To identify therapeutic targets limiting glioblastoma invasion, we applied druggable genome CRISPRi screens and multiomic analysis to patient-derived glioblastoma cells in micro-dissectible biomimetic 3D hydrogels that permitted separation and analysis of core versus invasive fractions. Of 2,550 genes screened, 12 encoded druggable targets whose suppression limited invasion, of which AURKB (encoding aurora kinase B) and ACP1 (encoding low molecular weight protein tyrosine phosphatase, LMW-PTP) were validated in neurosphere assays and in vivo. Proximity labeling identified cortactin as a link between LMW-PTP and aurora B, and we observed that cortactin underwent serine phosphorylation by aurora B and tyrosine dephosphorylation by LMW-PTP. Targeting ACP1 or AURKB via CRISPRi or inhibitors in culture and in vivo shifted the cortactin phosphorylation balance in glioblastoma, reducing levels of cortactin and the actin-related protein 2/3 (Arp2/3) complex that mediates cortactin-induced actin stabilization, thereby reducing actin-cortactin-Arp2/3 colocalization and subsequent actin polymerization. AURKB or ACP1 targeting shifted actin from cytoplasm to the nucleus, reducing mesenchymal gene expression. Biophysical analysis implicated AURKB in glioblastoma cell adhesion and stiffness needed for initial migration and ACP1 in mechanical stress resistance required for later migration. These findings revealed a targetable axis balancing kinase and phosphatase activities to regulate actin polymerization during glioblastoma invasion.

Hereditary renal cancer syndromes are rare, yet contribute to early-onset renal cell carcinoma (RCC) and require vigilant imaging surveillance. These syndromes, including Von Hippel-Lindau, Birt-Hogg-Dubé, hereditary papillary RCC, are linked to germline mutations affecting tumor suppressor pathways. Imaging techniques, such as MR imaging and computed tomography, play a crucial role in early diagnosis, characterization, and surveillance of hereditary RCC. A multidisciplinary approach is essential for individualized screening and management strategies. This review highlights the genetic associations, imaging features, and most up-to-date recommendations for screening and surveillance of hereditary RCC syndromes.

Breast cancer remains a major cause of morbidity and mortality in women, with around 2.3 million new cases and 670,000 deaths worldwide in 2022. Daidzin, a soy isoflavone glycoside from Glycine max, is a candidate bioactive scaffold, but its breast cancer-relevant mechanisms remain poorly defined. This study used an integrated in silico strategy combining network pharmacology and molecular modeling to prioritize daidzin targets and validate key interactions, with sirtinol as a reference compound. Target prediction identified 101 putative daidzin targets, and intersection with breast cancer-associated genes yielded 97 common targets. Protein-protein interaction analysis highlighted hub genes including ALB, TNF, MMP9, CASP3, SRC, ITGB1, MMP2, ESR1, IL2, and HSP90AA1. Enrichment analyses suggested convergence on extracellular/vesicle-related functions, metallopeptidase activity, and pathway modules spanning metabolism, inflammation, endocrine signaling, and cancer circuitry. Docking against ten hub proteins produced binding energies from -6.00 to -11.49 kcal/mol, with the strongest affinity for MMP9 (6ESM; -11.49 kcal/mol), exceeding B9Z (-10.54 kcal/mol) and sirtinol (-10.59 kcal/mol). Molecular dynamics simulations indicated stable complexes, and Molecular Mechanics Generalized Born Surface Area (MMGBSA) supported stronger binding for daidzin-MMP9 (-46.86 ± 3.83 kcal/mol) than sirtinol-MMP9 (-14.12 ± 8.99 kcal/mol). Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) prediction indicated favorable safety-related flags for daidzin, although lower predicted intestinal absorption and Caco2 permeability than sirtinol suggest potential exposure-related limitations. Density Functional Theory (DFT) analysis supported comparatively greater electronic stability. Collectively, the results prioritize a daidzin-MMP9 axis for experimental validation.

