Biology subjects

Fosu, K.

Publications and source records attributed to Fosu, K..

3 recordsLinked to original sources

bioRxiv2026

Genomic Correlates of APOBEC-Associated Mutagenesis in Esophageal Squamous Cell Carcinoma

Background and Aims: APOBEC-associated mutagenesis is prominent in esophageal squamous cell carcinoma (ESCC), but genomic features associated with its intertumoral variability remain incompletely characterized. We investigated genomic correlates of APOBEC-associated mutagenesis while accounting for the compositional structure of mutational signature data. Methods: Mutational signatures were analyzed in 552 ESCC tumors from eight countries. APOBEC-associated mutagenesis was quantified as SBS2 plus SBS13 using absolute mutation counts and proportional contributions. Associations with co-occurring mutational signatures, total SBS burden, recurrent driver-gene alterations, and country were evaluated using correlation, sensitivity, and multivariable analyses. Principal component and regression-model robustness were additionally assessed. Results: APOBEC burden varied markedly across tumors (median, 2,002 mutations; IQR, 987-4,346). Several associations observed using signature proportions were not maintained in absolute-count analyses: SBS1, SBS3, and SBS5 changed direction, indicating sensitivity to compositional representation. In contrast, SBS18 remained inversely associated with APOBEC-associated mutagenesis in all variable pairings examined: proportion versus proportion (Spearman rho = -0.527), APOBEC proportion versus SBS18 absolute count (r = -0.435), and absolute count versus absolute count (Pearson r = -0.319, P = 1.59 x 10^-14; Spearman rho = -0.317). These are distinct comparisons rather than discrepant estimates. Notably, this cohort-wide relationship was primarily characterized by higher APOBEC burden in SBS18-negative than SBS18-positive tumors rather than a continuous inverse relationship among SBS18-positive tumors. The multivariable model had an in-sample R^2 of 0.400 but lower and variable 10-fold cross-validated performance (mean R^2 = 0.273). Country added little explanatory information to this model (delta R^2 = 0.008; global P = 0.402). ZNF750-mutant tumors had higher APOBEC burden than wild-type tumors (BH-FDR q = 0.0032), although only 12 tumors carried ZNF750 alterations. Conclusion: Genomic correlates of APOBEC-associated mutagenesis in ESCC are sensitive to the representation of mutational signature activity. SBS18 showed the most consistent inverse association, whereas the ZNF750 association warrants independent validation.

genomics↗

bioRxiv2025

Hepatoprotective Effects of Vernonia amygdalina Leaf Extract: In Vivo and In Silico Evidence Against Ethanol-Induced Liver Injury

Alcoholic liver disease (ALD) remains a major global health burden with limited therapeutic options. In this study, we investigated the hepatoprotective effects of Vernonia amygdalina (VA) leaf extract against ethanol-induced liver injury using integrated in vivo and in silico approaches. Wistar rats were exposed to ethanol to induce liver damage, followed by treatment with VA extract (100-300 mg/kg) or silymarin (50 mg/kg). Liver function indices were evaluated through biochemical analysis. Network pharmacology analysis was performed to identify active compounds and their protein targets, and molecular docking assessed the binding affinities of key compounds. Ethanol exposure markedly increased serum SGOT, SGPT, ALKP, and total bilirubin while decreasing total protein and albumin. VA treatment significantly corrected these alterations in a dose-dependent manner. At 300 mg/kg, VA reduced SGPT from 110.31 to 88.65 U/mL, ALKP from 52.20 to 28.14 U/mL, and total bilirubin from 1.19 to 0.59 g/dL. Network pharmacology revealed flavonoids and sesquiterpene lactones as key active compounds targeting ALD-relevant proteins, including AKT1, CASP3, and HSP90AA1. Molecular docking demonstrated strong binding affinities (-9.5 kcal/mol) of cryptolepine, luteolin, and apigenin with AKT1 and HSP90AA1. VA provides both biochemical and mechanistic protection against ethanol-induced liver damage, highlighting its therapeutic potential in ALD management.

pharmacology and toxicology↗

bioRxiv2025

Neurobiological and Chemical Characterization of the Cyanobacterial Metabolite Veraguamide E

Ver Es structure was validated by {superscript 1}H NMR, HRMS, and molecular networking analyses. Computational docking and NMR titration confirmed direct, saturable, and tight binding of Ver E to the human Sigma-2 receptor/transmembrane protein 97 ({sigma}2R/TMEM97). Functional calcium imaging in primary mouse sensory neurons revealed that Ver E increases intracellular Ca{superscript 2} levels without modulating store-operated calcium entry (SOCE). Multi-well microelectrode array experiments using human induced pluripotent stem cell (hiPSC) derived nociceptors showed that Ver E significantly reduced neuronal activity at physiological temperatures, but not under heat-stress conditions. Ver E exhibited no cytotoxicity at concentrations up to 30 {micro}M in HEK293 cells, and immunocytochemistry confirmed that it does not alter phosphorylated eIF2 (p-eIF2) expression, indicating a mechanism distinct from integrated stress response modulators. Collectively, these findings position Ver E as a non-toxic compound capable of selectively modulating neuronal excitability, thereby advancing the development of novel therapeutics for pain management. SignificanceNatural products have long been recognized as a rich source of therapeutics, accounting for over 60% of currently approved small-molecule drugs and underscoring their pivotal role in drug discovery. Marine cyanobacteria produce structurally diverse secondary metabolites with a wide array of biological activities. Among these are the veraguamides, a family of depsipeptides that have shown promise as future therapeutics in our recent studies. This work presents a detailed biological and chemical characterization of veraguamide E (Ver E), isolated from a Panamanian marine cyanobacterial collection. The {sigma}2R/TMEM97 system has been identified as a promising target to address unmet need for non-opioid therapeutics which can modulate neuronal excitability in the context of chronic pain. Discovery and identification of novel compounds which modulate this system can help us better understand its function as well as allow us to develop future therapeutics targeting this pathway. HighlightsO_LIVeraguamide E specifically binds {sigma}2R/TMEM97 receptor with high affinity. C_LIO_LIComputational docking and NMR confirm a distinct binding mechanism. C_LIO_LIVer E modulates calcium signaling in mouse DRG neurons and human iPSC-derived nociceptors. C_LIO_LIVer E demonstrates no detectable cytotoxicity in human cell lines. C_LI

neuroscience↗