Regulation of Transcription by Circular RNAs

Systematic loss-of-function screens identify pathway-specific functional circular RNAs

Circular RNA (circRNA) is covalently closed, single-stranded RNA produced by back-splicing. A few circRNAs have been implicated as functional; however, we lack understanding of pathways that are regulated by circRNAs. Here we generated a pooled short-hairpin RNA library targeting the back-splice junction of 3,354 human circRNAs that are expressed at different levels (ranging from low to high) in humans. We used this library for loss-of-function proliferation screens in a panel of 18 cancer cell lines from four tissue types harbouring mutations leading to constitutive activity of defined pathways. Both context-specific and non-specific circRNAs were identified. Some circRNAs were found to directly regulate their precursor, whereas some have a function unrelated to their precursor. We validated these observations with a secondary screen and uncovered a role for circRERE(4-10) and circHUWE1(22,23), two cell-essential circRNAs, circSMAD2(2-6), a WNT pathway regulator, and circMTO1(2,RI,3), a regulator of MAPK signalling. Our work sheds light on pathways regulated by circRNAs and provides a catalogue of circRNAs with a measurable function.

CircGNAO1 strengthens its host gene GNAO1 expression for suppression of hepatocarcinogenesis

Background

Hepatocellular carcinoma (HCC) is one of the most prevalent primary liver carcinoma. Guanine nucleotide-binding protein, α-activating activity polypeptide O (GNAO1) was reported to be under-expressed in HCC tissues. This study aimed to investigate the GNAO1-derived circular RNA (circRNA) and its molecular mechanisms in HCC.

Methods

Real-time quantitative polymerase chain reaction (RT-qPCR) and Western blot were applied to examine RNA and protein levels. Functional experiments were performed to study HCC cell proliferation, cell cycle and cellular senescence. The interactions among circGNAO1, GNAO1 and DNA methyltransferase 1 (DNMT1) were examined by mechanism assays. The methylation level was analyzed by bisulfite sequencing PCR (BSP).

Results

CircGNAO1 is down-regulated and positively associated with GNAO1 in HCC tissues. Overexpression of circGNAO1 inhibits cell proliferation, induces cell cycle arrest and facilitates cell senescence in HCC cells. CircGNAO1 facilitates the progression of HCC via modulating GNAO1. Mechanistically, circGNAO1 enhances the transcription of GNAO1 by sequestering DNMT1, thereby up-regulating GNAO1 expression in HCC cells.

Conclusions

CircGNAO1 up-regulates its host gene GNAO1 expression for suppression of hepatocarcinogenesis.

Integrative lncRNA, circRNA, and mRNA analysis reveals expression profiles of six forensic body fluids/tissue

RNAs have attracted much attention in forensic body fluid/tissue identification (BFID) due to their tissue-specific expression characteristics. Among RNAs, long RNAs (e.g., mRNA) have a higher probability of containing more polymorphic sites that can be used to assign the specific donor of the body fluid/tissue. However, few studies have characterized their overall profiles in forensic science. In this study, we sequenced the transcriptomes of 30 samples from venous blood, menstrual blood, semen, saliva, vaginal secretion, and skin tissue, obtaining a comprehensive picture of mRNA, lncRNA, and circRNA profiles. A total of 90,305 mRNAs, 102,906 lncRNAs (including 19,549 novel lncRNAs), and 40,204 circRNAs were detected. RNA type distribution, length distribution, and expression distribution were presented according to their annotation and expression level, and many novel body fluid/tissue-specific RNA markers were identified. Furthermore, the cognate relations among the three RNAs were analyzed according to gene annotations. Finally, SNPs and InDels from RNA transcripts were genotyped, and 21,611 multi-SNP and 4,471 multi-InDel transcriptomic microhaplotypes (tMHs) were identified. These results provide a comprehensive understanding of transcriptome profiles, which could provide new avenues for tracing the origin of the body fluid/tissue and identifying an individual.

Global identification of mRNA-interacting circular RNAs by CLiPPR-Seq

Although the functional role of circular RNA (circRNA) interaction with microRNAs and proteins has been studied extensively, circRNA interactions with the protein-coding mRNAs in intact cells remain largely unknown. Here, by employing AMT-mediated proximity ligation of RNA-RNA duplexes followed by circRNA enrichment and deep sequencing, we report a novel Cross-Linking Poly(A) Pulldown RNase R Sequencing (CLiPPR-seq) technology which identified hundreds of mRNA-interacting circRNAs in three different cell types, including βTC6, C2C12 and HeLa cells. Furthermore, CLiPP-seq without RNase R treatment was also performed to identify the mRNA expression in these cells. BLAST analysis of circRNAs in CLiPPR-seq sample with the mRNAs in CLiPP-seq samples determined their potential complementary sequences for circRNA-mRNA interaction. Pulldown of circRNAs and poly(A) RNAs confirmed the direct interaction of circRNAs with target mRNAs. Silencing of mRNA-interacting circRNAs led to the altered expression of target mRNAs in βTC6 cells, suggesting the role of direct interaction of circRNAs with mRNAs in gene expression regulation. CLiPPR-seq thus represents a novel method for illuminating the myriad of uncharacterized circRNA-mRNA hybrids that may regulate gene expression.

Role of circular RNA/miRNA axes in the pathophysiology of polycystic ovary syndrome

Polycystic ovary syndrome (PCOS) is a disorder resulted from interactions between genetic and environmental factors. Based on the importance of epigenetic factors in the pathoetiology of PCOS, the current review focused on identification of circular RNAs (circRNAs) that are involved in PCOS through acting as molecular sponges for microRNAs (miRNAs). The literature search led to identification of circ_0043533/miR-1179, circ_0030018/miR-136, circ_FURIN/miR-423-5p, circ-FURIN/miR-195-5p, circ_0043532/miR-182, circ_RANBP9/miR-136-5p, circRHBG/miR-515-5p, circMTO1/miR-320b, circASPH/miR-375, circPSMC3/miR-296-3p, circLDLR/miR-1294, circPUM1/miR-760, and hsa_circ_0118530/miR-136 as molecular axes contributing to the pathogenesis of PCOS. To set the stage for future research on the role of the ceRNA network in PCOS, in-silico analyses were performed using miRWalk, miRNet, and miRDIP databases. miRWalk identified 80 genes regulated by 5 miRNAs, miRNet revealed 6449 circRNAs potentially controlling 11 miRNAs, and miRDIP identified 11 miRNAs associated with 35 human pathways. These targets can be used in the treatment options, design of personalized medicine and prediction of prognosis of PCOS.

Circular RNA in cervical cancer: Fundamental mechanism and clinical potential

CC (CC) remains a significant global health concern, imposing a substantial health burden on women worldwide due to its high incidence and mortality rates. To address this issue, there is a need for ongoing research to uncover the underlying molecular mechanisms of CC and to discover novel diagnostic and therapeutic strategies. Recent progress in non-coding RNAs (ncRNAs) has opened new avenues for investigation, and circular RNAs (circRNAs) have emerged as molecules with diverse roles in various cellular processes. These circRNAs are distinct in structure, forming a closed loop, setting them apart from their linear counterparts. They are intricately involved in regulating different aspects of cellular functions, particularly in cell growth and development. Remarkably, circRNAs can have varying functions, either promoting or inhibiting oncogenic processes, depending on the specific cellular context. Recent studies have identified abnormal circRNAs expression patterns associated with CC, indicating their significant involvement in disease development. The differing circRNAs profiles linked to CC present promising opportunities for early detection, precise prognosis evaluation, and personalized treatment strategies. In this comprehensive review, we embark on a detailed exploration of CC-related circRNAs, elucidating their distinct roles and providing insights into the intricate molecular mechanisms governing CC's onset and progression. A growing body of evidence strongly suggests that circRNAs can serve as valuable biomarkers for early CC detection and hold potential as therapeutic targets for intervention. By delving into the complex interplay between circRNAs and CC, we are paving the way for innovative, individualized approaches to combat this serious disease, with the goal of reducing its impact on women's health globally and improving patient outcomes. As our understanding of circRNAs in the context of CC continues to deepen, the outlook for breakthroughs in diagnosis and treatment becomes increasingly promising.

