Screening of Programmed Cell Death-Related Biomarkers and Exploration of Mechanisms in Zhenwu Decoction for Treating Chronic Kidney Disease
Ruiping Li, Tao Zhang, Liuyun Li, Xingyao Li, Qi Gao, Xili Wu, Sicen Wang, Peng AnIntroduction:
Programmed Cell Death (PCD) is pivotal in Chronic Kidney Disease (CKD), yet the therapeutic mechanism of Zhenwu Decoction (ZWD) targeting PCD remains unclear. This study integrated CKD transcriptomics (GSE15072 dataset) and network pharmacology to identify PCD-related biomarkers and elucidate ZWD's action.
Methods:
Differential expression analysis identified CKD-related genes. Active ZWD ingredients and targets were screened via TCMSP. Overlapping genes from PCD-Related Genes (PCDRGs), Differentially Expressed Genes (DEGs), and ZWD targets were subjected to machine learning for biomarker selection. Biomarkers were validated through nomogram construction, enrichment analysis, immune infiltration assessment, molecular docking, and RT-qPCR.
Results:
TCMSP identified 61 active ingredients and 777 targets for ZWD; 14 candidate genes were screened from 822 DEGs, 1548 PCD-RGs, and ZWD targets. Machine learning yielded 5 downregulated CKD biomarkers (SQLE, PRKACA, PARP2, RPS6KB1, ALOX12) with a wellperforming nomogram. GSEA linked SQLE, PRKACA, and ALOX12 to SARS-CoV-2 nsp1- related translation initiation; PARP2/RPS6KB1 negatively correlated with effector memory CD8 T cells, γδ T cells, NK cells, and neutrophils. PARP2 bound ignavine (Aconiti Lateralis Radix Praeparata) with -11.6 kcal/mol; RT-qPCR confirmed significant downregulation of 4 biomarkers, with PRKACA showing no difference.
Discussion:
CKD is a global burden with unclear mechanisms, in which dysregulated PCD worsens renal injury; ZWD has clinical efficacy in CKD, but its PCD-related targets were unknown. This study identified five downregulated biomarkers (SQLE, PRKACA, PARP2, RPS6KB1, ALOX12) via integrative bioinformatics and machine learning, which participate in lipid metabolism, inflammation, oxidative stress, and ferroptosis. PARP2 binds ZWD-derived ignavine (-11.6 kcal/mol), biomarkers correlate with immune cells, and ZWD exerts renoprotection by regulating PCD, immune homeostasis, and DNA repair, providing novel therapeutic insights.
Conclusion:
SQLE, PRKACA, PARP2, RPS6KB1, and ALOX12 were recognized as PCDrelated biomarkers for ZWD treatment of CKD, providing important references for the mechanism and clinical application of ZWD treatment of CKD.