Beyond Back Splicing, a Still Poorly Explored World: Non-Canonical Circular RNAs

Exploring the Key Signaling Pathways and ncRNAs in Colorectal Cancer

Colorectal cancer (CRC) is the third most prevalent cancer to be diagnosed, and it has a substantial mortality rate. Despite numerous studies being conducted on CRC, it remains a significant health concern. The disease-free survival rates notably decrease as CRC progresses, emphasizing the urgency for effective diagnostic and therapeutic approaches. CRC development is caused by environmental factors, which mostly lead to the disruption of signaling pathways. Among these pathways, the Wingless/Integrated (Wnt) signaling pathway, Phosphatidylinositol 3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) signaling pathway, Mitogen-Activated Protein Kinase (MAPK) signaling pathway, Transforming Growth Factor-β (TGF-β) signaling pathway, and p53 signaling pathway are considered to be important. These signaling pathways are also regulated by non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). They have emerged as crucial regulators of gene expression in CRC by changing their expression levels. The altered expression patterns of these ncRNAs have been implicated in CRC progression and development, suggesting their potential as diagnostic and therapeutic targets. This review provides an overview of the five key signaling pathways and regulation of ncRNAs involved in CRC pathogenesis that are studied to identify promising avenues for diagnosis and treatment strategies.

Circular RNAs: characteristics, functions, mechanisms, and potential applications in thyroid cancer

Thyroid cancer (TC) is one of the most common endocrine malignancies, and its incidence has increased globally. Despite extensive research, the underlying molecular mechanisms of TC remain partially understood, warranting continued exploration of molecular markers for diagnostic and prognostic applications. Circular RNAs (circRNAs) have recently garnered significant attention owing to their distinct roles in cancers. This review article introduced the classification and biological functions of circRNAs and summarized their potential as diagnostic and prognostic markers in TC. Further, the interplay of circRNAs with PI3K/Akt/mTOR, Wnt/β-catenin, MAPK/ERK, Notch, JAK/STAT, and AMPK pathways is elaborated upon. The article culminates with an examination of circRNA's role in drug resistance of TC and highlights the challenges in circRNA research in TC.

Innovative construction of the first reliable catalogue of bovine circular RNAs

The aim of this study was to compare the circular transcriptome of divergent tissues in order to understand: i) the presence of circular RNAs (circRNAs) that are not exonic circRNAs, i.e. originated from backsplicing involving known exons and, ii) the origin of artificial circRNA (artif_circRNA), i.e. circRNA not generated in-vivo. CircRNA identification is mostly an in-silico process, and the analysis of data from the BovReg project (https://www.bovreg.eu/) provided an opportunity to explore new ways to identify reliable circRNAs. By considering 117 tissue samples, we characterized 23,926 exonic circRNAs, 337 circRNAs from 273 introns (191 ciRNAs, 146 intron circles), 108 circRNAs from small non-coding genes and nearly 36.6K circRNAs classified as other_circRNAs. Furthermore, for 63 of those samples we analysed in parallel data from total-RNAseq (ribosomal RNAs depleted prior to library preparation) with paired mRNAseq (library prepared with poly(A)-selected RNAs). The high number of circRNAs detected in mRNAseq, and the significant number of novel circRNAs, mainly other_circRNAs, led us to consider all circRNAs detected in mRNAseq as artificial. This study provided evidence of 189 false entries in the list of exonic circRNAs: 103 artif_circRNAs identified by total RNAseq/mRNAseq comparison using two circRNA tools, 26 probable artif_circRNAs, and 65 identified by deep annotation analysis. Extensive benchmarking was performed (including analyses with CIRI2 and CIRCexplorer-2) and confirmed 94% of the 23,737 reliable exonic circRNAs. Moreover, this study demonstrates the effectiveness of a panel of highly expressed exonic circRNAs (5-8%) in analysing the tissue specificity of the bovine circular transcriptome.

