating ferroptosis in endometrial cancer

BACKGROUND

Transcription initiation factor IIE subunit beta (GTF2E2) is a crucial component of the RNA polymerase II transcription initiation complex. There is a lack of more detailed research on the biological function of GTF2E2 in pan-cancer.

METHODS

We conducted a comprehensive pan-cancer analysis using data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) project. Employing a multi-pronged approach with tools including R, Cytoscape, TISIDB, cBioPortal, STRING, GSCALite, and CancerSEA, we investigated GTF2E2's expression patterns, prognostic value, mutational landscape, functional enrichment, and immunological associations across 33 cancer types. Besides, we further validated the bioinformatic results through in vitro experiments in Uterine corpus endometrial carcinoma (UCEC), including western blotting (WB), cell proliferation assays and transwell. DCFH-DA, C11-BODIPY 581/591 and FeRhoNox-1 probes were performed to identify ferroptosis levels in vitro.

RESULTS

GTF2E2 expression was significantly elevated in most cancers compared to normal tissues, with notable diagnostic potential (AUC > 0.7) in 20 cancer types. GTF2E2 expression varied across molecular and immune subtypes and correlated with tumor stage and patient age in several cancers. Functional enrichment analyses highlighted GTF2E2's involvement in key cancer-related and immunological pathways. Notably, GTF2E2 promoted UCEC progression in vitro, and knockdown of GTF2E2 significantly inhibited the proliferation, migration and invasion of UCEC cells. Compared with the control group, GPX4 expression was down-regulated and ACSL4 expression was up-regulated in the GTF2E2-knockdown group. Knockdown of GTF2E2 also increased the intracellular levels of Fe2+, lipid peroxides (LPOs) and reactive oxygen species (ROS).

CONCLUSIONS

Our findings underscore GTF2E2's multifaceted roles in cancer biology, highlighting its potential as a diagnostic biomarker, prognostic indicator, and immunotherapeutic target across various malignancies. This investigation has the potential to contribute significantly to a deeper understanding of the substantial involvement of GTF2E2 in human malignancies, particularly UCEC.

The metabolic dialogue between intratumoural microbes and cancer: implications for immunotherapy

The tumour microenvironment (TME) exerts a profound influence on cancer progression and treatment outcomes. Recent investigations have elucidated the crucial role of intratumoural microbiota and their metabolites in shaping the TME and modulating anti-tumour immunity. This review critically assesses the influence of intratumoural microbial metabolites on the TME and cancer immunotherapy. We systematically analyse how microbial-derived glucose, amino acid, and lipid metabolites modulate immune cell function, cytokine secretion, and tumour growth. The roles of specific metabolites, including lactate, short-chain fatty acids, bile acids, and tryptophan derivatives, are comprehensively examined in regulating immune responses and tumour progression. Furthermore, we investigate the potential of these metabolites to augment the efficacy of cancer immunotherapies, with particular emphasis on immune checkpoint inhibitors. By delineating the mechanisms through which microbial metabolites influence the TME, this review provides insights into novel microbiome-based therapeutic strategies, thereby highlighting a promising frontier in personalised cancer medicine.

Imaging 3D cell cultures with optical microscopy

Three-dimensional (3D) cell cultures have gained popularity in recent years due to their ability to represent complex tissues or organs more faithfully than conventional two-dimensional (2D) cell culture. This article reviews the application of both 2D and 3D microscopy approaches for monitoring and studying 3D cell cultures. We first summarize the most popular optical microscopy methods that have been used with 3D cell cultures. We then discuss the general advantages and disadvantages of various microscopy techniques for several broad categories of investigation involving 3D cell cultures. Finally, we provide perspectives on key areas of technical need in which there are clear opportunities for innovation. Our goal is to guide microscope engineers and biomedical end users toward optimal imaging methods for specific investigational scenarios and to identify use cases in which additional innovations in high-resolution imaging could be helpful.

Quantitative cancer-immunity cycle modeling for predicting disease progression in advanced metastatic colorectal cancer

Patients with advanced metastatic colorectal cancer (mCRC) typically exhibit significant interindividual differences in treatment responses and face poor survival outcomes. To systematically analyze the heterogeneous tumor progression and recurrence observed in advanced mCRC patients, we developed a quantitative cancer-immunity cycle (QCIC) model. The QCIC model employs differential equations to capture the biological mechanisms underlying the cancer-immunity cycle and predicts tumor evolution dynamics under various treatment strategies through stochastic computational methods. We introduce the treatment response index (TRI) to quantify disease progression in virtual clinical trials and the death probability function (DPF) to estimate overall survival. Additionally, we investigate the impact of predictive biomarkers on survival prognosis in advanced mCRC patients, identifying tumor-infiltrating CD8+ cytotoxic T lymphocytes (CTLs) as key predictors of disease progression and the tumor-infiltrating CD4+ Th1/Treg ratio as a significant determinant of survival outcomes. This study presents an approach that bridges the gap between diverse clinical data sources and the generation of virtual patient cohorts, providing valuable insights into interindividual treatment variability and survival forecasting in mCRC patients.

Elucidation of the mechanism of carcinogenic transformation of human gastric epithelial cells in atrophic gastritis

BACKGROUND

Helicobacter pylori infection and subsequent atrophic gastritis (AG) and intestinal metaplasia (IM) are regarded as precursor conditions for gastric cancer (GC). Though diverse mechanisms of carcinogenesis from AG and IM have been clarified using mouse models, few studies using human models have been reported. Here, we describe in vitro modeling of IM, as well as in vivo modeling of the oncogenic transformation from AG using human gastric organoids.

METHODS

Organoids derived from patients with AG were established and characterized by immunohistochemistry and in situ hybridization. Niche factor withdrawal and genetic engineering using CRISPR/Cas9 were conducted for modeling IM, and manipulated organoids were xenografted subcutaneously in mice to establish a GC model.

RESULTS

AG organoids (AGOs) were maintained by Wnt niche factors; withdrawal of these factors led to differentiation toward foveolar cells. Knockout of Runt-related transcription factor 3 (RUNX3), or activation of bone morphogenetic protein (BMP) signaling, resulted in accumulation of the key IM markers caudal-type homeobox 2 (CDX2) and mucin 2 (MUC2) in AGOs; disruption of SMAD4 counteracted the induction of these markers. Organoids doubly deficient for TP53 and SMAD4 formed larger and more proliferative p21 -negative subcutaneous tumors than did RUNX3-deficient organoids, suggesting that induction of a senescent state is a key barrier in stepwise carcinogenesis from AG.

CONCLUSIONS

Wnt signaling is essential for homeostasis of AG, and SMAD4-dependent activation of BMP signaling promotes intestinal differentiation. Combined disruption of TP53 and SMAD4 confers tumorigenic potential to AGOs by inhibiting p21 induction.

Single-cell and bulk RNA-sequence identify an immune-derived lncRNA-mRNA signature for predicting clinical outcomes and immunotherapeutic response of prostate cancer

Immunotherapy has limited effectiveness in prostate cancer (PCa), often classified as a "cold tumor" due to immune-related long non-coding RNAs (lncRNAs) and mRNAs. We developed and validated a consensus immune-related lncRNA and mRNA signature (ILMS) to enhance immunotherapy efficacy for PCa patients. By analyzing seven independent datasets, including our own, we confirmed that ILMS is a robust predictor of biochemical recurrence (BCR). Compared to 70 other published signatures, ILMS showed the highest ability to anticipate PCa prognosis. Single-cell analysis indicated that ILMS-high patients had abundant immune cell infiltration, suggesting a favorable response to immunotherapy. Additionally, ILMS was positively associated with immune checkpoints LAG3, TIM3, and TIGIT, identifying patients likely to benefit from immunotherapy. This model will be further validated and refined in subsequent studies.

