Our understanding of kidney disease pathogenesis is limited by an incomplete molecular characterization of the cell types responsible for the organ’s multiple homeostatic functions. To help fill this knowledge gap, we characterized 57,979 cells from healthy mouse kidneys using unbiased single-cell RNA sequencing. Based on gene expression patterns, we infer that inherited kidney diseases that arise from distinct genetic mutations but have similar phenotypic manifestations share the same cell of origin. We also found that the kidney collecting duct in adult mice generates a spectrum of cell types via a newly identified transitional cell. Computational cell trajectory analysis and in vivo lineage tracing revealed that intercalated cells and principal cells undergo transitions mediated by the Notch signaling pathway. In mouse and human kidney disease, these transitions were shifted toward a principal cell fate and were associated with metabolic acidosis.

Fibrosis of the kidney is the final common pathway leading to end stage renal failure. By analyzing kidneys of patients and animal models with fibrosis we observed a significant mitochondrial defect, including the loss of the mitochondrial transcription factor A (TFAM) in kidney tubule cells. Here, we generated mice with tubule-specific deletion of TFAM (Ksp-Cre/ Tfam flox/flox ). While these mice developed severe mitochondrial loss and energetic deficit (ATP *

Kidney fibrosis is the histological manifestation of functional decline in the kidney. Fibrosis is a reactive process that develops in response to excessive epithelial injury and inflammation. Here, we describe how three key developmental signalling pathways—Notch, Wnt and Hedgehog—are reactivated in response to kidney injury. Although transient activation of these pathways is needed for repair of injured tissue, their sustained activation promotes fibrosis. Excessive Wnt and Notch expression prohibit epithelial differentiation whereas increased Wnt and Hh expression induce fibroblast proliferation and myofibroblastic transdifferentiation. Notch, Wnt and Hedgehog are fundamentally different signalling mechanisms, but their choreographed activation seems to be just as important for fibrosis as it is for embryonic kidney development. Decreasing the activity of Notch, Wnt, or Hh signalling could potentially be a new therapeutic strategy to ameliorate the development of chronic kidney disease.

The kidney has a tremendous capacity to regenerate following injury, but factors that govern this response are still largely unknown. We isolated cells from mouse kidneys with high proliferative and multi-lineage differentiation capacity. These cells expressed high level of Sox9. In regenerating kidneys, Sox9 expression was induced early and 89% of proliferating cells were Sox9 positive. In vitro, Sox9 positive cells showed unlimited proliferation and multi-lineage differentiation capacity. Using an inducible Sox9 cre line and lineage tagging methods, we show that Sox9 positive cells can supply new daughter cells, contributing to the regeneration of proximal tubule, loop of Henle and distal tubule segments, but not to collecting duct and glomerular cells. Furthermore, inducible deletion of Sox9 resulted in reduced epithelial proliferation, more severe injury and fibrosis development. In summary, we demonstrate that in the kidney, Sox9 positive cells show progenitor-like properties in vitro, and contribute to epithelial regeneration following injury in vivo.

Chronic kidney disease (CKD), a condition when the kidneys are unable to clear waste products, affects 700 million people globally. Genome-wide association (GWA) studies identified sequence variants for CKD; however, the biological basis of GWAS remains poorly understood. To address this issue, we created an expression quantitative trait loci (eQTL) atlas for the glomerular and tubular compartments of the human kidney. Integrating the CKD GWAS with eQTL, single-cell RNA sequencing and regulatory region maps, we identified novel genes for CKD. Putative causal genes were enriched for proximal tubule expression and endo-lysosomal function, where DAB2, an adaptor protein in the TGFβ pathway, formed a central node. Functional experiments confirmed that reducing Dab2 expression in renal tubules protected mice from CKD. In conclusion, compartment-specific eQTL analysis is an important avenue for the identification of novel genes and cellular pathways involved in CKD development and thus potential new opportunities for its treatment.

Supplementary InformaƟon (ESI) available: FT-IR spectrum, Raman spectrum, XRD patterns, XPS survey spectra, TEM and SEM images, the first three CV curves, Cycle performance, and rate capabilities of NG and RGO See Nitrogen and fluorine co-doped graphene (NFG) with the N and F content as high as 3.24 and 10.9 at.% was prepared through the hydrothermal reaction of trimethylamine tri(hydrofluoride) [(C2H5)3N·3HF] and aqueous-dispersed graphene oxide (GO) as the anode material for lithium ion batteries (LIBs). The N and F co-doping in graphene increased the disorder and defects of the framework, enlarged the space of the interlayer, wrinkled the nanosheets with many open-edge sites, and thus faciliated Li ion diffusion through the electrode compared with sole-N or F doped graphene. X-ray photoelectron spectroscopy (XPS) analysis of NFG demonstrated the presence of active pyridine and pyrrolic types N, and highly electrical conductive graphitic N and semi-ionic C-F bond in the structure. The N and F doping content and the component types of N and F functional groups could be controlled by the hydrothermal temperature. The NFG prepared at 150°C exhibited the best electrochemical performances tested as the anode of LIBs, including the high coulombic efficiency in the first cycle (56.7%), superior reversible specific discahrge capacity (1075 mAh g −1 at 100 mA g −1 ), excellent rate capabilities (305 mAh g −1 at 5 A g −1 ), and outstanding cycling stability (capacity retention of ~95% at 5 A g −1 after 2000 cycles), which demonstrated NFG was a promising candidate for anode materials of high-rate LIBs. 18,20,25 Recently, it has been realized that doping graphene with two or more kinds of heteroatoms can further improve its electrochemical performances because Li-ion storage is not only related with the contents of heteroatoms but also with

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Chronic kidney disease (CKD) is a complex gene-environmental disease affecting close to 10% of the US population. Genome-wide association studies (GWASs) have identified sequence variants, localized to non-coding genomic regions, associated with kidney function. Despite these robust observations, the mechanism by which variants lead to CKD remains a critical unanswered question. Expression quantitative trait loci (eQTL) analysis is a method to identify genetic variation associated with gene expression changes in specific tissue types. We hypothesized that an integrative analysis combining CKD GWAS and kidney eQTL results can identify candidate genes for CKD. We performed eQTL analysis by correlating genotype with RNA-seq-based gene expression levels in 96 human kidney samples. Applying stringent statistical criteria, we detected 1,886 genes whose expression differs with the sequence variants. Using direct overlap and Bayesian methods, we identified new potential target genes for CKD. With respect to one of the target genes, lysosomal beta A mannosidase (MANBA), we observed that genetic variants associated with MANBA expression in the kidney showed statistically significant colocalization with variants identified in CKD GWASs, indicating that MANBA is a potential target gene for CKD. The expression of MANBA was significantly lower in kidneys of subjects with risk alleles. Suppressing manba expression in zebrafish resulted in renal tubule defects and pericardial edema, phenotypes typically induced by kidney dysfunction. Our analysis shows that gene-expression changes driven by genetic variation in the kidney can highlight potential new target genes for CKD development.