The role of cilia in the pathogenesis of cystic kidney disease

Fluid shear stress triggers cholesterol biosynthesis and uptake in inner medullary collecting duct cells, independently of nephrocystin-1 and nephrocystin-4

Renal epithelial cells are subjected to fluid shear stress of urine flow. Several cellular structures act as mechanosensors-the primary cilium, microvilli and cell adhesion complexes-that directly relay signals to the cytoskeleton to regulate various processes including cell differentiation and renal cell functions. Nephronophthisis (NPH) is an autosomal recessive tubulointerstitial nephropathy leading to end-stage kidney failure before adulthood. NPHP1 and NPHP4 are the major genes which code for proteins that form a complex at the transition zone of the primary cilium, a crucial region required for the maintenance of the ciliary composition integrity. These two proteins also interact with signaling components and proteins associated with the actin cytoskeleton at cell junctions. Due to their specific subcellular localization, we wondered whether NPHP1 and NPHP4 could ensure mechanosensory functions. Using a microfluidic set up, we showed that murine inner medullary collecting ductal cells invalidated for Nphp1 or Nphp4 are more responsive to immediate shear exposure with a fast calcium influx, and upon a prolonged shear condition, an inability to properly regulate cilium length and actin cytoskeleton remodeling. Following a transcriptomic study highlighting shear stress-induced gene expression changes, we showed that prolonged shear triggers both cholesterol biosynthesis pathway and uptake, processes that do not seem to involve neither NPHP1 nor NPHP4. To conclude, our study allowed us to determine a moderate role of NPHP1 and NPHP4 in flow sensation, and to highlight a new signaling pathway induced by shear stress, the cholesterol biosynthesis and uptake pathways, which would allow cells to cope with mechanical stress by strengthening their plasma membrane through the supply of cholesterol.

Cystic Diseases of the Kidneys: From Bench to Bedside

Exploration into the causes of hereditary renal cystic diseases demonstrates a deep-rooted connection with the proteomic components of the cellular organelle cilia. Cilia are essential to the signaling cascades, and their dysfunction has been tied to a range of renal cystic diseases initiating with studies on the oak ridge polycystic kidney (ORPK) mouse model. Here, we delve into renal cystic pathologies that have been tied with ciliary proteosome and highlight the genetics associated with each. The pathologies are grouped based on the mode of inheritance, where inherited causes that result in cystic kidney disease phenotypes include autosomal dominant and autosomal recessive polycystic kidney disease, nephronophthisis (Bardet-Biedl syndrome and Joubert Syndrome), and autosomal dominant tubulointerstitial kidney disease. Alternatively, phakomatoses-, also known as neurocutaneous syndromes, associated cystic kidney diseases include tuberous sclerosis (TS) and Von Hippel-Lindau (VHL) disease. Additionally, we group the pathologies by the mode of inheritance to discuss variations in recommendations for genetic testing for biological relatives of a diagnosed individual.

Inhibition of proliferation and migration of hepatocellular carcinoma by knockdown of KIF3A via NF-κB signal pathway.. [DOI: 10.21203/rs.3.rs-2421333/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Background The up-regulation of KIF3A possibly predicts the dismal prognostic outcome of hepatocellular carcinoma (HCC). The present work is focused on investigating KIF3A’s function in the growth and migration of HCC cells. Methods KIF3A expression and its role in predicting HCC prognosis were assessed using the TCGA and Genotype-Tissue Expression (GTEx) databases. KIF3A detection conditions in HCC patients were studied using an immunohistochemical panel. siKIF3A was created and then transfected into HepG2 HCC cells. Cell proliferation was examined with the use of the EDU and CCK8. Using the scratch wound healing assays, cell migration was assessed. RT-PCR and Western-blot (WB) assays were adopted for evaluating the expression of genes and proteins. Results KIF3A expression increased in HCC tissues as compared to matched non-carcinoma samples, and it was tightly associated with poor survival and risk factors (Ps < 0.05). KIF3A knockdown hindered the proliferation and migration of HCC cells (Ps < 0.05). KIF3A silencing reduced RelA (NF-κBp65) expression, thus, affecting the activity of HCC cells (Ps < 0.05). Conclusion In this study, the oncogene of hepatocellular carcinoma is KIF3A. Silencing KIF3A inhibited HCC cell growth and migration by suppressing the NF-κB signal pathway. KIF3A was identified as a potential new anti-HCC therapeutic target.

