Identification and verification of a novel signature that combines cuproptosis-related genes with ferroptosis-related genes in osteoarthritis using bioinformatics analysis and experimental validation.

BACKGROUND: Exploring the pathogenesis of osteoarthritis (OA) is important for its prevention, diagnosis, and treatment. Therefore, we aimed to construct novel signature genes (c-FRGs) combining cuproptosis-related genes (CRGs) with ferroptosis-related genes (FRGs) to explore the pathogenesis of OA and aid in its treatment. MATERIALS AND METHODS: Differentially expressed c-FRGs (c-FDEGs) were obtained using R software. Enrichment analysis was performed and a protein-protein interaction (PPI) network was constructed based on these c-FDEGs. Then, seven hub genes were screened. Three machine learning methods and verification experiments were used to identify four signature biomarkers from c-FDEGs, after which gene set enrichment analysis, gene set variation analysis, single-sample gene set enrichment analysis, immune function analysis, drug prediction, and ceRNA network analysis were performed based on these signature biomarkers. Subsequently, a disease model of OA was constructed using these biomarkers and validated on the GSE82107 dataset. Finally, we analyzed the distribution of the expression of these c-FDEGs in various cell populations. RESULTS: A total of 63 FRGs were found to be closely associated with 11 CRGs, and 40 c-FDEGs were identified. Bioenrichment analysis showed that they were mainly associated with inflammation, external cellular stimulation, and autophagy. CDKN1A, FZD7, GABARAPL2, and SLC39A14 were identified as OA signature biomarkers, and their corresponding miRNAs and lncRNAs were predicted. Finally, scRNA-seq data analysis showed that the differentially expressed c-FRGs had significantly different expression distributions across the cell populations. CONCLUSION: Four genes, namely CDKN1A, FZD7, GABARAPL2, and SLC39A14, are excellent biomarkers and prospective therapeutic targets for OA.

Relationships between stable isotope natural abundances (δ13C and δ15N) and water use efficiency in rice under alternate wetting and drying irrigation in soils with high clay contents.

Natural abundance of the stable isotope (δ13C and δ15N) in plants is widely used to indicate water use efficiency (WUE). However, soil water and texture properties may affect this relationship, which remains largely elusive. Therefore, the purpose of this study was to evaluate δ13C as affected by different combinations of alternate wetting and drying irrigation (AWD) with varied soil clay contents in different organs and whole plant and assess the feasibility of using δ13C and δ15N as a physiological indicator of whole-plant water use efficiency (WUEwhole-plant). Three AWD regimes, I100 (30 mm flooded when soil reached 100% saturation), I90 (30 mm flooded when reached 90% saturation) and I70 (30 mm flooded when reached 70% saturation) and three soil clay contents, 40% (S40), 50% (S50), and 60% (S60), were included. Observed variations in WUEwhole-plant did not conform to theoretical expectations of the organs δ13C (δ13Corgans) of plant biomass based on pooled data from all treatments. However, a positive relationship between δ13Cleaf and WUEET (dry biomass/evapotranspiration) was observed under I90 regime, whereas there were no significant relationships between δ13Corgans and WUEET under I100 or I70 regimes. Under I100, weak relationships between δ13Corgans and WUEET could be explained by (i) variation in C allocation patterns under different clay content, and (ii) relatively higher rate of panicle water loss, which was independent of stomatal regulation and photosynthesis. Under I70, weak relationships between δ13Corgans and WUEET could be ascribed to (i) bigger cracks induced by water-limited irrigation regime and high clay content soil, and (ii) damage caused by severe drought. In addition, a negative relationship was observed between WUEwhole-plant and shoot δ15N (δ15Nshoot) across the three irrigation treatments, indicating that WUEwhole-plant is tightly associated with N metabolism and N isotope discrimination in rice. Therefore, δ13C should be used cautiously as an indicator of rice WUEwhole-plant at different AWD regimes with high clay content, whereas δ15N could be considered an effective indicator of WUEwhole-plant.