Search Results (239)

Background/Objectives: Hepatic cancers, including hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), are major global health concerns due to rising incidence and limited therapeutic success. While traditional risk factors include chronic liver disease and environmental exposures, recent evidence underscores the significance of genetic alterations and gut microbiota in liver cancer development and progression. This review aims to integrate emerging knowledge on the interplay between host genomic changes and gut microbial dynamics in the pathogenesis and treatment of hepatic cancers. Methods: We conducted a comprehensive review of current literature on genetic and epigenetic drivers of HCC and CCA, focusing on commonly mutated genes such as TP53, CTNNB1, TERT, IDH1/2, and FGFR2. In parallel, we evaluated studies addressing the gut–liver axis, including the roles of dysbiosis, microbial metabolites, and immune modulation. Key clinical and preclinical findings were synthesized to explore how host–microbe interactions influence tumorigenesis and therapeutic response. Results: HCC and CCA exhibit distinct but overlapping genomic landscapes marked by recurrent mutations and epigenetic reprogramming. Alterations in the gut microbiota contribute to hepatic inflammation, genomic instability, and immune evasion, potentially enhancing oncogenic signaling pathways. Furthermore, microbiota composition appears to affect responses to immune checkpoint inhibitors. Emerging therapeutic strategies such as probiotics, fecal microbiota transplantation, and precision oncology based on mutational profiling demonstrate potential for personalized interventions. Conclusions: The integration of host genomics with microbial ecology provides a promising paradigm for advancing diagnostics and therapies in liver cancer. Targeting the gut–liver axis may complement genome-informed strategies to improve outcomes for patients with HCC and CCA. Full article

Worldwide, lung cancer is one of the most common cancers, with non-small cell lung cancer (NSCLC) including up to 80–85% of all lung cancer diagnoses. The landscape of NSCLC is characterized by a heterogeneous spectrum of gene alterations, with tyrosine kinase inhibitors (TKIs) and targeted treatments that significantly improve survival outcomes for patients with oncogene-addicted NSCLC, offering superior efficacy, and often favorable safety and tolerability profiles compared to chemotherapy-based treatments. However, the complexity of NSCLC extends to co-occurring genomic alterations or amplifications in tumor suppressors and other oncogenes, such as TP53, STK11, KEAP1, PIK3CA, RB1, and others, that significantly influence disease progression, therapeutic resistance, and clinical outcomes. These co-mutations often contribute to the development of primary and acquired resistance to targeted therapies, complicating decision-making strategies. This review provides a timely and comprehensive synthesis of current insights into co-mutations in NSCLC, with a particular focus on their clinical implications, and offers a novel perspective by integrating recent molecular insights with therapeutic challenges, addressing existing knowledge gaps through a more integrative and clinically oriented analysis of co-mutations. Advances in next-generation sequencing (NGS) and molecular profiling have enabled the identification of these co-alterations, paving the way for more personalized therapeutic approaches. However, challenges remain in interpreting the functional interplay of co-mutations and translating these insights into effective clinical interventions. This review also highlights the significance of co-mutations in shaping NSCLC biology, and discusses their impact on current therapeutic paradigms, emphasizing the need for integrative biomarker-driven approaches to improve outcomes in NSCLC. Full article

Brachial plexus root avulsion [BPRA] and concomitant spinal cord injury [SCI] represent devastating injuries that come with limited hope for recovery owing to the adult spinal cord’s loss of intrinsic ability to spontaneously regenerate. BPRA/SCI is an enormous public health issue the world over, and its catastrophic impact goes beyond the patient, the family, businesses, and national health budgets, draining billions of dollars annually. The rising population and economic growth have seen the incidence of SCI surging. Genomic, transcriptomic, and proteomic studies have yielded loads of information on the various molecular events that precede, regulate, and support both regenerative and degenerative pathways post-SCI. Metabolomics, on the other hand, comes in as the search for a cure and the objective monitoring of SCI severity and prognosis remains on the horizon. Despite the large number of review articles on metabolomics and its application fields such as in cancer and diabetes research, there is no comprehensive review on metabolite profiling to study disease mechanisms, biomarkers, or neuroprotection in SCI. First, we present a short review on BPRA/SCI. Second, we discuss potential benefits of metabolomics as applied in BPRA/SCI cases. Next, a look at the analytical techniques that are used in metabolomics. Next, we present an overview of the studies that have used metabolomics to reveal SCI metabolic fingerprints and point out areas of further investigation. Finally, we discuss future research directions. Full article

