NLRC3 serves as a critical negative regulator of inflammatory signalling pathways and is implicated in the pathogenesis of multiple disorders, including inflammatory diseases and malignancies. However, the specific functions and underlying mechanisms of NLRC3 in hepatocellular carcinoma (HCC) development remain largely elusive. Here, we report that the expression of NLRC3 was downregulated in HCC tissues and was associated with poor prognosis. Mice deficient in NLRC3 were hypersusceptible to chemically induced hepatocarcinogenesis, and NLRC3 exerted a tumour-suppressive function during HCC development by inhibiting the TRAF6/MYC/NF-κB signalling cascade. Mechanistically, the NLRC3-HSP90 interaction competitively inhibited the binding of the HSP90 chaperone to TRAF6/MYC and impaired the K63-linked ubiquitination and stabilization of the TRAF6/MYC proteins. In the absence of NLRC3, TRAF6 and MYC reciprocally regulated the expression of the other and triggered a TRAF6-MYC positive feedback loop that accelerated the progression of HCC. Our study reveals a novel functional link between NLRC3 and MYC signalling and indicates that HSP90 is a potential target for hindering the progression of NLRC3-deficient HCC.

The application of Multiple Instance Learning (MIL) for classifying Whole Slide Images (WSIs) has gained extensive use in recent years, primarily due to the high cost and time consumption associated with pixel-level annotation of WSIs, which is challenging to accomplish. The advancements in MIL for WSIs have predominantly concentrated on two fronts: the development of superior feature extractors (for instance, utilizing self-supervised learning for training feature extractors) and the formulation of enhanced instance aggregation strategies. Regrettably, the majority of the most advanced approaches have neglected phenotypic variances among instances when employing attention mechanisms. To capitalize on the disparities between instance tissues, we have introduced a phenotypic self-distillation approach to MIL. Our framework is composed of three components: i) a self-supervised feature extractor based on contrastive learning and a phenotype extractor pre-trained on the Kather100K dataset, which automatically provides 9-class tissue phenotype labels (e.g., tumor epithelium, stroma, lymphocytes) without requiring manual annotation, ii) the incorporation of a self-distillation loss between the features of instances and their phenotypes to augment the informational content of both perspectives, and iii) the aggregation of MIL instances for the final MSI prediction. The efficacy of this framework was evaluated on two datasets: the TCGA-CRC dataset was used for training and internal testing with a fixed 70%/30% split, while the Tangshan People's Hospital cohort served as an independent external validation set. On the TCGA-CRC dataset (n = 360; 65 MSI-H, 295 MSS), our model achieved an AUC of 0.8846 and an accuracy of 0.84, using a fixed 70%/30% train-test split. On the Tangshan People's Hospital dataset (n = 472; 56 MSI-H, 426 MSS), the model attained an AUC of 0.7258 and an accuracy of 0.70.

The effect of genetic polymorphisms on survival outcomes in nasopharyngeal carcinoma (NPC) has not been fully elucidated. This study aimed to identify genetic variants associated with NPC survival using a genome-wide association study (GWAS) approach.

Fusobacterium nucleatum (Fn) drives chemotherapy resistance in colorectal cancer (CRC) by activating hypoxia-mimicking signaling pathways, yet the molecular mechanisms linking Fn to 5-fluorouracil (5-FU) resistance remain unclear. We investigated how Fn-induced hypoxia-related gene expression contributes to 5-FU resistance and identified a pharmacological strategy to overcome it.

