Comprehensive analysis of circular RNAs in pathological states: biogenesis, cellular regulation, and therapeutic relevance

Exploring the impact of circRNAs on cancer glycolysis: Insights into tumor progression and therapeutic strategies

Cancer cells exhibit altered metabolic pathways, prominently featuring enhanced glycolytic activity to sustain their rapid growth and proliferation. Dysregulation of glycolysis is a well-established hallmark of cancer and contributes to tumor progression and resistance to therapy. Increased glycolysis supplies the energy necessary for increased proliferation and creates an acidic milieu, which in turn encourages tumor cells' infiltration, metastasis, and chemoresistance. Circular RNAs (circRNAs) have emerged as pivotal players in diverse biological processes, including cancer development and metabolic reprogramming. The interplay between circRNAs and glycolysis is explored, illuminating how circRNAs regulate key glycolysis-associated genes and enzymes, thereby influencing tumor metabolic profiles. In this overview, we highlight the mechanisms by which circRNAs regulate glycolytic enzymes and modulate glycolysis. In addition, we discuss the clinical implications of dysregulated circRNAs in cancer glycolysis, including their potential use as diagnostic and prognostic biomarkers. All in all, in this overview, we provide the most recent findings on how circRNAs operate at the molecular level to control glycolysis in various types of cancer, including hepatocellular carcinoma (HCC), prostate cancer (PCa), colorectal cancer (CRC), cervical cancer (CC), glioma, non-small cell lung cancer (NSCLC), breast cancer, and gastric cancer (GC). In conclusion, this review provides a comprehensive overview of the significance of circRNAs in cancer glycolysis, shedding light on their intricate roles in tumor development and presenting innovative therapeutic avenues.

Osteosarcoma in a ceRNET perspective

Osteosarcoma (OS) is the most prevalent and fatal type of bone tumor. It is characterized by great heterogeneity of genomic aberrations, mutated genes, and cell types contribution, making therapy and patients management particularly challenging. A unifying picture of molecular mechanisms underlying the disease could help to transform those challenges into opportunities.This review deeply explores the occurrence in OS of large-scale RNA regulatory networks, denominated "competing endogenous RNA network" (ceRNET), wherein different RNA biotypes, such as long non-coding RNAs, circular RNAs and mRNAs can functionally interact each other by competitively binding to shared microRNAs. Here, we discuss how the unbalancing of any network component can derail the entire circuit, driving OS onset and progression by impacting on cell proliferation, migration, invasion, tumor growth and metastasis, and even chemotherapeutic resistance, as distilled from many studies. Intriguingly, the aberrant expression of the networks components in OS cells can be triggered also by the surroundings, through cytokines and vesicles, with their bioactive cargo of proteins and non-coding RNAs, highlighting the relevance of tumor microenvironment. A comprehensive picture of RNA regulatory networks underlying OS could pave the way for the development of innovative RNA-targeted and RNA-based therapies and new diagnostic tools, also in the perspective of precision oncology.

Current advances in circular RNA detection and investigation methods: Are we running in circles?

Circular RNAs (circRNAs), characterized by their closed-loop structure, have emerged as significant transcriptomic regulators, with roles spanning from microRNA sponging to modulation of gene expression and potential peptide coding. The discovery and functional analysis of circRNAs have been propelled by advancements in both experimental and bioinformatics tools, yet the field grapples with challenges related to their detection, isoform diversity, and accurate quantification. This review navigates through the evolution of circRNA research methodologies, from early detection techniques to current state-of-the-art approaches that offer comprehensive insights into circRNA biology. We examine the limitations of existing methods, particularly the difficulty in differentiating circRNA isoforms and distinguishing circRNAs from their linear counterparts. A critical evaluation of various bioinformatics tools and novel experimental strategies is presented, emphasizing the need for integrated approaches to enhance our understanding and interpretation of circRNA functions. Our insights underscore the dynamic and rapidly advancing nature of circRNA research, highlighting the ongoing development of analytical frameworks designed to address the complexity of circRNAs and facilitate the assessment of their clinical utility. As such, this comprehensive overview aims to catalyze further advancements in circRNA study, fostering a deeper understanding of their roles in cellular processes and potential implications in disease. This article is categorized under: RNA Methods > RNA Nanotechnology RNA Methods > RNA Analyses in Cells RNA Methods > RNA Analyses In Vitro and In Silico.

Multiple novel functions of circular RNAs in diabetes mellitus

Circular RNAs (circRNAs), as an emerging group of non-coding RNAs (ncRNAs), have received the attention given evidence indicating that these novel ncRNAs are implicated in various biological processes. Due to the absence of 5' and 3' ends in circ-RNAs, their two ends are covalently bonded together, and they are synthesised from pre-mRNAs in a process called back-splicing, which makes them more stable than linear RNAs. There is accumulating evidence showing that circRNAs play a critical role in the pathogenesis of diabetes mellitus (DM). Moreover, it has been indicated that dysregulation of circRNAs has made them promising diagnostic biomarkers for the detection of DM. Recently, increasing attention has been paid to investigate the mechanisms underlying the DM process. It has been demonstrated that there is a strong correlation between the expression of circRNAs and DM. Hence, our aim is to discuss the crosstalk between circRNAs and DM and its complications.

Virus-Encoded Circular RNAs: Role and Significance in Viral Infections

Circular RNAs (circRNAs) have been the focus of intense scientific research to understand their biogenesis, mechanisms of action and regulatory functions. CircRNAs are single stranded, covalently closed RNA molecules lacking the 5'-terminal cap and the 3'-terminal polyadenine chain, characteristics that make them very stable and resistant. Synthesised by both cells and viruses, in the past circRNAs were considered to have no precise function. Today, increasing evidence shows that circRNAs are ubiquitous, some of them are tissue- and cell-specific, and critical in multiple regulatory processes (i.e., infections, inflammation, oncogenesis, gene expression). Moreover, circRNAs are emerging as important biomarkers of viral infection and disease progression. In this review, we provided an updated overview of current understanding of virus-encoded and cellular-encoded circRNAs and their involvement in cellular pathways during viral infection.

Circ_0067934: a circular RNA with roles in human cancer

A circular RNA (circRNA) is a non-coding RNA (ncRNA) derived from reverse splicing from pre-mRNA and is characterized by the absence of a cap structure at the 5' end and a poly-adenylated tail at the 3' end. Owing to the development of RNA sequencing and bioinformatics approaches in recent years, the important clinical value of circRNAs has been increasingly revealed. Circ_0067934 is an RNA molecule of 170 nucleotides located on chromosome 3q26.2. Circ_0067934 is formed via the reverse splicing of exons 15 and 16 in PRKCI (protein kinase C Iota). Recent studies revealed the upregulation or downregulation of circ_0067934 in various tumors. The expression of circ_0067934 was found to be correlated with tumor size, TNM stage, and poor prognosis. Based on experiments with cancer cells, circ_0067934 promotes cancer cell proliferation, migratory activity, and invasion when overexpressed or downregulated. The potential mechanism involves the binding of circ_0067934 to microRNAs (miRNAs; miR-545, miR-1304, miR-1301-3p, miR-1182, miR-7, and miR-1324) to regulate the post-transcriptional expression of genes. Other mechanisms include inhibition of the Wnt/β-catenin and PI3K/AKT signaling pathways. Here, we summarized the biological functions and possible mechanisms of circ_0067934 in different tumors to enable further exploration of its translational applications in clinical diagnosis, therapy, and prognostic assessments.

