Search Results (9,735)

As a noninvasive liquid biopsy approach, extracellular vesicle (EV)-based detection offers significant advantages in reflecting real-time tumor dynamis and overcoming the limitations of conventional tissue biopsy. EVs, nanoscale vesicles secreted by cells, carry diverse biomolecules such as proteins and nucleic acids, playing key roles in tumor progression, metastasis, and immune evasion, and have emerged as promising biomarkers for cancer liquid biopsy. Surface-enhanced Raman spectroscopy (SERS), characterized by high sensitivity, resistance to photobleaching, minimal sample consumption, and multiplexing capability, has shown great potential in EV analysis. This review systematically summarizes current methods for EV isolation, characterization, and storage, with a focus on label-free and label-based SERS detection strategies for early cancer diagnosis, treatment response monitoring, and prognosis evaluation. Furthermore, the integration of SERS with machine learning and deep learning algorithms has substantially improved diagnostic accuracy and cancer subtyping. Despite remaining challenges, such as optimization of SERS substrate performance, intelligent processing of Raman spectral fingerprints, and clinical translation, EV-based SERS technology holds great promise for precision oncology. Full article

Background/Objectives: Breast cancer (BC) is the most frequently diagnosed malignancy and a leading cause of cancer-related mortality in women worldwide. This disease is highly heterogeneous and dynamic, and chromosomal instability (CIN) plays a key role in the acquisition of these traits by generating genetic diversity that promotes tumor adaptation and influences therapeutic response and prognosis. Although several methods have been developed to quantify CIN, they are not readily applicable to human tumors and are limited in resolution, hindering a comprehensive understanding of intratumoral heterogeneity. In this study, we aimed to quantify CIN levels and clonal heterogeneity (CH) in HER2-positive (HER2+) and triple-negative (TNBC) breast cancer using single-cell RNA sequencing (scRNA-seq) data. Methods: We analyzed publicly available scRNA-seq data from HER2+ and TNBC tumors and non-malignant controls. CIN was scored at single-cell resolution using transcriptomic signatures, clonal heterogeneity was estimated from single-cell diversity metrics, and copy number alterations were inferred computationally. Differential expression and functional enrichment analyses were performed between cells with very low and extreme CIN levels, with key comparisons confirmed at the patient level. Results: Our analyses revealed pronounced intra- and intertumoral heterogeneity, with higher CIN levels in TNBC than in HER2+ and control samples. Genes differentially expressed in cells with extreme CIN values were mainly involved in cell division and related processes, and included candidate biomarkers not previously reported in this context. Our findings suggest a positive but statistically non-significant trend was observed between CIN and CH. Conclusions: Single-cell approaches such as scRNA-seq provide a powerful framework to elucidate CIN-related mechanisms and to identify potential biomarkers of BC aggressiveness and prognosis, supporting their further application in the study of intratumoral heterogeneity. Full article

The benefits of lenalidomide, which leverages TP53-dependent apoptosis and promotion of megakaryocytic differentiation, in lower-risk MDS (LR-MDS) with del(5q) are well-established and drive its frequent use in clinical practice. In parallel, advances in molecular testing have elucidated the clear impact of TP53 mutations on response to therapies and prognosis, with diversity in the latter informed by variant allele frequency (VAF) and/or predicted allelic state. In this review, we discuss the converging pre-clinical and clinical evidence that implicates TP53 mutations not only as a driver of lenalidomide resistance in del(5q) LR-MDS, but as a source of selective clonal advantage under lenalidomide exposure. Lenalidomide-induced CK1α degradation triggers TP53-mediated apoptosis in wild-type clones, inadvertently favoring the survival and expansion of TP53-mutated cells. Clinically, this dynamic has been demonstrated across multiple studies, with rising TP53 variant allele frequency and clonal evolution observed following treatment. These findings underscore the importance of baseline molecular assessment in patients with MDS and, in select cases, serial monitoring during therapy. Investigational approaches for del(5q) LR-MDS with the TP53 mutation include GATA2-directed strategies aimed at restoring lenalidomide sensitivity, as well as immune-based therapies targeting the tumor microenvironment characteristic of TP53-mutated disease. Full article

