Circular RNA expression profiles of peripheral blood mononuclear cells in rheumatoid arthritis patients, based on microarray chip technology

Unveiling Novel Drug Targets and Emerging Therapies for Rheumatoid Arthritis: A Comprehensive Review

Rheumatoid arthritis (RA) is a chronic debilitating autoimmune disease, that causes joint damage, deformities, and decreased functionality. In addition, RA can also impact organs like the skin, lungs, eyes, and blood vessels. This autoimmune condition arises when the immune system erroneously targets the joint synovial membrane, resulting in synovitis, pannus formation, and cartilage damage. RA treatment is often holistic, integrating medication, physical therapy, and lifestyle modifications. Its main objective is to achieve remission or low disease activity by utilizing a "treat-to-target" approach that optimizes drug usage and dose adjustments based on clinical response and disease activity markers. The primary RA treatment uses disease-modifying antirheumatic drugs (DMARDs) that help to interrupt the inflammatory process. When there is an inadequate response, a combination of biologicals and DMARDs is recommended. Biological therapies target inflammatory pathways and have shown promising results in managing RA symptoms. Close monitoring for adverse effects and disease progression is critical to ensure optimal treatment outcomes. A deeper understanding of the pathways and mechanisms will allow new treatment strategies that minimize adverse effects and maintain quality of life. This review discusses the potential targets that can be used for designing and implementing precision medicine in RA treatment, spotlighting the latest breakthroughs in biologics, JAK inhibitors, IL-6 receptor antagonists, TNF blockers, and disease-modifying noncoding RNAs.

Long noncoding RNA/circular RNA regulates competitive endogenous RNA networks in rheumatoid arthritis: molecular mechanisms and traditional Chinese medicine therapeutic significances

Rheumatoid arthritis (RA) is a systemic and autoimmune disease that is mainly featured abnormal fibroblast-like synoviocyte (FLS) proliferation and inflammatory cell infiltration. Abnormal expression or function of long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) are closely related to human diseases, including RA. There has been increasing evidence showing that in the competitive endogenous RNA (ceRNA) networks, both lncRNA and circRNA are vital in the biological functions of cells. Nevertheless, the exact mechanism of ceRNA in RA remains to be investigated. Herein, we summarized the molecular potencies of lncRNA/circRNA-mediated ceRNA networks in RA, with emphasis on the phenotypic regulation of ceRNA in the progression of RA, including regulation of proliferation, invasion, inflammation and apoptosis, as well as the role of ceRNA in traditional Chinese medicine (TCM) in the treatment of RA. In addition, we also discussed the future direction and potential clinical value of ceRNA in the treatment of RA, which may provide potential reference value for clinical trials of TCM therapy for the treatment of RA.Key messagesLong noncoding RNA/circular RNA can work as the competitive endogenous RNA sponge and participate in the pathogenesis of rheumatoid arthritis.Traditional Chinese medicine and its agents have shown potential roles in the prevention and treatment of rheumatoid arthritis via competitive endogenous RNA.

Exploring the theranostic potentials of miRNA and epigenetic networks in autoimmune diseases: A comprehensive review

BACKGROUND

Autoimmune diseases (AD) are severe pathophysiological ailments that are stimulated by an exaggerated immunogenic response towards self-antigens, which can cause systemic or site-specific organ damage. An array of complex genetic and epigenetic facets majorly contributes to the progression of AD, thus providing significant insight into the regulatory mechanism of microRNA (miRNA). miRNAs are short, non-coding RNAs that have been identified as essential contributors to the post-transcriptional regulation of host genome expression and as crucial regulators of a myriad of biological processes such as immune homeostasis, T helper cell differentiation, central and peripheral tolerance, and immune cell development.

AIMS

This article tends to deliberate and conceptualize the brief pathogenesis and pertinent epigenetic regulatory mechanism as well as miRNA networks majorly affecting five different ADs namely rheumatoid arthritis (RA), type 1 diabetes, multiple sclerosis (MS), systemic lupus erythematosus (SLE) and inflammatory bowel disorder (IBD) thereby providing novel miRNA-based theranostic interventions.

RESULTS & DISCUSSION

Pertaining to the differential expression of miRNA attributed in target tissues and cellular bodies of innate and adaptive immunity, a paradigm of scientific expeditions suggests an optimistic correlation between immunogenic dysfunction and miRNA alterations.

CONCLUSION

Therefore, it is not astonishing that dysregulations in miRNA expression patterns are now recognized in a wide spectrum of disorders, establishing themselves as potential biomarkers and therapeutic targets. Owing to its theranostic potencies, miRNA targets have been widely utilized in the development of biosensors and other therapeutic molecules originating from the same.

Exploring CircRNA N6-methyladenosine in human rheumatoid arthritis: Hyper-methylated hsa_circ_0007259 as a potential biomarker and its involvement in the hsa_circ_0007259/hsa_miR-21-5p/STAT3 axis

BACKGROUND

N6-methyladenosine (m6A) is a highly enriched modification found in circular RNAs (CircRNAs); however, the ability and mechanism of CircRNAs to encode for m6A function in rheumatoid arthritis (RA) remain poorly understood.

METHODS

We utilized an epitranscriptomic microarray to measure levels and quantities of m6A methylated CircRNAs in synovial tissues of patients with RA and osteoarthritis (OA). We then utilized methylated RNA immunoprecipitation- and MazF-quantitative PCR to identify and validate differentially m6A-methylated RNAs between the groups, conducted a functional enrichment analysis, and selected protein-protein interaction hub genes. Lastly, we predicted and validated the CircRNA/miRNA/mRNA interaction networks.

RESULTS

We detected 4,845 CircRNAs containing m6A in our samples, with 53 CircRNAs upregulated, and 139 CircRNAs downregulated compared to human OA synovial tissue (|fold change| ≥ 1.2 and p ≤ 0.05). The differentially m6A-modified CircRNAs were associated with the interleukin-6-mediated signaling pathway, with an increase in relative m6A-methylated levels of hsa_circ_0007259 in human RA, a significant decrease in hsa_miR-21-5p, and an increase in signal transducer and activator of transcription 3（STAT3）. The Luciferase Reporter Gene assay verified the binding of hsa_circ_0007259 to hsa_miR-21-5p and the subsequent binding of hsa_miR-21-5p to STAT3.

CONCLUSION

We showed a notable increase in the relative m6A-methylated levels of hsa_circ_0007259 in human RA, indicating a potential role of hypermethylated hsa_circ_0007259 in RA pathogenesis. This may provide valuable insight into the mechanism of RA and the possibility of utilizing hsa_circ_0007259 as a valuable biomarker.

Dysregulation of circRNAs in rheumatoid arthritis, with special emphasis on circRNAs secreted by exosomes and the crosstalk between circRNAs and RNA methylations

BACKGROUND

Rheumatoid arthritis (RA) is an autoimmune disease caused by a variety of unknown factors. It mainly occurs in the small joints of hands and feet, leading to cartilage destruction and bone erosion. Various pathologic mechanisms such as exosomes and RNA methylations are involved in the pathogenesis of RA.

METHODS

This work searches PubMed, Web of Science (SCIE) and Science Direct Online (SDOL) databases, it role of abnormally expressed circulating RNAs (circRNAs) in the pathogenesis of RA was summarized. And the relationship between circRNAs and exosomes and methylations.

RESULTS

Both the abnormal expression of circRNAs and the sponge effect of circRNAs on microRNAs (miRNAs) affect the pathogenesis of RA by regulating target genes. CircRNAs affect the proliferation, migration and inflammatory reaction of RA-fibroblast-like synovial cells (FLSs), circRNAs in peripheral blood mononuclear cells (PBMCs) and macrophages also participate in the pathological mechanism of RA (Fig. 1). CircRNAs in exosomes are closely related to the pathogenesis of RA. In addition, exosomal circRNAs and the relationship between circRNAs and RNA methylations are closely related to the pathogenesis of RA.

CONCLUSION

CircRNAs play an important role in the pathogenesis of RA and have the potential to be a new target for the diagnosis and treatment of RA. However, the development of mature circRNAs for clinical application is not a small challenge.