Newly discovered mechanisms that mediate tumorigenesis and tumour progression: circRNA-encoded proteins

Proteins produced by cap-independent translation mediated by an internal ribosome entry site (IRES) in circular RNAs (circRNAs) play important roles in tumour progression. To date, numerous studies have been performed on circRNAs and the proteins they encode. In this review, we summarize the biogenesis of circRNAs and the mechanisms regulating circRNA-encoded proteins expression. We also describe relevant research methods and their applications to biological processes such as tumour cell proliferation, metastasis, epithelial-mesenchymal transition (EMT), apoptosis, autophagy and chemoresistance. This paper offers deeper insights into the roles that circRNA-encoded proteins play in tumours. It also provides a theoretical basis for the use of circRNA-encoded proteins as biomarkers of tumorigenesis and for the development of new targets for tumour therapy.

Clinical Delivery of Circular RNA: Lessons Learned from RNA Drug Development

Circular RNAs (circRNA) represent a distinct class of covalently closed-loop RNA molecules, which play diverse roles in regulating biological processes and disease states. The enhanced stability of synthetic circRNAs compared to their linear counterparts has recently garnered considerable research interest, paving the way for new therapeutic applications. While clinical circRNA technology is still in its early stages, significant advancements in mRNA technology offer valuable insights into its potential future applications. Two primary obstacles that must be addressed are the development of efficient production methods and the optimization of delivery systems. To expedite progress in this area, this review aims to provide an overview of the current state of knowledge on circRNA structure and function, outline recent techniques for synthesizing circRNAs, highlight key delivery strategies and applications, and discuss the current challenges and future prospects in the field of circRNA-based therapeutics.

LncRNA DNAJC3-AS1 promotes the biological functions of papillary thyroid carcinoma via regulating the microRNA-27a-3p/CCBE1 axis

Long noncoding RNA DNAJC3-AS1 (lncRNA DNAJC3-AS1) has been probed in many studies, while the regulatory mechanism of DNAJC3-AS1 on papillary thyroid carcinoma (PTC) via regulating microRNA (miR)-27a-3p remains inadequate. This research aims to depict the role of DNAJC3-AS1, miR-27a-3p, collagen, and calcium-binding EGF domain-containing protein 1 (CCBE1) on PTC development. DNAJC3-AS1, miR-27a-3p, and CCBE1 expression levels in PTC tissues and adjacent normal tissues were tested. The relation of DNAJC3-AS1, miR-27a-3p, and CCBE1 was analyzed. DNAJC3-AS1 and miR-27a-3p and CCBE1-related oligonucleotides were transfected into IHH-4 cells to investigate their role in PTC development. Cell tumorigenicity was detected by in vivo assay. DNAJC3-AS1 and CCBE1 expressed highly and miR-27a-3p expressed lowly in PTC. Downregulation of DNAJC3-AS1, upregulating miR-27a-3p or downregulating CCBE1 impaired the malignant behaviors of IHH-4 cells. Depletion of miR-27a-3p reversed the DNAJC3-AS1 suppression-induced phenotypic inhibition of IHH-4 cells. DNAJC3-AS1 bound to miR-27a-3p and CCBE1 as a target of miR-27a-3p. Our study highlights that DNAJC3-AS1 inhibits miR-27a-3p to promote CCBE1 expression, thereby facilitating PTC development. This study affords distinguished therapeutic strategies and novel research directions for PTC treatment.

CircRNA_0017076 acts as a sponge for miR-185-5p in the control of epithelial-to-mesenchymal transition of tubular epithelial cells during renal interstitial fibrosis

Renal interstitial fibrosis (RIF) is a common pathological hallmark of progressive chronic kidney disease (CKD). Circular RNAs (circRNAs) are involved in certain renal diseases, but their role in RIF is largely unknown. The present study investigated the effects and potential mechanisms of circRNA_0017076 in RIF. CircRNA_0017076 expression was markedly upregulated in transforming growth factor-β1 (TGF-β1)-treated renal tubular epithelial cells (RTECs) and kidney biopsy samples from patients with RIF. Functional assays showed that circRNA_0017076 colocalized with microRNA-185-5p (miR-185-5p) and inhibited miR-185-5p function via direct binding to miR-185-5p. In vitro, the knockdown of circRNA_0017076 inhibited the calcium ion (Ca²⁺) influx-mediated epithelial-to-mesenchymal transition (EMT) of RTECs and downregulated the expression of stromal interaction molecule 1 (STIM1), which is a target protein of miR-185-5p. Silencing mmu_circ_0004488 reduced fibrotic lesions in the kidneys of unilateral ureteral obstruction (UUO) mice by targeting the miR-185-5p/Stim1 axis. For the first time, we identified circRNA_0017076 as a sponge for miR-185-5p, which regulates STIM1 gene expression and is involved in RIF. Our results support circRNA_0017076 as a potential therapeutic target for RIF disease.

Epigenetic regulation of autophagy by non-coding RNAs in gastrointestinal tumors: Biological functions and therapeutic perspectives

Cancer is the manifestation of changes and mutations in genetic and epigenetic levels. Non-coding RNAs (ncRNAs) are commonly dysregulated in disease pathogenesis, and their role in cancer has been well-documented. The ncRNAs regulate various molecular pathways and mechanisms in cancer that can lead to induction/inhibition of carcinogenesis. Autophagy is a molecular "self-digestion" mechanism its function can be pro-survival or pro-death in tumor cells. The aim of the present review is to evaluate the role of ncRNAs in regulating autophagy in gastrointestinal tumors. The role of the ncRNA/autophagy axis in affecting the progression of gastric, liver, colorectal, pancreatic, esophageal, and gallbladder cancers is investigated. Both ncRNAs and autophagy mechanisms can function as oncogenic or onco-suppressor and this interaction can determine the growth, invasion, and therapy response of gastrointestinal tumors. ncRNA/autophagy axis can reduce/increase the proliferation of gastrointestinal tumors via the glycolysis mechanism. Furthermore, related molecular pathways of metastasis, such as EMT and MMPs, are affected by the ncRNA/autophagy axis. The response of gastrointestinal tumors to chemotherapy and radiotherapy can be suppressed by pro-survival autophagy, and ncRNAs are essential regulators of this mechanism. miRNAs can regulate related genes and proteins of autophagy, such as ATGs and Beclin-1. Furthermore, lncRNAs and circRNAs down-regulate miRNA expression via sponging to modulate the autophagy mechanism. Moreover, anti-cancer agents can affect the expression level of ncRNAs regulating autophagy in gastrointestinal tumors. Therefore, translating these findings into clinics can improve the prognosis of patients.

circRAB3IP modulates cell proliferation by reorganizing gene expression and mRNA processing in a paracrine manner

Circular RNAs are an endogenous long-lived and abundant noncoding species. Despite their prevalence, only a few circRNAs have been dissected mechanistically to date. Here, we cataloged nascent RNA-enriched circRNAs from primary human cells and functionally assigned a role to circRAB3IP in sustaining cellular homeostasis. We combined "omics" and functional experiments to show how circRAB3IP depletion deregulates hundreds of genes, suppresses cell cycle progression, and induces senescence-associated gene expression changes. Conversely, excess circRAB3IP delivered to endothelial cells via extracellular vesicles suffices for accelerating their division. We attribute these effects to an interplay between circRAB3IP and the general splicing factor SF3B1, which can affect transcript variant expression levels of cell cycle-related genes. Together, our findings link the maintenance of cell homeostasis to the presence of a single circRNA.

