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International Journal of Molecular Sciences
  • Review
  • Open Access

13 April 2020

Potential Roles of Long Noncoding RNAs as Therapeutic Targets in Renal Fibrosis

,
and
1
Department of Urology, College of Medicine, Catholic University of Daegu, Gyeongsan 42472, Korea
2
Department of Pathology, College of Medicine, Catholic University of Daegu, Gyeongsan 42472, Korea
*
Author to whom correspondence should be addressed.
This article belongs to the Special Issue Fibrosis-Related lncRNA

Abstract

Many studies have made clear that most of the genome is transcribed into noncoding RNAs, including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), both of which can affect different cell features. LncRNAs are long heterogeneous RNAs that regulate gene expression and a variety of signaling pathways involved in cellular homeostasis and development. Several studies have demonstrated that lncRNA is an important class of regulatory molecule that can be targeted to change cellular physiology and function. The expression or dysfunction of lncRNAs is closely related to various hereditary, autoimmune, and metabolic diseases, and tumors. Specifically, recent work has shown that lncRNAs have an important role in kidney pathogenesis. The effective roles of lncRNAs have been recognized in renal ischemia, injury, inflammation, fibrosis, glomerular diseases, renal transplantation, and renal-cell carcinoma. The present review focuses on the emerging role and function of lncRNAs in the pathogenesis of kidney inflammation and fibrosis as novel essential regulators. Although lncRNAs are important players in the initiation and progression of many pathological processes, their role in renal fibrosis remains unclear. This review summarizes the current understanding of lncRNAs in the pathogenesis of kidney fibrosis and elucidates the potential role of these novel regulatory molecules as therapeutic targets for the clinical treatment of kidney inflammation and fibrosis.

1. Introduction

Data analyses from genome projects have shown that less than 2% of transcribed genes encode protein-coding RNA, and that most noncoding transcripts are more than 200 base pairs and make up a group of long noncoding RNA (lncRNA) [,,]. These lncRNAs may have their own promoters and be located between protein-coding genes []. Emerging evidence shows that lncRNAs play key roles in a variety of biological processes such as proliferation and/or apoptosis through complicated mechanisms, and are also important in the development of kidney diseases []. Recently, lncRNAs were found to have potential use in diagnosis, and as biological markers in predicting prognosis and targets for the treatment of incurable diseases [], particularly as highly disease-specific ideal targets in kidney disease [,]. Although lncRNAs are important players in the initiation and progression of many diseases, the role of those associated with renal fibrosis remains largely undefined [].
LncRNAs are tissue-specific, and their expressions in human organs is lower than protein-coding genes []. Compared to protein-coding RNAs, lncRNAs are highly specific to organs and cell types, making them candidates as diagnostic biomarkers and gene-therapy targets []. Although lncRNAs are found in both the nucleus and cytoplasm, many of them are predominantly found in the nucleus, suggesting their important role in gene transcription [,,]. Many studies have demonstrated that lncRNA is an important regulatory molecule that can be targeted to modulate cellular physiology and functions in the pathophysiological progress of tumors, and of autoimmune and cardiovascular diseases [,,,,,]. The functional roles of lncRNAs in kidney pathogenesis have been unfolded in the past few years [,].
The effective roles of lncRNAs in kidney disease have been recognized in renal ischemia, injury, inflammation, fibrosis, glomerular diseases, renal transplantation, and renal-cell carcinoma []. Huang et al. [] reported that lncRNA, activated by TGF-β1, is a promising biomarker in predicting the acute rejection (AR) of renal allografts. However, their underlying mechanisms are still poorly understood. Recent application of next-generation sequencing has increased our knowledge of lncRNAs relating to various chronic fibrosis-related diseases []. Zhou et al. [,] identified a number of Smad3-associated lncRNAs that are related to renal inflammation and fibrosis in mouse models of kidney disease, suggesting that TGF-β/Smad3-associated lncRNAs may have regulatory roles in renal fibrosis and inflammation. However, little is known about how lncRNAs regulate TGF-β1/Smad signaling in kidney disease. Then, a total of 17 lncRNAs were selected after searching the PubMed for the key words of kidney, fibrosis, and lncRNA (Table 1).
Table 1. LncRNAs related to renal fibrosis.
The present review summarizes the latest advances in understanding the regulatory functions of lncRNAs, and their roles in the prevention and processes of renal fibrosis. Understanding the molecular mechanism of lncRNAs in pathophysiological kidney processes may contribute to developing more effective therapeutics to prevent renal fibrosis.