Drug sensitivity prediction is an important issue within the precision medicine field. IC50, which is the molar drug dose needed to decrease the viability of cells by half compared to the drug-free control, is the main pharmacodynamics parameter used for drug sensitivity analysis in large-scale pharmacogenomics screenings. Computational estimation of IC50s based on molecular and genomic factors significantly reduces costs associated with experiments for measuring cell viability and allows for accelerating the process of drug discovery. Traditional methods of IC50 calculation do not allow integrating the three-dimensional chemical structure of drugs and the biological context of particular cell lines, resulting in suboptimal model performance when using different pharmacogenomics data sources. In this work, we propose an innovative dual-branch approach based on Graph Isomorphism Network (GIN) drug representations coupled with a Multilayer Perceptron (MLP) for 50-dimensional ssGSEA pathway activities calculated from CCLE gene expression. After training on cell-line-drug pair combinations from the Genomics of Drug Sensitivity in Cancer 2 (GDSC2) dataset across various cancers, the proposed GIN+Pathway MLP model attains an R2 of 0.8553 and a Pearson Correlation Coefficient (PCC) of 0.9249 on the testing split of the same dataset. In a variant ablation study of six variants, we find that eliminating the pathway MLP component lowers the R2 value by more than 0.15, thus proving the importance of biological features in the two-branch model. The performance of our proposed model exceeds benchmark scores for models such as GraphDRP (PCC = 0.870, R2 = 0.756) and DeepCDR (PCC = 0.847, R2 = 0.720) when tested on the same GDSC2 dataset.

Colorectal cancer (CRC) is the second most common cause of cancer-related deaths in the United States. The incidence of early-onset CRC (EOCRC) has been rising in the past few decades. Given the multifaceted nature of EOCRC, the genetic and environmental factors contributing to this malignancy have remained elusive. Systems genetics is a multi-omics tool that analyzes multiple genes as a collective network. Transcriptional correlation, protein-protein interaction network, functional annotation, and drug-gene interaction analyzes enable investigators to explore the functional roles of target genes and aid with discovery of novel diagnostic biomarkers and potential therapeutics. To clarify the objective of this work, this manuscript serves three purposes: a narrative review of recent systems genetics applications in EOCRC research, a step-by-step protocol for conducting these analyses, and a discussion of current advances in systems genetics to address limitations in generalizability and context dependence. Through this manuscript, we envision a future in which emerging oncology researchers adopt these tools into their investigations of EOCRC and other malignancies.

Acquired temozolomide (TMZ) resistance remains a major challenge in glioblastoma and may involve the emergence or enrichment of cancer stem cell (CSC)-like characteristics. However, whether stem-like characteristics differ across increasing levels of acquired TMZ resistance remains unclear. This study compared stem-like characteristics among parental TMZ-sensitive glioblastoma cells and two sequentially generated TMZ-adapted populations with different levels of acquired TMZ resistance.

The systemic influence of tumor-derived secretomes on the nervous system remains poorly understood. We investigated whether differences in TP53 status are associated with altered cellular stress-handling states and amyloid precursor protein (APP) processing in colon cancer cells.

Oral squamous cell carcinoma (OSCC) arises in the context of diverse etiological exposures, such as tobacco, alcohol, areca nut use and viral infections. This etiological heterogeneity drives distinct molecular alterations, contributing to tumor complexity and significant challenges in identifying robust, clinically applicable biomarkers.

Non-small cell lung cancer (NSCLC) remains a leading cause of cancer-related mortality worldwide, largely due to the supportive role of the tumor microenvironment (TME). Tumor-associated macrophages, particularly the M2 phenotype, are pivotal in promoting NSCLC progression. Exosomes, key mediators of intercellular communication, can transfer functional cargo from M2 macrophages to cancer cells, thereby regulating malignant behaviors. However, the specific mechanisms by which M2 macrophage-derived exosomes modulate NSCLC progression are not fully understood.

