The bioinformatics toolbox for circRNA discovery and analysis

CircDDX17 inhibits invasive progression of pituitary adenomas by sponging miR-1279 and regulating CADM2 expression

Purpose

Increasing evidence has revealed that circDDX17 plays significant regulatory roles in tumor progression. In the present study, we investigated the role of circDDX17 in pituitary adenomas (PAs).

Methods

Reverse transcription-quantitative PCR was performed to detect the expression of Circular RNA DDX17 (circDDX17), microRNA-1279 (miR-1279), and cell adhesion molecule 2 (CADM2) in PA tissues. Cell abilities of migration and invasion were examined by wound healing and transwell assays. Dual-luciferase reporter, RNA immunoprecipitation, and RNA pull-down assays were applied to confirm the associations among circDDX17, miR-1279, and CADM2. Xenograft tumor experiments were performed to investigate the roles of circDDX17 in vivo.

Results

In the present study, we found that circDDX17 was downregulated in PA tissues correlated with invasion, tumor size, and progression-free survival of patients with PA. Enforced expression of circDDX17 significantly inhibited migration and invasion through miR-1279. Notably, CADM2 was verified as the direct binding target of miR-1279, and silencing the expression of CADM2 reverses the tumor suppressing effects induced by circDDX17 overexpression. We demonstrated that circDDX17 upregulated the expression of CADM2 by sponging miR-1279, which suppressed the invasive biological behaviors of PA.

Conclusion

CircDDX17 may serve as a tumor suppressor and potential promising biomarker and effectively therapeutic target for the management of PA.

Hsa_circ_0137652 Regulates miR-1205/CCNB1 Axis to Accelerate the Malignancy of Breast Cancer

CircRNAs have become a hotspot in tumor research owing to their high stability and specific functions. We investigated the function of hsa_circ_0137652 in the onset and progression of breast cancer (BC). The expression of circ_0137652, miR-1205, and CCNB1 in BC tissues and cell lines were detected using RT-qPCR and/or western blotting. Dual-luciferase reporter and RNA immunoprecipitation chip assays were used to confirm any potential connections between circ_0137652, miR-1205, and CCNB1. CCK-8 and clone formation assays (CFA) were used to measure the proliferation of BC cells. The Transwell assay was used to investigate the migration of BC cells, and the impact of circ_0137652 on BC tumor formation in vivo was validated using animal experiments. RT-qPCR results showed that circ_0137652 and CCNB1 in breast cancer tissues were notably upregulated in normal tissues, whereas miR-1205 was prominently downregulated. After silencing circ_0137652, the growth and migration of BC cells were reduced. Animal experiments showed that circ_0137652 hampers the tumorigenesis of BC cells in vivo. Additionally, we found that circ_0137652 functions as a sponge for miR-1205. Moreover, the miR-1205 inhibitor notably facilitated cell proliferation and migration and attenuated the action of circ_0137652 knockdown. Furthermore, miR-1205 inhibits BC progression by targeting CCNB1. Circ_0137652 controls the miR-1205/CCNB1 axis to induce increased breast cancer malignancy. Our findings suggest that circ_0137652 may be a novel target for BC therapy.

New insight into circRNAs: characterization, strategies, and biomedical applications

Circular RNAs (circRNAs) are a class of covalently closed, endogenous ncRNAs. Most circRNAs are derived from exonic or intronic sequences by precursor RNA back-splicing. Advanced high-throughput RNA sequencing and experimental technologies have enabled the extensive identification and characterization of circRNAs, such as novel types of biogenesis, tissue-specific and cell-specific expression patterns, epigenetic regulation, translation potential, localization and metabolism. Increasing evidence has revealed that circRNAs participate in diverse cellular processes, and their dysregulation is involved in the pathogenesis of various diseases, particularly cancer. In this review, we systematically discuss the characterization of circRNAs, databases, challenges for circRNA discovery, new insight into strategies used in circRNA studies and biomedical applications. Although recent studies have advanced the understanding of circRNAs, advanced knowledge and approaches for circRNA annotation, functional characterization and biomedical applications are continuously needed to provide new insights into circRNAs. The emergence of circRNA-based protein translation strategy will be a promising direction in the field of biomedicine.

Differentially expressed circRNAs in peripheral blood samples as potential biomarkers and therapeutic targets for acute angle-closure glaucoma

Glaucoma is the leading cause of irreversible blindness globally. Circular RNAs (circRNAs) play vital roles in various biological processes as microRNA (miRNA) sponges and, thus, have been investigated as potential biomarkers and therapeutic targets in numerous human diseases. However, the underlying mechanisms of circRNAs in the pathogenesis of glaucoma remain unclear. Therefore, transcriptome sequencing was performed to identify relevant circRNAs in peripheral blood samples from patients with primary angle-closure glaucoma. Bioinformatics analysis was performed to investigate the potential roles of differentially expressed circRNAs (DEcircRNAs) in the pathogenesis of glaucoma. In total, 481 differentially expressed genes in addition to 345 DEcircRNAs were identified in patients with glaucoma. Based on a public database, targeted gene analysis identified 11 DEcircRNAs that potentially regulate the expression of five genes as miRNA sponges in glaucoma. In addition, quantitative reverse transcription PCR analysis verified that expression of the circRNA hsa-circ-0000745 was positively correlated with the expression of NEAT1 as a potential target gene. These results suggest that DEcircRNAs are involved in a gene expression regulatory network related to immune cell function and progression of glaucoma. Thus, DEcircRNAs in peripheral blood are potential biomarkers and therapeutic targets for glaucoma.

Translation of Circular RNAs: Functions of Translated Products and Related Bioinformatics Approaches

Over the past two decades, studies have discovered a special form of alternative splicing (AS) that produces a circular form of RNA. This stands in contrast to normal AS, which produces a linear form of RNA. Although these circRNAs have garnered considerable attention in the scientific community for their biogenesis and functions, the focus of these studies has been on the regulatory role of circRNAs with the assumption that circRNAs are non-coding. As non-coding RNAs, they may regulate mRNA transcription, tumor initiation, and translation by sponging miRNAs and RNA-binding proteins (RBPs). In addition to these regulatory roles of circRNAs, however, recent studies have provided strong evidence for their translation. The translation of circRNAs is expected to have an important role in promoting cancer cell growth and activating molecular pathways related to cancer development. In some cases, the translation of circRNAs is shown to be efficiently driven by an internal ribosome entry site (IRES). The development of a computational tool for identifying and characterizing the translation of circRNAs using high-throughput sequencing and IRES increases identifiable proteins translated from circRNAs. In turn, it has a substantial impact on helping researchers understand the functional role of proteins derived from circRNAs. New web resources for aggregating, cataloging, and visualizing translational information of circRNAs derived from previous studies have been developed. In this paper, general concepts of circRNA, circRNA biogenesis, translation of circRNA, and existing circRNA tools and databases are summarized to provide new insight into circRNA studies.

