POLR2A Promotes the Proliferation of Gastric Cancer Cells by Advancing the Overall Cell Cycle Progression

A mutation in POLR2A gene associated with body size traits in Dezhou donkeys revealed with GWAS

The Dezhou donkey is a famous local donkey breed in China. The aim of the present study was to identify the genes associated with the body size traits of the Dezhou donkey and facilitate the breeding activities of the donkeys. A total of 349 donkeys from 2 generations (113 individuals in F0 and 236 in F1) were analyzed with restriction-site-associated DNA sequencing. A genome-wide association study revealed that the region between 13.7 and 15.6 Mb of chromosome 13 is significantly associated with body sizes. Candidate genes related to body size development, including POLR2A, CHRNB1, FGF11, and ZBTB4, were identified. The results of GO and KEGG analysis indicated that the genes involved in many GO terms were related to metabolic processes and developmental processes. Additionally, a T>C mutation (Chr13:14312485) was found at intron 10 of the POLR2A gene. The association analysis showed significant differences among genotypes for the size traits. The body size of the individuals with the TT genotype was significantly higher than that with the CC genotype. The results showed that the polymorphism of POLR2A has the potential to be used as a marker in the breeding programs of the Dezhou donkeys.

Integrated Bioinformatic Analysis of Differentially Expressed Genes Associated with Wound Healing

OBJECTIVE

Wound healing is a complex process involving the coordinated interaction of various genes and molecular
pathways. The study aimed to uncover novel therapeutic targets, biomarkers and candidate genes for drug development
to improve successful wound repair interventions.
Materials and Methods: This study is a network-meta analysis study. Nine wound healing microarray datasets obtained
from the Gene Expression Omnibus (GEO) database were used for this study. Differentially expressed genes (DEGs)
were described using the Limma package and shared genes were used as input for weighted gene co-expression
network analysis. The Gene Ontology analysis was performed using the EnrichR web server, and construction of a
protein-protein interaction (PPI) network was achieved by the STRING and Cytoscape.
Results: A total of 424 DEGs were determined. A co-expression network was constructed using 7692 shared genes
between nine data sets, resulting in the identification of seven modules. Among these modules, those with the top 20
genes of up and down-regulation were selected. The top down-regulated genes, including TJP1, SEC61A1, PLEK,
ATP5B, PDIA6, PIK3R1, SRGN, SDC2, and RBBP7, and the top up-regulated genes including RPS27A, EEF1A1,
HNRNPA1, CTNNB1, POLR2A, CFL1, CSNk1E, HSPD1, FN1, and AURKB, which can potentially serve as therapeutic
targets were identified. The KEGG pathway analysis found that the majority of the genes are enriched in the "Wnt
signaling pathway".
Conclusion: In our study of nine wound healing microarray datasets, we identified DEGs and co-expressed modules
using WGCNA. These genes are involved in important cellular processes such as transcription, translation, and posttranslational
modifications. We found nine down-regulated genes and ten up-regulated genes, which could serve as
potential therapeutic targets for further experimental validation. Targeting pathways related to protein synthesis and cell
adhesion and migration may enhance wound healing, but additional experimental validation is needed to confirm the
effectiveness and safety of targeted interventions.

Network-Derived Radioresistant Breast Cancer Target with Candidate Inhibitors from Brown Algae: A Sequential Assessment from Target Selection to Quantum Chemical Calculation

Despite significant progress in early detection and treatment, a few aggressive breast cancers still exhibit resistance to therapy. This study aimed to identify a therapeutic target for radioresistant breast cancer (RRbc) through a protein network from breast cancer genes and to evaluate potent phytochemicals against the identified target. Our approach includes the integration of differential expression genes from expression datasets to create a protein network and to use survival analysis to identify the crucial RRbc protein in order to discover a therapeutic target. Next, the phytochemicals sourced from brown algae were screened through molecular docking, ADME (absorption, distribution, metabolism, and excretion), molecular dynamics (MD) simulation, MM-GBSA, and quantum mechanics against the identified target. As a result of our protein network investigation, the proto-oncogene c-KIT (KIT) protein was identified as a potent radioresistant breast cancer target. Further, phytochemical screening establishes that nahocol-A1 from brown algae has high binding characteristics (-8.56 kcal/mol) against the KIT protein. Then, quantum chemical analysis of nahocol-A1 provided insights into its electronic properties favorable for protein binding. Also, MD simulation comprehends the conformational stability of the KIT-nahocol-A1 complex. Overall, our findings suggest nahocol-A1 could serve as a promising therapeutic candidate for radioresistant breast cancer.

RNF6 promotes gastric cancer progression by regulating CCNA1/CREBBP transcription

Ring finger protein 6 (RNF6) is a member of the E3 ubiquitin ligase family. Previous studies have reported the involvement of RNF6 as a ubiquitin ligase in the progression of gastric cancer (GC). However, this study found that RNF6 has a clear localization in the nucleus of GC, indicating a role other than ubiquitin ligase. Further chromatin immunoprecipitation sequencing (ChIP-seq) analysis revealed that RNF6 has DNA binding and transcriptional regulatory effects and is involved in important pathways such as tumor cell cycle and apoptosis. Cyclin A1 (CCNA1) and CREB binding protein (CREBBP) are downstream targets for RNF6 transcription regulation in GC. RNF6 binds to the promoter region of CCNA1/CREBBP and is actively regulating their expression in GC cells. Silencing CCNA1/CREBBP partially reversed the promoting effect of RNF6 overexpression on the biological function of GC cells. Our study suggests that RNF6 promotes the progression of GC by regulating CCNA1/CREBBP transcription.