Background/Objectives: Hepatocellular carcinoma (HCC) is the most prevalent primary liver tumor and is often diagnosed at advanced stages with very poor therapeutic response, leading to high mortality. Thus, new therapeutic strategies and biomarkers are urgently needed. We previously showed that the combination of loratadine, raloxifene, and sorafenib exerts synergistic cytotoxicity on HCC cells. Here, we explored potential molecular mechanisms underlying the anticancer effects of this combination using multiomics analyses. Methods: We performed proteomic analyses based on mass spectrometry, transcriptomic analyses using the Clariom D Plus human microarray (Affymetrix), and metabolomic analyses based on nuclear magnetic resonance to investigate the profile changes induced by the drug combination in HuH7 cells. Bioinformatic analyses were applied to associate the omics changes with biological functions, molecular interactions, and clinical relevance in terms of patient survival. Results: We identified several molecules whose expression changed in response to treatment across the three omics profiles analyzed. Some of them were found to be involved in hallmarks of cancer, including sustained proliferation, evasion of growth suppressors, and resistance to cell death. Integrated multi-omics analyses revealed that the drug combination suppresses critical oncogenic drivers (C7orf50, NUP188, and HS2ST1) and that the mitotic cell cycle process, DNA synthesis and cholesterol biosynthesis are the primary pathways affected. Protein–protein interaction analysis revealed five key hubs (KIF2C, PCNA, TRIP13, NDC80, and RPA3), whose expression in HCC is associated with poor clinical prognosis. Conclusions: The combined treatment rewired molecular networks involved in HCC progression. These findings identify clinically relevant molecular targets associated with poor prognosis and provide mechanistic insights into the synergistic anticancer activity of this drug combination. Full article

Glioblastoma and diffuse gliomas pose major therapeutic challenges due to marked intratumoral heterogeneity, limited tissue accessibility, and the blood–brain barrier. Tissue-based next-generation sequencing (NGS) remains essential for WHO CNS5 molecular classification, yet it is invasive and poorly suited to serial monitoring. Two complementary non- or minimally invasive approaches have advanced rapidly: radiogenomics, which correlates multiparametric MRI features with genomic alterations, and cerebrospinal fluid (CSF) liquid biopsy sequencing, which detects circulating tumor DNA with high tissue concordance. This review examines the independent progress and synergistic integration of radiogenomics and CSF-NGS. Imaging signatures can non-invasively predict key drivers (IDH1/2, EGFR, TERT, PTEN, TP53) and molecular subtypes, while CSF-ctDNA sequencing enables real-time assessment of clonal evolution, therapy resistance (including post-temozolomide hypermutation), and residual disease. We discuss technical considerations, performance metrics, multimodal artificial-intelligence fusion, and emerging clinical applications for diagnosis, prognosis, treatment selection, and longitudinal surveillance. Critical challenges, standardization, prospective validation, and workflow integration are highlighted. By combining the spatial phenotypic information of radiogenomics with the temporal genomic resolution of CSF sequencing, this multimodal strategy offers a promising path toward precision neuro-oncology and reduced reliance on repeated invasive sampling. Full article

Background: Portal vein tumor thrombus (PVTT) marks advanced hepatocellular carcinoma (HCC) and carries a dismal prognosis. Survival varies widely even within this stage, yet simple tools for individualized risk stratification remain scarce. Methods: We retrospectively enrolled 134 HCC patients with PVTT and randomly divided them into a training set (n = 94) and a validation set (n = 40). Clinical predictors were selected by variance inflation factor screening and backward elimination Cox regression. A radiomics score (Rad-score) was constructed from portal-venous phase computed tomography (CT) images using Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression with 10-fold cross-validation. Three Cox models were built: a clinical model, an imaging model based solely on the Rad-score, and a combined model integrating both. Discrimination was assessed by C-index and time-dependent area under the curve (AUC). Calibration was examined with bootstrap-based calibration curves. Decision curve analysis evaluated net benefit. A nomogram was developed from the combined model. Results: Four clinical variables (alpha-fetoprotein (AFP), body mass index (BMI), high-density lipoprotein cholesterol (HDL-C), and alkaline phosphatase (ALP)) and two CT texture features (GLRLM_SRHGE and GLZLM_SZHGE) were retained as independent predictors. The combined model gave the highest C-index in both the training set (0.843) and the internal validation set (0.815). Its 1-year AUC reached 0.953 and 0.947 in the two sets. Calibration slopes ranged from 1.044 to 1.291 across time points, indicating a tendency toward mild overdispersion; nevertheless, decision curve analysis confirmed net benefit across clinically relevant thresholds. The combined model offered greater net benefit than either single-domain model across a 0–50% threshold range. A nomogram incorporating all five predictors was generated for individualized 12- and 24-month survival prediction. Conclusions: A combined model integrating routine laboratory variables and a CT-based radiomics score improved survival prediction over clinical or imaging models alone. The corresponding nomogram uses inputs from a basic blood panel and a single portal-venous phase CT, suggesting its potential as a low-cost prognostic stratification tool for HCC patients with PVTT, although external validation in prospective multicenter cohorts is required before clinical implementation. Full article