Circular RNA SMARCA5 inhibits cholangiocarcinoma via microRNA-95-3p/tumor necrosis factor receptor associated factor 3 axis

Enhancing research indicatedthat circular RNA (circRNA) acted a critical part in cholangiocarcinoma (CHOL) development. This research aims to discover the role of circRNA SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a, member 5 (SMARCA5) in CHOL bio-progression, which has been proved to be downregulated in CHOL tissues. In this study, quantitative reverse transcription polymerase chain reaction was used to reveal the level and linkage of circRNA SMARCA5, miRNA-95-3p and TNF receptor-associated factor 3 gene (TRAF3) in CHOL tissues and cancer cells. The target sites of circRNA SMARCA5 and miRNA-95-3p were forecast by Starbase, and Targetscan was conducted to forecast the potential linkage points of TRAF3 and miRNA-95-3p, and which is affirmed by double luciferase reporter assay. CCK-8 and flow cytometry assay was carried to indicate cell viability. And apoptosis-related protein was counted by caspase3 activity and Western blot assay. CircRNA SMARCA5 was downregulated in CHOL cell lines and cancer samples. Besides, over-expression of SMARCA5 inhibited cell growth and promoted apoptotic rate. Dual-luciferase reporter assays presented that miRNA-95-3p could link with circRNA SMARCA5. Moreover, miRNA-95-3p was discovered highly expressed in CHOL. Interference of miRNA-95-3p repressed cell proliferation and raised the apoptosis. Importantly, TRAF3 was validated to be a downstream of miRNA-95-3p. Strengthen of miRNA-95-3p reversed the inhibitory impact of circRNA SMARCA5-plasmid transfection, and the results of miRNA-95-3p inhibitor were reversed by si-TRAF3. CircRNA SMARCA5 is involved in CHOL development by interosculating miRNA-95-3p/TRAF3 axis and may become a novel approach for treating CHOL.

Nd-Mn Molecular Cluster with Searched Targets for Oral Cancer Imaging

In this research, we designed a novel NIR II luminescence imaging probe with targeting effect to accurately track oral squamous cell carcinoma (OSCC) cells. Massive gene expression data were processed by weighted gene co-expression network analysis to establish a network of relationships between genes. After clustering, correlation of clinical information, and gene functional enrichment analysis, MMP1 was predicted to be a biomarker/therapeutic target for OSCC cells. To obtain rare-earth probes with better luminescence in the NIR II region, we adjusted the doping ratio of the rare-earth element (Nd, Gd, Er, and Yb) fraction of the Nd-Mn molecular cluster to optimize its luminescence properties. The results of in vitro targeting experiments showed that Nd-Mn-MMP1Ab can target Cal-27 cells, demonstrating at the cellular level that the MMP1 gene is a biomarker for oral cancer, which also proves that the cancer targets predicted by the bioinformatics approach are correct.

Depletion of circPDSS1 inhibits ITGA11 production to confer cisplatin sensitivity through miR-515-5p in gastric cancer

Chemoresistance limits cisplatin (DDP)-mediated treatment for gastric cancer (GC). Circular RNA (circRNA) acts an important role in chemoresistance. However, the underlying mechanism of circPDSS1 regulating DDP sensitivity in GC remains unclear. The expression patterns of circPDSS1, miR-515-5p and integrin subunit alpha 11 (ITGA11) were analyzed by qRT-PCR. Protein expression was checked by Western blotting analysis. Cell viability was investigated by 3-(4,5-dimethylthazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Cell proliferation was evaluated by colony formation assay and 5-ethynyl-2'-deoxyuridine (EdU) assay. The analysis of cell apoptosis, migration and invasion was performed by flow cytometry analysis and transwell assays. Dual-luciferase reporter assay and RNA immunoprecipitation assay were conducted to identify the associations among circPDSS1, miR-515-5p and ITGA11. In vivo assay was implemented using a xenograft mouse model assay. CircPDSS1 and ITGA11 expression were significantly upregulated, whereas miR-515-5p was downregulated in DDP-resistant GC tissues and cells in comparison with controls. CircPDSS1 depletion reduced DDP resistance, cell proliferation, migration and invasion but induced cell apoptosis in DDP-resistant GC cells. CircPDSS1 directly bound to miR-515-5p. CircPDSS1-mediated actions were dependent on the regulation of miR-515-5p. Besides, miR-515-5p was associated with ITGA11, and circPDSS1 regulated ITGA11 expression by binding to miR-515-5p. Overexpression of miR-515-5p improved DDP sensitivity owing to the downregulation of ITGA11. Further, circPDSS1 mediated DDP sensitivity by regulating miR-515-5p and ITGA11 in vivo. CircPDSS1 conferred DDP resistance through the miR-515-5p/ITGA11 axis in GC cells.

Data Mining of Microarray Datasets in Translational Neuroscience

Data mining involves the computational analysis of a plethora of publicly available datasets to generate new hypotheses that can be further validated by experiments for the improved understanding of the pathogenesis of neurodegenerative diseases. Although the number of sequencing datasets is on the rise, microarray analysis conducted on diverse biological samples represent a large collection of datasets with multiple web-based programs that enable efficient and convenient data analysis. In this review, we first discuss the selection of biological samples associated with neurological disorders, and the possibility of a combination of datasets, from various types of samples, to conduct an integrated analysis in order to achieve a holistic understanding of the alterations in the examined biological system. We then summarize key approaches and studies that have made use of the data mining of microarray datasets to obtain insights into translational neuroscience applications, including biomarker discovery, therapeutic development, and the elucidation of the pathogenic mechanisms of neurodegenerative diseases. We further discuss the gap to be bridged between microarray and sequencing studies to improve the utilization and combination of different types of datasets, together with experimental validation, for more comprehensive analyses. We conclude by providing future perspectives on integrating multi-omics, to advance precision phenotyping and personalized medicine for neurodegenerative diseases.

Expression and function of CCN2-derived circRNAs in chondrocytes

Cellular communication network factor 2 (CCN2) molecules promote endochondral ossification and articular cartilage regeneration, and circular RNAs (circRNAs), which arise from various genes and regulate gene expression by adsorbing miRNAs, are known to be synthesized from CCN2 in human vascular endothelial cells and other types of cells. However, in chondrocytes, not only the function but also the presence of CCN2-derived circRNA remains completely unknown. In the present study, we investigated the expression and function of CCN2-derived circRNAs in chondrocytes. Amplicons smaller than those from known CCN2-derived circRNAs were observed using RT-PCR analysis that could specifically amplify CCN2-derived circRNAs in human chondrocytic HCS-2/8 cells. The nucleotide sequences of the PCR products indicated novel circRNAs in the HCS-2/8 cells that were different from known CCN2-derived circRNAs. Moreover, the expression of several Ccn2-derived circRNAs in murine chondroblastic ATDC5 cells was confirmed and observed to change alongside chondrocytic differentiation. Next, one of these circRNAs was knocked down in HCS-2/8 cells to investigate the function of the human CCN2-derived circRNA. As a result, CCN2-derived circRNA knockdown significantly reduced the expression of aggrecan mRNA and proteoglycan synthesis. Our data suggest that CCN2-derived circRNAs are expressed in chondrocytes and play a role in chondrogenic differentiation. Production and role of CCN2-derived RNAs in chondrocytes.

