bims-lorfki 2021-01-31 papers

bims-lorfki

Biomed News

on Long non-coding RNA functions in the kidney

Issue of 2021–01–31
seven papers selected by
Nikita Dewani, Max Delbrück Centre for Molecular Medicine

Long non-coding RNAs: a double-edged sword in aging kidney and renal disease.
A lncRNA TCL6-miRNA-155 interaction regulates the Src-Akt-EMT network to mediate kidney cancer progression and metastasis.
Silence of Long Noncoding RNA SNHG14 Alleviates Ischemia/Reperfusion-Induced Acute Kidney Injury by Regulating miR-124-3p/MMP2 Axis.
A Risk Score Model Based on Nine Differentially Methylated mRNAs for Predicting Prognosis of Patients with Clear Cell Renal Cell Carcinoma.
lncRNA SNHG14 Plays a Role in Sepsis-Induced Acute Kidney Injury by Regulating miR-93.
Androgen receptor promotes renal cell carcinoma (RCC) vasculogenic mimicry (VM) via altering TWIST1 nonsense-mediated decay through lncRNA-TANAR.
Comprehensive analysis of lncRNAs N6-methyladenosine modification in colorectal cancer.

Chem Biol Interact. 2021 Jan 25. pii: S0009-2797(21)00032-6. [Epub ahead of print] 109396

Long non-coding RNAs: a double-edged sword in aging kidney and renal disease.

Yan-Ni Wang, Chang-E Yang, Dan-Dan Zhang, Yuan-Yuan Chen, Xiao-Yong Yu, Ying-Yong Zhao, Hua Miao.

  Aging as one of intrinsic biological processes is a risk factor for many chronic diseases. Kidney disease is a global problem and health care burden worldwide. The diagnosis of kidney disease is currently based on serum creatinine and urea levels. Novel biomarkers may improve diagnostic accuracy, thereby allowing early prevention and treatment. Over the past few years, advances in genome analyses have identified an emerging class of noncoding RNAs that play critical roles in the regulation of gene expression and epigenetic reprogramming. Long noncoding RNAs (lncRNAs) are pervasively transcribed in the genome and could bind DNA, RNA and protein. Emerging evidence has demonstrated that lncRNAs played an important role in all stages of kidney disease. To date, only some lncRNAs were well identified and characterized, but the complexity of multilevel regulation of transcriptional programs involved in these processes remains undefined. In this review, we summarized the lncRNA expression profiling of large-scale identified lncRNAs on kidney diseases including acute kidney injury, chronic kidney disease, diabetic nephropathy and kidney transplantation. We further discussed a number of annotated lncRNAs linking with complex etiology of kidney diseases. Finally, several lncRNAs were highlighted as diagnostic biomarkers and therapeutic targets. Targeting lncRNAs may represent a precise therapeutic strategy for progressive renal fibrosis.

Keywords:  Long noncoding RNAs; aging kidney; biomarker; diabetic nephropathy; kidney disease; renal fibrosis

DOI:  https://doi.org/10.1016/j.cbi.2021.109396
Cancer Res. 2021 Jan 26. pii: canres.0832.2020. [Epub ahead of print]

A lncRNA TCL6-miRNA-155 interaction regulates the Src-Akt-EMT network to mediate kidney cancer progression and metastasis.

Priyanka Kulkarni, Pritha Dasgupta, Yutaka Hashimoto, Marisa Shiina, Varahram Shahryari, Z Laura Tabatabai, Soichiro Yamamura, Yuichiro Tanaka, Sharanjot Saini, Rajvir Dahiya, Shahana Majid.

Metastasis is the leading cause of mortality from kidney cancer, and understanding the underlying mechanism of this event will provide better strategies for its management. Here we investigated the biological, functional, and clinical significance of lncTCL6 and its interacting miR-155 in clear cell renal cell carcinoma (ccRCC). We employed a comprehensive approach to investigate the lncTCL6-miR155-Src/Akt-mediated EMT pathway as a novel regulatory mechanism in ccRCC progression. Expression analyses revealed that lncTCL6 is downregulated in ccRCC compared to normal tissues. Overexpression of lncTCL6 in ccRCC cell lines impaired their oncogenic functions such as cell proliferation and migration/invasion and induced cell cycle arrest and apoptosis; conversely, depletion of lncTCL6 rescued these phenotypic effects. Furthermore, lncTCL6 directly interacted with miR-155. Unlike lncTCL6, miR-155 was overexpressed in ccRCC. Stable knockdown of miR-155 phenocopied the effects of lncTCL6 overexpression. Conversely, reconstitution of miR-155 and suppression of lncTCL6 in non-cancerous renal cell HK2 induced tumorigenic characteristics. Patients with higher expression of lncTCL6 and lower expression of miR-155 had better survival probability. When overexpressed, lncTCL6 recruited STAU1 and mediated decay of Src mRNA, followed by a marked downregulation of an integrated network of Src target genes involved in migration, invasion, and EMT. However, the interaction between miR-155 and lncTCL6 attenuated the regulatory role of lncTCL6 on Src-mediated EMT. In conclusion, this study is the first report documenting the lncTCL6-miR155-Src/Akt/EMT network as a novel regulatory mechanism in aggressive ccRCC and a promising therapeutic target to inhibit renal cancer.