Background/Objectives: Ovarian cancer is a prevalent gynecological malignancy with high mortality rates worldwide. Harmine hydrochloride (HMH), a tricyclic β-carboline alkaloid derived from the seeds of the medicinal plant Peganum harmala L., has demonstrated anti-tumor activity. This study investigated the effect of HMH on ovarian cancer and elucidated its underlying molecular mechanism. Methods: The anti-ovarian cancer effects of HMH were evaluated using the CCK-8 assay, cell cycle and apoptosis analyses, as well as a cell migration assay. The RNA-seq was utilized to explore the mechanisms of HMH. Western blot, qRT-PCR and IF were employed for further validation of the expression levels of relevant molecules. The Kaplan–Meier (KM) curve was conducted to evaluate the possible link between NFAT1 levels and the prognosis of ovarian cancer. The biological functions of NFAT1 were explored through siRNA knockdown experiments. Auto-dock molecular docking and DARTS were used to analyze the direct interaction between HMH and NFAT1. The in vivo efficacy of HMH was examined through bioluminescence imaging of intraperitoneal xenografts established with luciferase-expressing HEY cells. Results: HMH induced apoptosis, arrested the cell cycle, and suppressed migration of HEY and CAOV3 cells. NFAT1 was highly expressed in the nucleus of HEY and CAOV3 cells and promoted ovarian cancer progression. In addition, low NFAT1 expression levels had significantly improved overall survival and progression-free survival. Moreover, HMH reduced NFAT1 expression and reversed Ion-induced NFAT1 levels in ovarian cancer cell nuclei. The molecular docking and DARTS results suggested that HMH binds to NFAT1. Treatment with MG132 effectively blocked HMH-induced NFAT1 downregulation. Furthermore, HMH effectively blocked intraperitoneal xenograft development, and extended the life span of animals bearing HEY/Luc cells, when used alone or in combination with CDDP. Conclusions: The research indicated that HMH exerts anti-ovarian cancer effects, at least in part, by targeting NFAT1. Additionally, our research revealed that NFAT1 promotes ovarian cancer progression, and plays a significant role in HMH’s anti-cancer activity. These results may aid in the development of novel candidates for ovarian cancer and identify a new target for ovarian cancer treatment. Full article

Background/Objectives: Prostate cancer remains one of the most common malignancies in men, and prognosis remains particularly challenging in patients with lymph node metastases. Cyclooxygenase-2 (COX-2), an inducible enzyme involved in inflammation and tumor progression, has been investigated as a potential prognostic biomarker and therapeutic target, but its expression in lymph node metastases remains unclear. While COX-2 overexpression in primary prostate tumors has been reported, its expression in lymph node metastases has not been thoroughly investigated. Therefore, this study aimed to compare COX-2 expression in primary prostate tumors and corresponding lymph node metastases and to evaluate its association with clinicopathological characteristics and survival. Methods: This study included 77 treatment-naïve patients with prostate cancer and histologically confirmed lymph node metastases who underwent radical prostatectomy with extended lymphadenectomy. COX-2 expression was assessed using immunohistochemistry in paired samples from primary tumors and corresponding lymph node metastases. Statistical comparisons were conducted using the Mann–Whitney U test and survival analyses were performed using Kaplan–Meier curves with the log-rank test. Results: COX-2 expression was detected in both primary tumors and lymph node metastases, with no significant difference in staining intensity between the two sites. High COX-2 expression in primary tumors was significantly associated with a higher percentage of involved lymph nodes (30.0% vs. 11.8%, p = 0.026), elevated postoperative PSA levels (1.98 vs. 0.10 ng/mL, p = 0.007), and reduced surgical radicality (11.1% vs. 63.2%, p = 0.008). Moreover, elevated COX-2 expression in both primary and metastatic tissues correlated with worse five-year overall survival (41.7% vs. 92.8%, p = 0.033; and 40.0% vs. 95.6%, p < 0.001, respectively). Conclusions: High COX-2 expression is associated with adverse clinicopathological features and poorer survival in lymph node–positive prostate cancer. The association of COX-2 expression with the extent of lymph node involvement and survival suggests that COX-2 may have prognostic value in this setting. However, the present findings do not establish a causal role of COX-2 in disease progression or lymphangiogenesis. Further studies are warranted to validate the prognostic significance of COX-2 and to clarify its potential biological and therapeutic relevance in lymph node–positive prostate cancer. Full article