Circ_0006324 regulates cell proliferation, cell-cycle progression, apoptosis, and glycolysis of non-small cell lung cancer cells through miR-496/TRIM59 axis

Increasing evidence suggests that circular RNA (circRNA) plays an important role in non-small cell lung cancer (NSCLC) progression. This study aimed to investigate the role and potential molecular mechanism of circ_0006324 in NSCLC. The expression levels of circ_0006324, miR-496, miR-488-5p, and tripartite motif-containing 59 (TRIM59) mRNA were determined by quantitative real-time polymerase chain reaction (PCR). 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide assay, EdU assay, and flow cytometry were carried out to evaluate cell proliferation and apoptosis. The extracellular acidification rate and lactic acid production were examined to assess cell glycolysis. Western blot assay was used to detect protein levels. The target relationship of circ_0006324/miR-496/TRIM59 axis was validated by RNA pull-down assay, dual luciferase reporter assay, and radio immunoprecipitation assay. Xenograft tumor assay was performed to reveal the function of circ_0006324 in vivo. Circ_0006324 was upregulated in NSCLC and related to tumor node metastasis stage and distant metastasis. Knockdown of circ_00006324 impeded NSCLC cell proliferation, glycolysis, and promoted cell apoptosis. MiR-496 was verified as a target of circ_0006324 and circ_00006324 mediated the altering of cell proliferation, apoptosis, and glycolysis of NSCLC cells through targeting miR-496. TRIM59 was verified as a target of miR-496, and circ_0006324 positively regulated TRIM59 expression by targeting miR-496. Overexpression of TRIM59 could reverse the effects of circ_0006324 silencing on the proliferation, apoptosis, and glycolysis of NSCLC cells. Circ_0006324 knockdown impeded NSCLC tumor growth in vivo. Circ_0006324 functioned as a tumor promoter in NSCLC to promote cell proliferation, cell cycle progression, and glycolysis and inhibit cell apoptosis via miR-496/TRIM59 axis.

Discovery and Comprehensive Characterization of Novel Circular RNAs of the Apoptosis-Related BOK Gene in Human Ovarian and Prostate Cancer Cells, Using Nanopore Sequencing

CircRNAs have become a novel scientific research hotspot, and an increasing number of studies have shed light on their involvement in malignant progression. Prompted by the apparent scientific gap in circRNAs from apoptosis-related genes, such as BOK, we focused on the identification of novel BOK circRNAs in human ovarian and prostate cancer cells. Total RNA was extracted from ovarian and prostate cancer cell lines and reversely transcribed using random hexamer primers. A series of PCR assays utilizing gene-specific divergent primers were carried out. Next, third-generation sequencing based on nanopore technology followed by extensive bioinformatics analysis led to the discovery of 23 novel circRNAs. These novel circRNAs consist of both exonic and intronic regions of the BOK gene. Interestingly, the exons that form the back-splice junction were truncated in most circRNAs, and multiple back-splice sites were found for each BOK exon. Moreover, several BOK circRNAs are predicted to sponge microRNAs with a key role in reproductive cancers, while the presence of putative open reading frames indicates their translational potential. Overall, this study suggests that distinct alternative splicing events lead to the production of novel BOK circRNAs, which could come into play in the molecular landscape and clinical investigation of ovarian and prostate cancer.

Non-Coding RNAs Modulating Estrogen Signaling and Response to Endocrine Therapy in Breast Cancer

The largest part of human DNA is transcribed into RNA that does not code for proteins. These non-coding RNAs (ncRNAs) are key regulators of protein-coding gene expression and have been shown to play important roles in health, disease and therapy response. Today, endocrine therapy of ERα-positive breast cancer (BC) is a successful treatment approach, but resistance to this therapy is a major clinical problem. Therefore, a deeper understanding of resistance mechanisms is important to overcome this resistance. An increasing amount of evidence demonstrate that ncRNAs affect the response to endocrine therapy. Thus, ncRNAs are considered versatile biomarkers to predict or monitor therapy response. In this review article, we intend to give a summary and update on the effects of microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) on estrogen signaling in BC cells, this pathway being the target of endocrine therapy, and their role in therapy resistance. For this purpose, we reviewed articles on these topics listed in the PubMed database. Finally, we provide an assessment regarding the clinical use of these ncRNA types, particularly their circulating forms, as predictive BC biomarkers and their potential role as therapy targets to overcome endocrine resistance.