The role of LncRNA-MANCR induced by HIF-1α drive the malignant progression of pancreatic cancer by targeting miRNA-494/SIRT1 signaling axis under hypoxic conditions

This study revealed the prospective biological role and fundamental mechanisms of hypoxia-induced lncRNA-MANCR (MANCR), which is notably upregulated in pancreatic cancer (PC). This work uncovered the potential biological function and underlying mechanisms of hypoxia-induced MANCR, which is significantly elevated in PC. Microarray assays confirmed MANCR expression in the tissues of patients with PC and patients with chronic pancreatitis (CP), which positively correlated with sirtuin-1 (SIRT1) mRNA levels. Chromatin immunoprecipitation and luciferase assays were employed to gauge binding within the hypoxia-inducible factor-1α (HIF-1α)/MANCR/miRNA-494/SIRT1 pathway. Additionally, the association between MANCR expression and the clinical outcomes of patients with PC was confirmed. MANCR is significantly upregulated in PC cells under hypoxic conditions, which is closely linked to poor prognosis in patients with PC. Depletion of MANCR repressed in vitro proliferation, migration, and invasion of PC cells and in vivo growth of PC xenograft tumours. We further demonstrated that MANCR is localised in the cytoplasm and competitively binds miR-494, which directly targets SIRT1. Mechanically, the overexpression of SIRT1 improved the stability of the HIF-1α protein through deacetylation, leading to enhanced HIF-1α assembly. Moreover, MANCR underwent transcriptional regulation by HIF-1α in a hypoxic setting. This modulation was ascribed to HIF-1α binding to hypoxia response elements present in the MANCR promoter sequence. Data revealed the potential possibility of feedback between MANCR and HIF-1α, which may be conducive to hypoxia-induced oncogenicity and PC tumorigenesis, thereby providing a suitable therapeutic target.

ARIH2 serves as a potential prognostic biomarker for hepatocellular carcinoma associated with immune infiltration and ferroptosis

Background

Ariadne homolog 2 (ARIH2) has been demonstrated to be upregulated in various human cancer tissues. Nevertheless, the underlying biological function of ARIH2 in the progression of hepatocellular carcinoma (HCC) remains ambiguous. Hence, we conducted a comprehensive bioinformatics analysis on the liver hepatocellular carcinoma (LIHC) dataset to explore the role of ARIH2 in tumorigenesis.

Methods

The mRNA and protein expression of ARIH2 was analyzed by using data from public databases and verified through immunohistochemical staining and Western blot. Logistic regression, Cox regression, receiver operating characteristic curve (ROC), Kaplan-Meier analysis and nomogram model were employed to assess the association between ARIH2 and the clinicopathological characteristics of HCC. We utilized functional enrichment analysis to investigate the potential pathways of ARIH2 in the progression of HCC. The association of ARIH2 with immune infiltration, ferroptosis and immune checkpoint genes was further evaluated. Finally, the correlation between ARIH2 and the IC50 of chemotherapeutic drugs was analyzed in HCC.

Results

Our study discovered that ARIH2 was up-regulated in HCC tumor tissues compared with the control group. ARIH2 expression could effectively distinguish tumor tissues from normal liver tissues. The genes related to ARIH2 showed differential expression in pathways involving immune system-related pathways and ion channels. We identified a significant association between the expression level of ARIH2 in HCC tissues and immune infiltration, immune checkpoint genes and ferroptosis. The expression level of ARIH2 was significantly correlated with the clinical stage, histological pathological grade and clinical characteristics of HCC, and could independently predict overall survival.

Conclusions

The expression level of ARIH2 may serve as a promising biomarker for the diagnosis and prognosis of HCC, as well as a potential drug target, which holds great significance for the development of targeted therapy for HCC.

Cancer cell-derived exosomal miR-34a inhibits the malignant progression of pancreatic adenocarcinoma cells by restraining the M2 polarization of macrophages

This study aimed to investigate the crosstalk mechanism between pancreatic cancer (PAC) cells and M2 tumor-associated macrophages induced by tumor-derived exosomal miR-34a. MicroRNA and mRNA expression levels were detected using RT-qPCR. Cell Counting Kit-8, wound-healing, transwell assays and flow cytometry were respectively employed to assess cell proliferation, migration, invasion and apoptosis. Enzyme-linked immunosorbent assay was utilized to determine cytokine secretion. Transmission electron microscopy and nanoparticle tracking analyses were performed to detect the exosome morphology and particle size. Phagocytosis of exosomes by macrophages was verified by PKH26 labeling. The effects of exosome-treated macrophages on the epithelial-mesenchymal transition, invasion, and migration of PANC-1 cells were investigated using coculture experiments. The identification of miR-34a's potential targets were determined with TargetScan and validated by a dual-luciferase reporter assay. miR-34a was expressed at low levels in PAC tissues, cells, and exosomes. The overexpression of miR-34a restrains the malignant progression of PANC-1 cells. After miR-34a-overexpressed PANC-1-derived exosomes were phagocytosed by macrophages, the process of M2 polarization in macrophages was obstructed, leading to the suppression of epithelial-mesenchymal transition, migration, and invasion of the cocultured PANC-1 cells. Suppressor of cytokine signaling 3 is a direct target of miR-34a. MiR-34a negatively modulates the suppressor of cytokine signaling 3 to prevent the M2 polarization of macrophages by engaging the Janus kinase/signal transducers and activators of the transcription pathway and influencing the malignancy of PAC cells.  miR-34a in cancer cell-derived exosomes inhibits the malignant progression of pancreatic cancer cells by restraining M2 polarization of macrophages.

Comprehensive bioinformatics analysis identified HMGB3 as a promising immunotherapy target for glioblastoma multiforme

OBJECTIVE

Glioblastoma multiforme (GBM) presents significant therapeutic challenges due to its heterogeneous tumorigenicity, drug resistance, and immunosuppression. Although several molecular markers have been developed, there still lack of sensitive molecular for accurately detection. Studying the mechanisms underlying the development of GBM and finding relevant prognostic biomarkers remains crucial.

METHODS

Single-cell RNA sequencing, bulk RNA-seq, and cancer immune cycle activities of GBM were used to assess the expression of different molecular related to GBM. Bioinformatics analyses were carried to evaluate the functional of the high mobility group protein B3 (HMGB3) in GBM.

RESULTS

HMGB3 was highly expressed in GBM tissues and influenced the interpatient and intratumoral transcriptomic heterogeneity as well as immunosuppression in GBM. HMGB3 also contributes to a no inflamed tumor microenvironment (TME) and has an inhibitory effect on tumor-associated immune cell infiltration. Besides, HMGB3 participated GBM chemotherapeutic sensitivity and negative correlation with 140 medicines.

CONCLUSION

HMGB3 as a heterogeneous and immunosuppressive molecule in the GBM TME, making it a potential target for precision therapy for GBM.

Prognostic value of neutrophil-lymphocyte ratio in gastroenteropancreatic neuroendocrine neoplasm: a systematic review and meta-analysis

Purpose

A high neutrophil-to-lymphocyte ratio (NLR) might be connected with an unfavorable tumor prognosis. We sought to conduct a meta-analysis of published studies exploring the prognostic value of NLR in patients with gastroenteropancreatic neuroendocrine neoplasm (GEP-NEN).

