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The relationship between cellular senescence and fibrosis in the kidney is being elucidated and we have identified it as therapeutic target in recent studies. Chronic kidney disease has also become a lifestyle disease, often developing on the background of hypertension and dyslipidemia. In this study, we clarify the effect of interaction between these two conditions on kidney fibrosis and senescence. Wild type mice (WT), apolipoprotein E-/- mice (ApoEKO), and endothelial nitric oxide synthase (eNOS)-/- ApoE-/- mice (DKO) were obtained by breeding. Unilateral ureteral obstruction (UUO) was performed on 8-10 week old male mice and the degree of renal tubular injury, fibrosis and kidney senescence were evaluated. DKO manifested elevated blood pressure, higher total cholesterol and lower HDL than WT. DKO showed sustained kidney injury molecule-1 protein expression. Kidney fibrosis was significantly higher in ApoEKO and DKO. mRNA expression of genes related to kidney fibrosis was the highest in DKO. The mRNA expression of Zinc-α2-Glycoprotein and heme oxygenase-1 were significantly decreased in DKO. Furthermore, mRNA expression of p53, p21 and p16 were increased both in ApoEKO and DKO, with DKO being the highest. Senescence associated β-gal positive tubule area was significantly increased in DKO. Increased DNA damage and target of rapamycin-autophagy spatial coupling compartments (TASCCs) formation was found in DKO. Mice with endothelial dysfunction and dyslipidemia developed kidney fibrosis and accelerated senescence even in young mice after injury. These data highlight the fact managing lifestyle-related diseases from a young age is important for CKD prevention.

Abnormal mitochondrial function is a well-recognized feature of acute and chronic kidney diseases. To gain insight into the role of mitochondria in kidney homeostasis and pathogenesis, we targeted mitochondrial transcription factor A (TFAM), a protein required for mitochondrial DNA replication and transcription that plays a critical part in the maintenance of mitochondrial mass and function. To examine the consequences of disrupted mitochondrial function in kidney epithelial cells, we inactivated TFAM in sine oculis-related homeobox 2-expressing kidney progenitor cells. TFAM deficiency resulted in significantly decreased mitochondrial gene expression, mitochondrial depletion, inhibition of nephron maturation and the development of severe postnatal cystic disease, which resulted in premature death. This was associated with abnormal mitochondrial morphology, a reduction in oxygen consumption and increased glycolytic flux. Furthermore, we found that TFAM expression was reduced in murine and human polycystic kidneys, which was accompanied by mitochondrial depletion. Thus, our data suggest that dysregulation of TFAM expression and mitochondrial depletion are molecular features of kidney cystic disease that may contribute to its pathogenesis.

BACKGROUND: The root of many kidney diseases in humans can be traced to alterations or damage to subcellular organelles. Mitochondrial fragmentation, endoplasmic reticulum (ER) stress, and lysosomal inhibition, among others, ultimately contribute to kidney injury and are the target of therapeutics in development. Although recent technological advancements allow for the understanding of disease states at the cellular level, investigating changes in subcellular organelles from kidney tissue remains challenging. METHODS: Using structured illumination microscopy, we imaged mitochondria and other organelles from paraffin sections of mouse tissue and human kidney biopsy specimens. The resulting images were 3D rendered to quantify mitochondrial size, content, and morphology. Results were compared with those from transmission electron microscopy and segmentation. RESULTS: Super-resolution imaging reveals kidney tubular epithelial cell mitochondria in rodent and human kidney tissue form large, interconnected networks under basal conditions, which are fragmented with injury. This approach can be expanded to other organelles and cellular structures including autophagosomes, ER, brush border, and cell morphology. We find that, during unilateral ischemia, mitochondrial fragmentation occurs in most tubule cells, and they remain fragmented for >96 hours. Promoting mitochondrial fusion with the fusion promotor M1 preserves mitochondrial morphology and interconnectivity and protects against cisplatin-induced kidney injury. CONCLUSIONS: We provide, for the first time, a nonbiased, semiautomated approach for quantification of the 3D morphology of mitochondria in kidney tissue. Maintaining mitochondrial interconnectivity and morphology protects against kidney injury. Super-resolution imaging has the potential to both drive discovery of novel pathobiologic mechanisms in kidney tissue and broaden the diagnoses that can be made on human biopsy specimens.