Functions of Circular RNA in Human Diseases and Illnesses

Circular RNAs (circRNAs) represent single-stranded RNA species that contain covalently closed 3' and 5' ends that provide them more stability than linear RNA, which has free ends. Emerging evidence indicates that circRNAs perform essential functions in many DNA viruses, including coronaviruses, Epstein-Barr viruses, cytomegalovirus, and Kaposi sarcoma viruses. Recent studies have confirmed that circRNAs are present in viruses, including DNA and RNA viruses, and play various important functions such as evading host immune response, disease pathogenesis, protein translation, miRNA sponges, regulating cell proliferation, and virus replication. Studies have confirmed that circRNAs can be biological signatures or pathological markers for autoimmune diseases, neurological diseases, and cancers. However, our understanding of circRNAs in DNA and RNA viruses is still limited, and functional evaluation of viral and host circRNAs is essential to completely understand their biological functions. In the present review, we describe the metabolism and cellular roles of circRNA, including its roles in various diseases and viral and cellular circRNA functions. Circular RNAs are found to interact with RNA, proteins, and DNA, and thus can modulate cellular processes, including translation, transcription, splicing, and other functions. Circular RNAs interfere with various signaling pathways and take part in vital functions in various biological, physiological, cellular, and pathophysiological processes. We also summarize recent evidence demonstrating cellular and viral circRNA's roles in DNA and RNA viruses in this growing field of research.

Interaction between the expression of hsa_circRPRD1A and hsa_circHERPUD2 and classical coronary risk factors promotes the development of coronary artery disease

BACKGROUND

Recent studies suggest that classical coronary risk factors play a significant role in the pathogenesis of coronary artery disease. Our study aims to explore the interaction of circRNA with classical coronary risk factors in coronary atherosclerotic disease.

METHOD

Combined analysis of RNA sequencing results from coronary segments and peripheral blood mononuclear cells of patients with coronary atherosclerotic disease was employed to identify critical circRNAs. Competing endogenous RNA networks were constructed by miRanda-3.3a and TargetScan7.0. The relative expression quantity of circRNA in peripheral blood mononuclear cells was determined by qRT-PCR in a large cohort including 256 patients and 49 controls. Spearman's correlation test, receiver operating characteristic curve analysis, multivariable logistic regression analysis, one-way analysis of variance, and crossover analysis were performed.

RESULTS

A total of 34 circRNAs were entered into our study, hsa_circRPRD1A, hsa_circHERPUD2, hsa_circLMBR1, and hsa_circDHTKD1 were selected for further investigation. A circRNA-miRNA-mRNA network is composed of 20 microRNAs and 66 mRNAs. The expression of hsa_circRPRD1A (P = 0.004) and hsa_circHERPUD2 (P = 0.003) were significantly down-regulated in patients with coronary artery disease compared to controls. The area under the curve of hsa_circRPRD1A and hsa_circHERPUD2 is 0.689 and 0.662, respectively. Univariate and multivariable logistic regression analyses identified hsa_circRPRD1A (OR = 0.613, 95%CI:0.380-0.987, P = 0.044) as a protective factor for coronary artery disease. Based on the additive model, crossover analysis demonstrated that there was an antagonistic interaction between the expression of hsa_circHERPUD2 and alcohol consumption in subjects with coronary artery disease.

CONCLUSION

Our findings imply that hsa_circRPRD1A and hsa_circHERPUD2 could be used as biomarkers for the diagnosis of coronary artery disease and provide epidemiological support for the interactions between circRNAs and classical coronary risk factors.

Interrelated grid of non-coding RNA: An important aspect in Rheumatoid Arthritis pathogenesis

Inflammation and autoimmunity are the root cause of rheumatoid arthritis, a destructive disease of joints. Multiple biomolecules are involved in the pathogenesis of RA and are related to various events of molecular biology. RNA is a versatile biomolecule, playing numerous roles at structural, functional, and regulatory stages to maintain cellular homeostasis. The involvement of RNA (coding/non-coding) in disease development and progression has left a wide whole to fill with newer approaches. Non-coding RNAs belong to the housekeeping and regulatory categories and both have their specific roles, and their alteration causes specific implications in disease pathogenesis. Housekeeping RNAs, rRNA, tRNA and regulatory RNA, micro-RNA, circular RNA, piRNA and long non-coding RNA were found to be important regulators of inflammation. They work at the pre-and post-transcriptional levels and were found to be more intriguing to study their regulatory impact on disease pathogenesis. The review addresses a question on how the non-coding RNA gets involved in early RA pathogenesis and can be utilized to know their targets to understand the disease better and make way towards the unresolved mystery of RA development.

Detailed profiling of m6A modified circRNAs and synergistic effects of circRNA and environmental risk factors for coronary artery disease

The modification of N6-methyladenosine (m6A) modification is implicated in human diseases. However, considerable uncertainty is associated with the regulatory mechanisms of m6A circRNAs in coronary artery disease (CAD), which require further clarification. In this study, m6A-modified RNA immunoprecipitation sequencing (MeRIP-seq) was conducted to investigate m6A-modified circRNAs in human coronary artery smooth muscle cells (HCASMCs) and to identify potential biomarkers for CAD. A total of 830 and 331 up- and down-regulated m6A peaks, (corresponding to 463 and 243 up- and down-regulated circRNAs, respectively), were identified in HCASMCs in a pathological condition. Functional analysis suggested that these circRNAs appeared to participate in intracellular protein, histone deacetylase complex, ATP-dependent activity, autophagy, and AMPK signaling pathway. Four candidate circRNAs were selected for further evaluation in HCASMCs and human samples. The results suggested that hsa_circHECTD1 and hsa_circZBTB46 were significantly increased in patients with CAD (p-value = 0.039 and p-value = 0.014) and may act as potential diagnostic biomarkers of CAD. Furthermore, statistical results showed that hsa_circHECTD1 and hsa_circSEC62 were positively correlated with triglyceride (TG) (r = 0.213, p-value = 0.014) and Gensini Score (used to quantify the severity of CAD) (r = 0.349, p-value <0.001), respectively. Logistic regression revealed that hsa_circZBTB46 was strongly correlated with the incidence of CAD, and the synergistic effects of circRNAs and hypertension enhanced the risk of CAD. These results show that hsa_circHECTD1 and hsa_circZBTB46 may be new targets for further studies, and this study enhances our understanding of the effects of m6A-circRNAs on the pathogenesis of CAD.

The functions and networks of non-coding RNAs in the pathogenesis of Rheumatoid Arthritis

Rheumatoid Arthritis (RA) is a chronic autoimmune disease. Its main feature is inflammation of synovial tissue with irreversible joint damage and severe physical damage. Non-coding RNAs (ncRNAs) are a class of RNAs that do not have the ability to encode proteins but are vital regulators that mediate many fundamental cellular processes and play an essential role in the pathogenesis of RA. Multiple verified ncRNAs have been confirmed as a prospective biomarkers for diagnosing and treating RA. In this paper, we aim to sort out the role of ncRNAs in the pathogenesis of RA and provide new ideas for the diagnosis and treatment of RA.

Bioinformatics analysis of rheumatoid arthritis tissues identifies genes and potential drugs that are expressed specifically

Studies have implicated necroptosis mechanisms in orthopaedic-related diseases, since necroptosis is a unique regulatory cell death pattern. However, the role of Necroptosis-related genes in rheumatoid arthritis (RA) has not been well described. We downloaded RA-related data information and Necroptosis-related genes from the Gene Expression Omnibus (GEO), Kyoto Gene and Genome Encyclopedia (KEGG) database, and Genome Enrichment Analysis (GSEA), respectively. We identified 113 genes associated with RA-related necroptosis, which was closely associated with the cytokine-mediated signaling pathway, necroptosis and programmed necrosis. Subsequently, FAS, MAPK8 and TNFSF10 were identified as key genes among 48 Necroptosis-associated differential genes by three machine learning algorithms (LASSO, RF and SVM-RFE), and the key genes had good diagnostic power in distinguishing RA patients from healthy controls. According to functional enrichment analysis, these genes may regulate multiple pathways, such as B-cell receptor signaling, T-cell receptor signaling pathways, chemokine signaling pathways and cytokine-cytokine receptor interactions, and play corresponding roles in RA. Furthermore, we predicted 48 targeted drugs against key genes and 31 chemical structural formulae based on targeted drug prediction. Moreover, key genes were associated with complex regulatory relationships in the ceRNA network. According to CIBERSORT analysis, FAS, MAPK8 and TNFSF10 may be associated with changes in the immune microenvironment of RA patients. Our study developed a diagnostic validity and provided insight to the mechanisms of RA. Further studies will be required to test its diagnostic value for RA before it can be implemented in clinical practice.

Circular RNA in autoimmune diseases: special emphasis on regulation mechanism in RA and SLE

BACKGROUND

Autoimmune diseases are diseases caused by tissue damage caused by the body's immune response to autoantibodies. Circular RNAs (CircRNAs) are a kind of special endogenous non-coding RNA that play a biological role by regulating gene transcription.

