Proximal Tubule Differentiation Research Articles

Transcriptomic, epigenomic, and spatial metabolomic cell profiling redefines regional human kidney anatomy

A large-scale multimodal atlas that includes major kidney regions is lacking. Here, we employed simultaneous high-throughput single-cell ATAC/RNA sequencing (SHARE-seq) and spatially resolved metabolomics to profile 54 human samples from distinct kidney anatomical regions. We generated transcriptomes of 446,267 cells and chromatin accessibility profiles of 401,875 cells and developed a package to analyze 408,218 spatially resolved metabolomes. We find that the same cell type, including thin limb, thick ascending limb loop of Henle and principal cells, display distinct transcriptomic, chromatin accessibility, and metabolomic signatures, depending on anatomic location. Surveying metabolism-associated gene profiles revealed non-overlapping metabolic signatures between nephron segments and dysregulated lipid metabolism in diseased proximal tubule (PT) cells. Integrating multimodal omics with clinical data identified PLEKHA1 as a disease marker, and its invitro knockdown increased gene expression in PT differentiation, suggesting possible pathogenic roles. This study highlights previously underrepresented cellular heterogeneity underlying the human kidney anatomy.

Studies with Human-Induced Pluripotent Stem Cells Reveal That CTNS Mutations Can Alter Renal Proximal Tubule Differentiation

Cystinosis is an autosomal recessive disease resulting from mutations in ctns, which encodes for cystinosin, a proton-coupled cystine transporter that exports cystine from lysosomes. The major clinical form, infantile cystinosis, is associated with renal failure due to the malfunctioning of the renal proximal tubule (RPT). To examine the hypothesis that the malfunctioning of the cystinotic RPT arises from defective differentiation, human-induced pluripotent stem cells (hiPSCs) were generated from human dermal fibroblasts from an individual with infantile cystinosis, as well as a normal individual. The results indicate that both the cystinotic and normal hiPSCs are pluripotent and can form embryoid bodies (EBs) with the three primordial germ layers. When the normal hiPSCs were subjected to a differentiation regime that induces RPT formation, organoids containing tubules with lumens emerged that expressed distinctive RPT proteins, including villin, the Na+/H+ Exchanger (NHE) isoform 3 (NHE3), and the NHE Regulatory Factor 1 (NHERF1). The formation of tubules with lumens was less pronounced in organoids derived from cystinotic hiPSCs, although the organoids expressed villin, NHE3, and NHERF1. These observations can be attributed to an impairment in differentiation and/or by other defects which cause cystinotic RPTs to have an increased propensity to undergo apoptosis or other types of programmed cell death.

Elucidating the Proximal Tubule HNF4A Gene Regulatory Network in Human Kidney Organoids.

HNF4 genes promote proximal tubule differentiation in mice, but their function in human nephrogenesis is not fully defined. This study uses human pluripotent stem cell (PSC)-derived kidney organoids as a model to investigate HNF4A and HNF4G functions. The loss of HNF4A , but not HNF4G , impaired reabsorption-related molecule expression and microvilli formation in human proximal tubules. Cleavage under targets and release using nuclease (CUT&RUN) sequencing and CRISPR-mediated transcriptional activation (CRISPRa) further confirm that HNF4A directly regulates its target genes. Human kidney organoids provide a good model for studying transcriptional regulation in human kidney development. The proximal tubule plays a major role in electrolyte homeostasis. Previous studies have shown that HNF4A regulates reabsorption-related genes and promotes proximal tubule differentiation during murine kidney development. However, the functions and gene regulatory mechanisms of HNF4 family genes in human nephrogenesis have not yet been investigated. We generated HNF4A -knock out (KO), HNF4G -KO, and HNF4A/4G -double KO human pluripotent stem cell lines, differentiated each into kidney organoids, and used immunofluorescence analysis, electron microscopy, and RNA-seq to analyze them. We probed HNF4A-binding sites genome-wide by cleavage under targets and release using nuclease sequencing in both human adult kidneys and kidney organoid-derived proximal tubular cells. Clustered Regularly Interspaced Short Palindromic Repeats-mediated transcriptional activation validated HNF4A and HNF4G function in proximal tubules during kidney organoid differentiation. Organoids lacking HNF4A , but not HNF4G , showed reduced expression of transport-related, endocytosis-related, and brush border-related genes, as well as disorganized brush border structure in the apical lumen of the organoid proximal tubule. Cleavage under targets and release using nuclease revealed that HNF4A primarily bound promoters and enhancers of genes that were downregulated in HNF4A -KO, suggesting direct regulation. Induced expression of HNF4A or HNF4G by CRISPR-mediated transcriptional activation drove increased expression of selected target genes during kidney organoid differentiation. This study reveals regulatory mechanisms of HNF4A and HNF4G during human proximal tubule differentiation. The experimental strategy can be applied more broadly to investigate transcriptional regulation in human kidney development.