Exploring the interplay between PARP1 and circRNA biogenesis and function

PARP1 (poly-ADP-ribose polymerase 1) is a multidomain protein with a flexible and self-folding structure that allows it to interact with a wide range of biomolecules, including nucleic acids and target proteins. PARP1 interacts with its target molecules either covalently via PARylation or non-covalently through its PAR moieties induced by auto-PARylation. These diverse interactions allow PARP1 to participate in complex regulatory circuits and cellular functions. Although the most studied PARP1-mediated functions are associated with DNA repair and cellular stress response, subsequent discoveries have revealed additional biological functions. Based on these findings, PARP1 is now recognized as a major modulator of gene expression. Several discoveries show that this multifunctional protein has been intimately connected to several steps of mRNA biogenesis, from transcription initiation to mRNA splicing, polyadenylation, export, and translation of mRNA to proteins. Nevertheless, our understanding of PARP1's involvement in the biogenesis of both coding and noncoding RNA, notably circular RNA (circRNA), remains restricted. In this review, we outline the possible roles of PARP1 in circRNA biogenesis. A full examination of the regulatory roles of PARP1 in nuclear processes with an emphasis on circRNA may reveal new avenues to control dysregulation implicated in the pathogenesis of several diseases such as neurodegenerative disorders and cancers. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Processing > Splicing Regulation/Alternative Splicing.

Hsa_circ_0001479 accelerates tumorigenesis of gastric cancer and mediates immune escape

Gastric cancer (GC) is a common fatal malignant tumor of the digestive tract, particularly in Asia. Circular RNA (circRNA) has been proved to regulate malignancy progression and immunotherapeutic efficacy in multiple tumors, including GC. Notably, the function of circRNAs in GC has not been completely revealed. Therefore, exploration of more GC related circRNAs may provide potential strategies for GC treatment. In the study, it was observed that hsa_circ_0001479 exhibited a high level of expression in GC and was subsequently found to be associated with the depth of invasion, lymph node metastasis, and TNM stage. Functionally, the overexpression of hsa_circ_0001479 was found to enhance the proliferation and migration of GC cells, as evidenced by various experiments such as CCK-8, EdU, colony forming and transwell. Dual-luciferase reporter assay verified that hsa_circ_0001479 upregulated DEK expression by sponge targeting miR-133a-5p. Further investigations indicated DEK affected the entry of β-catenin into the nucleus by activating Wnt/β-catenin signaling pathway to promote accumulation of downstream c-Myc. As a transcription factor, c-Myc combined with the promoter of hsa_circ_0001479 parent gene to stimulate hsa_circ_0001479 generation. Besides, hsa_circ_0001479 inhibited theinfiltration with CD8+T cells in GC and associated with immune checkpoints. In summary, hsa_circ_0001479 accelerated the development and metastasis of GC and mediates immune escape of CD8+T cells. Targeting it may provide a novel immunotherapy to better locally treat GC and reduce the incidence of metastases.

CircRNA-SCAF8 promotes vascular endothelial cell pyroptosis by regulating the miR-93-5p/TXNIP axis

OBJECTIVES

To investigate the role and mechanism of circRNA-SR-related CTD associated factor 8 (SCAF8) in regulating endothelial cell pyroptosis in high glucose environment.

METHODS

Human umbilical vein endothelial cells (HUVECs) were cultured and divided into six groups. The normal control group and high glucose control group were cultured in cell culture medium with 5 and 33 mmol/L glucose, respectively. The RNA control group, circRNA-SCAF8 inhibition group, miR-93-5p overexpression group and miR-93-5p inhibition group were added with non-functional siRNA, circRNA-SCAF8 inhibitor, miR-93-5p overexpression molecule and miR-93-5p inhibitor in high glucose environment, respectively. Cell viability and pyroptosis were detected by cell counting kit-8 (CCK-8) assay, flow cytometry and Hoechst 33342/propidium iodide fluorescence double staining. Western blotting and enzyme-linked immunosorbent assay were used to detect the expression of pyroptosis-related factors including apoptosis-associated speck-like protein containing a CARD (ASC), cysteine aspartic acid specific protease-1 (caspase-1) and Gasdermin D (GSDMD), NOD like receptor protein 3 (NLRP-3), thioredoxin interacting proteins (TXNIP), IL-18 and IL-1β. The expression of circRNA-SCAF8, miR-93-5p and TXNIP was detected by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Fluorescence in situ hybridization (FISH) was used to locate circRNA-SCAF8 and miR-93-5p. Dual luciferase assay was used to verify the targeted regulatory relationship between miR-93-5p and upstream and downstream molecules.

RESULTS

Compared with the RNA control group, the cell survival rate of circRNA-SCAF8 inhibition group and miR-93-5p overexpression group increased (both P<0.01), the pyroptosis decreased (both P<0.01), and the expressions of pyroptosis-related factors such as TXNIP, NLRP-3, caspase-1, GSDMD, ASC, IL-18 and IL-1β were significantly decreased (all P<0.05). The expression of miR-93-5p was significantly increased after inhibition of circRNA-SCAF8 (P<0.01), and the expression of circRNA-SCAF8 tended to decrease after overexpression of miR-93-5p, but with no statistical significance (P>0.05). Dual luciferase assay showed that miR-93-5p downre-gulated circRNA-SCAF8 expression by binding to the 3 ´ UTR region of circRNA-SCAF8, and miR-93-5p downregulated TXNIP expression by binding to the 3 ´ UTR region of TXNIP. FISH showed that circRNA-SCAF8 and miR-93-5p were both located in the cytoplasm and were highly associated in the cells. qRT-PCR showed that the relative expression of TXNIP increased or decreased after overexpression or inhibition of miR-93-5p compared with the RNA control group, respectively (both P<0.05), suggesting that miR-93-5p could regulate TXNIP gene expression.

CONCLUSIONS

CircRNA-SCAF8/miR-93-5p/TXNIP axis is involved in the regulation of pyroptosis in HUVECs under high glucose.

CircUSP48 promotes malignant behavior by regulating CYR61 via miR-365 in osteosarcoma

Even though circular RNAs (circRNAs), a class of non-coding endogenous RNA, play a crucial role in the progression of osteosarcoma (OS), the specific function of hsa_circ_0000028 (circUSP48) remains unclear. This study aims to elucidate the mechanism by which circUSP48 regulates OS. We employed qRT-PCR and western blot techniques to quantify circDOCK1, miR-186, and DNMT3A levels. Cell proliferation was assessed using the cell counting kit-8 (CCK-8), 5-Ethynyl-20-deoxyuridine (EdU) assay, and colony formation assay. Cell migration and invasion were evaluated through Transwell and cell scratch assays. Furthermore, we performed dual-luciferase reporter, RIP, and RNA pull-down assays to investigate the association between circUSP48, miR-365, and CYR61. In addition, an in vivo xenograft model was utilized to assess the functional role of circUSP48. High levels of circUSP48 and CYR61 were observed in OS tissues and cells, while miR-365 levels were low. Knockdown of circUSP48 suppressed the multiplication, motility, and invasion of OS cells, thereby reducing carcinoma growth. Moreover, inhibition of miR-365 reversed the OS cell-suppressive effect caused by circUSP48 knockdown through direct interaction with circUSP48. Additionally, circUSP48 upregulated the expression of CYR61 by sponging miR-365. The findings suggest that circUSP48 promotes malignant behavior in OS by regulating the expression of CYR61 through miR-365, making it a potential therapeutic target for OS.