In November 2024, the fourth annual Symposium focusing on early-age onset cancer (EAOC) was hosted by the Colorectal Cancer Resource & Action Network (CCRAN), assembling clinicians, researchers, and patients virtually to discuss challenges in early detection and diagnosis of individuals afflicted with EAOC across tumour types. The meeting addressed the rising rates of EAOC and identified strategies to overcome barriers to timely detection and diagnosis by closing gaps in public and healthcare provider knowledge on symptoms of cancer in younger adults and reducing inequities in standard screening for younger age groups. Discussions also encompassed the various factors that serve as impediments to accessing diagnostic testing and obtaining results, as well as the critical need for access to diagnostics such as comprehensive genomic profiling (CGP), the results of which could be imperative in helping to guide clinical decisions regarding effective and well-tolerated targeted therapies. The Symposium generated key calls to action regarding increasing EAOC education and awareness among primary care providers and the public, re-evaluation of cancer screening programs’ eligibility criteria to include younger populations, and mechanisms to reduce waiting times for diagnostic testing by addressing technologist shortages and improving access to CGP through national collaborative strategies and increased funding. Full article

Background/Objectives: Laryngeal squamous cell carcinoma (LSCC) is a common malignancy with unsatisfactory survival rates, highlighting the need for reliable biomarkers to improve its diagnosis and prognosis. Growth differentiation factor 15 (GDF15), a protein implicated in various cancers, has not been thoroughly investigated in LSCC. This study aimed to evaluate the significance of GDF15 expression in LSCC by integrating immunohistochemical analysis of archival tissue samples with RNA sequencing data from public databases (TCGA and GEO) to provide comprehensive clinical insights. Methods: We analyzed archival tissue samples from 65 patients with LSCC using immunohistochemistry and evaluated GDF15 expression profiles from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Statistical analyses included Kaplan–Meier survival analysis and Cox proportional hazards regression to assess the correlation between GDF15 expression, clinicopathological variables, and survival outcomes. Results: GDF15 expression did not significantly differ between tumor and adjacent normal tissues. However, in the tissue macroarray (TMA) cohort, high GDF15 expression was significantly associated with a lower TNM stage and less advanced pT status. Kaplan–Meier analysis revealed that high GDF15 expression correlated with reduced overall survival in the TMA cohort, suggesting its utility in risk stratification. Multivariate analysis identified GDF15 as an independent prognostic factor for disease-free survival in LSCC. Conclusions: Our findings suggest that GDF15 may serve as a prognostic biomarker for LSCC, particularly in early-stage disease. Elevated GDF15 levels, which are associated with poorer overall survival, could be integrated into diagnostic panels to enhance risk stratification and inform treatment decisions. Furthermore, GDF15 may be a promising target for therapeutic intervention. Further research is warranted to validate these results and explore their potential in clinical practice. Full article

Background/Objectives: Spinal metastatic disease is a life-altering problem for individuals with cancer. Prognostication is key for tailored treatment of spinal metastases. This manuscript provides a comprehensive overview of the genomic profiles of metastatic spine tumors and investigates the potential of mutational data to stratify overall survival (OS) across various histologies. Methods: This is a cohort study of consecutive patients with spine metastatic disease whose tumors were sequenced on a next generation sequencing platform; a machine learning (ML) algorithm was used to stratify OS risk. Results: Targeted sequencing and stratification of OS risk of 282 spine metastases (breast (84), non-small cell lung (56), prostate (49), other (93)) was performed. TP53 (HR 1.80; 95% CI 1.26, 2.56) and KEAP1 (HR 3.95, 95% CI 2.24, 6.98) mutations were associated with poor survival across the entire cohort in univariate Cox proportional hazards models. The ML algorithm categorized breast cancer metastasis into low- and high-risk groups, revealing a median OS of 71 compared to 22 months (HR 3.3, p < 0.001). TP53 mutations and ESR1 mutations conferred poor prognosis. In lung cancer, low- and high-risk groups with median OS of 30 and 6 months (HR 8.3, p < 0.001), respectively, were identified with poor prognosis linked to MET amplification. No significant prognostic associations were identified for spinal prostate metastases. Conclusions: Metastatic spine tumor molecular data allows for the identification of prognostic groups. We present an open-source machine learning algorithm utilizing genomic mutational data that may aid in prognostication and tailored decision making. Full article