Chronic kidney disease (CKD) is a global health problem. CKD patients are at high risk of developing cardiovascular disease (CVD), including coronary artery disease, heart failure and stroke. Several factors invoke a vicious cycle of CKD and CVD, which is referred as to "cardiorenal syndrome". Among these factors, the compounds retained through loss of renal excretion play a pathological role in causing atherosclerosis and CVD. These compounds have been broadly classified as uremic toxins because of their accumulation with declining renal function and cytotoxicity. The major uremic toxins contributing to CVD are asymmetric dimethylarginine (ADMA), advanced glycation endproducts (AGE), and trimethyl amine N-oxide (TMAO). ADMA is linked to CVD through regulation of nitric oxide, reactive oxygen species, and renal anemia. AGE not only directly accumulates in the heart and kidney, but interacts with the receptor for AGE (RAGE), leading to cell damage in CVD. TMAO correlates with a high prevalence of CVD and promotes organ fibrosis by itself. The levels of these and other uremic toxins rise with worsening CKD, inducing multiplicative damage in the heart and kidney. Therefore, a better understanding of uremic toxins has great clinical importance for preventing cardiorenal syndrome. This review highlights the molecular mechanism by which these uremic toxins are implicated in CVD and suggests the possible mutual relationship between them.

Because injured mitochondria can accelerate cell death through the elaboration of oxidative free radicals and other mediators, it is striking that proliferator γ coactivator 1-α (PGC1α), a stimulator of increased mitochondrial abundance, protects stressed renal cells instead of potentiating injury. Here, we report that PGC1α’s induction of lysosomes via transcription factor EB (TFEB) may be pivotal for kidney protection. CRISPR and stable gene transfer showed that PGC1α-KO tubular cells were sensitized to the genotoxic stressor cisplatin, whereas Tg cells were protected. The biosensor mitochondrial-targeted Keima (mtKeima) unexpectedly revealed that cisplatin blunts mitophagy both in cells and mice. PGC1α and its downstream mediator NAD+ counteracted this effect. PGC1α did not consistently affect known autophagy pathways modulated by cisplatin. Instead RNA sequencing identified coordinated regulation of lysosomal biogenesis via TFEB. This effector pathway was sufficiently important that inhibition of TFEB or lysosomes unveiled a striking harmful effect of excess PGC1α in cells and conditional mice. These results uncover an unexpected effect of cisplatin on mitophagy and PGC1α’s reliance on lysosomes for kidney protection. Finally, the data illuminate TFEB as a potentially novel target for renal tubular stress resistance., PGC1α is renoprotective in the setting of platinum-based chemotherapy through the induction of mitophagy and lysosomal biogenesis via transcription factor EB.

The human kidney, which consists of up to 2 million nephrons, is critical for blood filtration, electrolyte balance, pH regulation, and fluid balance in the body. Animal experiments, particularly mice and rats, combined with advances in genetically modified technology have been the primary mechanism to study kidney injury in recent years. Mouse or rat kidneys, however, differ substantially from human kidneys at the anatomical, histological, and molecular levels. These differences combined with increased regulatory hurdles and shifting attitudes towards animal testing by non-specialists have led scientists to develop new and more relevant models of kidney injury. Although in vitro tissue culture studies are a valuable tool to study kidney injury and have yielded a great deal of insight, they are not a perfect model. Perhaps, the biggest limitation of tissue culture is that it cannot replicate the complex architecture, consisting of multiple cell types, of the kidney, and the interplay between these cells. Recent studies have found that pluripotent stem cells (PSCs), which are capable of differentiation into any cell type, can be used to generate kidney organoids. Organoids recapitulate the multicellular relationships and microenvironments of complex organs like kidney. Kidney organoids have been used to successfully model nephrotoxin-induced tubular and glomerular disease as well as complex diseases such as chronic kidney disease (CKD), which involves multiple cell types. In combination with genetic engineering techniques, such as CRISPR-Cas9, genetic diseases of the kidney can be reproduced in organoids. Thus, organoid models have the potential to predict drug toxicity and enhance drug discovery for human disease more accurately than animal models.

