To detect precise DNA methylation patterns in long-read DNA sequencing analysis, an efficient target enrichment method is needed. In this study, we established t-nanoEM, a practical method that integrates a hybridization-based capture step into a long-read enzymatic methyl (EM)-seq library for nanopore sequencing. We achieved a high sequencing coverage of up to ×570 at 5 kb N50 in length. We applied this method to the long-read methylation analysis of cancers. Using breast cancer as an example, we demonstrated that the signature changes in DNA methylation occurring in local cell populations could be displayed in a haplotype-aware manner. In lung cancer, the spatial diversity in gene expression as detected by the spatial expression profiling analysis may be associated with changes in DNA methylation.

Establish and validate a radiomics models based on computed tomography (CT) images to predict NRAS status in colorectal cancer patients.

Our previous findings indicate Semaphorin 4D (Sema4D) as a potential pediatric leukemia biomarker, promoting leukemogenesis via PI3K/AKT and ERK pathways, but its upstream regulatory mechanisms remain unclear. This study was conducted to explore the potential regulatory relationship between Insulin growth factor 2 mRNA binding protein 3 (IGF2BP3) and Sema4D in acute myeloid leukemia (AML).

The functional significance and clinical relevance of the translesion DNA synthesis polymerase subunit REV3L in bladder urothelial carcinoma (BLCA) require comprehensive characterization.

Lung cancer accounts for the highest number of cancer-related deaths globally, largely due to its high propensity for early and widespread metastasis. Calpains, a family of calcium-dependent cysteine proteases, are involved in various physiological processes, including cytoskeletal remodeling, migration, and invasion. Among them, calpain-2 has been implicated in promoting cancer cell invasiveness and metastatic behavior, although its precise role in non-small cell lung cancer (NSCLC) remains poorly understood. In this study, calpain-2-deficient cells were generated from the A549 lung adenocarcinoma cell line using CRISPR/Cas9 technology, and the effects of calpain-2 loss on cell migration, invasion, and epithelial-mesenchymal transition (EMT) were evaluated in comparison with control cells. We also evaluated the effects of transforming growth factor-β (TGF-β), a cytokine known to regulate diverse cellular processes, including proliferation, migration, and differentiation. Our results demonstrated that calpain-2 deficiency significantly reduced cell migratory capacity, EMT progression, and invasive potential following TGF-β stimulation. These effects were mediated by multiple molecular mechanisms, including impaired actin filament remodeling due to calpain-2 deficiency, reduced activation of Matrix Metalloproteinase (MMP)-2 and MMP-9, and decreased expression of EMT-related transcription factors such as Snail, Slug, and ZEB1. Collectively, these findings suggest that calpain-2 plays a central role in TGF-β-mediated cancer cell migration, invasion, and EMT progression, and that targeting calpain-2 function may represent a potential therapeutic strategy for inhibiting lung cancer metastasis.

The penetrant D463H mutation in PRKCA, which encodes the kinase PKCα, is a biomarker and driver of chordoid glioma, a type of brain cancer. Here, we found that heterozygous knock-in expression of the D463H mutant in mice elicited the development of chondrosarcomas. The mutant protein kinase was catalytically inactive, but no such oncogenic phenotype was observed for the related inactivating mutation D463N, indicating that the lack of activity per se was not the cause of the oncogenicity of the D463H mutant. In cultured glioma cells, the behavior of the D463H mutant closely mirrored that of wild-type PKCα and retained ATP binding, unlike the related D463N mutant. Mechanistically, PKCα D463H displayed quantitative alterations in its interactome compared with that of the wild-type kinase, with enhanced association with epigenetic regulators. This change in the interactome aligned with transcriptomic changes that resembled an increased PKCα-induced expression program, with enhanced gene signatures mediated by BRD4, MYC, and TGF-β. D463H expression reduced the sensitivity of cells to the BET inhibitors JQ1 and AZD5153, indicating the functional importance of these pathways. The findings indicate that D463H is a dominant gain-of-function oncogenic mutant that operates through a noncatalytic allosteric mechanism.