The spatial organization of the genome within the nucleus is a fundamental regulator of gene expression, genome stability, and cell identity. This review addresses the central question of how nuclear genome architecture contributes to disease mechanisms and diagnostics, and how technological advances enable its clinical exploration. We first outline the principles of nuclear genome architecture, including chromosome territories, replication timing, and 3D domains, and their role in gene regulation and disease. We then explore the mechanisms and consequences of chromosomal rearrangements, and how replication dynamics intersect with epigenetic regulation and genome stability. Diagnostic tools are presented in chronological progression, from conventional cytogenetics to high-resolution genomic and single-cell techniques. A dedicated section focuses on cancer cytogenomics and its clinical implications. We further highlight emerging technologies for 3D genome and epigenome profiling and their integration into diagnostic workflows. Finally, we discuss current challenges, such as standardization and cost, and the transformative potential of multi-omics and artificial intelligence for future precision diagnostics. Overall, we provide a comprehensive overview of how cytogenetics and cytogenomics contribute to the understanding and clinical diagnosis of genetic and neoplastic diseases. Full article

Stereotactic body radiotherapy (SBRT) delivers ablative radiation doses with sub-millimeter precision. Radiogenomic studies, meanwhile, provide insights into how tumor-intrinsic genetic factors influence responses to such high-dose treatments. This review explores the radiobiological mechanisms underpinning SBRT efficacy, emphasizing the roles of DNA damage response (DDR) pathways, tumor suppressor gene alterations, and inflammatory signaling in shaping tumor radiosensitivity or resistance. SBRT induces complex DNA double-strand breaks (DSBs) that robustly activate DDR signaling cascades, particularly via the ATM and ATR kinases. Tumors with proficient DNA repair capabilities often resist SBRT, whereas deficiencies in key repair genes can render them more susceptible to radiation-induced cytotoxicity. Mutations in tumor suppressor genes may impair p53-dependent apoptosis and disrupt cell cycle checkpoints, allowing malignant cells to evade radiation-induced cell death. Furthermore, SBRT provokes the release of pro-inflammatory cytokines and activates innate immune pathways, potentially leading to immunogenic cell death and reshaping the tumor microenvironment. Radiogenomic profiling has identified genomic alterations and molecular signatures associated with differential responses to SBRT and immune activation. These insights open avenues for precision radiotherapy approaches, including the use of genomic biomarkers for patient selection, the integration of SBRT with DDR inhibitors or immunotherapies, and the customization of treatment plans based on individual tumor genotypes and immune landscapes. Ultimately, these strategies aim to enhance SBRT efficacy and improve clinical outcomes through biologically tailored treatment. This review provides a comprehensive summary of current knowledge on the genetic determinants of response to stereotactic radiotherapy and discusses their implications for personalized cancer treatment. Full article

Background: Gastric cancer is a leading cause of cancer-related mortality worldwide, with approximately one million new cases diagnosed annually. While Helicobacter pylori infection remains a primary etiological factor, mounting evidence implicates obesity and lipid metabolic dysregulation, particularly in hypercholesterolemia, as emerging drivers of gastric tumorigenesis. This study investigates the molecular intersections between gastric cancer, obesity, and hypercholesterolemia through a comprehensive multi-omics and systems biology approach. Methods: We conducted integrative transcriptomic analysis of gastric adenocarcinoma using The Cancer Genome Atlas (TCGA) RNA-sequencing dataset (n = 623, 8863 genes), matched with standardized clinical metadata (n = 413). Differential gene expression between survival groups was assessed using Welch’s t-test with Benjamini–Hochberg correction (FDR < 0.05, |log₂FC| ≥ 1). High-confidence gene sets for obesity (n = 128) and hypercholesterolemia (n = 97) were curated from the OMIM, STRING (confidence ≥ 0.7), and KEGG databases using hierarchical evidence-based prioritization. Overlapping gene signatures were identified, followed by pathway enrichment via Enrichr (KEGG 2021 Human) and protein–protein interaction (PPI) analysis using STRING v11.5 and Cytoscape v3.9.0. CD36’s prognostic value was evaluated via Kaplan–Meier and log-rank testing alongside clinicopathological correlations. Results: We identified 36 genes shared between obesity and gastric cancer, and 31 genes shared between hypercholesterolemia and gastric cancer. CD36 emerged as the only gene intersecting all three conditions, marking it as a unique molecular integrator. Enrichment analyses implicated dysregulated fatty acid uptake, adipocytokine signaling, cholesterol metabolism, and NF-κB-mediated inflammation as key pathways. Elevated CD36 expression was significantly correlated with higher tumor stage (p = 0.016), reduced overall survival (p = 0.001), and race-specific expression differences (p = 0.007). No sex-based differences in CD36 expression or survival were observed. Conclusions: CD36 is a central metabolic–oncogenic node linking obesity, hypercholesterolemia, and gastric cancer. It functions as both a mechanistic driver of tumor progression and a clinically actionable biomarker, particularly in metabolically comorbid patients. These findings provide a rationale for targeting CD36-driven pathways as part of a precision oncology strategy and highlight the need to incorporate metabolic profiling into gastric cancer risk assessment and treatment paradigms. Full article