Triple Amplification Strategy of CHA-PER-DNAzyme for Ultrasensitive Detection of circRNA Associated with Hepatocellular Carcinoma

Biological and clinical studies have indicated that aberrant expression of circMTO1 served as a crucial biomarker for the diagnosis and prognosis of hepatocellular carcinoma (HCC) patients as well as a potential therapeutic target. However, the detection of circRNAs currently faces challenges such as homologous linear RNA interference and low-expression abundance of certain circRNAs. Therefore, we developed a triple amplification method based on catalytic hairpin assembly (CHA) activation by back-splice junction (BSJ), resulting in CHA products that triggered primer exchange reaction to generate DNAzyme. Subsequently, DNAzyme cleaved the fluorescent reporter chain, enabling ultrasensitive detection of hepatocellular carcinoma-associated circMTO1 through the output fluorescence signal. The catalytic hairpin opening sequence within CHA specifically targeted the BSJ sequence in circRNA, thereby avoiding false positive signals observed in circRNA assays due to the recognition of homologous linear RNA molecules. Moreover, this triple amplification method facilitated sensitive detection of circRNA and addressed the issue of low-abundance expression levels associated with circMTO1 in HCC samples. Notably, our newly designed assay for detecting circRNA exhibited a linear range from 1 fM to 100 nM with a detection limit of 0.265 fM. Furthermore, it demonstrated excellent and consistent performance even within complex systems. Our proposed method enabled the specific and sensitive detection of circMTO1 in various cancer cells and blood samples from HCC patients, providing an innovative approach for investigating the role of circRNA in tumorigenesis and development while promoting its clinical application.

Going circular: history, present, and future of circRNAs in cancer

To date, thousands of highly abundant and conserved single-stranded RNA molecules shaped into ring structures (circRNAs) have been identified. CircRNAs are multifunctional molecules that have been shown to regulate gene expression transcriptionally and post-transcriptionally and exhibit distinct tissue- and development-specific expression patterns associated with a variety of normal and disease conditions, including cancer pathogenesis. Over the past years, due to their intrinsic stability and resistance to ribonucleases, particular attention has been drawn to their use as reliable diagnostic and prognostic biomarkers in cancer diagnosis, treatment, and prevention. However, there are some critical caveats to their utility in the clinic. Their circular shape limits their annotation and a complete functional elucidation is lacking. This makes their detection and biomedical application still challenging. Herein, we review the current knowledge of circRNA biogenesis and function, and of their involvement in tumorigenesis and potential utility in cancer-targeted therapy.

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.

LH/hCG Regulation of Circular RNA in Mural Granulosa Cells during the Periovulatory Period in Mice

Ovarian follicles undergo a series of dynamic changes following the ovulatory surge of luteinizing hormone including cumulus expansion, oocyte maturation, ovulation, and luteinization. Post-transcriptional gene regulatory events are critical for mediating LH follicular responses, and among all RNA isoforms, circular RNA (circRNA) is one of the most abundant forms present in cells, yet they remain the least studied. Functionally, circRNA can act as miRNA sponges, protein sponges/decoys, and regulators of transcription and translation. In the context of ovarian follicular development, the identity and roles of circRNA are relatively unknown. In the present study, high throughput RNA sequencing of granulosa cells immediately prior to and 4-h after the LH/hCG surge identified 42,381 circRNA originating from 7712 genes. A total of 54 circRNA were identified as differentially expressed between 0-h and 4-h time points (Fold Change ± 1.5, FDR ≤ 0.1), among them 42 circRNA were upregulated and 12 circRNA were downregulated. All differentially expressed circRNA between the 0-h and 4-h groups were subjected to circinteractome analysis and identified networks of circRNA-protein and circRNA-miRNA were further subjected to "micro-RNA target filter analysis" in Ingenuity Pathway Analyses, which resulted in the identification of miRNA targeted mRNAs. A comparison of these circRNA target mRNAs with LH-induced mRNAs identified Runx2, Egfr, Areg, Sult1el, Cyp19a1, Cyp11a1, and Hsd17b1 as targets of circKif2, circVcan, circMast4, and circMIIt10. These newly identified LH/hCG-induced circRNA, their target miRNA and protein networks provide new insights into the complex interactions associated with periovulatory follicular development.

Advances in the role of epigenetics in homocysteine-related diseases

Homocysteine has a wide range of biological effects. However, the specific molecular mechanism of its pathogenicity is still unclear. The diseases induced by hyperhomocysteinemia (HHcy) are called homocysteine-related diseases. Clinical treatment of HHcy is mainly through folic acid and B-complex vitamins, which are not effective in reducing the associated end point events. Epigenetics is the alteration of heritable genes caused by DNA methylation, histone modification, noncoding RNAs and chromatin remodeling without altering the DNA sequence. In recent years the role of epigenetics in homocysteine-associated diseases has been gradually discovered. This article summarizes the latest evidence on the role of epigenetics in HHcy, providing new directions for its prevention and treatment.

Salidroside suppresses the multiple oncogenic activates and immune escape of lung adenocarcinoma through the circ_0009624-mediated PD-L1 pathway

BACKGROUND

Lung adenocarcinoma (LUAD) is a fatal malignancy all over the world. Salidroside (SAL) is an active component extracted from Rhodiola rosea that has been reported to exert antitumor activity against several human cancers, containing lung adenocarcinoma (LUAD). The purpose of this study was to explore the effect and underlying mechanism of SAL in LUAD.

METHODS

Cell viability, proliferation, migration, and invasion were measured using cell counting kit-8 (CCK-8), 5-ethynyl-2'-deoxyuridine (EdU), and transwell assays. Effects of LUAD cells on the cytotoxicity, percentage, and death of CD8+ cells were detected using lactate dehydrogenase (LDH) and flow cytometry assays. Programmed cell death ligand 1 (PD-L1) protein level was examined using western blot. Circ_0009624, enolase 1 (ENO1), and PD-L1 levels were determined using real-time quantitative polymerase chain reaction (RT-qPCR). The biological role of SAL on LUAD tumor growth was assessed using the xenograft tumor model in vivo.

RESULTS

SAL restrained LUAD cell proliferation, migration, invasion, and immune escape in vitro via modulating PD-L1. Circ_0009624 expression was increased in LUAD. Applying SAL repressed circ_0009624 and PD-L1 expression in LUAD cells. SAL treatment hindered suppressed various oncogenic activates and immune escape of LUAD cells by regulating the circ_0009624/PD-L1 pathway. SAL blocked LUAD xenograft growth in vivo.

CONCLUSION

Applying SAL might constrain malignant phenotypes and immune escape of LUAD cells partially through the circ_0009624-mediated PD-L1 pathway, providing a novel insight for LUAD treatment.

circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging

Motivation

Circular RNAs (circRNAs) are long noncoding RNAs (lncRNAs) often associated with diseases and considered potential biomarkers for diagnosis and treatment. Among other functions, circRNAs have been shown to act as microRNA (miRNA) sponges, preventing the role of miRNAs that repress their targets. However, there is no pipeline to systematically assess the sponging potential of circRNAs.

Results

We developed circRNA-sponging, a nextflow pipeline that (i) identifies circRNAs via backsplicing junctions detected in RNA-seq data, (ii) quantifies their expression values in relation to their linear counterparts spliced from the same gene, (iii) performs differential expression analysis, (iv) identifies and quantifies miRNA expression from miRNA-sequencing (miRNA-seq) data, (v) predicts miRNA binding sites on circRNAs, (vi) systematically investigates potential circRNA-miRNA sponging events, (vii) creates a network of competing endogenous RNAs and (viii) identifies potential circRNA biomarkers. We showed the functionality of the circRNA-sponging pipeline using RNA sequencing data from brain tissues, where we identified two distinct types of circRNAs characterized by a specific ratio of the number of the binding site to the length of the transcript. The circRNA-sponging pipeline is the first end-to-end pipeline to identify circRNAs and their sponging systematically with raw total RNA-seq and miRNA-seq files, allowing us to better indicate the functional impact of circRNAs as a routine aspect in transcriptomic research.

