Transcriptomic analysis and laboratory experiments reveal potential critical genes and regulatory mechanisms in sepsis-associated acute kidney injury

Abstract

Background Sepsis-associated acute kidney injury (SA-AKI) is one of the most frequent and serious complications of sepsis. However, the transcriptional regulatory network of the pathophysiological mechanism of the kidney has not been revealed. This study identified new mechanisms in SA-AKI using bioinformatics analyses and laboratory-based experiments. Methods We performed transcriptomic profiling of mouse kidneys after cecal ligation and puncture (CLP) to mimic clinical sepsis. RNA from kidney samples from the CLP and control groups was isolated and analyzed using bulk messenger RNA (mRNA)-seq. Differentially expressed genes (DEGs) between the two groups were identified, and GO, KEGG and GSEA pathway enrichment analyses were performed. The protein-protein interaction (PPI) network of DEGs and hub genes was analyzed. The hub genes were verified using quantitative real-time polymerase chain reaction (qPCR) or Western blotting. The interaction network, targeted microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) of hub genes were predicted, and the critical miRNA-hub gene regulatory axis was verified using qPCR, Western blotting, malondialdehyde (MDA) determination and flow cytometry. Correlation analyses of N6-adenosine methylation (m6A) RNA methylation regulators and hub genes and m6A modification analysis were performed. Results A total of 4,754 DEGs were identified between the two groups using high-throughput sequencing. The pathways in which DEGs were enriched included ferroptosis (the highest enrichment score), apoptosis, and the PI3K-Akt, NF-kappa B and IL-17 signaling pathways. Seven ( Hmox1, Spp1, Socs3, Mapk14, Lcn2, Cxcl1 and Cxcl12 ) of the 15 hub genes were involved in the KEGG pathway. mmu-miR-7212-5p-Hmox1 was a key RNA regulatory axis in ferroptosis. m6A RNA methylation modifications were involved in SA-AKI. The correlation analyses showed the close interactions among the m6A RNA methylation regulators and important hub genes. Conclusions The findings of this study provide new insights into the mechanism regulating the occurrence and progression of SA-AKI. The mmu-miR-7212-5p-Hmox1 axis in ferroptosis and m6A RNA methylation regulators may have potential clinical significance for the future treatment of SA-AKI. The datasets generated for this study can be found in the repository of the GEO database (Series number: GSE186822).

Single‐Cell Transcriptomic Analysis Reveals the Alleviating Effect of Anemoside B4 on Murine Diabetic Nephropathy

“…It is well known that the proximal tubule has the significant capacity for repair after damage, such as hyperglycemia, inflammation and oxidative stress. [ 27 ] In contrast to the PT, the proportions of other nephron segments exhibited varying changes followed by B4 treatment.…”

“…Next, we performed DEG analysis on PT epithelial cells by comparing the DKD group with both WT and B4 treatment (Figure 3F), and found that upregulated early growth response 1 (Egr1), the injury marker Spp1 promotes the attracting immune cells, including leukocytes, macrophages, and T cells, [ 27 ] and the expression levels of spliceosome regulator serine/arginine‐rich splicing factor (SR) were inhibited in the DKD group, including Srsf2 , Srsf3 , Srsf5 , Srsf6 , Srsf7 and Srsf11 . Among of them, the SR gene upregulated in PT cells by B4 treatment, Srsf5 , that is associated with glucose metabolism.…”

The role of N6-methyladenosine (m6A) in kidney diseases

“…In one study, mmu-miR-7,212-5p-Hmox1 in iron death has been demonstrated as a significant RNA regulatory pathway implicated in the pathophysiological process of SA-AKI in a mouse model of septic AKI. The promotion of AKI development by m 6 A RNA methylation alteration in SA-AKI has been shown (84). A growing number of studies in recent years have revealed that ncRNAs, particularly microRNAs (miRNAs), are connected to AKI (85).…”

Effects of DNA, RNA, and Protein Methylation on the Regulation of Ferroptosis

“…Furthermore, the role of the RNA m 6 A modification in many biological processes and diseases has been elucidated in the past decade; these processes include autophagy, cell proliferation, stem-cell renewal and differentiation, and the diseases include tumorigenesis, and cardiovascular diseases [139,146,148,149]. In the past three years, several studies have shown that RNA m 6 A marks are involved in the regulation of ferroptosis and thus affects the progression of diseases such as tumor growth and acute kidney injury [133,150,151] and that m 6 A modification regulators used in combination with ferroptosis-related genes can be diagnostic or prognostic markers for tumors in humans [130,[152][153][154][155]. Multiple m 6 A modification regulators have been shown to be aberrantly expressed in various types of tumors, and a prediction model comprising these regulators and ferroptosis-associated genes has been shown to effectively reflect the progression and prognosis of these tumor patients [23,[156][157][158][159].…”