Downregulation of circ-ZNF609 Promotes Heart Repair by Modulating RNA N6-Methyladenosine-Modified Yap Expression

Circular RNAs take crucial roles in several pathophysiological processes. The regulatory role and its underlying mechanisms of circ-ZNF609 in the heart remains largely unknown. Here, we report that circ-ZNF609 is upregulated during myocardial ischemia/reperfusion (I/R) remodeling. Knockdown of circ-ZNF609 protects against acute I/R injury and attenuates left ventricle dysfunction after I/R remodeling in vivo. In vitro, circ-ZNF609 regulates cardiomyocyte survival and proliferation via modulating the crosstalk between Hippo-YAP and Akt signaling. Mechanically, N⁶-methyladenosine-modification is involved in the regulatory role of circ-ZNF609 on YAP. An in-depth study indicates that knockdown of circ-ZNF609 decreases the expression of YTHDF3 and further fine-tuned the accessibility of Yap mRNA to YTHDF1 and YTHDF2 to regulate YAP expression. circ-ZNF609 knockdown represents a promising therapeutic strategy to combat the pathological process of myocardial I/R injury.

Noncoding RNAs Interplay in Ovarian Cancer Therapy and Drug Resistance

Noncoding RNAs (ncRNAs) are several types of RNA that do not encode proteins, but are essential for cell regulation. Ovarian cancer (OC) is a type of gynecological cancer with a high mortality rate and a 5-year prognosis. OC is becoming more common with each passing year, and the symptoms of early-stage OC are sometimes undetectable. Meanwhile, early-stage OC has no symptoms and is difficult to diagnose. Because ncRNA has been shown to affect the development of OC and is widely distributed, it could be employed as a new biomarker for early OC. Furthermore, ncRNA has the potential to promote or inhibit drug resistance in OC, potentially giving a solution to multiple drug resistance. Various prior studies have found that different ncRNAs perform differently in OC. This article examines how mainstream ncRNAs have been expressed in OC in recent years, as well as their function in tumor growth.

Circ_UTRN ameliorates caerulein-induced acute pancreatitis in vitro via reducing inflammation and promoting apoptosis through miR-320-3p/PTK2 axis

OBJECTIVES

Circular RNAs (circRNAs) have been demonstrated to play important roles in acute pancreatitis (AP). Herein, this study aimed to investigate the role and mechanism of circRNAs utrophin (circ_UTRN) in AP.

METHODS

In vitro cultured rat pancreatic acinar cell line AR42J was exposed to caerulein (10 nmol/L) to mimic an AP cell model. The levels of circ_UTRN and microRNA (miR)-320-3p and protein tyrosine kinase 2 (PTK2) were examined using quantitative real-time polymerase chain reaction and Western blot assays. Cell apoptosis was analysed by flow cytometry and Western blot assays. ELISA was employed to detect the levels of tumour necrosis factor-α (TNF-α), IL-1β and IL-6. The binding interaction between miR-320-3p and circ_UTRN or PTK2 was verified using dual-luciferase reporter assay.

KEY FINDINGS

The expression of circ_UTRN was decreased by caerulein in pancreatic acinar cells, ectopic overexpression of circ_UTRN reduced inflammation and promoted apoptosis in caerulein-mediated pancreatic acinar cells. In a mechanical study, circ_UTRN served as a sponge of miR-320-3p, and miR-320-3p directly targeted PTK2. Rescue assay suggested that the promotion of apoptosis and inhibition of inflammation induced by circ_UTRN re-expression in caerulein-mediated pancreatic acinar cells were partially abolished by miR-320-3p overexpression or PTK2 knockdown. Besides that, miR-320-3p inhibition impaired caerulein-induced cell apoptosis arrest and inflammation via targeting PTK2.

CONCLUSIONS

Up-regulation of circ_UTRN in pancreatic acinar cells attenuates caerulein-evoked cell apoptosis arrest and inflammation enhancement via miR-320-3p/PTK2, suggesting that circ_UTRN/miR-320-3p/PTK2 axis might be engaged in caerulein-induced AP.

A novel circular RNA circ_HN1/miR-628-5p/Ecto-5'-nucleotidase competing endogenous RNA network regulates gastric cancer development

The competing endogenous RNA (ceRNA) activity of circular RNAs (circRNAs) has been implicated in the development of gastric cancer. Here, we sought to explore the ceRNA function of circRNA Jupiter microtubule associated homolog 1 (circ_HN1) in gastric tumorigenesis. Circ_HN1, microRNA (miR)-628-5p, and NT5E expression levels were quantified by qRT-PCR and western blot. Dual-luciferase reporter assays were used to assess the direct relationship between miR-628-5p and circ_HN1 or NT5E. Our data showed that circ_HN1 expression was enhanced in human gastric cancer. Depletion of circ_HN1 impeded cell proliferation, spheroid formation, invasion, and migration and promoted apoptosis in vitro, as well as diminished tumor growth in vivo. NT5E was a downstream effector of circ_HN1 function. NT5E was targeted and inhibited by miR-628-5p through the perfect complementary site in NT5E 3ʹUTR, and circ_HN1 affected NT5E expression through miR-628-5p competition. Moreover, depletion of miR-628-5p reversed the effects of circ_HN1 silencing on regulating cell functional behaviors. Our findings identify a novel ceRNA network, the circ_HN1/miR-628-5p/NT5E axis, for the oncogenic activity of circ_HN1 in gastric cancer, highlighting circ_HN1 inhibition as a promising targeted treatment against gastric cancer.

Muscle Regeneration and RNA: New Perspectives for Ancient Molecules

The ability of the ribonucleic acid (RNA) to self-replicate, combined with a unique cocktail of chemical properties, suggested the existence of an RNA world at the origin of life. Nowadays, this hypothesis is supported by innovative high-throughput and biochemical approaches, which definitively revealed the essential contribution of RNA-mediated mechanisms to the regulation of fundamental processes of life. With the recent development of SARS-CoV-2 mRNA-based vaccines, the potential of RNA as a therapeutic tool has received public attention. Due to its intrinsic single-stranded nature and the ease with which it is synthesized in vitro, RNA indeed represents the most suitable tool for the development of drugs encompassing every type of human pathology. The maximum effectiveness and biochemical versatility is achieved in the guise of non-coding RNAs (ncRNAs), which are emerging as multifaceted regulators of tissue specification and homeostasis. Here, we report examples of coding and ncRNAs involved in muscle regeneration and discuss their potential as therapeutic tools. Small ncRNAs, such as miRNA and siRNA, have been successfully applied in the treatment of several diseases. The use of longer molecules, such as lncRNA and circRNA, is less advanced. However, based on the peculiar properties discussed below, they represent an innovative pool of RNA biomarkers and possible targets of clinical value.

CircRNA FUT10 regulates the regenerative potential of aged skeletal muscle stem cells by targeting HOXA9

Skeletal muscle is capable of repairing itself after injury to maintain the stability of its own tissue, but this ability declines with aging. Circular RNAs (circRNAs) are involved in cell aging. However, there is little research into their role and underlying mechanisms, especially in skeletal muscle stem cells (SkMSCs). In this study, we assessed circRNA FUT10 expression in aged and adult SkMSCs. We observed that circRNA FUT10 was upregulated in aged SkMSCs compared with that in adult SkMSCs. Furthermore, we identified putative miR-365-3p binding sites on circRNA FUT10, suggesting that this circRNA sponges miR-365a-3p. We also found that HOXA9 is a downstream target of miR-365a-3p and confirmed that miR-365a-3p can bind to circRNA FUT10 and the 3′-untranslated region of HOXA9 mRNA. This finding indicated that miR-365a-3p might serve as a “bridge” between circRNA FUT10 and HOXA9. Finally, we found that the circRNA FUT10/miR365a-3p/HOXA9 axis is involved in SkMSC aging. Collectively, our results show that the circRNA FUT10/miR365a-3p/HOXA9 axis is a promising therapeutic target and are expected to facilitate the development of therapeutic strategies to improve the prognosis of degenerative muscle disease.