SETD2-mediated H3K36me3 reprogramming is involved in homologous recombination (HR) repair; however, the dynamics of this repair process remain unclear. Here, we report that the scaffold protein menin, encoded by the Men1 gene, plays a crucial bridging role in H3K36-mediated HR repair. Genetic ablation of Men1 resulted in spontaneous lung carcinogenesis and was accompanied by severe genomic instability. Mechanistically, menin directly recognizes histone H2A.X via its Val371-Gln400 motif, and DNA damage markedly promotes the specific interaction between menin and γH2A.X. Subsequently, SETD2 is recruited to DNA damage sites by menin and acts as a writer to catalyze H3K36me3 reprogramming at local chromatin. LEDGF, as a reader, recognizes the H3K36me3 marker and further recruits CtIP as an effector to perform DNA end resection, ultimately activating the RPA2/Rad51 pathway. Restoring H3K36me3 via pharmacological intervention rescued impaired HR repair in Men1-deficient cells, further validating that menin governs HR repair in an H3K36me3-dependent manner. The results of the present study provide the detailed molecular mechanism underlying the previously described functions of H3K36me3 remodeling in HR repair.

Clonal hematopoiesis of indeterminate potential (CHIP) causes the expansion of mutated hematopoietic stem cells and produces immunophenotypically altered leukocytes, which induce a tumor-promoting inflammatory condition. However, the causal effect of CHIP on cancer remains unclear. We assessed the relationship of genetically predicted CHIP with the risk of 18 cancer types involving 612,576 cases using two-sample Mendelian randomization (MR). Genetic instruments for overall and sub-types of CHIP were obtained from the a large-scale genome-wide association study using independent (r2 < 0.001) SNPs at genome-wide significance (p < 5.0 × 10-8). Summary statistics for 18 cancers were obtained from the FinnGen, MVP, PLCO study, and large consortia. Inverse-variance weighted random-effects models were used as the primary method for estimating causal effects. Findings from independent datasets were combined using the fixed-effect model and Bonferroni corrections were applied for multiple testing. We found genetic predicted overall and DNMT3A CHIP was significantly associated with an increased risk of thyroid cancer, lung cancer, kidney cancer, brain cancer, basal cell carcinoma, and malignant melanoma after corrections. In addition, we found the causal estimate of CHIP varied across histological sub-types of cancer. Sensitivity analyses confirmed that these findings were robust. Strong associations were found between genetic predicted CHIP and an increased risk of a broad range of cancers, highlighting the importance of timely screening for CHIP in cancer early detection and prevention.

Tuberous sclerosis complex (TSC) is an autosomal dominant multisystem genetic disorder caused by pathogenic variants in the TSC1 or TSC2 genes, resulting in dysregulation of the mTOR signaling pathway and subsequent hamartoma formation. Although the genetic basis of TSC is well established, population-specific data on TSC1 and TSC2 variants are still emerging. The aim of this study was to characterize the variant spectrum of the TSC1 and TSC2 genes in a cohort of 34 unrelated probands from Greece, 26 of whom had a definite TSC diagnosis, whereas eight had a possible TSC diagnosis. Targeted next-generation sequencing (NGS) was performed to analyze all coding exons and flanking exon-intron boundaries of TSC1 and TSC2. Identified variants were subsequently validated by Sanger sequencing. Pathogenic or likely pathogenic variants were identified in 22 of 34 probands, corresponding to an overall diagnostic yield of 65% using the testing strategy applied in this study. Of these variants, 32% (7/22) occurred in TSC1 and 68% (15/22) in TSC2; seven variants (7/22; 32%) were previously unreported. The molecular detection rate was 77% (20/26) for patients meeting the criteria for definite clinical TSC diagnosis and 25% (2/8) for those with a possible TSC diagnosis. Exploratory genotype-phenotype analysis revealed a trend toward a more severe clinical presentation among patients harboring TSC2 variants. These findings expand the known molecular landscape of TSC and support the clinical utility of genetic testing for diagnosis, genetic counseling, and patient management.