Characterization of cell-type specific circular RNAs associated with colorectal cancer metastasis

Colorectal cancer (CRC) is the most common gastrointestinal malignancy and a leading cause of cancer deaths in the United States. More than half of CRC patients develop metastatic disease (mCRC) with an average 5-year survival rate of 13%. Circular RNAs (circRNAs) have recently emerged as important tumorigenesis regulators; however, their role in mCRC progression remains poorly characterized. Further, little is known about their cell-type specificity to elucidate their functions in the tumor microenvironment (TME). To address this, we performed total RNA sequencing (RNA-seq) on 30 matched normal, primary and metastatic samples from 14 mCRC patients. Additionally, five CRC cell lines were sequenced to construct a circRNA catalog in CRC. We detected 47 869 circRNAs, with 51% previously unannotated in CRC and 14% novel candidates when compared to existing circRNA databases. We identified 362 circRNAs differentially expressed in primary and/or metastatic tissues, termed circular RNAs associated with metastasis (CRAMS). We performed cell-type deconvolution using published single-cell RNA-seq datasets and applied a non-negative least squares statistical model to estimate cell-type specific circRNA expression. This predicted 667 circRNAs as exclusively expressed in a single cell type. Collectively, this serves as a valuable resource, TMECircDB (accessible at https://www.maherlab.com/tmecircdb-overview), for functional characterization of circRNAs in mCRC, specifically in the TME.

Circular RNAs: Promising Targets in Osteoporosis

PURPOSE OF REVIEW

Circular RNAs (circRNAs) are RNA transcripts derived from fragments of pre-messenger RNAs through a back-splicing process. An advantage that rises from their circular covalently closed conformation is their high stability, when compared with their linear counterparts. The current review focuses on the emerging roles of circRNAs in osteoporosis, including in osteogenic differentiation and osteoclastogenesis. Their potential as osteoporosis biomarkers will also be discussed.

RECENT FINDINGS

Although firstly described as non-coding, some of these single-stranded RNAs were recently reported to possess protein-coding capacity. On the other hand, the circRNAs exhibit cell and tissue-specific patterns at the transcriptome level in eukaryotes and are regulated throughout the development or disease progression. Even though thousands of these circular transcripts are listed and annotated, only a limited number of studies describe their biological role in bone processes. Recent evidence indicates inhibitory activator roles in both osteoblasts and osteoclasts differentiation and function. Latest screenings in the blood, plasma, or serum of osteoporosis patients support the potential for circRNA signature to be used as biomarkers in osteoporosis, but further validation is required. While intense research into circRNAs has been detailing their biological roles, there remains a need for standardization and further research to fulfil the future potential of this emerging and highly promising class of regulatory molecules.

Crosstalk between circRNAs and the PI3K/AKT and/or MEK/ERK signaling pathways in digestive tract malignancy progression

Evidence indicates that circular RNAs (circRNAs) may play an important role in regulating gene expression by binding to miRNAs through miRNA response elements. circRNAs are formed by back-splicing and have a covalently closed structure. The biogenesis of circRNAs also appears to be regulated by certain cell-specific and/or gene-specific mechanisms, and thus some circRNAs are tissue specific and tumor-expression specific. Furthermore, the high stability and tissue specificity of circRNAs may be of value for early diagnosis, survival prediction and precision medicine. This review summarizes current knowledge regarding the classification and functions of circRNAs and the role of circRNAs in regulating the PI3K/AKT and/or MEK/ERK signaling pathways in digestive tract malignancy tumors.

Exon-intron split analysis reveals posttranscriptional regulatory signals induced by high and low n-6/n-3 polyunsaturated fatty acid ratio diets in piglets

Polyunsaturated fatty acids (PUFA), such as omega-6 (n-6) and omega-3 (n-3), play a vital role in nutrient metabolism, inflammatory response, and gene regulation. microRNAs (miRNA), which can potentially degrade targeted messenger RNAs (mRNA) and/or inhibit their translation, might play a relevant role in PUFA-related changes in gene expression. Although differential expression analyses can provide a comprehensive picture of gene expression variation, they are unable to disentangle when in the mRNA life cycle the regulation of expression is taking place, including any putative functional miRNA-driven repression. To capture this, we used an exon-intron split analysis (EISA) approach to account for posttranscriptional changes in response to extreme values of n-6/n-3 PUFA ratio. Longissimus dorsi muscle samples of male and female piglets from sows fed with n-6/n-3 PUFA ratio of 13:1 (SOY) or 4:1 (LIN), were analyzed in a bidirectional contrast (LIN vs. SOY, SOY vs. LIN). Our results allowed the identification of genes showing strong posttranscriptional downregulation signals putatively targeted by significantly upregulated miRNA. Moreover, we identified genes primarily involved in the regulation of lipid-related metabolism and immune response, which may be associated with the pro- and anti-inflammatory functions of the n-6 and n-3 PUFA, respectively. EISA allowed us to uncover regulatory networks complementing canonical differential expression analyses, thus providing a more comprehensive view of muscle metabolic changes in response to PUFA concentration.

Role of lncRNAs and circRNAs in epilepsy

Epilepsy is a chronic disorder of with a high prevalence and extensive health burden in almost all age groups of the population. This condition is resulted from disturbance in the balance between excitatory and inhibitory factors in the brain. Genetic elements that affect synaptic connectivity, receptors functions or ion channels have been shown to predispose individuals to the epilepsy. More recently, a body of evidence points to the role of non-coding part of the transcriptome in the pathology of epilepsy. Expression levels of NEAT1, H19, PVT1, ILF3-AS1, GAS5, ZFAS1, UCA1, MALAT1 and SNHG1 have been changed in epileptic patients or animal models of epilepsy. Moreover, circ_ANKMY2, circRNA-0067835 and circHivep2 are among circRNAs which are involved in the pathogenesis of epilepsy. Although the mechanistical impact of these transcripts in the pathogenesis of epilepsy has not been fully explored, disturbances in neuron plasticity, apoptosis or differentiation might be implicated in this process. Expression levels of lncRNAs can be used for discrimination of epileptic patients from normal controls or refractory patients from non-refractory ones. JAK/STAT, Wnt, PI3K/AKT and NF-κB signaling pathways are among the regulated pathways by lncRNAs in the context of epilepsy. In the present review, we summarize the role of lncRNAs and circRNAs in the pathogenesis of epilepsy.

CircRNAs Related to Breast Muscle Development and Their Interaction Regulatory Network in Gushi Chicken

Circular RNAs (circRNAs) play a significant regulatory role during skeletal muscle development. To identify circRNAs during postnatal skeletal muscle development in chickens, we constructed 12 cDNA libraries from breast muscle tissues of Chinese Gushi chickens at 6, 14, 22, and 30 weeks and performed RNA sequencing. In total, 2112 circRNAs were identified, and among them 79.92% were derived from exons. CircRNAs are distributed on all chromosomes of chickens, especially chromosomes 1-9 and Z. Bioinformatics analysis showed that each circRNA had an average of 38 miRNA binding sites, 61.32% of which have internal ribosomal entry site (IRES) elements. Furthermore, in total 543 differentially expressed circRNAs (DE-circRNAs) were identified. Functional enrichment analysis revealed that DE-circRNAs source genes are engaged in biological processes and muscle development-related pathways; for example, cell differentiation, sarcomere, and myofibril formation, mTOR signaling pathway, and TGF-β signaling pathway, etc. We also established a competitive endogenous RNA (ceRNA) regulatory network associated with skeletal muscle development. The results in this report indicate that circRNAs can mediate the development of chicken skeletal muscle by means of a complex ceRNA network among circRNAs, miRNAs, genes, and pathways. The findings of this study might help increase the number of known circRNAs in skeletal muscle tissue and offer a worthwhile resource to further investigate the function of circRNAs in chicken skeletal muscle development.

Circular RNA in multiple myeloma: A new target for therapeutic intervention

Circular RNAs (circRNAs) are RNA molecules with a stable closed-loop structure that are found in a variety of organisms. CircRNAs are highly stable and conserved, and they play important roles in transcriptional regulation and splicing. Multiple Myeloma (MM) is a malignant proliferative disease for which there are currently no effective and comprehensive treatments. Numerous circRNAs may contribute to the development and progression of MM by acting as oncogenes or regulators. Due to the unique function of circRNAs, they have a high potential for regulating the biological functions (including proliferation and apoptosis) of MM cells, and their expression levels and molecular mechanism are closely related to their diagnostic value, therapeutic sensitivity, and clinical prognosis of MM patients. In this review, we aim to provide a detailed overview of the structure and function of circRNAs and demonstrate the potential therapeutic value and potential mechanism of circRNAs in MM via experiments and clinical trials.

