Downregulation of fibrosis related hsa-miR-29c-3p in human CAKUT

Macak, Natasa; Jovanovic, Ivan; Zivkovic, Maja; Mitrovic, Kristina; Cvetkovic, Mirjana; Kostic, Mirjana; Stankovic, Aleksandra

doi:10.1080/15257770.2023.2218430

Cited by 3 publications

(1 citation statement)

References 47 publications

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“…46 miR-29c-3p, in particular, showed an interesting pattern where it was significantly downregulated in ADPKD urinary extracellular vesicles compared to the healthy individuals. This particular miRNA have been shown to be downregulated in renal fibrosis, 47 which is one of the physiological contributors to ADPKD progression. 48 This particular marker was also shown to be downregulated in PKD1 cystic tissue (Figure 6C) and its potential diagnostic was implicated the ROC curve analysis (Figure 3).…”

Section: Discussionmentioning

confidence: 99%

Global analysis of urinary extracellular vesicle small RNAs in autosomal dominant polycystic kidney disease

Ali,

Malik,

Abu‐Farha

et al. 2024

The Journal of Gene Medicine

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BackgroundAutosomal dominant polycystic kidney disease (ADPKD) is the most prevalent monogenic renal disease progressing to end‐stage renal disease. There is a pressing need for the identification of early ADPKD biomarkers to enable timely intervention and the development of effective therapeutic approaches. Here, we profiled human urinary extracellular vesicles small RNAs by small RNA sequencing in patients with ADPKD and compared their differential expression considering healthy control individuals to identify dysregulated small RNAs and analyze downstream interaction to gain insight about molecular pathophysiology.MethodsThis is a cross‐sectional study where urine samples were collected from a total of 23 PKD1‐ADPKD patients and 28 healthy individuals. Urinary extracellular vesicles were purified, and small RNA was isolated and sequenced. Differentially expressed Small RNA were identified and functional enrichment analysis of the critical miRNAs was performed to identify driver genes and affected pathways.ResultsmiR‐320b, miR‐320c, miR‐146a‐5p, miR‐199b‐3p, miR‐671‐5p, miR‐1246, miR‐8485, miR‐3656, has_piR_020497, has_piR_020496 and has_piR_016271 were significantly upregulated in ADPKD patient urine extracellular vesicles and miRNA‐29c was significantly downregulated. Five ‘driver’ target genes (FBRS, EDC3, FMNL3, CTNNBIP1 and KMT2A) were identified.ConclusionsThe findings of the present study make significant contributions to the understanding of ADPKD pathogenesis and to the identification of novel biomarkers and potential drug targets aimed at slowing disease progression in ADPKD.

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Section: Discussionmentioning

confidence: 99%

Global analysis of urinary extracellular vesicle small RNAs in autosomal dominant polycystic kidney disease

Ali,

Malik,

Abu‐Farha

et al. 2024

The Journal of Gene Medicine

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Interaction of estradiol and renin–angiotensin system with microRNAs-21 and -29 in renal fibrosis: focus on TGF-β/smad signaling pathway

Rajabi,

Saberi,

Najafipour

et al. 2024

Mol Biol Rep

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Identification of hub genes through integrated single-cell and microarray transcriptome analysis in osteoarthritic meniscus

Shen,

Jiang,

Huang

et al. 2024

J Orthop Surg Res

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Background Osteoarthritis (OA) is marked by the progressive degradation of joint cartilage and subchondral bone. The precise molecular mechanisms driving meniscus deterioration in OA, especially at the single-cell level, remain poorly understood. Method We analyzed two datasets from the GEO database, GSE220243 and GSE98918, focusing on meniscus tissue sequencing data from OA and non-OA patients. The standard Seurat procedure was employed to process single-cell data and identify differentially expressed genes (DEGs). Immune cell infiltration was assessed using the Microenvironment Cell Populations (MCP) counter and CIBERSORT algorithms. For the microarray data, DEGs were identified with the limma package, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using ClusterProfiler. The overlapping DEGs from both datasets were imported into Cytoscape to generate protein-protein interaction (PPI) networks and identify hub genes. Transcription factor (TF) and miRNA interaction networks were analyzed using NetworkAnalyst, and gene-related predictive drugs were enriched through the DSigDB platform. Result After quality control, 34,763 cells from the OA patients and 34,145 cells from the healthy controls were analyzed. UMAP identified and SingleR annotated 14 cell clusters. The 10 largest cell clusters were selected for further analysis. The OA group exhibited a notable increase in macrophages and a reduction in cytotoxic lymphocytes and endothelial cells in the meniscus. In GSE98918, 220 DEGs were identified, and the MCODE plug-in in Cytoscape pinpointed a key module containing 12 candidate genes. The MCC methodfiltered the top 20 DEGs in each GSE220243 cluster. Overlapping DEGs from GSE220243 and GSE98918 identified COL1A1, COL3A1, COL5A2, COL6A3, LOX, and VEGFA as significantly decreased in OA, with COL3A1, COL5A2, LOX, and VEGFA upregulated in meniscal chondrocytes. The interaction network highlighted 3 key miRNAs and 13 shared TFs. Ten gene-related predictive drug molecules were identified. Conclusion This research highlights crucial genes in the OA meniscus and uncovers their differing regulatory patterns between chondrocytes and non-chondrocytes. These findings enhance our understanding of the molecular mechanisms driving OA pathogenesis and aid in identifying potential drug targets. Supplementary Information The online version contains supplementary material available at 10.1186/s13018-024-05175-z.

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Downregulation of fibrosis related hsa-miR-29c-3p in human CAKUT

Cited by 3 publications

References 47 publications

Global analysis of urinary extracellular vesicle small RNAs in autosomal dominant polycystic kidney disease

Global analysis of urinary extracellular vesicle small RNAs in autosomal dominant polycystic kidney disease

Interaction of estradiol and renin–angiotensin system with microRNAs-21 and -29 in renal fibrosis: focus on TGF-β/smad signaling pathway

Identification of hub genes through integrated single-cell and microarray transcriptome analysis in osteoarthritic meniscus

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