bims-lorfki 2022-04-03 papers

Issue of 2022‒04‒03
five papers selected by
Nikita Dewani
Max Delbrück Centre for Molecular Medicine

Front Physiol. 2022 ;13 849403

An Update of Long-Noncoding RNAs in Acute Kidney Injury.

Acute kidney injury (AKI) is a global public health concern with high morbidity, mortality, and medical costs. Despite advances in medicine, effective therapeutic regimens for AKI remain limited. Long non-coding RNAs (lncRNAs) are a subtype of non-coding RNAs, which longer than 200 nucleotides and perform extremely diverse functions in biological processes. Recently, lncRNAs have emerged as promising biomarkers and key mediators to AKI. Meanwhile, existing research reveals that the aberrant expression of lncRNAs has been linked to major pathological processes in AKI, including the inflammatory response, cell proliferation, and apoptosis, via forming the lncRNA/microRNA/target gene regulatory axis. Following a comprehensive and systematic search of the available literature, 87 relevant papers spanning the years 2005 to 2021 were identified. This review aims to provide and update an overview of lncRNAs in AKI, and further shed light on their potential utility as AKI biomarkers and therapeutic targets.

Keywords: acute kidney injury; drug induced AKI; ischemia–reperfusion; kidney transplant; long non-coding RNA; post-contrast AKI; sepsis

DOI: https://doi.org/10.3389/fphys.2022.849403

Transl Oncol. 2022 Mar 24. pii: S1936-5233(22)00018-3. [Epub ahead of print]20 101356

LncRNA GIHCG promoted the proliferation and migration of renal cell carcinoma through regulating miR-499a-5p/XIAP axis.

Shu-Ying Zhu, Hong-Chang Zou, Ming-Ming Gao, Yan-Xia Chen, Man Xu, Xiao-Hua Qin.

BACKGROUND: Our previous study demonstrated that lncRNA GIHCG is upregulated in renal cell carcinoma (RCC) and that knockdown of lncRNA GIHCG suppresses the proliferation and migration of RCC cells. However, the mechanism of lncRNA GIHCG in RCC needs further exploration.METHODS: The proliferation, cell cycle, migration, and apoptosis of RCC cells were tested using CCK-8, flow cytometry, wound healing and Annexin-V/-FITC/PI flow cytometry assays, respectively. Dual-luciferase reporter and RNA pull-down or RNA immunoprecipitation assays (RIPs) were performed to analyze the interactions among lncRNA GIHCG, miR-499a-5p and XIAP. A tumour xenograft study was conducted to verify the function of lncRNA GIHCG in RCC development in vivo.
RESULTS: Knockdown of lncRNA GIHCG inhibited cell proliferation and migration and induced G0/G1 arrest while promoting apoptosis. Overexpression of lncRNA GIHCG led to the opposite results. LncRNA GIHCG sponged miR-499a-5p and downregulated its expression in RCC cells. MiR-499a-5p overexpression suppressed RCC cell growth. MiR-499a-5p targeted XIAP and inhibited its expression. LncRNA GIHCG knockdown reduced the growth of tumour xenografts in vivo and the expression of XIAP while increasing miR-499a-5p levels.
CONCLUSION: LncRNA GIHCG accelerated the development of RCC by targeting miR-499a-5p and increasing XIAP levels.

Keywords: LncRNA GIHCG; Migration; Proliferation; Renal cell carcinoma; XIAP; miR-499a-5p

DOI: https://doi.org/10.1016/j.tranon.2022.101356

Front Genet. 2022 ;13 787884

Identification and Validation of a Ferroptosis-Related Long Non-Coding RNA (FRlncRNA) Signature to Predict Survival Outcomes and the Immune Microenvironment in Patients With Clear Cell Renal Cell Carcinoma.

Zhongbao Zhou, Zhenpeng Yang, Yuanshan Cui, Shuai Lu, Yongjin Huang, Xuanyan Che, Liqing Yang, Yong Zhang.

Background: The incidence of clear cell renal cell carcinoma (ccRCC) is increasing worldwide, contributing to 70-85% of kidney cancer cases. Ferroptosis is a novel type of programmed cell death and could predict prognoses in cancers. Here, we developed a ferroptosis-related long non-coding RNA (FRlncRNA) signature to improve the prognostic prediction of ccRCC. Methods: The transcriptome profiles of FRlncRNAs and clinical data of ccRCC were obtained from The Cancer Genome Atlas and ICGC databases. Patients were randomly assigned to training cohorts, testing cohorts, and overall cohorts. The FRlncRNA signature was constructed by Lasso regression and Cox regression analysis, and Kaplan-Meier (K-M) analysis was used to access the prognosis of each group. The accuracy of this signature was evaluated by the receiver operating characteristic (ROC) curve. The visualization of functional enrichment was carried out by the gene set enrichment analysis (GSEA). Internal and external datasets were performed to verify the FRlncRNA signature. Results: A FRlncRNA signature comprising eight lncRNAs (AL590094.1, LINC00460, LINC00944, AC024060.1, HOXB-AS4, LINC01615, EPB41L4A-DT, and LINC01550) was identified. Patients were divided into low- and high-risk groups according to the median risk score, in which the high-risk group owned a dramatical shorter survival time than that of the low-risk group. Through ROC analysis, it was found that this signature had a greater predictive capability than traditional evaluation methods. The risk score was an independent risk factor for overall survival suggested by multivariate Cox analysis (HR = 1.065, 95%CI = 1.036-1.095, and p < 0.001). We constructed a clinically predictive nomogram based on this signature and its clinical features, which is of accurate prediction about the survival rate of patients. The GSEA showed that primary pathways were the P53 signaling pathway and tumor necrosis factor-mediated signaling pathway. The major FRlncRNAs (LINC00460, LINC00944, LINC01550, and EPB41L4A-DT) were verified with the prognosis of ccRCC in the GEPIA and K-M Plotter databases. Their major target genes (BNIP3, RRM2, and GOT1) were closely related to the stage, grade, and survival outcomes of ccRCC by the validation of multiple databases. Additionally, we found two groups had a significant distinct pattern of immune function, immune checkpoint, and immune infiltration, which may lead to different survival benefits. Conclusions: The FRlncRNA signature was accurate and act as reliable tools for predicting clinical outcomes and the immune microenvironment of patients with ccRCC, which may be molecular biomarkers and therapeutic targets.