This study focuses on the systematization and integration of ovarian cancer multi-omics data, revealing patterns in the application of different omics-based approaches and assessing factors that affect the identification of potential biomarkers. An integrative analysis of 51 publications revealed 1649 potential biomarkers. The findings emphasized the molecular diversity of ovarian cancer. They demonstrated the importance of performing the comprehensive integration of molecular and clinical data to search for diagnostic alternatives and molecular patterns underlying ovarian cancer. The heterogeneity of data sources, differences in data acquisition and analysis protocols, and the lack of uniform standards affect the reproducibility of the results of genomic and post-genomic profiling. Multi-omics studies are more promising than mono-omics-based ones. Despite technological advances, researchers continue to focus on results obtained over a decade ago, which may hinder the scientific community from exploring new horizons in ovarian cancer research. Full article

In the era of precision oncology, comprehensive molecular profiling is critical for guiding targeted and immunotherapy strategies. This study presents the analytical and clinical validation of a 1021-gene next-generation sequencing (NGS) panel, designed for use with both formalin-fixed paraffin-embedded (FFPE) tissue- and liquid-biopsy specimens. Analytical validation confirmed the assay’s high sensitivity and specificity across variant types—including SNVs (Single Nucleotide Variations), indels, CNVs (Copy Number Variations), and fusions—down to a 0.5% variant allele frequency. The assay also accurately identified microsatellite instability (MSI) and tumor mutational burden (TMB), essential biomarkers for immunotherapy. Clinical validation was performed on over 1300 solid tumor samples from diverse histologies, revealing actionable alterations in over 50% of cases. The panel detected on-label treatment biomarkers in 12.57% of patients, increasing to 20.15% when immunotherapy markers were included. Additionally, the assay demonstrated strong concordance with orthogonal methods and was effective in detecting variants in plasma-derived circulating tumor DNA in 70% of evaluable cases. These findings support the robust performance and broad clinical applicability of the 1021-gene panel for comprehensive genomic profiling in both tissue and liquid biopsies, offering a valuable tool for personalized cancer treatment. Full article

The upcoming wave of personalized medicine, driven by genomic diagnostics and artificial intelligence, demands clearly defined pre-laboratory and laboratory procedures to ensure the acquisition of DNA and RNA of sufficient quantity and quality. In prostate cancer oncogenetics, diagnostic and prognostic assessments increasingly rely on personalized approaches, including Comprehensive Genomic Profiling (CGP). In this pilot study, we aimed to establish optimal pre-analytical and analytical conditions for selected genetic diagnostic methods using tissue samples acquired through multiparametric MRI-guided biopsy. Tissue specimens from thirteen patients were processed for DNA isolation, fluorescence in situ hybridization (FISH), and next-generation sequencing (NGS). Comparative analyses were performed on DNA derived from both fresh and formalin-fixed, paraffin-embedded (FFPE) samples. Sequencing quality metrics demonstrated markedly superior performance in fresh tissue compared to FFPE. These results highlight the importance of standardized tissue collection and processing protocols to enable reliable molecular diagnostics in prostate cancer. Our findings support the feasibility of integrating high-quality genomic testing into routine biopsy workflows and emphasize the need for further large-scale validation. Full article