METHODS

In this work, we searched the PubMed, Web of Science (SCIE), National Science and Technology Library (NSTL), and ScienceDirect Online (SDOL) databases to summarize the impact of circRNAs on autoimmune diseases, especially the results of circRNAs in rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE).

RESULTS

The study on the function of circRNAs and autoimmune diseases further deepened our understanding of the development and pathogenesis of autoimmune diseases. CircRNAs may act as miRNA sponges to regulate biological processes and affect the occurrence and development of autoimmune diseases. CircRNAs are closely related to the pathogenesis of RA and SLE and may become potential biomarkers for the diagnosis and treatment of RA and SLE.

CONCLUSION

CircRNAs play an important role in the pathogenesis of RA, SLE and other autoimmune diseases, and are expected to provide new biomarkers for the diagnosis and treatment of autoimmune diseases. However, the function and mechanism of circRNAs in autoimmune diseases need more comprehensive research.

The circRNA-miRNA-mRNA regulatory network in plasma and peripheral blood mononuclear cells and the potential associations with the pathogenesis of systemic lupus erythematosus

OBJECTIVES

This study aimed to explore the possible role of plasma and peripheral blood mononuclear cells (PBMCs) circular RNA (circRNA) in systemic lupus erythematosus (SLE).

METHOD

Total RNA was extracted from blood plasma samples obtained from 10 patients with SLE and 10 healthy controls and subjected to microarray analysis to define the profile of circRNA expression. The quantitative reverse transcription-polymerase chain reaction (qRT-PCR) amplification was conducted. The overlapped circRNA between PBMCs and plasma was performed, the interactions with microRNAs were predicted, the miRNA target mRNA was predicted, and the GEO database was used. The Gene ontology and pathway analysis was performed.

RESULTS

One hundred thirty-one upregulated and 314 significantly downregulated circRNAs were identified in the plasma of patients with SLE by the Fold change criteria (≥ 2.0) and P < 0.05. The qRT-PCR results showed that the expression of has-circRNA-102531, has-circRNA-103984, and has-circRNA-104262 was increased in plasma of SLE, and the expression of has-circRNA-102972, has-circRNA-102006, has-circRNA-104313 was decreased in plasma of SLE. Twenty-eight upregulated circRNAs and 119 downregulated circRNAs were overlapped from PBMCs and plasma, and ubiquitination was enriched. Furthermore, the circRNA-miRNA-mRNA network was constructed in SLE after analyzing dataset GSE61635 from GEO. The circRNA-miRNA-mRNA network comprises 54 circRNAs, 41 miRNAs, and 580 mRNAs. In addition, the TNF signaling pathway and the MAPK pathway were enriched from the mRNA of the miRNA target.

CONCLUSION

We first revealed the differentially expressed circRNAs in plasma and PBMCs, and then the circRNA-miRNA-mRNA network was constructed. The network's circRNAs could be a potential diagnostic biomarker and potentially play an important role in the pathogenesis and development of SLE. Key Points • This study analyzed the circRNAs expression profiles combined with the plasma and PBMCs, which provided a comprehensive overview of circRNAs expression patterns in SLE. • The network of the circRNA-miRNA-mRNA in SLE was constructed, which contributes to a better understanding of the pathogenesis and development of SLE.

Rheumatoid arthritis and non-coding RNAs; how to trigger inflammation

Rheumatoid arthritis (RA) is a systemic and chronic inflammatory disease categorized by continuous synovitis in the joints and systemic inflammatory responses that can cause lifelong disability. The major cause of RA is the dysregulation of the immune response. The development of RA disease includes multiplex association of several interleukins and cells, which leads to synovial cell growth, cartilage and bone damage. The primary stage of RA disease is related to the modification of both the innate and adaptive immune systems, which leads to the formation of autoantibodies. This process results in many damaged molecules and epitope spreading. Both the innate (e.g., dendritic cells, macrophages, and neutrophils) and acquired immune cells (e.g., T and B lymphocytes) will increase and continue the chronic inflammatory condition in the next stages of the RA disease. In recent years, non-coding RNAs have been proved as significant controllers of biological functions, especially immune cell expansion and reactions. Non-coding RNAs were primarily containing microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA). Various studies confirmed non-coding RNAs as hopeful markers for diagnosing and curing RA. This review will describe and cover existing knowledge about RA pathogenesis, which might be favorable for discovering possible ncRNA markers for RA.

Non-coding RNAs in immunoregulation and autoimmunity: Technological advances and critical limitations

Immune cell function is critically dependent on precise control over transcriptional output from the genome. In this respect, integration of environmental signals that regulate gene expression, specifically by transcription factors, enhancer DNA elements, genome topography and non-coding RNAs (ncRNAs), are key components. The first three have been extensively investigated. Even though non-coding RNAs represent the vast majority of cellular RNA species, this class of RNA remains historically understudied. This is partly because of a lag in technological and bioinformatic innovations specifically capable of identifying and accurately measuring their expression. Nevertheless, recent progress in this domain has enabled a profusion of publications identifying novel sub-types of ncRNAs and studies directly addressing the function of ncRNAs in human health and disease. Many ncRNAs, including circular and enhancer RNAs, have now been demonstrated to play key functions in the regulation of immune cells and to show associations with immune-mediated diseases. Some ncRNAs may function as biomarkers of disease, aiding in diagnostics and in estimating response to treatment, while others may play a direct role in the pathogenesis of disease. Importantly, some are relatively stable and are amenable to therapeutic targeting, for example through gene therapy. Here, we provide an overview of ncRNAs and review technological advances that enable their study and hold substantial promise for the future. We provide context-specific examples by examining the associations of ncRNAs with four prototypical human autoimmune diseases, specifically rheumatoid arthritis, psoriasis, inflammatory bowel disease and multiple sclerosis. We anticipate that the utility and mechanistic roles of these ncRNAs in autoimmunity will be further elucidated in the near future.

Circular RNAs: typical biomarkers for bone-related diseases

Bone is a connective tissue that has important functions in the human body. Cells and the extracellular matrix (ECM) are key components of bone and are closely related to bone-related diseases. However, the outcomes of conventional treatments for bone-related diseases are not promising, and hence it is necessary to elucidate the exact regulatory mechanisms of bone-related diseases and identify novel biomarkers for diagnosis and therapy. Circular RNAs (circRNAs) are single-stranded RNAs that form closed circular structures without a 5' cap or 3' tail and polycyclic adenylate tails. Due to their high stability, circRNAs have the potential to be typical biomarkers. Accumulating evidence suggests that circRNAs are involved in bone-related diseases, including osteoarthritis, osteoporosis, osteosarcoma, multiple myeloma, intervertebral disc degeneration, and rheumatoid arthritis. Herein, we summarize the recent research progress on the characteristics and functions of circRNAs, and highlight the regulatory mechanism of circRNAs in bone-related diseases.

Newly discovered circRNAs in rheumatoid arthritis, with special emphasis on functional roles in inflammatory immunity

Circular RNA (circRNA) is a unique type of endogenous RNA. It does not have free 3 ′or 5′ ends, but forms covalently closed continuous rings. Rheumatoid arthritis (RA) is a common chronic autoimmune joint disease, characterized by chronic inflammation of the joint synovial membrane, joint destruction, and the formation of pannus. Although the pathogenesis of rheumatoid arthritis remains incompletely understood, a growing amount of research shows that circRNA has a close relationship with RA. Researchers have found that abnormally expressed circRNAs may be associated with the occurrence and development of RA. This article reviews the inflammatory immune, functions, mechanisms, and values of the circRNAs in RA to provide new ideas and novel biomarkers for the diagnosis and treatment of RA.

Male mice exposed to chronic intermittent ethanol exposure exhibit significant upregulation or downregulation of circular RNAs

B a ckground: Circular RNAs (circRNAs) have been crucially implicated in various diseases, however, their involvement in chronic intermittent ethanol (CIE) exposure remains unclear.O bjective: The present study was conducted to evaluate the circular RNA expression alteration in brain samples and to identify the molecular mechanisms underlying chronic intermittent ethanol exposure.M ethods: Male C57BL/6J mice (10 for each group) were given 4 weeks of chronic intermittent ethanol exposure. Whole brain samples were collected for high-throughput sequencing and circRNA bioinformatic analysis. Real-time quantitative PCR (RI-qPCR) and agarose electrophoresis were used to validate the differentially expressed circRNAs. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) analysis were performed. A p level < 0.05 was considered statistically significant.R esults: Compared with the control group and baseline values, the CIE group showed a significant increase in ethanol intake. High-throughput sequencing revealed 399 significantly different circRNAs in CIE mice, including 150 up-regulated circRNAs and 249 down-regulated circRNAs. GO analysis showed that the most significantly enriched term for biological process, cellular component, and molecular function were GO:0050885, GO:0016020 and GO:0005515, respectively. The most enriched pathways in KEGG analysis were GABAergic synapse (mmu04727), followed by retrograde endocannabinoid (eCB) signaling (mmu04723) and morphine addiction (mmu05032). Among the circRNAs, RT-qPCR confirmed 14 upregulated and 13 downregulated circRNAs in the brain tissues with 9 upregulated and 10 downregulated circRNAs being observed in blood samples.C onclusions: Our study suggests that chronic ethanol exposure upregulates or downregulates circRNAs in the brain, which, in turn, could alter neurotransmitter release and signal transduction.

