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Apolipoprotein L1 (APOL1)-miR193a axis has been reported to play a role in the maintenance of podocyte homeostasis. In the present study, we analyzed transcription factors relevant to miR193a in human podocytes and their effects on podocytes’ molecular phenotype. The motif scan of the miR193a gene provided information about transcription factors, i...
Citations
... In vitro studies suggest that miR-193a binds to WT-1 mRNA, preventing its expression. Molecular dynamic simulations showed an interaction between miR-193a and other transcription factors like apolipoprotein 1 (APOL1), vitamin D receptor-retinoid X receptor (VDR-RXR) heterodimer, Yin Yang (YY) 1, and sex-determining region Y-Box2 (Sox2) [49]. Elevated miR-193a is directly associated with FSGS and crescentic glomerulonephritis in animal models. ...
... The role of miR-193a in promoting PEC-to-podocyte transdifferentiation in human glomerular diseases is unknown, and the speculations are discussed in detail elsewhere [6]. The effects of miR-193a on various podocyte-relevant molecules and pathways are shown in Figure 2. Effects of miR-193a on target messenger RNAs and its impact on podocytes [7,49,53,54]; miR-193a inhibits APOL1G0 [49,55,56]; miR-193a downregulates WT-1 [54] and VDR [49,57]. Attenuation of WT1 results in the downregulation of the expression of podocyte proteins (nephrin and CD2AP), which form adherens junction complexes and decreased expression of VDR, resulting in compromised heterodimerization of VDR with RXR [49] and activation of the RAAS [57]; RAAS blockers such as losartan increase VDR [57]. ...
... The role of miR-193a in promoting PEC-to-podocyte transdifferentiation in human glomerular diseases is unknown, and the speculations are discussed in detail elsewhere [6]. The effects of miR-193a on various podocyte-relevant molecules and pathways are shown in Figure 2. Effects of miR-193a on target messenger RNAs and its impact on podocytes [7,49,53,54]; miR-193a inhibits APOL1G0 [49,55,56]; miR-193a downregulates WT-1 [54] and VDR [49,57]. Attenuation of WT1 results in the downregulation of the expression of podocyte proteins (nephrin and CD2AP), which form adherens junction complexes and decreased expression of VDR, resulting in compromised heterodimerization of VDR with RXR [49] and activation of the RAAS [57]; RAAS blockers such as losartan increase VDR [57]. ...
MicroRNAs (miRNAs) are noncoding small RNAs that regulate the protein expression of coding messenger RNAs. They are used as biomarkers to aid in diagnosing, prognosticating, and surveillance of diseases, especially solid cancers. MiR-193a was shown to be directly pathogenic in an experimental mouse model of focal segmental glomerulosclerosis (FSGS) during the last decade. Its specific binding and downregulation of Wilm’s tumor-1 (WT-1), a transcription factor regulating podocyte phenotype, is documented. Also, miR-193a is a regulator switch causing the transdifferentiation of glomerular parietal epithelial cells to a podocyte phenotype in in vitro study. Interaction between miR-193a and apolipoprotein 1 (APOL1) mRNA in glomeruli (filtration units of kidneys) is potentially involved in the pathogenesis of common glomerular diseases. Since the last decade, there has been an increasing interest in the role of miR-193a in glomerular diseases, including diabetic nephropathy and membranous nephropathy, besides FSGS. Considering the lack of biomarkers to manage FSGS and diabetic nephropathy clinically, it is worthwhile to invest in evaluating miR-193a in the pathogenesis of these diseases. What causes the upregulation of miR-193a in FSGS and how the mechanism is different in different glomerular disorders still need to be elucidated. This narrative review highlights the pathogenic mechanisms of miR-193a elevation in various glomerular diseases and its potential use in clinical management.
... Podocyte miRNAs have been studied in primary podocytopathy, 35 and in the context of APOL1 variants. Several groups have investigated the role of miR-193a, [36][37][38][39] for which we have observed higher expression in differentiated podocytes compared to undifferentiated J o u r n a l P r e -p r o o f podocytes. APOL1 is a predicted target gene for both miR-629-3p and miR-1285-3p, according to the TargetScanHuman 8.0 application. ...
Introduction
The mechanisms in podocytes which mediate the pathologic effects of the APOL1 high-risk variants remain incompletely understood, although various molecular and cellular mechanisms have been proposed. We previously established conditionally immortalized human urine-derived podocyte-like cell lines (HUPEC) to investigate APOL1 high-risk variant induced podocytopathy.
