Pan-Cancer Multi-Omics and Structure-Guided Drug Discovery Identify TUBG1 as a Clinically and Immunologically Relevant Target

The Role of ULK3 in Cancer Progression: A Pan-Cancer Bioinformatics Analysis Integrated with Experimental Validation in Prostate Cancer

Unc-51-like kinase 3 (ULK3) is a key member of the ULK serine/threonine kinase family. Aberrant ULK3 expression has been increasingly linked to tumorigenesis and malignant progression in multiple cancer types. However, the precise role of ULK3 in tumor initiation and progression remains incompletely understood. Leveraging integrated multi-omics data from The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression (GTEx) project, and the Clinical Proteomic Tumor Analysis Consortium (CPTAC), we systematically characterized the expression of ULK3 at both the transcript and protein levels across 33 cancer types. We also evaluated genomic alterations, prognostic significance, alternative splicing, pathway enrichment, tumor stemness, immune infiltration, and immunotherapy-related biomarkers. In parallel, we investigated the function of ULK3 in prostate cancer PC-3 cells using cellular localization analysis, wound-healing assays, and MTT assays. We further applied Connectivity Map (CMap) screening and molecular docking to identify candidate ULK3 activators. ULK3 was significantly upregulated in 13 cancer types, including Bladder Urothelial Carcinoma, Breast Invasive Carcinoma, and Lung Adenocarcinoma. In contrast, ULK3 was downregulated in Cholangiocarcinoma and Head and Neck Squamous Cell Carcinoma. High ULK3 expression was associated with poor overall survival in Adrenocortical Carcinoma, Kidney Renal Clear Cell Carcinoma, and Skin Cutaneous Melanoma. Copy number amplification contributed to ULK3 overexpression. A recurrent A206V missense mutation was detected in the protein kinase (Pkinase) domain. Genes co-expressed with ULK3 were enriched in RNA splicing, methylation, oxidative phosphorylation, and energy metabolism. ULK3 expression showed positive correlations with tumor stemness indices and m1A/m5C/m6A RNA modification regulators. From an immunological perspective, high ULK3 expression was associated with lower Immune Score, increased M2 macrophage infiltration, and co-expression of PD-L1, CTLA4, and LAG3 in most cancers. ULK3 expression was also correlated with Tumor Mutational Burden in Kidney Renal Clear Cell Carcinoma and Rectum Adenocarcinoma. In addition, ULK3 expression was associated with Microsatellite Instability in Brain Lower Grade Glioma, Lung Adenocarcinoma, and Uterine Corpus Endometrial Carcinoma. ULK3 overexpression promoted proliferation and migration in PC-3 cells. Cephaeline was screened as a putative ULK3 activator. Overall, ULK3 expression and amplification were associated with poor clinical outcomes, tumor stemness, immunosuppression, and RNA dysregulation. These findings highlight the potential value of ULK3 as a pan-cancer diagnostic and prognostic biomarker and as a predictor of immunotherapy response, particularly in prostate cancer.

A pan-cancer analysis reveals the multifaceted role of PABPC1L in immune regulation and therapy response

A multi-omics integrative analyses reveals CYBB-mediated apoptotic and immune dysregulation as a key target of berberine in diffuse large B-cell lymphoma

Berberine has shown antitumor activity across multiple malignancies, yet its molecular targets and mechanisms of action in diffuse large B-cell lymphoma (DLBCL) remain incompletely defined. We integrated genetic causality, multi-omics data, and functional validation to identify berberine-related molecular pathways relevant to DLBCL. We identify bioinformatic screening and Mendelian randomization (MR) on 760 candidate berberine-related genes; 315 with adequate instruments underwent MR for causal links to DLBCL. Follow-up analyses included pathway enrichment, Protein-Protein Interaction (PPI) networks, machine-learning prognostic modeling, molecular docking and dynamics, single-cell RNA sequencing, cell–cell communication inference, bulk transcriptomic validation, and in vitro assays. MR identified several berberine-related genes with putative causal associations with DLBCL. ABCA1 , ITK, MAPK3, TGM2, and DAPK1 were associated with decreased DLBCL risk, whereas CYBB, RAC1, JUN, and CPT1A were associated with increased risk. Enriched pathways encompassed B-cell receptor signaling, immune checkpoints, apoptosis, and MAPK signaling. Apoptosis pathway activity correlated with favorable prognosis across cohorts. Integrative analyses prioritized CYBB as a central hub. Molecular docking and dynamics indicated stable berberine– CYBB binding. Single-cell analyses showed CYBB + B cells had distinct apoptotic, immunoregulatory, and communication features, including BTLA–TNFRSF14 signaling. Bulk deconvolution linked high CYBB to worse prognosis, proliferation, and an immunosuppressive microenvironment. Functionally, CYBB knockdown reduced DLBCL cell viability and increased apoptosis; berberine inhibited growth dose-dependently, and cellular thermal shift assays supported berberine– CYBB target engagement in cells. This integrative study identifies berberine-related genes with potential causal relevance to DLBCL and prioritizes CYBB as a functionally relevant target linked to apoptosis, immune regulation, and prognosis, highlighting the potential involvement of berberine– CYBB axis underlying berberine activity in DLBCL, although rescue experiments are needed to confirm its specificity and relative contribution.