Defective Cystinosin, Aberrant Autophagy-Endolysosome Pathways, and Storage Disease: Towards Assembling the Puzzle.

Epithelial cells that form the kidney proximal tubule (PT) rely on an intertwined ecosystem of vesicular membrane trafficking pathways to ensure the reabsorption of essential nutrients—a key requisite for homeostasis. The endolysosome stands at the crossroads of this sophisticated network, internalizing molecules through endocytosis, sorting receptors and nutrient transporters, maintaining cellular quality control via autophagy, and toggling the balance between PT differentiation and cell proliferation. Dysregulation of such endolysosome-guided trafficking pathways might thus lead to a generalized dysfunction of PT cells, often causing chronic kidney disease and life-threatening complications. In this review, we highlight the biological functions of endolysosome-residing proteins from the perspectives of understanding—and potentially reversing—the pathophysiology of rare inherited diseases affecting the kidney PT. Using cystinosis as a paradigm of endolysosome disease causing PT dysfunction, we discuss how the endolysosome governs the homeostasis of specialized epithelial cells. This review also provides a critical analysis of the molecular mechanisms through which defects in autophagy pathways can contribute to PT dysfunction, and proposes potential interventions for affected tissues. These insights might ultimately accelerate the discovery and development of new therapeutics, not only for cystinosis, but also for other currently intractable endolysosome-related diseases, eventually transforming our ability to regulate homeostasis and health.

PBRM1 loss in kidney cancer unbalances the proximal tubule master transcription factor hub to repress proximal tubule differentiation

SUMMARYPBRM1, a subunit of the PBAF coactivator complex that transcription factors use to activate target genes, is genetically inactivated in almost all clear cell renal cell cancers (RCCs). Using unbiased proteomic analyses, we find that PAX8, a master transcription factor driver of proximal tubule epithelial fates, recruits PBRM1/PBAF. Reverse analyses of the PAX8 interactome confirm recruitment specifically of PBRM1/PBAF and not functionally similar BAF. More conspicuous in the PAX8 hub in RCC cells, however, are corepressors, which functionally oppose coactivators. Accordingly, key PAX8 target genes are repressed in RCC versus normal kidneys, with the loss of histone lysine-27 acetylation, but intact lysine-4 trimethylation, activation marks. Re-introduction of PBRM1, or depletion of opposing corepressors using siRNA or drugs, redress coregulator imbalance and release RCC cells to terminal epithelial fates. These mechanisms thus explain RCC resemblance to the proximal tubule lineage but with suppression of the late-epithelial program that normally terminates lineage-precursor proliferation.

Aligned Silk Sponge Fabrication and Perfusion Culture for Scalable Proximal Tubule Tissue Engineering.