Given the urgent need for more specific, sensitive, and non-invasive markers for prostate cancer screening and differential diagnosis, circulating miRNAs have emerged as valuable candidates. Sixty seven prostate cancer subjects in different stages were included in this study. The participants were categorized into groups based on their pathological characteristics as local, biochemical relapse and metastatic. We retrieved eligible datasets from GEO database to identify stage-specific differentially expressed up/down-regulated genes. Cytohubba, built-in application of Cytoscape software, and Reactome pathway database were applied to select hub genes. To select upstream miRNAs, we utilized the MiRWalk and miRNet online tools. To construct the miRNA-mRNA regulatory networks, we employed rna22. Finally, three miRNAs and five target genes were validated in peripheral blood mononuclear cells of PCa patients compared with benign prostate hyperplasia. PSA level was also measured using ELISA. Our findings revealed the potential role of PRC1 and UBA52 to be used as biomarkers for the metastatic stage, RCC1 for both biochemical relapse, and metastatic subjects. Furthermore, elevated levels of miR-124-3p and downregulation of miR-133a-3p can be introduced as biochemical relapse stage identifier. We also identified the tumor suppressor role of miR-17-5p, which was associated with higher Gleason scores. We propose PRC1, UBA52, RCC1, miR-124-3p and miR133a-3p as stage-specific PCa identifiers.

Lung adenocarcinoma (LUAD) is a highly aggressive lung cancer with poor prognosis due to lack of reliable biomarkers. Resistance to anoikis drives tumor progression and metastasis. This study aims to develop and validate an anoikis-related prognostic model for LUAD. We employed univariate Cox regression analysis, LASSO regression, and random forest algorithms to identify anoikis-related genes (ARG) from bulk transcriptomic datasets, and establish a 7-gene prognostic signature, validated in two LUAD cohorts from GEO database. We evaluated immune infiltration, molecular functions, and genomic alterations between risk groups and analyzed single-cell RNA sequencing data. IHC and mIF validated TIMP1 expression and its interaction with Treg cells. We developed a 7-gene prognostic model (LDHA, PLK1, TRAF2, ITGB4, SLCO1B3, TIMP1, ZEB2) using machine learning to predict survival in LUAD patients. The model accurately predicted 1-year survival rates (GSE31210: AUC = 0.805; GSE30219: AUC = 0.787), 2-year survival rates (GSE31210: AUC = 0.769; GSE30219: AUC = 0.681), and 3-year survival rates (GSE31210: AUC = 0.695; GSE30219: AUC = 0.735) and correlated with clinical features, immune infiltration, and tumor microenvironment (TME) remodeling. Single-cell sequencing data showed that LUAD patients exhibited an immunosuppressive TME phenotype, which was exacerbated by high TIMP1 expression in epithelial cells, promoting Treg cell activity. The 7-gene ARG prognostic model established in this study shows promising potential as a clinically applicable tool for decision-making.

Background Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death worldwide. Lenvatinib is a common first-line treatment for advanced HCC. However, resistance to lenvatinib is the greatest challenge limiting its clinical application. Currently, the molecular mechanisms of resistance remain poorly understood. Methods The expression of DDX1 and Ephrin-A3 in lenvatinib-resistant HCC cells was identified via RNA-seq and Western blotting. Bioinformatic analyses were applied to explore its expression and prognostic role. The biological role of DDX1 was evaluated via CCK8, EdU, flow cytometry analyses and xenograft tumor model. The regulation between DDX1 and Ephrin-A3 was determined by mass spectrometry, coimmunoprecipitation, RNA Immunoprecipitation, and RNA stability assay. Results We successfully established lenvatinib-resistant HCC cells. The results of RNA-seq showed DDX1 and Ephrin-A3 were significantly increased in lenvatinib-resistant HCC cells compared to parental cell. The DDX1 expression in HCC tissues is positively associated with worse prognosis. DDX1 knockdown increased the sensitivity of cells to lenvatinib by inhibiting proliferation and promoting apoptosis in vitro and in vivo. Conversely, overexpression of DDX1 exhibited the opposite regulation. Moreover, DDX1 bound to Ephrin-A3 and regulated its expression levels. The effects of DDX1 overexpression on cell proliferation, apoptosis, and lenvatinib resistance were significantly blocked by Ephrin-A3 knockdown. Mechanistically, DDX1 promotes lenvatinib resistance in HCC by regulating Ephrin-A3 mRNA stability and activating the Wnt/β-catenin pathway. Conclusion: The increased DDX1 expression in HCC cells promotes lenvatinib resistance via regulating Ephrin-A3 mRNA stability and activating the Wnt/β-catenin pathway, indicating that targeting DDX1 may be an important strategy for overcoming lenvatinib resistance.

