A Subpopulation of Label-Retaining Cells of the Kidney Papilla Regenerates Injured Kidney Medullary Tubules

Fewer medullary pyramids in the living kidney donor are associated with graft failure in the recipient

This study aimed to identify the parenchymal structural features by both computed tomography (CT) and histology that are associated with death-censored graft failure in recipients of living donor kidneys. We analyzed kidney recipients of ABO-compatible living donor kidneys from 2000-2020 with follow-up through 2023. Cortical volume and thickness, individual medullary pyramid volume and count, glomerular volume, nephrosclerosis, and nephron number were assessed by deep learning models applied to the predonation CT and by morphometric histology analysis from the biopsy at the time of transplantation. There were 3098 recipients followed for a median of 5 years with 346 graft failure events. In adjusted analyses, the only structural measures associated with graft failure were fewer medullary pyramids on CT and a higher fraction of interstitial fibrosis and tubular atrophy on histology. Having ≤15 pyramids donated occurred in 9% and was associated with a graft failure incidence of 2.5 per 100 person-years compared to 1.6 per 100 person-years in the 17% with ≥26 pyramids donated. Fewer medullary pyramids were associated with a lower 1-year estimated glomerular filtration rate, which mediated the subsequent risk of graft failure. Interstitial fibrosis and tubular atrophy >1% is also associated with graft failure. Medullary pyramid count is a potentially useful predonation prognostic biomarker for graft failure in transplant recipients.

Regenerative Role of Lrig1+ Cells in Kidney Repair

Key Points

Lrig1 + cells exist long term during kidney homeostasis and become activated upon injury, contributing to regeneration. Lrig1 + cells and their progeny emerge during tubulogenesis and contribute to proximal tubule and inner medullary collecting duct development. Lrig1 + cells expand and differentiate into a mature nephron lineage in response to AKI to repair the proximal tubule.

Background

In response to severe kidney injury, the kidney epithelium displays remarkable regenerative capabilities driven by adaptable resident epithelial cells. To date, it has been widely considered that the adult kidney lacks multipotent stem cells; thus, the cellular lineages responsible for repairing proximal tubule damage are incompletely understood. Leucine-rich repeats and immunoglobulin-like domain protein 1–expressing cells (Lrig1 + cells) have been identified as a long-lived cell in various tissues that can induce epithelial tissue repair. Therefore, we hypothesized that Lrig1 + cells participate in kidney development and tissue regeneration.

Methods

We investigated the role of Lrig1 + cells in kidney injury using mouse models. The localization of Lrig1 + cells in the kidney was examined throughout mouse development. The function of Lrig1 + progeny cells in AKI repair was examined in vivo using a tamoxifen-inducible Lrig1 -specific Cre recombinase-based lineage tracing in three different kidney injury mouse models. In addition, we conducted single-cell RNA sequencing to characterize the transcriptional signature of Lrig1 + cells and trace their progeny.

Results

Lrig1 + cells were present during kidney development and contributed to formation of the proximal tubule and collecting duct structures in mature mouse kidneys. In three-dimensional culture, single Lrig1 + cells demonstrated long-lasting propagation and differentiated into the proximal tubule and collecting duct lineages. These Lrig1 + proximal tubule cells highly expressed progenitor-like and quiescence-related genes, giving rise to a novel cluster of cells with regenerative potential in adult kidneys. Moreover, these long-lived Lrig1 + cells expanded and repaired damaged proximal tubule in response to three types of AKIs in mice.

Conclusions

These findings highlight the critical role of Lrig1 + cells in kidney regeneration.