Hepatocellular carcinoma (HCC) is one of the malignant tumors with high incidence and mortality rates worldwide. Given the poor prognosis of patients with HCC, it is crucial to explore the molecular mechanisms underlying HCC development and to evaluate prognostic markers. Differential expression analysis followed by univariate Cox, LASSO, and multivariate Cox regression identified four genes (EPO, SOCS2, IL18RAP, and KPNA2), and a Cox-based risk score was evaluated in the TCGA-LIHC cohort and externally in GSE14520 using Kaplan–Meier and time-dependent ROC analyses. Bulk, single-cell, and protein resources provided convergent expression context. Survival machine-learning analysis using observed overall-survival time and censoring status identified Cox–Ridge as the best-performing model in TCGA-LIHC, with more modest performance in GSE14520, and immune profiling revealed risk-group-associated differences in estimated immune and stromal components, immune-cell composition, and immune-checkpoint expression. The oncoPredict/GDSC2 screen highlighted five potential drug candidates for experimental prioritization. Because the drug screen is based on computationally predicted sensitivities, these findings should be regarded as hypothesis-generating and require validation in prospective cohorts and experimental systems before clinical translation. Full article

Background: Lymph node metastasis (LNM) is a major determinant of prognosis in gastric adenocarcinoma. Although lymphovascular invasion (LVI) and perineural invasion (PNI) are established markers of aggressive tumor behavior, their combined association with nodal dissemination has not been systematically evaluated. This study investigated the relationship between invasive histopathologic features and LNM and developed a composite invasion score. Methods: This retrospective study included 395 patients with gastric adenocarcinoma. Clinicopathological analyses involving LNM were performed in the surgical resection cohort. A composite invasion score (0–2) was generated based on the presence of LVI and PNI. Associations with LNM, metastatic lymph node burden, and lymph node ratio (LNR) were evaluated using non-parametric tests and multivariable logistic regression. Predictive performance was assessed using receiver operating characteristic (ROC) analysis. An exploratory external transcriptomic analysis was performed using the GSE15459 dataset. Results: Both LVI and PNI were significantly associated with LNM (both p < 0.001). The composite invasion score showed a stepwise association with nodal dissemination, with median metastatic lymph node counts increasing from 0 in score-0 tumors to 3.5 in score-1 and 9 in score-2 tumors (p < 0.001). After adjustment for pathological T stage, histological grade, Lauren classification, age, and tumor location, the composite invasion score remained an independent predictor of LNM (OR = 4.53, 95% CI: 1.81–13.00, p = 0.002). LNR also increased significantly across score categories (p < 0.001). The composite invasion score demonstrated good discriminatory performance for LNM (AUC = 0.848, 95% CI: 0.773–0.923). The exploratory transcriptomic analysis demonstrated significant upregulation of MMP11, MMP14, and FAP in advanced-stage tumors, consistent with increased extracellular matrix remodeling and stromal activation. Conclusions: A simple composite invasion score integrating LVI and PNI is independently associated with lymph node metastasis and metastatic burden in gastric adenocarcinoma. The accompanying exploratory transcriptomic analysis provides biological context for these clinicopathological findings by demonstrating stage-associated extracellular matrix remodeling rather than direct molecular validation of the proposed score. These findings support the potential utility of the composite invasion score as a postoperative pathology-derived risk stratification tool. Full article