Methods

We have referred to the PRISMA 2020 for the Abstracts checklist and have registered our review at the International Prospective Register of Systematic Reviews (registration number CRD42020187679). The PubMed, Embase, and Web of Science databases were screened using words like 'neutrophil to lymphocyte ratio', 'neuroendocrine tumors', and others up to July 2024. In our study, we evaluated the significance of NLR on overall survival (OS), recurrence-free survival (RFS), and progression-free survival (PFS) of patients with GEP-NEN. Subgroup analysis were conducted to identify the origins of heterogeneity and examine the impact of factor grouping.

Results

We gathered 18 cohorts with 2,995 cases. All included studies were high quality, with Newcastle Ottawa Scale (NOS) scores ranging from 6 to 8. The pooled analysis revealed that a higher NLR related to worse OS (hazard ratio (HR): 4.59, 95% confidence interval (CI) [3.35-6.29], p < 0.00001) and poor RFS (HR: 4.05, 95% CI [2.78-5.90], p < 0.00001) in patients with GEP-NEN. Subgroup analysis of race, tumor sites, and therapy showed good predictive significance, however, NLR is not effective in predicting the overall survival time of non-operative patients.

Conclusion

This meta-analysis showed that a high NLR predicted poor OS, RFS, and PFS in patients with GEP-NEN and can be used as a promising predictor.

Novel bioengineered drugs with immunotherapies for malignant pleural effusion: Remodulate tumor immune microenvironment and activate immune system

Malignant pleural effusion (MPE) remains a clinical issue since it is associated with advanced-stage cancers and dismal survival, with immunosuppressive tumor microenvironment (TME) and ineffective drug delivery. Conventional therapies such as thoracentesis and pleurodesis are for symptom relief but palliative, without inducing immunity and prolonging survival. Emerging new bioengineered drugs, synergizing with immunotherapies, offer a new paradigm by dual-targeting TME remodeling and immune activation. These technologies leverage nanotechnology, gene editing, and biomaterials to offer precise spatiotemporal control. This review illustrates the molecular mechanism of the immunosuppressive TME in MPE. It examines the newest bioengineering platforms-such as cytokine-encapsulated nanoparticles and oncolytic viruses-that can reactivate immune mechanisms. We highlight preclinical and clinical evidence of the effectiveness of combinatorial strategies in overcoming local immune tolerance and potential risks in adverse events. While the clinical transformation challenge remains, future directions necessitate cross-disciplinary convergence to engineer intelligent delivery vehicles and predictive biomarkers for patient stratification. By integrating immunotherapy with bioengineering, this strategy not only restores antitumor immunity but also portends a new epoch of precision medicine for MPE.

Bufalin inhibits immune escape in metastatic colorectal cancer by regulating M2 macrophage polarization

The prognosis for patients with metastatic colorectal cancer (mCRC) remains poor primarily owing to immune escape caused by immunosuppressive tumor microenvironment (TME). M2 tumor-associated macrophages (TAMs) have been considered as a pivotal role in sustaining the immunosuppressive character in TME. Our previous studies have found that highly mCRC cells could promote M2 TAMs polarization, leading to the exhaustion of T cell antitumor immunity. Studies have reported that Bufalin (BU) could reverse the immunosuppressive TME via regulating TAMs polarization, but the mechanisms underlying remain elusive. In this study, we demonstrated that KLF4 secreted by highly mCRC cells not only promoted the polarization to M2 TAMs but also up-regulated the PD-L1 expression in TAMs, leading to suppressing cytotoxic T lymphocyte (CTL) function to facilitate tumor immune escape. Mechanistically, BU targeted the SRC-3 protein to reduce KLF4 release in highly mCRC cells to regulate the polarization of M2 TAMs and down-regulate PD-L1 expression in TAMs, resulting in reprogramming of the TME and enhancing the anti-tumor immunity. These results have also been validated in both subcutaneous tumor models and orthotopic tumor models. Overall, this research further elucidates the anti-tumor mechanism of BU for inhibiting immune escape in mCRC and facilitate exploitation of a new potential macrophage-based mCRC immunotherapeutic modality.

KIF14 plays a role in the regulation of the cell cycle and has implications for prognosis in clear cell renal cell carcinoma

BACKGROUND

Kinesin family member 14 (KIF14) is a significant multifunctional protein that has been linked to several malignancies. However, the varied expression profiles of KIF14 and its prognostic relevance in Clear cell renal cell carcinoma (ccRCC) have yet to be elucidated.

METHODS

Patients with ccRCC were obtained from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and ArrayExpress databases. A comparison of KIF14 expression levels between ccRCC and normal tissues was conducted using the Wilcoxon rank sum test. Logistic regression analysis was subsequently employed to evaluate the relationship between KIF14 expression and clinicopathological features. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) term analysis, gene set enrichment analysis (GSEA) and single sample gene set enrichment analysis (ssGSEA), as well as CIBERSORT, were utilized to elucidate the enriched pathways and functions linked to KIF14 and to quantify the level of immune cell infiltration. Kaplan-Meier analysis was conducted to assess the correlation between KIF14 expression and survival. Additionally, KIF14 expression was downregulated in A498 ccRCC cells, and their proliferation, expansion capacity, cell cycle, and apoptosis were assessed through CCK-8 assays, colony formation assays, 7-AAD staining, and Annexin V/PI staining, respectively.

RESULTS

The findings of this study demonstrate that KIF14 mRNA levels are notably increased in ccRCC. Furthermore, a positive association was observed between KIF14 expression and cancer stage, nodal metastasis, and the infiltration of various immune cells in ccRCC. High levels of KIF14 were also found to be indicative of poor survival outcomes among ccRCC patients. Knockdown of KIF14 in A498 cells resulted in reduced proliferation, diminished colony formation capacity, cell cycle arrest, increased apoptosis, and downregulation of CyclinD1 and CDK4.

CONCLUSIONS

KIF14 down-regulates cell cycle proteins CyclinD1 and CDK4 to facilitate the proliferation of ccRCC cells, suggesting its potential as a therapeutic target and prognostic biomarker in ccRCC.

Development and validation of basement membrane-related signatures for predicting postoperative recurrence, tumor microenvironment and drug candidates in chordomas

BACKGROUND

Skull base chordoma is a rare and aggressive bone tumor with a poor prognosis. The basement membrane (BM) plays an pivotal role in tumor progression. However, the involvement of BM-related genes in assessing the prognosis and influencing the biological behavior of skull base chordomas remains unclear.

METHODS

Patients with skull base chordoma undergoing endoscopic endonasal surgery were included in the study (77 patients for bulk transcriptome sequencing and 6 patients for single-cell RNA sequencing). A BM-related genes signature was established and validated using bulk transcriptome data. Additionally, we investigated the oncogenic potential of a key BM-related gene in chordoma cells in vitro.

RESULTS

A prognostic signature consisting of five BM-related genes was identified through LASSO Cox regression analysis. The accuracy and reliability of this signature were validated by the validation cohort. Multivariate Cox analysis and a nomogram demonstrated that the risk score serves as an independent and reliable prognostic factor for skull base chordoma. Moreover, the BM-related gene signature was significantly associated with the immune microenvironment, immune checkpoint expression, and drug sensitivity. Single-cell RNA sequencing analysis revealed both the chordoma tumor cell and the fibroblast contributed to the overall BM signature. Finally, in vitro experiments demonstrated that the knockdown of ITGB3, the hub gene in the signature, inhibited the proliferation and migration of chordoma cells via the PI3K-Akt pathway.

CONCLUSION

This study explored the critical role of BM-related genes in skull base chordoma, which affected postoperative recurrence and maligant behavior of chordoma via the PI3K-Akt signaling pathway.