Circ_0004712 Silencing Suppresses the Aggressive Changes of Rheumatoid Arthritis Fibroblast-Like Synoviocytes by Targeting miR-633/TRAF6 Axis

Circular RNA_0004712 (circ_0004712) is reported to be up-regulated in rheumatoid arthritis (RA) patients. Nevertheless, its role and mechanism in RA pathology remain to be clarified. RNA and protein expression was determined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blot assay. Cell viability, proliferation, apoptosis, migration, and inflammation were assessed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, 5-ethynyl-20-deoxyuridine assay, flow cytometry, scratch test, and enzyme-linked immunosorbent assay. The target correlation between microRNA-633 (miR-633) and circ_0004712 or TNF receptor associated factor 6 (TRAF6) was verified by dual-luciferase reporter assay and RNA immunoprecipitation assay. Circ_0004712 was up-regulated in RA synovial tissues and RA fibroblast-like synoviocytes (RA-FLSs). Circ_0004712 silencing suppressed the viability, proliferation, migration and inflammatory response and facilitated the apoptosis of RA-FLSs. miR-633 was confirmed to be a direct target of circ_0004712, and miR-633 knockdown reversed circ_0004712 silencing-mediated protective effects on the dysfunction and inflammation of RA-FLSs. TRAF6 was a direct target of miR-633, and miR-633 overexpression suppressed the aggressive changes of RA-FLSs by down-regulating TRAF6. Circ_0004712 could up-regulate TRAF6 expression by sponging miR-633 in RA-FLSs. Circ_0004712 interference inactivated nuclear factor (NF)-κB signaling by targeting miR-633/TRAF6 axis. Circ_0004712 silencing inhibited the aggressive changes of RA-FLSs by targeting miR-633/TRAF6 axis and NF-κB signaling, which provided new targets for RA therapy.

Roles of Non-Coding RNAs in Primary Biliary Cholangitis

Primary biliary cholangitis (PBC) is an autoimmune-mediated chronic cholestatic liver disease, fatigue, and skin itching are the most common clinical symptoms. Its main pathological feature is the progressive damage and destruction of bile duct epithelial cells. Non-coding RNA (NcRNA, mainly including microRNA, long non-coding RNA and circular RNA) plays a role in the pathological and biological processes of various diseases, especially autoimmune diseases. Many validated ncRNAs are expected to be biomarkers for the diagnosis or treatment of PBC. This review will elucidate the pathogenesis of PBC and help to identify potential ncRNA biomarkers for PBC.

Significance of circRNAs as biomarkers for systemic lupus erythematosus: a systematic review and meta-analysis

Objective

To comprehensively evaluate the significance of circular RNAs (circRNAs) as potential diagnostic biomarkers for systemic lupus erythematosus (SLE) via pooled analyses of data from published studies that focussed on the association between circRNAs and SLE.

Methods

The systematic review and meta-analysis protocol was registered in PROSPERO (registration No. CRD42021229383). Relevant studies published before 3 April 2022 were selected to verify the relationship between circRNA expression levels and SLE. Extracted data were analysed using a random-effects model with Meta-DiSc 1.4 and Stata 16 software. Transcription factors related to hsa_circ_0000479 and its parental gene were extracted from the TRCirc and hTFtarget databases, respectively.

Results

A total of 10 studies, involving 438 patients with SLE and 434 controls, were included in the meta-analysis. The pooled sensitivity, specificity, and diagnostic odds ratio of circRNAs in detecting SLE were 0.66 (95% confidence interval [CI] 0.63, 0.70), 0.79 (95% CI 0.76, 0.82), and 10.80 (95% CI 6.58, 17.73), respectively. The area under the summary receiver operating characteristic curve was 0.8366.

Conclusions

Meta-analysis of pooled data indicated a moderate accuracy of circRNAs in diagnosing SLE. The exact diagnostic value of circRNAs and the mechanisms of interaction between circRNAs and their parental genes should be confirmed in further studies.

Bioinformatics Analysis Identified the Hub Genes, mRNA–miRNA–lncRNA Axis, and Signaling Pathways Involved in Rheumatoid Arthritis Pathogenesis

Objective

Rheumatoid arthritis (RA) is a nonspecific, chronic, systemic autoimmune disease characterized by symmetric polyarticular synovitis. Bioinformatics analysis of potential biomarkers, mRNA–miRNA–lncRNA axes, and signaling pathways in the pathogenesis of RA provides potential targets and theoretical basis for further research on RA.

Methods

The GSE1919 and GSE77298 datasets were downloaded from the Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo). Perl was used to perform data merging, and R was used to perform batch correction. The “limma” package of R was used to screen differentially expressed genes, and the “clusterProfiler” package was used to perform enrichment analysis of the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Search Tool for the Retrieval of Interacting Genes/Proteins was used to construct the protein–protein interaction network, Cytoscape was used for module analysis, and R was used to screen for hub genes. GraphPad Prism was used to plot the receiver operating characteristic curve of the hub genes. Gene set enrichment analysis and competitive endogenous RNA network analysis were performed on hub genes with the greatest diagnostic values. The hub gene with the greatest diagnostic value was verified using immunohistochemical staining.

Results

We obtained nine hub genes (ITGB2, VAMP8, HLA-A, PTAFR, SYK, FCER1G, HLA-DPB1, LCP2, and ACTR2) and four mRNA–miRNA–lncRNA axes (ITGB2-hsa-miR-486-3p-SNHG3, ITGB2-hsa-miR-338-5p-XIST, ITGB2-hsa-miR-5581-3p-XIST, and ITGB2-hsa-miR-1226-5p-XIST) related to the pathogenesis of RA. The nine hub genes were highly expressed, and ITGB2 had the highest diagnostic value for RA. We also identified signaling pathways related to the pathogenesis of RA: Fc epsilon Rl and chemokine signaling pathways. The immunohistochemical results showed that ITGB2 expression was significantly upregulated in RA.

Conclusion

The hub genes, mRNA–miRNA–lncRNA axes, and signaling pathways related to RA pathogenesis identified in this study provide a new research direction for the mechanism, diagnosis, and treatment of RA.

Circ_0088036 facilitates the proliferation and inflammation and inhibits the apoptosis of fibroblast-like synoviocytes through targeting miR-326/FZD4 axis in rheumatoid arthritis

BACKGROUND

The function and pathological significance of circular RNAs (circRNAs) in autoimmune diseases, such as rheumatoid arthritis (RA), are barely known. Here, we explored the role of circ_0088036 in RA progression and its associated mechanism.

METHODS

The synovial lining layer tissues of RA patients and non-RA control patients were collected for clinical study in vivo, and tumour necrosis factor α (TNF-α)-induced RA-fibroblast-like synoviocytes (RA-FLSs) were used for the experiments in vitro. Cell proliferation was assessed by Cell Counting Kit 8 (CCK8) assay and flow cytometry. Cell apoptosis was analyzed by flow cytometry. Enzyme-linked immunosorbent assay (ELISA) was conducted to analyze the release of pro-inflammatory cytokines. Dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay were performed to verify the target interaction between microRNA-326 (miR-326) and circ_0088036 or frizzled class receptor 4 (FZD4).

RESULTS

Circ_0088036 expression was elevated in the synovial lining layer tissues of RA patients and TNF-α-treated RA-FLSs. Circ_0088036 interference largely reversed TNF-α-induced proliferation and inflammation in RA-FLSs. The interaction between circ_0088036 and miR-326 was verified, and miR-326 silencing largely reversed circ_0088036 knockdown-mediated effects in TNF-α-treated RA-FLSs. MiR-326 bound to the 3' untranslated region (3'UTR) of FZD4 in RA-FLSs. FZD4 overexpression largely diminished miR-326 accumulation-mediated influences in TNF-α-treated RA-FLSs. Circ_0088036 could up-regulate FZD4 by sponging miR-326 in RA-FLSs.