Mechanism underlying circRNA dysregulation in the TME of digestive system cancer

Circular RNAs (circRNAs) are a new series of noncoding RNAs (ncRNAs) that have been reported to be expressed in eukaryotic cells and have a variety of biological functions in the regulation of cancer pathogenesis and progression. The TME, as a microscopic ecological environment, consists of a variety of cells, including tumor cells, immune cells and other normal cells, ECM and a large number of signaling molecules. The crosstalk between circRNAs and the TME plays a complicated role in affecting the malignant behaviors of digestive system cancers. Herein, we summarize the mechanisms underlying aberrant circRNA expression in the TME of the digestive system cancers, including immune surveillance, angiogenesis, EMT, and ECM remodelling. The regulation of the TME by circRNA is expected to be a new therapeutic method.

Promising Roles of Circular RNAs as Biomarkers and Targets for Potential Diagnosis and Therapy of Tuberculosis

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) infection, remains one of the most threatening infectious diseases worldwide. A series of challenges still exist for TB prevention, diagnosis and treatment, which therefore require more attempts to clarify the pathological and immunological mechanisms in the development and progression of TB. Circular RNAs (circRNAs) are a large class of non-coding RNA, mostly expressed in eukaryotic cells, which are generated by the spliceosome through the back-splicing of linear RNAs. Accumulating studies have identified that circRNAs are widely involved in a variety of physiological and pathological processes, acting as the sponges or decoys for microRNAs and proteins, scaffold platforms for proteins, modulators for transcription and special templates for translation. Due to the stable and widely spread characteristics of circRNAs, they are expected to serve as promising prognostic/diagnostic biomarkers and therapeutic targets for diseases. In this review, we briefly describe the biogenesis, classification, detection technology and functions of circRNAs, and, in particular, outline the dynamic, and sometimes aberrant changes of circRNAs in TB. Moreover, we further summarize the recent progress of research linking circRNAs to TB-related pathogenetic processes, as well as the potential roles of circRNAs as diagnostic biomarkers and miRNAs sponges in the case of Mtb infection, which is expected to enhance our understanding of TB and provide some novel ideas about how to overcome the challenges associated TB in the future.

Internal Introns Promote Backsplicing to Generate Circular RNAs from Spinal Muscular Atrophy Gene

Human survival motor neuron 1 (SMN1) codes for SMN, an essential housekeeping protein involved in most aspects of RNA metabolism. Deletions or mutations of SMN1 lead to spinal muscular atrophy (SMA), a devastating neurodegenerative disease linked to a high rate of infant mortality. SMN2, a near identical copy of SMN1 present in humans, cannot compensate for the loss of SMN1 due to predominant skipping of SMN2 exon 7. Restoration of SMN by splicing modulation of SMN2 exon 7 or gene replacement are currently approved therapies of SMA. Human SMN genes produce a vast repertoire of circular RNAs (circRNAs). However, the mechanism of SMN circRNA generation has not yet been examined in detail. For example, it remains unknown if forward splicing impacts backsplicing that generates circRNAs containing multiple exons. Here, we employed SMN as a model system to examine the impact of intronic sequences on the generation of circRNAs. We performed our experiments in HeLa cells transiently transfected with minigenes expressing three abundantly represented circRNAs containing two or more SMN exons. We observed an enhanced rate of circRNA generation when introns joining exons to be incorporated into circRNAs were present as compared to the intronless context. These results underscore the stimulatory effect of forward splicing in the generation of circRNAs containing multiple exons. These findings are consistent with the reported low abundance of SMN circRNAs comprised of single exons. We confirmed our findings using inducible HEK 293 cells stably expressing the SMN circRNAs. Our results support the role of the exon junction complex in the generation of the exon-only-containing circRNAs. We showed that SMN circRNAs were preferentially localized in the cytoplasm. These findings provide new insights regarding our understanding of circRNA generation and open avenues to uncover novel functions of the SMN genes.

Relation between the circular and linear form of the Elongator Acetyltransferase Complex Subunit 3 in the progression of triple-negative breast cancer

Triple-negative breast cancer (TNBC) is the most aggressive type of breast cancer (BC) that hardly responds to common treatment. Recent studies show that circ-ELP3 (Elongator Acetyltransferase Complex Subunit 3 or hsa-circ-0001785) is involved in the pathogenesis of several malignancies. The present study aimed to evaluate the possible role of this circRNA in the progression of TNBC cells and the possible relation between the circular and linear forms of the ELP3. We evaluated the circ-ELP3 and its host gene expression level in clinical samples and breast cancer cell lines. Using an expression vector, hsa-circ-0001785 was upregulated to investigate its role on cancer cell progression. After a transient transfection, we evaluated possible alterations in the cell cycle progression, cell viability, and cell proliferation. Quantitative real-time polymerase chain reaction analyses verified that circ-ELP3 and its host gene were significantly upregulated in TNBC tissues and breast cancer cells. Overexpression of circ-ELP3 markedly increases the cell viability and proliferation and also the formation of colonies in transfected cells compared to the controls. Briefly, our results showed that Circ-ELP3 and its host gene were significantly upregulated in TNBC. Circ-ELP3 is involved in TNBC progression and may exert its effects by indirectly regulating of ELP3 expression.

Regulation of Non-Coding RNA in the Growth and Development of Skeletal Muscle in Domestic Chickens

Chicken is the most widely consumed meat product worldwide and is a high-quality source of protein for humans. The skeletal muscle, which accounts for the majority of chicken products and contains the most valuable components, is tightly correlated to meat product yield and quality. In domestic chickens, skeletal muscle growth is regulated by a complex network of molecules that includes some non-coding RNAs (ncRNAs). As a regulator of muscle growth and development, ncRNAs play a significant function in the development of skeletal muscle in domestic chickens. Recent advances in sequencing technology have contributed to the identification and characterization of more ncRNAs (mainly microRNAs (miRNAs), long non-coding RNAs (LncRNAs), and circular RNAs (CircRNAs)) involved in the development of domestic chicken skeletal muscle, where they are widely involved in proliferation, differentiation, fusion, and apoptosis of myoblasts and satellite cells, and the specification of muscle fiber type. In this review, we summarize the ncRNAs involved in the skeletal muscle growth and development of domestic chickens and discuss the potential limitations and challenges. It will provide a theoretical foundation for future comprehensive studies on ncRNA participation in the regulation of skeletal muscle growth and development in domestic chickens.

Past, Present and Future: The Relationship Between Circular RNA and Immunity

The immune system has evolved since the birth of humans. However, immune-related diseases have not yet been overcome due to the lack of expected indicators and targeting specificity of current medical technology, subjecting patients to very uncomfortable physical and mental experiences and high medical costs. Therefore, the requirements for treatments with higher specificity and indicative ability are raised. Fortunately, the discovery of and continuous research investigating circular RNAs (circRNAs) represent a promising method among numerous methods. Although circRNAs wear regarded as metabolic wastes when discovered, as a type of noncoding RNA (ncRNA) with a ring structure and wide distribution range in the human body, circRNAs shine brilliantly in medical research by virtue of their special nature and structure-determined functions, such as high stability, wide distribution, high detection sensitivity, acceptable reproducibility and individual differences. Based on research investigating the role of circRNAs in immunity, we systematically discuss the hotspots of the roles of circRNAs in immune-related diseases, including expression profile analyses, potential biomarker research, ncRNA axis/network construction, impacts on phenotypes, therapeutic target seeking, maintenance of nucleic acid stability and protein binding research. In addition, we summarize the current situation of and problems associated with circRNAs in immune research, highlight the applications and prospects of circRNAs in the treatment of immune-related diseases, and provide new insight into future directions and new strategies for laboratory research and clinical applications.