Immune checkpoint blockade (ICB) therapy has dramatically improved the survival outcomes of patients with locally advanced unresectable and metastatic non-small cell lung cancer (NSCLC). In particular, accumulated clinical trials and systematic reviews have further verified that induction ICB regimen following surgery confers superior benefits for IIIB-N3 NSCLC. Herein, we present a clinical case of a patient diagnosed with bulky contralateral mediastinal N3 (cT1bN3M0) left upper lung adenocarcinoma and devoid of actionable driver gene alterations. The patient achieved pathological complete response following anti-PD-1 treatment and subsequently underwent left upper lobectomy, followed by anti-PD-1 therapy for three consecutive years. To date, the patient has maintained a recurrence-free survival status for more than 5 years. Notably, we dynamically monitored the T-cell receptor (TCR) repertoire throughout the entire treatment course. Further analysis of TCR profiles revealed distinct dynamic patterns of certain specific T-cell clonotypes during treatment. These clonal alterations may help interpret sustained immune responses and warrant further exploration as candidate indicators for therapeutic outcome.

Post-translational modifications (PTMs) are pivotal in tumor biology, yet their role in papillary thyroid cancer (PTC) remains unclear. We integrated bulk and single-cell transcriptomes with clinical data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases to analyze 17 PTMs and construct a prognostic model using 12 machine learning algorithms for predicting the thyroid cancer-free interval (TCFi). Enrichment analysis, single-cell analysis, and immune-related analysis were performed to elucidate the biological role of PTMs. Therapeutic responses of PTC patients were predicted based on the model. We validated the expression of model genes and identified the key signature associated with the malignant phenotypes of PTC. We filtered out 12 genes to construct a post-translational modification index (PTMI) and identified three molecular clusters of PTC. Shapley additive explanations (SHAP) and nomogram models confirmed the predictive efficacy of PTMI. Integrated analyses revealed significant associations between PTMI and immune features. High-PTMI patients showed sensitivity to FDA-approved drugs and chemotherapeutics but resistance to radioactive iodine therapy. Notably, we identified TYMS as a key functional PTMI signature. The PTMI proposed in this study holds strong potential as a prognostic biomarker and therapeutic predictor, offering valuable insights for personalized management of PTC patients.

CD73 is an enzyme that generates extracellular adenosine and has been implicated in tumor-associated immune suppression, but its biological and clinical significance in pancreatic ductal adenocarcinoma (PDAC) remains incompletely understood. We investigated the prognostic relevance and biological functions of CD73 in PDAC using transcriptomic analyses, in vitro functional assays, and in vivo mouse models. Transcriptomic analyses consistently showed that CD73 expression was correlated with hypoxia, glycolysis related, and cell-cycle programs. In agreement with these findings, hypoxic exposure induced CD73 mRNA expression in a subset of PDAC cell lines, and CD73 knockdown modestly affected glycolysis related extracellular acidification (ECAR) in a cell line dependent manner, and modulation of CD73 expression altered PDAC cell growth. CD73 expression was also associated with reduced intratumoral CD8+ T cell infiltration and cytolytic activity in human PDAC cohorts. In vivo, CD73 overexpression accelerated cancer progression and shortened survival in immunocompetent mice, whereas this effect was abrogated in immunodeficient NSG mice. Flow cytometric analysis further demonstrated reduced intratumoral CD8+ T cell infiltration in CD73 overexpressing tumors. Clinically, high CD73 expression was consistently associated with worse survival in multiple PDAC cohorts. Collectively, these findings suggest that CD73 is associated with multiple features of PDAC progression, including hypoxia-related metabolic programs, tumor growth, and suppression of anti-tumor immunity. CD73 may therefore represent a biologically relevant biomarker and a potential therapeutic target in PDAC.

Benefit from first-line immunotherapy-based treatment in advanced biliary tract cancer (BTC) is heterogeneous, and selection biomarkers are lacking. We investigated whether genomic features could stratify benefit from intensified immunotherapy-based treatment versus chemotherapy.