Single-cell lineage tracing approaches to track kidney cell development and maintenance

The kidney is a complex organ consisting of various cell types. Previous studies have aimed to elucidate the cellular relationships among these cell types in developing and mature kidneys using Cre-loxP-based lineage tracing. However, this methodology falls short of fully capturing the heterogeneous nature of the kidney, making it less than ideal for comprehensively tracing cellular progression during kidney development and maintenance. Recent technological advancements in single-cell genomics have revolutionized lineage tracing methods. Single-cell lineage tracing enables the simultaneous tracing of multiple cell types within complex tissues and their transcriptomic profiles, thereby allowing the reconstruction of their lineage tree with cell state information. Although single-cell lineage tracing has been successfully applied to investigate cellular hierarchies in various organs and tissues, its application in kidney research is currently lacking. This review comprehensively consolidates the single-cell lineage tracing methods, divided into 4 categories (clustered regularly interspaced short palindromic repeat [CRISPR]/CRISPR-associated protein 9 [Cas9]-based, transposon-based, Polylox-based, and native barcoding methods), and outlines their technical advantages and disadvantages. Furthermore, we propose potential future research topics in kidney research that could benefit from single-cell lineage tracing and suggest suitable technical strategies to apply to these topics.

Reduced urine volume and changed renal sphingolipid metabolism in P2ry14-deficient mice

The UDP-glucose receptor P2RY14, a rhodopsin-like G protein-coupled receptor (GPCR), was previously described as receptor expressed in A-intercalated cells of the mouse kidney. Additionally, we found P2RY14 is abundantly expressed in mouse renal collecting duct principal cells of the papilla and epithelial cells lining the renal papilla. To better understand its physiological function in kidney, we took advantage of a P2ry14 reporter and gene-deficient (KO) mouse strain. Morphometric studies showed that the receptor function contributes to kidney morphology. KO mice had a broader cortex relative to the total kidney area than wild-type (WT) mice. In contrast, the area of the outer stripe of the outer medulla was larger in WT compared to KO mice. Transcriptome comparison of the papilla region of WT and KO mice revealed differences in the gene expression of extracellular matrix proteins (e.g., decorin, fibulin-1, fibulin-7) and proteins involved in sphingolipid metabolism (e.g., small subunit b of the serine palmitoyltransferase) and other related GPCRs (e.g., GPR171). Using mass spectrometry, changes in the sphingolipid composition (e.g., chain length) were detected in the renal papilla of KO mice. At the functional level, we found that KO mice had a reduced urine volume but an unchanged glomerular filtration rate under normal chow and salt diets. Our study revealed P2ry14 as a functionally important GPCR in collecting duct principal cells and cells lining the renal papilla and the possible involvement of P2ry14 in nephroprotection by regulation of decorin.

Age-Associated Loss in Renal Nestin-Positive Progenitor Cells

The decrease in the number of resident progenitor cells with age was shown for several organs. Such a loss is associated with a decline in regenerative capacity and a greater vulnerability of organs to injury. However, experiments evaluating the number of progenitor cells in the kidney during aging have not been performed until recently. Our study tried to address the change in the number of renal progenitor cells with age. Experiments were carried out on young and old transgenic nestin-green fluorescent protein (GFP) reporter mice, since nestin is suggested to be one of the markers of progenitor cells. We found that nestin⁺ cells in kidney tissue were located in the putative niches of resident renal progenitor cells. Evaluation of the amount of nestin⁺ cells in the kidneys of different ages revealed a multifold decrease in the levels of nestin⁺ cells in old mice. In vitro experiments on primary cultures of renal tubular cells showed that all cells including nestin⁺ cells from old mice had a lower proliferation rate. Moreover, the resistance to damaging factors was reduced in cells obtained from old mice. Our data indicate the loss of resident progenitor cells in kidneys and a decrease in renal cells proliferative capacity with aging.

Aqp2+ Progenitor Cells Maintain and Repair Distal Renal Segments

BACKGROUND

Adult progenitor cells presumably demonstrate clonogenicity, self-renewal, and multipotentiality, and can regenerate cells under various conditions. Definitive evidence demonstrating the existence of such progenitor cells in adult mammalian kidneys is lacking.