Adoptive cell transfer of tumor infiltrating CD4+ T cells or T cells genetically modified to express antitumor CD4+ T cell receptors (TCRs) has shown clinical efficacy in patients with advanced solid tumors. We previously defined unique transcriptomic states of antitumor, neoantigen-specific CD8+ and CD4+ tumor infiltrating lymphocytes (TIL) in human cancer. However, optimal cell surface protein markers that identify and would enable viable cell isolation and selective enrichment of antitumor CD4+ T cells have yet to be identified. Here, we define transcriptomic and corresponding cell surface protein profiles of antitumor CD4+ TIL within metastatic colorectal tumors using high dimensional single cell transcriptomic and proteomic analysis. Comprehensive analysis of 45 antitumor CD4+ TCR clonotypes demonstrated uniquely high cell surface protein expression of ADGRG1, CD86, and CD57. In all samples containing tumor neoantigen-reactive CD4+ TIL clonotypes, ADGRG1- and CD86-based cell surface enrichment of known reactive TCR clonotypes were 11-fold and 9-fold higher than bulk CD4+ TIL, respectively. ADGRG1- and CD86-based cell surface enrichment identified >60 validated antitumor CD4+ TCR-clonotypes including tumor organoid-reactive TCRs, as well as neoantigen-specific TCRs targeting private tumor mutations and cancer driver mutations. While both ADGRG1 and CD86 enriched CD4+ TIL displayed an exhausted neoantigen-specific gene expression signature, CD86 also enriched for cytotoxic CD4+ TIL phenotypes. CD4+ TIL isolated based on ADGRG1 expression and expanded in vitro also demonstrated neoantigen reactivity in two samples. Thus, ADGRG1 and CD86 appear to be effective protein markers for isolating human tumor-specific CD4+ TCR clonotypes and studying antitumor CD4+ TIL.

Liver cancer is the fourth leading cause of global cancer mortality, with hepatocellular carcinoma (HCC) accounting for most primary liver cancers. The nucleolus, as the primary site of ribosome biogenesis, plays a crucial role in HCC development. Here, we report that the nucleolar protein KRR1 interacting protein (KRI1) is aberrantly overexpressed in HCC tissues and interacts with nucleophosmin 1 (NPM1) via phase separation to maintain nucleolar structure and ribosome biogenesis. Downregulation of KRI1 significantly impairs HCC cell proliferation and increases apoptosis, accompanied by disrupted nucleolar structure and ribosome biogenesis. Moreover, we show that KRI1 phase separation is enhanced by the phosphorylation of three serine residues (S94, S95, and S97) in its N-terminal intrinsically disordered region, and pyruvate kinase M2 (PKM2) is identified as the key kinase. PKM2 inhibitor shikonin markedly attenuates KRI1 phase separation and its interaction with NPM1, disrupts nucleolar structure and ribosome biogenesis, thereby inhibiting HCC progression. This study uncovers the crucial role of KRI1 in HCC progression and provides theoretical and experimental evidence for the development of nucleolar protein-targeted therapeutic strategies for HCC treatment.

Non-small cell lung cancer (NSCLC) exhibits stem-like characteristics that drive tumor aggressiveness and treatment resistance. The molecular chaperone Glucose-Regulated Protein 78 (GRP78) is substantially elevated in NSCLC compared to normal tissues and cell lines. In clinical samples, GRP78 protein levels correlated with advanced tumor stage and lymph node metastasis. Pharmacological inhibition of GRP78 using BAPTA-AM and GRP78-IN-3 significantly suppressed NSCLC cell viability while promoting apoptosis. The inhibitors effectively attenuated cell migration by downregulating matrix metalloproteinases and reversed epithelial-mesenchymal transition by modulating key cadherin expression profiles. Importantly, GRP78 inhibition substantially reduced cancer stem cell markers and impaired spheroid formation capability. Genetic knockdown of GRP78 in A549 and H1975 cells recapitulated the effects of pharmacological inhibition, reducing cell migration, reversing EMT, attenuating stemness, and suppressing β-catenin signaling. Conversely, GRP78 overexpression in A549 and H1975 cells induced opposite effects, promoting mesenchymal markers, enhancing stemness proteins, and increasing spheroid size. Mechanistic studies revealed that this anti-tumor activity operates through suppression of β-catenin signaling mediated by SIX1, as evidenced by SIX1-overexpression rescue experiments. These findings demonstrate that GRP78 acts as a key regulator of NSCLC stemness and metastatic potential by coordinating epithelial plasticity and stemness pathways, positioning it as a promising therapeutic target for NSCLC treatment.