Availability and implementation

https://github.com/biomedbigdata/circRNA-sponging.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

CircRNA: a rising star in leukemia

Non-coding RNA are a class of RNA that lack the potential to encode proteins. CircRNAs, generated by a post-splicing mechanism, are a newly discovered type of non-coding RNA with multi-functional covalent loop structures. CircRNAs may play an important role in the occurrence and progression of tumors. Research has shown that circRNAs are aberrantly expressed in various types of human cancers, including leukemia. In this review, we summarize the expression and function of circRNAs and their impact on different types of leukemia. We also illustrate the function of circRNAs on immune modulation and chemoresistance in leukemia and their impact on its diagnosis and prognosis. Herein, we provide an understanding of recent advances in research that highlight the importance of circRNAs in proliferation, apoptosis, migration, and autophagy in different types of leukemia. Furthermore, circRNAs make an indispensable difference in the modulation of the immunity and chemoresistance of leukemia. Increasing evidence suggests that circRNAs may play a vital role in the diagnostic and prognostic markers of leukemia because of their prominent properties. More detailed preclinical studies on circRNAs are needed to explore effective ways in which they can serve as biomarkers for the diagnosis and prognosis of leukemia in vivo.

Expression Profile and Regulatory Properties of m6A-Modified circRNAs in the Longissimus Dorsi of Queshan Black and Large White Pigs

It is well known that N6-methyladenosine (m6A) is the most abundant modification in linear RNA molecules, but many circRNA molecules have now been found to have a wide range of m6A modification sites as well. However, there are few relevant studies and information on the expression profile and functional regulatory properties of m6A-modified circRNAs (m6A-circRNAs) in longissimus dorsi. In this study, a total of 12 putative m6A-circRNAs were identified and characterized in the longissimus dorsi of Queshan Black and Large White pigs-8 of them were significantly more expressed in the longissimus dorsi of Queshan Black than in Large White pigs, while the other 4 were the opposite. These 12 putative m6A-circRNAs were also found to act as miRNA sponge molecules to regulate fat deposition by constructing the ceRNA regulatory network. Enrichment analysis also revealed that the 12 m6A-circRNAs parent genes and their adsorbed miRNA target genes were widely involved in fat deposition and cell proliferation and differentiation-related pathways, such as the HIF-1 signaling pathway, the pentose phosphate pathway, the MAPK signaling pathway, the glycosphingolipid biosynthesis-lacto and neolacto series, and the TNF signaling pathway, suggesting that the analyzed m6A-circRNAs may be largely involved in the formation of pork quality. These results provide new information to study the regulatory properties of m6A-circRNAs in the formation of pork quality.

Noncoding RNAs in asthmatic airway smooth muscle cells

Asthma is a complex and heterogeneous airway disease caused by genetic, environmental and epigenetic factors treated with hormones and biologics. Irreversible pathological changes to airway smooth muscle cells (ASMCs) such as hyperplasia and hypertrophy can occur in asthmatic patients. Determining the mechanisms responsible is vital for preventing such changes. In recent years, noncoding RNAs (ncRNAs), especially microRNAs, long noncoding RNAs and circular RNAs, have been found to be associated with abnormalities of the ASMCs. This review highlights recent ncRNA research into ASMC pathologies. We present a schematic that illustrates the role of ncRNAs in pathophysiological changes to ASMCs that may be useful in future research in diagnostic and treatment strategies for patients with asthma.

circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging

MOTIVATION

Circular RNAs (circRNAs) are long non-coding RNAs (lncRNAs) often associated with diseases and considered potential biomarkers for diagnosis and treatment. Among other functions, circRNAs have been shown to act as microRNA (miRNA) sponges, preventing the role of miRNAs that repress their targets. However, there is no pipeline to systematically assess the sponging potential of circRNAs.

RESULTS

We developed circRNA-sponging, a nextflow pipeline that (1) identifies circRNAs via backsplicing junctions detected in RNA-seq data, (2) quantifies their expression values in relation to their linear counterparts spliced from the same gene, (3) performs differential expression analysis, (4) identifies and quantifies miRNA expression from miRNA-sequencing (miRNA-seq) data, (5) predicts miRNA binding sites on circRNAs, (6) systematically investigates potential circRNA-miRNA sponging events, (7) creates a network of competing endogenous RNAs, and (8) identifies potential circRNA biomarkers. We showed the functionality of the circRNA-sponging pipeline using RNA sequencing data from brain tissues, where we identified two distinct types of circRNAs characterized by a specific ratio of the number of the binding site to the length of the transcript. The circRNA-sponging pipeline is the first end-to-end pipeline to identify circRNAs and their sponging systematically with raw total RNA-seq and miRNA-seq files, allowing us to better indicate the functional impact of circRNAs as a routine aspect in transcriptomic research.

AVAILABILITY

https://github.com/biomedbigdata/circRNA-sponging Contact: markus.daniel.hoffmann@tum.de; markus.list@tum.de Supplementary Material: Supplementary data are available at Bioinformatic Advances online.

A Unique Circular RNA Expression Pattern in the Peripheral Blood of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Patients

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating disease with obscure aetiology. The underdiagnosis rate of ME/CFS is high due to the lack of diagnostic criteria based on objective markers. In recent years, circRNAs have emerged as potential genetic biomarkers for neurological diseases, including Parkinson's disease and Alzheimer's disease, making them likely to have the same prospect of being biomarkers in ME/CFS. However, despite the extensive amount of research that has been performed on the transcriptomes of ME/CFS patients, all of them are solely focused on linear RNAs, and the profiling of circRNAs in ME/CFS has been completely omitted. In this study, we investigated the expression profiles of circRNAs, comparing ME/CFS patients and controls before and after two sessions of cardiopulmonary exercise longitudinally. In patients with ME/CFS, the number of detected circRNAs was higher compared to healthy controls, indicating potential differences in circRNA expression associated with the disease. Additionally, healthy controls showed an increase in the number of circRNAs following exercise testing, while no similar pattern was evident in ME/CFS patients, further highlighting physiological differences between the two groups. A lack of correlation was observed between differentially expressed circRNAs and their corresponding coding genes in terms of expression and function, suggesting the potential of circRNAs as independent biomarkers in ME/CFS. Specifically, 14 circRNAs were highly expressed in ME/CFS patients but absent in controls throughout the exercise study, indicating a unique molecular signature specific to ME/CFS patients and providing potential diagnostic biomarkers for the disease. Significant enrichment of protein and gene regulative pathways were detected in relation to five of these 14 circRNAs based on their predicted miRNA target genes. Overall, this is the first study to describe the circRNA expression profile in peripheral blood of ME/CFS patients, providing valuable insights into the molecular mechanisms underlying the disease.