Organoid-on-a-chip model of human ARPKD reveals mechanosensing pathomechanisms for drug discovery

Organoids serve as a novel tool for disease modeling in three-dimensional multicellular contexts. Static organoids, however, lack the requisite biophysical microenvironment such as fluid flow, limiting their ability to faithfully recapitulate disease pathology. Here, we unite organoids with organ-on-a-chip technology to unravel disease pathology and develop therapies for autosomal recessive polycystic kidney disease. PKHD1-mutant organoids-on-a-chip are subjected to flow that induces clinically relevant phenotypes of distal nephron dilatation. Transcriptomics discover 229 signal pathways that are not identified by static models. Mechanosensing molecules, RAC1 and FOS, are identified as potential therapeutic targets and validated by patient kidney samples. On the basis of this insight, we tested two U.S. Food and Drug Administration-approved and one investigational new drugs that target RAC1 and FOS in our organoid-on-a-chip model, which suppressed cyst formation. Our observations highlight the vast potential of organoid-on-a-chip models to elucidate complex disease mechanisms for therapeutic testing and discovery.

Multiomic identification of factors associated with progression to cystic kidney disease in mice with nephron Ift88 disruption

Ift88 gene mutations cause primary cilia loss and polycystic kidney disease (PKD) in mice. Nephron intraflagellar transport protein 88 (Ift88) knockout (KO) at 2 mo postnatal does not affect renal histology at 4 mo postnatal and causes PKD only in males by 11 mo postnatal. To identify factors associated with PKD development, kidneys from 4-mo-old male and female control and Ift88 KO mice underwent transcriptomic, proteomic, Western blot, metabolomic, and lipidomic analyses. mRNAs involved in extracellular matrix (ECM) synthesis and degradation were selectively upregulated in male KO mice. Proteomic analysis was insufficiently sensitive to detect most ECM components, while Western blot analysis paradoxically revealed reduced fibronectin and collagen type I in male KO mice. Only male KO mice had upregulated mRNAs encoding fibrinogen subunits and receptors for vascular endothelial growth factor and platelet-derived growth factor; period 2, period 3, and nuclear receptor subfamily 1 group D member 1 clock mRNAs were selectively decreased in male KO mice. Proteomic, metabolomic, and lipidomic analyses detected a relative (vs. the same-sex control) decrease in factors involved in fatty acid β-oxidation in female KO mice, while increased or unchanged levels in male KO mice, including medium-chain acyl-CoA dehydrogenase, 3-hydroxybutyrate, and acylcarnitine. Three putative mRNA biomarkers of cystogenesis in male Ift88 KO mice (similar control levels between sexes and uniquely altered by KO in males) were identified, including high levels (fibrinogen α-chain and stromal cell-derived factor 2-like 1) and low levels (BTG3-associated nuclear protein) in male KO mice. These findings suggest that relative alterations in renal ECM metabolism, fatty acid β-oxidation, and other pathways precede cystogenesis in Ift88 KO mice. In addition, potential novel biomarkers of cystogenesis in Ift88 KO mice have been identified.NEW & NOTEWORTHY Male, but not female, mice with nephron intraflagellar transport protein 88 (Ift88) gene knockout (KO) develop polycystic kidneys by ∼1 yr postnatal. We performed multiomic analysis of precystic male and female Ift88 KO and control kidneys. Precystic male Ift88 KO mice exhibited differential alterations (vs. females) in mRNA, proteins, metabolites, and/or lipids associated with renal extracellular matrix metabolism, fatty acid β-oxidation, circadian rhythm, and other pathways. These findings suggest targets for evaluation in the pathogenesis of Ift88 KO polycystic kidneys.

Primary cilium in kidney development, function and disease

The primary cilium is a hair-like, microtubule-based organelle that is covered by the cell membrane and extends from the surface of most vertebrate cells. It detects and translates extracellular signals to direct various cellular signaling pathways to maintain homeostasis. It is mainly distributed in the proximal and distal tubules and collecting ducts in the kidney. Specific signaling transduction proteins localize to primary cilia. Defects in cilia structure and function lead to a class of diseases termed ciliopathies. The proper functioning of primary cilia is essential to kidney organogenesis and the maintenance of epithelial cell differentiation and proliferation. Persistent cilia dysfunction has a role in the early stages and progression of renal diseases, such as cystogenesis and acute tubular necrosis (ATN). In this review, we focus on the central role of cilia in kidney development and illustrate how defects in cilia are associated with renal disease progression.