Circular RNAs: Expression, localization, and therapeutic potentials

Circular RNAs (circRNAs) are RNAs with a unique circular structure that is generated from back-splicing processes. These circular molecules were discovered more than 40 years ago but failed to raise scientific interest until lately. Increasing studies have found that these circular RNAs might not just be byproducts of the splicing process but possess important regulatory functions through different cellular events. Most circular RNAs are currently being studied in the field of cancer, and many of them have been confirmed to be involved in the process of tumorigenesis. However, many circular RNAs are implicated in the developmental stages of diseases other than cancer. In this review, we focus on discussing the role of circular RNAs in non-cancer diseases, especially in cardiovascular diseases. Following the summary of the life cycle of circRNAs, we provide input on studying circRNA-protein interactions based on our experience, which modulate protein translocation. Furthermore, we outline the potential of circRNAs to be potent biomarkers, effective therapeutic targets, and potential treatments in cardiovascular diseases as well as other non-cancer fields.

Circular RNAs and Hepatocellular Carcinoma: New Epigenetic Players With Diagnostic and Prognostic Roles

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death worldwide. Due to the lack of potent diagnosis and prognosis biomarkers and effective therapeutic targets, the overall prognosis of survival is poor in HCC patients. Circular RNAs (circRNAs) are a class of novel endogenous non-coding RNAs with covalently closed loop structures and implicated in diverse physiological processes and pathological diseases. Recent studies have demonstrated the involvement of circRNAs in HCC diagnosis, prognosis, development, and drug resistance, suggesting that circRNAs may be a class of novel targets for improving HCC diagnosis, prognosis, and treatments. In fact, some artificial circRNAs have been engineered and showed their therapeutic potential in treating HCV infection and gastric cancer. In this review, we introduce the potential of circRNAs as biomarkers for HCC diagnosis and prognosis, as therapeutic targets for HCC treatments and discuss the challenges in circRNA research and chances of circRNA application.

Overexpression of hsa_circ_0094742 inhibits IL-1β-induced decline in CHON-001 cell viability by targeting microRNA-127-5p

Osteoarthritis (OA) is a public health problem that affects 240 million people globally; however, the current treatment options for OA are not effective. Therefore, there is still an urgent need to identify novel strategies to reduce the incidence and progression of OA. The circular RNA hsa_circ_0094742 was reported to be downregulated in patients with OA. However, the underlying mechanism remains unclear. The levels of hsa_circ_0094742 in CHON-001 were detected by reverse transcription quantitative polymerase chain reaction. Moreover, Cell Counting Kit-8 assay and Ki67 staining were used to determine the cell viability. The protein expression of biomarkers was detected by western blot analysis. In addition, the putative downstream target of hsa_circ_0094742 was predicted using the Circinteractome and TargetScan online databases. The putative targeting relationship was verified by dual luciferase reporter assay and fluorescence in situ hybridization. Next, cell apoptosis was determined by Annexin V/PI staining. hsa_circ_0094742 overexpression (OE) inhibited interleukin (IL)-1β-induced decline in the viability of CHON-001 cells and primary human chondrocytes. Furthermore, IL-1β-induced alterations in aggrecan, matrix metallopeptidase 13, X-linked inhibitor of apoptosis protein (XIAP), Bax and active caspase 3 were reversed by hsa_circ_0094742 OE. Luciferase reporter assay indicated that miR-127-5p was the downstream target of hsa_circ_0094742, and latexin was the target of miR-127-5p. hsa_circ_0094742 OE inhibited IL-1β-induced decline in CHON-001 cell viability by targeting miRNA-127-5p. The findings of the present study revealed the biological rational of the use of hsa_circ_0094742 OE as an anti-IL-1β effector in human chondrocytes. These findings may prompt further research on hsa_circ_0094742 as a potent circRNA target for the treatment of OA.

Hsa_circ_0099198 facilitates the progression of retinoblastoma by regulating miR-1287/LRP6 axis

Retinoblastoma (RB) is an intraocular malignancy that occurs in children. Circular RNAs (circRNAs) have been confirmed to play an essential role in tumorigenesis and development. This study aimed to ascertain the role and potential mechanism of hsa_circ_0099198 in RB. The levels of circ_0099198, microRNA-1287 (miR-1287) and low-density lipoprotein receptor-related protein 6 (LRP6) were determined by real-time quantitative polymerase chain reaction and Western blot. Cell proliferation was assessed by colony formation assay. Cell cycle arrest and apoptosis were evaluated by flow cytometry. Cell migration and invasion were tested using transwell assay. The activity of caspase-3/caspase-9 was examined with commercial kits. The interaction among circ_0099198, miR-1287 and LRP6 were verified by dual-luciferase reporter assay, RNA immunoprecipitation (RIP) assay or RNA pull-down assay. Xenograft experiment was used to assess tumor growth in vivo. circ_0099198 and LRP6 levels were increased, while miR-1287 level was reduced in RB cells. circ_0099198 silencing suppressed proliferation and metastasis and expedited cell cycle arrest and apoptosis in Y79 and So-RB50 cells. In addition, depletion of circ_0099198 inhibited RB cell progression via regulating miR-1287/LRP6 axis. Moreover, knockdown of circ_0099198 blocked the growth of xenograft tumors. circ_0099198 contributed to RB progression by sponging miR-1287 and up-regulating LRP6, which provided novel biomarkers for RB therapy.

tsRNAs: Novel small molecules from cell function and regulatory mechanism to therapeutic targets

tsRNAs are small fragments of RNAs with specific lengths that are generated by particular ribonucleases, such as dicer and angiogenin (ANG), clipping on the rings of transfer RNAs (tRNAs) in specific cells and tissues under specific conditions. Depending on where the splicing site is, tsRNAs can be segmented into two main types, tRNA‐derived stress‐induced RNAs (tiRNAs) and tRNA‐derived fragments (tRFs). Many studies have shown that tsRNAs are functional molecules, not the random degradative products of tRNAs. Notably, due to their regulatory mechanism in regulating mRNA stability, transcription, ribosomal RNA (rRNA) synthesis and RNA reverse transcription, tsRNAs are significantly involved in the cell function, such as cell proliferation, migration, cycle and apoptosis, as well as the occurrence and development of a variety of diseases. In addition, tsRNAs may represent a new generation of clinical biomarkers or therapeutic targets because of their stable structures, high conservation and widely distribution, particularly in the peripheral tissues, bodily fluids and exosomes. In this review, we describe the generation, function and mechanism of tsRNAs and illustrate the current research progress of tsRNAs in various diseases, highlight their potentials as biomarkers and therapeutic targets in clinical application. Although our understanding of tsRNAs is still in infancy, the application prospects shown in this field deserve further exploration.

circFOXO3: Going around the mechanistic networks in cancer by interfering with miRNAs regulatory networks

Circular RNAs (circRNA) have gained recent interest due to their functional versatility due to their interactions with other RNA species and proteins, all of which underline complex regulatory networks involved in pathogenic mechanisms. As a result, recent insights in circRNA biology are investigating their biomarker and therapeutic potential. One such circRNA is CircFOXO3, which consists of the circularized second exon of the FOXO3 mRNA, a member of the forkhead box transcription factor family involved in the regulation of developmental programs. Recent research focused on the role of circFOXO3 in the context of cancer has highlighted several implications in key tumorigenesis mechanisms, thus consolidating its relevance among other identified circRNAs. In this paper, we will focus on the currently identified case-specific implications of circFOXO3 in cancer, with a focus on the circFOXO3-miRNA-mRNA regulatory networks, its interactions with different proteins, and their cumulated biological effects upon tumor development. Therefore, we aim to provide an integrated perspective of the mechanistic implications of circFOXO3 in different cancers while also highlighting its biomarker or therapeutic potential based on the current evidence.