Roles of circRNA dysregulation in esophageal squamous cell carcinoma tumor microenvironment

Esophageal squamous cell carcinoma (ESCC) is the most prevalent histological esophageal cancer characterized by advanced diagnosis, metastasis, resistance to treatment, and frequent recurrence. In recent years, numerous human disorders such as ESCC, have been linked to abnormal expression of circular RNAs (circRNAs), suggesting that they are fundamental to the intricate system of gene regulation that governs ESCC formation. The tumor microenvironment (TME), referring to the area surrounding the tumor cells, is composed of multiple components, including stromal cells, immune cells, the vascular system, extracellular matrix (ECM), and numerous signaling molecules. In this review, we briefly described the biological purposes and mechanisms of aberrant circRNA expression in the TME of ESCC, including the immune microenvironment, angiogenesis, epithelial-to-mesenchymal transition, hypoxia, metabolism, and radiotherapy resistance. As in-depth research into the processes of circRNAs in the TME of ESCC continues, circRNAs are promising therapeutic targets or delivery systems for cancer therapy and diagnostic and prognostic indicators for ESCC.

CircRNAs in colorectal cancer: potential biomarkers and therapeutic targets

Globally, colorectal cancer (CRC) is the third most prevalent cancer and the second leading cause of cancer-related deaths. Circular RNAs (circRNAs) are single-stranded RNA with covalently closed-loop structures and are highly stable, conserved, and abundantly expressed in various organs and tissues. Recent research found abnormal circRNA expression in CRC patients' blood/serum, cells, CRC tissues, and exosomes. Furthermore, mounting data demonstrated that circRNAs are crucial to the development of CRC. CircRNAs have been shown to exert biological functions by acting as microRNA sponges, RNA-binding protein sponges, regulators of gene splicing and transcription, and protein/peptide translators. These characteristics make circRNAs potential markers for CRC diagnosis and prognosis, potential therapeutic targets, and circRNA-based therapies. However, further studies are still necessary to improve the understanding of the roles and biological mechanisms of circRNAs in the development of CRC. In this review, up-to-date research on the role of circRNAs in CRC was examined, focusing on their potential application in CRC diagnosis and targeted therapy, which would advance the knowledge of the functions of circRNAs in the development and progression of CRC.

CircEGFR reduces the sensitivity of pirarubicin and regulates the malignant progression of triple-negative breast cancer via the miR-1299/EGFR axis

Circular RNAs (circRNAs) have been found to be involved in cancer progression and chemotherapy sensitivity. However, the biological function of circRNAs in triple-negative breast cancer (TNBC) and its effect on the sensitivity to pirarubicin (THP) chemotherapy are still unclear. CircEGFR (hsa_circ_0080220) was screened and verified by bioinformatics analysis, proving it was highly expressed in TNBC cell lines, patient tissues, and plasma exosomes, and was associated with poor prognosis of patients. The expression level of circEGFR in patient tissue has potential diagnostic value to distinguish TNBC tissue from normal breast tissue. In vitro studies confirmed that overexpression of circEGFR promoted the proliferation, migration, invasion, and EMT of TNBC cells and decreased the sensitivity of THP treatment while silencing circEGFR showed the opposite effect. The circEGFR/miR-1299/EGFR pathway was cascaded and verified. CircEGFR regulated malignant progression of TNBC by regulating EGFR via sponging miR-1299. THP can inhibit the malignant phenotype of MDA-MB-231 cells by downregulating the expression of circEGFR. In vivo studies confirmed that overexpression of circEGFR can promote tumor growth and EMT and reduce tumor sensitivity to THP treatment. Silencing circEGFR inhibited the malignant progression of the tumor. These results revealed circEGFR is a promising biomarker for TNBC diagnosis, therapeutic and prognosis.

Current status and future perspectives in dysregulated miR-492

MicroRNAs (miRNAs) are a class of single-stranded small non-coding RNAs with a length of 21-23 nucleotides. One such miRNA, miR-492, is located in the KRT19 pseudogene 2 (KRT19P2) of chromosome 12q22 and can also be generated from the processing of the KRT19 transcript at chromosome 17q21. Aberrant expression of miR-492 has been observed in cancers of various physiological systems. miR-492 has been shown to target at least 11 protein-coding genes, which are involved in the regulation of cellular behaviors such as growth, cell cycle, proliferation, epithelial- mesenchymal transition (EMT), invasion and migration. The expression of miR-492 can be regulated by both endogenous and exogenous factors. Furthermore, miR-492 is involved in the regulation of several signaling pathways including the PI3K/AKT signaling pathway, WNT/β-catenin signaling pathway, and MAPK signaling pathway. High expression of miR-492 has been closely associated with shorter overall survival in patients with gastric cancer, ovarian cancer, oropharyngeal carcinoma, colorectal cancer, and hepatocellular carcinoma. This study systematically summarizes the related research findings on miR-492, providing potential insights for future investigations.

circRNA_0001006 predicts prognosis and regulates cellular processes of triple-negative breast cancer via miR-424-5p

BACKGROUND

circular RNAs (circRNAs) have been considered novel biomarker candidates for human cancers, such as triple-negative breast cancer (TNBC). circ_0001006 was identified as a differentially expressed circRNA in metastatic breast cancer, but its significance and function in TNBC were unclear. The significance of circ_0001006 in TNBC was assessed and exploring its potential molecular mechanism to provide a therapeutic target for TNBC.

RESULTS

circ_0001006 showed significant upregulation in TNBC and close association with patients' histological grade, Ki67 level, and TNM stage. Upregulated circ_0001006 could predict a worse prognosis and high risk of TNBC patients. In TNBC cells, silencing circ_0001006 suppressed cell proliferation, migration, and invasion. In mechanism, circ_0001006 could negatively regulate miR-424-5p, which mediated the inhibition of cellular processes by circ_0001006 knockdown.

CONCLUSIONS

Upregulated circ_0001006 in TNBC served as a poor prognosis predictor and tumor promoter via negatively regulating miR-424-5p.

Computational approaches for circRNAs prediction and in silico characterization

Circular RNAs (circRNAs) are single-stranded and covalently closed non-coding RNA molecules originated from RNA splicing. Their functions include regulatory potential over other RNA species, such as microRNAs, messenger RNAs and RNA binding proteins. For circRNA identification, several algorithms are available and can be classified in two major types: pseudo-reference-based and split-alignment-based approaches. In general, the data generated from circRNA transcriptome initiatives is deposited on public specific databases, which provide a large amount of information on different species and functional annotations. In this review, we describe the main computational resources for the identification and characterization of circRNAs, covering the algorithms and predictive tools to evaluate its potential role in a particular transcriptomics project, including the public repositories containing relevant data and information for circRNAs, recapitulating their characteristics, reliability and amount of data reported.

Alternative splicing in bladder cancer: potential strategies for cancer diagnosis, prognosis, and treatment

Bladder cancer is the most common malignancy of the urinary tract worldwide. The therapeutic options to tackle this disease comprise surgery, intravesical or systemic chemotherapy, and immunotherapy. Unfortunately, a wide number of patients ultimately become resistant to these treatments and develop aggressive metastatic disease, presenting a poor prognosis. Therefore, the identification of novel therapeutic approaches to tackle this devastating pathology is urgently needed. However, a significant limitation is that the progression and drug response of bladder cancer is strongly associated with its intrinsic molecular heterogeneity. In this sense, RNA splicing is recently gaining importance as a critical hallmark of cancer since can have a significant clinical value. In fact, a profound dysregulation of the splicing process has been reported in bladder cancer, especially in the expression of certain key splicing variants and circular RNAs with a potential clinical value as diagnostic/prognostic biomarkers or therapeutic targets in this pathology. Indeed, some authors have already evidenced a profound antitumor effect by targeting some splicing factors (e.g., PTBP1), mRNA splicing variants (e.g., PKM2, HYAL4-v1), and circular RNAs (e.g., circITCH, circMYLK), which illustrates new possibilities to significantly improve the management of this pathology. This review represents the first detailed overview of the splicing process and its alterations in bladder cancer, and highlights opportunities for the development of novel diagnostic/prognostic biomarkers and their clinical potential for the treatment of this devastating cancer type. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Disease.

