Circular RNAs in Cancer: Biogenesis, Function, and Clinical Significance

doi:10.1016/j.trecan.2020.01.012

Trends in Cancer

Volume 6, Issue 4, April 2020, Pages 319-336

https://doi.org/10.1016/j.trecan.2020.01.012 Get rights and content

Highlights

Circular RNA (circRNA) is a class of single-stranded RNAs with a covalently closed loop structure generated from back-splicing of precursor mRNA (pre-mRNA), a process highly regulated by cis-acting elements and trans-acting factors.
CircRNA regulates gene expression and/or protein function in a diversity of cellular processes via acting as miRNA sponges, protein decoys, encoding peptides, or other action modes.
CircRNAs are aberrantly expressed in cancers and these dysregulated circRNAs may play oncogenic or tumor suppressive roles in cancer initiation and progression.
Due to their abundance, high stability, and distinctive expression pattern, circRNAs may potentially serve as biomarkers and therapeutic targets for cancer patients.

Circular RNA (circRNA) is a class of single-stranded molecules with tissue/development-specific expression patterns. Unlike linear RNA, circRNA forms a covalently closed loop produced from ‘back-splicing’ of primary transcripts, conferring on them inherent resistance to exonucleolytic RNA decay. Increasing evidence demonstrates that many circRNAs exert important biological functions by acting as miRNA inhibitors (‘sponges’), protein ‘decoys’, or by encoding small peptides. Importantly, circRNAs are aberrantly expressed in cancer and play indispensable oncogenic or tumor suppressive roles during tumor development and progression. In this review, we summarize the biogenesis, turnover, and involvements of circRNAs in cancer and also discuss their potential as diagnostic biomarkers or therapeutic targets.

Section snippets

Overview

Cancer involves broad variations in genome, transcriptome, and proteome. The majority of transcriptome studies focus on dynamic changes of linear transcripts during cancer initiation and progression, overlooking the landscape of circular RNA (circRNA). Unlike linear RNA with 5′ and 3′ ends, circRNA generates a covalently closed loop structure. As early as the 1970s, circRNAs were found in the genome of viruses and in the cytoplasm of eukaryotic cells [1., 2., 3.]. Due to limitations in

CircRNA Biogenesis

CircRNAs are primarily generated from exonic or/and intronic sequences of primary transcripts by back-splicing that competes with canonical mRNA splicing. Based on the diversity of source sequences, circRNA can be grouped into three major categories: exonic circRNAs (EcRNAs), exon–intron circRNAs (EIciRNAs), and intron-derived circRNAs [6,7,10,11,22]. The latter includes circular intronic RNAs (ciRNAs) from pre-mRNAs and tRNA intronic circular RNAs (tricRNAs) [10,22,23]. For most circRNAs,

Biological Function of CircRNA

CircRNAs appear primarily as regulatory noncoding RNAs, either: (i) directly through regulating gene transcription and splicing, or (ii) indirectly through modulating other regulators such as miRNA and protein. A subset of circRNAs are also characterized as regulatory coding RNAs encoding small functional peptides.

Dysregulation of CircRNA in Cancer

Recently, the focus on characterizing the role of circRNA in disease is growing. Accumulating evidence indicates that circRNA expression is commonly dysregulated in a large number of malignancies, with distinct expression patterns in different cancer types (Table 1). For instance, circMTO1 is dramatically downregulated in hepatocellular carcinoma (HCC) and cervical cancer [58,59], whereas circPVT1 is significantly upregulated in gastric cancer, leukemia, as well as head and neck squamous cell

The Role of CircRNA in Cancer

Emerging evidence demonstrates that dysregulated circRNAs play tumor suppressive or oncogenic roles in cancer initiation and progression to affect many cellular functions, such as (i) sustaining proliferative signaling, (ii) promotion of cell migration and invasion, (iii) resistance to cell apoptosis, and (iv) induction of angiogenesis.

Clinical Significance of CircRNA in Cancer

The high abundance, stability, as well as the unique expression signatures associated with cancer progression and outcome, highlight the potentials of circRNA as diagnostic and prognostic biomarkers. Moreover, certain circRNAs have been characterized as functional molecules contributing to cancer progression, rendering them as promising therapeutic targets. Here, we discuss the clinical implications of circRNAs in cancer.

