Seeing Is Believing: Visualizing Circular RNAs

Unveiling Pharmacogenomics Insights into Circular RNAs: Toward Precision Medicine in Cancer Therapy

Pharmacogenomics is revolutionizing precision medicine by enabling tailored therapeutic strategies based on an individual genetic and molecular profile. Circular RNAs (circRNAs), a distinct subclass of endogenous non-coding RNAs, have recently emerged as key regulators of drug resistance, tumor progression, and therapeutic responses. Their covalently closed circular structure provides exceptional stability and resistance to exonuclease degradation, positioning them as reliable biomarkers and novel therapeutic targets in cancer management. This review provides a comprehensive analysis of the interplay between circRNAs and pharmacogenomics, focusing on their role in modulating drug metabolism, therapeutic efficacy, and toxicity profiles. We examine how circRNA-mediated regulatory networks influence chemotherapy resistance, alter targeted therapy responses, and impact immunotherapy outcomes. Additionally, we discuss emerging experimental tools and bioinformatics techniques for studying circRNAs, including multi-omics integration, machine learning-driven biomarker discovery, and high-throughput sequencing technologies. Beyond their diagnostic potential, circRNAs are being actively explored as therapeutic agents and drug delivery vehicles. Recent advancements in circRNA-based vaccines, engineered CAR-T cells, and synthetic circRNA therapeutics highlight their transformative potential in oncology. Furthermore, we address the challenges of standardization, reproducibility, and clinical translation, emphasizing the need for rigorous biomarker validation and regulatory frameworks to facilitate their integration into clinical practice. By incorporating circRNA profiling into pharmacogenomic strategies, this review underscores a paradigm shift toward highly personalized cancer therapies. circRNAs hold immense potential to overcome drug resistance, enhance treatment efficacy, and optimize patient outcomes, marking a significant advancement in precision oncology.

Live-cell imaging of circular and long noncoding RNAs associated with FUS pathological aggregates by Pepper fluorescent RNA

Lately, important advancements in visualizing RNAs in fixed and live cells have been achieved. Although mRNA imaging techniques are well-established, the development of effective methods for studying noncoding RNAs (ncRNAs) in living cells is still challenging but necessary, as they show a variety of functions and intracellular localizations, including participation in highly dynamic processes like phase transition, which is still poorly studied in vivo. Addressing this issue, we tagged two exemplary ncRNAs with the fluorescent RNA (fRNA) Pepper. Specifically, we showed that circ-HDGFRP3 interacts with p-bodies and is recruited in pathological FUS aggregates in a dynamic fashion, and we super-resolved its distribution in such condensates via structured illumination microscopy. Moreover, we tracked the long noncoding RNA (lncRNA) nHOTAIRM1, a motor neuron-specific constituent of stress granules, monitoring its behavior throughout the oxidative-stress response in physiological and pathological conditions. Overall, as fRNA development progresses, our work demonstrates an effective use of Pepper for monitoring complex processes, such as phase transition, in living cells through the visualization of circular RNAs (circRNAs) and lncRNAs with super-resolution power.

Past, present, and future strategies for detecting and quantifying circular RNA variants

Circular RNAs (circRNAs) are a family of covalently closed RNA transcripts ubiquitous across the eukaryotic kingdom. CircRNAs are generated by a class of alternative splicing called backsplicing, with the resultant circularization of a part of parental RNA producing the characteristic backsplice junction (BSJ). Because of the noncontiguous sequence of the BSJ with respect to the DNA genome, circRNAs remained hidden in plain sight through over a decade of RNA next-generation sequencing, yet over 3 million unique circRNA transcripts have been illuminated in the past decade alone. CircRNAs are expressed in a cell type-specific manner, are highly stable, with many examples of circRNAs being evolutionarily conserved and/or functional in specific contexts. However, circRNAs can be very lowly expressed and predictions of the circRNA context from BSJ-spanning reads alone can confound extrapolation of the exact sequence composition of the circRNA transcript. For these reasons, specific and ultrasensitive detection, combined with enrichment, bespoke bioinformatics pipelines and, more recently, long-read, highly processive sequencing is becoming critical for complete characterization of all circRNA variants. Concomitantly, the need for targeted detection and quantification of specific circRNAs has sparked numerous laboratory-based and commercial approaches to visualize circRNAs in cells and quantify them in biological samples, including biospecimens. This review focuses on advancements in the detection and quantification of circRNAs, with a particular focus on recent next-generation sequencing approaches to bolster detection of circRNA variants and accurately normalize between sequencing libraries.