METHOD

We performed in vivo lineage tracing and thymidine analogue labeling using adult tamoxifen-inducible (Aqp2^ECE/+ RFP/+, Aqp2^ECE/+ Brainbow/+, and Aqp2^ECE/+ Brainbow/Brainbow) and WT mice. The tamoxifen-inducible mice were analyzed between 1 and 300 days postinduction. Alternatively, WT and tamoxifen-induced mice were subjected to unilateral ureteral obstruction and thymidine analogue labeling and analyzed 2-14 days post-surgery. Multiple cell-specific markers were used for high-resolution immunofluorescence confocal microscopy to identify the cell types derived from Aqp2⁺ cells.

RESULTS

Like their embryonic counterparts, adult cells expressing Aqp2 and V-ATPase subunits B1 and B2 (Aqp2⁺ B1B2⁺) are the potential Aqp2⁺ progenitor cells (APs). Adult APs rarely divide to generate daughter cells, either maintaining the property of the AP (self-renewal) or differentiating into DCT2/CNT/CD cells (multipotentiality), forming single cell-derived, multiple-cell clones (clonogenicity) during tissue maintenance. APs selectively and continuously regenerate DCT2/CNT/CD cells in response to injury resulting from ureteral ligation. AP proliferation demonstrated direct correlation with Notch activation and was inversely correlated with development of kidney fibrosis. Derivation of both intercalated and DCT2 cells was found to be cell division-dependent and -independent, most likely through AP differentiation which requires cell division and through direct conversion of APs and/or regular principal cells without cell division, respectively.

CONCLUSION

Our study demonstrates that Aqp2⁺ B1B2⁺ cells behave as adult APs to maintain and repair DCT2/CNT1/CNT2/CD segments.

Drosophila renal stem cells enhance fitness by delayed remodeling of adult Malpighian tubules

Drosophila renal stem cells (RSCs) contradict the common expectation that stem cells maintain tissue homeostasis. RSCs are abundant, quiescent, and confined to the peri-ureter region of the kidney-like Malpighian tubules (MTs). Although derived during pupation-like intestinal stem cells, RSCs initially remodel the larval MTs only near the intestinal junction. However, following adult injury to the ureter by xanthine stones, RSCs remodel the damaged region in a similar manner. Thus, RSCs represent stem cells encoding a developmental redesign. The remodeled tubules have a larger luminal diameter and shorter brush border, changes linked to enhanced stone resistance. However, RSC-mediated modifications also raise salt sensitivity and reduce fecundity. Our results suggest that RSCs arose by arresting developmental progenitors to preserve larval physiology until a time in adulthood when it becomes advantageous to complete the development by RSC activation.

Potential renal stem/progenitor cells identified by in vivo lineage tracing

Mammalian kidneys consist of more than 30 different types of cells. A challenging task is to identify and characterize the stem/progenitor subpopulations that establish the lineage relationships among these cellular elements during nephrogenesis in the embryonic and neonate kidneys and during tissue homeostasis and/or injury repair in the mature kidney. Moreover, the potential clinical utility of stem/progenitor cells holds promise for development of new regenerative medicine approaches for the treatment of renal diseases. Stem cells are defined by unlimited self-renewal capacity and pluripotentiality. Progenitor cells have pluripotentiality, but no or limited self-renewal potential. Cre-LoxP-based in vivo genetic lineage tracing is a powerful tool to identify the stem/progenitor cells in their native environment. Hypothetically, this technique enables investigators to accurately track the progeny of a single cell, or a group of cells. The Cre/loxP system has been widely employed to uncover the function of genes in various mammalian tissues and to identify stem/progenitor cells through in vivo lineage tracing analyses. In this review, we summarize the recent advances in the development and characterization of various Cre drivers, and their use in identifying potential renal stem/progenitor cells in both developing and mature mouse kidneys.

Identification of a foetal epigenetic compartment in adult human kidney

The mammalian kidney has extensive repair capacity; however, identifying adult renal stem cells has proven elusive. We applied an epigenetic marker of foetal cell origin (FCO) in diverse human tissues as a probe for developmental cell persistence, finding a 5.4-fold greater FCO proportion in kidney. Normal kidney FCO proportions averaged 49% with extensive interindividual variation. FCO proportions were significantly negatively correlated with immune-related gene expression and positively correlated with genes expressed in the renal medulla, including those involved in renal organogenesis (e.g., FGF2, PAX8, and HOXB7). FCO associated genes also mapped to medullary nephron segments in mouse and rat, suggesting evolutionary conservation of this cellular compartment. Renal cancer patients whose tumours contained non-zero FCO scores survived longer. The kidney appears unique in possessing substantial foetal epigenetic features. Further study of FCO-related gene methylation may elucidate regenerative regulatory programmes in tissues without apparent discrete stem cell compartments.