Methods
We conducted comprehensive transcriptomic analysis, including messenger RNA (mRNA), microRNA (miRNA) and transfer RNA fragments (tRFs), to characterize the transcriptional profiles in undifferentiated and differentiated HUPEC with APOL1 high-risk (G1/G2, two cell lines) and APOL1 low-risk (G0/G0, two cell lines) genotypes. We re-analyzed single-cell RNA-seq data from urinary podocytes from focal segmental glomerulosclerosis (FSGS) subjects to characterize the effect of APOL1 genotypes on podocyte transcriptomes.
Results
Differential expression analysis showed that the ribosomal pathway was one of the top enriched pathways, suggesting that altered function of the translation initiation machinery may contribute to APOL1 variant-induced podocyte injury. Expression of genes related to the elongation initiation factor 2 (EIF2) pathway were also enriched in the APOL1 high-risk urinary podocytes from single-cell RNA-seq, supporting a prior report on the role of this pathway in APOL1-associated cell injury. Expression of microRNA and transfer RNA fragments were analyzed, and the profile of small RNAs differed by both differentiation status and APOL1 genotype.
Conclusion
We have profiled the transcriptomic landscape of human podocytes, including mRNA, miRNA, and tRF, in order to characterize the effects of differentiation and of different APOL1 genotypes. The candidate pathways, miRNAs and tRFs described here expand understanding of APOL1-associated podocytopathies.
... Both glomerular parietal epithelial cells (PECs) and podocytes Frontiers in Physiology frontiersin.org 03 develop from the same mesenchymal cells during development (Jha et al., 2020). Moreover, the expression of miR-193a-5p affects whether cells take on the phenotype of PECs or podocytes. ...
MicroRNAs (miRNAs) are endogenous, small, non-coding RNA molecules that act as epigenetic modifiers to regulate the protein levels of target messenger RNAs without altering their genetic sequences. The highly complex role of miRNAs in the epigenetics of lupus nephritis (LN) is increasingly being recognized. DNA methylation and histone modifications are focal points of epigenetic research. miRNAs play a critical role in renal development and physiology, and dysregulation may result in abnormal renal cell proliferation, inflammation, and fibrosis of the kidneys in LN. However, epigenetic and miRNA-mediated regulation are not mutually exclusive. Further research has established a link between miRNA expression and epigenetic regulation in various disorders, including LN. This review summarizes the most recent evidence regarding the interaction between miRNAs and epigenetics in LN and highlights potential therapeutic and diagnostic targets.
... Indeed, we observed a complete rescue of the MBM suggesting a role of YY1 in the differentiation of podocytes. That YY1 might play an important role in the transition of undifferentiated into differentiated podocytes was nicely shown by Jha and colleagues [66]. Furthermore, it was shown that the expression of YY1 ameliorates podocyte damage in diabetic nephropathy (DN) [67]. ...
Background/aims:
Podocyte differentiation is essential for proper blood filtration in the kidney. It is well known that transcription factors play an essential role to maintain the differentiation of podocytes. The present study is focused on the basic helix-loop-helix (bHLH) transcription factor Tcf21 (Pod1) which is essential for the development of podocytes in vivo. Since parietal epithelial cells (PECs) are still under debate to be progenitor cells which can differentiate into podocytes, we wanted to find out whether the expression of Tcf21 induces a transition of PECs into podocytes.
Methods:
We transfected PECs with Tcf21-GFP and analyzed the expression of PEC- and podocyte-specific markers. Furthermore, we performed ChIP-Seq analysis to identify new putative interaction partners and target genes of Tcf21.
Results:
By gene arrays analysis, we found that podocytes express high levels of Tcf21 in vivo in contrast to cultured podocytes and parietal epithelial cells (PECs) in vitro. After the expression of Tcf21 in PECs, we observed a downregulation of specific PEC markers like caveolin‑1, β-catenin and Pax2. Additionally, we found that the upregulation of Tcf21 induced multi-lobulation of cell nuclei, budding and a formation of micronuclei (MBM). Furthermore, a high number of PECs showed a tetraploid set of chromosomes. By qRT-PCR and Western blot analysis, we revealed that the transcription factor YY1 is downregulated by Tcf21. Interestingly, co-expression of YY1 and Tcf21 rescues MBM and reduced tetraploidy. By ChIP-Seq analysis, we identified a genome-wide Tcf21-binding site (CAGCTG), which matched the CANNTG sequence, a common E-box binding motif used by bHLH transcription factors. Using this technique, we identified additional Tcf21 targets genes that are involved in the regulation of the cell cycle (e.g. Mdm2, Cdc45, Cyclin D1, Cyclin D2), on the stability of microtubules (e.g. Mapt) as well as chromosome segregation.
Conclusion:
Taken together, we demonstrate that Tcf21 inhibits the expression of PEC-specific markers and of the transcription factor YY1, induces MBM as well as regulates the cell cycle suggesting that Tcf21 might be important for PEC differentiation into podocyte-like cells.