Chronic kidney disease and kidney failure are on the rise globally, yet there has not been a corresponding improvement in available therapies. A key challenge in a biological approach to developing kidney tissue is to identify scaffolding materials that support cell growth both in vitro and in vivo to facilitate translational goals. Scaffolds composed of silk fibroin protein possess the biocompatibility, mechanical robustness, and stability required for tissue engineering. Here, we use a silk sponge system to support kidney cells in a perfused bioreactor system. Silk fibroin protein underwent directional freezing to form parallel porous structures that mimic the native kidney structure of aligned tubules and are able to support more cells than nonaligned silk sponges. Adult immortalized renal proximal tubule epithelial cells were seeded into the sponges and cultured under static conditions for 1 week, then grown statically or with perfusion with culture media flowing through the sponge to enhance cell alignment and maturation. The sponges were imaged with confocal and scanning electron microscopies to analyze and quantify cell attachment, alignment, and expression of proteins important to proximal tubule differentiation and function. The perfused tissue constructs showed higher number of cells that are more evenly distributed through the construct and increased gene expression of several key markers of proximal tubule epithelial cell function compared to sponges grown under static conditions. These perfused tissue constructs represent a step toward a scalable approach to engineering proximal tubule structures with the potential to be used as in vitro models or as in vivo implantable tissues to supplement or replace impaired kidney function.

Transcriptional Programs Driving Shear Stress-Induced Differentiation of Kidney Proximal Tubule Cells in Culture.

Cultured cell models are an essential complement to dissecting kidney proximal tubule (PT) function in health and disease but do not fully recapitulate key features of this nephron segment. We recently determined that culture of opossum kidney (OK) cells under continuous orbital shear stress (OSS) significantly augments their morphological and functional resemblance to PTs in vivo. Here we used RNASeq to identify temporal transcriptional changes upon cell culture under static or shear stress conditions. Comparison of gene expression in cells cultured under static or OSS conditions with a database of rat nephron segment gene expression confirms that OK cells cultured under OSS are more similar to the PT in vivo compared with cells maintained under static conditions. Both improved oxygenation and mechanosensitive stimuli contribute to the enhanced differentiation in these cells, and we identified temporal changes in gene expression of known mechanosensitive targets. We observed changes in mRNA and protein levels of membrane trafficking components that may contribute to the enhanced endocytic capacity of cells cultured under OSS. Our data reveal pathways that may be critical for PT differentiation in vivo and validate the utility of this improved cell culture model as a tool to study PT function.

Spatio-temporal patterning of different connexins in developing and postnatal human kidneys and in nephrotic syndrome of the Finnish type (CNF)

Connexins (Cxs) are membrane-spanning proteins which enable flow of information important for kidney homeostasis. Changes in their spatiotemporal patterning characterize blood vessel abnormalities and chronic kidney diseases (CKD). We analysed spatiotemporal expression of Cx37, Cx40, Cx43 and Cx45 in nephron and glomerular cells of developing, postnatal kidneys, and nephrotic syndrome of the Finnish type (CNF) by using immunohistochemistry, statistical methods and electron microscopy. During kidney development, strong Cx45 expression in proximal tubules and decreasing expression in glomeruli was observed. In developing distal nephron, Cx37 and Cx40 showed moderate-to-strong expression, while weak Cx43 expression gradually increased. Cx45/Cx40 co-localized in mesangial and granular cells. Cx43 /Cx45 co-localized in podocytes, mesangial and parietal epithelial cells, and with podocyte markers (synaptopodin, nephrin). Different Cxs co-expressed with endothelial (CD31) and VSMC (α –SMA) markers in vascular walls. Peak signalling of Cx37, Cx43 and Cx40 accompanied kidney nephrogenesis, while strongest Cx45 signalling paralleled nephron maturation. Spatiotemporal Cxs patterning indicate participation of Cx45 in differentiation of proximal tubules, and Cx43, Cx37 and Cx40 in distal tubules differentiation. CNF characterized disorganized Cx45 expression in proximal tubules, increased Cx43 expression in distal tubules and overall elevation of Cx40 and Cx37, while Cx40 co-localized with increased number of interstitial myofibroblasts.

Renal tubular dysgenesis: An unusual cause of anhydramnios

We present case of renal tubular dysgenesis, a rare fetal disorder of abnormal renal tubule development which causes anhydramnios and neonatal death. Kidneys are of normal size, with non-specific, subtle, ultrasound abnormalities, but show absence or incomplete differentiation of proximal tubules due to abnormalities of the renin angiotensin system. We highlight the need for post-mortem for accurate diagnosis, targeted genetic testing, genetic counselling and subsequent antenatal screening for this usually autosomal recessive condition.