The Bidirectional Interplay between T Cell-Based Immunotherapies and the Tumor Microenvironment

T cell-based therapies, including tumor-infiltrating lymphocyte therapy, T-cell receptor-engineered T cells, and chimeric antigen receptor T cells, are powerful therapeutic approaches for cancer treatment. Whereas these therapies are primarily known for their direct cytotoxic effects on cancer cells, accumulating evidence indicates that they also influence the tumor microenvironment (TME) by altering the cytokine milieu and recruiting additional effector populations to help orchestrate the antitumor immune response. Conversely, the TME itself can modulate the behavior of these therapies within the host by either supporting or inhibiting their activity. In this review, we provide an overview of clinical and preclinical data on the bidirectional influences between T-cell therapies and the TME. Unraveling the interactions between T cell-based therapies and the TME is critical for a better understanding of their mechanisms of action, resistance, and toxicity, with the goal of optimizing efficacy and safety.

Unleashing the Potential of Metal Ions in cGAS-STING Activation: Advancing Nanomaterial-Based Tumor Immunotherapy

Immunotherapy is a critical modality in cancer treatment with diverse activation pathways. In recent years, the stimulator of interferon genes (STING) signaling pathway has exhibited significant potential in tumor immunotherapy. This pathway exerts notable antitumor effects by activating innate and adaptive immunity and regulating the tumor immune microenvironment. Various metal ions have been identified as effective activators of the STING pathway and, through the design and synthesis of nanodelivery platforms, have been applied in immunotherapy as well as in combination therapies, such as chemotherapy, chemodynamic therapy, photodynamic therapy, and cancer vaccines. Metal nanomaterials showcase unique advantages in immunotherapy; however, there are still aspects that require optimization. This review systematically examines existing metal-based nanomaterials, elaborates on the mechanisms by which different metal ions activate the STING pathway, and discusses their application models in tumor combination therapies. We also provide a comparative analysis of the advantages of metal nanomaterials over other treatment methods. Our exploration highlights the broad application prospects of metal nanomaterials in cancer treatment, offering new insights and directions for the advancement of tumor immunotherapy.

Advancements in immunotherapy for gastric cancer: Unveiling the potential of immune checkpoint inhibitors and emerging strategies

Gastric cancer (GC) is linked to high morbidity and mortality rates. Approximately two-thirds of GC patients are diagnosed at an advanced or metastatic stage. Conventional treatments for GC, including surgery, radiotherapy, and chemotherapy, offer limited prognostic improvement. Recently, immunotherapy has gained attention for its promising therapeutic effects in various tumors. Immunotherapy functions by activating and regulating the patient's immune cells to target and eliminate tumor cells, thereby reducing the tumor burden in the body. Among immunotherapies, immune checkpoint inhibitors (ICIs) are the most advanced. ICIs disrupt the inhibitory protein-small molecule (PD-L1, CTLA4, VISTA, TIM-3 and LAG3) interactions produced by immune cells, reactivating these cells to recognize and attack tumor cells. However, adverse reactions and resistance to ICIs hinder their further clinical and experimental development. Therefore, a comprehensive understanding of the advancements in ICIs for GC is crucial. This article discusses the latest developments in clinical trials of ICIs for GC and examines combination therapies involving ICIs (targeted therapy, chemotherapy, radiotherapy), alongside ongoing clinical trials. Additionally, the review investigates the tumor immune microenvironment and its role in non-responsiveness to ICIs, highlighting the function of tumor immune cells in ICI efficacy. Finally, the article explores the prospects and limitations of new immunotherapy-related technologies, such as tumor vaccines, nanotechnologies, and emerging therapeutic strategies, aiming to advance research into personalized and optimized immunotherapy for patients with locally advanced gastric cancer.

The Presence of Pigment Incontinence in Sinonasal Mucosal Melanoma

BACKGROUND

Regression is an immunological phenomenon described in cutaneous melanoma whereby tumor is replaced with tumor-infiltrating lymphocytes, granulation tissue, and mature fibroblasts often accompanied by pigment incontinence (accumulation of melanin in the upper dermis). Pigment incontinence results in grossly pigmented lesions that may be mistaken for viable tumor and has not been described in sinonasal mucosal melanoma (SNMM). This study investigates the presence of regression and pigment incontinence in patients with SNMM.

METHODS

A retrospective chart review was conducted on SNMM patients from 2007 to 2023. Pathology slides from surgical resection were examined by two pathologists blinded to treatment information for the presence and extent of pigment-laden macrophages and other histopathologic features of regression.

RESULTS

Seventeen patients with SNMM were included in this study who underwent surgical resection. Three patients received neoadjuvant therapy followed by surgical resection. Regression was present in 94% of patients and pigment incontinence was present in 65% of patients and occurred in both neoadjuvant treated patients and treatment naïve patients. All three patients with neoadjuvant treatment had evidence of pigment incontinence.

DISCUSSION

This study highlights that SNMM often displays characteristics of regression. This study is one of the first to describe the presence of pigment incontinence in patients with SNMM. Pigment incontinence can be a part of the natural tumor life cycle and grossly pigmented lesions could easily be confused for melanoma especially after neoadjuvant therapy. Developing an understanding of regression and pigment incontinence within SNMM is important for diagnosis and clinical management.

LEVEL OF EVIDENCE

4 Laryngoscope, 135:1321-1325, 2025.

CTCF enhances pancreatic cancer progression via FLG-AS1-dependent epigenetic regulation and macrophage polarization

CCCTC-binding factor (CTCF) regulates chromatin organization and is upregulated in pancreatic ductal adenocarcinoma (PDAC). We found that CTCF interacts with HNRNPU through a FLG-AS1-dependent mechanism, facilitating the recruitment of EP300 and activation of the m6A reader IGF2BP2. This activation promotes histone lactylation at the promoter region of IGF2BP2 stimulating the proliferation of PDAC cells. IGF2BP2 enhanced the mRNA stability of CSF1 and MYC. Moreover, FLG-AS1 directly interacts with HNRNPU to modulate alternative splicing of CSF1, thus promoting the M2 polarization of tumor associated macrophages (TAMs) in PDAC. The results indicated that CTCF-induced oncogenic modification of histone lactylation, m6A and alternative spilcing as multi-regulation modes of TAMs reprogramming in PDAC and identifies CTCF as a potential therapeutic target for PDAC immunotherapy whose inhibition M2 polarization through the IGF2BP2/CSF1/CSF1R axis. Curaxin combined with gemcitabine treatment has shown promising antitumor efficacy against PDAC.

Identification and dissection of prostate cancer grounded on fatty acid metabolism-correlative features for predicting prognosis and assisting immunotherapy

BACKGROUND

Fatty acid metabolism (FAM) plays a critical role in tumor progression and therapeutic resistance by enhancing lipid biosynthesis, storage, and catabolism. Dysregulated FAM is a hallmark of prostate cancer (PCa), enabling cancer cells to adapt to extracellular signals and metabolic changes, with the tumor microenvironment (TME) playing a key role. However, the prognostic significance of FAM in PCa remains unexplored.

METHODS

We analyzed 309 FAM-related genes to develop a prognostic model using least absolute shrinkage and selection operator (LASSO) regression based on The Cancer Genome Atlas (TCGA) database. This model stratified PCa patients into high- and low-risk groups and was validated using the Gene Expression Omnibus (GEO) database. We constructed a nomogram incorporating risk score, clinical variables (T and N stage, Gleason score, age), and assessed its performance with calibration curves. The associations between risk score, tumor mutation burden (TMB), immune checkpoint inhibitors (ICIs), and TME features were also examined. Finally, a hub gene was identified via protein-protein interaction (PPI) networks and validated.