Despite evidence linking histone lactylation to tumorigenesis, its specific regulatory role in laryngeal squamous cell carcinoma (LSCC) is still not well defined. Histone H3K18 lactylation (H3K18la) levels in LSCC tissues were analyzed by immunohistochemistry (IHC) and western blot, showing significantly higher levels than non-tumor tissues. Treatment with the sodium oxamate (SO) effectively reduced H3K18la level, thereby suppressing LSCC cell proliferation and migration while inducing apoptosis. Mechanistically, H3K18la upregulated Runt-related transcription factor 2 (RUNX2) expression, which in turn activated the phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) signaling pathway to promote aggressive LSCC phenotypes. Our findings demonstrate that H3K18la facilitates LSCC progression by enhancing malignant cellular behaviors, thereby offering potential therapeutic targets for LSCC intervention.

The widespread use of pesticides such as deltamethrin (a pyrethroid) and acetamiprid (a neonicotinoid) has sparked concerns regarding their effects on human health, particularly their potential role in carcinogenesis. This study investigated the cytotoxic, molecular, and functional effects of these pesticides, individually and in combination, on the MDA-MB-231 triple-negative breast cancer (TNBC) cell line. This model was chosen to specifically investigate estrogen recpetor (ER)-independent mechanisms due to its expression of targets such as aryl hydrocarbon receptor (AhR), peroxisome proliferator-activated receptor gamma (PPARγ), and G protein-coupled estrogen receptor (GPER); however, it does not reflect normal mammary cell responses. Cytotoxicity was assessed via XTT assays, migration was analyzed using wound-healing assays, and gene expression changes in AhR, PPARγ, and Caspase-3 were measured using RT-qPCR. Molecular docking was performed to predict pesticide-protein interactions, and in silico toxicity assessments using ProTox-II supplemented the in vitro results by predicting toxicity profiles relevant to public health. Both pesticides exhibited dose-dependent cytotoxicity, and their combination produced an additive effect on cell viability. Importantly, suppression of cell migration and downregulation of AhR and PPARγ expression reflected toxic stress responses at high pesticide concentrations, rather than therapeutic or anti-cancer potential. While apoptosis-related gene expression (Caspase-3) was increased, this effect did not reach statistical significance. Molecular docking supported strong interactions with key pathways related to xenobiotic metabolism and apoptosis. These findings emphasize that, at high and non-environmentally relevant concentrations, deltamethrin and acetamiprid induce additive cytotoxic effects and disrupt molecular processes in a mechanistic cancer model. The results highlight the need for further investigation using normal cell systems and environmentally relevant exposures to clarify real-world risk and biological mechanisms, and should not be interpreted as evidence of therapeutic activity. This study underscores the mechanistic relevance of pesticide exposure in environmental toxicology rather than any potential therapeutic application.

