bims-lorfki 2021-09-19 papers

bims-lorfki

Biomed News

on Long non-coding RNA functions in the kidney

Issue of 2021–09–19
nine papers selected by
Nikita Dewani, Max Delbrück Centre for Molecular Medicine

Effect of Aberrant Long Noncoding RNA on the Prognosis of Clear Cell Renal Cell Carcinoma.
The ceRNA PVT1 inhibits proliferation of ccRCC cells by sponging miR-328-3p to elevate FAM193B expression.
Identification of autophagy-related long non-coding RNA prognostic and immune signature for clear cell renal cell carcinoma.
Long non-coding RNA ARAP1-AS1 contributes to cell proliferation and migration in clear cell renal cell carcinoma via the miR-361-3p/placental growth factor axis.
Sp1-Induced lncRNA Rmrp Promotes Mesangial Cell Proliferation and Fibrosis in Diabetic Nephropathy by Modulating the miR-1a-3p/JunD Pathway.
Long non-cording RNA XIST promoted cell proliferation and suppressed apoptosis by miR-423-5p/HMGA2 axis in diabetic nephropathy.
Construction of a Novel Immune-Related lncRNA Pair Signature with Prognostic Significance for Kidney Clear Cell Renal Cell Carcinoma.
Long noncoding RNA and protein abundance in lncRNPs.
Comprehensive analysis of lncRNAs as biomarkers for diagnosis, prognosis, and treatment response in clear cell renal cell carcinoma.

Comput Math Methods Med. 2021 ;2021 6533049

Effect of Aberrant Long Noncoding RNA on the Prognosis of Clear Cell Renal Cell Carcinoma.

Han Wu, Haixiao Wu, Peng Sun, Desheng Zhu, Min Ma, Wentao Fan.

Clear cell renal cell carcinoma (ccRCC) is a kind of lethal cancer. Although there are mature treatment methods, there is still a lack of rigorous and scientific means for cancer diagnosis. Long noncoding RNAs (lncRNAs) are a kind of noncoding RNA (ncRNA). Recent studies find that alteration of lncRNA expression is related to the occurrence of many cancers. In order to find lncRNAs which can effectively predict the prognosis of ccRCC, RNA-seq count data and clinical information were downloaded from TCGA-KIRC, and gene expression profiles from 530 patients were included. Then, K-means was used for clustering, and the number of clusters was determined to be 5. The R-package "edgeR" was used to perform differential expression analysis. Subsequently, a risk model composed of 10 lncRNA biomarkers significantly related to prognosis was identified via Cox and LASSO regression analyses. Then, patients were divided into two groups according to the model-based risk score, and then, GSEA pathway enrichment was performed. The results showed that metabolism- and mTOR-related pathways were activated while immune-related pathways were inhibited in the high-risk patients. Combined with previous studies, it is believed that these 10 lncRNAs are potential targets for the treatment of ccRCC. In addition, Cox regression analysis was used to verify the independence of the risk model, and as results revealed, the risk model can be used to independently predict the prognosis of patients. In conclusion, our study found 10 lncRNAs related to the prognosis of ccRCC and provided new ideas for clinical diagnosis and drug development.

DOI: https://doi.org/10.1155/2021/6533049
Aging (Albany NY). 2021 Sep 13. 13(undefined):

The ceRNA PVT1 inhibits proliferation of ccRCC cells by sponging miR-328-3p to elevate FAM193B expression.

Guohai Xie, Xinyi Zheng, Zhong Zheng, Ruoyu Wu, Zhixian Yao, Wenjie Huang, Feng Sun, Xingyu Mu, Ke Wu, Junhua Zheng.

  Clear cell renal cell carcinoma (ccRCC) is a common and fatal malignancy. Long noncoding RNAs (lncRNAs) have emerged as crucial biomarkers and regulators in many cancers, warranting the detailed investigation of their biological functions and molecular mechanisms. In this study, we explored the role and mechanism of plasmacytoma variant translocation 1 (PVT1), a competitive endogenous RNA (ceRNA) in ccRCC tissues in vitro and in vivo. We found that PVT1 is upregulated in ccRCC cells and promoted cell proliferation. Bioinformatic analysis, dual-luciferase reporter assays, argonaute 2-RNA immunoprecipitation (AGO2-RIP), quantitative PCR arrays, western blot assay, and rescue experiments were conducted to explore the underlying mechanisms of PVT1. Our analyses revealed that miR-328-3p was a direct target of PVT1 and that FAM193B was a direct target of miR-328-3p. FAM193B is upregulated in ccRCC tissues and promotes cell proliferation by activating the MAPK/ERK and PI3K/AKT pathways. Our results indicated that PVT1 promotes ccRCC cells proliferation by sponging miR-328-3p to upregulate FAM193B and activate the MAPK/ERK and PI3K/AKT pathways. Collectively, these results suggest that PVT1- miR-328-3p-FAM193B loop could serve as a potential biomarker and therapeutic target for ccRCC.