Summary Tubulointerstitial abnormalities are predictive of the progression of diabetic kidney disease (DKD), and their targeting may be an effective means for prevention. Proximal tubular (PT) expression of kidney injury molecule (KIM)-1, as well as blood and urinary levels, are increased early in human diabetes and can predict the rate of disease progression. Here, we report that KIM-1 mediates PT uptake of palmitic acid (PA)-bound albumin, leading to enhanced tubule injury with DNA damage, PT cell-cycle arrest, interstitial inflammation and fibrosis, and secondary glomerulosclerosis. Such injury can be ameliorated by genetic ablation of the KIM-1 mucin domain in a high-fat-fed streptozotocin mouse model of DKD. We also identified TW-37 as a small molecule inhibitor of KIM-1-mediated PA-albumin uptake and showed in vivo in a kidney injury model in mice that it ameliorates renal inflammation and fibrosis. Together, our findings support KIM-1 as a new therapeutic target for DKD.

The mineralocorticoid receptor (MR) and its downstream signaling play an important role in hypertensive renal injury. The interaction of advanced glycation end products (AGE) with their receptor (RAGE) is involved in the progression of renal disease. However, the pathological crosstalk between AGE–RAGE axis and MR system in kidney derangement remains unclear. We screened DNA-aptamer directed against RAGE (RAGE-apt) in vitro and examined its effects on renal injury in uninephrectomized deoxycorticosterone acetate (DOCA)/salt-induced hypertensive mice. RAGE, GTP-bound Rac-1 (Rac1), and MR were co-localized in the podocytes of DOCA mice. The deletion of RAGE gene significantly inhibited mesangial matrix expansion and tubulointerstitial fibrosis in DOCA mice, which was associated with the reduction of glomerular oxidative stress, MR, Rac1, and urinary albumin excretion (UAE) levels. RAGE-apt attenuated the increase in carboxymethyllysine (CML), RAGE, nitrotyrosine, Rac1, and MR levels in the kidneys and reduced UAE in DOCA mice. Aldosterone (Aldo) increased nitrotyrosine, CML, and RAGE gene expression in murine podocytes, whereas CML stimulated MR and Rac1 levels, which were blocked by RAGE-apt. The present study indicates the crosstalk between the AGE–RAGE axis and Aldo–MR system, suggesting that RAGE-apt may be a novel therapeutic tool for the treatment of MR-associated renal diseases.

A critical event during kidney organogenesis is the differentiation of podocytes, specialized epithelial cells that filter blood plasma to form urine. Podocytes derived from human pluripotent stem cells (hPSC-podocytes) have recently been generated in nephron-like kidney organoids, but the developmental stage of these cells and their capacity to reveal disease mechanisms remains unclear. Here, we show that hPSC-podocytes phenocopy mammalian podocytes at the capillary loop stage (CLS), recapitulating key features of ultrastructure, gene expression, and mutant phenotype. hPSC-podocytes in vitro progressively establish junction-rich basal membranes (nephrin+podocin+ZO-1+) and microvillus-rich apical membranes (podocalyxin+), similar to CLS podocytes in vivo. Ultrastructural, biophysical, and transcriptomic analysis of podocalyxin-knockout hPSCs and derived podocytes, generated using CRISPR/Cas9, reveals defects in the assembly of microvilli and lateral spaces between developing podocytes, resulting in failed junctional migration. These defects are phenocopied in CLS glomeruli of podocalyxin-deficient mice, which cannot produce urine, thereby demonstrating that podocalyxin has a conserved and essential role in mammalian podocyte maturation. Defining the maturity of hPSC-podocytes and their capacity to reveal and recapitulate pathophysiological mechanisms establishes a powerful framework for studying human kidney disease and regeneration.