Advances in spatial transcriptomics (ST) technologies enable spatially resolved gene expression profiling, yet most platforms remain limited to spot-level resolution, where each measurement aggregates signals from multiple cells and obscures cell-specific programs and microenvironmental interactions. Existing computational approaches either provide limited sub-spot refinement or rely on matched single-cell RNA sequencing references that are costly and difficult to obtain. Here, we present DeSpaST (Deconvoluting Spatial Transcriptomics Signals to Cell-Level Resolution Using Histology Images), a dynamic edge-conditioned graph convolutional network that deconvolves spot-level ST data into cell-level gene expression profiles using only paired histology images. DeSpaST extracts nucleus-level morphological features, constructs directed cellular interaction graphs, and integrates spatial and transcriptional information through message passing. Validated across four cancer datasets with orthogonal Xenium, immunofluorescence, ablation, and interslice evaluations, DeSpaST enhances spatial resolution, facilitates downstream cellular-level analyses, and provides deeper insights into tissue biology.

Linking clinically derived risk signals to reproducible molecular states across independent cohorts remains a major challenge in translational bioinformatics. Existing approaches often rely on cohort-specific model fitting, limiting cross-dataset comparability and downstream biological interpretation. We developed a cross-cohort projection framework that maps baseline clinical variables to a clinically anchored latent risk coordinate, $\mu$, enabling application across external datasets without refitting. The fixed projector was trained in a local imaging cohort and applied unchanged to independent cohorts. Projected $\mu$ was evaluated across multiple molecular layers, including bulk transcriptomics, single-cell-guided deconvolution, spatial transcriptomics, and circulating cell-free DNA (cfDNA). In an independent external cohort, projected $\mu$ preserved separation of time to castration resistance across predefined strata (P = .002), with 30-month risk increasing from 0.13 to 0.86 across ordered $\mu$ bins. In bulk transcriptomics, higher projected $\mu$ was associated with increased proliferation-related signaling and reduced androgen receptor/lineage programs ($\rho$ = 0.40 and -0.26; both P < .001). Deconvolution analyses linked higher projected $\mu$ to reduced AR-high epithelial cell fractions ($\rho$ = -0.17, P = .001). Spatial transcriptomics demonstrated organized tissue-level structure of prespecified molecular programs. In cfDNA, higher projected $\mu$ was associated with a more negative RB1 copy-number signal in the detectable subset ($\rho$ = -0.49, P = .0278). This study presents a projection-based framework for cross-cohort translation of clinically anchored latent risk into interpretable multi-omics context. By enabling reuse of a fixed coordinate without refitting, the approach provides a practical strategy for linking clinical risk to molecular programs and blood-based readouts across datasets.

To address the limited tissue specificity of extracellular vesicles (EVs) derived from blood and other body fluids, this study isolated small EVs (sEVs) from the tissue interstitial fluid (TIF) of hepatocellular carcinoma (HCC) and adjacent tissues. The expression profiles of non-coding RNAs (ncRNAs) were analyzed to identify more specific diagnostic biomarkers.

RAD51 is a central protein in the homologous recombination (HR) pathway and is essential for the accurate repair of DNA double-strand breaks (DSBs). Following DSB formation, DNA end resection generates single-stranded DNA substrates that facilitate the recruitment and assembly of RAD51 nucleoprotein filaments at sites of damage. This process results in the formation of discrete nuclear RAD51 foci, which serve as a widely accepted functional readout of HR activity and a surrogate marker of HR proficiency. Because defects in HR are common in several malignancies, particularly ovarian and breast cancers, assessment of RAD51 foci formation has emerged as an important approach for evaluating DNA repair capacity and predicting response to DNA-damaging therapies, including platinum compounds and poly(ADP-ribose) polymerase (PARP) inhibitors, whose efficacy is strongly influenced by HR repair status. This manuscript describes a simple, reliable, and reproducible immunofluorescence-based protocol for the detection and quantification of RAD51 nuclear foci in cultured ovarian cancer cells. The method involves induction of DNA damage by ionizing radiation (IR), followed by fixation, immunostaining with antibodies against RAD51 and γH2AX, confocal microscopy, and manual quantitative analysis of RAD51/γH2AX co-localized foci. The protocol can be applied under basal conditions or after genetic and pharmacological perturbations to determine their effects on HR function. Representative results demonstrate robust induction of RAD51 foci in HR-proficient ovarian cancer cells following DNA damage, whereas RAD51 depletion markedly reduces foci formation despite comparable levels of DSBs, confirming assay specificity. Overall, this protocol provides a robust and reproducible functional assay for assessing HR competency, with broad applications in preclinical and potentially translational cancer research.