Keywords:  FAM193B; PVT1; clear cell renal cell carcinoma; miR-328-3p; proliferation

DOI:  https://doi.org/10.18632/aging.203514
Transl Androl Urol. 2021 Aug;10(8): 3317-3331

Identification of autophagy-related long non-coding RNA prognostic and immune signature for clear cell renal cell carcinoma.

Yankang Cui, Shaobo Zhang, Chenkui Miao, Chao Liang, Xiaochao Chen, Tao Yan, Hengtao Bu, Huiyu Dong, Junchen Li, Jie Li, Zengjun Wang, Bianjiang Liu.

   Background: Studies over the past decade have shown that long non-coding RNAs (lncRNAs) play an essential role in the tumorigenesis and progression of kidney renal clear cell carcinoma (KIRC). Meanwhile, autophagy has been demonstrated to regulate KIRC pathogenesis and targeting therapy resistance. However, the prognostic value of autophagy-related lncRNAs in KIRC patients has not been reported before.
Methods: In this study, we obtained transcriptome data of 611 KIRC cases from the TCGA database and 258 autophagy-related mRNAs from the HADb database to identify autophagy-related lncRNAs by co-expression network. A prognostic model was then established basing on these autophagy-related lncRNAs, dividing patients into high-risk and low-risk groups. Survival analysis, clinical variables dependent receiver operating characteristic (ROC) analyses, univariate/multivariate Cox analyses, and clinical correlation analysis were performed based on risk signature with R language. Gene set enrichment analysis (GSEA) was then performed to investigate the potential mechanism of the risk signature promoting KIRC progression with GSEA software. CIBERSORT algorithm was performed to assess the impact of these lncRNAs on the infiltration of immune cells.
Results: A total of 17 lncRNAs were screened out and all these lncRNAs were found significantly related to KIRC patients' overall survival in subsequent survival analyses. Besides, the overall survival time in the high-risk group was much poorer than in the low-risk group. The ROC analysis revealed that the prognostic value of risk signature was better than age, gender, grade, and N stage. Univariate/multivariate analyses suggested that the risk signature was an independent predictive factor for KIRC patients. Immune and autophagy related pathways were dramatically enriched in high-risk and low-risk groups, respectively, and lncRNAs related immune cells were identified by CIBERSORT.
Conclusions: In summary, our identified 17 autophagy-related lncRNAs had prognostic value for KIRC patients which may function in immunomodulation.

Keywords:  Kidney renal clear cell carcinoma (KIRC); autophagy; immune; lncRNA; prognosis

DOI:  https://doi.org/10.21037/tau-21-278
Bioengineered. 2021 Dec;12(1): 6629-6642

Long non-coding RNA ARAP1-AS1 contributes to cell proliferation and migration in clear cell renal cell carcinoma via the miR-361-3p/placental growth factor axis.

Liping Zhong, Xiuwen Zhong.

  Clear cell renal cell carcinoma (ccRCC) is an aggressive malignancy with a poor prognosis. Therefore, investigating the molecular mechanism of ccRCC is important for ccRCC treatment. Here, we aimed to explore the effect of the long non-coding RNA ARAP1-AS1/miR-361-3p/PGF axis on ccRCC. The expression of lncRNA ARAP1-AS1, miR-361-3p, and placental growth factor (PGF) in ccRCC cells was verified by real-time quantitative PCR (RT-qPCR). The influence of the ARAP1-AS1/miR-361-3p/PGF axis on ccRCC cells was identified using the Cell Counting Kit-8 (CCK-8) assay, colony formation assay, flow cytometry, and wound healing assay. The interaction between ARAP1-AS1, miR-361-3p, and PGF was confirmed by bioinformatics analysis and luciferase assay. The results showed that the levels of ARAP1-AS1 and PGF increased in ccRCC cells, while miR-361-3p expression decreased. Cell functional experiments showed that cell proliferation and migration were inhibited by silencing ARAP1-AS1 or PGF, while miR-361-3p inhibitor or PGF overexpression could relieve the inhibitory effect of silencing ARAP1-AS1 on ccRCC cells. Moreover, ARAP1-AS1 sponges miR-361-3p to increase PGF expression. In conclusion, our study revealed that ARAP1-AS1 enhanced the malignancy of ccRCC cells by regulating the miR-361-3p/PGF axis.