CONCLUSION

Circ_0088036 contributed to TNF-α-induced RA progression partly by targeting miR-326/FZD4 signalling.

Long Noncoding RNA and Circular RNA Expression Profiles of Monocyte-Derived Dendritic Cells in Autoimmune Hepatitis

Autoimmune hepatitis (AIH) is a chronic liver disease caused by disruption of liver immune homeostasis. The effect of dendritic cells (DCs) on the pathogenesis of AIH is not fully understood. Long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) have been shown to play critical roles in the regulation of cell function. In this study, we analyzed the immunophenotypic characteristics of DCs in the peripheral blood. The percentage of mature DCs was higher in AIH patients than in healthy controls (HCs), and the proportion of mature DCs decreased after treatment. We isolated monocyte-derived DCs (moDCs) from the peripheral blood, obtained whole RNA-sequencing (RNA-seq) data for the moDCs from the two groups, and identified differentially expressed (DE) lncRNAs, circRNAs, miRNAs and mRNAs. In addition, we performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses for the DE mRNAs and constructed competing endogenous RNA (ceRNA) networks. ENST00000543334, hsa_circ_0000279, and hsa_circ_0005076 were selected and validated by RT-qPCR. These results provide a possible molecular mechanism of DCs in the pathogenesis of AIH and identify some potential therapeutic targets.

EIF4A3-mediated hsa_circ_0088088 promotes the carcinogenesis of breast cancer by sponging miR-135-5p

Circular RNAs have participated in oncology progress. Nevertheless, the potential mechanisms are not completely understood. We intended to inspect the functions of hsa_circ_0088088 on breast malignancy, together with the possible mechanism(s). hsa_circ_0088088 expression in breast malignancy was studied using quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR). The overall survival was studied by the Kaplan-Meier curve. The biological functions of hsa_circ_0088088 aberrant expression on cell growth and metastasis were evaluated in MDA-MB-231 cells. Bioinformatics analysis, RNA immunoprecipitation (RIP), and qRT-PCR were accomplished to confirm the possible regulatory effects of eukaryotic initiation factor 4A3 (EIF4A3) on the biogenesis of hsa_circ_0088088. Furthermore, a dual-luciferase reporter assay, qRT-PCR, and RNA pull-down assay were used to confirm the association between the hsa_circ_0088088 and miR-135-5p in MDA-MB-231 cells. hsa_circ_0088088 was upregulated in the tumor tissues and cells, and higher expression presented an unfavorable prognosis. hsa_circ_0088088 overexpression promoted cell growth and metastasis in MDA-MB-231 cells. EIF4A3 was found to positively regulate hsa_circ_0088088. Furthermore, we confirmed that hsa_circ_0088088 sponges miR-135-5p and directly targets miR-135-5p with respect to the cell growth and metastasis in MDA-MB-231 cells. Our data suggest that EIF4A3-induced hsa_circ_0088088 stimulates the carcinogenic effects of breast tumors by sponging miR-135-5p.

circPTPN22 as a novel biomarker and ceRNA in peripheral blood mononuclear cells of rheumatoid arthritis

The role of circular RNAs (circRNAs) in rheumatoid arthritis (RA) remains to be elucidated. To determine the expression of circRNAs in peripheral blood mononuclear cells (PBMCs) and to identify novel biomarkers for RA and explore their potential effects in RA, the present study conducted high-throughput RNA sequencing to analyze circRNA expression profiles in PBMCs from 4 RA patients and 3 healthy controls (HCs). Reverse transcription-quantitative PCR was used to verify the expression of circPTPN22 in 42 RA patients, 44 HCs and 45 systemic lupus erythematosus (SLE) patients. In addition, bioinformatics analysis and Pearson's correlation test were conducted to assess the correlation of the relationships between circPTPN22 and RA progression. A receiver operating characteristic curve was calculated to evaluate the diagnostic value. Multilevel integrated analysis identified 41 upregulated and 30 downregulated circRNAs in RA patients compared with HCs. circPTPN22 was confirmed to be a common differentially expressed gene in RA and SLE compared with HCs. Area under the curve analysis suggested the diagnostic value of circPTPN22 expression to distinguish RA patients from both HCs and SLE patients. In addition, circPTPN22 levels in RA PBMCs were correlated with RA-IgG, RA-IgM, RA-IgA, anti-cyclic citrullinated peptide (anti-CCP), rheumatoid factor and C reactive protein levels. A total of four putative microRNAs (miRNAs or miRs), namely, hsa-miR-3074-5p, hsa-miR-373-3p, hsa-miR-766-3p and hsa-miR-34c-5p, were screened to be sponged by circPTPN22 via bioinformatics analysis and then experimentally verified to be upregulated in RA PBMCs compared with controls. The data suggested that circPTPN22 might be a novel biomarker for the diagnosis of RA and participate in RA pathogenesis through a sponge mechanism.

Hsa_circ_0044235 regulates the pyroptosis of rheumatoid arthritis via MiR-135b-5p-SIRT1 axis

Studies have found that cell pyroptosis is involved in the occurrence and development of rheumatoid arthritis (RA). Hsa_circ_0044235 has been found to be significantly low-expressed in RA patients. The purpose of this research was to reveal the regulatory mechanism of hsa_circ_0044235 in the pyroptosis pathway of RA. Serum expressions of hsa_circ_0044235 and SIRT were detected by RT-qPCR, and the relationship of the two genes was analyzed by Pearson. Next, a collagen-induced arthritis (CIA) mouse model was constructed to examine the effect of hsa_circ_0044235 on knee joint injury. The number of apoptotic cells and the level of inflammatory cytokines in synovial tissue were detected by TUNEL and ELISA. Fibroblast-like synoviocytes (FLSs) were extracted as in vitro study subject. Functional assays including flow cytometry and immunofluorescence staining, molecular experiments including RT-qPCR, Western blot and dual luciferase assay, and bioinformatics analysis were performed to analyze the mechanism of hsa_circ_0044235 in pyroptosis in FLSs. Hsa_circ_0044235 and SIRT1 expressions were suppressed in RA patients and the two were positively correlated. Overexpressed hsa_circ_0044235 attenuated joint inflammation, cell apoptosis, and joint damage, reduced foot pad thickness, clinical case scores, inhibited the NLRP3-mediated pyroptosis pathway but promoted SIRT1 expression in CIA mice. Overexpressed hsa_circ_0044235 inhibited caspase-1 content and the NLRP3-mediated pyroptosis pathway. Moreover, hsa_circ_0044235 promoted SIRT1 expression by sponging miR-135b-5p in FLSs. Additionally, the effect of overexpressed hsa_circ_0044235 on FLSs was reversed by miR-135b-5p mimic and siSIRT1, while the effect of siSIRT1 was reversed by miR-135b-5p inhibitor. Hsa_circ_0044235 regulated NLRP3-mediated pyroptosis through miR-135b-5p-SIRT1 axis to regulate the development of RA.

The Expression of Non-Coding RNAs and Their Target Molecules in Rheumatoid Arthritis: A Molecular Basis for Rheumatoid Pathogenesis and Its Potential Clinical Applications

Rheumatoid arthritis (RA) is a typical autoimmune-mediated rheumatic disease presenting as a chronic synovitis in the joint. The chronic synovial inflammation is characterized by hyper-vascularity and extravasation of various immune-related cells to form lymphoid aggregates where an intimate cross-talk among innate and adaptive immune cells takes place. These interactions facilitate production of abundant proinflammatory cytokines, chemokines and growth factors for the proliferation/maturation/differentiation of B lymphocytes to become plasma cells. Finally, the autoantibodies against denatured immunoglobulin G (rheumatoid factors), EB virus nuclear antigens (EBNAs) and citrullinated protein (ACPAs) are produced to trigger the development of RA. Furthermore, it is documented that gene mutations, abnormal epigenetic regulation of peptidylarginine deiminase genes 2 and 4 (PADI2 and PADI4), and thereby the induced autoantibodies against PAD2 and PAD4 are implicated in ACPA production in RA patients. The aberrant expressions of non-coding RNAs (ncRNAs) including microRNAs (miRs) and long non-coding RNAs (lncRNAs) in the immune system undoubtedly derange the mRNA expressions of cytokines/chemokines/growth factors. In the present review, we will discuss in detail the expression of these ncRNAs and their target molecules participating in developing RA, and the potential biomarkers for the disease, its diagnosis, cardiovascular complications and therapeutic response. Finally, we propose some prospective investigations for unraveling the conundrums of rheumatoid pathogenesis.

