BackgroundCurrent management of AKI, a potentially fatal disorder that can also initiate or exacerbate CKD, is merely supportive. Therefore, deeper understanding of the molecular pathways perturbed in AKI is needed to identify targets with potential to lead to improved treatment.MethodsWe performed single-cell RNA sequencing (scRNA-seq) with the clinically relevant unilateral ischemia-reperfusion murine model of AKI at days 1, 2, 4, 7, 11, and 14 after AKI onset. Using real-time quantitative PCR, immunofluorescence, Western blotting, and both chromogenic and single-molecule in situ hybridizations, we validated AKI signatures in multiple experiments.ResultsOur findings show the time course of changing gene expression patterns for multiple AKI stages and all renal cell types. We observed elevated expression of crucial injury response factors—including kidney injury molecule-1 (Kim1), lipocalin 2 (Lcn2), and keratin 8 (Krt8)—and of several novel genes (Ahnak, Sh3bgrl3, and Col18a1) not previously examined in kidney pathologies. AKI induced proximal tubule dedifferentiation, with a pronounced nephrogenic signature represented by Sox4 and Cd24a. Moreover, AKI caused the formation of “mixed-identity cells” (expressing markers of different renal cell types) that are normally seen only during early kidney development. The injured tubules acquired a proinflammatory and profibrotic phenotype; moreover, AKI dramatically modified ligand-receptor crosstalk, with potential pathologic epithelial-to-stromal interactions. Advancing age in AKI onset was associated with maladaptive response and kidney fibrosis.ConclusionsThe scRNA-seq, comprehensive, cell-specific profiles provide a valuable resource for examining molecular pathways that are perturbed in AKI. The results fully define AKI-associated dedifferentiation programs, potential pathologic ligand-receptor crosstalk, novel genes, and the improved injury response in younger mice, and highlight potential targets of kidney injury.

BACKGROUND: Acute kidney injury (AKI) is a short-term life-threatening condition that, if survived, can lead to renal insufficiency and development of chronic kidney disease. The pathogenesis of AKI and chronic kidney disease involves direct effects on the heart and the development of hypertrophy and cardiomyopathy. METHODS: We used mouse models of ischemia/reperfusion AKI and unilateral ureteral obstruction to investigate the role of IL-33 (interleukin-33) and its receptor-encoding gene Il1rl1 (also called ST2L [suppression of tumorigenicity 2]) in cardiac remodeling after AKI. Mice with cell type–specific genetic disruption of the IL-33/ST2L axis were used, and IL-33 monoclonal antibody, adeno-associated virus encoding IL-33 or ST2L, and recombinant IL-33, as well. RESULTS: Mice deficient in Il33 were refractory to cardiomyopathy associated with 2 models of kidney injury. Treatment of mice with monoclonal IL-33 antibody also protected the heart after AKI. Moreover, overexpression of IL-33 or injection of recombinant IL-33 induced cardiac hypertrophy or cardiomyopathy, or both, but not in mice lacking Il1rl1 . AKI-induced cardiomyopathy was also reduced in mice with cardiac myocyte–specific deletion of Il1rl1 but not in endothelial cell- or fibroblast-specific deletion of Il1rl1 . Last, overexpression of the ST2L receptor in cardiac myocytes recapitulated induction of cardiac hypertrophy. CONCLUSIONS: These results indicate that IL-33 released from the kidney during AKI underlies cardiorenal syndrome by directly signaling to cardiac myocytes, suggesting that antagonism of IL-33/ST2 axis would be cardioprotective in patients with kidney disease.

Examining kidney fibrosis is crucial for mechanistic understanding and developing targeted strategies against chronic kidney disease (CKD). Persistent fibroblast activation and tubular epithelial cell (TEC) injury are key CKD contributors. However, cellular and transcriptional landscapes of CKD and specific activated kidney fibroblast clusters remain elusive. Here, we analyzed single cell transcriptomic profiles of two clinically relevant kidney fibrosis models which induced robust kidney parenchymal remodeling. We dissected the molecular and cellular landscapes of kidney stroma and newly identified three distinctive fibroblast clusters with “secretory”, “contractile” and “vascular” transcriptional enrichments. Also, both injuries generated failed repair TECs (frTECs) characterized by decline of mature epithelial markers and elevation of stromal and injury markers. Notably, frTECs shared transcriptional identity with distal nephron segments of the embryonic kidney. Moreover, we identified that both models exhibited robust and previously unrecognized distal spatial pattern of TEC injury, outlined by persistent elevation of renal TEC injury markers including Krt8, while the surviving proximal tubules (PTs) showed restored transcriptional signature. Furthermore, we found that long-term kidney injuries activated a prominent nephrogenic signature, including Sox4 and Hox gene elevation, which prevailed in the distal tubular segments. Our findings might advance understanding of and targeted intervention in fibrotic kidney disease.

Background: Persistent kidney fibroblast activation and tubular epithelial cell (TEC) injury are key contributors to CKD. However, transcriptional and cellular identities of advanced kidney disease, along with renal fibroblast specific markers and molecular targets contributing to persistent tubular injury, remain elusive. Methods: We performed single-cell RNA sequencing with two clinically relevant murine kidney fibrosis models. Day 28 post-injury was chosen to ensure advanced fibrotic disease. Identified gene expression signatures were validated using multiple quantitative molecular analyses. Results: We revealed comprehensive single cell transcriptomic profiles of two independent kidney fibrosis models compared to normal control. Both models exhibited key CKD characteristics including renal blood flow decline, inflammatory expansion and proximal tubular loss. We identified novel populations including secretory, migratory and contractile activated fibroblasts, specifically labelled by newly identified fibroblast-specific Gucy1a3 expression. Fibrotic kidneys elicited elevated embryonic and pro-fibrotic signaling, including separate Embryonic and Pro-fibrotic TEC clusters. Also, fibrosis caused enhanced cell-to-cell crosstalk, particularly between activated fibroblasts and pro-fibrotic TECs. Analysis of factors mediating mesenchymal phenotype in the injured epithelium identified persistent elevation of Ahnak, previously reported in AKI, in both CKD models. AHNAK knockdown in primary human renal proximal tubular epithelial cells induced a pro-fibrotic phenotype and exacerbated TGFb response via p38, p42/44, pAKT, BMP and MMP signaling. Conclusions: Our study comprehensively examined kidney fibrosis in two independent models at the singe-cell resolution, providing a valuable resource for the field. Moreover, we newly identified Gucy1a3 as a kidney activated fibroblast specific marker and validated AHNAK as a putative disease target.