This manuscript presents a letter to the editor addressing the study by Lv et al. (J Mol Histol 56(2):129, 2025), which identifies PDZ-binding kinase (PBK) as a diagnostic and prognostic biomarker for hepatocellular carcinoma (HCC). While commending the article's comprehensive approach-including bioinformatics integration and validation of PBK's role in immune infiltration and methylation-the authors highlight three critical areas for improvement to enhance the study's rigor and clarity. First, they identify methodological issues in differential gene analysis, recommending RNA-seq-specific tools (e.g., DESeq2) over misapplied microarray frameworks like limma. Second, they critique the presentation of statistical significance, urging clearer reporting of P-values (e.g., P < 0.001) instead of P < 0.000. Third, they dispute the unrealistic survival curve in Fig. 2, suggesting evidence-based adjustments to reflect clinical plausibility. The letter emphasizes that addressing these concerns would strengthen the findings' impact on HCC research.

Osteosarcoma (OS) is a highly aggressive malignant bone tumor predominantly affecting adolescents and children. Extracellular vesicles (EVs) significantly contribute to the progression of osteosarcoma by promoting intercellular communication via the transportation of biomolecules and activation of signaling pathways. However, the specific role of tenascin-C (TNC) transmitted by EVs in osteosarcoma remains poorly understood. In this study, we reanalyzed mass spectrometry data of osteosarcoma-derived EV proteins from public databases. EVs were isolated and characterized using standard protocols. The expression levels of EV-derived TNC (EVs-TNC) were measured by western blot or enzyme-linked immunosorbent assay. Functional assays were used to elucidate the role of EVs-TNC in promoting OS malignancy. Transcriptome sequencing was conducted to identify downstream effectors of EVs-TNC. Our results revealed elevated circulating EVs-TNC concentrations in OS patients versus healthy controls. Furthermore, EVs-TNC derived from OS cell lines (SJSA-1 and 143B) were internalized by MG-63 cells, enhancing their proliferative and migratory capabilities. Mechanistically, EVs-TNC was found to regulate angiotensin II receptor type 1 (AGTR1) expression, suggesting a potential signaling pathway involved in OS progression. This study highlights the role of EVs-TNC in promoting OS proliferation and migration, indicating that targeting EVs-TNC may offer a novel treatment strategy for osteosarcoma.

Breast cancer is the leading cancer type that is reported in women worldwide, with its 2.3 million annual incidence and 685,000-related deaths (WHO, 2023). Although genetic mutations have proven to be major driving agents of tumorigenesis, the tumor microenvironment (TME) is increasingly being considered as the definitive indicator of disease progression, metastasis, immune evasion and therapeutic resistance. It is an active, diverse cellular webwork of substances cancer-related fibroblasts, (CAFs), tumor-related macrophages, (TAMs), regulatory T cells, (Tregs), myeloid-derived suppressor cells (MDSCs), and cancer-related adipocytes; (CAAs). These cellular processes interact reciprocally with not only malignant cells through paracrine communication but also through the composition of the extracellular matrix, (ECM). Recent research indicates that CAFs produce pro-invasive factors i.e. TGF-B and HGF whereas TAMs tend to be M2-like and secret VEGF and IL-10 to encourage angiogenesis and immune subversion. Cytokines, chemokines, ECM proteins, and tumor-derived EVs are non-cellular factors serving to alter cellular phenotypes and facilitate construction of metastatic niche. Besides oncogenic microRNAs (e.g., miR-21, miR-10b) that is released in exosome, hypoxia-mediated activation of HIF-1a induces both neovascularization and metabolic reprogramming. The repolarization of TAM (e.g. CSF1R inhibitors) and depletion of CAF and inhibition of EV pathway are also being explored as therapeutic mechanisms against TME resistance and are in preclinical and clinical development. In particular, the combination procedures with immunomodulation and TME disruption have demonstrated some success in conquering resistance in TNBC models. Therefore, it is paramount to understand how the surrounding tissue, the immune system, the immune system, and other elements behave over time and space as cofounding partners of tumors, in a way that would create better precision and clinical outcomes in breast cancer patients.