Chronic myelomonocytic leukemia (CMML) is a clonal myelodysplastic/myeloproliferative neoplasm characterized by sustained monocytosis, recurrent gene mutations, and a risk of transformation to acute myeloid leukemia (AML). This review examines the historical evolution of CMML as a diagnostic entity, its genetic landscape, fundamental controversies in definition, including the contentious boundaries of oligomonocytic CMML (OM-CMML), and the spectrum of associated phenomena, such as plasmacytoid dendritic cell proliferations, systemic mastocytosis, extramedullary disease, and autoimmune manifestations.

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with limited therapeutic options, driven in part by its immunosuppressive tumor microenvironment (TME). Tumor-associated macrophages (TAMs) and neutrophils (TANs) contribute to tumor progression and immune evasion. A Disintegrin and Metalloproteinase 8 (ADAM8), a zinc-dependent protease, is strongly upregulated in PDAC and correlates with poor clinical outcomes, suggesting a regulatory role in tumor progression.

Medullary thyroid carcinoma (MTC) is characterized by frequent RET mutations, while non-RET alterations remain less well studied. Previous reports have identified a recurrent STK11 c.1062 C > G (p.Phe354Leu) variant in MTC, but its clinicopathologic and functional significance remains uncertain.

This study describes the development and analytical validation of a DNA-based quantitative PCR (qPCR) assay for detecting the NPM1 Type A mutation (NPM1-A mut) in acute myeloid leukemia (AML). The assay employs a modified wild-type blocker (WTB) to preferentially suppress amplification of wild-type (WT) alleles, thereby enriching mutant targets.

Dihydropyrimidine dehydrogenase (DPD), which is encoded by the DPYD gene, plays an important role in the metabolism of fluoropyrimidine (FP) drugs, including tegafur, in S-1. A decrease in DPD activity can cause severe FP-related toxicity. The Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines for FP and DPYD polymorphisms recommend FP dose adjustments based on the four major DPYD polymorphisms. However, multiple rare variants of DPYD have been reported. We present the case of a man in his 50s with cT3N0M0 tongue squamous cell carcinoma who developed severe myelosuppression and diarrhea after the initiation of S-1 (tegafur/gimeracil/oteracil) despite appropriate dosing. On day 20 of treatment, the patient developed grade 4 neutropenia and septic shock and required ICU admission. Genetic testing identified a rare heterozygous DPYD variant (c. 812delT) that causes a frameshift and a presumed loss of enzyme function, suggesting an underlying cause of the severe adverse events. Although severe toxicity occurred, marked tumor shrinkage allowed for less invasive surgery. This case highlights the need for expanded genetic screening beyond the guideline-listed variants, particularly in Asian populations, where common variants differ. Combining genotypic and phenotypic evaluations of DPD activity may improve the prediction and prevention of FP-related toxicities, supporting safer and more effective use of FP drugs.