Regenerative medicine therapies: lessons from the kidney

We focus on three strategies for renal regenerative medicine; administering cells to replace damaged tissue, promoting endogenous regeneration, and growing stem cell-derived organs. Mouse kidney regeneration can be promoted by stem cells injected into the circulation which do not become new kidney tissue but seem to secrete regeneration-promoting humoral factors. This argues against direct replacement but encourages developing pharmacological stimulators of endogenous regeneration. Simple ‘kidneys’ have been made from stem cells, but there is a large gap between what has been achieved and a useful transplantable organ. Most current work aims to stimulate endogenous regeneration or to grow new organs but much remains to be done; misplaced hype about short-term prospects of regenerative medicine helps neither researchers nor patients.

Kidney Cells Regeneration: Dedifferentiation of Tubular Epithelium, Resident Stem Cells and Possible Niches for Renal Progenitors

A kidney is an organ with relatively low basal cellular regenerative potential. However, renal cells have a pronounced ability to proliferate after injury, which undermines that the kidney cells are able to regenerate under induced conditions. The majority of studies explain yielded regeneration either by the dedifferentiation of the mature tubular epithelium or by the presence of a resident pool of progenitor cells in the kidney tissue. Whether cells responsible for the regeneration of the kidney initially have progenitor properties or if they obtain a “progenitor phenotype” during dedifferentiation after an injury, still stays the open question. The major stumbling block in resolving the issue is the lack of specific methods for distinguishing between dedifferentiated cells and resident progenitor cells. Transgenic animals, single-cell transcriptomics, and other recent approaches could be powerful tools to solve this problem. This review examines the main mechanisms of kidney regeneration: dedifferentiation of epithelial cells and activation of progenitor cells with special attention to potential niches of kidney progenitor cells. We attempted to give a detailed description of the most controversial topics in this field and ways to resolve these issues.

Current State of Renal Regenerative Therapies

The worldwide increase in the number of patients with end-stage renal disease leads to a growing waiting list for kidney transplantation resulting from the scarcity of kidney donors. Therefore, alternative treatment options for patients with end-stage renal disease are being sought. In vitro differentiation of stem cells into renal tissue is a promising approach to repair nonfunctional kidney tissue. Impressive headway has been made in the use of stem cells with the use of adult renal progenitor cells, embryonic stem cells, and induced pluripotent stem cells for the development toward primitive kidney structures. Currently, efforts are directed at improving long-term maintenance and stability of the cells. This review aims to provide a comprehensive overview of the cell sources used for the generation of kidney cells and strategies used for transplantation in in vivo models. Furthermore, it provides a perspective on stability and safety during future clinical application of in vitro generated kidney cells.

Isolation and Characterization of Multipotent CD24+ Cells From the Renal Papilla of Swine