RESULTS

The risk score was an independent prognostic factor for PCa. High-risk patients showed worse survival outcomes but were more responsive to immunotherapy, chemotherapy, and targeted therapies. A core gene with high expression correlated with poor prognosis, unfavorable clinicopathological features, and immune cell infiltration.

CONCLUSION

These findings reveal the prognostic importance of FAM in PCa, providing novel insights into prognosis and potential therapeutic targets for PCa management.

High antigen-presenting CAF levels correlate with reduced glycosaminoglycan biosynthesis-heparan sulfate/heparin metabolism in immune cells and poor prognosis in esophageal squamous cell carcinoma: Insights from bulk and single-cell transcriptome profiling

In esophageal squamous cell carcinoma (ESCC), the tumor microenvironment (TME) is characterized by a significant accumulation of cancer-associated fibroblasts (CAFs), which play a pivotal role in the host response against tumor cells. While fibroblasts are known to be crucial in the metabolic reprogramming of the TME, the specific metabolic alterations induced by these cells remain largely undefined. Utilizing single-cell RNA sequencing, we have identified a distinct subpopulation of antigen-presenting CAF (apCAF) within ESCC tumors. Our findings reveal that apCAF contribute to adverse patient outcomes by remodeling the tumor metabolic environment. Notably, apCAF modulate the glycosaminoglycan biosynthesis-heparan sulfate/heparin metabolism pathway in T cells, B cells, and macrophages. Disruption of this pathway may facilitate immune evasion by the tumor. These insights underscore the critical role of CAFs in shaping the metabolic landscape of the TME and lay the groundwork for developing therapeutic strategies aimed at enhancing anti-tumor immunity.

Carvacrol potentiates immunity and sorafenib anti-cancer efficacy by targeting HIF-1α/STAT3/ FGL1 pathway: in silico and in vivo study

Hypoxia and tumor cell immunological escape greatly hinder the hepatocellular carcinoma (HCC) treatment efficiency. This study is designed to investigate the capability of carvacrol (CVR) to enhance sorafenib (SOR) anti-cancer efficacy and modulate anti-HCC immunity. CVR target and biological activities were predicted using Swiss Target Prediction website and PASS web server. UALCAN and LinkedOmics databases were used to examine hypoxia-inducible factor 1-alpha (HIF-1α) expression and the relationship between studied genes and tumor clinical features. Kaplan-Meier plotter (KM plotter) and TISIDB databases were used to illustrate correlation of HIF-1α with HCC prognosis and immune infiltration. The binding affinities of CVR to p300, KAT2B, CREBBP, and Hsp90 were demonstrated by molecular docking. In vivo analysis was performed in male Sprague-Dawley rats. The STAT3, JAK2, and fibrinogen-like protein 1 (FGL1) expressions were assessed by qRT-PCR. FGL1 was determined by ELISA. CD8+ T cell number was counted by flow cytometry. HIF-1α was determined by immunohistochemistry. CVR showed an HIF-1α inhibitory potential, which is highly expressed in HCC tissues. Also, elevated HIF-1α expression has been found to be correlated with clinicopathological characteristics, poor survival in HCC patients, and tumor immune cell infiltration. CVR/SOR enhanced liver functions and decreased AFP level. CVR/SOR hindered HCC progression by downregulating STAT3, JAK2, and FGL1. CVR/SOR induced tumor immunity via increasing CD8+ T cells. CVR/SOR is a powerful combination for tumor repression and enhancing SOR efficiency in HCC by modulating FGL1. Moreover, CVR/SOR might exert the aforementioned effects through HIF-1α/STAT3/FGL1 pathway.

Drug resistance in TKI therapy for hepatocellular carcinoma: Mechanisms and strategies

Tyrosine kinase inhibitors (TKIs) are such as sorafenib the first-line therapeutic drugs for patients with advanced hepatocellular carcinoma. However, patients with TKI-resistant advanced liver cancer are insensitive to TKI treatment, resulting in limited survival benefits. This paper comprehensively reviewed the mechanisms underlying TKI resistance in hepatocytes, investigating activation of tumor signaling pathways, epigenetic regulation, tumor microenvironment, and metabolic reprogramming. Based on resistance mechanisms, it also reviews preclinical and clinical studies of drug resistance strategies and summarizes targeted therapy combined with immunotherapy currently in investigational clinical trials. Understanding the interactions and clinical studies of these resistance mechanisms offers new hope for improving and prolonging patient survival.

Alterations of the microenvironment of hepatocellular carcinoma in different unfolded protein response activity states

BACKGROUND

The unfolded protein response (UPR) is an adaptive and cytoprotective sensing-signaling network. Numerous studies have indicated the crucial role of UPR in the anti-tumor drug resistance and the modification of tumor microenvironment (TME). The aim of this study is to analyze the alterations of microenvironment and key regulatory genes in hepatocellular carcinoma (HCC) with high UPR activity.

METHODS

We profiled differentially expressed genes (DEGs) by UPR activity, and the biological functions of DEGs and the alterations of signaling pathways were explored. The Immune/Stromal scores and relative abundance of infiltrating cells of HCC tissues with RNA sequencing data downloaded from The Cancer Genome Atlas (TCGA) were calculated by the xCell and ESTIMATE algorithm. The correlations between the prognostic UPR-related genes with the microenvironment scores and infiltrating cells were analyzed using R package "corrplot".

RESULTS

Our results demonstrated that UPR-related genes mainly involved in immune-related signaling pathways. Microenvironment analysis revealed that HCC tissues with higher UPR activity had lower Stromal scores and the relative abundance of various infiltrating cells including hematopoietic stem cells (HSC), lymphatic endothelial cells (LECs), microvascular endothelial cells, endothelial cells (ECs) and adipocytes decreased most significantly. Kaplan-Meier survival analysis indicated that the decline of Stromal scores and corresponding infiltrating stromal cells would result in worse prognosis. The expression levels of CLEC3B, RAMP3, GPR182 and DNASE1L3 were significantly positively correlated with Stromal scores and various infiltrating stromal cells, and down-regulation of these genes were also associated with worse prognosis of HCC.

CONCLUSIONS

HCC with high UPR activity had lower Stromal scores and worse prognosis. Down-regulated genes CLEC3B, RAMP3, GPR182 and DNASE1L3 may play an important regulatory role in the modification of microenvironment of HCC with high UPR activity.

A tumor-infiltrating B lymphocytes -related index based on machine-learning predicts prognosis and immunotherapy response in lung adenocarcinoma

Introduction

Tumor-infiltrating B lymphocytes (TILBs) play a pivotal role in shaping the immune microenvironment of tumors (TIME) and in the progression of lung adenocarcinoma (LUAD). However, there remains a scarcity of research that has thoroughly and systematically delineated the characteristics of TILBs in LUAD.

Method

The research employed single-cell RNA sequencing from the GSE117570 dataset to identify markers linked to TILBs. A comprehensive machine learning approach, utilizing ten distinct algorithms, facilitated the creation of a TILB-related index (BRI) across the TCGA, GSE31210, and GSE72094 datasets. We used multiple algorithms to evaluate the relationships between BRI and TIME, as well as immune therapy-related biomarkers. Additionally, we assessed the role of BRI in predicting immune therapy response in two datasets, GSE91061 and GSE126044.

Result

BRI functioned as an independent risk determinant in LUAD, demonstrating a robust and reliable capacity to predict overall survival rates. We observed significant differences in the scores of B cells, M2 macrophages, NK cells, and regulatory T cells between the high and low BRI score groups. Notably, BRI was found to inversely correlate with cytotoxic CD8+ T-cell infiltration (r = -0.43, p < 0.001) and positively correlate with regulatory T cells (r = 0.31, p = 0.008). We also found that patients with lower BRI were more likely to respond to immunotherapy and were associated with reduced IC50 values for standard chemotherapy and targeted therapy drugs, in contrast to higher BRI. Additionally, the BRI-based survival prediction nomogram demonstrated significant promise for clinical application in predicting the 1-, 3-, and 5-year overall survival rates among LUAD patients.