Circular RNAs as potential biomarkers for male severe sepsis

Circular RNAs (circRNAs) play important roles in many human diseases. However, their role in the development of severe sepsis, a condition that remains one of the main causes of death in intensive care units, has not yet been defined. In this study, we interrogated the molecular mechanisms of circRNAs in severe sepsis. We profiled the expression levels of 5,680 circRNAs in plasma extracted from blood samples of 9 severe sepsis cases or 9 controls (male, age 78 ± 7) using the Human circRNA Array. To enrich protein-coding genes hosting severe sepsis-related circRNAs, we conducted gene ontology and pathways analyses. Out of the identified 760 differentially expressed circRNAs, 404 were upregulated while 356 were downregulated (fold change [FC] ≥2 or ≤-2, and false discovery ratio <0.05). Circ-0008285 (located in exons of CDYL), showed significant upregulation in severe sepsis with an FC of 13.7, and Bonferroni-corrected P < 0.05/5. In silico analysis identified Circ-0008285 interacting microRNAs as well as protein-coding genes. We systematically investigated the differential expression pattern of circRNAs in severe sepsis. The circRNAs we identified might serve as potential biomarkers for diagnosis and prognosis of sepsis.

CircR-loop: a novel RNA:DNA interaction on genome instability

CircR-loop, a recently unearthed regulatory mechanism situated at the crossroads of circular RNA and DNA interactions, constitute a subset of R-loop. This circR-loop have emerged as a crucial player in pivotal regulatory functions within both animal and plant systems. The journey into the realm of circR-loop commenced with their discovery within the human mitochondrial genome, where they serve as critical directors of mitochondrial DNA replication. In the plant kingdom, circR-loop wield influence over processes such as alternative splicing and centromere organization, impacting the intricacies of floral development and genome stability, respectively. Their significance extends to the animal domain, where circR-loop has captured attention for their roles in cancer-related phenomena, exerting control over transcription, chromatin architecture, and orchestrating responses to DNA damage. Moreover, their involvement in nuclear export anomalies further underscores their prominence in cellular regulation. This article summarizes the important regulatory mechanisms and physiological roles of circR-loop in plants and animals, and offers a comprehensive exploration of the methodologies employed for the identification, characterization, and functional analysis of circR-loop, underscoring the pressing need for innovative approaches that can effectively distinguish them from their linear RNA counterparts while elucidating their precise functions. Lastly, the article sheds light on the challenges and opportunities that lie ahead in the field of circR-loop research, emphasizing the vital importance of continued investigations to uncover their regulatory roles and potential applications in the realm of biology. In summary, circR-loop represents a captivating and novel regulatory mechanism with broad-reaching implications spanning the realms of genetics, epigenetics, and disease biology. Their exploration opens new avenues for comprehending gene regulation and holds significant promise for future therapeutic interventions.

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.

Dysregulated Expression Patterns of Circular RNAs in Cancer: Uncovering Molecular Mechanisms and Biomarker Potential

Circular RNAs (circRNAs) are stable, enclosed, non-coding RNA molecules with dynamic regulatory propensity. Their biogenesis involves a back-splicing process, forming a highly stable and operational RNA molecule. Dysregulated circRNA expression can drive carcinogenic and tumorigenic transformation through the orchestration of epigenetic modifications via extensive RNA and protein-binding domains. These multi-ranged functional capabilities have unveiled extensive identification of previously unknown molecular and cellular patterns of cancer cells. Reliable circRNA expression patterns can aid in early disease detection and provide criteria for genome-specific personalized medicine. Studies described in this review have revealed the novelty of circRNAs and their biological ss as prognostic and diagnostic biomarkers.

