Probing the Effect of Bulky Lesion-Induced Replication Fork Conformational Heterogeneity Using 4-Aminobiphenyl-Modified DNA

Unveiling Anoikis-related genes: A breakthrough in the prognosis of bladder cancer

BACKGROUND

Bladder cancer (BLCA) is a prevalent malignancy worldwide. Anoikis remains a new form of cell death. It is necessary to explore Anoikis-related genes in the prognosis of BLCA.

METHODS

We obtained RNA expression profiles from the The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases for dimensionality reduction analysis and isolated epithelial cells, T cells and fibroblasts for copy number variation analysis, pseudotime analysis and transcription factor analysis based on R package. We integrated machine-learning algorithms to develop the artificial intelligence-derived prognostic signature (AIDPS).

RESULTS

The performance of AIDPS with clinical indicators was stable and robust in predicting BLCA and showed better performance in every validation dataset compared to other models. Mendelian randomization analysis was conducted. Single nucleotide polymorphism (SNP) sites of rs3100578 (HK2) and rs66467677 (HSP90B1) exhibited significant correlation of bladder problem (not cancer) and bladder cancer, whereasSNP sites of rs3100578 (HK2) and rs947939 (BAD) had correlation between bladder stone and bladder cancer. The immune infiltration analysis of the TCGA-BLCA cohort was calculated via the ESTIMATE (i.e. Estimation of STromal and Immune cells in MAlignantTumours using Expression data) algorithm which contains stromal, immune and estimate scores. We also found significant differences in the IC50 values of Bortezomib_1191, Docetaxel_1007, Staurosporine_1034 and Rapamycin_1084 among the high- and low-risk groups.

CONCLUSIONS

In conclusion, these findings indicated Anoikis-related prognostic genes in BLCA and constructed an innovative machine-learning model of AIDPS with high prognostic value for BLCA.

Effect of Guanine Adduct Size, Shape, and Linker Type on the Conformation of Adducted DNA: A DFT and Molecular Dynamics Study

DNA is damaged through various exogenous sources (e.g., automobile exhaust, tobacco smoke, and processed foods), which can yield diverse C8-dG bulky aryl adducts. Adducts are known to induce structural changes to DNA that can lead to various biological outcomes, ranging from cell death to diseases such as cancer. Unfortunately, the relationship between the chemical composition of the damaged product, the adducted DNA structure, and the biological consequences is not well understood, which limits the development of disease detection and prevention strategies. The present study uses density functional theory (DFT) calculations and quintuplicate 1 μs molecular dynamics (MD) simulations to characterize the structure of DNA containing 21 model C8-dG adducts that systematically differ in size (phenyl to pyrenyl), shape (α (2,3), β (3,4) fusion, or ring substitution), and nucleobase-aryl group linkage (N, O, and C-linked). DFT calculations reveal that the inherent structural features of the G nucleobase adducts are impacted by linker type and bulky moiety shape, but not size, with the conformational flexibility reducing with α-ring fusion and linker composition as N > O > C. These structural properties are maintained in nucleoside models, which also reveal an increased propensity for anti-to-syn rotation about the glycosidic bond with N < O < C linker type. Although these diverse chemical features do not influence the global structure of adducted DNA, the adducts differentially impact the conformation local to the adducted site, including the relative populations of structures with the bulky moiety in the major groove (B conformer) and intercalated (stacked) into the helix (S conformer). Specifically, while the smallest phenyl adducts favor the B conformation and the largest pyrenyl-derived adducts stabilize the S conformation, the B/S ratio decreases with an increase in ring size and N > O > C linker composition. The shape and size (length) of the adduct can further finetune the B/S ratio, with β-fused naphthyl or α-fused phenanthryl N-linked adducts and O or C-linked adducts containing ring substitution increasing the prevalence of the S adducted DNA conformation. Overall, this work uncovers the significant effect of bulky moiety size and linker type, as well as the lesser impact of aryl group shape, on adducted DNA structure, which suggests differential replication and repair outcomes, and thereby represents an important step toward rationalizing connections between the structure and biological consequences of diverse DNA adducts.

HSPB8 is a Potential Prognostic Biomarker that Correlates With Immune Cell Infiltration in Bladder Cancer

Background: Heat shock protein B8 (HSPB8) is expressed in various cancers. However, the functional and clinicopathological significance of HSPB8 expression in bladder cancer (BC) remains unclear. The present study sought to elucidate the clinicopathological features and prognostic value of HSPB8 in BC.

Methods: A BC RNA-seq data set was obtained from The Cancer Genome Atlas Urothelial Bladder Carcinoma (TCGA-BLCA) database, and the external validation dataset GSE130598 was downloaded from the GEO database. Samples in the TCGA-BLCA were categorized into two groups based on HSPB8 expression. Differentially expressed genes (DEGs) between the two groups were defined as HSPB8 co-expressed genes. Gene set enrichment analysis (GSEA), protein-protein interaction networks, and mRNA-microRNA (miRNA) interaction networks were generated to predict the function and interactions of genes that are co-expressed with HSPB8. Finally, we examined immune cell infiltration and constructed a survival prediction model for BC patients.

Results: The expression level of HSBP8 has a significant difference between cancer samples and normal samples, and its diagnosis effect was validated by the ROC curve. 446 differential expressed genes between HSBP8 high-expression and HSBP8 low expression groups were identified. Gene enrichment analysis and GSEA analysis show that these differential gene functions are closely related to the occurrence and development of BC and the metabolic pathways of BC. The cancer-related pathways included Cytokine-cytokine receptor Interaction, Focal adhesion, and Proteoglycans in cancer. PPI and protein-coding gene-miRNA network visualized the landscape for these tightly bounded gene interactions. Immune cell infiltration shows that B cells, CD4+T cells, and CD8+T cells have strongly different infiltration levels between the HSBP8 high exp group and low exp group. The survival prediction model shows that HSBP8 has strong prognosis power in the BLCA cohort.

Conclusion: Identifying DEGs may enhance understanding of BC development’s causes and molecular mechanisms. HSPB8 may play an essential role in BC progression and prognosis and serve as a potential biomarker for BC treatment.