Electronic Journal of Biotechnology

Identification and validation of a pyroptosis-relevant model for the prognosis of cutaneous melanoma

YaSu Jiang — 2026-05-15

Background: Cutaneous melanoma (CM) is a highly aggressive skin malignancy with marked molecular heterogeneity and poor prognosis. Pyroptosis, an inflammatory form of programmed cell death, has been implicated in tumor progression and immune regulation; however, its prognostic value in CM remains incompletely understood.

Results: Gene expression data from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas skin cutaneous melanoma (TCGA-SKCM) cohorts were analyzed to identify pyroptosis-related differentially expressed genes (PRGs). Eight CM-associated PRGs were identified through integrated differential expression and intersection analyses. Functional enrichment analyses revealed that these genes were involved in inflammatory responses, immune regulation, and cell cycle-related pathways. A prognostic model was constructed using univariate Cox and least absolute shrinkage and selection operator (LASSO) regression analyses in the TCGA-SKCM cohort. Six PRGs were incorporated into the prognostic signature, of which ISG15, GZMB, and EGFR were independently associated with patient survival. The model demonstrated good predictive performance, as confirmed by receiver operating characteristic curves, Kaplan-Meier survival analysis, calibration plots, and decision curve analysis at 1-, 3-, and 5-year time points. Immune infiltration analysis revealed that ISG15, GZMB, and EGFR expression were positively correlated with the enrichment of multiple immune cell populations. Mutation profiling further supported the clinical relevance of these prognostic genes.

Conclusions: In summary, we developed a pyroptosis-related prognostic model for cutaneous melanoma and identified ISG15, GZMB, and EGFR as clinically relevant prognostic biomarkers. Our findings enhance the understanding of pyroptosis-associated molecular mechanisms in CM and support their potential utility in prognostic stratification.

Study on the effect of catalytic rotting and returning of rice straw to the field on rhizosphere soil and rice yield

Bing Yang — 2026-05-15

Background: In-situ straw return is an effective agronomic practice for improving soil quality and increasing crop yields. However, in Northeast China, prolonged seasonal freezing lasting more than 6 months markedly restricts straw decomposition, thereby limiting the benefits of straw return in saline-alkali soils. To overcome this constraint, cold-tolerant bacterial agents were applied to promote the decomposition and in-situ return of rice straw under frozen and low-temperature conditions.

Results: The results demonstrated that under freezing and low-temperature conditions, the application of the microbial agent (CF) increased the rice straw decomposition rate to 51.22%, which was significantly higher than that observed in the control treatment (34.64%). The germination index of seeds exposed to the decomposed straw reached 102.87%, indicating that the decomposition products met safety standards. CF treatment reduced rhizosphere soil pH and salinity, while significantly increasing the diversity and abundance of rhizosphere microorganisms. In particular, it promoted the enrichment of bacterial genera associated with nitrogen fixation and straw decomposition. At the same time, the CF application enhanced rhizosphere soil nutrient levels, which in turn significantly improved rice growth parameters, including tiller number, plant height, and dry weight. Consequently, rice yield increased by 5.84% compared with the control treatment.

Conclusions: In summary, the application of cold-tolerant bacterial agents enables efficient in-situ decomposition and return of rice straw under freezing and low-temperature conditions. This approach effectively enhances rice productivity in saline-alkali farmland and provides a simple, practical, and scalable strategy for overcoming straw decomposition limitations in cold regions worldwide.

Identification and verification of diagnostic biomarkers related to matrisome in patients with knee osteoarthritis based on machine learning algorithms

Jianqiao Sun — 2026-05-15

Background: It is reported that matrisome exerts a significant function in the pathogenesis of knee osteoarthritis (KOA). Thus, this study was conducted to screen the matrisome-associated diagnostic genes for KOA.