DOI: https://doi.org/10.1158/0008-5472.CAN-20-0832
Biomed Res Int. 2021 ;2021 8884438

Silence of Long Noncoding RNA SNHG14 Alleviates Ischemia/Reperfusion-Induced Acute Kidney Injury by Regulating miR-124-3p/MMP2 Axis.

Qianlong Xue, Lipeng Yang, Hui Wang, Shuchi Han.

Purpose: Ample evidence has proved that lncRNAs are pivotal regulators in acute kidney injury (AKI). Here, we focus on the role and mechanism of lncRNA SNHG14 in ischemia/reperfusion- (I/R-) caused AKI.
Methods: I/R and hypoxia/reoxygenation (H/R) were applied to induce rats and HK-2 cells to establish AKI models in vivo and in vitro. Relative expression of SNHG14, miR-124-3p, and MMP2 was determined by qRT-PCR. HE staining was used to evaluate pathological changes in renal tissues, and acute tubular necrosis (ATN) score was calculated. Renal function was evaluated by measuring serum creatinine content and blood urea nitrogen content. Levels of IL-1β, IL-6, and TNF-α were measured by ELISA. Cell viability was examined by MTT assay. Oxidative stress was assessed by measuring SOD, MDA, and ROS levels. The target of SNHG14 or miR-124-3p was verified by DLR assay. Protein expression of MMP2 was examined by western blot.
Results: SNHG14 was boosted in renal tissues of I/R-stimulated rats and H/R-induced HK-2 cells, while miR-124-3p was diminished in H/R-stimulated HK-2 cells. Si-SNHG14 or miR-124-3p mimics repressed inflammation and oxidative stress and enhanced cell viability in H/R-stimulated HK-2 cells. Sh-SNHG14 mitigated I/R-induced AKI in rats. MiR-124-3p was targeted by SNHG14, and MMP2 was targeted by miR-124-3p. Inhibition of miR-124-3p or upregulation of MMP2 reversed inhibitory effects of SNHG14 silence on inflammation and oxidative stress as well as the promoting effect of SNHG14 silence on cell viability in H/R-induced HK-2 cells.
Conclusion: Knockdown of SNHG14 alleviated I/R-induced AKI by miR-124-3p-mediated downregulation of MMP2.

DOI: https://doi.org/10.1155/2021/8884438
Dis Markers. 2021 ;2021 8863799

A Risk Score Model Based on Nine Differentially Methylated mRNAs for Predicting Prognosis of Patients with Clear Cell Renal Cell Carcinoma.

Jingmin Zhou, Guanghua Liu, Xingcheng Wu, Zhien Zhou, Jialin Li, Zhigang Ji.

Purpose: DNA methylation alterations play important roles in initiation and progression of clear cell renal cell carcinoma (ccRCC). In this study, we attempted to identify differentially methylated mRNA signatures with prognostic value for ccRCC.
Methods: The mRNA methylation and expression profiling data of 306 ccRCC tumors were downloaded from The Cancer Genome Atlas (TCGA) to screen differentially methylated lncRNAs and mRNAs (DMLs and DMMs) between bad and good prognosis patients. Uni- and multivariable Cox regression analyses and LASSO Cox-PH regression analysis were used to select prognostic lncRNAs and mRNAs. Corresponding risk scores were calculated and compared for predictive performance in the training set using Kaplan-Meier OS and ROC curve analyses. The optimal risk score was then identified and validated in the validation set. Function enrichment analysis was conducted.
Results: This study screened 461 DMMs and 63 DMLs between good prognosis and bad prognosis patients, and furthermore, nine mRNAs and six lncRNAs were identified as potential prognostic molecules. Compared to nine-mRNA status risk score model, six-lncRNA methylation risk score model, and six-lncRNA status risk score model, the nine-mRNA methylation risk score model showed superiority for prognosis stratification of ccRCC patients in the training set. The prognostic ability of the nine-mRNA methylation risk score model was validated in the validation set. The nine prognostic mRNAs were functionally associated with neuroactive ligand receptor interaction and inflammation-related pathways.
Conclusion: The nine-mRNA methylation signature (DMRTA2, DRGX, FAM167A, FGGY, FOXI2, KRTAP2-1, TCTEX1D1, TTBK1, and UBE2QL1) may be a useful prognostic biomarker and tool for ccRCC patients. The present results would be helpful to elucidate the possible pathogenesis of ccRCC.

DOI: https://doi.org/10.1155/2021/8863799
Mediators Inflamm. 2021 ;2021 5318369

lncRNA SNHG14 Plays a Role in Sepsis-Induced Acute Kidney Injury by Regulating miR-93.