Discussion

Our study developed a BRI model using ten different algorithms and 101 algorithm combinations. The BRI could be a valuable tool for risk stratification, prognosis, and selection of treatment approaches.

A comprehensive review on targeting diverse immune cells for anticancer therapy: Beyond immune checkpoint inhibitors

Although immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment, primary resistance and acquired resistance continue to limit their efficacy for many patients. To address resistance and enhance the anti-tumor activity within the tumor immune microenvironment (TIME), numerous therapeutic strategies targeting both innate and adaptive immune cells have emerged. These include combination therapies with ICIs, chimeric antigen receptor T-cell (CAR-T), chimeric antigen receptor macrophages (CAR-Ms) or chimeric antigen receptor natural killer cell (CAR-NK) therapy, colony stimulating factor 1 receptor (CSF1R) inhibitors, dendritic cell (DC) vaccines, toll-like receptor (TLR) agonists, cytokine therapies, and chemokine inhibition. These approaches underscore the significant potential of the TIME in cancer treatment. This article provides a comprehensive and up-to-date review of the mechanisms of action of various innate and adaptive immune cells within the TIME, as well as the therapeutic strategies targeting each immune cell type, aiming to deepen the understanding of their therapeutic potential.

Epigenetic regulators combined with tumour immunotherapy: current status and perspectives

Immunotherapy, particularly immune checkpoint inhibitor therapy, has demonstrated clinical benefits in solid tumours. Despite its satisfactory clinical efficacy, it still faces several issues, such as limited eligibility, low response rates and cytotoxicity. Cancer epigenetics implies that tumour cells exhibit unique phenotypes because of their unique characteristics, thus reprogramming of the epigenome holds promise for cancer therapy. Epigenetic regulation plays an important role in regulating gene expression during tumour development and maintenance. Epigenetic regulators induce cancer cell cycle arrest, apoptosis and differentiation of cancer cells, thereby exerting anti-tumour effects. Recent studies have revealed a significant correlation between epigenetic regulatory factors and immune checkpoint therapy. Epigenetics can modulate various aspects of the tumour immune microenvironment and immune response to enhance the sensitivity of immunotherapy, such as lowering the concentration required and mitigating cytotoxicity. This review primarily discusses DNA methyltransferase inhibitors, histone deacetylase inhibitors, enhancer of zeste homolog 2 inhibitors and lysine-specific demethylase 1 inhibitors, which are associated with transcriptional repression. This repression alters the expression of genes involved in the immune checkpoint, thereby enhancing the effectiveness of immunotherapy. We also discuss the potential and challenges of tumour immunotherapy and highlight its advantages, application challenges and clinical research on integrating epigenetic regulatory factors with tumour immunotherapy.

Exploration of SUSD3 in pan-cancer: studying its role, predictive analysis, and biological significance in various malignant tumors in humans

Background

The SUSD3 protein, marked by the Sushi domain, plays a key role in cancer progression, with its expression linked to tumor advancement and patient prognosis. Altered SUSD3 levels could serve as a predictive biomarker for cancer progression. Recognized as a novel susceptibility marker, SUSD3 presents a promising target for antibody-based therapies, offering a potential approach for the prevention, diagnosis, and treatment of breast cancer.

Methods

Using the HPA and GeneMANIA platforms, the distribution of SUSD3 protein across tissues was analyzed, while expression levels in tumor and healthy tissues were compared using The Cancer Genome Atlas data. The TISCH and STOmics DB databases facilitated the mapping of SUSD3 expression in different cell types and its spatial relationship with cancer markers. Univariate Cox regression assessed the prognostic significance of SUSD3 expression in various cancers. Genomic alterations of SUSD3 were explored through the cBioPortal database. The potential of SUSD3 as a predictor of immunotherapy response was investigated using TIMER2.0, and GSEA/GSVA identified related biological pathways. Drugs targeting SUSD3 were identified through CellMiner, CTRP, and GDSC databases, complemented by molecular docking studies. In vitro experiments demonstrated that SUSD3 knockdown in breast cancer cell lines significantly reduced proliferation and migration.

Results

SUSD3 expression variations in pan-cancer cohorts are closely linked to the prognosis of various malignancies. In the tumor microenvironment (TME), SUSD3 is predominantly expressed in monocytes/macrophages and CD4+ T cells. Research indicates a strong correlation between SUSD3 expression and key cancer immunotherapy biomarkers, immune cell infiltration, and immunomodulatory factors. To explore its immune regulatory role, StromalScore, ImmuneScore, ESTIMATE, and Immune Infiltration metrics were employed. Molecular docking studies revealed that selumetinib inhibits tumor cell proliferation. Finally, SUSD3 knockdown reduced cancer cell proliferation and migration.

Conclusion

These findings provide valuable insights and establish a foundation for further exploration of SUSD3's role in pan-carcinomas. Additionally, they offer novel perspectives and potential targets for the development of innovative therapeutic strategies in cancer treatment.

Establishing a Prognostic Model Correlates to Inflammatory Response Pathways for Prostate Cancer via Multiomic Analysis of Lactylation-Related Genes

Prostate cancer (PCa) continues to pose substantial clinical challenges, with molecular heterogeneity significantly impacting therapeutic decision-making and disease trajectories. Emerging evidence implicates protein lactylation-a novel epigenetic regulatory mechanism-in oncogenic processes, though its prognostic relevance in PCa remains underexplored. Through integrative bioinformatics interrogation of lactylation-associated molecular signatures, we established prognostic correlations using multivariable feature selection methodologies. Initial screening via differential expression analysis (limma package) coupled with Cox proportional hazards modeling revealed 11 survival-favorable regulators and 16 hazard-associated elements significantly linked to biochemical recurrence. To enhance predictive precision, ensemble machine learning frameworks were implemented, culminating in a 10-gene lactylation signature demonstrating robust discriminative capacity (concordance index = 0.738) across both primary (TCGA-PRAD) and external validation cohorts (DKFZ). Multivariable regression confirmed the lactylation score's prognostic independence, exhibiting prominent associations with clinicopathological parameters including tumor staging and metastatic potential. The developed clinical-molecular nomogram achieved superior predictive accuracy (C - index > 0.7) through the synergistic integration of biological and clinical covariates. Tumor microenvironment deconvolution uncovered distinct immunological landscapes, with high-risk stratification correlating with enriched stromal infiltration and immunosuppressive phenotypes. Pathway enrichment analyses implicated chromatin remodeling processes and cytokine-mediated inflammatory cascades as potential mechanistic drivers of prognostic divergence. Therapeutic vulnerability profiling demonstrated differential response patterns: low-risk patients exhibited enhanced immune checkpoint inhibitor responsiveness, whereas high-risk subgroups showed selective chemosensitivity to docetaxel and mitoxantrone. Functional validation in PC-3 models revealed AK5 silencing induced proapoptotic effects, suppressed metastatic potential of migration and invasion, and modulated immune checkpoint regulation through CD276 coexpression. These multimodal findings position lactylation dynamics, particularly AK5-mediated pathways, as promising therapeutic targets and stratification biomarkers in PCa management.