CircADAMTS16 Inhibits Differentiation and Promotes Proliferation of Bovine Adipocytes by Targeting miR-10167-3p

Circular RNAs (CircRNAs) are covalently closed-loop non-coding RNA (ncRNA) molecules present in eukaryotes. Numerous studies have demonstrated that circRNAs are important regulators of bovine fat deposition, but their precise mechanisms remain unclear. Previous transcriptome sequencing studies have indicated that circADAMTS16, a circRNA derived from the a disintegrin-like metalloproteinases with the thrombospondin motif 16 (ADAMTS16) gene, is high expressed in bovine adipose tissue. This gives a hint that the circRNA may be involved in the process of bovine lipid metabolism. In this study, the targeting relationship between circADAMTS16 and miR-10167-3p was verified using a dual-luciferase reporter assay. Then, the functions of circADAMTS16 and miR-10167-3p in bovine adipocytes were explored through gain-of-function and lose-of-function. The mRNA expression levels of genes were detected by real-time quantitative PCR (qPCR), and lipid droplet formation was phenotypically evaluated by Oil Red O staining. Cell proliferation and apoptosis were detected using CCK-8, EdU, and flow cytometry. We demonstrated that circADAMTS16 targeted binding to miR-10167-3p. The up-regulation of circADAMTS16 inhibited the differentiation of bovine preadipocytes, and the overexpression of miR-10167-3p promoted the differentiation of bovine preadipocytes. Meanwhile, CCK-8 and EdU results indicated that circADAMTS16 promoted adipocyte proliferation. Subsequently, flow cytometry analysis showed that circADAMTS16 promoted cell transition from G0/G1 phase to S phase, and inhibited cell apoptosis. However, up-regulation of miR-10167-3p inhibited cell proliferation and promoted apoptosis. Briefly, circADAMTS16 inhibited the differentiation and promotes the proliferation of bovine adipocytes by targeting miR-10167-3p during bovine fat deposition, which provides new insights into the mechanism of circRNAs regulation of beef quality.

Circ_0060967 contributes to colorectal cancer progression by sponging miR-1184 to up-regulate SRC proto-oncogene

BACKGROUND AND STUDY AIMS

Circular RNAs (circRNAs) are closely associated with cancer pathogenesis. The purpose of our current study was to explore the role and mechanism of circ_0060967 in colorectal cancer (CRC) development.

PATIENTS AND METHODS

Human CRC specimens and paired healthy tissues were used to examine variable expression. The expression of circ_0060967 and microRNA (miR)-1184 was examined by quantitative reverse transcription-PCR. The protein levels of proliferating cell nuclear antigen, BCL2-associated X, apoptosis regulator (Bax), proto-oncogene nonreceptor tyrosine kinase Src (SRC), nuclear factor-κB inhibitor alpha (IκBα), phosphorylated-IκBα (p-IκBα), RELA proto-oncogene, nuclear factor-κB subunit (p65), and phosphorylated-p65 (p-p65) were determined by western blot. Proliferation and motility of HCT-116 and SW480 CRC cells were assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) and transwell assays, respectively. Dual-luciferase reporter assay and RNA immunoprecipitation assay were used to determine the binding relation between miR-1184 and circ_0060967 or SRC. Animal studies were used to detect the role of circ_0060967 in CRC cell tumorigenicity.

RESULTS

Circ_0060967 abundance was enhanced in human CRC tissue samples versus paired normal colorectal tissues and in HCT-116 and SW480 CRC cells versus normal HCO cells. Decreased expression of circ_0060967 could suppress cell growth, motility, and invasiveness of CRC cells in vitro and tumor growth in vivo. Circ_0060967 sponged miR-1184, and miR-1184 targeted SRC. Furthermore, we also found circ_0060967 affected cell growth by modulating miR-1184/SRC axis in CRC.

CONCLUSION

This study demonstrates a novel circ_0060967/miR-1184/SRC regulatory cascade in affecting CRC cell malignant behaviors, which can have a broad effect on the field of molecularly targeted therapeutics.

Identification of a prognostic biomarker predicting biochemical recurrence and construction of a novel nomogram for prostate cancer

Background

Biochemical recurrence (BCR) is common in prostate cancer (PCa), but its prediction is based predominantly on clinicopathological characteristics with low accuracy. We intend to identify a potential prognostic biomarker related to the BCR and construct a nomogram for improving the risk stratification of PCa patients.

Methods

The transcriptome and clinical data of PCa patients were obtained from TCGA and GEO databases. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were used to screen out differentially expressed genes (DEGs) related to the BCR of PCa. Cox regression analysis was further applied to screen out DEGs related to BCR-free survival (BFS). Time-dependent receiver operating curve (ROC) analysis and Kaplan–Meier (K-M) survival analysis were conducted to assess the prognostic value. Then, a prognostic nomogram was established and evaluated. The clinicopathological correlation analysis, GSEA analysis, and immune analysis were used to explore the biological and clinical significance of the biomarker. Finally, the qRT-PCR, western blotting, and immunohistochemistry (IHC) were conducted to validate the expression of the biomarker.

Results

BIRC5 was identified to be the potential prognostic biomarker. The clinical correlation analysis and K-M survival analysis found that the BIRC5 mRNA expression was positively associated with disease progression and negatively associated with the BFS rate. Time-dependent ROC curves verified its accurate prediction performance. The GSEA and immune analysis suggested that the BIRC5 was related to immunity. A nomogram with an accurate prediction for BFS of PCa patients was constructed. qRT-PCR, western blotting, and IHC results validated the expression level of BIRC5 in PCa cells and tissues.

Conclusion

Our study identified BIRC5 as a potential prognostic biomarker related to BCR of PCa and constructed an efficacy nomogram for predicting BFS to assist clinical decision-making.

Investigating Circular RNAs Using qRT-PCR; Roundup of Optimization and Processing Steps

Circular RNAs (circRNAs) have gained recent attraction due to their functional versatility and particular structure connected to human diseases. Current investigations are focused on the interplay between their ability to sponge smaller species of RNAs, such as microRNAs (miRNAs), thus influencing their regulatory activity on gene expression and protein templates. Therefore, their reported implication in various biological processes axis has resulted in an accumulating number of studies. While the testing and annotation methods of novel circular transcripts are still under development, there is still a plethora of transcript candidates suitable for investigation in human disease. The discordance in the literature regarding the approaches used in circRNAs quantification and validation methods, especially regarding qRT-PCR, the current golden standard procedure, leads to high result variability and undermines the replicability of the studies. Therefore, our study will offer several valuable insights into bioinformatic data for experimental design for circRNA investigation and in vitro aspects. Specifically, we will highlight key aspects such as circRNA database annotation divergent primer design and several processing steps, such as RNAse R treatment optimization and circRNA enrichment assessment. Additionally, we will provide insights into the exploration of circRNA-miRNA interactions, a prerequisite for further functional investigations. With this, we aim to contribute to the methodological consensus in a currently expanding field with possible implications for assessing therapeutic targets and biomarker discovery.

