bims-lorfki Biomed News
on Long non-coding RNA functions in the kidney
Issue of 2021–01–03
seven papers selected by
Nikita Dewani, Max Delbrück Centre for Molecular Medicine
  1. LncRNA Gm12840 mediates WISP1 to regulate ischemia-reperfusion-induced renal fibrosis by sponging miR-677-5p.
  2. Effects of LncRNA HCP5/miR-214-3p/MAPK1 Molecular Network on Renal Cell Carcinoma Cells.
  3. Identifying 4 Novel lncRNAs as Potential Biomarkers for Acute Rejection and Graft Loss of Renal Allograft.
  4. Identification of Smad3-related transcriptomes in type-2 diabetic nephropathy by whole transcriptome RNA sequencing.
  5. Gene regulation by long non-coding RNAs and its biological functions.
  6. Downregulating LncRNA XIST attenuated contrast-induced nephropathy injury via regulating miR-133a-3p/NLRP3 axis.
  7. Urinary expression of long non-coding RNA TUG1 in non-diabetic patients with glomerulonephritides.
  1. Epigenomics. 2020 Dec 22.
    LncRNA Gm12840 mediates WISP1 to regulate ischemia-reperfusion-induced renal fibrosis by sponging miR-677-5p.
    Hongtao Chen, Youling Fan, Huan Jing, Simin Tang, Zhenxing Huang, Meijuan Liao, Sen Lin, Jiying Zhong, Jun Zhou.
      Aim: We aimed to identify that long noncoding RNAs (lncRNAs) are involved in ischemia-reperfusion (IR)-induced late fibrosis of kidney and may constitute novel therapeutic strategies for acute kidney injury-induced chronic kidney disease. Materials & methods: We performed the mouse model of IR later induced renal fibrosis and analyzed lncRNA profiles using second-generation sequencing during the pathogenesis. Results: The expression levels of 43 lncRNAs and 141 lncRNAs were respectively changed significantly 7 days and 2 weeks after IR treatment. Based on the correlation analysis of the differentially expressed genes, the interaction networks of lncRNAs, miRNAs and mRNA were structured. Conclusion: LncRNA (Gm12840) could act as a sponge for miR-677-5p to mediate fibroblast activation induced by TGF-β1 via the WISP1/PKB (Akt) signaling pathway.
    Keywords:  fibrosis; ischemia; lncRNA; renal; reperfusion
    DOI:  https://doi.org/10.2217/epi-2020-0054
  2. Cancer Manag Res. 2020 ;12 13347-13356
    Effects of LncRNA HCP5/miR-214-3p/MAPK1 Molecular Network on Renal Cell Carcinoma Cells.
    Jun-Feng Hao, Pei Chen, He-Yi Li, Ya-Jing Li, Yu-Ling Zhang.
       Background: Recent researches have shown that long non-coding RNA (LncRNA) is often disordered and acts in many carcinomas. Clear cell renal cell carcinoma (ccRCC) is the main reason for carcinoma-related deaths, which are mainly caused by the metastasis. HCP5 is a newly discovered LcnRNA. Early studies have found that HCP5 acts in neoplasm metastasis, but the mechanism of HCP5 in ccRCC is still unclear.
    Methods: The expression of HCP5 in human renal cell carcinoma (RCC) was detected by real-time quantitative PCR. The biological effect of LncRNAs in proliferation, migration, invasion and metastasis of RCC cells was explored by gain-of-function and loss-of-function tests. The molecular mechanism of LncRNAs was explored by RNA immunoprecipitation and Western blot.
    Results: qRT-PCR revealed that HCP5 was enhanced in neoplasm tissues of ccRCC patients and correlated with the metastatic characteristics of RCC. Over-expression of HCP5 promoted the proliferation, migration and invasion of renal carcinoma cells. The deletion of HCP5 inhibited the proliferation, migration and invasion of RCC in vitro and the metastasis of RCC in vivo. Mechanically, HCP5 inhibited the growth and metastasis of ccRCC cells by regulating miR-214-3p/MAPK1 axis.
    Conclusion: HCP5, as a key LncRNA, can promote ccRCC metastasis by regulating miR-214-3p/MAPK1 axis and may be a biomarker and be helpful for judging the prognosis of ccRCC.
    Keywords:  HCP5; MAPK1; clear cell renal cell carcinoma; miR-214-3p
    DOI:  https://doi.org/10.2147/CMAR.S274426
  3. J Immunol Res. 2020 ;2020 2415374
    Identifying 4 Novel lncRNAs as Potential Biomarkers for Acute Rejection and Graft Loss of Renal Allograft.