Advancement and properties of circular RNAs in prostate cancer: An emerging and compelling frontier for discovering

Prostate cancer (PC) is the most common carcinoma among men worldwide which results in 26% of leading causes of cancer-related death. However, the ideal and effective molecular marker remains elusive. CircRNA, initially observed in plant-infected viruses and Sendai virus in 1979, is generated from pre-mRNA back-splicing and comes in to play by adequate expression. The differential expression in prostate tissues compared with the control reveals the promising capacity in modulating processes including carcinogenesis and metastasis. However, the biological mechanisms of regulatory network in PC needs to systemically concluded. In this review, we enlightened the comprehensive studies on the definite mechanisms of circRNAs affecting tumor progression and metastasis. What's more, we validated the potential clinical application of circRNAs serving as diagnostic and prognostic biomarker. The discussion and analysis in circRNAs will broaden our knowledge of the pathogenesis of PC and further optimize the current therapies against different condition.

Knockdown of circPRKCA Restrained Cell Growth, Migration, and Invasion of NSCLC Cells Both in vitro and in vivo via Regulating miR-330-5p/PDK1/AKT Pathway

Background

Protein kinase Cα (PRKCA) is an oncogene in multiple cancers including non-small-cell lung cancer (NSCLC) and can be transcribed into a number of circular PRKCAs (circPRKCAs). Here, we aimed to elaborate the role and mechanism of circPRKCA_024 (circPRKCA) in malignant progression of NSCLC.

Methods

Expression of circPRKCA, miRNA (miR)-330-5p and 3-phosphoinositide-dependent protein kinase-1 (PDK1) was measured by real-time quantitative PCR and Western blotting, and their relationship was testified by dual-luciferase reporter assay, RNA immunoprecipitation, and RNA pull-down assay. Cell behaviors were evaluated by cell counting kit (CCK)-8, flow cytometry, and transwell assays. AKT activity was confirmed by Western blotting. Xenograft experiment assessed tumor growth.

Results

Expression of circPRKCA and PDK1 was upregulated, and miR-330-5p was downregulated in NSCLC tissues and cell lines. High circPRKCA was correlated with TNM stage and lymph node metastasis of NSCLC patients. Silencing circPRKCA could suppress cell viability, migration, and invasion in A549 and H1299 cells, accompanied with apoptosis rate promotion. Moreover, circPRKCA knockdown retarded tumor growth of A549 cells in vivo. Molecularly, miR-330-5p was sponged by circPRKCA, and PDK1 was a target of miR-330-5p. Inhibiting miR-330-5p could attenuate the suppression of circPRKCA knockdown on cell growth, migration, and invasion; contrarily, promoting miR-330-5p caused inhibition on those cell behaviors by downregulating PDK1. Analogously, AKT activity was suppressed by circPRKCA downregulation and miR-330-5p upregulation in NSCLC cells both in vitro and in vivo.

Conclusion

Depleting circPRKCA inhibited PDK1 to suppress NSCLC cell malignant behaviors through miR-330-5p/PDK1/AKT pathway.

Circular RNAs: New Epigenetic Signatures in Viral Infections

Covalent closed circular RNAs (circRNAs) can act as a bridge between non-coding RNAs and coding messenger RNAs. CircRNAs are generated by a back-splicing mechanism during post-transcriptional processing and are abundantly expressed in eukaryotic cells. CircRNAs can act via the modulation of RNA transcription and protein production, and by the sponging of microRNAs (miRNAs). CircRNAs are now thought to be involved in many different biological and pathological processes. Some studies have suggested that the expression of host circRNAs is dysregulated in several types of virus-infected cells, compared to control cells. It is highly likely that viruses can use these molecules for their own purposes. In addition, some viral genes are able to produce viral circRNAs (VcircRNA) by a back-splicing mechanism. However, the viral genes that encode VcircRNAs, and their functions, are poorly studied. In this review, we highlight some new findings about the interaction of host circRNAs and viral infection. Moreover, the potential of VcircRNAs derived from the virus itself, to act as biomarkers and therapeutic targets is summarized.

Implications of Long Non-Coding RNAs in Age-Altered Proteostasis

This review aims to summarize the current knowledge on how lncRNAs are influencing aging and cancer metabolism. Recent research has shown that senescent cells re-enter cell-cycle depending on intrinsic or extrinsic factors, thus restoring tissue homeostasis in response to age-related diseases (ARDs). Furthermore, maintaining proteostasis or cellular protein homeostasis requires a correct quality control (QC) of protein synthesis, folding, conformational stability, and degradation. Long non-coding RNAs (lncRNAs), transcripts longer than 200 nucleotides, regulate gene expression through RNA-binding protein (RBP) interaction. Their association is linked to aging, an event of proteostasis collapse. The current review examines approaches that lead to recognition of senescence-associated lncRNAs, current methodologies, potential challenges that arise from studying these molecules, and their crucial implications in clinical practice.

Analysis of the Molecular Mechanism of Acute Coronary Syndrome Based on circRNA-miRNA Network Regulation

BACKGROUND

With the development of biological technology, biomarkers for the prevention and diagnosis of acute coronary syndrome (ACS) have become increasingly evident. However, the study of novel circular RNAs (circRNAs) in ACS is still in progress. This study aimed to investigate whether the regulation of circRNA-miRNA networks is involved in ACS pathogenesis.

METHODS

We used microarray analysis to detect significantly expressed circRNAs and miRNAs in the peripheral blood of patients in the control group (CG) and ACS groups, including an unstable angina pectoris (UAP) group and an acute myocardial infarction (AMI) group. A circRNA-miRNA interaction network analysis was carried out with open-source bioinformatics. The gene ontology (GO), pathway, and disease enrichment analyses for differentially expressed circRNAs were further analysed with hierarchical clustering.

RESULTS

A total of 266 circRNAs (121 upregulated and 145 downregulated, P < 0.05, fold change FC ≥2) and 3 miRNAs (1 upregulated and 2 downregulated, P < 0.05, FC ≥ 1.2) were differentially expressed in the ACS groups compared with those in the CG. In addition, among these expressed circRNAs and miRNAs, a single circRNA could bind to more than 1-100 miRNAs, and vice versa. Next, an AMI-UAP network, an AMI-CG network, a UAP-CG network, and an AMI-CG-UAP network were constructed. The top 30 enriched GO terms among the three groups were emphasized as differentially expressed. Disease enrichment analysis showed that these differentially expressed circRNAs are involved in the pathogenesis of cardiovascular diseases. KEGG pathway analysis was performed to identify pathways associated with circRNAs targeting mRNAs.

CONCLUSION

CircRNAs are closely related to the pathological process of ACS via a mechanism that may be related to the up- or down-regulation of circRNAs and miRNAs and circRNA-miRNA coexpression. The metabolic pathways, signalling pathways, and diseases affected by these circRNAs can be predicted by enrichment analysis.

Circular RNAs: from biogenesis and function to diseases

OBJECTIVE

Evidence suggests that various diseases may contribute to the circular RNAs (circRNAs) expression disorder. This review was aimed at looking for appropriate biomarkers for the treatment of diseases.