Circular RNAs and Their Role in Exosomes

As a novel class of endogenous non-coding RNAs discovered in recent years, circular RNAs (circRNAs) are highly conserved and stable covalently closed ring structures with no 5'-end cap or 3'-end poly(A) tail. CircRNAs are formed by reverse splicing, mainly by means of a noose structure or intron complementary pairing. Exosomes are tiny discoid vesicles with a diameter of 40-100 nm that are secreted by cells under physiological and pathological conditions. Exosomes play an important role in cell-cell communication by carrying DNA, microRNAs, mRNAs, proteins and circRNAs. In this review, we summarize the biological functions of circRNAs and exosomes, and further reveal the potential roles of exosomal circRNAs in different diseases, providing a scientific basis for the diagnosis, treatment, and prognosis of a wide variety of diseases.

Circular RNAs as novel biomarkers in triple-negative breast cancer: a systematic review

More effective prognostic and diagnostic tools are urgently required for early detecting and treating triple-negative breast cancer, which is the most acute type of breast cancer because of its lower survival rate, aggressiveness, and non-response to various common treatments. So, it remains the most harmful malignancy for women worldwide. Recently, circular RNAs, as a group of non-coding RNAs, with covalently closed loop and high stability have been discovered, which can modulate gene expression through competing with endogenous microRNA sponges. This finding provided further insight into novel approaches for controlling genes affected in many disorders and malignancies. This review concentrates on the dysregulated expression of circRNAs like their diagnostic and prognostic values in TNBC. This review aims to focus on the abnormal expression of circRNAs and their diagnostic and prognostic values in TNBC. We used PubMed, Embase, and Web of Science databases and ClinicalTrials.gov to systematically search for all relevant clinical studies. This review is based on articles published in databases up to April 2022 with the following keywords: "Circular RNA", "CircRNA", "Triple-Negative Breast Cancer" and "TNBC". We conducted a review of published CircRNA profiled-research articles to identify candidate CircRNA biomarkers for TNBC. The review is registered on JBI at https://jbi.global/systematic-review-register . Accumulating evidence has shown that several circRNAs are downregulated and some are upregulated in TNBC. The results of these studies confirm that circRNAs might be potential biomarkers with the diagnostic, prognostic, and therapeutic target value for TNBC. We also consider the connection between circRNAs and TNBC cell proliferation, apoptosis, metastasis, and chemotherapy resistance and sensitivity.

Arabidopsis apoplastic fluid contains sRNA- and circular RNA-protein complexes that are located outside extracellular vesicles

Previously, we have shown that apoplastic wash fluid (AWF) purified from Arabidopsis leaves contains small RNAs (sRNAs). To investigate whether these sRNAs are encapsulated inside extracellular vesicles (EVs), we treated EVs isolated from Arabidopsis leaves with the protease trypsin and RNase A, which should degrade RNAs located outside EVs but not those located inside. These analyses revealed that apoplastic RNAs are mostly located outside and are associated with proteins. Further analyses of these extracellular RNAs (exRNAs) revealed that they include both sRNAs and long noncoding RNAs (lncRNAs), including circular RNAs (circRNAs). We also found that exRNAs are highly enriched in the posttranscriptional modification N6-methyladenine (m6A). Consistent with this, we identified a putative m6A-binding protein in AWF, GLYCINE-RICH RNA-BINDING PROTEIN 7 (GRP7), as well as the sRNA-binding protein ARGONAUTE2 (AGO2). These two proteins coimmunoprecipitated with lncRNAs, including circRNAs. Mutation of GRP7 or AGO2 caused changes in both the sRNA and lncRNA content of AWF, suggesting that these proteins contribute to the secretion and/or stabilization of exRNAs. We propose that exRNAs located outside of EVs mediate host-induced gene silencing, rather than RNA located inside EVs.

High Expression of RRM1 Mediated by ncRNAs Correlates with Poor Prognosis and Tumor Immune Infiltration of Hepatocellular Carcinoma

Introduction

Hepatocellular carcinoma (HCC) is one of several tumors with poor prognosis and causes a significant social burden. A growing number of studies have shown that RRM1 plays a crucial role in the development and progression of multiple human cancers. However, the specific role and mechanism of RRM1 have not been fully defined in HCC.

Methods

TCGA and GTEx data were used for the first time to conduct a pan-cancer analysis of RRM1 expression and prognosis, and identified RRM1 as a possible potential oncogene in HCC. At the same time, a combination of analyses (including expression analysis, correlation analysis or survival analysis) identified non-coding RNAs (ncRNAs) that contribute to RRM1 overexpression.

Results

MIR4435-2HG/miR-22-3p and SNHG6/miR-101-3p were identified as the most promising RRM1 upstream ncRNA-related pathways in HCC. In addition, RRM1 levels were significantly and positively correlated with tumor immune cell infiltration, immune cell biomarker or immune checkpoint expression.

Conclusion

These results suggest that high expression of RRM1 mediated by ncRNAs is associated with poor prognosis and tumor immune infiltration in HCC.

Circ-PKD2 promotes Atg13-mediated autophagy by inhibiting miR-646 to increase the sensitivity of cisplatin in oral squamous cell carcinomas

Autophagy is an evolutionally conserved catabolic process that degrades cells to maintain homeostasis. Cisplatin-activated autophagy promotes the expression of circ-PKD2, which plays a role as a tumor suppressor gene in the proliferation, migration, and invasion in oral squamous cell carcinoma (OSCC). However, the role of circ-PKD2 in regulating the sensitivity of OSCC patients to cisplatin remains to be elucidated. Overexpression of circ-PKD2 increased the formation of autophagosomes in OSCC cells and activation of proteins, such as LC3 II/I. Its activation effect on autophagy was, however, alleviated by 3-MA. Bioinformatics analyses and double luciferases reporter assays conducted in this study confirmed the existence of targeted relationships between circ-PKD2 and miR-646 and miR-646 and Atg13. Functional experiments further revealed that miR-646 reversed the autophagy and apoptosis effects of circ-PKD2 in OSCC cells treated with cisplatin. In addition, circ-PKD2 promoted the expression of ATG13 by adsorption of miR-646. Its interference with Atg13 alleviated the activation effects of circ-PKD2 on autophagy and apoptosis of miR-646. Notably, the in vivo animal experiments also confirmed that circ-PKD2 inhibited tumor proliferation and activated autophagy in OSCC cells. This study provides a theoretical basis for using circ-PKD2 as a target to regulate the sensitivity of OSCC patients to cisplatin, thus increasing its chemotherapeutic effects.

Emerging Roles of Circular RNAs in Vascular Smooth Muscle Cell Dysfunction

Atherosclerosis is the major pathophysiological basis of cerebrovascular and cardiovascular diseases. Vascular smooth muscle cells (VSMCs) constitute the main structure of vasculature and play important roles in maintaining vascular tone and blood pressure. Many biological processes and cellular signaling events involved in atherosclerogenesis have been shown to converge on deregulating VSMC functions. However, the molecular mechanisms underlying dysfunctional VSMC in atherosclerosis are still poorly defined. Recent evidence revealed that circular RNAs (circRNAs) are closely related to diseases such as degenerative diseases, tumor, congenital diseases, endocrine diseases and cardiovascular diseases. Several studies demonstrated that circRNAs (e.g., circACTA2, Circ-SATB2, circDiaph3, circ_0020397, circTET3, circCCDC66) played critical roles in the regulation of VSMC proliferation, migration, invasion, and contractile-to-synthetic phenotype transformation by sponging microRNAs (e.g., miR-548f-5p, miR-939, miR-148a-5p, miR-138, miR-351-5p, miR-342-3p). This review describes recent progress in the profiling of circRNAs by transcriptome analysis in VSMCs and their molecular functions in regulating VSMC proliferation and migration.