Identification of circular RNAs hosted by the RPGR ORF15 genomic locus

Mutations in the retina-specific isoform of the gene encoding retinitis pigmentosa GTPase regulator (RPGRorf15) cause X-linked retinitis pigmentosa, a severe and early onset inherited retinal degeneration. The underlying pathogenic mechanisms and variability in disease severity remain to be fully elucidated. The present study examines structural features of the ORF15 exonic region to provide new insights into the disease pathogenesis. Using canine and human RNA samples, we identified several novel RPGR ORF15-like linear RNA transcripts containing cryptic introns (exitrons) within the annotated exon ORF15. Furthermore, using outward-facing primers designed inside exitrons in the ORF15 exonic region, we found many of previously unidentified circular RNAs (circRNAs) that formed via back fusion of linear parts of the RPGRorf15 pre-mRNAs. These circRNAs (resistant to RNAse R treatment) were found in all studied cells and tissues. Notably, some circRNAs were present in cytoplasmic and polysomal RNA fractions. Although certain RPGR circRNAs may be cell type specific, we found some of the same circRNAs expressed in different cell types, suggesting similarities in their biogenesis and functions. Sequence analysis of RPGR circRNAs revealed several remarkable features, including identification of N6-methyladenosine (m6A) consensus sequence motifs and high prevalence of predictive microRNA binding sites pointing to the functional roles of these circRNAs. Our findings also illustrate the presence of non-canonical RPGR circRNA biogenesis pathways independent of the known back splicing mechanism. The obtained data on novel RPGR circRNAs further underline structural complexity of the RPGR ORF15 region and provide a potential molecular basis for the disease phenotypic heterogeneity.

From the comparative study of a circRNA originating from an mammalian ATXN2L intron to understanding the genesis of intron lariat-derived circRNAs

Circular intronic RNAs (ciRNAs) are still unexplored regarding mechanisms for their emergence. We considered the ATXN2L intron lariat-derived circular RNA (ciRNA-ATXN2L) as an opportunity to conduct a cross-species examination of ciRNA genesis. To this end, we investigated 207 datasets from 4 tissues and from 13 mammalian species. While in eight species, ciRNA-ATXN2L was never detected, in pigs and rabbits, ciRNA-ATXN2L was expressed in all tissues and sometimes at very high levels. Bovine tissues were an intermediate case and in macaques and cats, only ciRNA-ATXN2L traces were detected. The pattern of ciRNA-ATXN2L restricted to only five species is not related to a particular evolution of intronic sequences. To empower our analysis, we considered 221 additional introns including 80 introns where a lariat-derived ciRNA was previously described. The primary driver of micro-ciRNA genesis (< 155 nt as ciRNA-ATXN2L) appears to be the absence of a canonical "A" (i.e. a "tnA" located in the usual branching region) to build the lariat around this adenosine. The balance between available "non canonical-A" (no ciRNA genesis) and "non-A" (ciRNA genesis) for use as a branch point to build the lariat could modify the expression level of ciRNA-ATXN2L. In addition, the rare localization of the 2'-5' bond in an open RNA secondary structure could also negatively affect the lifetime of ciRNAs (macaque ciRNA-ATXN2L). Our analyses suggest that ciRNA-ATXN2L is likely a functionless splice remnant. This study provides a better understanding of the ciRNAs origin, especially drivers for micro ciRNA genesis.