Xenopus to the rescue: A model to validate and characterize candidate ciliopathy genes

Cilia are present on most vertebrate cells and play a central role in development, growth, and homeostasis. Thus, cilia dysfunction can manifest into an array of diseases, collectively termed ciliopathies, affecting millions of lives worldwide. Yet, our understanding of the gene regulatory networks that control cilia assembly and functions remain incomplete. With the advances in next-generation sequencing technologies, we can now rapidly predict pathogenic variants from hundreds of ciliopathy patients. While the pace of candidate gene discovery is exciting, most of these genes have never been previously implicated in cilia assembly or function. This makes assigning the disease causality difficult. This review discusses how Xenopus, a genetically tractable and high-throughput vertebrate model, has played a central role in identifying, validating, and characterizing candidate ciliopathy genes. The review is focused on multiciliated cells (MCCs) and diseases associated with MCC dysfunction. MCCs harbor multiple motile cilia on their apical surface to generate extracellular fluid flow inside the airway, the brain ventricles, and the oviduct. In Xenopus, these cells are external and present on the embryonic epidermal epithelia, facilitating candidate genes analysis in MCC development in vivo. The ability to introduce patient variants to study their effects on disease progression makes Xenopus a powerful model to improve our understanding of the underlying disease mechanisms and explain the patient phenotype.

Exploring the Spectrum of Kidney Ciliopathies

Ciliopathies are a group of multi-organ diseases caused by the disruption of the primary cilium. This event leads to a variety of kidney disorders, including nephronophthisis, renal cystic dysplasia, and renal cell carcinoma (RCC). Primary cilium contributes to the regulation of the cell cycle and protein homeostasis, that is, the balance between protein synthesis and degradation by acting on the ubiquitin-proteasome system, autophagy, and mTOR signaling. Many proteins are involved in renal ciliopathies. In particular, fibrocystin (PKHD1) is involved in autosomal recessive polycystic kidney disease (ARPKD), while polycystin-1 (PKD1) and polycystin-2 (PKD2) are implicated in autosomal dominant polycystic kidney disease (ADPKD). Moreover, primary cilia are associated with essential signaling pathways, such as Hedgehog, Wnt, and Platelet-Derived Growth Factor (PDGF). In this review, we focused on the ciliopathies associated with kidney diseases, exploring genes and signaling pathways associated with primary cilium and the potential role of cilia as therapeutic targets in renal disorders.

Primary Cilia and Calcium Signaling Interactions

The calcium ion (Ca2+) is a diverse secondary messenger with a near-ubiquitous role in a vast array of cellular processes. Cilia are present on nearly every cell type in either a motile or non-motile form; motile cilia generate fluid flow needed for a variety of biological processes, such as left-right body patterning during development, while non-motile cilia serve as the signaling powerhouses of the cell, with vital singling receptors localized to their ciliary membranes. Much of the research currently available on Ca2+-dependent cellular actions and primary cilia are tissue-specific processes. However, basic stimuli-sensing pathways, such as mechanosensation, chemosensation, and electrical sensation (electrosensation), are complex processes entangled in many intersecting pathways; an overview of proposed functions involving cilia and Ca2+ interplay will be briefly summarized here. Next, we will focus on summarizing the evidence for their interactions in basic cellular activities, including the cell cycle, cell polarity and migration, neuronal pattering, glucose-mediated insulin secretion, biliary regulation, and bone formation. Literature investigating the role of cilia and Ca2+-dependent processes at a single-cellular level appears to be scarce, though overlapping signaling pathways imply that cilia and Ca2+ interact with each other on this level in widespread and varied ways on a perpetual basis. Vastly different cellular functions across many different cell types depend on context-specific Ca2+ and cilia interactions to trigger the correct physiological responses, and abnormalities in these interactions, whether at the tissue or the single-cell level, can result in diseases known as ciliopathies; due to their clinical relevance, pathological alterations of cilia function and Ca2+ signaling will also be briefly touched upon throughout this review.

