In this study, we used Mendelian randomization analysis to explore the causal relationships between drug targets and cutaneous melanoma (CM) and subsequently screened for new drug targets for CM. In addition, we verified whether targeted drugs could inhibit the development of CM in CM cells by suppressing the expression of target genes.

This study aims to elucidate the mechanism through which prostate cancer-associated transcript 6 (PCAT6) modulates immune escape in triple-negative breast cancer (TNBC), focusing on its interaction with IGF2BP1 and PD-L1.

The 2021 WHO classification reclassified "IDH-mutant glioblastoma (GBM)" as "Astrocytoma, IDH-mutant, grade 4." This study aims to provide real-world validation of this reclassification using the specific ICD-O-3 code (9445/3) from the Surveillance, Epidemiology, and End Results (SEER) "Transition Era" (2018-2022) and develop a machine learning (ML)-based prognostic model.

Skin cutaneous melanoma (SKCM) is a highly aggressive malignancy with a poor prognosis, necessitating the exploration of novel molecular mechanisms driving its progression. CircRNA, which have emerged as critical regulators in cancer biology, have been implicated in various tumorigenic processes. However, their specific roles in SKCM remain inadequately understood.

Few studies have evaluated the impact of organ-specific tumor microenvironments (TMEs) on clinical outcomes in diffuse large B-cell lymphoma (DLBCL). This study investigated potential molecular markers, the immune cell composition within the TME, and their associations with clinical outcomes in patients with primary intestinal DLBCL (PI-DLBCL). We initially analyzed RNA expression in tumor cells from 19 patients with PI-DLBCL in the experimental cohort. Candidate biomarkers were then assessed in lymphoma tissue from a total of 48 patients in the same cohort, including the 19 with RNA-expression data, and validated in an independent cohort of 29 patients with PI-DLBCL. Associations between these markers and clinicopathological features, event-free survival (EFS), and overall survival (OS) in the two cohorts were analyzed. In the RNA expression panel, CCL5 expression was higher in patients with advanced-stage PI-DLBCL and was associated with inferior EFS and OS. Its principal receptor, CCR5, expressed in approximately one-third of patients, was associated with lower complete response rates to first-line immunochemotherapy: 50% in the experimental cohort and 10% in the validation cohort and correlated with the 7-year worse OS rate in both the experimental (49.8% versus 71.4%, p = 0.082) and validation (0% versus 76.2%, p < 0.001) cohorts. In both the experimental and validation cohorts, CCR5-positive tumors exhibited decreased CD86-positive (M1-like) and increased CD206-positive (M2-like) macrophage infiltration, consistent with an immunosuppressive TME. Multivariate analyses revealed that CCR5 expression was independently associated with worse EFS (p < 0.001) and OS (p = 0.004) in patients with PI-DLBCL (combined experimental and validation cohorts). CCR5 expression indicates a biologically aggressive subtype of PI-DLBCL with poor clinical outcomes and M2 macrophage-dominant immunosuppression.

Innate immunity constitutes the body's first line of defense, deploying evolutionarily conserved mechanisms to detect and respond to pathogenic threats and tissue injury. In contrast to the adaptive immune system's specificity and memory, innate immunity relies on germline-encoded pattern recognition receptors (PRRs) to sense pathogen-associated molecular patterns (PAMPs) and danger-associated molecular patterns (DAMPs). This review outlines the major PRR families and their downstream signaling pathways, culminating in the production of cytokines and inflammasome activation. Additionally, this review explores the functional integration of cellular responses and examines the sophisticated regulatory circuits, including transcriptional, posttranscriptional, epigenetic, and metabolic mechanisms, that calibrate innate immune responses. Importantly, we highlight how dysregulated innate immunity underlies a wide spectrum of diseases, from autoinflammatory and autoimmune disorders to chronic inflammatory states and cancer. Recent insights into trained immunity and innate immune memory further redefine the scope of innate defenses, revealing that metabolic and epigenetic remodeling can prime innate cells for enhanced secondary responses. Finally, we discuss the therapeutic potential of modulating innate pathways, including PRR agonists as vaccine adjuvants or anticancer agents, and PRR inhibitors in autoimmune and inflammatory diseases. By integrating current mechanistic knowledge with emerging therapeutic strategies, this review underscores the central role of innate immunity in health and disease while pointing toward promising avenues for future research and clinical translation.