... Over expression of miR193a results in podocytes undifferentiation. 39 Urine samples of patients with MN at different stages were compared with healthy controls, and patients were followed for up to 4 years. Patients with MN had significantly elevated urinary miR193a level; the more advanced the pathologic stage of MN, the higher the urinary level of miRNA193a. ...
Membranous nephropathy (MN) as one of the most common glomerulonephritis still relies on an invasive procedure of kidney biopsy for precise recognition. Over the recent past years noninvasive methods using wide range of biomarkers have been developed in order to diagnose and estimating the final prognosis of MN. Plasma, urine and tissue are readily accessible specimens for identification of these biomarkers. In order to utilize a single biomarker or a panel of them for detection of a specific entity, many factors should taking into consideration like the accuracy, precision, and validity, accompanying with being available and cost effective. This review is focused on recently developed biomarkers and their application on the diagnosis besides determining the prognosis of MN. The clinical utilities and limitations of each biomarker are discussed in details.
Background
Atherosclerosis is a widespread disorder of the cardiovascular system. The early detection of plaques by circulating biomarkers is highly clinically relevant to prevent the occurrence of major complications such as stroke or heart attacks. It is known that extracellular vesicles (EVs) are important in intercellular communication in atherosclerotic disorders and carry many components of their cells of origin, including microRNAs (miRNAs). In this study, we test the assumption that miRNAs present in material acquired from plaques in patients undergoing surgery for atherosclerotic carotid artery stenosis are also expressed in circulating EVs obtained from the identical patients. This would allow the adoption of a liquid biopsy approach for the detection of plaques.
Methods
We studied 22 surgical patients with atherosclerotic carotid arterial stenosis and 28 healthy controls. EVs were isolated from serum by precipitation. miRNA expression profiles of serum-derived EVs were obtained by small RNA sequencing and in plaque material simultaneously acquired from patients. A comparative analysis was performed to identify circulating atherosclerosis-associated miRNAs that are also detectable in plaques.
Results
Seven miRNAs were found to be differentially regulated in patient serum compared with the serum of healthy controls. Of these, miR-193b-5p, miR-193a-5p, and miR-125a-3p were significantly upregulated in patients compared with that in healthy controls and present in both, circulating EVs and plaque material. An overrepresentation analysis of experimentally validated mRNA targets revealed an increased regulation of inflammation and vascular growth factors, key players in atherosclerosis and plaque formation.
Conclusion
Our findings suggest that circulating EVs reflect plaque development in patients with symptomatic carotid artery stenosis, which can serve as biomarker candidates for detecting the presence of atherosclerotic plaques.
Non-coding RNAs (ncRNAs) are a growing class of transcripts, with lengths ranging from tens to several thousand of bases, involved in the regulation of a large number of biological processes and diseases. Many of these ncRNAs have emerged as the molecules of interest for prognostic, diagnostic, and therapeutic purposes in many diseases including cancer. Although ncRNAs do not encode proteins, they fold into complex structures to interact with target proteins, DNA, or other RNAs. In contrast to microRNAs (miRNAs) where researchers mainly focused on the nucleotide sequence for target prediction in the past, folding and structural conservation seems to be important to encode functions and interactions of long non-coding RNA (lncRNA). In this chapter, we discuss methods and tools available for the structural modeling of ncRNAs together with various examples from the literature where structural modeling helped decipher the function of ncRNAs. We also provide a step-by-step procedure to design 3D structures of ncRNAs combining state-of-the-art tools available toward the design of novel RNA therapeutics.KeywordsNon-coding RNAsStructure modelingmiRNA-mRNAMolecular dockingMolecular dynamic simulationDeep learning
The elucidation of internal dynamics in proteins is essential for the understanding of their stability and functionality. Breaking the symmetry of the degenerate rotation of the phenyl side chain provides additional structural information and allows a detailed description of the dynamics. Based on this concept, we propose a combination of synthetic and computational methods, to study the rotational mobility of the Phe ring in a sensitive zinc finger motif. The systematic methyl hopping around the phenylalanine ring yields o-, m-, p-tolyl and xylyl side chains that provide a vast array of additional NOE contacts, allowing the precise determination of the orientation of the aromatic ring. MD simulations and metadynamics complement these findings and facilitate the generation of free energy profiles for each derivative. Previous studies used a wide temperature window in combination with NMR spectroscopy to elucidate the side chain mobility of stable proteins. The zinc finger moiety exhibits a limited thermodynamic stability in a temperature range of only 40 K, making this approach impractical for this compound class. Therefore, we have developed a method that can be applied even to thermolabile systems and facilitates the detailed investigation of protein dynamics.