Expression of VHL Causes Three-Dimensional Morphological Changes in Renal Cells Indicative of Proximal Tubule Differentiation

Mutations in the von Hippel-Lindau (VHL) tumor suppressor gene are responsible for the VHL hereditary cancer syndrome, and are associated with the majority of clear cell renal cell carcinomas. In this study, scanning electron microscopy of VHL-negative renal carcinoma cells was utilized to examine the effects of VHL re-expression on the morphology of these cells. Significant differences were observed between the morphology of VHL-negative control cells and those with reintroduced VHL, with VHL expression mediating an apical surface that mounded upward, as opposed to the flat surfaces seen with VHL-negative cells. In long term cultures, rounded VHL-expressing cells grew in clusters on top the monolayer, and microvilli were observed on the apical face of these cells, in a manner suggestive of proximal tubule differentiation. In contrast, VHL-negative cells remained flat and did not develop microvilli in long-term cultures. Since VHL is a key member of an ubiquitin E3 ligase complex whose best known target is hypoxia-inducible factor alpha (HIF-α), we looked at the effects of HIF-α expression on cell morphology. Knockdown of HIF-2α in cells that only express this isoform had no effect on the morphology of the cells. These results indicate that VHL expression directs three dimensional morphological changes in renal cells indicative of differentiation, and while dysregulation of HIF-α may be necessary for tumorigenesis following VHL loss, it is not the major determinant of these VHL-mediated morphological changes.

Spectrum of mutations in the renin-angiotensin system genes in autosomal recessive renal tubular dysgenesis

Autosomal recessive renal tubular dysgenesis (RTD) is a severe disorder of renal tubular development characterized by early onset and persistent fetal anuria leading to oligohydramnios and the Potter sequence, associated with skull ossification defects. Early death occurs in most cases from anuria, pulmonary hypoplasia, and refractory arterial hypotension. The disease is linked to mutations in the genes encoding several components of the renin-angiotensin system (RAS): AGT (angiotensinogen), REN (renin), ACE (angiotensin-converting enzyme), and AGTR1 (angiotensin II receptor type 1). Here, we review the series of 54 distinct mutations identified in 48 unrelated families. Most of them are novel and ACE mutations are the most frequent, observed in two-thirds of families (64.6%). The severity of the clinical course was similar whatever the mutated gene, which underlines the importance of a functional RAS in the maintenance of blood pressure and renal blood flow during the life of a human fetus. Renal hypoperfusion, whether genetic or secondary to a variety of diseases, precludes the normal development/ differentiation of proximal tubules. The identification of the disease on the basis of precise clinical and histological analyses and the characterization of the genetic defects allow genetic counseling and early prenatal diagnosis.

Organic anion and cation transporter expression and function during embryonic kidney development and in organ culture models

Organic anion and cation transporters (OATs, OCTs, and OCTNs) mediate the proximal tubular secretion of numerous clinically important compounds, including various commonly prescribed pharmaceuticals. Here, we report determination of the ontogeny of these transporters and of NaP(i)2 and SGLT1, using quantitative polymerase chain reaction (QPCR) to determine expression levels of transporter genes in rat embryonic kidneys on each day of gestation from embryonic day (ed) 13 to ed18, in cultures of induced and uninduced metanephric mesenchyme (MM), and on each day of 1 week of whole embryonic kidney (WEK) culture. We also examined ontogeny of Oat1 protein expression in rat embryonic kidney by immunohistochemistry. Finally, we used uptake of fluorescein (FL) as a novel in vitro functional assay of OAT expression in WEK and MM. Developmental induction of OAT and OCT genes does not occur uniformly: some genes are induced early (e.g., Oat1 and Oat3, potential early markers of proximal tubulogenesis), and others after kidney development is relatively advanced (e.g., Oct1, a potential marker of terminal differentiation). The ontogeny of transporter genes in WEK and MM is similar to that observed in vivo, indicating that these organ culture systems may represent convenient in vitro models to study the developmental induction of OATs, OCTs, and OCTNs. Functional transport was evidenced by accumulation of FL in the developing tubule in WEK and MM organ cultures. Our findings on the renal ontogeny of OATs and OCTs could carry implications both for the development of more rational therapeutics for premature infants, as well as for our understanding of proximal tubule differentiation.