Circular RNA Expression and Regulation Profiling in Testicular Tissues of Immature and Mature Wandong Cattle (Bos taurus)

Wandong cattle are an autochthonous Chinese breed used extensively for beef production. The breed tolerates extreme weather conditions and raw feed and is resistant to tick-borne diseases. However, the genetic basis of testis development and sperm production as well as breeding management is not well established in local cattle. Therefore, improving the reproductive efficiency of bulls via genetic selection is crucial as a single bull can breed thousands of cows through artificial insemination (AI). Testis development and spermatogenesis are regulated by hundreds of genes and transcriptomes. However, circular RNAs (circRNAs) are the key players in many biological developmental processes that have not been methodically described and compared between immature and mature stages in Bovine testes. In this study, we performed total RNA-seq and comprehensively analyzed the circRNA expression profiling of the testis samples of six bulls at 3 years and 3 months of developmental age. In total, 17,013 circRNAs were identified, of which 681 circRNAs (p-adjust < 0.05) were differentially expressed (DE). Among these DE circRNAs, 579 were upregulated and 103 were downregulated in calf and bull testes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that the identified target genes were classified into three broad functional categories, including biological process, cellular component, and molecular function, and were enriched in the lysine degradation, cell cycle, and cell adhesion molecule pathways. The binding interactions between DE circRNAs and microRNAs (miRNAs) were subsequently constructed using bioinformatics approaches. The source genes ATM, CCNA1, GSK3B, KMT2C, KMT2E, NSD2, SUCLG2, QKI, HOMER1, and SNAP91 were found to be actively associated with bull sexual maturity and spermatogenesis. In addition, a real-time quantitative polymerase chain reaction (RT-qPCR) analysis showed a strong correlation with the sequencing data. Moreover, the developed model of Bovine testes in the current study provides a suitable framework for understanding the mechanism of circRNAs in the development of testes and spermatogenesis.

CircRNA-001241 Mediates Sorafenib Resistance of Hepatocellular Carcinoma Cells by Sponging miR-21-5p and Regulating TIMP3 Expression

Hepatocellular carcinoma (HCC) is one of the major malignancies worldwide and its incidence is on the rise, closely related to advanced liver disease¹. Sorafenib chemotherapy is one of the main treatment options for patients with advanced HCC. Despite several reports on HCC multidrug resistance, the underlying regulatory mechanisms are still unclear. In this study, we found circ-001241 was significantly upregulated in HCC tissues and cells. Knockdown of circ-001241 markedly inhibited HCC cell proliferation and decreased sorafenib-resistance. More importantly, circRNA acts as a ceRNA to suppress the expression and activity of miR-21-5p, leading to the increase in TIMP3 expression. In addition, circRNA-001241 facilitated HCC sorafenib-resistance by regulating the miR-21-5p/TIMP3 axis.Taken together, our study elucidated the oncogenic role of circ-001241 in mediating sorafenib resistance in HCC, providing insights and opportunities to overcome sorafenib resistance in patients with advanced hepatocellular carcinoma.

Identification of Potential circRNA-microRNA-mRNA Regulatory Network in Skeletal Muscle

Circular RNAs (circRNAs) are a newly discovered family of regulatory RNAs generated through backsplicing. Genome-wide profiling of circRNAs found that circRNAs are ubiquitously expressed and regulate gene expression by acting as a sponge for RNA-binding proteins (RBPs) and microRNAs (miRNAs). To identify circRNAs expressed in mouse skeletal muscle, we performed high-throughput RNA-sequencing of circRNA-enriched gastrocnemius muscle RNA samples, which identified more than 1,200 circRNAs. In addition, we have identified more than 14,000 and 15,000 circRNAs in aging human skeletal muscle tissue and satellite cells, respectively. A subset of abundant circRNAs was analyzed by RT-PCR, Sanger sequencing, and RNase R digestion assays to validate their expression in mouse skeletal muscle tissues. Analysis of the circRNA-miRNA-mRNA regulatory network revealed that conserved circNfix might associate with miR-204-5p, a suppressor of myocyte enhancer factor 2c (Mef2c) expression. To support the hypothesis that circNfix might regulate myogenesis by controlling Mef2c expression, silencing circNfix moderately reduced Mef2c mRNA expression and inhibited C2C12 differentiation. We propose that circNfix promotes MEF2C expression during muscle cell differentiation in part by acting as a sponge for miR-204-5p.

Circular RNA Mitochondrial Translation Optimization 1 homologue (CircMTO1) induced by Zinc Finger Protein 460 (ZNF460) promotes oral squamous cell carcinoma progression through the microRNA miR-320a / Alpha Thalassemia/Mental Retardation, X-linked (ATRX) axis

Oral squamous cell carcinoma (OSCC) is one of the most common cancer types of head and neck cancer, accounting for 95% of all cases. However, the mechanisms underlying the pathogenesis of OSCC remain unclear. Circular RNA (CircRNA) has been extensively studied in the past decades and is a promising direction for the development of OSCC therapeutic targets. In this study, we aimed to investigate the role of circMTO1 in OSCC progression. First, we validated the characterization and expression of circMTO1 in OSCC. It was found that circMTO1 was upregulated in OSCC tumor tissues and cells. Subsequently, we conducted biological experiments. It was found that circMTO1 knockdown inhibited OSCC cell proliferation, migration, and invasion. Furthermore, we conducted a series of experiments to elucidate the underlying mechanisms. A novel circMTO1/miR-320a/ATRX axis was identified. Our results suggest that circMTO1 modulates ATRX expression to accelerate OSCC progression by sponging miR-320a. Moreover, we found that circMTO1 expression in OSCC was transcriptionally regulated by Zinc Finger Protein 460 (ZNF460). Our study showed a novel ZNF460/circMTO1/miR-320a/ATRX signaling in OSCC development.

CircRNAs: Insights into Gastric Cancer

Background

Gastric cancer (GC) is recorded as the fifth most common cancer globally. The classic resemblance of early symptoms of chronic gastritis including nausea, dysphagia, and dyspepsia with GC is the current challenge limiting the early diagnosis of GC. The current diagnostic procedures of GC are limited due to their invasive nature. This directs the research question toward alternative approaches, specifically at the molecular level. Recent advances in molecular regulation of cancer suggest the prominence of circular RNAs (circRNAs) in the multistep process of tumourigenesis.

Summary

CircRNAs are a class of non-coding RNAs, abundant in eukaryotes, with key roles in regulating genes and miRNAs as well as the alteration of processes involved in pathological conditions. Research studies have demonstrated the participation of circRNAs in the initiation and progression of tumours. This review provides a comprehensive insight into the potential of circRNAs as disease biomarkers for the early detection and treatment of GC.

Key Messages

This study is an amalgamation of the implications and future prospects of circRNAs for the detection and potential treatment of GC.

The Dual Role of Circular RNAs as miRNA Sponges in Breast Cancer and Colon Cancer

Breast cancer (BC) and colon cancer (CRC) are the two most deadly cancers in the world. These cancers partly share the same genetic background and are partially regulated by the same genes. The outcomes of traditional chemoradiotherapy and surgery remain suboptimal, with high postoperative recurrence and a low survival rate. It is, therefore, urgent to innovate and improve the existing treatment measures. Many studies primarily reported that the microRNA (miRNA) sponge functions of circular RNA (circRNA) in BC and CRC have an indirect relationship between the circRNA–miRNA axis and malignant behaviors. With a covalent ring structure, circRNAs can regulate the expression of target genes in multiple ways, especially by acting as miRNA sponges. Therefore, this review mainly focuses on the roles of circRNAs as miRNA sponges in BC and CRC based on studies over the last three years, thus providing a theoretical reference for finding new therapeutic targets in the future.

Identification of circular RNAs hsa_circ_0140271 in peripheral blood mononuclear cells as a novel diagnostic biomarker for female rheumatoid arthritis

Background

Rheumatoid arthritis (RA) is a chronic autoimmune disease, which commonly affects women. Accumulating evidence shows that differentially expressed circular RNAs (circRNAs) play crucial roles in the progress of RA. However, the roles of circRNAs in female RA remains unclear. This study explores potential role and diagnostic value of hsa_circ_0140271 from peripheral blood mononuclear cells (PBMC) in female RA.