Exosome-mediated delivery of small interfering RNA (siRNA) has emerged as a promising therapeutic strategy for cancer treatment, offering precise gene silencing with minimal off-target effects. Exosomes, naturally secreted extracellular vesicles, provide biocompatible carriers that protect siRNA from enzymatic degradation and facilitate efficient uptake by tumor cells. Their natural tropism, driven by surface proteins such as integrins and tetraspanins, promotes cellular adhesion and interactions within the tumor microenvironment, facilitating the delivery of therapeutic cargo. Preclinical studies have demonstrated that exosome-delivered siRNAs can suppress oncogenes, inhibit tumor growth, reverse chemoresistance, and modulate immune responses by targeting stromal and immune components. Engineering approaches, including surface functionalization and hybrid exosome-nanoparticle systems, further enhance stability, payload capacity, and tumor-homing efficiency. Combination strategies with chemotherapy, immunotherapy, or phototherapy have shown synergistic effects, allowing simultaneous inhibition of survival pathways, promotion of apoptosis, and remodeling of the immunosuppressive microenvironment. Early-phase clinical studies indicate safety, effective biodistribution, and functional gene silencing, highlighting the translational potential of exosome-mediated siRNA therapeutics. Challenges such as scalable production, cargo heterogeneity, and regulatory considerations remain, but ongoing advances in exosome engineering and patient-derived vesicles are poised to overcome these barriers. This review aims to comprehensively summarize the current state, therapeutic applications, and translational prospects of exosome-mediated siRNA delivery in cancer.

Osteosarcoma (OS) is the most common bone cancer, known for its aggressive nature, high chemoresistance, and strong metastatic potential responsible for poor clinical outcomes. In this context, identifying reliable biomarkers and therapeutic targets is therefore critical. This study investigates the role of paraoxonase-2 (PON2), an intracellular enzyme known for its anti-oxidative and anti-apoptotic properties. PON2 overexpression has been observed in various cancers and is implicated in tumor development and progression.

The NOTCH1 gene and its signaling pathway play a critical role in the oncogenesis and progression of various carcinomas through complex cellular and molecular mechanisms. This integrative literature review examines 21 selected studies across multiple carcinoma types, including head and neck, prostate, penis, breast, and hepatocellular carcinomas, to elucidate the functional impact of notch1 alterations on tumor behavior and clinical outcomes. NOTCH1 functions as a context-dependent regulator, acting either as an oncogene or tumor suppressor according to cellular environment and molecular context. Aberrations in notch1 signaling influence cell proliferation, differentiation, apoptosis, and angiogenesis, thereby contributing to cancer initiation and progression. Despite some variability in findings, the majority of studies indicate that notch1-related molecular changes have significant implications for prognosis and potential therapeutic targeting. This review highlights the importance of understanding notch1 signaling pathways in the cellular and molecular biology of carcinomas, aiming to pave the way for novel diagnostic and treatment strategies.

Colon cancer is one of the most prevalent cancers globally, characterized by the abnormal growth of cells in the intestines. Numerous studies have explored the effects of pomegranate-derived products, such as pomegranate seed oil (PSO), as anti-proliferative, anti-invasive, and pro-apoptotic agents against various cancer cell lines. Additionally, previous research has highlighted the anti-cancer properties of low-frequency electromagnetic fields (LF-EMF). In the present study, we investigated the combined effects of these two factors on the expression of the Caspase 3, Caspase 9, BAX, and Bcl2 genes. Human colon cancer cells of the HT29 line were sourced from the Pasteur Institute of Iran cell bank and maintained in a complete culture medium. The cells were categorized into four groups: control, PSO, EMF, and PSO+EMF. To assess cell viability and the type of cell death, MTT and Annexin V-FITC assays were employed. Changes in the expression levels of Caspase 3, Caspase 9, BAX, and Bcl2 were analyzed using Real-Time PCR. The results from the MTT and Annexin V-FITC assays indicated that both PSO and EMF reduced cell viability and promoted apoptosis in colon cancer cells. The Real-Time PCR results showed an upregulation of Caspase 3, Caspase 9, and BAX genes, along with a downregulation of Bcl2 expression in the treatment groups compared to the control group. This study demonstrated that the combination of PSO and EMF enhances apoptotic gene expression, thereby diminishing the proliferation and viability of cancer cells. Based on these findings, both PSO and LF-EMF exhibit cytotoxic effects on colon cancer cells, suggesting their potential as candidates for future research in the field of colon cancer.