DATA SOURCES

The comprehensive search used online literature databases including PubMed of National Center for Biotechnology Information and Web of Science.

STUDY SELECTION

The study selection was based on the following keywords: circRNAs, biogenesis, biologic function, and disease. The time limit for literature retrieval was from the year 1976 to 2019, with language restriction in English. Relevant articles were carefully reviewed, with no exclusions applied to study design and publication type.

RESULTS

CircRNAs are one of the critical non-coding RNAs (ncRNAs), which are covalently closed continuous loops that do not possess 5' and 3' ends. This makes them resistant to exoribonuclease activity and potentially more stable than their cognate linear transcripts, thus making them ideal candidates for biomarker development. Due to the stable and extensive tissue-specific expression of circRNAs, they can function as microRNA sponges and bind to RNA-binding proteins, regulate transcription and splicing, and translate into proteins to participate in the regulation of physiologic and pathologic processes. Moreover, the expression disorders of circRNAs in diseases, such as neurodegenerative disease, cardiovascular disease, and cancer, make them have potential applications for the diagnosis and treatment of diseases.

CONCLUSIONS

Changes in circRNA expression profiles related to various diseases, and circRNAs often exhibit low expression in cancer tissues. In addition, circRNAs can be detected in patient's body fluids to indicate that circRNAs are effective biomarkers for disease diagnosis. These characteristics make circRNAs have potential applications as novel therapeutic targets for diseases.

CircHIPK3 Promotes Pyroptosis in Acinar Cells Through Regulation of the miR-193a-5p/GSDMD Axis

Acute pancreatitis (AP), especially severe acute pancreatitis (SAP), is an extremely dangerous illness with a high mortality rate. Pyroptotic cells release their cellular contents and inflammatory factors, aggravating the inflammatory response. Pyroptosis may be the main mode of acinar cell death during AP. The circular RNA circHIPK3 is expressed in pancreatic tissue and is associated with inflammatory response. In this study, we focused on the role and underlying mechanism of circHIPK3 in AP. We found that the expression of circHIPK3 was significantly elevated in serum of patients with AP and in caerulein-stimulated AR42J cells and was associated with caspase-1 and caspase-11 activation. circHIPK3 silencing ameliorated caerulein-induced cell damage and reduced the release of inflammatory factors IL-1β, IL-6, IL-8, and TNF-α and inhibited the activation of caspase-1 and caspase-11. In addition, circHIPK3 bound to miR-193a-5p and negatively regulated its expression. Inhibition of miR-193a-5p increased the release of IL-1β, IL-6, IL-8, and TNF-α and activated caspase-1 and caspase-11, thereby counteracting the effect of circHIPK3 silencing on caerulein-induced cell damage. Furthermore, we identified GSDMD as a target gene of miR-193a-5p, which is the key gene for pyroptosis. Interfering with the expression of GSDMD can increase cell viability, reduce the secretion of inflammatory cytokines, and suppress the activation of cleaved caspase-1 and caspase-11. Silencing GSDMD reversed the effects of miR-193a-5p inhibitors on caerulein-induced damage. In conclusion, circHIPK3 promotes pyroptosis in acinar cells through regulation of the miR-193a-5p/GSDMD axis, which eventually aggravates AP disease.

Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

BACKGROUND

Eimeria necatrix, the most highly pathogenic coccidian in chicken small intestines, can cause high morbidity and mortality in susceptible birds and devastating economic losses in poultry production, but the underlying molecular mechanisms in interaction between chicken and E. necatrix are not entirely revealed. Accumulating evidence shows that the long-non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are key regulators in various infectious diseases. However, the expression profiles and roles of these two non-coding RNAs (ncRNAs) during E. necatrix infection are still unclear.

METHODS

The expression profiles of mRNAs, lncRNAs and circRNAs in mid-segments of chicken small intestines at 108 h post-infection (pi) with E. necatrix were analyzed by using the RNA-seq technique.

RESULTS

After strict filtering of raw data, we putatively identified 49,183 mRNAs, 818 lncRNAs and 4153 circRNAs. The obtained lncRNAs were classified into four types, including 228 (27.87%) intergenic, 67 (8.19%) intronic, 166 (20.29%) anti-sense and 357 (43.64%) sense-overlapping lncRNAs; of these, 571 were found to be novel. Five types were also predicted for putative circRNAs, including 180 exonic, 54 intronic, 113 antisense, 109 intergenic and 3697 sense-overlapping circRNAs. Eimeria necatrix infection significantly altered the expression of 1543 mRNAs (707 upregulated and 836 downregulated), 95 lncRNAs (49 upregulated and 46 downregulated) and 13 circRNAs (9 upregulated and 4 downregulated). Target predictions revealed that 38 aberrantly expressed lncRNAs would cis-regulate 73 mRNAs, and 1453 mRNAs could be trans-regulated by 87 differentially regulated lncRNAs. Additionally, 109 potential sponging miRNAs were also identified for 9 circRNAs. GO and KEGG enrichment analysis of target mRNAs for lncRNAs, and sponging miRNA targets and source genes for circRNAs identified associations of both lncRNAs and circRNAs with host immune defense and pathogenesis during E. necatrix infection.

CONCLUSIONS

To the best of our knowledge, the present study provides the first genome-wide analysis of mRNAs, lncRNAs and circRNAs in chicken small intestines infected with E. necatrix. The obtained data will offer novel clues for exploring the interaction mechanisms between chickens and Eimeria spp.

Plasma and Tissue Specific miRNA Expression Pattern and Functional Analysis Associated to Colorectal Cancer Patients

An increasing number of studies suggest the implication of microRNAs (miRNAs) in colorectal (CRC) carcinogenesis and disease progression. Nevertheless, the basic mechanism is not yet clear. We determined plasma miRNA expression levels using Agilent microarray technology followed by overlapping with The Cancer Genome Atlas (TCGA) tissue data and a qRT-PCR validation step and analysis of the altered miRNA signatures to emphasize new mechanistic insights. For TGCA dataset, we identified 156 altered miRNAs (79 downregulated and 77 upregulated) in colorectal tissue samples versus normal tissue. The microarray experiment is based on 16 control samples, 38 CRC plasma samples from colorectal cancer patients who have not undergone chemotherapy, and 17 chemo-treated samples. In the case of the analysis of CRC cancer versus healthy control we identified 359 altered miRNAs (214 downregulated and 60 upregulated), considering as the cutoff value a fold-change of ±1.5 and p < 0.01. An additional microarray analysis was performed on plasma from untreated colorectal cancer (n = 38) and chemotherapy-treated colorectal cancer patients (n = 17), which revealed 15 downregulated miRNAs and 53 upregulated miRNAs, demonstrating that the plasma miRNA pattern is affected by chemotherapy and emphasizing important regulators of drug resistance mechanisms. For the validation of the microarray data, we selected a panel of 4 miRNAs from the common miRNA signatures for colon and rectal cancer (miR-642b-3p, miR-195-5p and miR-4741). At the tissue level, the expression levels were in agreement with those observed in colorectal plasma. miR-1228-3p, the top upregulated miRNA in CRC, was chosen to be validated on tissue and plasma samples, as it was demonstrated to be downregulated at tissue level in our patient cohort. This was confirmed by TCGA data and was one example of ta ranscript that has a different expression level between tumor tissue and plasma. Developing more efficient investigation methods will help explain the mechanisms responsible for miRNAs released in biofluids, which is the most upregulated transcript in colorectal plasma samples and which can function as a prediction tool within the oncological field.