Background: Comprehensive molecular profiling is essential for precision oncology in non-small cell lung cancer (NSCLC). However, genomic data from Eastern European populations, including Romania, remain limited. Methods: We analyzed 398 consecutive NSCLC cases tested at the PATHOS Molecular Pathology Laboratory (Cluj-Napoca, Romania) between April 2024 and February 2025 using the Ion Torrent™ Genexus™ System and the Oncomine™ Dx Target Test, which evaluates SNVs/indels in 46 genes, fusions in 23 genes, and CNVs in 19 genes from FFPE samples. Results: The cohort was predominantly male (66%) with a median age of 67 years. Adenocarcinoma represented 70% of cases with known histology. Genomic profiling revealed a high frequency of actionable alterations. KRAS mutations were the most common (29.1%), with p.G12C detected in 10.3% of all the cases. EGFR mutations were present in 14.3% of patients, mostly exon 19 deletions and L858R substitutions. BRAF alterations (5.3%) included both V600E and non-V600E variants. RET alterations were detected as eight missense mutations, two canonical fusions (KIF5B–RET, CCDC6–RET), one amplification, and three transcript imbalances. EML4-ALK fusions (1.77%), ERBB2 mutations/amplifications (3.0%), and FGFR1/FGFR3 amplifications were also observed. Conclusions: This study provides the first large-scale molecular snapshot of NSCLC in Romania. While the overall genomic profiles align with Western populations, the higher frequency of KRAS p.G12C and FGFR amplifications highlights the value of region-specific data to support targeted therapies in Eastern Europe. Full article

Colorectal cancer (CRC) remains a major health burden in Japan, with precision medicine playing an increasingly critical role in treatment optimization. Key biomarkers, including RAS, BRAF, microsatellite instability/mismatch repair, and human epidermal growth factor receptor 2, can be used as a guide for molecularly targeted therapies and immunotherapy. Advances in molecular diagnostics, including comprehensive genomic profiling, have enabled more precise treatment selection such as RET and NTRK fusions. Nationwide initiatives, such as c-CAT and SCRUM-Japan, can leverage real-world data to refine clinical strategies. Recent developments in circulating tumor DNA analysis have led to novel approaches for minimal residual disease monitoring, as demonstrated by the CIRCULATE-Japan GALAXY study. However, certain challenges persist, including the time required for genetic testing, the limited availability of targeted therapies, and disparities in access to molecular tumor boards. This review summarizes the current landscape of precision medicine in CRC in Japan, emphasizing key biomarkers, genetic testing strategies, targeted therapies, and emerging technologies. Future research should focus on expanding clinical trial access, accelerating drug approvals, and integrating real-world data into clinical practice to further advance precision medicine. Full article

Background: Docetaxel is the standard of care for advanced non-small cell lung cancer (NSCLC) after platinum-based chemotherapy and/or immunotherapy but is associated with modest clinical outcomes and considerable toxicity. Sacituzumab govitecan and datopotamab deruxtecan are trophoblast cell surface antigen (TROP)-2-directed antibody–drug conjugates (ADCs) that showed encouraging activity in pretreated patients with advanced NSCLC. This systematic review and pooled analysis aims to comprehensively assess the efficacy and safety of anti-TROP-2 ADCs compared to docetaxel in pretreated patients with advanced NSCLC. Methods: A systematic search through PubMed and EMBASE before 31 January 2025 was performed to identify eligible studies. Randomized controlled phase III trials comparing an anti-TROP-2 regimen to docetaxel in patients with pretreated advanced NSCLC were included. Overall survival (OS), progression-free survival (PFS), and grade ≥ 3 treatment-related adverse events (TRAEs) were extracted from the identified trials. A pooled analysis of reconstructed patient data and meta-analysis employing the random-effect model were used to summarize the efficacy and safety outcomes. Results: Across the two trials included, 1207 patients were enrolled, 598 in the TROP-2 ADC arm and 609 in the docetaxel arm. Anti-TROP-2 treatment did not produce significant improvements in OS (HR: 0.90; 95% CI, 0.78–1.03; P = 0.13) and PFS (HR: 0.84; 95% CI, 0.68–1.02; P = 0.08), compared to docetaxel, even in patients with a nonsquamous histology (OS HR: 0.86; 95% CI, 0.73–1.01; P = 0.06; PFS HR: 0.76; 95% CI, 0.52–1.12; P = 0.17). Across the subgroup analyses, a statistically significant improvement in OS was observed in patients with actionable genomic alterations (AGAs) (HR: 0.63; 95% CI, 0.41–0.95; P = 0.03). Compared to docetaxel, the anti-TROP-2 regimen demonstrated a lower risk of developing grade ≥ 3 TRAEs (RR: 0.76; 95% CI, 0.55–1.05; P = 0.09). Conclusions: The anti-TROP-2 regimen showed a better safety profile but failed to demonstrate a relevant clinical improvement over docetaxel. Anti-TROP-2 ADCs could find a role in the management of patients with AGAs. Full article