Chuanchuan Shi, Yuqian Zhao, Qi Li, Jianguo Li.

Acute kidney injury (AKI) is a common organ injury in sepsis, which leads to poor prognosis. Long noncoding RNA (lncRNA) small nucleolus RNA host gene 14 (SNHG14) was recognized to induce cell injury in LPS-induced acute lung injury and Parkinson's disease. We want to investigate the functions and mechanisms of SNHG14 in sepsis-induced AKI. Increased expression of SNHG14 was observed in LPS-induced HK-2 cells, and this was due to the activation of the TLR4/NF-κB pathway. In vitro studies showed that SNHG14 was involved in the oxidative stress, inflammation, and apoptosis of LPS-induced HK-2 cells. Further investigations confirmed that SNHG14 exerted the functions via miR-93 which could regulate the activation of NF-κB and STAT3 signaling by targeting IRAK4 and IL-6R. We also found that silencing SNHG14 also alleviated cellular injury processes of IL-1β and IL-6 in HK-2 cells via miR-93. We demonstrate that SNHG14 accelerates cellular injury in sepsis-induced AKI by activating IRAK4/NF-κB and IL-6R/STAT3 signaling via miR-93.

DOI: https://doi.org/10.1155/2021/5318369
Oncogene. 2021 Jan 28.

Androgen receptor promotes renal cell carcinoma (RCC) vasculogenic mimicry (VM) via altering TWIST1 nonsense-mediated decay through lncRNA-TANAR.

Bosen You, Yin Sun, Jie Luo, Keliang Wang, Qing Liu, Ruizhe Fang, Bingmei Liu, Fuju Chou, Ronghao Wang, Jialin Meng, Chi-Ping Huang, Shuyuan Yeh, Chawnshang Chang, Wanhai Xu.

While the androgen receptor (AR) may influence the progression of clear cell renal cell carcinoma (ccRCC), its role to impact vasculogenic mimicry (VM) to alter the ccRCC progression and metastasis remains obscure. Here, we demonstrated that elevated AR expression was positively correlated with tumor-originated vasculogenesis in ccRCC patients. Consistently, in vitro research revealed AR promoted VM formation in ccRCC cell lines via modulating lncRNA-TANAR/TWIST1 signals. Mechanism dissection showed that AR could increase lncRNA-TANAR (TANAR) expression through binding to the androgen response elements (AREs) located in its promoter region. Moreover, we found that TANAR could impede nonsense-mediated mRNA decay (NMD) of TWIST1 mRNA by direct interaction with TWIST1 5'UTR. A preclinical study using in vivo mouse model with orthotopic xenografts of ccRCC cells further confirmed the in vitro data. Together, these results illustrated that AR-mediated TANAR signals might play a crucial role in ccRCC VM formation and metastasis, and targeting this newly identified AR/TANAR/TWIST1 signaling may help in the development of a novel anti-angiogenesis therapy to better suppress the ccRCC progression.

DOI: https://doi.org/10.1038/s41388-020-01616-1
Aging (Albany NY). 2021 Jan 20. 12

Comprehensive analysis of lncRNAs N6-methyladenosine modification in colorectal cancer.

Luo Zuo, Hui Su, Qiao Zhang, Wei-Yu Wu, Yan Zeng, Xue-Mei Li, Jing Xiong, Lan-Fang Chen, Yan Zhou.

   BACKGROUND: Long non-coding RNAs (lncRNAs) and their N6-methyladenosine (M6A) modifications are involved in cancer occurrence and development.
METHODS: lncRNA M6A modification in colorectal cancer (CRC) was comprehensively analyzed for the first time.
RESULTS: M6A levels of lnRNAs in CRC tissues were higher than those in tumor-adjacent normal tissues. A total of 8,332 M6A peaks were detected in 6,690 lncRNAs in CRC tissues. Approximately 91% of the modified lncRNAs had unique M6A modification peaks. A total of 383 lncRNAs were differentially methylated in CRC, of which 48.24% had a length of 1-1,000 bp. Most of these were located on chromosomes 1, 2, 7, 11, 16 and 19; 42.3% were within a sense-overlapping exon. RNA sequencing identified 163 differentially expressed lncRNAs in CRC. GO and KEGG analyses revealed that genes near differentially-methylated or -expressed lncRNAs were associated with CRC occurrence and development. Methylation was positively correlated with lncRNA expression levels in CRC and tumor-adjacent normal tissues. More unmethylated than M6A methylated lncRNA molecules were detected. A competing endogenous RNA (ceRNA) and lncRNA-mRNA expression-regulation network revealed a regulatory relationship between lncRNAs, microRNAs (miRNAs), and mRNAs.
CONCLUSIONS: The findings may help improve our understanding of lncRNA function in colorectal cancer.

Keywords:  colorectal cancer; lncRNAs; m6A

DOI:  https://doi.org/10.18632/aging.202383