    Zedan Zhang, Yanlin Tang, Hongkai Zhuang, Enyu Lin, Lu Xie, Xiaoqiang Feng, Jiayi Zeng, Yanjun Liu, Jiumin Liu, Yuming Yu.
      Acute rejection (AR) after kidney transplant is one of the major obstacles to obtain ideal graft survival. Reliable molecular biomarkers for AR and renal allograft loss are lacking. This study was performed to identify novel long noncoding RNAs (lncRNAs) for diagnosing AR and predicting the risk of graft loss. The several microarray datasets with AR and nonrejection specimens of renal allograft downloaded from Gene Expression Omnibus database were analyzed to screen differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs). Univariate and multivariate Cox regression analyses were used to identify optimal prognosis-related DElncRNAs for constructing a risk score model. 39 common DElncRNAs and 185 common DEmRNAs were identified to construct a lncRNA-mRNA regulatory relationship network. DElncRNAs were revealed to regulate immune cell activation and proliferation. Then, 4 optimal DElncRNAs, ATP1A1-AS1, CTD-3080P12.3, EMX2OS, and LINC00645, were selected from 17 prognostic DElncRNAs to establish the 4-lncRNA risk score model. In the training set, the high-risk patients were more inclined to graft loss than the low-risk patients. Time-dependent receiver operating characteristics analysis revealed the model had good sensitivity and specificity in prediction of 1-, 2-, and 3-year graft survival after biopsy (AUC = 0.891, 0.836, and 0.733, respectively). The internal testing set verified the result well. Gene set enrichment analysis which expounded NOD-like receptor, the Toll-like receptor signaling pathways, and other else playing important role in immune response was enriched by the 4 lncRNAs. Allograft-infiltrating immune cells analysis elucidated the expression of 4 lncRNAs correlated with gamma delta T cells and eosinophils, etc. Our study identified 4 novel lncRNAs as potential biomarkers for AR of renal allograft and constructed a lncRNA-based model for predicting the risk of graft loss, which would provide new insights into mechanisms of AR.
    DOI:  https://doi.org/10.1155/2020/2415374
  4. J Cell Mol Med. 2020 Dec 25.
    Identification of Smad3-related transcriptomes in type-2 diabetic nephropathy by whole transcriptome RNA sequencing.
    Qin Zhou, Honghong Guo, Chaolun Yu, Xiao-Ru Huang, Liying Liang, Puhua Zhang, Jianwen Yu, Jizhou Zhang, Ting-Fung Chan, Ronald C W Ma, Hui-Yao Lan.
      Smad3 deficiency prevents the development of type 2 diabetic nephropathy; however, the underlying molecular mechanisms remain unknown. In this study, we aimed to identify Smad3-related genes involved in the pathogenesis of diabetic kidney disease. High-throughput RNA sequencing was performed to profile the whole transcriptome in the diabetic kidney of Smad3 WT-db/db, Smad3 KO-db/db, Smad3+/- db/db and their littermate control db/m mice at 20 weeks. The gene ontology, pathways and alternative splicing of differentially expressed protein-coding genes and long non-coding RNAs related to Smad3 in diabetic kidney were analysed. Compared to Smad3 WT-db/db mice, Smad3 KO-db/db mice exhibited an alteration of genes associated with RNA splicing and metabolism, whereas heterozygosity deletion of Smad3 (Smad3+/- db/db mice) significantly altered genes related to cell division and cell cycle. Notably, three protein-coding genes (Upk1b, Psca and Gdf15) and two lncRNAs (NONMMUG023520.2 and NONMMUG032975.2) were identified to be Smad3-dependent and to be associated with the development of diabetic nephropathy. By using whole transcriptome RNA sequencing, we identified novel Smad3 transcripts related to the development of diabetic nephropathy. Thus, targeting these transcripts may represent a novel and effective therapy for diabetic nephropathy.
    Keywords:  Smad3 deficiency; alternative splicing; diabetic kidney disease; whole transcriptome
    DOI:  https://doi.org/10.1111/jcmm.16133
  5. Nat Rev Mol Cell Biol. 2020 Dec 22.
    Gene regulation by long non-coding RNAs and its biological functions.
    Luisa Statello, Chun-Jie Guo, Ling-Ling Chen, Maite Huarte.