A strategy for synergistic enhancement of immune circulation in head and neck squamous cell carcinoma by novel nucleic acid drug therapy and immunotherapy

Studies have shown that in the pathogenesis of head and neck squamous cell carcinoma, immune circulation obstruction caused by various factors including metabolic abnormalities, gene mutations, and matrix barrier, is a critical factor for the induction of tumor development and progression. Therefore, the immunotherapy strategy of killing head and neck squamous cell carcinoma cells by an enhanced immune circulation mechanism has attracted much attention. In addition, the rapid development of new nucleic acid drug therapy, such as mRNA, oligonucleotide and small guide RNA (sgRNA), has taken immunotherapy of head and neck squamous cell carcinoma (immune checkpoint inhibitors, tumor vaccines, cellular immunotherapy, cytokines and adjuvants, etc.) to a new level. The combination of nucleic acid therapy with immunotherapy developed for its therapeutic properties has brought a new direction for the diagnosis and treatment of head and neck squamous cell carcinoma, and the combination of the two has had considerable curative effect to patients with refractory/recurrent head and neck squamous cell carcinoma. In this review, we summarized the latest progress of nucleic acid therapy applied to conventional immunotherapy for head and neck squamous cell carcinoma, discussed its mechanism of action and efficacy, and looked into the future development trend.

Prediction and analysis of tumor infiltrating lymphocytes across 28 cancers by TILScout using deep learning

The density of tumor-infiltrating lymphocytes (TILs) serves as a valuable indicator for predicting anti-tumor responses, but its broad impact across various types of cancers remains underexplored. We introduce TILScout, a pan-cancer deep-learning approach to compute patch-level TIL scores from whole slide images (WSIs). TILScout achieved accuracies of 0.9787 and 0.9628, and AUCs of 0.9988 and 0.9934 in classifying WSI patches into three categories-TIL-positive, TIL-negative, and other/necrotic-on validation and independent test sets, respectively, surpassing previous studies. The biological significance of TILScout-derived TIL scores across 28 cancers was validated through comprehensive functional and correlational analyses. A consistent decrease in TIL scores with an increase in cancer stage provides direct evidence that the lower TIL content may stimulate cancer progression. Additionally, TIL scores correlated with immune checkpoint gene expression and genomic variation in common cancer driver genes. Our comprehensive pan-cancer survey highlights the critical prognostic significance of TILs within the tumor microenvironment.

p53: A player in the tumor microenvironment

Approximately half of all cancers have p53 inactivating mutations, in addition to which most malignancies inactivate the p53 pathway by increasing p53 inhibitors, decreasing p53 activators, or inactivating p53 downstream targets. A growing number of researches have demonstrated that p53 can influence tumor progression through the tumor microenvironment (TME). TME is involved in the process of tumor development and metastasis and affects the clinical prognosis of patients. p53 participates in host immunity and engages in the immune landscape of the TME, but the specific mechanisms remain to be investigated. This review briefly explores the interactions between different states of p53 and TME components and their mechanisms, as well as their effects on tumor progression. To understand the progress of drug development and clinical studies related to p53 and tumor microenvironment.

Tumor microenvironment: recent advances in understanding and its role in modulating cancer therapies

Tumor microenvironment (TME) denotes the non-cancerous cells and components presented in the tumor, including molecules produced and released by them. Interactions between cancer cells, immune cells, stromal cells, and the extracellular matrix within the TME create a dynamic ecosystem that can either promote or hinder tumor growth and spread. The TME plays a pivotal role in either promoting or inhibiting tumor growth and dissemination, making it a critical factor to consider in the development of effective cancer therapies. Understanding the intricate interplay within the TME is crucial for devising effective cancer therapies. Combination therapies involving inhibitors of immune checkpoint blockade (ICB), and/or chemotherapy now offer new approaches for cancer therapy. However, it remains uncertain how to best utilize these strategies in the context of the complex tumor microenvironment. Oncogene-driven changes in tumor cell metabolism can impact the TME to limit immune responses and present barriers to cancer therapy. Cellular and acellular components in tumor microenvironment can reprogram tumor initiation, growth, invasion, metastasis, and response to therapies. Components in the TME can reprogram tumor behavior and influence responses to treatments, facilitating immune evasion, nutrient deprivation, and therapeutic resistance. Moreover, the TME can influence angiogenesis, promoting the formation of blood vessels that sustain tumor growth. Notably, the TME facilitates immune evasion, establishes a nutrient-deprived milieu, and induces therapeutic resistance, hindering treatment efficacy. A paradigm shift from a cancer-centric model to a TME-centric one has revolutionized cancer research and treatment. However, effectively targeting specific cells or pathways within the TME remains a challenge, as the complexity of the TME poses hurdles in designing precise and effective therapies. This review highlights challenges in targeting the tumor microenvironment to achieve therapeutic efficacy; explore new approaches and technologies to better decipher the tumor microenvironment; and discuss strategies to intervene in the tumor microenvironment and maximize therapeutic benefits.

Multi-omics analysis identifies OSGEPL1 as an oncogene in hepatocellular carcinoma

PURPOSE

N6-Threonylcarbamoyladenosine (t6A) modification irregularities and their associated enzymes genes (OSGEP, OSGEPL1, TPRKB, GON7, TP53RK, YRDC, and LAGE3) are linked to various malignancies development, including Hepatocellular Carcinoma (HCC), yet the specific mechanisms remain obscure. This gap in knowledge is significant, as understanding the mechanisms of t6A modification could reveal new insights into HCC pathogenesis and potentially identify novel therapeutic targets.

METHODS

We leveraged data from The Cancer Genome Atlas (TCGA) to analyze the expression of t6A-associated genes, with a focus on OSGEPL1 in HCC. Our analyses included survival outcome, gene expression, functional enrichment, immune cell infiltration, and somatic mutation data.

RESULTS

We discovered that OSGEPL1 is upregulated in HCC and is correlated with tumor grade, pathological T stage, and overall stage. It inversely impacts overall survival and immune cell infiltration. In vitro experiments confirmed the role of OSGEPL1 in promoting HCC cell proliferation.

CONCLUSIONS

This study implicates t6A modification pathway dysregulation in HCC prognosis, identifying OSGEPL1 as a potential therapeutic target. These findings provide novel insights into HCC pathogenesis and may guide future treatment strategies.

Bi-level graph learning unveils prognosis-relevant tumor microenvironment patterns in breast multiplexed digital pathology

The tumor microenvironment (TME) is widely recognized for its central role in driving cancer progression and influencing prognostic outcomes. Increasing efforts have been dedicated to characterizing it, including its analysis with modern deep learning. However, identifying generalizable biomarkers has been limited by the uninterpretable nature of their predictions. We introduce a data-driven yet interpretable approach for identifying cellular patterns in the TME associated with patient prognoses. Our method relies on constructing a bi-level graph model: a cellular graph, which models the TME, and a population graph, capturing inter-patient similarities given their respective cellular graphs. We demonstrate our approach in breast cancer, showing that the identified patterns provide a risk-stratification system with new complementary information to standard clinical subtypes, and these results are validated in two independent cohorts. Our methodology could be applied to other cancer types more generally, providing insights into the spatial cellular patterns associated with patient outcomes.

Single-cell transcriptomic analyses reveal heterogeneity and key subsets associated with survival and response to PD-1 blockade in cervical squamous cell carcinoma

BACKGROUND

Understanding the intricate tumor microenvironment (TME) is crucial for elucidating the mechanisms underlying the progression of cervical squamous cell carcinoma (CSCC) and its response to anti-PD-1 therapy.

METHODS

In this study, we characterized 50,649 cells obtained from the CSCC for single-cell RNA sequencing and integrated bulk sequencing data from The Cancer Genome Atlas (TCGA) and clinical samples to explore their cell composition, metabolic processes, signaling pathways, specific transcription factors, lineage tracking and response to immunotherapy. In vivo experiments were performed to validate the function of key cell subsets.