Cystic Nephroma: A Histologic and Immunohistochemical Study of 10 Cases

Cystic nephroma is a rare and controversial benign multicystic renal tumor. While the clinical, radiologic, and histologic features of cystic nephroma are well described, the immunohistochemical features are not. The role of immunohistochemistry in the differential diagnosis, which includes multicystic renal cell carcinoma, is also unknown. To define the histologic and immunohistochemical features of cystic nephroma. Ten cases of cystic nephroma diagnosed at 2 institutions during a period of 10 years were stained with an immunohistochemical panel consisting of 20 immunostains. Median age at diagnosis was 61 years, with a range from 31 to 79 years. The female-to-male ratio was 9:1. Grossly, the tumors were multicystic masses without solid nodules. Histologic features included cysts lined by flat, cuboidal, or hobnail epithelium and septa variably lined by fibrous (10/10 cases) and/or ovarian-like (7/10 cases) stroma. Corpus albicans-like acellular hyalinized structures were noted in the septa in 9 of 10 cases. The cyst epithelium showed consistent positivity for distal tubule/collecting duct markers (cytokeratin 19, cytokeratin AE1/AE3, epithelial membrane antigen) and variable positivity for proximal tubule markers (alpha1-antitrypsin, lysozyme, CD15, CD10). The ovarian-like stroma (present in 7/10 cases) stained positively for progesterone receptors (6/7 cases) and estrogen receptors (4/7 cases). Our immunohistochemical findings confirm a previous report of both distal tubule/collecting duct and proximal tubule differentiation in cystic nephroma. Stromal estrogen and/or progesterone receptor positivity in the majority of cases of cystic nephroma is a novel finding.

Developmentally regulated expression of organic ion transporters NKT (OAT1), OCT1, NLT (OAT2), and Roct.

Several xenobiotic (organic cation and anion) transporters have recently been identified, although their endogenous substrates, if such exist, remain unknown. When we initially identified NKT, also known as OAT1, the first member of the organic anion transporter (OAT) family (Lopez-Nieto CE, You G, Bush KT, Barros EJ, Beier DR, and Nigam SK. J Biol Chem 272: 6471-6478, 1997), we noted its expression in the embryonic kidney. We have now demonstrated its transporter function and more fully examined the spatiotemporal expression patterns of representative organic ion transporters, [NKT (OAT1), Roct, OCT1, and NLT, also known as OAT2] during murine development. In the kidney, NKT (OAT1), OCT1, and Roct transcripts appeared at midgestation, coinciding with proximal tubule differentiation, and gradually increased during nephron maturation. A similar pattern was observed for NLT (OAT2) in the liver and kidney, although, in the kidney, NLT (OAT2) transcription did not increase as dramatically. The roughly cotemporal expression of these related transporters in the developing proximal tubule may indicate common transcriptional regulation. Expression during embryogenesis in extrarenal sites could suggest a role in the formation and maintenance of nonrenal tissues. Importantly, all four genes were expressed in unexpected places during nonrenal organogenesis: Roct in the fetal liver (temporally coinciding with the onset of hematopoiesis) and neural tissue; NKT (OAT1) in the fetal brain; OCT1 in the ascending aorta and atrium; and NLT (OAT2) in the fetal lung, intestine, skin, and developing bone. Because these gene products mediate the transport of a broad range of metabolites and toxins, it seems likely that, apart from their known functions, these transporters play a role in transport of organic molecules, perhaps including those with morphogenetic activity. These genes could also play important developmental roles independent of transport function.