The Qing-Re-Yi-Liu decoction (QRYLD) is a clinically effective prescription for treatment of breast cancer. Our preliminary studies found that QRYLD treatment interfered with the Warburg effect in breast cancer cells. However, its chemical components and molecular mechanisms have not been clarified. This study analyzed the bioactive components of QRYLD aqueous extracts by HPLC. The effects of QRYLD on the malignant behaviors of MCF-7 cells and potential mechanisms were analyzed by CCK-8, transwell invasion, wound-healing assays, flow cytometry, Western blot assays and transcriptomic analysis as well as in vivo mouse tumor model. QRYLD aqueous extracts contained several bioactive components. Transcriptomic analysis indicated that QRYLD treatment altered the expression of several genes involved in biological processes and signaling pathways, such as manganese superoxide dismutase (MnSOD). Functionally, QRYLD, similar to MnSOD silencing, inhibited the malignant behaviors of MCF-7 cells and enhanced their apoptosis, whereas MnSOD overexpression had the opposite effects. Moreover, QRYLD treatment inhibited the Warburg effect by limiting glucose uptake and lactic acid production, and decreasing the relative expression of glucose transporter-1, hypoxia-inducible factor 1α, c-Myc, hexokinase-2, phosphofructokinase 1, lactate dehydrogenase A, pyruvate kinase isozyme 2, MnSOD, calmodulin-dependent kinase II (CaMKII), and AMP-activated protein kinase (AMPK) in MCF-7 cells. Finally, treatment with QRYLD significantly inhibited the growth of xenografted MCF-7 tumors in mice and reduced the tumor expression of MnSOD, CaMKII, and AMPK. These data suggest that QRYLD may target MnSOD to attenuate the MnSOD/CaMKII/AMPK signaling, inhibiting the Warburg effect and malignant behaviors in breast cancer.

Diagnosing papillary thyroid carcinoma (PTC) remains challenging, particularly due to limitations in fine-needle aspiration biopsy (FNAB), which yields up to 10% nondiagnostic results. The objective of this study was to evaluate the diagnostic and prognostic potential of four candidate microRNAs (miR-21, miR-31, miR-187-3p, and miR-200a-5p) in PTC from multinodular goiter (MNG) and normal. Fresh tissue samples from PTC and MNG patients were analyzed using quantitative RT-PCR, followed by ROC analysis to assess diagnostic accuracy and correlation with clinical, histopathological, and hormonal parameters. Compared to normal tissue, miR-21 and miR-187-3p were significantly upregulated in PTC, while miR-31 and miR-200a-5p were downregulated. MNG samples showed similar but less pronounced trends. All four miRNAs differed significantly between PTC and MNG. ROC analysis revealed strong diagnostic performance, particularly for miR-187-3p (AUC = 0.937) and miR-21 (AUC = 0.914), with their combination achieving an AUC of 0.968. Expression levels correlated with age, tumor stage, surgical status, and thyroid hormones (TSH, ATG, TG), highlighting novel regulatory patterns. This miRNA panel offers promising diagnostic value and insight into PTC pathogenesis, suggesting potential for non-invasive diagnostics and targeted therapies.

Prostate cancer (PC) remains a leading cause of cancer-related mortality in men, with recurrence contributing significantly to poor outcomes. Its molecular heterogeneity complicates effective risk stratification. We evaluated Sig27, a novel 27-gene panel, across 13 bulk RNA-seq datasets (n = 3,133 tumors) and 6 single-cell RNA-seq (scRNA-seq) datasets (n = 53 patients). Sig27 expression was elevated in PC compared to normal tissue and further increased in high-grade Gleason tumors, node-positive, and recurrent tumors. Sig27 demonstrated recurrence prediction comparable to Oncotype DX, with strong enrichment in immune regulatory pathways. To further investigate immune associations, we developed SigIC, a 22-gene immune checkpoint panel. Sig27 showed strong correlations with SigIC and individual immune checkpoints (e.g., HAVCR2, CD96, TIGIT) in both primary and metastatic PC. In scRNA-seq data, Sig27 was enriched in tumor-associated monocytes/macrophages (TAMs) and endothelial cells. We identified five key Sig27 genes - TFEC, FPR3, NOD2, LAMP3, and MCTP1 - and constructed Sig27IMG, a multigene panel formed by these five genes, and demonstrated their robust correlations with immune checkpoints and their strong enrichment in TAMs and endothelial cells. Sig27IMG strongly predicted PC recurrence and was dominantly expressed in TAMs, dendritic cells, and endothelial cells across 26 cancer types (n = 386 patients) in scRNA-seq studies and 17 cancer types (n = 5,672 patients) in bulk RNA-seq investigations. Notably, Sig27IMG stratified patients with a poor prognosis risk in these 17 cancer types. In summary, Sig27 and its derivative panel, Sig27IMG, offer a robust assessment of PC recurrence, highlighting immunosuppressive features mediated by TAMs, dendritic cells, and endothelial cells across multiple cancer types.