GATCDA: Predicting circRNA-Disease Associations Based on Graph Attention Network

CircRNAs (circular RNAs) are a class of non-coding RNA molecules with a closed circular structure. CircRNAs are closely related to the occurrence and development of diseases. Due to the time-consuming nature of biological experiments, computational methods have become a better way to predict the interactions between circRNAs and diseases. In this study, we developed a novel computational method called GATCDA utilizing a graph attention network (GAT) to predict circRNA-disease associations with disease symptom similarity, network similarity, and information entropy similarity for both circRNAs and diseases. GAT learns representations for nodes on a graph by an attention mechanism, which assigns different weights to different nodes in a neighborhood. Considering that the circRNA-miRNA-mRNA axis plays an important role in the generation and development of diseases, circRNA-miRNA interactions and disease-mRNA interactions were adopted to construct features, in which mRNAs were related to 88% of miRNAs. As demonstrated by five-fold cross-validation, GATCDA yielded an AUC value of 0.9011. In addition, case studies showed that GATCDA can predict unknown circRNA-disease associations. In conclusion, GATCDA is a useful method for exploring associations between circRNAs and diseases.

iCircDA-LTR: identification of circRNA-disease associations based on Learning to Rank

MOTIVATION

Due to the inherent stability and close relationship with the progression of diseases, circRNAs are serving as important biomarkers and drug targets. Efficient predictors for identifying circRNA-disease associations are highly required. The existing predictors consider circRNA-disease association prediction as a classification task or a recommendation problem, failing to capture the ranking information among the associations and detect the diseases associated with new circRNAs. However, more and more circRNAs are discovered. Identification of the diseases associated with these new circRNAs remains a challenging task.

RESULTS

In this study, we proposed a new predictor called iCricDA-LTR for circRNA-disease association prediction. Different from any existing predictor, iCricDA-LTR employed a ranking framework to model the global ranking associations among the query circRNAs and the diseases. The Learning to Rank (LTR) algorithm was employed to rank the associations based on various predictors and features in a supervised manner. The experimental results on two independent test datasets showed that iCircDA-LTR outperformed the other competing methods, especially for predicting the diseases associated with new circRNAs. As a result, iCircDA-LTR is more suitable for the real world applications.

AVAILABILITY

For the convenience of researchers to detect new circRNA-disease associations. The web server of iCircDA-LTR was established and freely available at http://bliulab.net/iCircDA-LTR/.

CircASH2L facilitates tumor-like biologic behaviours and inflammation of fibroblast-like synoviocytes via miR-129-5p/HIPK2 axis in rheumatoid arthritis

Background

Previous study showed that circular RNA Absent-Small-Homeotic-2--Like protein (circASH2L) was higher in rheumatoid arthritis (RA) patients. However, the roles and mechanisms of circASH2L in RA progression remain unclear.

Methods

Levels analysis was conducted using western blot and qRT-PCR. The proliferation, apoptosis, cell cycle progression, migration, invasiveness, and inflammation of RA fibroblast-like synoviocytes (RA-FLSs) were determined via MTT, flow cytometry, western blot, transwell, and ELISA assays.

Results

CircASH2L knockdown in RA-FLSs suppressed cell proliferative, migratory, and invasive capacities, triggered cell cycle arrest, promoted apoptosis, and inhibited inflammation. Mechanistically, circASH2L targeted miR-129-5p, and repression of miR-129-5p abolished the functions of circASH2L silencing on the growth, motility, and inflammation of RA-FLSs. Besides, miR-129-5p was found to directly target HIPK2, and suppressed the tumor-like biologic behaviors and inflammation of RA-FLSs via regulating HIPK2. Importantly, we proved that circASH2L could modulate HIPK2 expression via miR-129-5p.

Conclusion

CircASH2L promoted RA-FLS growth, motility, and inflammation through miR-129-5p/HIPK2 axis.

The role of exosomal non-coding RNAs in aging-related diseases

Aging is a biological process caused by the accumulation of senescent cells with a permanent proliferative arrest. To the influence of aging on human life expectancy, there is essential for new biomarkers which possibly will assistance in recognizing age-associated pathologies. Exosomes, which are cell-secreted nanovesicles, make available a new biomarker detection and therapeutic approach for the transfer of different molecules with high capacity. Recently, non-coding RNAs (ncRNA) which are contained in exosomes have developed as important molecules regulating the complexity of aging and relevant human diseases. The discovery of ncRNA provided perceptions into an innovative regulatory platform that could interfere with cellular senescence. The non-coding transcriptome includes a different of RNA species, spanning from short ncRNAs (<200 nucleotides) to long ncRNAs, that are >200 bp long. Upgraded evidence displays that targeting ncRNAs possibly will influence senescence pathways. In this article, we will address ncRNAs that participated in age-related and cellular senescence diseases. Growing conception of ncRNAs in the aging process possibly will be responsible for new understandings into the improvement of age-related diseases and elongated life span.

Promising diagnostic and therapeutic circRNAs for skeletal and chondral disorders

Circular RNAs (circRNAs) belong to a highly conserved subtype of non-coding RNAs, produced by the back-splicing of specific regions of pre-mRNA. CircRNAs have wide-ranging effects on eukaryotic physiology and pathology by acting as transcription regulators, miRNA sponges, protein sponges, and templates for translation. Skeletal and chondral disorders are the leading causes of pain and disability, especially for elders, affecting hundreds of millions of people worldwide. Plenty of evidence have shown that circRNAs are dysregulated and play vital roles in the occurrence and progression of skeletal and chondral disorders. Herein, we systematically summarize the emerging roles and underlying molecular mechanisms of hub circRNAs in the pathogenesis of several representative skeletal and chondral disorders. Our findings may provide further insight into the mechanistic details of the role of circRNA in bone or cartilage metabolism, and highlight the promising application of circRNAs in serving as potential diagnostic or therapeutic targets for the prevention and treatment of skeletal and chondral disorders.

Current Status of Functional Studies on Circular RNAs in Rheumatoid Arthritis and Their Potential Role as Diagnostic Biomarkers

Circular RNAs (circRNAs), a new class of endogenous non-coding RNAs (ncRNAs), are highly stable and exhibit tissue-specific expression. Accumulating evidence has indicated that circRNAs play crucial roles in the development and progression of multiple diseases. Notably, circRNAs, important epigenetic modulators of gene expression in inflammation and autoimmune regulation, have a close association with the pathogenesis of rheumatoid arthritis (RA). RA, one of the most common systemic autoimmune diseases, is characterized by synovial hyperplasia and inflammation, and cartilage and bone destruction. Here, we focus on the roles of circRNAs in macrophage, synovial tissues, fibroblast-like synoviocytes (FLSs), and cartilage tissues in pathogenesis and progression of RA, highlighting the potential of circRNAs in the blood as diagnostic biomarkers, and aiming at providing new insights into the diagnosis and therapy of this disease.

Hsa_circ_0056558 regulates cyclin-dependent kinase 6 by sponging microRNA-1290 to suppress the proliferation and differentiation in ankylosing spondylitis

The aims of this study was to investigate the influences of hsa_circ_0056558/miR-1290/CDK6 axis in ankylosing spondylitis (AS). The differentially expressed has_circ_0056558 and miR-1290 in AS tissue were analysed based on RNA-seq data and microarray data, respectively. qRT-PCR was performed for detection of relative expression levels of hsa_circ_0056558, miR-1290, CDK6, osteogenic differentiation markers (Runx2 and Osterix) and other inflammatory factors (TNF-α, IL-1β, and IL-6). Western blotting analysis was conducted to test the protein levels of CDK6, osteogenic differentiation markers (Runx2 and Osterix), and PI3K/AKT/NF-κB pathway-associated proteins. CCK8 assay and flow cytometry were conducted to determine cell proliferation and cell apoptotic ability, respectively. Targeted relationships were predicted by bioinformatic analysis and verified by dual-luciferase reporter assay. The differentiation of fibroblast cells was analysed by alkaline phosphatase (ALP) activity assay. Our findings revealed that the expression levels of both circ_0056558 and CDK6 in AS tissue were significantly higher than that in normal samples. Besides, hsa_circ_0056558 could suppress cell proliferation and differentiation by facilitating CDK6 expression and suppressing miR-1290 expression in AS. Over-expression of miR-1290 negatively regulated CDK6 expression to enhance cell proliferation. The protein levels of p-AKT, p-NF-κB p65, and p-IκBα were promoted by hsa_circ_0056558 or CDK6 over-expression while suppressed by miR-1290 up-regulation. In conclusion, our study demonstrated that hsa_circ_0056558 and CDK6 suppressed cell proliferation and differentiation while enhanced cell apoptosis by competitive binding to miR-1290 in AS, which might be possibly achieved by PI3K/AKT/NF-κB pathway, providing us novel therapeutic strategy for AS.