Results: A total of 158 matrisome-related genes in KOA were obtained, then 5 diagnostic genes were screened, namely collagen type 1 alpha 1 (COL1A1), high temperature requirement factor A1 (HTRA1), SPARC (osteonectin), cwcv and kazal-like domains proteoglycan 1 (SPOCK1), sulfatase 1 (SULF1) and extracellular matrix protein 1 (ECM1). These 5 diagnostic genes were both obviously overexpressed in KOA groups relative to those in the healthy group, and both strongly associated with most immune cells, such as macrophage, eosinophil, and activated B cell. The targeted drugs for the 5 diagnostic genes contained 9-Octadecenamide, Diacerein, and Rifaximin. The mRNA and protein expression levels of the 5 diagnostic genes were consistent with the bioinformatics analysis results. Also, the viability of monosodium iodoacetate (MIA)-treated SW1353 cells was significantly decreased after upregulation of ECM1, while apoptosis showed the opposite trend. Moreover, MIA remarkably increased the phosphorylation levels of PI3K and Akt in SW1353 cells.

Conclusions: Five matrisome-associated diagnostic genes were identified with better diagnostic values, including COL1A1, HTRA1, SPOCK1, SULF1 and ECM1. ECM1 exacerbates the progression of KOA, and PI3K-Akt signaling pathway is involved in the progression of KOA. The drugs, containing 9-Octadecenamide, Diacerein, and Rifaximin, etc., might be used for KOA treatment by targeting COL1A1, HTRA1, SPOCK1, SULF1 and ECM1.

Glutathione peroxidase 3 as a predictor of immune modulation in gastric adenocarcinoma

Ying Shao — 2026-05-15

Background: Gastric cancer is a highly prevalent and lethal malignancy worldwide, with its immune microenvironment playing a crucial role in tumor initiation and progression. Among selenoproteins, glutathione peroxidase 3 (GPX3) is an important antioxidant enzyme that has recently attracted attention for its roles in various cancers. However, the function of GPX3 and its impact on the immune microenvironment in stomach adenocarcinoma (STAD) remain insufficiently explored.

Results: Deep STAD tissues were more enriched in immune cells compared to superficial tumor tissues, particularly myeloid cells and fibroblasts. GPX3 was predominantly expressed in fibroblasts and myeloid cells, while its expression in T cells was relatively low, with no significant differences across different tumor layers. Moreover, GPX3 exhibited weak correlations with PD-1 and CTLA-4, suggesting that GPX3 may not directly mediate immune evasion via immune checkpoint pathways. These findings characterize the cellular distribution of GPX3 within the STAD immune microenvironment and provide initial insights into its potential regulatory function.

Conclusions: Although GPX3 may not directly influence immune checkpoint pathways, its high expression in myeloid cells and fibroblasts suggests that it might indirectly modulate immune responses by regulating the tumor microenvironment. These results lay a theoretical foundation for future research on GPX3 in gastric cancer and its potential as a therapeutic target.

Periodontal ligament stem cell-derived exosomes promote alveolar bone defect repair in periodontitis by mediating M2 macrophage polarization via regulation of the SEMA4D/PLXNB1 axis

YanZong Yang — 2026-05-15

Background: Periodontitis is a chronic inflammatory disease characterized by progressive alveolar bone loss. This study explored the role of exosomes derived from periodontal ligament stem cells (PDLSCs-Exo) in repairing alveolar bone defects in periodontitis.

Results: PDLSCs-Exo significantly promoted new bone formation and collagen deposition in the defect area while reducing pro-inflammatory factors and enhancing M2 macrophage polarization. The knockdown of semaphorin 4D (SEMA4D) or plexin B1 (PLXNB1) further enhanced exosome-mediated repair, whereas their overexpression attenuated it. Additionally, the upregulation of PLXNB1 reversed the reparative effects of SEMA4D downregulation on alveolar bone defects in periodontitis.

Conclusions: PDLSCs-Exo promotes M2 macrophage polarization by inhibiting the SEMA4D/PLXNB1 axis, alleviating local inflammation and accelerating alveolar bone defect repair in periodontitis. This finding provides a novel theoretical basis for the clinical treatment of periodontitis-related alveolar bone defects and identifies potential therapeutic targets for improving the efficacy of bone defect repair.