Concluding Remarks

High-throughput sequencing technology accelerated the illustration of the circRNA landscape in eukaryotic cells. Increasing evidence indicates that circRNAs play pivotal roles in physiological and pathological processes, particularly in cancer. Although great progress has been achieved in identifying and characterizing circRNAs, many critical unknowns and limitations need to be addressed in further exploration (see Outstanding Questions).

CircRNA dysregulation occurs in a variety of cancer

Acknowledgments

This work was supported by National Key R&D Program of China (2016YFA0502204 and 2017YFA0504304), National Natural Science Foundation of China (81772960 and 81903082), Fundamental Research Funds for the Central Universities (2018SCUH0018), Sichuan Science and Technology Program (2019JDTD0013), the 1.3.5 Project for Disciplines of Excellence, West China Hospital, Sichuan University (ZYJC18030), and National Postdoctoral Program for Innovative Talents of China (BX20190225).

Glossary

Alu repeats: sequences that are about 280 bp in length and considered as the most abundant class of dispersed repeat elements in the human genome.
Back-splicing: a splicing event in which a 5′ splice site is joined to an upstream 3′ splice site rather than a downstream 3′ splice site.
Canonical splicing: a form of RNA processing in which introns are removed from pre-mRNA and exons are connected together to produce a mature mRNA. During splicing, a 5′ splice site of an exon is joined to a 3′ splice site