Circular RNAs in atherosclerosis

Atherosclerosis (AS) is a chronic inflammatory lesion of the arterial vessel wall caused by a variety of complex factors. Furthermore, it is a major cause of cardiovascular disease and a leading cause of death. Circular RNAs (circRNAs) are a new family of endogenous non-coding RNAs with unique covalently closed loops that have sparked interest due to their unique characteristics and potential diagnostic and therapeutic applications in various diseases. A growing number of studies have shown that circRNAs can be used as biomarkers for the diagnosis and treatment of AS. In this article, we review the biogenesis, classification as well as functions of circRNA and summarize the research on circRNA as a diagnostic biomarker for AS. Finally, we describe the regulatory capacity of circRNA in AS pathogenesis through its pathogenesis and demonstrate the potential therapeutic role of circRNA for AS.

Circ_0002623 promotes bladder cancer progression by regulating the miR-1276/SMAD2 axis

Circular RNAs (circRNAs) are key regulatory factors in the development of multiple cancers. This study is targeted at exploring the effect of circ_0002623 on bladder cancer (BCa) progression and its mechanism. Circ_0002623 was screened out by analyzing the expression profile of circRNAs in BCa tissues. Circ_0002623, miR-1276 and SMAD2 mRNA expression levels in clinical sample tissues and cell lines were detected through quantitative real-time polymerase chain reaction (qRT-PCR). After circ_0002623 was overexpressed or silenced in BCa cells, the cell proliferation, migration and cell cycle were evaluated by CCK-8, BrdU, Transwell assay and flow cytometry. Tumor xenograft model was used to validate the biological function of circ_0002623 in vivo. Bioinformatics analysis and dual-luciferase reporter gene assay were conducted for analyzing and confirming, respectively, the targeted relationship between circ_0002623 and miR-1276, as well as between miR-1276 and SMAD2. The regulatory effects of circ_0002623 and miR-1276 on the expression levels of TGF-β, WNT1 and SMAD2 in BCa cells were detected by Western blot. We reported that, in BCa tissues and cell lines, circ_0002623 was up-regulated, whereas miR-1276 was down-regulated. Circ_0002623 positively regulated BCa cell proliferation, migration and cell cycle progression. Additionally, circ_0002623 could competitively bind with miR-1276 to increase the expression of SMAD2, the target gene of miR-1276. Furthermore, circ_0002623 could regulate the expression of TGF-β and WNT1 via modulating miR-1276 and SMAD2. This study helps to better understand the molecular mechanism underlying BCa progression.

Computational Analysis of Transposable Elements and CircRNAs in Plants

This chapter provides two main contributions: (1) a description of computational tools and databases used to identify and analyze transposable elements (TEs) and circRNAs in plants; and (2) data analysis on public TE and circRNA data. Our goal is to highlight the primary information available in the literature on circular noncoding RNAs and transposable elements in plants. The exploratory analysis performed on publicly available circRNA and TEs data help discuss four sequence features. Finally, we investigate the association on circRNAs:TE in plants in the model organism Arabidopsis thaliana.

The design and synthesis of circular RNAs

Circular RNAs (circRNAs) are a novel class of RNAs distinguished by their single-stranded, covalently-closed topology. Although initially perceived as rare byproducts of aberrant splicing, circRNAs are now recognized as ubiquitously expressed and functionally significant. These discoveries have led to a growing need for ways to model circRNAs in living cells to advance our understanding of their biogenesis, regulation, and function, and to adopt them as new technologies for application within research and medicine. In this review, we provide an updated summary of approaches used to produce circRNAs in vitro and in vivo, the latter of which has grown considerably in recent years. Given increased interest in the unique functions carried out by individual circRNAs, we further dedicate a section on how to customize synthesized circRNAs for specific biological roles. We focus on the most common applications, including designing circRNAs for protein delivery, to target miRNAs and proteins, to act as fluorescent reporters, and to modulate cellular immunity.