Over 100,000 patients in the United States are currently waiting for a kidney transplant. With just over 10,000 cadaveric kidneys transplanted annually, it is of the utmost importance to optimize kidney viability upon transplantation. One exciting avenue may be xenotransplantation, which has rejuvenated interest after advanced gene editing techniques have been successfully used in swine. Simultaneously, acute kidney injury (AKI) is associated with high morbidity and mortality and currently lacks effective treatment. Animal models have been used extensively to address both of these issues, with recent emphasis on renal progenitor cells (RPCs). Due to anatomical similarities to humans we aimed to examine progenitor cells from the renal papillae of swine kidneys. To do this, RPCs were dissected from the renal papillae of healthy swine. Cell surface marker expression, proliferation, and differentiation of the RPCs were tested in vitro. Additionally, a mixed lymphocyte reaction was performed to examine immunomodulatory properties. RPCs displayed spindle shaped morphology with limited self-renewing capacity. Isolated RPCs were positive for CD24 and CD133 at early passages, but lost expression with subsequent passaging. Similarly, RPCs displayed myogenic, osteogenic, and adipogenic differentiation capacities at passage 2, but largely lost this by passage 6. Lastly, direct contact of RPCs with human lymphocytes increased release of IL6 and IL8. Taken together, RPCs from the papilla of porcine kidneys display transient stem cell properties that are lost with passaging, and either represent multiple types of progenitor cells, or a multipotent progenitor population. In instances of ischemic insult, augmentation of/with RPCs may potentiate regenerative properties of the kidney. While the use of swine for transplantation and ischemia studies confers obvious advantages, the populations of different progenitor cell populations within pig kidneys warrants further investigation. Ultimately, while gene editing techniques enhance the potential for xenotransplantation of organs or cells, the ultimate success of this strategy may be determined by the (dis)similarities of RPCs from different species.

Highly tamoxifen-inducible principal cell-specific Cre mice with complete fidelity in cell specificity and no leakiness

An ideal inducible system should be cell specific and have absolutely no background recombination without induction (i.e., no leakiness), a high recombination rate after induction, and complete fidelity in cell specificity (i.e., restricted recombination exclusively in cells where the driver gene is expressed). However, such an ideal mouse model remains unavailable for collecting duct research. Here, we report a mouse model that meets these criteria. In this model, a cassette expressing ERT2CreERT2 ( ECE) is inserted at the ATG of the endogenous Aqp2 locus to disrupt Aqp2 function and to express ECE under the control of the Aqp2 promoter. The resulting allele is named Aqp2ECE. There was no indication of a significant impact of disruption of a copy of Aqp2 on renal function and blood pressure control in adult Aqp2ECE/+ heterozygotes. Without tamoxifen, Aqp2ECE did not activate a Cre-dependent red fluorescence protein (RFP) reporter in adult kidneys. A single injection of tamoxifen (2 mg) to adult mice enabled Aqp2ECE to induce robust RFP expression in the whole kidney 24 h postinjection, with the highest recombination efficiency of 95% in the inner medulla. All RFP-labeled cells expressed principal cell markers (Aqp2 and Aqp3), but not intercalated cell markers (V-ATPase B1B2, and carbonic anhydrase II). Hence, Aqp2ECE confers principal cell-specific tamoxifen-inducible recombination with absolutely no leakiness, high inducibility, and complete fidelity in cell specificity, which should be an important tool for temporospatial control of target genes in the principal cells and for Aqp2+ lineage tracing in adult mice.

Kidney-Derived c-Kit+ Cells Possess Regenerative Potential

Kidney-derived c-Kit+ cells exhibit progenitor/stem cell properties in vitro (self-renewal capacity, clonogenicity, and multipotentiality). These cells can regenerate epithelial tubular cells following ischemia-reperfusion injury and accelerate foot processes effacement reversal in a model of acute proteinuria in rats. Several mechanisms are involved in kidney regeneration by kidney-derived c-Kit+ cells, including cell engraftment and differentiation into renal-like structures, such as tubules, vessels, and podocytes. Moreover, paracrine mechanisms could also account for kidney regeneration, either by stimulating proliferation of surviving cells or modulating autophagy and podocyte cytoskeleton rearrangement through mTOR-Raptor and -Rictor signaling, which ultimately lead to morphological and functional improvement. To gain insights into the functional properties of c-Kit+ cells during kidney development, homeostasis, and disease, studies on lineage tracing using transgenic mice will unveil their fate. The results obtained from these studies will set the basis for establishing further investigation on the therapeutic potential of c-Kit+ cells for treatment of kidney disease in preclinical and clinical studies. Stem Cells Translational Medicine 2018;7:317-324.