Epb41l5 interacts with Iqcb1 and regulates ciliary function in zebrafish embryos

Erythrocyte protein band 4.1 like 5 (EPB41L5) is an adaptor protein beneath the plasma membrane that functions to control epithelial morphogenesis. Here we report a previously uncharacterized role of EPB41L5 in controlling ciliary function. We found that EPB41L5 forms a complex with IQCB1 (previously known as NPHP5), a ciliopathy protein. Overexpression of EPB41L5 reduced IQCB1 localization at the ciliary base in cultured mammalian epithelial cells. Conversely, epb41l5 knockdown increased IQCB1 localization at the ciliary base. epb41l5-deficient zebrafish embryos or embryos expressing C-terminally modified forms of Epb41l5 developed cilia with reduced motility and exhibited left-right patterning defects, an outcome of abnormal ciliary function. We observed genetic synergy between epb41l5 and iqcb1. Moreover, EPB41L5 decreased IQCB1 interaction with CEP290, another ciliopathy protein and a component of the ciliary base and centrosome. Together, these observations suggest that EPB41L5 regulates the composition of the ciliary base and centrosome through IQCB1 and CEP290.

The Role of Wnt Signalling in Chronic Kidney Disease (CKD)

Chronic kidney disease (CKD) encompasses a group of diverse diseases that are associated with accumulating kidney damage and a decline in glomerular filtration rate (GFR). These conditions can be of an acquired or genetic nature and, in many cases, interactions between genetics and the environment also play a role in disease manifestation and severity. In this review, we focus on genetically inherited chronic kidney diseases and dissect the links between canonical and non-canonical Wnt signalling, and this umbrella of conditions that result in kidney damage. Most of the current evidence on the role of Wnt signalling in CKD is gathered from studies in polycystic kidney disease (PKD) and nephronophthisis (NPHP) and reveals the involvement of β-catenin. Nevertheless, recent findings have also linked planar cell polarity (PCP) signalling to CKD, with further studies being required to fully understand the links and molecular mechanisms.

The primary cilia in diabetic kidney disease: A tubulocentric view?

Diabetic kidney disease is growing exponentially. This review aims to discuss alternate therapeutic approaches beyond the glomerulocentric view and to consider a novel tubulocentric approach with focus on the primary cilia. Renin-angiotensin-aldosterone system blockade to decrease glomerular capillary pressure and prevent albuminuria has been the mainstay of treatment for diabetic and non-diabetic proteinuric kidney disease. Landmark clinical trials have also shown cardiorenal benefit with sodium-glucose linked co-transporter 2 inhibitors and glucagon-like peptide 1 receptor analogues in patients with type 2 diabetes. Effective renoprotective drugs seem to have a common mechanistic mode of reducing glomerular hyperfiltration/hypertension. In the tubules, primary cilia act as "antennae" to detect mechanosensory changes such as glomerular hyperfiltration and trgger intracellular signalling pathways. They are also implicated in obesity and metabolic disorders linked to diabetes. To conclude, primary cilia of the kidney tubules offer a novel therapeutic target and may complement the current glomerulocentric approaches.

Physiology, Development, and Disease Modeling in the Drosophila Excretory System

The insect excretory system contains two organ systems acting in concert: the Malpighian tubules and the hindgut perform essential roles in excretion and ionic and osmotic homeostasis. For over 350 years, these two organs have fascinated biologists as a model of organ structure and function. As part of a recent surge in interest, research on the Malpighian tubules and hindgut of Drosophila have uncovered important paradigms of organ physiology and development. Further, many human disease processes can be modeled in these organs. Here, focusing on discoveries in the past 10 years, we provide an overview of the anatomy and physiology of the Drosophila excretory system. We describe the major developmental events that build these organs during embryogenesis, remodel them during metamorphosis, and repair them following injury. Finally, we highlight the use of the Malpighian tubules and hindgut as accessible models of human disease biology. The Malpighian tubule is a particularly excellent model to study rapid fluid transport, neuroendocrine control of renal function, and modeling of numerous human renal conditions such as kidney stones, while the hindgut provides an outstanding model for processes such as the role of cell chirality in development, nonstem cell-based injury repair, cancer-promoting processes, and communication between the intestine and nervous system.

28 novel mutations identified from 33 Chinese patients with cilia-related kidney disorders

BACKGROUND

Cilia play an important role in cellular signaling pathways. Defective ciliary function causes a variety of disorders involve retina, skeleton, liver, kidney or others. Cilia-related kidney disorders are characterized by cystic renal disease, nephronophthisis and renal failure in general.

METHODS

In this study, we collected 33 families clinically suspected of cilia-related kidney disorders. Capture-based next-generation sequencing (NGS) of 88 related genes, Sanger sequencing, pedigree analysis and functional study were performed to analyze their genetic cause.