      Evidence accumulated over the past decade shows that long non-coding RNAs (lncRNAs) are widely expressed and have key roles in gene regulation. Recent studies have begun to unravel how the biogenesis of lncRNAs is distinct from that of mRNAs and is linked with their specific subcellular localizations and functions. Depending on their localization and their specific interactions with DNA, RNA and proteins, lncRNAs can modulate chromatin function, regulate the assembly and function of membraneless nuclear bodies, alter the stability and translation of cytoplasmic mRNAs and interfere with signalling pathways. Many of these functions ultimately affect gene expression in diverse biological and physiopathological contexts, such as in neuronal disorders, immune responses and cancer. Tissue-specific and condition-specific expression patterns suggest that lncRNAs are potential biomarkers and provide a rationale to target them clinically. In this Review, we discuss the mechanisms of lncRNA biogenesis, localization and functions in transcriptional, post-transcriptional and other modes of gene regulation, and their potential therapeutic applications.
    DOI:  https://doi.org/10.1038/s41580-020-00315-9
  6. J Thromb Thrombolysis. 2021 Jan 02.
    Downregulating LncRNA XIST attenuated contrast-induced nephropathy injury via regulating miR-133a-3p/NLRP3 axis.
    Xingli Liu, Wei Song, Xiangmin Zhang, Fangmin Long, Junkun Yin, Xiao He, Liang Lv.
      Long non-coding RNA X-inactive specific transcript (LncRNA XIST) is involved in several diseases. However, the molecular mechanism of XIST and its relation with miR-133a-3p in contrast-induced nephropathy (CIN) remained vague. Sprague-Dawley (SD) rats were assigned to Control, Sham, and CIN groups at random (n = 15 for each group). Histological examination on the kidney tissues was performed using hematoxylin and eosin (HE) and periodic acid-Schiff (PAS) staining. Mean serum creatinine (SCr) and blood urea nitrogen (BUN) contents was measured by colorimetric microplate method. Levels of inflammatory cytokines were detected by enzyme-linked immunosorbent assay (ELISA). The cells viability and apoptosis were respectively detected by MTT assay and flow cytometry. Target gene and potential binding sites between XIST, miR-133a-3p and NLR Family Pyrin Domain Containing 3 (NLRP3) were predicted using online databases and confirmed by dual-luciferase reporter assay. Relative mRNA and protein expressions of XIST, miR-133a-3p, NLRP3, apoptosis-associated speck-like protein (ASC) and Cleaved caspase-1 were measured with quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot as needed. In the rat CIN model, Ioversol induced kidney morphology changes, with increase on SCr and BUN contents, elevated levels of inflammatory cytokines and upregulated expressions of XIST, NLRP3, ASC and Cleaved caspase-1. Silencing XIST reversed the effects of Ioversol on cells. MiR-133a-3p could bind with XIST and target NLRP3, and downregulating miR-133a-3p reversed the effect of silencing XIST on Ioversol-treated cells. Moreover, downregulating XIST attenuated CIN injury via regulating miR-133a-3p/NLRP3 axis.
    Keywords:  Contrast-induced nephropathy; NLR family pyrin domain containing 3; X-inactive specific transcript; miR-133a-3p
    DOI:  https://doi.org/10.1007/s11239-020-02369-0
  7. Biomed Rep. 2021 Jan;14(1): 17
    Urinary expression of long non-coding RNA TUG1 in non-diabetic patients with glomerulonephritides.
    Fernando Javier Salazar-Torres, Miguel Medina-Perez, Zesergio Melo, Claudia Mendoza-Cerpa, Raquel Echavarria.
      Metabolic alterations serve a significant role in the pathogenesis of kidney disease. Long non-coding RNA (lncRNA) taurine upregulated gene 1 (TUG1) is a known regulator of podocyte health and mitochondrial biogenesis. Although TUG1 protects against podocyte loss in models of diabetic nephropathy, it is unknown if urinary TUG1 expression is associated with clinical and histopathological findings in non-diabetic patients diagnosed with glomerulonephritides. In the present study, the expression of TUG1, podocyte-specific markers (nephrin and podocin) and mitochondrial biogenesis-associated mRNAs (transcription factor A mitochondrial, cytochrome C oxidase subunit 5A and peroxisome proliferator-activated receptor γ coactivator 1α) were examined in urinary sediment of non-diabetic patients with biopsy-confirmed glomerulonephritides and healthy controls. Urinary expression of TUG1 was significantly lower in patients with glomerulonephritides, particularly those diagnosed with Focal Segmental Glomerulosclerosis (FSGS). Furthermore, TUG1 levels were associated with urinary expression of podocyte-specific markers and mRNAs associated with mitochondrial biogenesis. Loss of TUG1 expression in urinary sediment was strongly associated with FSGS, highlighting the potential of this lncRNA and its mitochondrial biogenesis-associated targets as non-invasive biomarkers of assessing podocytopathy.
    Keywords:  FSGS; TUG1; glomerulonephritides; lncRNA; urinary sediment
    DOI:  https://doi.org/10.3892/br.2020.1393
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