Exosomal Non-Coding RNAs: Novel Regulators of Macrophage-Linked Intercellular Communication in Lung Cancer and Inflammatory Lung Diseases

Macrophages are innate immune cells and often classified as M1 macrophages (pro-inflammatory states) and M2 macrophages (anti-inflammatory states). Exosomes are cell-derived nanovesicles that range in diameter from 30 to 150 nm. Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), are abundant in exosomes and exosomal ncRNAs influence immune responses. Exosomal ncRNAs control macrophage-linked intercellular communication via their targets or signaling pathways, which can play positive or negative roles in lung cancer and inflammatory lung disorders, including acute lung injury (ALI), asthma, and pulmonary fibrosis. In lung cancer, exosomal ncRNAs mediated intercellular communication between lung tumor cells and tumor-associated macrophages (TAMs), coordinating cancer proliferation, migration, invasion, metastasis, immune evasion, and therapy resistance. In inflammatory lung illnesses, exosomal ncRNAs mediate macrophage activation and inflammation to promote or inhibit lung damage. Furthermore, we also discussed the possible applications of exosomal ncRNA-based therapies for lung disorders.

Łabaj P, Mangul S. RNA-seq data science: From raw data to effective interpretation

RNA sequencing (RNA-seq) has become an exemplary technology in modern biology and clinical science. Its immense popularity is due in large part to the continuous efforts of the bioinformatics community to develop accurate and scalable computational tools to analyze the enormous amounts of transcriptomic data that it produces. RNA-seq analysis enables genes and their corresponding transcripts to be probed for a variety of purposes, such as detecting novel exons or whole transcripts, assessing expression of genes and alternative transcripts, and studying alternative splicing structure. It can be a challenge, however, to obtain meaningful biological signals from raw RNA-seq data because of the enormous scale of the data as well as the inherent limitations of different sequencing technologies, such as amplification bias or biases of library preparation. The need to overcome these technical challenges has pushed the rapid development of novel computational tools, which have evolved and diversified in accordance with technological advancements, leading to the current myriad of RNA-seq tools. These tools, combined with the diverse computational skill sets of biomedical researchers, help to unlock the full potential of RNA-seq. The purpose of this review is to explain basic concepts in the computational analysis of RNA-seq data and define discipline-specific jargon.

CircDNAJC11 interacts with TAF15 to promote breast cancer progression via enhancing MAPK6 expression and activating the MAPK signaling pathway

BACKGROUND

Breast cancer (BC) is a common malignant tumor in women worldwide. Circular RNA (circRNA) has been proven to play a critical role in BC progression. However, the exact biological functions and underlying mechanisms of circRNAs in BC remain largely unknown.

METHODS

Here, we first screened for differentially expressed circRNAs in 4 pairs of BC tissues and adjacent non-tumor tissues using a circRNA microarray. Functionally, gain- and loss-of-function experiments in vitro and in vivo showed that circDNAJC11 promoted BC cell proliferation, migration, invasion, and tumor growth. Mechanistically, RNA pull-down, mass spectrum, RNA immunoprecipitation, fluorescence in situ hybridization assays, and rescue experiments were executed.

RESULTS

We found that circDNAJC11 was significantly upregulated in triple-negative breast cancer tissues and cells. Clinical data revealed that the high expression of circDNAJC11 was closely correlated with a poor prognosis of BC patients and could be an independent risk factor for BC prognosis. Functionally, gain- and loss-of-function experiments in vitro and in vivo showed that circDNAJC11 promoted BC cell proliferation, migration, invasion, and tumor growth. Mechanistically, RNA pull-down, mass spectrum, RNA immunoprecipitation, fluorescence in situ hybridization assays, and rescue experiments were executed. We demonstrated that circDNAJC11 combined with TAF15 to promote BC progression via stabilizing MAPK6 mRNA and activating the MAPK signaling pathway.

CONCLUSIONS

The circDNAJC11/TAF15/MAPK6 axis played a crucial role in the progression and development of BC, suggesting that circDNAJC11 might be a novel biomarker and therapeutical target for BC.

Exosomal circular RNAs: A chief culprit in cancer chemotherapy resistance

Chemotherapy is one of the primary treatments for malignant tumors. However, the acquired drug resistance hinders clinical efficacy and leads to treatment failure in most patients. Exosomes are cell-derived vesicles with a diameter of 30-150 nm carrying and delivering substances such as DNAs, RNAs, lipids, and proteins for cellular communication in tumor development. Circular RNAs (circRNAs) present covalently closed-loop RNA structures, which regulate tumor cell proliferation, apoptosis, and metastasis by controlling different genes and signaling pathways. CircRNAs are abundant and stably expressed in exosomes. Recent studies have shown that they play critical roles in chemotherapy resistance in various cancers. In this review, we summarized the origin of exosomes and discussed the regulation mechanism of exosomal circRNAs in cancer drug resistance.

Microarray profiling identifies hsa_circ_0082003 as a novel tumor promoter for papillary thyroid carcinoma

BACKGROUND

Circular RNAs (circRNAs) are non-coding RNAs that have essential regulatory roles in the development of various tumors. This study explored whether circRNAs are involved in the progression of papillary thyroid carcinoma (PTC).

METHODS

Differentially expressed circRNAs (DECs) in four pairs of PTC and matched normal thyroid tissues were screened using a circRNA microarray. The potential functions of dysregulated circRNAs were predicted by bioinformatic analyses. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used to determine hsa_circ_0082003 expression in 80 pairs of PTC and matched normal thyroid tissues. Cell counting kit-8, colony formation, wound healing, and Transwell assays were performed to evaluate the biological functions of hsa_circ_0082003 in PTC cells. The role of hsa_circ_0082003 in PTC tumorigenesis in vivo was validated in nude mice.

RESULTS

In total, 3150 DECs (2317 upregulated and 833 downregulated) were identified. Pathway enrichment analyses indicated that the dysregulated circRNAs may play roles in PTC development. RT-qPCR validation demonstrated that hsa_circ_0082003 expression was significantly increased in PTC tissues and correlated with poor clinicopathological parameters. Receiver operating characteristic curve analysis showed that hsa_circ_0082003 had good performance for diagnosing PTC and judging whether it was accompanied by lymph node metastasis. Knockdown of hsa_circ_0082003 inhibited PTC cell proliferation, migration, and invasion. Tumor formation assays in vivo showed that downregulation of hsa_circ_0082003 significantly suppressed the growth of PTC.

CONCLUSION

Hsa_circ_0082003 may serve as a novel diagnostic biomarker and potential therapeutic target for PTC.

Regulation of Glial Function by Noncoding RNA in Central Nervous System Disease

Non-coding RNAs (ncRNAs) are a class of functional RNAs that play critical roles in different diseases. NcRNAs include microRNAs, long ncRNAs, and circular RNAs. They are highly expressed in the brain and are involved in the regulation of physiological and pathophysiological processes of central nervous system (CNS) diseases. Mounting evidence indicates that ncRNAs play key roles in CNS diseases. Further elucidating the mechanisms of ncRNA underlying the process of regulating glial function that may lead to the identification of novel therapeutic targets for CNS diseases.