Insights Into the Involvement of Circular RNAs in Autoimmune Diseases

Circular RNAs (circRNAs) are single-stranded, endogenous, non-coding RNA (ncRNA) molecules formed by the backsplicing of messenger RNA (mRNA) precursors and have covalently closed circular structures without 5′-end caps and 3′-end polyadenylation [poly(A)] tails. CircRNAs are characterized by abundant species, stable structures, conserved sequences, cell- or tissue-specific expression, and widespread and stable presence in many organisms. Therefore, circRNAs can be used as biomarkers for the prediction, diagnosis, and treatment of a variety of diseases. Autoimmune diseases (AIDs) are caused by defects in immune tolerance or abnormal immune regulation, which leads to damage to host organs. Due to the complexity of the pathophysiological processes of AIDs, clinical therapeutics have been suboptimal. The emergence of circRNAs sheds new light on the treatment of AIDs. In particular, circRNAs mainly participate in the occurrence and development of AIDs by sponging targets. This review systematically explains the formation, function, mechanism, and characteristics of circRNAs in the context of AIDs. With a deeper understanding of the pathophysiological functions of circRNAs in the pathogenesis of AIDs, circRNAs may become reasonable, accurate, and effective biomarkers for the diagnosis and treatment of AIDs in the future.

Circ_0088194 Promotes the Invasion and Migration of Rheumatoid Arthritis Fibroblast-Like Synoviocytes via the miR-766-3p/MMP2 Axis

Dysregulation of circular RNAs (circRNAs) is involved in various human diseases. Fibroblast-like synoviocytes (FLSs), which form the lining of the joint, are epigenetically imprinted with an aggressive phenotype and contribute to joint destruction in rheumatoid arthritis (RA). In the present study, we identified a novel circRNA, Circ_0088194, which was upregulated in RA fibroblast-like synoviocytes (RA-FLSs) and correlated with the disease activity score in 28 joints. Overexpression of Circ_0088194 promoted RA-FLS migration and invasion, while inhibition of Circ_0088194 had the opposite effect. Mechanistically, Circ_0088194 acted as a miR-766-3p sponge to relieve the repressive effect of miR-766-3p on its target, MMP2 (encoding matrix metalloproteinase 2), thereby promoting migration and invasion. The expression level of Circ_0088194 was inversely correlated with that of miR-766-3p in RA-FLSs. Importantly, overexpression of miR-766-3p partially blocked the migration and invasion induced by Circ_0088194 overexpression. Collectively, this study identified a novel circRNA Circ_0088194 that promotes RA-FLS invasion and migration via the miR-766-3p/MMP2 axis. Circ_0088194 might represent a novel therapeutic target to prevent and treat RA.

Expression and clinical significance of circular RNAs related to immunity and inflammation in patients with rheumatoid arthritis

The aim of this study was to investigate the changes in and clinical significance of circular RNAs (circRNAs) expression related to immunity and inflammation in patients with rheumatoid arthritis (RA). We analyzed the circRNAs related to immunity and inflammation in peripheral blood mononuclear cells (PBMCs) from three RA patients and three healthy controls using high-throughput sequencing and bioinformatics analysis. Subsequently, four differentially expressed circRNAs were verified by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR). We selected hsa_circ_0003353 for functional phenotype analysis in fibroblast-like synoviocytes (FLS) according to correlation tests and logistic regression analysis. The results identified and verified the expression of circRNAs (0003353, 0005732, 0072428, 0091685) that were significantly changed in PBMCs from RA patients. ROC analysis suggested that these circRNAs have significant value in RA diagnosis. Spearman analysis revealed that significant relationships between these circRNAs and clinical indicators as well as SPP. The logistic regression analysis showed that clinical indicators and SPP were risk factors for hsa_circ_0003353 expression, which is worthy of further investigation. As predicted, hsa_circ_0003353 had significantly higher expression in RA-FLS. The cell proliferation, migration, invasion, apoptosis, and inflammatory cytokine production of RA-FLS showed significant alterations after hsa_circ_0003353 suppression and overexpression. Our results indicate that hsa_circ_0003353 may play an essential role in promoting immunity, inflammation, synovial invasion, and joint destruction and that hsa_circ_0003353 may act as a biomarker of RA.

CircRNA_103765 acts as a proinflammatory factor via sponging miR-30 family in Crohn's disease

Increasing evidence suggests that circular RNAs (circRNAs) play critical roles in various pathophysiological activities. However, the role of circRNAs in inflammatory bowel disease (IBD) remains unclear. Here we report the potential roles of hsa_circRNA_103765 in regulating cell apoptosis induced by TNF-α in Crohn’s disease (CD). We identify that CircRNA_103765 expression was significantly upregulated in peripheral blood mononuclear cells (PBMCs) of patients with active IBD. A positive correlation with TNF-α significantly enhanced circRNA_103765 expression in CD, which was significantly reversed by anti-TNF-α mAb (infliximab) treatment. In vitro experiments showed that TNF-α could induce the expression of circRNA_103765, which was cell apoptosis dependent, while silencing of circRNA_103765 could protect human intestinal epithelial cells (IECs) from TNF-α-induced apoptosis. In addition, circRNA_103765 acted as a molecular sponge to adsorb the miR-30 family and impair the negative regulation of Delta-like ligand 4 (DLL4). Collectively, CircRNA_103765 is a novel important regulator of the pathogenesis of IBD via sponging miR-30 family-mediated DLL4 expression changes. Blockade of circRNA_103765 could serve as a novel approach for the treatment of IBD patients.

Circ_0000396 inhibits rheumatoid arthritis synovial fibroblast growth and inflammatory response via miR-203/HBP1 axis

Background

Circ_0000396 was found to be down-regulated in the rheumatoid arthritis (RA) patients and had a high diagnostic value. However, the function and mechanisms underlying circ_0000396 in RA progression remain unclear.

Methods

The expression of circ_0000396, microRNA (miR)-203 and HMG-box transcription factor 1 (HBP1) was detected using qRT-PCR and western blot. The proliferative and apoptotic capabilities of rheumatoid arthritis synovial fibroblasts (RASFs) were measured by colony formation, CCK-8, flow cytometry and western blot assays, respectively. The levels of interleukins (IL)-6, IL-1β, IL-8 and tumor necrosis factor-α (TNF-α) were detected using enzyme-linked immunosorbent assay (ELISA). The target correlations between miR-203 and circ_0000396 or HBP1 were validated using pull-down and dual-luciferase reporter assay.

Results

Circ_0000396 was decreased in RA synovial tissues and RASFs, and overexpression of circ_0000396 suppressed cell proliferation, induced cell apoptosis and reduced the release of inflammatory cytokine IL-6, IL-1β, IL-8 and TNF-α in RASFs, while circ_0000396 deletion functioned oppositely. MiR-203 was confirmed to be a target of circ_0000396, and miR-203 reversed the protective effects of circ_0000396 on the dysfunction and inflammation of RASFs. HBP1 was a target of miR-203, and silencing miR-203 inhibited RASFs malignant changes by regulating HBP1. In addition, circ_0000396 could regulate HBP1 by sponging miR-203, and HBP1 decrease attenuated the effects of circ_0000396 on RASF growth and inflammation.

Conclusion

Circ_0000396 inhibited the growth and inflammation in RASFs by regulating miR-203/HBP1 axis, providing a potential therapeutic target for RA.

Biodegradable nanoparticle-assisted and multiplexed imaging of asymmetric RNA expressions in live cells for precise cancer diagnosis and prognosis

The simultaneous imaging of the dynamic expression variations of regulatory RNAs in cells, which remains a major challenge, has important applications in precise disease diagnosis, treatment and prognosis. Here, we describe the establishment of a biodegradable ZnO nanoparticle (NP)-assisted asymmetric amplification approach for the simultaneous imaging of microRNA-21 (miRNA-21) and programmed cell death 4 (PDCD4) mRNA at distinct expression levels in live cells. The DNA signal probe complexes are immobilized on the ZnO NPs and readily delivered into the target cancer cells via the endocytosis pathway. The acidic microenvironment in cancer cells leads to the dissolution of the ZnO NPs to release Zn²⁺ ions and the intracellular miRNA-21 activates the Zn²⁺-dependent DNAzyme to cleave the substrate signal probes with the assistance of the Zn²⁺ cofactor to show green fluorescence for imaging miRNA-21. Meanwhile, the PDCD4 mRNA can displace the other quenched signal probes to generate red fluorescence. Importantly, the PDCD4 mRNA sequences can be recycled and reused by using the DNAzyme-cleaved sequences as the fuel strands through two strand displacement reactions to yield amplified red fluorescence for detecting low levels of PDCD4 mRNA. Moreover, our approach can be used to evaluate the varied expression levels of miRNA-21 and PDCD4 mRNA responsive to different drugs in cells, reflecting its usefulness for precise cancer diagnosis and prognosis upon anticancer drug treatment.