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Unraveling the crosstalk: circRNAs and the wnt signaling pathway in cancers of the digestive system
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Circular RNA (circRNA) is a unique type of noncoding RNA molecule characterized by its closed-loop structure. Functionally versatile, circRNAs play pivotal roles in gene expression regulation, protein activity modulation, and participation in cell signaling processes. In the context of cancers of the digestive system, the Wnt signaling pathway holds particular significance. Anomalous activation of the Wnt pathway serves as a primary catalyst for the development of colorectal cancer. Extensive research underscores the notable participation of circRNAs associated with the Wnt pathway in the progression of digestive system tumors. These circRNAs exhibit pronounced dysregulation across esophageal cancer, gastric cancer, liver cancer, colorectal cancer, pancreatic cancer, and cholangiocarcinoma. Furthermore, the altered expression of circRNAs linked to the Wnt pathway correlates with prognostic factors in digestive system tumors. Additionally, circRNAs related to the Wnt pathway showcase potential as diagnostic, therapeutic, and prognostic markers within the realm of digestive system tumors. This comprehensive review outlines the interplay between circRNAs and the Wnt signaling pathway in cancers of the digestive system. It seeks to provide a comprehensive perspective on their association while delving into ongoing research that explores the clinical applications of circRNAs associated with the Wnt pathway.
Potential therapeutic applications of circular RNA in acute kidney injury
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Acute kidney injury (AKI) is a common clinical syndrome characterized by a rapid deterioration in renal function, manifested by a significant increase in creatinine and a sharp decrease in urine output. The incidence of morbidity and mortality associated with AKI is on the rise, with most patients progressing to chronic kidney disease or end-stage renal disease. Treatment options for patients with AKI remain limited. Circular RNA (circRNA) is a wide and diverse class of non-coding RNAs that are present in a variety of organisms and are involved in gene expression regulation. Studies have shown that circRNA acts as a competing RNA, is involved in disease occurrence and development, and has potential as a disease diagnostic and prognostic marker. CircRNA is involved in the regulation of important biological processes, including apoptosis, oxidative stress, and inflammation. This study reviews the current status and progress of circRNA research in the context of AKI.
Hsa_circ_0003356 suppresses gastric cancer progression via miR-556-5p/FKBP5 axis
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CircRNAs are implicated in the tumorigenesis of various human cancers. This study aims to explore how circ_0003356 contributes to the development of gastric cancer (GC).
Circ_0003356 expression was analyzed in GSE184882 dataset and validated in our cohort of GC patients and human GC cell lines. The correlations between circ_0003356 levels and prognostic parameters were analyzed. The contribution of circ_0003356 in GC cell malignant behaviors such as cell survival, apoptosis and invasion were investigated by circ_0003356 overexpression in GC cell lines. The downstream targets of circ_0003356 were predicted and verified in vitro and in vivo. The in vivo function of circ_0003356 was studied as well in a xenograft mouse model.
Circ_0003356 expressed at a low level in human GC tissues and cells, which was closely associated with poor outcome of GC patients. Circ_0003356 overexpression induced GC cell apoptosis while depressed the growing, migration and invasive abilities through miR-556-5p/FKBP5 axis. In vivo model showed retarded tumor growth when circ_0003356-overexpressed cells were inoculated.
Circ_0003356 is identified as a potential biomarker of the prognosis of human gastric cancer, and circ_0003356/miR-556-5p/FKBP5 axis could be a promising target in gastric cancer treatment.
A unique circ_0067716/EIF4A3 double-negative feedback loop impacts malignant transformation of human bronchial epithelial cells induced by benzo(a)pyrene
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Benzo(a)pyrene as a pervasive environmental contaminant is characterized by its substantial genotoxicity, and epidemiological investigations have established a correlation between benzo(a)pyrene exposure and the susceptibility to human lung cancer. Notably, much research has focused on the link between epigenetic alterations and lung cancer induced by chemicals, although circRNAs are also emerging as relevant contributors to the carcinogenic process of benzo(a)pyrene. In this study, we identified circ_0067716 as being significantly upregulated in response to stress injury and downregulated during malignant transformation induced by benzo(a)pyrene-7,8-diol-9,10-epoxide (BPDE) in human bronchial epithelial cells. The observed differential expression of circ_0067716 in cells treated with BPDE for varying durations suggests a strong correlation between this circRNA and BPDE exposure. The tissue samples of lung cancer patients also suggest that a lower circ_0067716 expression is associated with BPDE-DNA adduct levels. Remarkably, we demonstrate that EIF4A3, located in the nucleus, interacts with the flanking sequences of circ_0067716 and inhibits its biogenesis. Conversely, circ_0067716 is capable of sequestering EIF4A3 in the cytoplasm, thereby preventing its translocation into the nucleus. EIF4A3 and circ_0067716 can form a double-negative feedback loop that could be affected by BPDE. During the initial phase of BPDE exposure, the expression of circ_0067716 was increased in response to stress injury, resulting in cell apoptosis through the involvement of miR-324-5p/DRAM1/BAX axis. Subsequently, as cellular adaptation progressed, long-term induction due to BPDE exposure led to an elevated EIF4A3 and a reduced circ_0067716 expression, which facilitated the proliferation of cells by stabilizing the PI3K/AKT pathway. Thus, our current study describes the effects of circ_0067716 on the genotoxicity and carcinogenesis induced by benzo(a)pyrene and puts forwards to the possible regulatory mechanism on the occurrence of smoking-related lung cancer, providing a unique insight based on epigenetics.
CircRAPGEF5 sponges miR-582-3p and targets KIF3A to regulate bladder cancer cell proliferation, migration and invasion
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Bladder cancer (BCa) is a common malignant disease with high recurrence and poor prognosis. Several circular RNAs (circRNAs) have been found to be associated with the malignant progression of bladder cancer (BCa). Here, the aim of this study was to investigate the expression, role and mechanism of circRAPGEF5 in BCa progression.
Quantitative real-time PCR (qRT-PCR) and immunoblotting were used to detect gene and protein expression levels. In vitro functional studies were performed using CCK-8, colony formation, wound healing and Transwell assays, respectively, and a mouse xenograft tumor model was established to perform in vivo experiments. Bioinformatic predictions as well as luciferase reporter assays and RNA pull-down assays were used to probe circRAPGEF5-mediated competitive endogenous RNA (ceRNA) network.
CircRAPGEF5 was significantly overexpressed in BCa patients (p < 0.05), indicating a potential unsatisfactory prognosis. Functionally, knockdown of circRAPGEF5 inhibited the growth, migration and invasion of BCa cells in vitro (p < 0.05), as well as BCa growth in vivo (p < 0.05). Mechanistically, circRAPGEF5 acted as a sponge for miR-582-3p and targeted kinesin family member 3A (KIF3A). In addition, rescue experiments showed that inhibition of miR-582-3p or overexpression of KIF3A reversed the anticancer effects of circRAPGEF5 knockdown on BCa cells (p < 0.05).
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Circular RNAs (circRNAs) have been recognized as key components in the intricate regulatory network of the KRAS pathway across various cancers. The KRAS pathway, a central signalling cascade crucial in tumorigenesis, has gained substantial emphasis as a possible therapeutic target. CircRNAs, a subgroup of non-coding RNAs known for their closed circular arrangement, play diverse roles in gene regulation, contributing to the intricate landscape of cancer biology. This review consolidates existing knowledge on circRNAs within the framework of the KRAS pathway, emphasizing their multifaceted functions in cancer progression. Notable circRNAs, such as Circ_GLG1 and circITGA7, have been identified as pivotal regulators in colorectal cancer (CRC), influencing KRAS expression and the Ras signaling pathway. Aside from their significance in gene regulation, circRNAs contribute to immune evasion, apoptosis, and drug tolerance within KRAS-driven cancers, adding complexity to the intricate interplay. While our comprehension of circRNAs in the KRAS pathway is evolving, challenges such as the diverse landscape of KRAS mutant tumors and the necessity for synergistic combination therapies persist. Integrating cutting-edge technologies, including deep learning-based prediction methods, holds the potential for unveiling disease-associated circRNAs and identifying novel therapeutic targets. Sustained research efforts are crucial to comprehensively unravel the molecular mechanisms governing the intricate interplay between circRNAs and the KRAS pathway, offering insights that could potentially revolutionize cancer diagnostics and treatment strategies.