Methods

Differential expression of circRNAs was determined by RNA-sequencing in PBMC from 4 healthy controls (HC) and 4 RA patients, and we further measured the level of hsa_circ_0140271 in a validation cohort consisting of 47 RA and 47 HC via RT-qPCR. Besides, correlation studies with clinical variables were also examined. What’s more, we performed bioinformatics analysis to predict the potential role of hsa_circ_0140271.

Results

PBMC expression of hsa_circ_0140271 of female RA was significantly higher than that of female HC, and it was positively correlated with antistreptolysin (ASO). Furthermore, the receiver operating characteristic (ROC) curve indicated that hsa_circ_0140271 could distinguish female RA from female HC and female patients with ankylosing spondylitis (AS) or osteoarthritis (OA). Besides, the combined diagnosis anti-cyclic citrullinated peptide (Anti-CCP) + hsa_circ_0140271 could improve diagnostic accuracy with an area under the curve (AUC) of 0.818 to compared with Anti-CCP. Furthermore, KEGG pathway enrichment analysis indicated hsa_circ_0140271 may act as microRNA sponge and participate in fatty acid metabolism pathways.

Conclusion

Hsa_circ_0140271 was likely to be used as a promising diagnostic biomarker for female RA; it may act as microRNA sponge to regulate fatty acid metabolism pathways in RA.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13018-021-02794-8.

Data Mining Identifies Differentially Expressed Circular RNAs in Skeletal Muscle of Thermally Challenged Turkey Poults

Precise regulation of gene expression is critical for normal muscle growth and development. Changes in gene expression patterns caused by external stressors such as temperature can have dramatic effects including altered cellular structure and function. Understanding the cellular mechanisms that underlie muscle growth and development and how these are altered by external stressors are crucial in maintaining and improving meat quality. This study investigated circular RNAs (circRNAs) as an emerging aspect of gene regulation. We used data mining to identify circRNAs and characterize their expression profiles within RNAseq data collected from thermally challenged turkey poults of the RBC2 and F-lines. From sequences of 28 paired-end libraries, 8924 unique circRNAs were predicted of which 1629 were common to all treatment groups. Expression analysis identified significant differentially expressed circRNAs (DECs) in comparisons between thermal treatments (41 DECs) and between genetic lines (117 DECs). No intersection was observed between the DECs and differentially expressed gene transcripts indicating that the DECs are not simply the result of expression changes in the parental genes. Comparative analyses based on the chicken microRNA (miRNA) database suggest potential interactions between turkey circRNAs and miRNAs. Additional studies are needed to reveal the functional significance of the predicted circRNAs and their role in muscle development in response to thermal challenge. The DECs identified in this study provide an important framework for future investigation.

Role of circRNAs in neurodevelopment and neurodegenerative diseases

With the rapid development of sequencing technology, scientists have been able to study and acquire a better understanding of non-coding RNAs (ncRNAs). Circular RNAs (circRNAs), a unique class of ncRNAs with a special loop structure, have been found to possess modulatory properties with respect to various biological processes, such as interacting with nucleic acids or proteins. In addition to their tissue-specific expression and high conservation across species, circRNAs are abundant and dynamically expressed in the nervous system, especially in nerve synapse, indicating their potential regulation in synaptic plasticity or neuronal disorders. In this review, we discuss the characteristics of circRNAs and their common biological functions, as well as their significant role in neurodevelopment, drug addiction and neurodegenerative diseases, aiming to guide further disease diagnoses and efficient therapy.

Expression Profiling and Bioinformatics Analysis of CircRNA in Mice Brain Infected with Rabies Virus

Rabies virus (RABV) induces acute, fatal encephalitis in mammals including humans. The circRNAs are important in virus infection process, but whether circRNAs regulated RABV infection remains largely unknown. Here, mice brain with or without the RABV CVS-11 strain were subjected to RNA sequencing and a total of 30,985 circRNAs were obtained. Among these, 9021 candidates were shared in both groups, and 14,610 and 7354 circRNAs were expressed specifically to the control and experimental groups, indicating that certain circRNAs were specifically inhibited or induced on RABV infection. The circRNAs mainly derived from coding exons. In total, 636 circRNAs were differentially expressed in RABV infection, of which 426 significantly upregulated and 210 significantly downregulated (p < 0.05 and fold change ≥2). The expression of randomly selected 6 upregulated and 6 downregulated circRNAs was tested by RT-qPCR, and the expression trend of the 11 out of 12 circRNAs was consistent in RT- qPCR and RNA-seq analysis. Rnase R-resistant assay and Sanger sequencing were conducted to verify the circularity of circRNAs. GO analysis demonstrated that source genes of all differentially regulated circRNAs were mainly related to cell plasticity and synapse function. Both KEGG and GSEA analysis revealed that these source genes were engaged in the cGMP–PKG and MAPK signaling pathway, and HTLV-I infection. Also, pathways related to glucose metabolism and synaptic functions were enriched in KEGG analysis. The circRNA–miRNA–mRNA network was built with 25 of 636 differentially expressed circRNAs, 264 mRNAs involved in RABV infection, and 29 miRNAs. Several miRNAs and many mRNAs in the network were reported to be related to viral infection and the immune response, suggesting that circRNAs could regulate RABV infection via interacting with miRNAs and mRNAs. Taken together, this study first characterized the transcriptomic pattern of circRNAs, and signaling pathways and function that circRNAs are involved in, which may indicate directions for further research to understand mechanisms of RABV pathogenesis.

Characteristics and expression profiles of circRNAs during abdominal adipose tissue development in Chinese Gushi chickens

Circular RNAs (circRNAs) play important roles in adipogenesis. However, studies on circRNA expression profiles associated with the development of abdominal adipose tissue are lacking in chickens. In this study, 12 cDNA libraries were constructed from the abdominal adipose tissue of Chinese domestic Gushi chickens at 6, 14, 22, and 30 weeks. A total of 1,766 circRNAs were identified by Illumina HiSeq 2500 sequencing. These circRNAs were primarily distributed on chr1 through chr10 and sex chromosomes, and 84.95% of the circRNAs were from gene exons. Bioinformatic analysis showed that each circRNA has 35 miRNA binding sites on average, and 62.71% have internal ribosome entry site (IRES) elements. Meanwhile, these circRNAs were primarily concentrated in TPM < 0.1 and TPM > 60, and their numbers accounted for 18.90% and 80.51%, respectively, exhibiting specific expression patterns in chicken abdominal adipose tissue. In addition, 275 differentially expressed (DE) circRNAs were identified by comparison analysis. Functional enrichment analysis showed that the parental genes of DE circRNAs were primarily involved in biological processes and pathways related to lipid metabolism, such as regulation of fat cell differentiation, fatty acid homeostasis, and triglyceride homeostasis, as well as fatty acid biosynthesis, fatty acid metabolism, and glycerolipid metabolism. Furthermore, ceRNA regulatory networks related to abdominal adipose development were constructed. The results of this study indicated that circRNAs can regulate lipid metabolism, adipocyte proliferation and differentiation, and cell junctions during abdominal adipose tissue development in chickens through complex ceRNA networks between circRNAs, miRNAs, genes, and pathways. The results of this study may help to expand the number of known circRNAs in abdominal adipose tissue and provide a valuable resource for further research on the function of circRNAs in chicken abdominal adipose tissue.

The Role of circRNAs in Human Papillomavirus (HPV)-Associated Cancers

Circular RNAs (circRNAs) are a new class of "non-coding RNAs" that originate from non-sequential back-splicing of exons and/or introns of precursor messenger RNAs (pre-mRNAs). These molecules are generally produced at low levels in a cell-type-specific manner in mammalian tissues, but due to their circular conformation they are unaffected by the cell mRNA decay machinery. circRNAs can sponge multiple microRNAs or RNA-binding proteins and play a crucial role in the regulation of gene expression and protein translation. Many circRNAs have been shown to be aberrantly expressed in several cancer types, and to sustain specific oncogenic processes. Particularly, in virus-associated malignancies such as human papillomavirus (HPV)-associated anogenital carcinoma and oropharyngeal and oral cancers, circRNAs have been shown to be involved in tumorigenesis and cancer progression, as well as in drug resistance, and some are useful diagnostic and prognostic markers. HPV-derived circRNAs, encompassing the HPV E7 oncogene, have been shown to be expressed and to serve as transcript for synthesis of the E7 oncoprotein, thus reinforcing the virus oncogenic activity in HPV-associated cancers. In this review, we summarize research advances in the biogenesis of cell and viral circRNAs, their features and functions in the pathophysiology of HPV-associated tumors, and their importance as diagnostic, prognostic, and therapeutic targets in anogenital and oropharyngeal and oral cancers.