RESULTS

We identified ten major cell type and 35 subsets of stromal and immune cells in TME and observed distinct patterns in the metabolic processes and signaling pathways of these cells between tumor and normal tissues. Furthermore, PCNA clamp-associated factor (PCLAF)+ tumor-associated epithelial cell (TAEpis) was negatively correlated with the number of C-X-C motif chemokine ligand 13 (CXCL13)+ CD8+ T cells, overall survival, and response to anti-programmed cell death-1(PD-1) therapy in patients with CSCC. Both in vivo and in vitro experiments demonstrated that PCLAF+ TAEpis promotes the apoptosis of CD8+ T and tumor growth, while also inhibiting T cell infiltration and function.

CONCLUSION

Our findings illuminate the heterogeneity of the complex TME in CSCC and offer evidence supporting PCLAF+ TAEpis as a promising therapeutic target.

Digging Through the Complexities of Immunological Approaches in Emerging Osteosarcoma Therapeutics: A Comprehensive Narrative Review with Updated Clinical Trials

Osteosarcoma (OS) is the predominant mesenchymal primary malignant bone tumor in oncology and pathology, impacting a wide age range from adolescents to older adults. It frequently advances to lung metastasis, ultimately resulting in the mortality of OS patients. The precise pathological pathways responsible for OS progression and dissemination are not fully understood due to its heterogeneity. The integration of surgery with neoadjuvant and postoperative chemotherapy has significantly increased the 5-year survival rate to more than 70% for patients with localized OS tumors. However, about 30% of patients experience local recurrence and/or metastasis. Hence, there is a requirement for innovative therapeutic approaches to address the limitations of traditional treatments. Immunotherapy has garnered increasing attention as a promising avenue for tumors resistant to standard therapies, including OS, despite the underlying mechanisms of disease progression and dissemination remaining not well elucidated. Immunotherapy may not have been suitable for use in patients with OS because of the tumor's immunosuppressive microenvironment and limited immunogenicity. Nevertheless, there are immune-based treatments now being developed for clinical use, such as bispecific antibodies, chimeric antigen receptor T cells, and immune checkpoint inhibitors. Also, additional immunotherapy techniques including cytokines, vaccines, and modified-Natural Killer (NK) cells/macrophages are in the early phases of research but will certainly be popular subjects in the nearest future. Our goal in writing this review was to spark new lines of inquiry into OS immunotherapy by summarizing the findings from both preclinical and current clinical studies examining different approaches.

HDAC1 Mediates Immunosuppression of the Tumor Microenvironment in Non-Small Cell Lung Cancer

Background

Studies have demonstrated that histone deacetylase 1 (HDAC1) enables cancer cells to evade killing mediated by cytotoxic T lymphocytes. However, there are no studies on the immunological aspects of HDAC1 in non-small cell lung cancer (NSCLC).

Methods

In this research, we used the Cancer Genome Atlas (TCGA) public database combined with tissue microarray (TMA) to investigate HDAC1 expression and prognosis in NSCLC. According to the median value of HDAC1 expression in the TCGA dataset, samples of patients with NSCLC were classified into high- and low-expression cohorts. Subsequently, the biological characteristics of HDAC1 in high- and low-expression cohorts in terms of signaling pathways, immune cell infiltration, immune cell function, and genomic stability were investigated to better understand the effect of HDAC1 in the tumor microenvironment (TME) of NSCLC. Additionally, we selected tissue samples with HDAC1 overexpression in TMA2 and performed immunohistochemical staining of CD8+ T cells to observe the distribution of CD8+ T cells in the tumor.

Results

The findings revealed that overexpression of HDAC1 in NSCLC was associated with poor prognosis. Analysis of signaling pathway enrichment indicated that HDAC1 downregulated immune-related signaling pathways in NSCLC. Immune cell infiltration, immune cell function, and genomic stability analyses suggested that the TME alteration mediated by HDAC1 in the high-expression cohort was consistent with the "immune desert" phenotype. Furthermore, CD8+ T immunohistochemical staining experiments of tissue samples with HDAC1 overexpression in NSCLC revealed few CD8+ T cells distributed in the tumor parenchyma and interstitium.

Conclusion

Conclusively, our findings from several biological analyses revealed that HDAC1 is overexpressed in NSCLC and induces TME immunosuppression.

The emerging role of glycolysis and immune evasion in ovarian cancer

Ovarian cancer (OC) is one of the three most common malignant tumors of the female reproductive system, with the highest mortality rate among gynecologic malignancies. Like other tumors, OC cells undergo metabolic reprogramming phenomenon and convert glucose metabolism into "aerobic glycolysis" and generate a high concentration of lactate, i.e., the "Warburg effect", which provides a large amount of energy and corresponding intermediary metabolites for their survival, reproduction and metastasis. Numerous studies have shown that targeted inhibition of aerobic glycolysis and lactate metabolism is a promising strategy to enhance the sensitivity of cancer cells to immunotherapy. Therefore, this review summarizes the metabolic features of glycolysis in OC cells and highlights how abnormal lactate concentration affects the differentiation, metabolism, and function of infiltrating immune cells, which contributes to immunosuppression, and how targeted inhibition of this phenomenon may be a potential strategy to enhance the therapeutic efficacy of OC.

MiR-769-5p of macrophage exosomes induced by GRP78 promotes stemness and chemoresistance in colorectal cancer

The tumor microenvironment (TME) plays an important role in tumorigenesis and development. Tumor-associated macrophages (TAMs) are essential members of the TME, the exosomes and miRNAs they secrete are crucial in tumor regulation. Our previous study showed that GRP78-induced macrophages infinitely tend to be M2-type TAMs. In this study, the exosomes of M0 and GRP78-induced macrophage were collected and co-incubated with colorectal cancer (CRC) cells. The results implied that macrophage exosomes induced by GRP78 (GRP78-exos) significantly promoted stemness and chemoresistance in CRC in vitro and in vivo. Further, the top 5 miRNAs upregulated in GRP78-exos were obtained from miRNA sequencing data. The qRT-PCR validation revealed that miR-769-5p was the most observably upregulated and could be directly transferred into CRC cells via GRP78-exos. Mechanistically, the study indicated that miR-769-5p targeted MAPK1 to regulate the cell cycle-related proteins RB1, cyclin D1, and cyclin E1. This contributes to CRC cells entering a quiescent state, which leads to the development of chemoresistance. Moreover, miR-769-5p is also expressed higher in the tissues of 5-FU-resistant CRC patients. In summary, the findings indicate a novel function of miR-769-5p as a potential marker for the diagnosis and treatment of chemotherapy resistance in CRC.

Killing the killers: Natural killer cell therapy targeting glioma stem cells in high-grade glioma

High-grade gliomas (HGGs), including glioblastoma (GBM) in adults and diffuse intrinsic pontine glioma (DIPG) in children, are among the most aggressive and deadly brain tumors. A key factor in their resilience is the presence of glioma stem cells (GSCs), which drive tumor initiation, progression, and resistance to treatment. Targeting and eradicating GSCs holds potential for curing both GBM and DIPG. Natural killer (NK) cells, as part of the innate immune system, naturally recognize and destroy malignant cells. Recent advances in NK cell-based therapies, such as chimeric antigen receptor (CAR)-NK cells, NK cell engagers, and NK cell-derived exosomes, offer promising approaches for treating GBM and DIPG, particularly by addressing the persistence of GSCs. This review highlights these advancements, explores challenges such as the blood-brain barrier and the immunosuppressive tumor microenvironment, and proposes future directions for improving and clinically advancing these NK cell-based therapies for HGGs.