Tubulointerstitial abnormalities are predictive of progression of diabetic kidney disease (DKD) . Proximal tubular (PT) kidney injury molecule (KIM)-1 expression and blood and urinary KIM-1 levels are increased early in human diabetes and can predict rate of progression of disease. We report that KIM-1 mediates PT uptake of fatty acids (FAs) bound to albumin leading to enhanced tubule injury with DNA damage, PT cell cycle arrest, interstitial inflammation and fibrosis, and secondary glomerulosclerosis. Injury is ameliorated by inhibition of uptake by genetic ablation of KIM-1 mucin domain or a newly discovered small molecule inhibitor of KIM-1-mediated FA uptake, TW-37. Our findings support KIM-1 as a new therapeutic target for DKD.

Kidney disease is estimated to affect 15% of the world's population. Autophagy is a key homeostatic pathway in eukaryotic cells, which has been linked to numerous pathological states. In the kidney, autophagy has been shown to modulate both acute and chronic injuries. Despite the importance of autophagy in kidney disease, few techniques to precisely monitor autophagic flux in kidney tissue are available. Here we describe an improved technique to quantify autophagic flux using an RFP-GFP-LC3 reporter mouse and super-resolution microscopy. Using structured illumination microscopy, we can resolve individual autophagosomes within kidney tubular cells. We describe the preparation of slides, staining, imaging and data processing. 3D surface rendering is utilized to categorize and quantify autophagosomes by number, size, fluorescence and autophagic flux in response to ischemia.

Fibrosis contributes to the progression of chronic kidney disease (CKD). Severe acute kidney injury can lead to CKD through proximal tubular cell (PTC) cycle arrest in the G2-M phase, with secretion of profibrotic factors. Here, we show that epithelial cells in the G2-M phase form target of rapamycin (TOR)–autophagy spatial coupling compartments (TASCCs), which promote profibrotic secretion similar to the senescence-associated secretory phenotype. Cyclin G1 (CG1), an atypical cyclin, promoted G2-M arrest in PTCs and up-regulated TASCC formation. PTC TASCC formation was also present in humans with CKD. Prevention of TASCC formation in cultured PTCs blocked secretion of profibrotic factors. PTC-specific knockout of a key TASCC component reduced the rate of kidney fibrosis progression in mice with CKD. CG1 induction and TASCC formation also occur in liver fibrosis. Deletion of CG1 reduced G2-M phase cells and TASCC formation in vivo. This study provides mechanistic evidence supporting how profibrotic G2-M arrest is induced in kidney injury and how G2-M–arrested PTCs promote fibrosis, identifying new therapeutic targets to mitigate kidney fibrosis.

Kidney disease is estimated to affect 15% of the world's population. Autophagy is a key homeostatic pathway in eukaryotic cells, which has been linked to numerous pathological states. In the kidney, autophagy has been shown to modulate both acute and chronic injuries. Despite the importance of autophagy in kidney disease, few techniques to precisely monitor autophagic flux in kidney tissue are available. Here we describe an improved technique to quantify autophagic flux using an RFP-GFP-LC3 reporter mouse and super-resolution microscopy. Using structured illumination microscopy, we can resolve individual autophagosomes within kidney tubular cells. We describe the preparation of slides, staining, imaging and data processing. 3D surface rendering is utilized to categorize and quantify autophagosomes by number, size, fluorescence and autophagic flux in response to ischemia.

Global or local ischemia contributes to the pathogenesis of acute kidney injury (AKI). Currently there are no specific therapies to prevent AKI. Potentiation of glycolytic metabolism and attenuation of mitochondrial respiration may decrease cell injury and reduce reactive oxygen species generation from the mitochondria. Meclizine, an over-the-counter anti-nausea and -dizziness drug, was identified in a ‘nutrient-sensitized’ chemical screen. Pretreatment with 100 mg/kg of meclizine, 17 h prior to ischemia protected mice from IRI. Serum creatinine levels at 24 h after IRI were 0.13 ± 0.06 mg/dl (sham, n = 3), 1.59 ± 0.10 mg/dl (vehicle, n = 8) and 0.89 ± 0.11 mg/dl (meclizine, n = 8). Kidney injury was significantly decreased in meclizine treated mice compared with vehicle group (p, Graphical abstract, Highlights • Pretreatment with meclizine protected mice from kidney ischemia–reperfusion injury. • Meclizine reduced mitochondrial oxygen consumption and upregulated glycolysis. • Meclizine caused accumulation of phosphoethanolamine, a mitochondrial respiration inhibitor. • Phosphoethanolamine recapitulated meclizine's effects on metabolism and renal protection. Kishi et al. demonstrate that meclizine, an over-the-counter anti-nausea drug, protects mouse against kidney ischemia. Pretreatment with 100 mg/kg of meclizine, 17 or 24 h prior to ischemia showed kidney protection in mice. Meclizine reduced mitochondrial oxygen consumption by directly inhibiting the Kennedy pathway of phosphatidylethanolamine biosynthesis and up-regulated glycolysis.

