Circulating RNA Profiling in Postreperfusion Plasma From Kidney Transplant Recipients

Exploration of the shared gene signatures and biological mechanisms between ischemia-reperfusion injury and antibody-mediated rejection in renal transplantation

BACKGROUND

Antibody-mediated rejection (ABMR) plays a crucial role in graft loss during allogeneic renal transplantation. In renal transplantation, ischemia-reperfusion injury (IRI) is unavoidable, serves as a major contributor to acute rejection, and is linked to graft loss. However, the mechanisms underlying IRI and ABMR are unclear. Therefore, this study aimed to investigate the shared genetic characteristics and biological mechanisms between IRI and ABMR.

METHODS

Gene expressions for IRI (GSE43974) and ABMR (GSE129166 and GSE36059) were retrieved from the Gene Expression Omnibus database. The shared differentially expressed genes (DEGs) of IRI and ABMR were identified, and subsequent functional enrichment analysis was performed. Immune cell infiltration in ABMR and its relationship with the shared DEGs were investigated using the CIBERSORT method. Random forest analysis, a protein-protein interaction network, and Cytoscape were used to screen hub genes, which were subsequently subjected to gene set enrichment analysis, miRNA prediction, and transcription factors analysis. The survival analysis was performed through Kaplan-Meier curves. Finally, drug compound prediction was performed on the shared DEGs using the Drug Signature Database.

RESULTS

Overall, 27 shared DEGs were identified between the renal IRI and ABMR groups. Among these, 24 genes exhibited increased co-expression, whereas none showed decreased co-expression. The shared DEGs were primarily enriched in the inflammation signaling pathways. Notably, CD4 memory T cells were identified as potential critical mediators of IRI, leading to ABMR. Tumor necrosis factor alpha-induced protein 3 (TNFAIP3), interferon regulatory factor 1 (IRF1), and early growth response 2 (EGR2) were identified as key components in the potential mechanism that link IRI and ABMR. Patients undergoing renal transplantation with higher expression levels of TNFAIP3, IRF1, and EGR2 exhibited decreased survival rates compared to those with lower expression levels.

CONCLUSION

Inflammation is a key mechanism that links IRI and ABMR, with a potential role played by CD4 memory T cells. Furthermore, TNFAIP3, IRF1, and EGR2 are implicated in the underlying mechanism between IRI and ABMR.

Understanding Propofol's Protective Mechanism in Tubular Epithelial Cells: Mitigating Pyroptosis via the miR-143-3p/ATPase Na + /K + Transporting Subunit Alpha 2 Pathway in Renal Ischemia-Reperfusion

Propofol (Pro), a prevalent intravenous anesthetic, has recently been recognized for its potential in mitigating ischemia-reperfusion (I/R) injuries. Despite a plethora of evidence suggesting the beneficial effects of low-dose Pro in renal I/R injury (RI/R), its role in modulating pyroptosis in renal tubular epithelial cells consequent to RI/R has not been thoroughly elucidated. In our investigation, we explored the therapeutic potential of Pro against pyroptosis in renal tubular epithelial cells under the duress of RI/R, employing both in vivo and in vitro models, while deciphering the intricate molecular pathways involved. Our results demonstrate an elevation in the expression of miR-143-3p, contrasted by a diminution in ATPase Na + /K + Transporting Subunit Alpha 2 (ATP1A2) under RI/R conditions. Pro effectively mitigates apoptosis in renal tubular epithelial cells induced by RI/R, principally characterized by the inhibition of pro-inflammatory cytokines interleukin (IL-)-1β and IL-18, enhancement of cellular viability, reduction in the ratio of pyroptotic cells, and suppression of nucleotide-binding domain and leucine-rich repeat-related family, pyrin domain containing 3 inflammasome activation along with the expression of cleaved caspase-1, and gasdermin D. Both knockdown and overexpression studies of miR-143-3p revealed its pivotal role in modulating RI/R-induced tubular cell pyroptosis. Notably, Pro's capacity to inhibit pyroptosis in renal tubular epithelial cells was found to be reversible following ATP1A2 knockdown. Furthermore, our study unveils miR-143-3p as a targeted regulator of ATP1A2 expression. From a mechanistic standpoint, Pro's therapeutic efficacy is attributed to its regulatory influence on miR-143-3p and ATP1A2 expression levels. In conclusion, our findings pioneer the understanding that Pro can significantly ameliorate pyroptosis in renal tubular epithelial cells in the context of RI/R, predominantly through the modulation of the miR-143-3p/ATP1A2 axis. This novel insight furnishes robust empirical support for the development of targeted therapeutics and clinical strategies in addressing RI/R.

Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs

BACKGROUND

Extrachromosomal circular deoxyribonucleic acid (eccDNA) is evolving as a valuable biomarker, while little is known about its presence in urine.

METHODS

Here, we report the discovery and analysis of urinary cell-free eccDNAs (ucf-eccDNAs) in healthy controls and patients with advanced chronic kidney disease (CKD) by Circle-Seq.

RESULTS

Millions of unique ucf-eccDNAs were identified and comprehensively characterised. The ucf-eccDNAs are GC-rich. Most ucf-eccDNAs are less than 1000 bp and are enriched in four pronounced peaks at 207, 358, 553 and 732 bp. Analysis of the genomic distribution of ucf-eccDNAs shows that eccDNAs are found on all chromosomes but enriched on chromosomes 17, 19 and 20 with a high density of protein-coding genes, CpG islands, short interspersed transposable elements (SINEs) and simple repeat elements. Analysis of eccDNA junction sequences further suggests that microhomology and palindromic repeats might be involved in eccDNA formation. The ucf-eccDNAs in CKD patients are significantly higher than those in healthy controls. Moreover, eccDNA with miRNA genes is highly enriched in CKD ucf-eccDNA.

CONCLUSIONS

This work discovers and provides the first deep characterisation of ucf-eccDNAs and suggests ucf-eccDNA as a valuable noninnvasive biomarker for urogenital disorder diagnosis and monitoring.

Epigenetic Regulation in Kidney Transplantation

Kidney transplantation is a standard care for end stage renal disease, but it is also associated with a complex pathogenesis including ischemia-reperfusion injury, inflammation, and development of fibrosis. Over the past decade, accumulating evidence has suggested a role of epigenetic regulation in kidney transplantation, involving DNA methylation, histone modification, and various kinds of non-coding RNAs. Here, we analyze these recent studies supporting the role of epigenetic regulation in different pathological processes of kidney transplantation, i.e., ischemia-reperfusion injury, acute rejection, and chronic graft pathologies including renal interstitial fibrosis. Further investigation of epigenetic alterations, their pathological roles and underlying mechanisms in kidney transplantation may lead to new strategies for the discovery of novel diagnostic biomarkers and therapeutic interventions.