(1) Background: Drug-eluting bead transarterial chemoembolization (DEB-TACE) is increasingly used for unresectable colorectal liver metastases (CRLM), yet individualized prognostic tools are lacking. We developed and internally validated nomograms predicting overall survival (OS) and hepatic progression-free survival (hPFS). (2) Methods: In this single-center retrospective cohort, reported per the TRIPOD guideline, OS and hPFS were estimated by Kaplan–Meier methods, and independent predictors from multivariable Cox regression were assembled into nomograms. Internal validation combined 1000-sample bootstrap optimism-corrected concordance indices (C-index), a uniform shrinkage factor, a bootstrap calibration slope, and a LASSO–Cox sensitivity analysis. (3) Results: Among 63 patients (44 deaths; 42 intrahepatic-progression events), median OS was 10.9 months and median hPFS was 5.8 months. Independent OS predictors were baseline CEA, high liver tumor burden (≥10 lesions), CEA decline (protective), and second-line-or-beyond interventional therapy (corrected C-index: 0.796). Independent hPFS predictors were high liver tumor burden, CEA decline, and age (corrected C-index: 0.718). Nomogram-defined high-risk groups had markedly shorter OS (5.3 vs. 22.8 months) and hPFS (3.3 vs. 8.6 months; both p < 0.001). Grade ≥3 toxicity occurred in 6%. (4) Conclusions: In real-world DEB-TACE-treated CRLM, liver tumor burden and CEA dynamics dominated prognosis; the internally validated nomograms provide individualized estimates and risk stratification, pending external validation. Full article

Liquid biopsy, the analysis of tumor-derived material in blood, saliva, and other body fluids, is increasingly explored for the diagnosis, surveillance, and molecular characterization of head and neck squamous cell carcinoma (HNSCC). Its performance, however, is not uniform across the disease, and the reason is fundamentally molecular. human papillomavirus (HPV)-positive oropharyngeal cancers carry viral oncogenes that are absent from the host genome and therefore provide a near ideal, tumor specific circulating marker, whereas HPV-negative tumors are driven by a heterogeneous somatic landscape that offers no single universal target. In this narrative review, we adopt a molecular perspective. We first examine the biological origin of circulating tumor DNA and of the other analytes that liquid biopsy can interrogate including circulating tumor HPV DNA, viral transcripts, microRNAs, extracellular vesicles, and methylation signatures. We then consider how analytical platforms, from droplet digital PCR to next generation and ultrasensitive whole-genome sequencing, translate these molecules into measurements. Only afterward do we discuss the clinical questions, organized by clinical objective rather than by individual study: diagnosis and early detection, prognosis and risk stratification, treatment response monitoring, minimal residual disease and surveillance, and biomarker guided de-escalation in HPV-positive disease. Twelve registered clinical trials, involving approximately 1183 patients, are presented as illustrations of these questions. We close on the biological and technical gaps that still separate promising signals from clinical practice, and on the multi analyte and dynamic strategies most likely to bridge them. At present, liquid biopsy should be regarded as a complementary tool rather than as a replacement for established clinicopathological assessment. Full article