Ischemia-reperfusion injury (IRI) evokes intragraft inflammatory responses, which markedly augment alloimmune responses against the graft. Understanding the mechanisms underlying these responses is fundamental to develop therapeutic regimens to prevent/ameliorate organ IRI. Here, we demonstrate that IRI results in a marked increase in mitochondrial damage and autophagy in dendritic cells (DCs). While autophagy is a survival mechanism for ischemic DCs, it also augments their production of interleukin (IL)-6. Allograft-derived dendritic cells (ADDCs) lacking autophagy-related gene 5 (Atg5) showed higher death rates posttransplantation. Transplanted ischemic hearts from CD11cCre/Atg5 conditional knockout mice showed marked reduction in intragraft expression of IL-6 compared with controls. To antagonize the effect of IL-6 locally in the heart, we synthesized novel anti-IL-6 nanoparticles with capacity for controlled release of anti-IL-6 over time. Compared with systemic delivery of anti-IL-6, localized delivery of anti-IL-6 significantly reduced chronic rejection with a markedly lower amount administered. Despite improved allograft histology, there were no changes to splenic T cell populations, illustrating the importance of local IL-6 in driving chronic rejection after IRI. These data carry potential clinical significance by identifying an innovative, targeted strategy to manipulate organs before transplantation to diminish inflammation, leading to improved long-term outcomes.