The potential role of hsa_circ_0001079 in androgenetic alopecia via sponging hsa-miR-136-5p

Background

Androgenetic alopecia (AGA) is an androgen‐dependent polygenic hereditary disease.

Methods

Diseased hair follicles from 5 AGA patients and normal hair follicles from 5 healthy individuals were selected as specimens to carry out whole transcriptome sequencing. Multiple high‐expression circular RNAs (circRNAs) were screened from the diseased group. We further verified the presence of the circRNAs in the clinical specimens by real‐time fluorescence quantitative PCR (qRT‐PCR).

Results

In total, 100 circRNAs were significantly upregulated, and 184 circRNAs were significantly downregulated. The top 10 upregulated circRNAs were hsa_circ_0101041, hsa_circ_0001578, hsa_circ_0135062, hsa_circ_0002980, hsa_circ_0005062, hsa_circ_0072688, hsa_circ_0133954, hsa_circ_0001079, hsa_circ_0005974, hsa_circ_0000489. The top 10 downregulated circRNAs were hsa_circ_0001278, hsa_circ_0031482, hsa_circ_0008285, hsa_circ_0003784, hsa_circ_0077096, hsa_circ_0001148, hsa_circ_0006886, hsa_circ_0000638, hsa_circ_0084521, and hsa_circ_0101074. Among top 10 upregulated circRNAs, hsa_circ_0001079 showed significantly high expression via large‐sample verification and clinical application potential. Based on a database comparison and base pairing analysis, we found that has‐miR‐136‐5p bound to hsa_circ_0001079 and that hsa‐miR‐136‐5p had potential binding sites with Wnt5A.

Conclusion

In summary, through high‐throughput sequencing and bioinformatic analysis, a potential diagnostic marker for alopecia and a key circRNA that might adsorb microRNA (miRNA) through a sponging mechanism, thus mediating alopecia, were discovered in this study.

Comparative Analysis of the Circular Transcriptome in Muscle, Liver, and Testis in Three Livestock Species

Circular RNAs have been observed in a large number of species and tissues and are now recognized as a clear component of the transcriptome. Our study takes advantage of functional datasets produced within the FAANG consortium to investigate the pervasiveness of circular RNA transcription in farm animals. We describe here the circular transcriptional landscape in pig, sheep and bovine testicular, muscular and liver tissues using total 66 RNA-seq datasets. After an exhaustive detection of circular RNAs, we propose an annotation of exonic, intronic and sub-exonic circRNAs and comparative analyses of circRNA content to evaluate the variability between individuals, tissues and species. Despite technical bias due to the various origins of the datasets, we were able to characterize some features (i) (ruminant) liver contains more exonic circRNAs than muscle (ii) in testis, the number of exonic circRNAs seems associated with the sexual maturity of the animal. (iii) a particular class of circRNAs, sub-exonic circRNAs, are produced by a large variety of multi-exonic genes (protein-coding genes, long non-coding RNAs and pseudogenes) and mono-exonic genes (protein-coding genes from mitochondrial genome and small non-coding genes). Moreover, for multi-exonic genes there seems to be a relationship between the sub-exonic circRNAs transcription level and the linear transcription level. Finally, sub-exonic circRNAs produced by mono-exonic genes (mitochondrial protein-coding genes, ribozyme, and sno) exhibit a particular behavior. Caution has to be taken regarding the interpretation of the unannotated circRNA proportion in a given tissue/species: clusters of circRNAs without annotation were characterized in genomic regions with annotation and/or assembly problems of the respective animal genomes. This study highlights the importance of improving genome annotation to better consider candidate circRNAs and to better understand the circular transcriptome. Furthermore, it emphasizes the need for considering the relative “weight” of circRNAs/parent genes for comparative analyses of several circular transcriptomes. Although there are points of agreement in the circular transcriptome of the same tissue in two species, it will be not possible to do without the characterization of it in both species.