Multiple myeloma (MM) persists within a specialized bone marrow niche in which malignant plasma cells, immune dysfunction, inflammatory signaling, and metabolic stress reinforce one another. To resolve this ecosystem at compartment-level resolution, we integrated public single-cell RNA sequencing data with pathway scoring, cell-cell communication inference, independent clinical validation, multiplex immunofluorescence, and metabolic perturbation experiments. Analysis of 95,940 bone marrow cells identified 32 annotated populations and revealed broad microenvironmental remodeling in MM, including plasma-cell expansion, altered cytotoxic and dendritic-cell compartments, TAM-associated inflammatory programs, and lineage-specific hematopoietic perturbations. Hallmark pathway analysis identified recurrent immunometabolic programs, including IL6-JAK-STAT3, TNFα-NFκB, mTORC1 signaling, oxidative phosphorylation, unfolded protein response, hypoxia, and checkpoint/exhaustion-associated pathways. CellChat analysis showed disease-associated rewiring of ligand-receptor networks involving malignant plasma cells, TAMs, dendritic cells, and T/NK subsets, with checkpoint-enriched communication and clinically relevant plasma-cell and CD274 survival associations. Serum IL-6 was elevated in an independent clinical validation cohort. Multiplex immunofluorescence confirmed PD-L1-positive plasma cells, C1QA/C1QB/C1QC-positive TAMs expressing LAG3, and CD8-positive/LAG3-positive cytotoxic T cells. Mechanistically, malignant plasma cells showed transcriptional activation of LDH-associated glycolytic/lactate programs and ASCT2/SLC1A5-GLS-linked glutamine-metabolic programs, nominating these pathways as functional vulnerabilities. Accordingly, the LDH inhibitor galloflavin and the ASCT2/SLC1A5 glutamine-transport inhibitor V-9302 suppressed RPMI-8226 viability in dose- and time-dependent manners; their combination produced synergistic anti-myeloma activity supported by Bliss synergy, combination-index analysis, observed-versus-expected inhibition, and apoptosis-related validation. Together, these findings support an IL6-centered immunometabolic communication circuit linking malignant plasma cells, TAMs, and dysfunctional T cells, and identify cooperative glycolytic/lactate and glutamine-dependent metabolic vulnerabilities with therapeutic relevance in MM.

In the OptiTROP-Lung04 trial, sacituzumab tirumotecan (sac-TMT) yielded a median progression-free survival of 8.3 months-a clinically significant outcome that has approval by the National Medical Products Administration. This study evaluates the cost-effectiveness of sac-TMT as a later-line therapy for patients with EGFR-mutant advanced NSCLC who have progressed on EGFR-TKIs, from the perspective of Chinese healthcare system.

This study aims to integrate network pharmacology, machine learning, and survival analysis to preliminarily explore the molecular mechanisms underlying the inhibitory effects of thalidomide on the malignant transformation of oral leukoplakia (OLK).

RAS mutations occur in patients with several types of vascular anomalies, but effective treatments remain limited. To address this need, we evaluated the RAS (ON) multi-selective inhibitor RMC-7977 in human endothelial cells (ECs) expressing the NRASQ61R mutation found in kaposiform lymphangiomatosis (KLA). RMC-7977 was evaluated using in vitro and in vivo models. Doxycycline-inducible NRASWT and NRASQ61R human ECs were treated with RMC-7977 (3.12-100 nM) or vehicle. We assessed signalling pathways, proliferation, migration, morphology, and angiopoietin-2 (ANG-2) production. NRASQ61R ECs in a 3D angiogenesis assay were also treated with RMC-7977. For in vivo studies, NRASQ61R ECs were injected into flanks of nude mice on a doxycycline diet to generate xenografts. Mice received oral RMC-7977 or vehicle, and xenografts were collected after 11 days. RMC-7977 inhibited NRASQ61R-induced ERK phosphorylation and reduced proliferation, migration, spindle-like morphology, and ANG-2 production in a dose-dependent manner. RMC-7977 reduced vascular area in the angiogenesis assay. In vivo, RMC-7977 reduced xenograft weight, vascular area, and p-ERK staining. Overall, RMC-7977 suppressed NRASQ61R-mediated signalling, aberrant EC behaviour, and ANG-2 production in vitro and reduced vascular overgrowth in angiogenesis assays and mouse xenografts. Therefore, RMC-7977 may be a promising therapeutic candidate for RAS-driven vascular anomalies, including KLA.