Kidney injury molecule-1/T cell IgG and mucin containing 1 (KIM-1/TIM-1) is a type 1 membrane receptor [1] which we identified as the most upregulated proximal tubular cell (PTC) protein following a variety of kidney injuries in animal models and human diseases [1] (Figure ​(Figure1A).1A). While KIM-1 (also known as hepatitis A virus cellular receptor-1 (HAVCR-1)) quickly was recognized as a promising biomarker, other proteins were subsequently discovered which, together with KIM-1/TIM-1 formed a new class of proteins (TIMs) whose function was unknown at the time of discovery. Work from our lab identified KIM-1′s function as an apoptotic cell phosphatidylserine phagocytosis and scavenger receptor [2], whereby it induces the binding and uptake of dead cells from the kidney tubule lumen in acute kidney injury (AKI) (Figure ​(Figure1B).1B). As is often the case, however, identifying the function of KIM-1 only led to more questions: Why do non-myeloid cells express a scavenger receptor? Can PTCs efficiently phagocytose in vivo? What are the functional consequences of PTC phagocytosis? In other words, what is the role of KIM-1 in kidney injury? Figure 1 KIM-1 is expressed by PTCs and mediates apoptotic cell phagocytosis To address these questions, we characterized a mouse model KIM-1Δmucin (in collaboration with Dr. Vijay Kuchroo's lab), which expressed a truncated, phagocytosis deficient KIM-1 molecule, by deleting the mucin domain, (the domain where most mutations leading to human disease occur), while retaining most of the protein intact [3]. Utilizing this novel animal model, we found that KIM-1 mediated phagocytosis is responsible for the clearance of much of the luminal apoptotic cells resulting from ischemic or nephrotoxic acute tubular injury [4]. In addition, KIM-1 expression down-regulates PTC cytokine secretion, which is further down-regulated with the KIM-1-mediated uptake of apoptotic cells. Using a systems biology approach, we identified post-translational modifications to the NFκB pathway as the most likely pathway modulated by KIM-1 to regulate cytokine secretion [4]. Indeed, KIM-1 expression and phagocytosis decreases NFκB phosphorylation and activity. KIM-1 phosphorylation regulates the NFκB pathway through interaction and regulation of the PI3 kinase subunit p85. In the KIM-1Δmucin mice, decreased apoptotic cell clearance, increased pro-inflammatory cytokine secretion and increased immune cell infiltration culminated in more severe injury, when compared to wild-type mice, indicating intact KIM-1 plays a protective role in AKI [4]. In addition to acting as non-professional phagocytes, PTCs constitutively express MHC II and can activate naive T cells; thus, PTCs are also semi-professional antigen presenting cells [5]. To determine if KIM-1-mediated phagocytosis promotes presentation of phagocytosed antigens, we first examined the uptake and processing of apoptotic cells in vitro by adding apoptotic cells to the apical surface of cultured PTCs and monitoring phagocytosis (Figure ​(Figure1C).1C). Apoptotic cells taken up by KIM-1 are quickly targeted by LC3 in the cytosol. LC3 localization to KIM-1 phagosomes required the expression of autophagy factors ATG5, Beclin1 and ULK1 [6]. Mutation to the KIM-1 ligand-binding domain (WFND, amino acids 115–118 in the mouse), deletion of the mucin domain or deletion of the cytosolic domain (containing the phosphorylation sites) prevents autophagy induction [6]. KIM-1 phosphorylation and interaction with p85 are critical to its regulation of autophagy, with KIM-1-induced autophagy being suppressed in p85 knockout cells [6]. Unlike professional phagocytes, KIM-1-mediated phagocytosis in PTCs resulted in slower acidification of the phagosome (compared to macrophages and dendritic cells) and did not induce dependent reactive oxygen species production [6]. Inhibition of NOX by diphenylene iodonium did not prevent LC3 localization to the phagosome [6]. These biochemical data support the role of autophagy in the clearance of KIM-1 phagosomes. We next examined if phagocytosed material was presented to MHC I and II. KIM-1 expressing PTCs present antigens at a higher level than did KIM-1Δmucin PTCs [6]. Despite the increase in antigen presentation, KIM-1 expressing PTCs are associated with inhibition of CD4+ T cell proliferation and activation and an increase in the number of T regulatory cells (Tregs) [6]. Removal of the Treg population reverses the ability KIM-1-dependent antigen presentation to inhibit T cell activation. Deletion of autophagy factors ATG5 and ULK1 also results in a pro-inflammatory MHC presentation [6]. In vivo, kidneys from wild-type mice have greater numbers of Tregs and reduced numbers of CD4+ and CD8+ T cells, compared to KIM-1Δmucin mice [6]. Thus, material phagocytosed by KIM-1 and processed via autophagy are presented to MHC I and II, creating a pro-tolerogenic milieu. Our earlier work demonstrated that long-term expression of KIM-1, even at low levels, is maladaptive, inducing spontaneous and progressive interstitial inflammation, fibrosis and chronic kidney disease in the mouse [7]. In models of severe AKI which progress to CKD, KIM-1 is expressed at high levels during the acute phase and remains elevated through the transition to CKD [7]. Therefore, the induction and progression of fibrosis by KIM-1 could help explain the AKI to CKD transition seen in human kidney diseases and animal models. What can explain the dichotomy between the protective role of KIM-1 in acute and maladaptive response in chronic kidney injuries? We believe the key to answering this question lies in the differences in the pathophysiology of acute vs chronic injury. AKI is associated with an abundance of apoptotic cells and necrotic debris, while CKD is associated with a more mild but sustained injury, breakdown of the glomerular filtration barrier, and marked increases in modified serum proteins, lipids and other factors entering into the tubule lumen which can be taken up by KIM-1 expressing cells [7]. These ligands for KIM-1 likely exert increasing levels of stress to the epithelial cell with a resultant generation of pro-fibrotic cytokines, culminating in inflammation, activation of interstitial cells, increased matrix production, vascular rarefaction and chronic kidney disease (CKD). In contrast to the uptake of apoptotic cells leading to KIM-1 phosphorylation and autophagy, we suggest that KIM-1 ligands found in glomerular filtrate in CKD do not induce autophagy. This is perhaps due to the fact that uptake of these ligands activate a distinctive KIM-1 signaling program which promotes inflammatory processes including cytokine production and pro-inflammatory antigen presentation. Taken together, these studies demonstrate that KIM-1 acts as a “double-edged sword” in the injured kidney. In acutely injured kidneys, KIM-1 facilitates repair by removal of luminal debris, leading to anti-inflammatory antigen presentation and down-regulation of the PTC immune response via NFκB suppression. By contast, in the chronically injured kidney, prolonged KIM-1 expression stimulates inflammation and fibrosis. Future studies are required to elucidate whether KIM-1′s phagocytic function to remove lumenal cellular debris or its ability to down-modulate inflammation is most important for its protective effect in AKI. The development of phospho-specific antibodies would enable the further exploration of divergent KIM-1 signaling in AKI and CKD, shedding light on potential mechanisms of KIM-1 action in the chronic setting. It is evident, however, that small molecules or biologics which can up or down-modulate KIM-1 activity should be explored as potential therapeutics in AKI and CKD.

