Chromatin Remodeling In Kidney Repair And Regeneration After Acute Kidney Injury

Acute kidney injury(AKI)is a severe clinical syndrome characterized by a sudden decrease in glomerular filtration rate(e GFR).It accounts for approximately 2million deaths per year worldwide.Even surviving from AKI,patients with AKI still have a high risk of developing chronic kidney disease(CKD),which ultimately leads to end-stage renal disease(ESRD).Currently,other than electronic AKI alerts or supportive care,no effective therapies are available for AKI patients to prevent tubular cell injury,promote regeneration and reverse the process of fibrosis.After kidney injury,renal tubule cells undergo dedifferentiation,proliferation,and re-differentiation,leading to tubular cell regeneration or transition to cellular senescence,referring to adaptive repair or maladaptive repair,respectively.However,the mechanisms underlying the cell-fate transition of tubular cells during the process of adaptive repair or maladaptive repair are unclear.Accumulating evidence indicates that alterations in chromatin state are associated with the cell-fate transition.Chromatin accessibility refers to the level of physical compaction of chromatin,accounting for transcription activity.In this work,we explored the role of chromatin remodeling in cell-fate transition during kidney regeneration and repair.We developed 20 min mild bilateral renal ischemia-reperfusion(b I/R)mouse model to mimic adaptive repair and 30 min severe b I/R mouse model to mimic maladaptive repair.Magnetic bead perfusion was performed to remove glomeruli before collecting renal tubules on day 2,day 7,and day 30 after kidney injury.Low cell number assays for Transposase-Accessible Chromatin by sequencing(ATAC-seq)of renal tubular cells was performed to define the dynamic change of chromatin accessibility in the process of renal regeneration and repair.Integrative analysis of ATAC-seq data and RNA-seq data revealed that the dynamic regulation of chromatin state correlated with the gene expression dynamics in the kidney repair process.We further explored the similarities and differences of chromatin state between the two AKI mouse models.Markedly differential chromatin accessibility was observed in two mouse models at different stages of the kidney repair process.We found chromatin accessibility altered genome-wide but without concomitant changes in gene expression during early injury response.In contrast,we observed that the alterations in chromatin accessibility correlated well with the changes in gene expression in the post-acute phase of AKI.Gene enrichment analysis revealed that genes whose expression sensitive to alteration of chromatin accessibility induced by adaptive repair were highly enriched in pathways associated with metabolism and cell differentiation,which may help the tubular epithelial cells to restore their normal structure and function.Conversely,the chromatin accessibility-regulated genes induced by maladaptive repair were enriched in the inflammatory pathway,which may contribute to tubular cell injury.We next mapped the TF-to-TF gene regulatory networks(GRNs)by integrating motif analysis and transcriptomic data.During the post-phase of renal repair,Rxra,Ppara,and Esrra were strongly enriched in the mild GRN whereas bZIP and ETS family members were strongly enriched in the severe GRN.After mapping GRNs,we found Rxrα plays an important role after mild injury.Thus,we analyzed the open chromatin regions regulated by Rxrα.It showed that Rxrα bound to the regions related to molecular transport and energy metabolism.Bexarotene,a Food and Drug Administration(FDA)-approved drug,is a potent and selective RXR agonist.Preoperative use of Bexarotene significantly decreased AKI mortality and ameliorated renal dysfunction.Therefore,we analyzed the correlation between renal function and RXRα expression in AKI patients and found that RXRα is inversely correlated with disease severity.Thus,RXRα,a master transcription factor,plays an important role in tubular epithelial cell state transition and regeneration after injury.In summary,by using recently developed Low-Cell ATAC-seq and RNA-seq,we systematically profiled the dynamic chromatin accessibility and transcriptome,as well as mapped the dynamic GRNs in the renal tubular epithelial cell during renal regeneration and repair.This study reveals an epigenetic mechanism underlying the cell-fate transition during kidney repair and regeneration after AKI and provides important insights for the development of rational strategies for AKI treatment.