The Biogenesis and Functions of circRNAs and Their Roles in Breast Cancer

Recent statistics show that breast cancer is among the most frequent cancers in clinical practice. It is also the second-leading cause of cancer-related deaths among women worldwide. CircRNAs are a new class of endogenous regulatory RNA molecules whose 5’ end and 3’ end are connected together to form a covalently closed single-stranded loop by back-splicing. CircRNAs present the advantages of disease-specific expression and excellent expression stability, and they can modulate gene expression at posttranscriptional and transcriptional levels. CircRNAs are abnormally expressed in multiple cancers, such as breast cancer, and drive the initiation and progression of cancer. In this review, we describe current knowledge about the functions of circRNAs and generalize their roles in various aspects of breast cancer, including cell proliferation, cell cycle, apoptosis, invasion and metastasis, autophagy, angiogenesis, drug resistance, and tumor immunity, and their prognostic and diagnostic value. This may add to a better understanding of the functions and roles of circRNAs in breast cancer, which may become new diagnostic and predictive biomarkers of breast cancer.

Circular RNA hsa_circ_0008003 facilitates tumorigenesis and development of non-small cell lung carcinoma via modulating miR-488/ZNF281 axis

As one of the most aggressive malignancies, non‐small cell lung carcinoma (NSCLC) has high risks of death. It has been demonstrated that circRNAs accelerate NSCLC progression, but the underlying molecular mechanisms of circRNAs in NSCLC were still obscure. In the first place, the circRNA microarray of NSCLC was investigated in this study, and hsa_circ_0008003 (circ‐0008003) was chosen as the research object. Then, it was unveiled that the expression of circ‐0008003 examined via qRT‐PCR was elevated in tumour tissues relative to the non‐tumour tissues, which was associated with TNM stage and lymphatic metastasis in NSCLC. Additionally, the prognosis of NSCLC patients with high circ‐0008003 level was poor. Besides, circ‐0008003 silencing dampened the invasion and proliferation of NSCLC cells. Next, according to the mechanistic studies, circ‐0008003 functioned as a ceRNA of ZNF281 in NSCLC by acting as the endogenous sponge for miR‐488, which was proved to be a tumour suppressor in NSCLC. Additionally, ZNF281 overexpression and miR‐488 suppression recovered the influences of repressed circ‐0008003 on NSCLC cellular processes. It was validated in this research that circ‐0008003 triggered tumour formation in NSCLC, which was adjusted via miR‐488/ZNF281 axis, casting a novel light on the resultful target for treating NSCLC and predicting the prognosis.

Role of LncRNAs and CircRNAs in Bone Metabolism and Osteoporosis

Bone is a mechanosensitive organ that provides strength and support. Many bone cells, various pathways, and signaling molecules coordinate bone metabolism and also determine the course of bone diseases, such as osteoporosis, osteonecrosis, osteopenia, etc. Osteoporosis is caused by increased bone resorption and reduced bone formation due to the changes in the level of different proteins and RNAs in osteoclast or/and osteoblasts. The available therapeutic interventions can significantly reduce bone resorption or enhance bone formation, but their prolonged use has deleterious side effects. Therefore, the use of non-coding RNAs as therapeutics has emerged as an interesting field of research. Despite advancements in the molecular field, not much is known about the role of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in bone homeostasis and osteoporosis. Therefore, in this article, we summarize the role of lncRNAs and circRNAs in different bone cells and osteoporosis so that it might help in the development of osteoporotic therapeutics.

Circular RNAs in Cardiac Regeneration: Cardiac Cell Proliferation, Differentiation, Survival, and Reprogramming

Circular RNAs (circRNAs) are classified as long non-coding RNAs (lncRNAs) that are characterized by a covalent closed-loop structure. This closed-loop shape is the result of a backsplicing event in which the 3' and 5' splice sites are ligated. Through the lack of 3' poly(A) tails and 5' cap structures, circRNAs are more stable than linear RNAs because these adjustments make the circular loop less susceptible to exonucleases. The majority of identified circRNAs possess cell- and tissue-specific expression patterns. In addition, high-throughput RNA-sequencing combined with novel bioinformatics algorithms revealed that circRNA sequences are often conserved across different species suggesting a positive evolutionary pressure. Implicated as regulators of protein turnover, micro RNA (miRNA) sponges, or broad effectors in cell differentiation, proliferation, and senescence, research of circRNA has increased in recent years. Particularly in cardiovascular research, circRNA-related discoveries have opened the door for the development of potential diagnostic and therapeutic tools. Increasing evidence links deviating circRNA expression patterns to various cardiovascular diseases including ischemic heart failure. In this mini-review, we summarize the current state of knowledge on circRNAs in cardiac regeneration with a focus on cardiac cell proliferation, differentiation, cardiomyocyte survival, and cardiac reprogramming.

The Biomarker and Therapeutic Potential of Circular Rnas in Schizophrenia

Circular RNAs (circRNAs) are endogenous, single-stranded, most frequently non-coding RNA (ncRNA) molecules that play a significant role in gene expression regulation. Circular RNAs can affect microRNA functionality, interact with RNA-binding proteins (RBPs), translate proteins by themselves, and directly or indirectly modulate gene expression during different cellular processes. The affected expression of circRNAs, as well as their targets, can trigger a cascade of events in the genetic regulatory network causing pathological conditions. Recent studies have shown that altered circular RNA expression patterns could be used as biomarkers in psychiatric diseases, including schizophrenia (SZ); moreover, circular RNAs together with other cell molecules could provide new insight into mechanisms of this disorder. In this review, we focus on the role of circular RNAs in the pathogenesis of SZ and analyze their biomarker and therapeutic potential in this disorder.

Exploring the regulatory roles of circular RNAs in Alzheimer's disease

Circular RNAs (circRNAs) are a type of covalently closed, single-stranded circular noncoding RNA that can affect the expression of many protein-coding genes. Growing evidence has shown that circRNAs play critical roles in Alzheimer's disease (AD) and may have therapeutic potentials for this disease. CircRNAs play regulatory roles in neural functions and neurological disorders through diverse mechanisms, including acting as microRNA sponges or interacting with proteins to regulate selective splicing or transcription, as well as through epigenetic modification. In this review, we discuss the biogenesis and functions of circRNAs and the research progress on circRNAs in AD to advance the understanding of how circRNAs contribute to this neurological disorder.

Protein-Related Circular RNAs in Human Pathologies

Circular RNAs (circRNAs) are a distinct family of RNAs derived from alternative splicing which play a crucial role in regulating gene expression by acting as microRNA (miRNA) and RNA binding protein (RBP) sponges. However, recent studies have also reported the multifunctional potential of these particles. Under different conditions, circRNAs not only regulate protein synthesis, destination, and degradation but can serve as protein scaffolds or recruiters and are also able to produce short peptides with active biological functions. circRNAs are under ongoing investigation because of their close association with the development of diseases. Some circRNAs are reportedly expressed in a tissue- and development stage-specific manner. Furthermore, due to other features of circRNAs, including their stability, conservation, and high abundance in bodily fluids, they are believed to be potential biomarkers for various diseases, including cancers. In this review, we focus on providing a summary of the current knowledge on circRNA-protein interactions. We present the properties and functions of circRNAs, the possible mechanisms of their translation abilities, and the emerging functions of circRNA-derived peptides in human pathologies.