Human-pluripotent-stem-cell-derived kidney cells (hPSC-KCs) have important potential for disease modelling and regeneration. Whether the hPSC-KCs can reconstitute tissue-specific phenotypes is currently unknown. Here we show that hPSC-KCs self-organize into kidney organoids that functionally recapitulate tissue-specific epithelial physiology, including disease phenotypes after genome editing. In three-dimensional cultures, epiblast-stage hPSCs form spheroids surrounding hollow, amniotic-like cavities. GSK3β inhibition differentiates spheroids into segmented, nephron-like kidney organoids containing cell populations with characteristics of proximal tubules, podocytes and endothelium. Tubules accumulate dextran and methotrexate transport cargoes, and express kidney injury molecule-1 after nephrotoxic chemical injury. CRISPR/Cas9 knockout of podocalyxin causes junctional organization defects in podocyte-like cells. Knockout of the polycystic kidney disease genes PKD1 or PKD2 induces cyst formation from kidney tubules. All of these functional phenotypes are distinct from effects in epiblast spheroids, indicating that they are tissue specific. Our findings establish a reproducible, versatile three-dimensional framework for human epithelial disease modelling and regenerative medicine applications., Generating organized kidney tissues from human pluripotent stem cell is a major challenge. Here, Freedman et al. describe a differentiation system forming spheroids and tubular structures, characteristic of these kidney structures, and using CRISPR/Cas9, delete PKD1/2, to model polycystic kidney disease.

Kidney injury molecule 1 (KIM-1, also known as TIM-1) is markedly upregulated in the proximal tubule after injury and is maladaptive when chronically expressed. Here, we determined that early in the injury process, however, KIM-1 expression is antiinflammatory due to its mediation of phagocytic processes in tubule cells. Using various models of acute kidney injury (AKI) and mice expressing mutant forms of KIM-1, we demonstrated a mucin domain-dependent protective effect of epithelial KIM-1 expression that involves downregulation of innate immunity. Deletion of the mucin domain markedly impaired KIM-1-mediated phagocytic function, resulting in increased proinflammatory cytokine production, decreased antiinflammatory growth factor secretion by proximal epithelial cells, and a subsequent increase in tissue macrophages. Mice expressing KIM-1Δmucin had greater functional impairment, inflammatory responses, and mortality in response to ischemia- and cisplatin-induced AKI. Compared with primary renal proximal tubule cells isolated from KIM-1Δmucin mice, those from WT mice had reduced proinflammatory cytokine secretion and impaired macrophage activation. The antiinflammatory effect of KIM-1 expression was due to the interaction of KIM-1 with p85 and subsequent PI3K-dependent downmodulation of NF-κB. Hence, KIM-1-mediated epithelial cell phagocytosis of apoptotic cells protects the kidney after acute injury by downregulating innate immunity and inflammation.