Appraising circular RNAs as novel biomarkers for the diagnosis and prognosis of gastric cancer: A pair-wise meta-analysis

Background

Circular RNAs (circRNAs), proven as single‐stranded closed RNA molecules, have been implicated in the onset and development of multiple cancers. This study aimed to summarize existing evidences regarding the clinicopathologic, diagnostic, and prognostic significances of circRNAs in gastric cancer (GC).

Methods

Eligible studies were identified using online databases. The quality of the included studies was judged, and patients' clinical characteristics, diagnostic data, and overall survival (OS) were extracted from the electronic medical record. Fisher's method was adopted to determine P values for clinicopathologic features. The diagnostic and prognostic data from all included studies were merged.

Results

Thirty eligible studies were comprised of 2687 GC patients were enrolled in the meta‐analyses. Altered expressions of circRNAs in GC tissues were significantly associated with worse clinicopathologic features. Abnormally expressed circRNAs yielded a pooled sensitivity of 0.76 (95% CI: 0.69‐0.81) and a specificity of 0.77 (95% CI: 0.70‐0.83) in distinguishing GC from noncancerous controls, which corresponded to an area under the curve (AUC) of 0.83. The survival analysis showed that the oncogenic circRNA signature could be an independent risk factor of OS (HR = 2.11, 95% CI: 1.60‐2.78, P = .000). Patients with down‐regulated circRNAs (tumor suppressor genes) presented a significantly shorter OS time than those with high‐level circRNAs (HR = 0.33, 95% CI: 0.27‐0.42, P = .000). Stratified analyses based on sample type, control source, circRNA expression status, and cutoff setting also produced robust results.

Conclusions

CircRNAs may play an important role as potential diagnostic and prognostic biomarkers of GC.

Critical function of circular RNAs in lung cancer

Lung cancer is one of the main causes of cancer-related death in the world, especially due to its frequency and ineffective therapeutically approaches in the late stages of the disease. Despite the recent advent of promising new targeted therapies, lung cancer diagnostic strategies still have difficulty in identifying the disease at an early stage. Therefore, the characterizations of more sensible and specific cancer biomarkers have become an important goal for clinicians. Circular RNAs (circRNAs), a type of RNA with covalently closed continuous loop structures that display high structural resistance and tissue specificity pointed toward a potential biomarker role. Current investigations have identified that circRNAs have a prominent function in the regulation of oncogenic pathways, by regulating gene expression both at transcriptional and post-transcriptional level. The aim of this review is to provide novel information regarding the implications of circRNAs in lung cancer, with an emphasis on the role in disease development and progression. Initially, we explored the potential utility of circRNAs as biomarkers, focusing on function, mechanisms, and correlation with disease progression in lung cancer. Further, we will describe the interaction between circRNAs and other non-coding species of RNA (particularly microRNA) and their biological significance in lung cancer. Describing the nature of these interactions and their therapeutic potential will provide additional insight regarding the altered molecular landscape of lung cancer and consolidate the potential clinical value of these circular transcripts. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.

A New World of Biomarkers and Therapeutics for Female Reproductive System and Breast Cancers: Circular RNAs

As one of the most recently (re)discovered types of non-coding RNAs (ncRNA), circular RNAs (circRNAs) differentiate from other ncRNAs by a specific biogenesis, high stability, and distinct functions. The biogenesis of circRNAs can be categorized into three mechanisms that permit the back-splicing reaction: exon-skipping, pairing of neighboring introns, and dimerization of RNA-binding proteins. Regarding their stability, circRNAs have no free ends, specific to linear RNA molecules, prompting a longer half-life and resistance to exonuclease-mediated activity by RNase R, bypassing the common RNA turnover process. Regarding their functions, circular transcripts can be categorized into four broad roles: miRNA sponging, protein binding, regulation of transcription, and coding for proteins and peptides. Female reproductive system (including mainly ovarian, corpus, and cervix uteri cancers) and breast cancers are the primary causes of death in women worldwide, accounting for over 1,212,772 deaths in 2018. We consider that a better understanding of the molecular pathophysiology through the study of coding and non-coding RNA regulators could improve the diagnosis and therapeutics of these cancers. Developments in the field of circRNA in regard to breast or gynecological cancers are recent, with most circRNA-related discoveries having been made in the last 2 years. Therefore, in this review we summarize the newly detected roles of circRNAs in female reproductive system (cervical cancer, ovarian cancer, and endometrial cancer) and breast cancers. We argue that circRNAs can become essential elements of the diagnostic and therapeutic tools for female reproductive system cancers in the future.

The ceRNA Network Has Potential Prognostic Value in Clear Cell Renal Cell Carcinoma: A Study Based on TCGA Database

Clear cell renal cell carcinoma (ccRCC) is a very common cancer in urology. Many evidences suggest that complex changed pathways take a nonnegligible part in the occurrence and development of ccRCC. Nevertheless, the underlying mechanism is not clear. In this study, the expression data between ccRCC and normal tissue samples in TCGA database were compared to distinguish differentially expressed genes (DEGs: mRNAs, miRNAs, and lncRNAs). Afterwards, we used GO enrichment and KEGG pathway enrichment analyses to explore the functions of these DEGs. We also found the correlation between three RNAs and created a competing endogenous RNA (ceRNA) network. Moreover, we used univariate Cox regression analysis to select DEGs that are connected with overall survival (OS) of ccRCC patients. We found 1652 mRNAs, 1534 lncRNAs, and 173 miRNAs that were distinguished in ccRCC compared with normal tissues. According to GO analysis, the maladjusted mRNAs are mainly concentrated in immune cell activation and kidney development, while according to KEGG, they are mainly concentrated in pathways related to cancer. A total of 5 mRNAs, 1 miRNA, and 4 lncRNAs were connected with patients' OS. In this article, a network of lncRNA-miRNA-mRNA was established; it is expected to be able to indicate possible molecular mechanisms for initial of ccRCC and provide a new viewpoint for diagnosis of ccRCC.

MicroRNA profiling in kidney in pigs fed ochratoxin A contaminated diet

OTA is a toxic metabolite produced by fungus belonging to Aspergillus and Penicillium genera. Kidney is the main target of this toxin; OTA is considered as one of the etiological factors at the origin of the human Balkan endemic nephropathy. microRNA are short non-coding transcrips (18-22 nucleotides in length) regulating key cellular processes. Various miRNAs have been established to play important roles in development of renal carcinoma and urothelial cancer. The objective of this study is to analyse the miRNA profiling in the kidney of piglets experimentally intoxicated with feed contaminated with OTA. Fifteen piglets (five pigs/group) were randomly distributed into 3 groups, fed normal diet (Group 1: control), or diets contaminated with OTA in two concentrations: 50 μg OTA/kg feed (Group 2: 50 μg OTA/kg feed) or 200 μg OTA/kg feed (Group 3: 200 μg OTA/kg feed) for 28 days. At the end of the experiment blood samples were taken for serological analyses. Animals from control group and 200 μg OTA/kg feed were sacrificed and kidney samples were taken for histological and molecular analyses. As resulted from molecular profiling study there are 8 miRNA differentially expressed in OTA kidney vs control kidney, in which five miRNA were overexpressed in the kidney of OTA intoxicated animals: miR-497 (FC = 6.34), miR-133a-3p (FC = 5.75), miR-423-3p (FC = 5.48), miR-34a (FC = 1.68), miR-542-3p (1.65) while three miRNA were downregulated: miR-421-3p (FC = -3.96); miR-490 (FC = -3.87); miR-9840-3p (FC = -2.13). The altered miRNAs as effect of OTA are strongly connected to the engine of cancer, disturbing nodal points in different pathways, as TP53 signalling. This proof-of-concept study proves the actual utility of miRNAs as biomarkers of mycotoxin exposure, including OTA.