Keywords:  ARAP1-AS1; PGF; clear cell renal cell carcinoma; miR-361-3p

DOI:  https://doi.org/10.1080/21655979.2021.1975019
Front Endocrinol (Lausanne). 2021 ;12 690784

Sp1-Induced lncRNA Rmrp Promotes Mesangial Cell Proliferation and Fibrosis in Diabetic Nephropathy by Modulating the miR-1a-3p/JunD Pathway.

Hansen Yang, Jia Wang, Zheng Zhang, Rui Peng, Dan Lv, Handeng Liu, Yan Sun.

  Diabetic nephropathy (DN) is a serious complication of diabetes mellitus. Long non-coding RNAs (lncRNAs) are regulators in DN progression. However, the regulatory mechanisms of multiple lncRNAs in DN remain to be determined. Our aim was to investigate the function and molecular mechanism of lncRNA RNA component of mitochondrial RNAase P (Rmrp) in DN. Here, we observed that the expression of Rmrp was up-regulated in the kidney of db/db DN mice and high glucose induced glomerular mesangial cells (MC). More importantly, the abnormal transcription of Rmrp was induced by nuclear transcription factor Sp1, which promotes the proliferation and production of fibrotic markers in MC. Subsequently, we screened the miRNAs related to Rmrp and found that Rmrp and miR-1a-3p are co-localized at the subcellular level of MC, and Rmrp could directly binds to miR-1a-3p. Further mechanism research demonstrated that the elevated miR-1a-3p significantly attenuated the proliferation and fibrosis-promoting effects induced by up-regulation of Rmrp. At the same time, we also investigated that miR-1a-3p can directly bind to Jun D proto-oncogene (JunD), thereby regulating the protein level of JunD. Rmrp-induced proliferation and fibrogenesis were reversed by co-transfection with JunD siRNA. In summary, Sp1 induced lncRNA Rmrp could drive the expression of JunD via sponging miR-1a-3p in DN progression.

Keywords:  JunD; Rmrp; diabetic nephropathy; mesangial cells; miR-1a-3p

DOI:  https://doi.org/10.3389/fendo.2021.690784
Mol Cell Biochem. 2021 Sep 16.

Long non-cording RNA XIST promoted cell proliferation and suppressed apoptosis by miR-423-5p/HMGA2 axis in diabetic nephropathy.

Hui Chen, Yuan Guo, Xingbo Cheng.

  This research studied the effect of long non-coding RNA X-inactive-specific transcript (XIST) on DN. The effect of high glucose (HG) on the expression of XIST and miR-423-5p was detected by quantitative real-time PCR (qRT-PCR) in human kidney (HK) cells (human glomerular mesangial cells (HMCs) and human kidney-2 (HK-2) cells). The effect of XIST depletion and miR-423-5p inhibition or overexpression on high mobility group protein A2 (HMGA2) protein level was examined by western blot in HG-induced HK cells. The impacts of XIST depletion on viability and apoptosis were assessed by 3-(4, 5-dimethyl-2-thiazolyl)-2, 5-diphenyl-2-H-tetrazolium bromide (MTT) and flow cytometry assays in HG-induced HK cells. We found the expression of XIST and HMGA2 protein was significantly upregulated in DN tissues and cells. Moreover, HG treatment induced the upregulation of XIST and HMGA2 protein level in HK cells. Besides, both XIST depletion and HMGA2 depletion decreased cell proliferation but increased apoptosis in HG-treated HK cells. Furthermore, HMGA2 upregulation or miR-423-5p inhibition partly eliminated the effects of XIST depletion on cell proliferation, apoptosis of HG-treated HK cells. Interestingly, HMGA2 upregulation partly reversed miR-423-5p overexpression-mediated suppression on viability and promotion on apoptosis in HG-treated HK cells. Mechanistically, XIST sponged miR-423-5p to regulate HMGA2 expression in DN cells. Taken together, XIST depletion suppressed proliferation and promoted apoptosis via miR-423-5p/HMGA2 axis in HG-treated HK cells, which may provide a potential therapeutic target for DN.

Keywords:  Diabetic nephropathy; HMGA2; High glucose; XIST; miR-423-5p

DOI:  https://doi.org/10.1007/s11010-021-04250-x
Dis Markers. 2021 ;2021 8800358

Construction of a Novel Immune-Related lncRNA Pair Signature with Prognostic Significance for Kidney Clear Cell Renal Cell Carcinoma.

Jian-Xuan Sun, Qi-Dong Xia, Chen-Qian Liu, Jin-Zhou Xu, Yang Xun, Jun-Lin Lu, Jia Hu, Shao-Gang Wang.