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²: These authors contributed equally to this work

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Trends in Cancer

ReviewCircular RNAs in Cancer: Biogenesis, Function, and Clinical Significance

Highlights

Section snippets

Overview

CircRNA Biogenesis

Biological Function of CircRNA

Dysregulation of CircRNA in Cancer

The Role of CircRNA in Cancer

Clinical Significance of CircRNA in Cancer

Concluding Remarks

Acknowledgments

Glossary

Cell

Mol. Cell

Mol. Cell

Mol. Cancer

Cell

Mol. Cancer

Cell

Cell Rep.

Cell

Cell Rep.

Biomed. Pharmacother.

Cancer Lett.

Biochem. Biophys. Res. Commun.

Int. J. Biochem. Cell Biol.

Cell

J. Hepatol.

Mol. Cancer

Genome Biol.

Cell

Biochem. Biophys. Res. Commun.

Cancer Lett.

Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures

Proc. Natl. Acad. Sci. U. S. A.

Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells

Nature

Mis-splicing yields circular RNA molecules

FASEB J.

Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types

PLoS One

Circular RNAs are abundant, conserved, and associated with ALU repeats

RNA

Cell-type specific features of circular RNA expression

PLoS Genet.

Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development

Genome Biol.

Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing

Nucleic Acids Res.

Exon-intron circular RNAs regulate transcription in the nucleus

Nat. Struct. Mol. Biol.

Circular RNAs are a large class of animal RNAs with regulatory potency

Nature

Natural RNA circles function as efficient microRNA sponges

Nature

Identifying and characterizing circRNA-protein interaction

Theranostics

The translational landscape of the human heart

Cell

Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function

Science

Circular RNAs open a new chapter in cardiovascular biology

Nat. Rev. Cardiol.

The landscape of circular RNA in cancer

Cell

The biogenesis, biology and characterization of circular RNAs

Nat. Rev. Genet.

Metazoan tRNA introns generate stable circular RNAs in vivo

RNA

Molecular determinants of metazoan tricRNA biogenesis

Nucleic Acids Res.

The biogenesis and emerging roles of circular RNAs

Nat. Rev. Mol. Cell Biol.

Short intronic repeat sequences facilitate circular RNA production

Genes Dev.

DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome

Nature

Circular RNA biogenesis can proceed through an exon-containing lariat precursor

Elife

Review
Circular RNAs in Cancer: Biogenesis, Function, and Clinical Significance

YTHDC1 mediates nuclear export of N⁶-methyladenosine methylated mRNAs