The extensive role of miR-155 in malignant and non-malignant diseases

MicroRNAs (miRNAs) have rapidly emerged as key molecules in cancer initiation and development, showing the capability to regulate pivotal oncogenic pathways. MiR-155 has gathered an increased attention especially in oncology, but also in non-malignanat pathologies. Nowadays, this noncoding RNA is one of the most important miRNAs in cancer, due to the extensive signaling network associated with it, implication in immune system regulation and also deregulation in disease states. Therefore, numerous research protocols are focused on preclinical modulation of miR-155 for therapeutic purposes, or investigation of its dynamic expression for diagnostic/prognostic assessments, with the final intention of bringing this miRNA into the clinical setting. This review comprehensively presents the extended role of miR-155 in cancer and other pathologies, where its expression is dysregulated. Finally, we assess the future steps toward miR-155 based therapeutics.

Comprehensive circular RNA profiling reveals the regulatory role of the hsa_circ_0137606/miR‑1231 pathway in bladder cancer progression

Bladder cancer (BC) is one of the most common malignant tumors in males globally. Its progression imposes a heavy burden on patients; however, the expression profile of circular (circ)RNAs in BC progression remains unclear. This study explored changes in circRNA expression during BC progression by sequencing different grade BC samples and normal controls to reveal the circRNA expression profiles of different BC grades. Gene Ontology (GO) and Kyoto Encyclopedia of Gens and Genomes (KEGG) pathway analyses, and protein-protein interaction network construction were used to predict pathways that the differentially expressed circRNAs may participate in. circRNA expression levels were detected using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and dual-luciferase reporter assays were used to investigate the interactions between circRNA and microRNA (miR). Cell Counting Kit-8 and Transwell assays were also performed to detect cell proliferation, migration, and invasion. In total, 244 circRNAs were found to be differentially expressed in high-grade BC compared to low-grade BC, whilst 316 dysregulated circRNAs were detected in high-grade BC compared with normal urothelium. Furthermore, 42 circRNAs overlapped between the two groups, seven of which were randomly selected and detected by RT-qPCR to validate the sequencing results. GO analysis and KEGG pathway analyses revealed that the differentially expressed circRNAs may participate in BC via 'GTPase activity regulation', 'cell junction', and 'focal adhesion' pathways. Of note, we proposed that a novel circRNA in BC progression, hsa_circ_0137606, could suppress BC proliferation and metastasis by sponging miR-1231. Through bioinformatics analysis, we predicted that PH domain and leucine rich repeat protein phosphatase 2 could be a target of the hsa_circ_0137606/miR-1231 axis in BC progression. Using high-throughput sequencing, this study revealed the circRNA expression profiles of different grades of BC and proposed that the novel circRNA, hsa_circ_0137606, suppresses BC proliferation and metastasis by sponging miR-1231. Our findings may provide novel insight into potential therapeutic targets for treating BC.

Progress in Research on the Role of Flavonoids in Lung Cancer

Lung cancer is the leading cause of cancer deaths worldwide. Therefore, for the prevention, diagnosis, prognosis and treatment of lung cancer, efficient preventive strategies and new therapeutic strategies are needed to face these challenges. Natural bioactive compounds and particular flavonoids compounds have been proven to have an important role in lung cancer prevention and of particular interest is the dose used for these studies, to underline the molecular effects and mechanisms at a physiological concentration. The purpose of this review was to summarize the current state of knowledge regarding relevant molecular mechanisms involved in the pharmacological effects, with a special focus on the anti-cancer role, by regulating the coding and non-coding genes. Furthermore, this review focused on the most commonly altered and most clinically relevant oncogenes and tumor suppressor genes and microRNAs in lung cancer. Particular attention was given to the biological effect in tandem with conventional therapy, emphasizing the role in the regulation of drug resistance related mechanisms.

RETRACTED: A novel circular RNA circ-ZNF652 promotes hepatocellular carcinoma metastasis through inducing snail-mediated epithelial-mesenchymal transition by sponging miR-203/miR-502-5p

This article has been retracted at the request of the authors: please see Elsevier policy on article withdrawal (https://www.elsevier.com/locate/withdrawalpolicy). The authors claim that other members of their lab attempted to repeat the experiments in this study several times and found that the activation ability of snail on circ-znf652 was significantly lower than reported, indicating that this regulation loop does not exist. The authors' incorrect experimental method and lack of reasonable control, coupled with the lack of experimental experience of the first author, led to the mistakes and mean the results cannot be relied upon. In order not to mislead other scientists, they requested to retract their manuscript. The Editor-in-Chief has approved this retraction. The authors apologise to the readership of the journal for these errors.

Circular exonic RNAs: When RNA structure meets topology

Although RNA circularization was first documented in the 1990s, the extent to which it occurs was not known until recent advances in high-throughput sequencing enabled the widespread identification of circular RNAs (circRNAs). Despite this, many aspects of circRNA biogenesis, structure, and function yet remain obscure. This review focuses on circular exonic RNAs, a subclass of circRNAs that are generated through backsplicing. Here, I hypothesize that RNA secondary structure can be the common factor that promotes both exon skipping and spliceosomal RNA circularization, and that backsplicing of double-stranded regions could generate topologically linked circRNA molecules. CircRNAs manifest themselves by the presence of tail-to-head exon junctions, which were previously attributed to post-transcriptional exon permutation and repetition. I revisit these observations and argue that backsplicing does not automatically imply RNA circularization because tail-to-head exon junctions give only local information about transcript architecture and, therefore, they are in principle insufficient to determine globally circular topology. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.

The Function of Non-Coding RNAs in Lung Cancer Tumorigenesis

Lung cancer is the most prevalent and deadliest cancer worldwide. A significant part of lung cancer studies is dedicated to the expression alterations of non-coding RNAs. The non-coding RNAs are transcripts that cannot be translated into proteins. While the study of microRNAs and siRNAs in lung cancer received a lot of attention over the last decade, highly efficient therapeutic option or the diagnostic methods based on non-coding RNAs are still lacking. Because of this, it is of utmost importance to direct future research on lung cancer towards analyzing other RNA types for which the currently available data indicates that are essential at modulating lung tumorigenesis. Through our review of studies on this subject, we identify the following non-coding RNAs as tumor suppressors: ts-46, ts-47, ts-101, ts-53, ts-3676, ts-4521 (tRNA fragments), SNORD116-26, HBII-420, SNORD15A, SNORA42 (snoRNAs), piRNA-like-163, piR-35127, the piR-46545 (piRNAs), CHIAP2, LOC100420907, RPL13AP17 (pseudogenes), and uc.454 (T-UCR). We also found non-coding RNAs with tumor-promoting function: tRF-Leu-CAG, tRNA-Leu, tRNA-Val (tRNA fragments), circ-RAD23B, circRNA 100146, circPVT1, circFGFR3, circ_0004015, circPUM1, circFLI1, circABCB10, circHIPK3 (circRNAs), SNORA42, SNORA3, SNORD46, SNORA21, SNORD28, SNORA47, SNORD66, SNORA68, SNORA78 (snoRNAs), piR-65, piR-34871, piR-52200, piR651 (piRNAs), hY4 5’ fragments (YRNAs), FAM83A-AS1, WRAP53, NKX2-1-AS1 (NATs), DUXAP8, SFTA1P (pseudogene transcripts), uc.338, uc.339 (T-UCRs), and hTERC.