Integrated transcriptomic and proteomic analysis reveals that the anti-endometriosis effects of Pingchong Jiangni recipe may involve pathways and genes/proteins related to inflammation, autophagy, mitochondrial function, and angiogenesis in ectopic endometrial stromal cells

ETHNOPHARMACOLOGICAL RELEVANCE: Pingchong Jiangni recipe (PJR) is a Chinese herbal formula that has been used clinically for decades in the treatment of endometriosis, with effects such as shrinking the lesions and reducing the recurrence rate. However, the mechanisms underlying the inhibition of ectopic endometrium by PJR remain unclear. AIM OF THE STUDY: This study aimed to explore the potential mechanism through which PJR ameliorates endometriosis by acting on ectopic endometrial stromal cells (EESCs). MATERIALS AND METHODS: The EESCs were obtained from endometriosis patients, and identified via immunocytochemistry. The cell counting kit-8 assay, along with morphological analysis, was used to quantify the effect of PJR on EESCs growth. Furthermore, RNA sequencing and proteomics were employed to detect the characteristics of EESCs following their treatment with PJR. Additionally, gene ontology enrichment analysis, Kyoto Encyclopedia of Genes and Genomes enrichment analysis, gene set enrichment analysis, individuation genes/proteins analysis, and correlation analysis were used to analyze the genes and proteins. These genes/proteins were also compared with endometriosis-related genes in other databases. Finally, the authenticity of the omics results was validated by detecting the expression of randomly selected focus genes/proteins via quantitative real-time polymerase chain reaction and western blotting. RESULTS: It was observed that PJR significantly inhibited EESCs growth in a dose-dependent manner (p < 0.05). A 10 % concentration of PJR inhibited EESCs viability by more than 50 % and significantly altered the cell morphology. Transcriptomic and proteomic analyses revealed 1470 differentially expressed genes and 1881 proteins (|fold-change|>2 and false discovery rate <0.05) in the PJR group compared with the control group. Furthermore, multiple signaling pathways were enriched and 162 crucial genes/proteins were subsequently identified. These were related to inflammation, angiogenesis, autophagy, mitochondrial function, as well as cell adhesion and invasion. Moreover, the expression of eight genes randomly selected was consistent with the omics results, whereas the expression of three proteins was also consistent. CONCLUSION: The inhibition of EESCs growth by PJR is a key step in PJR shrinking the lesions in patients with endometriosis. Furthermore, the inhibition mechanism of PJR in EESCs was associated with multiple pathways and genes/proteins, both related to inflammation, autophagy, mitochondrial function, and angiogenesis.