Background: Renal cell carcinoma (RCC) is one of the most common aggressive malignant tumors in the urinary system, among which the clear cell renal cell carcinoma (ccRCC) is the most common subtype. The immune-related long noncoding ribonucleic acids (irlncRNAs) which are abundant in immune cells and immune microenvironment (IME) have potential significance in evaluating the prognosis and effects of immunotherapy. The signature based on irlncRNA pairs and independent of the exact expression level seems to have a latent predictive significance for the prognosis of patients with malignant tumors but has not been applied in ccRCC yet.
Method: In this article, we retrieved The Cancer Genome Atlas (TCGA) database for the transcriptome profiling data of the ccRCC and performed coexpression analysis between known immune-related genes (ir-genes) and lncRNAs to find differently expressed irlncRNA (DEirlncRNA). Then, we adopted a single-factor test and a modified LASSO regression analysis to screen out ideal DEirlncRNAs and constructed a Cox proportional hazard model. We have sifted 28 DEirlncRNA pairs, 12 of which were included in this model. Next, we compared the area under the curve (AUC), found the cutoff point by using the Akaike information criterion (AIC) value, and distinguished the patients with ccRCC into a high-risk group and a low-risk group using this value. Finally, we tested this model by investigating the relationship between risk score and survival, clinical pathological characteristics, cells in tumor immune microenvironment, chemotherapy, and targeted checkpoint biomarkers.
Results: A novel immune-related lncRNA pair signature consisting of 12 DEirlncRNA pairs was successfully constructed and tightly associated with overall survival, clinical pathological characteristics, cells in tumor immune microenvironment, and reactiveness to immunotherapy and chemotherapy in patients with ccRCC. Besides, the efficacy of this signature was verified in some commonly used clinicopathological subgroups and could serve as an independent prognostic factor in patients with ccRCC.
Conclusions: This signature was proven to have a potential predictive significance for the prognosis of patients with ccRCC and the efficacy of immunotherapy.

DOI: https://doi.org/10.1155/2021/8800358
RNA. 2021 Sep 15. pii: rna.078971.121. [Epub ahead of print]

Long noncoding RNA and protein abundance in lncRNPs.

Man Wu, Liang-Zhong Yang, Ling-Ling Chen.

  Although long noncoding RNAs (lncRNAs) are generally expressed at low levels, emerging evidence has revealed that many play important roles in gene regulation by a variety of mechanisms as they engage with proteins. Given that the abundance of proteins often greatly exceeds that of their interacting lncRNAs, quantification of the relative abundance, or even the exact stoichiometry in some cases, within lncRNA-protein complexes is helpful for understanding of the mechanism(s) of action of lncRNAs. We discuss methods used to examine lncRNA and protein expression at the single cell, sub-cellular and sub-organelle levels, the average and local lncRNA concentration in cells, as well as how lncRNAs can modulate the functions of their interacting proteins even at a low stoichiometric concentration.

Keywords:  abundance; concentration; lncRNA; lncRNP; stoichiometry

DOI:  https://doi.org/10.1261/rna.078971.121
Mol Ther Oncolytics. 2021 Sep 24. 22 209-218

Comprehensive analysis of lncRNAs as biomarkers for diagnosis, prognosis, and treatment response in clear cell renal cell carcinoma.

Xiaoyu Chao, Pei Wang, Xiaoyu Ma, Zhenfen Li, Yubing Xia, Ying Guo, Linna Ge, Linzhu Tian, Hong Zheng, Yaowu Du, Jitian Li, Zhanjie Zuo, Longxiang Xie, Xiangqian Guo.

  Clear cell renal cell carcinoma (ccRCC) is the most common histological type of renal carcinoma and has a high recurrence rate and poor outcome. Accurate patient risk stratification based on genetic markers can help to identify the high-risk patient for early and further treatments and would promote patient survival. Long non-coding RNAs (lncRNAs) have attracted widespread attention as biomarkers for early diagnosis, treatment, and prognosis because of their high specificity and sensitivity. Here, we performed a systematic search in NCBI PubMed and found 44 lncRNAs as oncogenes, 18 lncRNAs as tumor suppressors, 199 lncRNAs as diagnostic biomarkers, 62 lncRNAs as prognostic biomarkers, and 3 lncRNAs as predictive biomarkers for ccRCC. We also comprehensively discuss the biological functions and molecular regulatory mechanisms of lncRNAs in ccRCC. Overall, the present study is a systemic analysis to assess the expression and clinical value of lncRNAs in ccRCC, and lncRNAs hold promise to be diagnostic, prognostic, and predictive biomarkers.

Keywords:  biomarker; ccRCC; ceRNA; diagnosis; lncRNAs; miRNA; oncogene; prognosis; treatment response; tumor suppressor

DOI:  https://doi.org/10.1016/j.omto.2021.08.003