Circular RNAs in Immune Response and Viral Infection

Circular RNAs (circRNAs) are a diverse class of RNAs with varying sizes, cellular abundance, and biological functions. Investigations from the past decade have revealed that circRNAs are ubiquitously found in eukaryotes and have defined the different biological roles of circRNAs to illuminate this previously unrecognized class of molecules. In the context of the immune system, immune responses and immune-related diseases alter circRNA expression. More recently, several oncogenic double-stranded DNA viruses have been found to encode circRNAs. In this review, we summarize the current understanding of circRNAs and their emerging functions in immune regulation and autoimmune disorders, and discuss the identification and potential roles of viral circRNAs during infections. Finally, we present promising areas for future investigations in the nascent field of circRNAs.

Circular RNAs: Promising Biomarkers for Age-related Diseases

Aging is a complex biological process closely linked with the occurrence and development of age-related diseases. Despite recent advances in lifestyle management and drug therapy, the late diagnosis of these diseases causes severe complications, usually resulting in death and consequently impacting social economies. Therefore, the identification of reliable biomarkers and the creation of effective treatment alternatives for age-related diseases are needed. Circular RNAs (circRNAs) are a novel class of RNA molecules that form covalently closed loops capable of regulating gene expression at multiple levels. Several studies have reported the emerging functional roles of circRNAs in various conditions, providing new perspectives regarding cellular physiology and disease pathology. Notably, accumulating evidence demonstrates the involvement of circRNAs in the regulation of age-related pathologies, including cardio-cerebrovascular disease, neurodegenerative disease, cancer, diabetes, rheumatoid arthritis, and osteoporosis. Therefore, the association of circRNAs with these age-related pathologies highlights their potential as diagnostic biomarkers and therapeutic targets for better disease management. Here, we review the biogenesis and function of circRNAs, with a special focus on their regulatory roles in aging-related pathologies, as well as discuss their potential as biological biomarkers and therapeutic targets for these diseases.

CircRNA_09505 aggravates inflammation and joint damage in collagen-induced arthritis mice via miR-6089/AKT1/NF-κB axis

A number of circular RNAs (circRNAs) have been implicated in rheumatoid arthritis (RA) pathogenesis; however, little is known about their function and hidden molecular mechanism in immune and inflammation regulation. We investigated the role and the underlying mechanism of circRNA_09505 in RA in this study. Real-time PCR and fluorescence in situ hybridization (FISH) are adopted to estimate the quantitative expression and localization of circRNA_09505 in macrophages. The altering effect of circRNA_09505 on inflammation is investigated in vitro and in vivo by use of macrophage cell models and collagen-induced arthritis (CIA) mice. Luciferase reporter assay and RNA-binding protein immunoprecipitation (RIP) are used to confirm the circRNA_09505/miR-6089 ceRNA network predicted by bioinformatics analysis. Compared with controls, the expression of circRNA_09505 is upregulated in peripheral blood mononuclear cells (PBMCs) from patients with RA. The proliferation and cell cycle are significantly promoted when circRNA_09505 is upregulated in macrophages, whereas knockdown of circRNA_09505 inhibits macrophage proliferation and cell- cycle progression. Besides, circRNA_09505 can act as a miRNA sponge for miR-6089 in macrophages, and promote the production of TNF-α, IL-6, and IL-12 through ceRNA mechanism. Moreover, AKT1 is a direct target of miR-6089. CircRNA_09505 can promote AKT1 expression by acting as a miR-6089 sponge via IκBα/NF-κB signaling pathway in macrophages. Most interestingly, knockdown of circRNA_09505 significantly alleviates arthritis and inflammation in vivo in CIA mice. These data support the hypothesis that circRNA_09505 can function as a miR-6089 sponge and regulate inflammation via miR-6089/AKT1/NF-κB axis in CIA mice.

New Insight of Circular RNAs in Human Musculoskeletal Diseases

Circular RNAs (circRNAs), a novel group of noncoding RNAs, are present in most eukaryotic cells. Different from messenger RNAs, circRNAs have a covalently closed single-stranded stable structure and often act in cell type and tissue-specific manners, indicating that they can be used as biomarkers. With the advance of high-throughput RNA sequencing technology and bioinformatics, a large number of circRNAs have been identified in association with musculoskeletal diseases, but the functions of most circRNAs have not been clarified. circRNAs regulate biological processes by adsorbing microRNA as "sponges," binding to proteins, acting as transcriptional regulators, and participating in translation of proteins. In this study, we discuss the latest understanding of biogenesis and gene regulatory mechanisms of circRNAs with special emphasis on new targets for musculoskeletal disease diagnosis and clinical treatment.

Circular RNAs associated with a mouse model of concanavalin A-induced autoimmune hepatitis: preliminary screening and comprehensive functional analysis

Without treatment, autoimmune hepatitis (AIH) often leads to cirrhosis, liver failure and, in some cases, death. However, the pathogenesis of AIH remains incompletely understood. Here, we explored the relationship between differentially expressed circular RNAs (DECs) and development of AIH by obtaining an expression profile of DECs in a concanavalin A‐induced AIH mouse model by microarray. In total, we identified 27 DECs; the host genes of these DECs were annotated with 140 Gene Ontology terms and 19 pathways, revealing potential roles in the metabolism of cellular ions and regulation of protein expression, as well as possible involvement in endocytosis and apoptosis. We constructed a circular RNA–microRNA network that was used to infer that a mmu_circ_0001520/mmu‐miR‐193b‐3p/MAPK10 network may be associated with the occurrence of AIH. These findings may help lay the foundation for validation of the potential roles of circular RNAs in AIH.

Circulating Cell-Free Nucleic Acids as Epigenetic Biomarkers in Precision Medicine

The circulating cell-free nucleic acids (ccfNAs) are a mixture of single- or double-stranded nucleic acids, released into the blood plasma/serum by different tissues via apoptosis, necrosis, and secretions. Under healthy conditions, ccfNAs originate from the hematopoietic system, whereas under various clinical scenarios, the concomitant tissues release ccfNAs into the bloodstream. These ccfNAs include DNA, RNA, microRNA (miRNA), long non-coding RNA (lncRNA), fetal DNA/RNA, and mitochondrial DNA/RNA, and act as potential biomarkers in various clinical conditions. These are associated with different epigenetic modifications, which show disease-related variations and so finding their role as epigenetic biomarkers in clinical settings. This field has recently emerged as the latest advance in precision medicine because of its clinical relevance in diagnostic, prognostic, and predictive values. DNA methylation detected in ccfDNA has been widely used in personalized clinical diagnosis; furthermore, there is also the emerging role of ccfRNAs like miRNA and lncRNA as epigenetic biomarkers. This review focuses on the novel approaches for exploring ccfNAs as epigenetic biomarkers in personalized clinical diagnosis and prognosis, their potential as therapeutic targets and disease progression monitors, and reveals the tremendous potential that epigenetic biomarkers present to improve precision medicine. We explore the latest techniques for both quantitative and qualitative detection of epigenetic modifications in ccfNAs. The data on epigenetic modifications on ccfNAs are complex and often milieu-specific posing challenges for its understanding. Artificial intelligence and deep networks are the novel approaches for decoding complex data and providing insight into the decision-making in precision medicine.

Emerging Roles for Noncoding RNAs in Autoimmune Thyroid Disease

Autoimmune thyroid disease (AITD) is one of the most frequent autoimmune disorders. However, the pathogenesis of AITD has not been fully elucidated. Recently, accumulating evidence has demonstrated that abnormal expression of noncoding RNAs (ncRNAs) is closely related to the etiopathogenesis of AITD. microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs) are 3 major groups of ncRNAs that are attracting increasing attention. Herein, we summarized our present knowledge on the role of miRNAs, lncRNAs, and circRNAs in AITD. This review focused on the importance of ncRNAs in development of the most prevalent AITD, such as Hashimoto disease and Graves' diseases. Altogether, the main purpose of this review is to provide new insights in the pathogenesis of AITD and the possibility of developing novel potential therapeutic targets.