RESULTS

40 mutations in PKD1, PKD2, PKHD1, DYNC2H1 and TMEM67 genes were identified from 27 of 33 affected families. 70% (28/40) of the mutations were first found in patients. We reported a very early-onset autosomal dominant polycystic kidney disease (ADPKD) family caused by a novel heterozygous PKD1 mutation; another fetus with DYNC2H1 compound heterozygous missense mutations showed mainly kidney dysplasia instead of skeletal abnormalities; and a novel PKD1 mutation, c.12445-3C > G, was confirmed to cause two wrong splicing modes. As for previously reported mutations, such as PKD1, c.6395 T > G (p.F2132C) and c.6868G > T (p.D2290Y), we had new and different findings.

CONCLUSION

The findings provided new references for genotype-phenotype analyses and broadened the mutation spectrum of detected genes, which were significantly valuable for prenatal diagnosis and genetic counseling.

Chronic kidney disease in the neonate: etiologies, management, and outcomes

Neonatal chronic kidney disease (CKD) occurs with an estimated incidence of 1 in 10,000 live births, whereas the incidence of neonatal end-stage renal disease (ESRD) is about 7.1 per million age-related population. The most frequent etiologies are renal hypoplasia/dysplasia, posterior urethral valves, and other congenital anomalies of the kidney and urinary tract. Other etiologies include polycystic kidney disease, cortical necrosis, and renal vascular thrombosis. Management of CKD focuses primarily on replacing renal functions such as erythropoietin, 1,25-hydroxylation of vitamin D, electrolyte homeostasis/excretion, and, in ESRD, waste product removal. Nutrition and growth monitoring are of utmost importance, with the majority of ESRD infants requiring gastrostomy tube for nutrition. Outcomes of neonates (<31 days) started on dialysis continue to improve, with large cohort studies showing 2-3-year survival rates of 79-81%. As in other neonatal disciplines, the gestational age and size limits for safe provision of dialysis continue to decrease.

Autosomal Dominant Polycystic Kidney Disease: A Path Forward

Autosomal dominant polycystic kidney disease (ADPKD) is the commonest inherited cause of renal failure in adults, and is due to loss-of-function mutations in either the PKD1 or PKD2 genes, which encode polycystin-1 and polycystin-2, respectively. These proteins have an essential role in maintaining the geometric structure of the distal collecting duct in the kidney in adult life, and their dysfunction predisposes to renal cyst formation. The typical renal phenotype of ADPKD is the insidious development of hundreds of renal cysts, which form in childhood and grow progressively through life, causing end-stage kidney failure in the fifth decade in about half affected by the mutation. Over the past 2 decades, major advances in genetics and disease pathogenesis have led to well-conducted randomized controlled trials, and observational studies that have resulted in an accumulation of evidence-based data, and raise hope that the lifetime risk of kidney failure due to ADPKD will be progressively curtailed during this century. This review will provide a contemporary summary of the current state of the field in disease pathogenesis and therapeutics, and also briefly highlights the importance of clinical practice guidelines, patient perspectives, patient-reported outcomes, uniform trial reporting, and health-economics in ADPKD.

Cilia in autophagy and cancer

Cancer cells are distinguished from normal cells by increased proliferation and metabolism, loss of polarity control, and the potential to invade other tissues of the body. As hubs of signaling transduction, primary cilia have been linked to diverse developmental and degenerative disorders. Interestingly, loss of cilia has been observed in multiple malignant tumors, suggesting a potential suppressive role of cilia in cancer development. More recently, emerging studies began to unveil the bidirectional interaction of cilia and autophagy, a basic cellular clearance and recycling mechanism to regulate cell homeostasis. Here, we summarize the interplay between cilia and autophagy and discuss the roles of cilia in both autophagy and cancer.

Ciliary/Flagellar Protein Ubiquitination

Cilia/flagella are conserved eukaryotic organelles that play an important role in the control of cell motility and detection of environmental cues. However, the molecular mechanisms underlying ciliary/flagellar assembly, maintenance, disassembly, and signal transduction are not yet completely understood. Recent studies demonstrated that post-translational modifications (PTMs) such as phosphorylation, methylation, glutamylation, and ubiquitination are involved in these processes. In this mini review, we present a summary of research progress in ciliary/flagellar protein ubiquitination, including the ubiquitin conjugation system identified by proteomics as well as the role of ciliary/flagellar protein ubiquitination in flagellar disassembly, motility, and signal transduction. Moreover, we described putative further research directions in the study of ciliary/flagellar protein ubiquitination.