Characterization and Comparative Analysis of Whole-Transcriptome Sequencing in High- and Low-Fecundity Chongming White Goat Ovaries during the Estrus Phase

Reproductive performance is one of the most important economic traits in the goat industry. Increasing the number of goats is an effective measure to improve production efficiency and reduce production costs. Ovaries are important reproductive organs in female mammals that directly affect the estrous cycle and reproductive abilities. Understanding the complex transcription network of non-coding RNAs (lncRNAs, circRNAs, and miRNAs) and messenger RNA (mRNA) could lead to significant insights into the ovarian regulation of the reproductive processes of animals. However, the whole-transcriptome analysis of the non-coding RNAs and mRNA of the ovaries in Chongming white goats between high-fecundity (HP) and low-fecundity (LP) groups is limited. In this study, a whole-transcriptome sequencing approach was used to identify lncRNA, circRNA, miRNA, and mRNA expression in the ovaries of Chongming white goats during the estrus phase using RNA-Seq technology. More than 20,000 messenger RNAs (mRNAs), 10,000 long non-coding RNAs (lncRNAs), 3500 circular RNAs (circRNAs), and 1000 micro RNAs (miRNAs) were identified. A total of 1024 differential transcripts (724 mRNAs, 112 lncRNAs, 178 circRNAs, and 10 miRNAs) existing between the HP and the LP groups were revealed through a bioinformatics analysis. They were enriched in the prolactin signaling pathway, the Jak-STAT signaling pathway, and the GnRH signaling pathway, as well as various metabolic pathways. Differentially expressed mRNAs (such as LYPD6, VEGFA, NOS3, TNXB, and EPHA2) and miRNAs (such as miR-10a-5p) play key roles in the regulation of goat ovaries during the estrus phase. The enrichment of pathways related to reproduction, such as the Hippo, Hedgehog, PI3K-AKT, and MAPK signaling pathways, suggests that they might be involved in the prolificacy of goat ovaries. Overall, we identified several gene modules associated with goat fecundity and provided a basis for a molecular mechanism in the ovaries of Chongming white goats.

The role of circular RNAs in pulmonary hypertension

Circular RNAs (circRNAs) are endogenous, covalently circularised, non-protein-coding RNAs generated from back-splicing. Most circRNAs are very stable, highly conserved, and expressed in a tissue-, cell- and developmental stage-specific manner. circRNAs play a significant role in various biological processes, such as regulation of gene expression and protein translation via sponging of microRNAs and binding with RNA-binding proteins. circRNAs have become a topic of great interest in research due to their close link with the development of various diseases. Their high stability, conservation and abundance in body fluids make them promising biomarkers for many diseases. A growing body of evidence suggests that aberrant expression of circRNAs and their targets plays a crucial role in pulmonary vascular remodelling and pulmonary arterial hypertension (group 1) as well as other forms (groups 3 and 4) of pulmonary hypertension (PH). Here we discuss the roles and molecular mechanisms of circRNAs in the pathogenesis of pulmonary vascular remodelling and PH. We also highlight the therapeutic and biomarker potential of circRNAs in PH.

Best practice standards for circular RNA research

Circular RNAs (circRNAs) are formed in all domains of life and via different mechanisms. There has been an explosion in the number of circRNA papers in recent years; however, as a relatively young field, circRNA biology has an urgent need for common experimental standards for isolating, analyzing, expressing and depleting circRNAs. Here we propose a set of guidelines for circRNA studies based on the authors' experience. This Perspective will specifically address the major class of circRNAs in Eukarya that are generated by a spliceosome-catalyzed back-splicing event. We hope that the implementation of best practice principles for circRNA research will help move the field forward and allow a better functional understanding of this fascinating group of RNAs.

CircFISH: A Novel Method for the Simultaneous Imaging of Linear and Circular RNAs

Circular RNAs (circRNAs) are regulatory RNAs which have recently been shown to have clinical significance in several diseases, including, but not limited to, various cancers, neurological diseases and cardiovascular diseases. The function of such regulatory RNAs is largely dependent on their subcellular localization. Several circRNAs have been shown to conduct antagonistic roles compared to the products of the linear isoforms, and thus need to be characterized distinctly from the linear RNAs. However, conventional fluorescent in situ hybridization (FISH) techniques cannot be employed directly to distinguish the signals from linear and circular isoforms because most circRNAs share the same sequence with the linear RNAs. In order to address this unmet need, we adapted the well-established method of single-molecule FISH by designing two sets of probes to differentiate the linear and circular RNA isoforms by virtue of signal colocalization. We call this method 'circular fluorescent in situ hybridization' (circFISH). Linear and circular RNAs were successfully visualized and quantified at a single-molecule resolution in fixed cells. RNase R treatment during the circFISH reduced the levels of linear RNAs while the circRNA levels remain unaltered. Furthermore, cells with shRNAs specific to circRNA showed the loss of circRNA levels, whereas the linear RNA levels were unaffected. The optimization of the in-situ RNase R treatment allowed the multiplexing of circFISH to combine it with organelle staining. CircFISH was found to be compatible with multiple sample types, including cultured cells and fresh-frozen and formalin-fixed tissue sections. Thus, we present circFISH as a versatile method for the simultaneous visualization and quantification of the distribution and localization of linear and circular RNA in fixed cells and tissue samples.