Daraxonrasib is an orally bioavailable RAS(ON) multi-selective tri-complex inhibitor of the oncogenic mutant and wild-type variants of N, H and KRAS. We previously reported encouraging efficacy in a phase 1/2 clinical trial evaluating daraxonrasib monotherapy at clinically active dose levels in patients with previously treated, RAS mutant metastatic pancreatic adenocarcinoma (PDAC), providing the basis for confirmatory evaluation in the randomized phase 3 RASolute 302 clinical trial. Here we report mechanisms of acquired resistance to daraxonrasib monotherapy observed through targeted sequencing of over 800 genes in paired pretreatment and end of treatment circulating tumor DNA samples from 44 patients in the phase 1/2 clinical trial. Treatment-emergent genomic alterations in the RAS signaling pathway were observed in more than half (26 of 44; 59%) of these patients, including, most notably, mutant KRAS amplifications in one-third (16 of 44; 36%), as well as alterations in receptor tyrosine kinase (RTK) (4 of 44; 9%), MAPK (11 of 44; 25%) and PI3K (4 of 44; 9%) pathways. Notably, no acquired secondary KRAS mutations were observed, distinct from resistance profiles of mutant-selective KRAS G12C(OFF) inhibitors. To corroborate these clinical findings, we found, or mechanistically established, concordant mechanisms of daraxonrasib resistance in human and murine preclinical models of PDAC, including mutant KRAS and MYC amplification and RTK upregulation, with these alterations guiding various combination therapy concepts. Notably, daraxonrasib combined with agents targeting DNA damage response, RTKs or the mutant-selective RAS(ON) G12D inhibitor zoldonrasib averted resistance in preclinical models. Collectively, these results show that most daraxonrasib genomic resistance mechanisms drive reactivation of RAS pathway signaling and guide potential combination strategies in PDAC for further investigation.

Tumor-specific targeting remains a major obstacle for the development of precision cancer therapies. For several tumors and specifically glioblastoma (GBM), an aggressive brain tumor with poor prognosis, more effective treatments are urgently needed. Recombinant adeno-associated viruses (rAAVs), with their established clinical utility and mutational capsid plasticity, offer a promising platform for targeted delivery. We engineered and evaluated modified AAV capsids derived from the established AAV2 with HSPG-tropism knockdown and two less-characterized, tropism-reduced AAV9 variants. The epidermal growth factor receptor (EGFR), a tumor marker often overexpressed in GBM, was targeted by inserting an affibody (ZEGFR:1907). Also chlorotoxin (CLTX) was inserted, a peptide from scorpion venom reported to bind GBM. Transduction efficiencies were initially assessed with established cell lines (A431, HeLa, U251MG, MCF7). Affibody-displaying capsids exhibited EGFR-dependent transduction, with AAV9-affibody variants surpassing AAV9 wild-type. Several affibody-displaying capsids also transduced patient-derived GBM explants, as confirmed by fluorescence microscopy. These findings highlight the potential of retargeting AAV9 variants and the use of human surgical tissue samples for the initial evaluation of newly designed AAV capsids.

Transarterial chemoembolization (TACE) remains a cornerstone therapy for intermediate-to-advanced hepatocellular carcinoma (HCC); however, the optimal embolic platform remains uncertain. This multicenter, retrospective, real-world study (Clinical trial registration number: ChiCTR2500113198) conducted across China compared a novel temperature-sensitive liquid embolic agent, TempSLE-TACE (T-TACE), with conventional drug-eluting bead TACE (D-TACE) in 328 patients with Barcelona Clinic Liver Cancer (BCLC) stage B/C HCC. Following inverse probability of treatment weighting (IPTW), T-TACE achieved significantly superior objective response rates (ORRs) compared with D-TACE according to both RECIST 1.1 criteria (54.11% vs. 27.78%, P < 0.001) and mRECIST criteria (73.56% vs. 54.93%, P = 0.002). T-TACE was additionally associated with significantly prolonged progression-free survival (median PFS: 12.0 vs. 9.0 months; HR = 0.67, P = 0.001) and overall survival (median OS, 24.0 vs. 15.0 months; HR = 0.49, P < 0.001). Moreover, T-TACE demonstrated a favorable safety profile, with lower incidences of hepatic and gastrointestinal toxicities, including any-grade alanine aminotransferase elevation and hyperbilirubinemia. Subgroup analyses further demonstrated consistent OS, PFS, and ORR benefits across major clinical subgroups, with effect sizes remaining significantly favorable in high-risk populations, including advanced portal vein tumor thrombosis type Vp4, baseline AFP > 1000 ng/mL, and PIVKA-II > 2000 mAU/mL. Exploratory histo-molecular and spatial transcriptomic analyses suggested that T-TACE may promote immune microenvironment remodeling through enhanced Th17-cell infiltration and CD8⁺ T-cell activation, whereas incomplete embolization after D-TACE was more frequently associated with residual intermediate-state tumor cells and an immunosuppressive microenvironment. Collectively, these findings provide preliminary evidence supporting T-TACE as a promising real-world therapeutic strategy for intermediate-to-advanced HCC.

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.