2. Classification and Mechanisms of lncRNA Functions

NcRNAs are classified according to size as small (shorter than 200 nucleotides) and long (longer than 200 nucleotides) transcripts. Small ncRNAs, including miRNAs and small interfering RNAs (siRNA) are involved in the regulation of various biological processes in kidney diseases []. Many lncRNAs are not easily classified across particular categories, and the same lncRNAs may be listed in different groups in all classifications [,]. Moreover, since the vast majority of lncRNAs remain functionally uncharacterized, the classification is difficult.
It was reported that lncRNAs can regulate the expression of target genes via a variety of mechanisms, although complete understanding is yet to be achieved [,,,]. Many studies demonstrated that these molecules play critical roles in the regulation of specific cellular processes, specifically in protein-coding gene expression at the epigenetic, transcriptional, and post-transcriptional levels [,,,,]. Taken together, these distinct molecular mechanisms allow dysregulated lncRNAs to up- or downregulate gene expression, thereby demonstrating their regulatory functions in various biological processes. The complicated mechanisms that underlie such regulatory behaviors require further investigation.
Here, on the basis of previous reports [], we suggest that the presumed molecular mechanisms of lncRNAs are divided into four categories according to their function at the nucleus or cytoplasm (Figure 1): (1) transcription activator, binding to the transcription factor, controls the epigenetic state of particular genes, and is involved in transcriptional regulation in the nucleus (Figure 1A); (2) transcription repressor, also binding to the transcription factor, inhibits gene expression by occupying the DNA-binding site of the transcription factor in the nucleus (Figure 1B); (3) miRNA sequester, binding with miRNAs, causes increased translation efficiency of mRNA in the cytoplasm (Figure 1C); and (4) RNA regulator competes with miRNA-mediated inhibition by, for example, having miRNA embedded in the lncRNA, leading to decreased mRNA expression in the cytoplasm (Figure 1D). There has been, however, no systematic and unambiguous classification of lncRNAs to date, and many existing classifications are conflicting and overlapping [].
Figure 1. Long noncoding RNA (lncRNA) functions at nucleus and cytoplasm. (A) Transcription activator involved in gene expression and transcription regulation in nucleus; (B) transcription repressor inhibits gene expression by occupying DNA binding site in nucleus; (C) miRNA sequester can function as miRNA decoy to sequester miRNAs from their mRNA targets; (D) RNA regulator decreases mRNA expression as RNA regulator in cytoplasm.
For their epigenetic role, the majority of lncRNAs localize to the nucleus, and increasing evidence indicates that nuclear lncRNAs epigenetically regulate gene expression by altering the activity of the transcription factor []. At the transcriptional level, lncRNAs regulate gene expression by guiding transcription factors to the promoter region of target genes to regulate their transcription, and by functioning as transcriptional activators or repressors to mediate gene transcription [,,,,,,]. At the post-transcriptional level, lncRNAs regulate the expression of genes responsible for biological functions by modulating mRNA stability, translation, and degradation [].
Unlike miRNAs, which are RNA segments of 22 nucleotides in length and function exclusively at the post-transcriptional level [], lncRNAs participate in both the transcriptional and post-transcriptional regulation of genes. LncRNAs can act as sponges for miRNAs and thereby negatively regulate them [,]. Another regulatory mechanism through which lncRNAs control gene expression is by controlling miRNA biogenesis, distribution, and degradation []. Although the underlying mechanisms are still largely unknown, the tissue- and disease-specific characteristics of lncRNAs make them a potential biomarker and therapeutic target for clinical settings.

4. Conclusions

Recent evidence indicated that lncRNAs represent a heterogeneous class of transcripts that are incompletely understood but rapidly emerging as potential drug targets and therapeutic candidates. Continued investigations based on the knowledge presented here will undoubtedly overcome the remaining challenges in the field of fibrosis-related diseases, and this review represents a potential research strategy for renal fibrosis-related lncRNAs. First, with the application of newly developed technologies such as next-generation sequencing, more new lncRNAs related with renal interstitial fibrosis could be found in the near future. Second, another new biological marker that can easily be detected in urine samples could be developed. Third, novel synthetic oligodeoxynucleotides, which are another ncRNA type that could prevent the function of fibrosis-related lncRNA, could be developed and used for clinical trials. Further studies are required to examine the toxicity and the pharmacokinetics of lncRNAs, and evaluating their biological properties is also important.

Author Contributions

Writing—original-draft preparation, H.J.J.; writing—review and editing, K.-K.P.; visualization, H.-J.K. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the National Research Foundation of Korea, grant funded by the Korean government (no. NRF-2019R1G1A1010882).

Conflicts of Interest

The authors declare no conflict of interest.

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