Proteomics and transcriptome reveal the key transcription factors mediating the protection of Panax notoginseng saponins (PNS) against cerebral ischemia/reperfusion injury

Background and purpose: Transcription factors (TFs) play a critical role in the cerebral ischemia/reperfusion injury (IRI). Panax notoginseng saponins (PNS) are extensively used in the treatment of acute cerebral ischemia in China, but the mechanism of their effects, especially at the TF level, remains unclear. In this study, a combination of transcriptomics, proteomics and network pharmacology analysis was used to identify the key TFs involved in the protection of PNS against middle cerebral artery occlusion (MCAO)-induced IRI. Methods and results: Sprague-Dawley rats which were subjected to 1.5 hours of MCAO-induced occlusionand then followed by reperfusion, were treated with PNS at a concentration of 36 mg/kg or 72 mg/kg daily for 7 days. PNS significantly decreased neurological deficient scores and infarction rate; prevented cerebral tissue damage; and reduced CASP3 activity, levels of TNF, IL1B and CCL2 after IRI. Through a combination of transcriptomics and proteomics, 9 critical TFs were identified, including Excision repair cross-complementing group 2 (ERCC2), Nuclear receptor subfamily 4 group A member 3 (NR4A3) and 7 other TFs. The targets of ERCC2 and NR4A3, such as Ubxn11, Ush2a, Numr2, Oxt, Ubxn11, Scrt2, Ttc34 and Lrrc23, were verified by using real-time PCR analysis. RNA-seq analyses indicated that PNS regulated nerve system development and inflammation, and the majority of the identified TFs were also involved in these processes. By using network pharmacology analysis, 73 chemical components in PNS were predicted to affect ERCC2, NR4A3 and 3 other identified TFs. Conclusion: ERCC2, NR4A3 and 7 other TFs were of importance in the protection of PNS against IRI. This study promoted the understanding of protective mechanism of PNS against cerebral IRI and facilitated the identification of possible targets of PNS.