Multiple myeloma (MM) remains an uncurable hematologic cancer due to neoplastic proliferation of plasma cells. The role and detailed mechanisms of Ubiquitin-Specific Protease 4 (USP4) in MM remain to be clarified. Cell viability and apoptosis were evaluated by CCK-8 and TUNEL. Molecular expression was determined by RT-qPCR, Western blotting, and immunohistochemistry. The morphology of endoplasmic reticulum (ER) was observed by ER tracker-red. The protein interaction and ubiquitination level were evaluated by Co-IP. The binding of myocyte enhancer factor 2A (MEF2A) to the USP4 promoter was confirmed by ChIP and dual luciferase reporter assay. The in vivo growth of MM was monitored by subcutaneous xenograft experiments. USP4 knockdown suppressed MM cell proliferation and triggered ER stress and apoptosis, whereas USP4 overexpression resulted in the opposite effect. Mechanistically, USP4 enhanced nuclear receptor subfamily 4 group A member 1 (NR4A1) protein stability by inhibiting its ubiquitination. MEF2A bound to the USP4 promoter to activate its transcription and expression. The promotive effect of sh-USP4 or sh-MEF2A on ER stress and apoptosis of MM cells was counteracted by NR4A1 or USP4 overexpression. MEF2A deficiency restrained in vivo MM growth by activating ER stress and apoptosis through modulation of the USP4/NR4A1 pathway. MEF2A activates USP4 to repress ER stress and apoptosis of MM cells via deubiquitination of NR4A1, thus favoring MM progression. Our findings identify USP4 as an attractive intervention target for MM therapy.

As neuroblastoma is a highly heterogeneous pediatric solid tumor, it is essential to select appropriate reference genes to compare the concentration of circulating free DNA (cfDNA) between patients with neuroblastoma and healthy individuals. cfDNA was extracted from peripheral blood and quantified using quantitative Polymerase Chain Reaction (qPCR). The stability of candidate reference genes (RGs) was analyzed using the ΔCt method, geNorm, NormFinder, and BestKeeper. The results from these four algorithms were integrated using the RefFinder tool to generate a comprehensive stability ranking and assess the stability of these candidate RGs across different sample groups. Alpha hemoglobin stabilizing protein (AHSP) and Hypoxanthine-Guanine Phosphoribosyltransferase 1 (HPRT1) exhibited the highest stability, whereas Beta-2-microglobulin(B2M) and HBS1-like protein(HBS1L) demonstrated the lowest stability. qPCR of cfDNA from patients with neuroblastoma revealed differences in the stability of various reference genes. Prioritizing reference genes with better stability may facilitate more accurate detection of intergroup differences in the samples.

The integration of regional hyperthermia into the multimodal treatment of patients with localized high-risk soft tissue sarcomas has been shown to improve overall survival. However, specific effects on the tumors' genetic makeup and biology are largely unknown. Since clonal selection of malignant cells capable of thermoresistance might contribute to disease progression, a better understanding of the induced tumor evolution could inform strategies for improving treatment efficacy.