Biomarker discovery for renal cancer stem cells

Characterised by high intra- and inter-tumor heterogeneity, metastatic renal cell carcinoma (RCC) is resistant to chemo- and radiotherapy. Therefore, the development of new prognostic and diagnostic markers for RCC patients is needed. Cancer stem cells (CSCs) are a small population of neoplastic cells within a tumor which present characteristics reminiscent of normal stem cells. CSCs are characterised by unlimited cell division, maintenance of the stem cell pool (self-renewal), and capability to give rise to all cell types within a tumor; and contribute to metastasis in vivo (tumourigenicity), treatment resistance and recurrence. So far, many studies have tried to establish unique biomarkers to identify CSC populations in RCC. At the same time, different approaches have been developed with the aim to isolate CSCs. Consequently, several markers were found to be specifically expressed in CSCs and cancer stem-like cells derived from RCC such as CD105, ALDH1, OCT4, CD133, and CXCR4. However, the contribution of genetic and epigenetic mechanisms, and tumor microenvironment, to cellular plasticity have made the discovery of unique biomarkers a very difficult task. In fact, contrasting results regarding the applicability of such markers to the isolation of renal CSCs have been reported in the literature. Therefore, a better understanding of the mechanism underlying CSC may help dissecting tumor heterogeneity and drug treatment efficiency.

Comparing adult renal stem cell identification, characterization and applications

Despite growing interest and effort, a consensus has yet to be reached in regards to the identification of adult renal stem cells. Organ complexity and low turnover of renal cells has made stem cell identification difficult and lead to the investigation of multiple possible populations. In this review, we summarize the work that has been done toward finding and characterizing an adult renal stem cell population. In addition to giving a general overview of what has been done, we aim to highlight the variation in methods and outcomes. The methods used to locate potential stem cell populations can vary widely, but even within the relatively standard practice of BrdU labeling of slowly dividing cells, there are significant differences in protocols and results. Additional diversity exists in cell marker profiles and apparent differentiation potential seen in potential stem cell sources. Cataloging the variety of methods and outcomes seen so far may help to streamline future investigation and stear the field toward consensus. But even without firmly defined populations, the application of renal stem cells holds tantalizing potential. Populations of highly proliferative, multipotent cells of renal origin show the ability to engraft in injured kidneys, mitigate functional loss and occasionally show the ability to generate nephrons de novo. The progress toward regenerative medicine applications is also summarized.

Fatty acid synthase cooperates with protrudin to facilitate membrane outgrowth of cellular protrusions

Cellular protrusion formation capacity is a key feature of developing neurons and many eukaryotic cells. However, the mechanisms underlying membrane growth in protrusion formation are largely unclear. In this study, photo-reactive unnatural amino acid 3-(3-methyl-3H-diazirin-3-yl)-propamino-carbonyl-Nε-l-lysine was incorporated by a genetic code expansion strategy into protrudin, a protein localized in acidic endosomes and in the endoplasmic reticulum, that induces cellular protrusion and neurite formation. The modified protrudin was used for covalent trapping of protrudin-interacting proteins in living cells. Fatty acid synthase (FASN), which synthesizes free fatty acids, was identified to transiently interact with protrudin. Further characterization revealed a unique cooperation mechanism in which protrudin cooperates with FASN to facilitate cellular protrusion formation. This work reveals a novel mechanism involved in protrusion formation that is dependent on transient interaction between FASN and protrudin, and establishes a creative strategy to investigate transient protein-protein interactions in mammalian cells.

Cellular plasticity in kidney injury and repair

Terminally differentiated cells can be reprogrammed to pluripotency or directly to another differentiated cell type in vitro, a capacity termed cellular plasticity. Plasticity is not limited to in vitro manipulations but rather represents an important aspect of the regenerative response to injury in organs. Differentiated adult cells retain the capacity to dedifferentiate, adopting a progenitor-like phenotype after injury or, alternatively, to transdifferentiate, directly converting to a different mature cell type. Emerging concepts on cellular plasticity have relevance to our understanding of repair after kidney injury, including epithelial regeneration. Here we discuss work published in the past 5 years on the cellular hierarchies and mechanisms underlying kidney injury and repair, with a particular focus on potential roles for cellular plasticity in this response.