Syntaxin 3 and Munc-18-2 in epithelial cells during kidney development

Differentiation of epithelial cells involves the assembly of polarized membrane transport machineries necessary for the generation and maintenance of the apical and basolateral membrane domains characteristic of this cell type. We have analyzed the expression patterns of vesicle-docking proteins of the syntaxin family in mouse kidney, focusing on syntaxin 3 and its interaction partner, the Sec1-related Munc-18-2. Expression patterns were studied by in situ hybridization and immunocytochemistry and the complex formation of syntaxin 3 and Munc-18-2 by coimmunoprecipitation and Western blotting. We have previously shown by in situ hybridization that Munc-18-2 is present in the proximal tubules and collecting ducts of embryonic day 17 mouse kidney. We compared this with the expression patterns of syntaxin 1A, 2, 3, 4, and 5, and found that syntaxin 3 was enriched in the same epithelial structures in which Munc-18-2 was abundant. By immunocytochemistry, the two proteins colocalized at the apical plasma membrane of proximal tubule and collecting duct epithelial cells, and they were shown to form a physical complex in the kidney. The expression of both proteins was up-regulated during kidney development. The most prominent changes in expression levels coincided with the differentiation of proximal tubules, suggesting a role in the generation of the highly active reabsorption machinery characterizing this segment of the nephron. The results show that Munc-18-2 and syntaxin 3 form a complex in vivo and suggest that they participate in epithelial cell differentiation and targeted vesicle transport processes in the developing kidney.

Renale tubul�re Dysgenesie mit fetaler Nierenvenenthrombose

Renal tubular dysgenesis is a rarely recognized condition characterized by oligohydramnios, Potter's sequence and congenital anuria leading to stillbirth or neonatal death from respiratory failure. It is thought to be inherited in an autosomal recessive manner. Definitive diagnosis is based on renal histology, revealing the lack of proximal tubule differentiation. Two additional cases of affected sibs in a family with parental consanguinity are reported. Lectin and immunohistochemical studies confirmed structural and functional immaturity of the proximal tubule. Further findings include bilateral renal vein thrombosis. The clinical and morphological parameters defining this disorder and the possible mechanisms of pathogenesis are discussed.

Variation in the electrical properties of cultured human proximal tubule cells

Monolayers of human proximal tubule (HPT) cells, when grown on permeable supports and mounted in Ussing chambers, spontaneously display a transepithelial potential difference (PD), short-circuit current (Isc), and transepithelial specific resistance (RT). These electrical parameters were used to determine the degree of heterogeneity among independent isolates of human proximal tubule cell cultures. Seventeen independent isolates of cells were assessed, totaling 260 individual determinations of spontaneous electrical properties. On average, these cell monolayers displayed an apical-negative PD of 1.5 +/- 0.1 mV, an Isc of 2.7 +/- 0.2 microA/cm2, and an RT of 480 +/- 19 ohms x cm2. Each independent cell isolate, however, displayed electrical values within a narrow range, in some cases allowing isolates to be distinguished from one another. The individual isolates were also assessed for Na-coupled glucose transport, Na+,K(+)-ATPase activity, cAMP stimulation by parathyroid hormone (PTH), forskolin stimulation of Isc, and ouabain inhibition. With the exception of a strong correlation between Na+,K(+)-ATPase activity and Isc, these parameters, in contrast to electrical properties, were found to be consistent and did not reveal distinctions among the isolates. HPT cell cultures seem to consistently retain important features of proximal tubule differentiation while maintaining the variability, as demonstrated by electrical properties, that might be expected of cells isolated from a random population.

Renal tubular dysgenesis and very large cranial fontanels in a family with acrocephalosyndactyly S. C. type

We describe the first case of renal tubular dysgenesis in a newborn female who survived 15 days. The immunohistochemical and lectin binding studies confirmed the lack of proximal tubule differentiation. Electron microscopy showed undifferentiated tubular epithelium. Widely patent cranial fontanels were present in the proposita. The father and sister showed acrocephalosyndactyly Saethre-Chotzen type. The parents were not related and there was no familial history of renal pathology.