Background/Objectives: Glioblastoma (GBM) is the most aggressive and lethal primary brain tumor, and elucidating the molecular determinants of its malignant progression is essential for improving patient outcomes. NTAN1 encodes N-terminal asparagine amidase 1, a component of the N-degron pathway involved in selective protein turnover; however, its role in GBM remains unclear. This study aimed to investigate the clinical significance and biological function of NTAN1 in GBM. Methods: Integrated analyses of The Cancer Genome Atlas (TCGA) transcriptomic and clinical data were performed, together with tissue microarray validation, to assess the association between NTAN1 expression and prognosis in GBM. Immunohistochemical analysis of GBM specimens was conducted to evaluate NTAN1 protein expression. Functional studies, including NTAN1 knockdown and overexpression experiments, were used to examine its effects on GBM cell proliferation, clonogenic growth, migration, and invasion. An orthotopic GBM model was established to assess the effect of NTAN1 inhibition on tumor growth. Transcriptomic analysis was further performed to explore the molecular changes associated with NTAN1 knockdown. Results: Elevated NTAN1 expression was associated with poor survival in GBM. Immunohistochemical analysis further demonstrated that high NTAN1 protein expression predicted unfavorable prognosis. Functional studies showed that NTAN1 knockdown inhibited GBM cell proliferation, clonogenic growth, migration, and invasion, whereas NTAN1 overexpression promoted these malignant phenotypes. In an orthotopic GBM model, NTAN1 inhibition significantly reduced tumor volume. Transcriptomic analysis showed that NTAN1 knockdown was associated with reduced expression of invasion-related genes, including SPINK1, MMP1, and LIF, and with enrichment changes in inflammation-associated pathways, suggesting that NTAN1 may promote GBM progression through pro-invasive molecular programs. Conclusions: Collectively, these findings identify NTAN1 as a potential promoter of GBM malignant progression and a prognostic biomarker of poor outcome. Full article

Breast cancer (BRCA) possesses prominent molecular heterogeneity, where aberrant expression of genes annotated to asparagine metabolism networks drives malignant progression and therapeutic resistance. However, systematic construction of prognostic signatures from a holistic asparagine metabolic pathway perspective remains scarce, limiting the clinical translation of metabolic insights into prognostic tools. We integrated TCGA and GEO BRCA transcriptomic datasets to screen asparagine metabolism-related differentially expressed genes and build a prognostic model. Six biomarkers, SLC35A2, SRD5A2, NT5E, CEL, IFNG and CNR1, were selected via univariate Cox, LASSO and multivariate Cox regression. SRD5A2 and IFNG were enriched in low-risk patients, while the other four genes were upregulated in high-risk subgroups. This signature reliably stratifies patient prognosis, with risk scores correlating strongly with pathway activity, immune infiltration, immune checkpoints, mutation landscapes and drug responsiveness. Bioinformatic results were validated via TCGA cohort analysis, in vitro cellular assays and Western blot. Two in vivo models were established: 4T1 xenografts in 6-week-old BALB/c mice and DMBA/hormone-induced spontaneous breast tumors in 8-week-old SD rats. Tumors were generated by cell injection or DMBA gavage plus cyclic hormone treatment, and tissue sections were processed for immunohistochemistry. Consistent differential expression of the six core genes was validated across all in vitro and in vivo systems. In conclusion, this asparagine metabolism-associated signature offers candidate biomarkers for personalized prognosis and provides preclinical evidence for metabolism-targeted BRCA therapy. Full article

Background/Objectives: Cutaneous melanoma prognosis is largely determined at diagnosis, with Breslow thickness, subtype and other histopathological aspects being key prognostic indicators. Variations in healthcare organization and environmental factors may influence melanoma presentation. This study aimed to compare epidemiological, clinical, and histopathological characteristics of primary cutaneous melanoma between two national referral centers in Southeastern Europe. Methods: A multicenter retrospective cohort study was conducted at the University Clinical Center of Serbia (Belgrade) and the Clinical Center of Montenegro (Podgorica). Consecutive patients treated for primary cutaneous melanoma between January 2018 and December 2022 were included. Data of interest were extracted from medical records. Annual regional sunshine hours were obtained from publicly available climatological databases. Group comparisons were performed using appropriate parametric and non-parametric tests, followed by a multivariable ordinal logistic regression analysis. Results: A total of 412 patients were analyzed. Age and sex distributions were comparable between cohorts. Nodular melanoma predominated in Montenegro, whereas superficial spreading melanoma was most common in Belgrade (p < 0.001). Median Breslow thickness was significantly higher in Montenegro (p = 0.001), with a greater proportion of tumors >4 mm (p = 0.001). In multivariable analysis, increasing age (p < 0.001), male sex (p = 0.027), and treatment in Montenegro (p = 0.001) were independently associated with higher Breslow thickness categories. Conclusions: Patients treated in Montenegro presented with thicker melanomas and a higher proportion of nodular subtype. These differences may reflect multifactorial influences, including healthcare accessibility and diagnostic pathways. Further prospective studies incorporating other histopathological aspects, time-to-diagnosis and survival outcomes are warranted. Full article