The Circ_0001367/miR-545-3p/LUZP1 Axis Regulates Cell Proliferation, Migration and Invasion in Glioma Cells

Glioma is the most common primary intracranial malignant tumour in adults. It has a high incidence and poses a serious threat to human health. Circular RNA is a hotspot of cancer research. In this study, we aimed to explore the role of circ_0001367 in gliomagenesis and the underlying mechanism. First, qRT-PCR was conducted, which showed that circ_0001367 level was downregulated in glioma tissues and cells. Next, gain-of-function and loss-of-function assays were performed, which indicated that circ_0001367 inhibited the proliferation, migration and invasion of glioma cells. Subsequent bioinformatics analysis, dual-luciferase reporter assays, RNA immunoprecipitation assays and cell function assays demonstrated that circ_0001367 inhibited the proliferation, migration and invasion of glioma cells by absorbing miR-545-3p and thereby regulating the expression of leucine zipper protein (LUZP1). Finally, an in vivo experiment was conducted, which demonstrated that circ_0001367 inhibited glioma growth in vivo by modulating miR-545-3p and LUZP1. Taken together, the results of this study demonstrate that the circ_0001367/miR-545-3p/LUZP1 axis may be a novel target for glioma therapy.

Circular RNAs as microRNA sponges: evidence and controversies

Gene expression in eukaryotic cells is a complex process encompassing several layers of regulation at the transcriptional and post-transcriptional levels. At the post-transcriptional level, microRNAs (miRs) are key regulatory molecules that function by binding directly to mRNAs. This generally leads to less efficient translation of the target mRNAs. More recently, an additional layer of gene regulation has been discovered, as other molecules, including circular RNAs (circRNAs), may bind to miRs and thereby function as sponges or decoys resulting in increased expression of the corresponding miR target genes. The circRNAs constitute a large class of mainly non-coding RNAs, which have been extensively studied in recent years, in particular in the cancer research field where many circRNAs have been proposed to function as miR sponges. Here, we briefly describe miR-mediated gene regulation and the extra layer of regulation that is imposed by the circRNAs. We describe techniques and methodologies that are commonly used to investigate potential miR sponging properties of circRNAs and discuss major pitfalls and controversies within this relatively new research field.

Methods to study circRNA-protein interactions

Circular RNAs (circRNAs) have been studied extensively in the last few years, uncovering functional roles in a diverse range of cell types and organisms. As shown for a few cases, these functions may be mediated by trans-acting factors, in particular RNA-binding proteins (RBPs). However, the specific interaction partners for most circRNAs remain unknown. This is mainly due to technical difficulties in their identification and in differentiating between interactors of circRNAs and their linear counterparts. Here we review the currently used methodology to systematically study circRNA-protein complexes (circRNPs), focusing either on a specific RNA or protein, both on the gene-specific or global level, and discuss advantages and challenges of the available approaches.

Identifying and characterizing virus-encoded circular RNAs

Circular forms of RNA were first discovered in plant viroids and later found in a variety of animal viruses. These circular RNAs lack free 5' and 3' ends, granting protection from exonucleases. This review is focused on the methods that are used to investigate virus-encoded circular RNAs. Using DNA viruses that are prevalent among human as examples, we begin with features of circular RNAs and the unique methods to enrich for circular RNAs. Next, we discuss the computational methods for RNA-sequencing analysis to discover new virus-encoded circular RNAs. Many strategies are similar to analyzing cellular RNAs, but some unique aspects of virus-encoded circular RNAs that are likely due to highly packed viral genomes and non-canonical use of splicing machinery, are described herein. We illustrate the various methods of validating expression of specific virus-encoded circular RNAs. Finally, we discuss novel methods to study functions of circular RNAs and the current technical challenges that remain for investigating virus-encoded circular RNAs.