Transcriptomic analysis of the mechanisms of alleviating renal interstitial fibrosis using the traditional Chinese medicine Kangxianling in a rat model

Abstract

Renal interstitial fibrosis (RIF) is currently recognized as a crucial mechanism of the pathogenesis of chronic kidney disease (CKD). Kangxianling (KXL, anti-fibrin) is a traditional Chinese medicine that has been proven to significantly reduce the levels of ECM deposition and inhibit renal fibrosis. To characterize the mechanisms and drug targets of KXL, we established a RIF rat model and treated the rats with KXL and losartan. Histological analyses validated the establishment of the RIF model and the treatment effect of KXL. Multiple levels of transcriptomic datasets were generated using lncRNA, mRNA and microRNA sequencing of kidney tissues. Functional annotations and pathway analyses were performed to unravel the therapeutic mechanisms. A multi-level transcriptomic regulatory network was built to illustrate the core factors in fibrosis pathogenesis and therapeutic regulation. KXL and losartan significantly reduced the progression of RIF, and a better therapeutic effect was shown with higher concentrations of KXL. According to the cluster analysis results of the RNA-seq data, the normal control (NC) and high concentration of KXL (HK) treatment groups were the closest in terms of differentially expressed genes. The WNT, TGF-β and MAPK pathways were enriched and dominated the pathogenesis and therapy of RIF. miR-15b, miR-21, and miR-6216 were upregulated and miR-107 was downregulated in the fibrosis model. These small RNAs were shown to play critical roles in the regulation of the above fibrosis-related genes and could be inhibited by KXL treatment. Finally, based on the lncRNA datasets, we constructed a mRNA-lncRNA-miRNA coexpression ceRNA network, which identified key regulatory factors in the pathogenesis of kidney fibrosis and therapeutic mechanisms of KXL. Our work revealed the potential mechanism of the Chinese medicine Kangxianling in inhibiting renal interstitial fibrosis and supported the clinical use of KXL in the treatment of kidney fibrosis. Chronic kidney disease (CKD) is a chronic disease characterized by the gradual and irreversible loss of renal function over months or years. The incidence of CKD has increased globally with the prolongation of human life expectancy and increased incidence of diabetes and hypertension. A 2012 study found that the incidence of CKD in the Chinese population was 10.8% 1,2 , and according to the WHO (World Health Organization), the number of people that died from CKD in 2012 was 864,226 (mortality rate of 1.5%), which has become a heavy burden on public health resources 3,4 .

Mechanism of protective effect of xuan-bai-cheng-qi decoction on LPS-induced acute lung injury based on an integrated network pharmacology and RNA-sequencing approach

“…TCM and other herbal medicines are characterized by multiple chemical components, multiple targets and multiple effects. Network pharmacology constructs the complex relationships between each components, targets, diseases, and molecular pathways [ 15 , 16 ]. High-throughput RNA sequencing technology (RNA-seq) is a robust transcriptional screening technology, which could identify differentially expressed genes (DEGs) through comparisons of different conditions, such as normal and disease states [ 17 , 18 ].…”

Elevation of LncRNA ENST00000453774.1 Prevents Renal Fibrosis by Upregulating FBN1, IGF1R, and KLF7

“…More recently, a study has noted that repressed expression of lncRNA XIST could upregulate the expression of microRNA (miR)-93-5p, thereby decreasing CDKN1A and suppressing renal interstitial fibrosis in diabetic nephropathy [12]. Moreover, the competing endogenous RNA (ceRNA) mechanism has been reported to play an important role in the renal fibrosis field [13]. Thus, miRs, which target key genes and targeted by lncRNA453774.1 at the same time, may take concern in this study.…”

Treatment with Tang-luo-ning altered the microRNA expression profile in rats with diabetic peripheral neuropathy

“…MicroRNAs (miRNAs) are a type of non-coding RNA of 21–25 nucleotides in length, which are involved in the post-transcriptional regulation of gene expression. miRNAs have been reported to mediate the therapeutic effects of natural herbs [ 10 , 11 ]. In the previous study, we performed a microarray bioinformatics analysis of genes that were differentially regulated by TLN, and cell survival genes ( NRG1, MTOR, GAB1 , and PI3KCB ) identified from the microarray analysis were validated by qPCR.…”