Keywords: clear cell renal cell carcinoma; ferroptosis; immune microenvironment; long non-coding RNAs; overall survival; prognostic signature

DOI: https://doi.org/10.3389/fgene.2022.787884

Int J Gen Med. 2022 ;15 3215-3235

Analysis of Ferroptosis-Related LncRNAs Signatures Associated with Tumor Immune Infiltration and Experimental Validation in Clear Cell Renal Cell Carcinoma.

Xinyi Chen, Jingyao Tu, Li Ma, Yongbiao Huang, Chunguang Yang, Xianglin Yuan.

Background: Clear cell renal cell carcinoma (ccRCC) is the most aggressive subtype of renal cell carcinoma. Ferroptosis is an iron-dependent programmed cell death. Long non-coding RNAs (lncRNAs) emerge as a critical role in regulating cancer progression.Objective: This study aimed to identify molecular regulation of ferroptosis-related lncRNAs (FRLs) in ccRCC.
Methods: The prognostic value of FRLs was investigated in ccRCC samples downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) dataset. The FRLs were screened out by Pearson correlation test. The 465 FRLs confirmed as potential prognostic factors through univariate Cox regression analysis were entered into Lasso and multivariate Cox regression to build a FRLs prognostic signature. A risk score based on the prognostic model divided ccRCC patients into low- and high-risk groups. A prognostic nomogram, derived from the prognostic signature and integrating clinical characteristics, was constructed. Gene set enrichment analysis (GSEA) revealed the immune- and tumor-associated pathways. Two distinct clusters were identified with different immune signatures through consensus clustering analysis. The prognostic value of some hub FRLs was externally validated via three GEO datasets (GSE46699, GSE53757 and GSE66272) and online databases. Finally, the three FRLs (LINC00460, LINC00941 and LINC02027) were verified through in vitro experiments.
Results: The FRLs prognostic signature, including 7 independent prognostic lncRNAs, exhibited good accuracy in predicting overall survival (OS) of ccRCC patients. This signature was correlated with immune infiltration and immune checkpoint blockade (ICB). We correlated two distinct clusters with immune infiltration signature of ccRCC. The worse prognosis of cluster 2 was probably mediated by immune evasion. We also found that the expression levels of LINC00460 and LINC00941 in ccRCC cell lines were higher than those in HK-2 cells, but LINC02027 showed the inverse trend.
Conclusion: Collectively, our study demonstrated a FRLs prognostic signature which had great clinical value in prognosis assessment.

Keywords: clear cell renal cell carcinoma; ferroptosis; immune microenvironment; long non-coding RNA; prognostic signature

DOI: https://doi.org/10.2147/IJGM.S354682

Int Urol Nephrol. 2022 Apr 01.

LncRNA NEAT1 knockdown ameliorates LPS-induced human kidney injury by mediating the miR-330-5p/FOXO3 axis.

Yi Gong, Xiao Dong, Jianjun Xu, Wei Yang.

BACKGROUND: Sepsis is a systemic process with multiple inflammatory responses and organ injuries, particularly in the damage of the kidney. Recently, numerous studies suggest that long non-coding RNAs (lncRNAs) are involved in sepsis-related kidney injury. This study aimed to investigate the functional role and mechanism of lncRNA nuclear paraspeckle assembly transcript 1 (NEAT1) in sepsis-related kidney injury.METHODS: Cell model of kidney injury was constructed in human kidney 2 (HK-2) cells with the treatment of lipopolysaccharide (LPS). The expression of NEAT1 was measured by quantitative real-time PCR (qRT-PCR). Cell viability was examined using CCK-8 assay. Flow cytometry was performed to detect cell apoptosis, and apoptosis-related proteins were quantified by western blot. The release of proinflammatory cytokines was assessed by ELISA. Oxidative stress was assessed by the levels of SOD and MDA using kits. The putative relationship between miR-330-5p and NEAT1 or FOXO3 was confirmed using dual-luciferase reporter assay, RIP assay and pull-down assay.
RESULT: The expression of NEAT1 was increased in LPS-treated HK-2 cells. LPS exposure promoted apoptotic rate, inflammatory responses and oxidative stress in HK-2 cells, which were largely ameliorated by NEAT1 knockdown. MiR-330-5p was verified as a target of NEAT1, and miR-330-5p inhibition reversed the effects of NEAT1 knockdown in LPS-treated HK-2 cells. Moreover, FOXO3 was a target of miR-330-5p, and miR-330-5p restoration-blocked cell apoptosis, inflammation and oxidative stress in LPS-treated HK-2 cells were recovered by FOXO3 overexpression.
CONCLUSION: NEAT1 downregulation meliorated LPS-induced HK-2 cell injuries partly by regulating the miR-330-5p/FOXO3 pathway.

Keywords: FOXO3; HK-2; Kidney injury; LPS; NEAT1; Sepsis; miR-330-5p

DOI: https://doi.org/10.1007/s11255-022-03179-4