Integrative network pharmacology and genomic analysis of esculin targeting PARP1 in cervical cancer: Insights from ADME profiling, molecular docking, and biomarker discovery.

Cervical cancer remains a serious global health issue, particularly in low- and middle-income countries, with inadequate access to early detection and diagnostics. This study investigates the anticancer effect of esculin, a coumarin known for its pharmacological benefits, as a safer and more effective alternative to standard chemotherapeutics. This research implements an integrative in silico method, which includes ADME profiling, toxicity prediction, molecular docking, molecular dynamics (MD) simulations, and network pharmacology analyses. Esculin performed well in drug-likeness properties and showed satisfactory water solubility and low predicted toxicity, which is even better than that of the reference drug paclitaxel in safety and pharmacokinetics. Although no direct connection was established between esculin's predicted targets and genes perturbed in cervical cancer, PARP1 came up as a candidate target that is functionally and biologically relevant, since the protein is involved in DNA repair and is overexpressed in cervical tumours. Molecular docking revealed that esculin binds strongly to PARP1and interacts with ASP770 and ARG878. A subsequent 100 ns molecular dynamics (MD) simulation experiment showed the constant RMSD and hydrogen bonding profiles that were consistent and thus proved the stability of the complex structure. Protein-protein interaction and enrichment analyses supported PARP1's role in critical cancer-associated pathways, particularly in DNA damage response and chromatin remodelling. Considering all the findings, the efforts to develop a targeted cervical cancer therapy with esculin as a potential candidate are gaining traction and being warranted by further experimental validation.

Unraveling the role of PPFIA1 in cancer: a comprehensive multi-omics analysis and functional validation from pan-cancer to pancreatic cancer

Background PTPRF interacting protein alpha 1 (PPFIA1), a cytoplasmic scaffold protein of the liprin family, modulates cell adhesion, signal transduction, and cytoskeletal dynamics. Its pan-cancer prognostic implications and functional roles, particularly in pancreatic cancer, remain underexplored. Methods Pan-cancer datasets including TCGA, GTEx and TISCH were integrated to assess PPFIA1 expression, genomic alterations, and pathway enrichment via Kaplan-Meier survival analysis, Cox regression, cBioPortal, and GSEA. In pancreatic cancer, external cohorts (e.g., GSE28735, GSE52452) were used for expression and prognosis validation. Besides, immunotherapy response was analyzed by using TIGER cohorts. Functional impacts were determined by using ShRNA-mediated knockdown in CFPAC-1, PANC-1 and Panc-02 cells and evaluating their proliferation, migration and invasion in vitro and in vivo. Results PPFIA1 exhibited differential expression across multiple cancer types, with overexpression in pancreatic adenocarcinoma (PAAD) versus non-tumor tissue at mRNA/protein levels, predominantly in malignant cells. High PPFIA1 correlated with adverse prognosis in PAAD across multiple endpoints. Genomic analyses revealed amplifications in head/neck cancers and mutations in endometrial carcinoma, clustering in SAM domains. GSEA enrichment analysis indicated pan-cancer activation of the mitotic spindle assembly pathway and Epithelial-Mesenchymal Transition (EMT) pathways in PAAD. Knockdown suppressed PAAD cell proliferation, colony formation, migration, invasion, and tumor growth in vivo. Notably, elevated PPFIA1 predicted superior responses to immunotherapy in pan-cancer cohorts rather than pancreatic cancer. Conclusions PPFIA1 emerges as a pan-cancer biomarker with prognostic significance and shows an oncogenic role in PAAD, potentially associating with EMT-related malignant phenotypes. Its association with immunotherapy efficacy suggests PPFIA1 warrants further investigation as a candidate biomarker and potential functional target for precision oncology.

METTL1/WDR4 Complex: A Novel Epitranscriptomic Target at the Crossroads of RNA Methylation and Drug Discovery

METTL1, in complex with its partner protein WDR4, is the principal writer of internal and RNA-associated N7-methylguanosine (m7G), an epitranscriptomic modification that remodels translation, RNA stability, and stress-response pathways. Across diverse cancer types, including hepatocellular carcinoma, cholangiocarcinoma, lung and bladder cancer, glioma, AML, and prostate cancer, METTL1/WDR4-driven expansion of m7G-modified tRNAs and stabilization of codon-biased mRNAs amplifies oncogenic programs governing cell-cycle progression, EMT, DNA repair, and immune evasion. Context-specific roles extend to autoimmune, cardiovascular, and neurological disorders, where METTL1 regulates hypertrophy, fibrosis, angiogenesis, neurodevelopment, and inflammation. Recent advances have established METTL1 as a tractable methyltransferase target: fragment-derived SAM-pocket ligands provide optimal starting points, and recently disclosed THIQ-based inhibitors report nanomolar inhibition, robust cellular target engagement, and functional suppression of tRNA m7G in cells. These advances provide the first chemical foothold for therapeutic modulation of m7G pathways and underscore METTL1 as a promising yet complex target requiring careful biological stratification.