Assessing the impacts of various factors on circular RNA reliability

Circular RNAs (circRNAs) are non-polyadenylated RNAs with a continuous loop structure characterized by a non-colinear back-splice junction (BSJ). Although millions of circRNA candidates have been identified, it remains a major challenge for determining circRNA reliability because of various types of false positives. Here, we systematically assess the impacts of numerous factors related to circRNA identification, conservation, biogenesis, and function on circRNA reliability by comparisons of circRNA expression from mock and the corresponding colinear/polyadenylated RNA-depleted datasets based on three different RNA treatment approaches. Eight important indicators of circRNA reliability are determined. The relative contribution to variability explained analyses reveal that the relative importance of these factors in affecting circRNA reliability in descending order is the conservation level of circRNA, full-length circular sequences, supporting BSJ read count, both BSJ donor and acceptor splice sites at the same colinear transcript isoforms, both BSJ donor and acceptor splice sites at the annotated exon boundaries, BSJs detected by multiple tools, supporting functional features, and both BSJ donor and acceptor splice sites undergoing alternative splicing. This study thus provides a useful guideline and an important resource for selecting high-confidence circRNAs for further investigations.

Autophagy-mediated circHIPK2 promotes lipopolysaccharide-induced astrocytic inflammation via SIGMAR1

Circular RNAs (circRNAs) are a subclass of noncoding RNAs and widely involve in the occurrence of multiple human diseases. It is an urgent task to clarify circRNA upstream regulation mechanism and seek their biofunction. Our previous study has confirmed that circular RNA HIPK2 (circHIPK2) promotes astrocyte activation via SIGMAR1, sigma non-opioid intracellular receptor 1, in a mouse model of single high-dose lipopolysaccharide (LPS) injection. However, what mechanism circHIPK2 is regulated by and whether it is involved in the inflammatory response of astrocytes remain unclear. In this study, we reported that circHIPK2 and SIGMAR1 were significantly increased in mouse prefrontal cortex after multiple intraperitoneal injection of LPS, with the elevation of inflammatory mediators. Knockdown circHIPK2 in primary astrocytes suppressed the SIGMAR1 expression and inflammation. Pretreatment of autophagy inducer rapamycin on astrocytes suppressed the circHIPK2 expression and inactivated inflammatory response. These results implied that autophagy inducer rapamycin could suppress astrocytic inflammation by inactivating circHIPK2-SIGMAR1 axis. Autophagy may be a promising upstream administrator of circHIPK2 and therapeutic target for central nervous system inflammation.

Hsa_circ_0001550 impairs decidualization by regulating the proliferation and apoptosis of endometrial stromal cells

RESEARCH QUESTION

What is the molecular function of hsa_circ_0001550 in decidualization?

DESIGN

Human endometrial stromal cells (HESC) were isolated from the endometrium tissues to build an in-vitro decidualization model. Different concentrations of medroxyprogesterone acetate (MPA) were used to observe whether the expression level of hsa_circ_0001550 was related to progesterone. Biological characteristics and distribution of hsa_circ_0001550 were determined by RNase R, actinomycin D (Act D) assay and cytoplasmic/nuclear fraction assay. Then the overexpression of hsa_circ_0001550 was achieved by adenovirus vector. Cell proliferation was determined by Cell Counting Kit-8 (CCK-8) assays. The cell cycle was assessed by flow cytometry analyses. Cell apoptosis was determined by annexin-V/propidium iodide double staining experiment and western blotting.

RESULTS

The expression of hsa_circ_0001550 was decreased in decidua and decidualized HESC (P < 0.001, P = 0.014). Hsa_circ_0001550 is a covalently closed RNA molecule that was verified by RNase R assay and Act D assay (P = 0.012). Nuclear and cytoplasmic separation experiments confirmed that hsa_circ_0001550 was mainly distributed in the cytoplasm. Overexpression of hsa_circ_0001550 inhibited decidualization of HESC (P < 0.0001). Furthermore, overexpression of hsa_circ_0001550 inhibited proliferation by decreasing the number of S phase cells (P = 0.033). Annexin-V/propidium iodide double staining experiment and western blotting revealed that overexpression of hsa_circ_0001550 promoted HESC apoptosis (P < 0.001, P = 0.0139).

CONCLUSIONS

Hsa_circ_0001550 impairs decidualization of HESC. Progesterone decreases the expression of hsa_circ_0001550. The results may provide new insights into the cause of decidualization.

Circular RNAs in and out of Cells: Therapeutic Usages of Circular RNAs

RNAs are versatile molecules that are primarily involved in gene regulation and can thus be widely used to advance the fields of therapeutics and diagnostics. In particular, circular RNAs which are highly stable, have emerged as strong candidates for use on next-generation therapeutic platforms. Endogenous circular RNAs control gene regulatory networks by interacting with other biomolecules or through translation into polypeptides. Circular RNAs exhibit cell-type specific expression patterns, which can be altered in tissues and body fluids depending on pathophysiological conditions. Circular RNAs that are aberrantly expressed in diseases can function as biomarkers or therapeutic targets. Moreover, exogenous circular RNAs synthesized in vitro can be introduced into cells as therapeutic molecules to modulate gene expression networks in vivo. Depending on the purpose, synthetic circular RNA sequences can either be identical to endogenous circular RNA sequences or artificially designed. In this review, we introduce the life cycle and known functions of intracellular circular RNAs. The current stage of endogenous circular RNAs as biomarkers and therapeutic targets is also described. Finally, approaches and considerations that are important for applying the available knowledge on endogenous circular RNAs to design exogenous circular RNAs for therapeutic purposes are presented.

Circular hsa_circ_0020377 regulates KLF7 by targeting miR-194-5p to facilitate tumor cell malignant behaviors and glycolysis in oral squamous cell carcinoma progression

Oral squamous cell carcinoma (OSCC) is a common malignant tumor with high recurrence, metastasis rates, and poor prognosis. Numerous studies discover that circular RNA (circRNA) is closely associated with OSCC progression. Hsa_circ_0020377 has been aberrantly expressed in OSCC, but its role in tumor growth and metastasis remains largely unclear. Hsa_circ_0020377, microRNA-194-5p (miR-194-5p), and Krüppel-like factor 7 (KLF7) contents were determined by real-time quantitative polymerase chain reaction (RT-qPCR). Cell proliferative, cycle progression migration, and invasion were measured using 5-ethynyl-2'-deoxyuridine (EdU), Cell Counting Kit-8 (CCK-8), flow cytometry, wound healing, and Transwell assays. The glycolysis level was detected via specific kits. Cyclin D1, E-cadherin, hexokinase 2 (HK2), and KLF7 protein levels were detected via western blot. Using predicting bioinformatics software, the binding between miR-194-5p and hsa_circ_0020377 or KLF7 was verified using a dual-luciferase reporter and RNA Immunoprecipitation (RIP). Beyond that, a xenograft tumor model was used to analyze the role of hsa_circ_0020377 on tumor cell growth in vivo. Increased hsa_circ_0020377 and KLF7 and reduced miR-194-5p were found in OSCC tissues and cell lines. Loss-of-function experiments proved that hsa_circ_0020377 depletion might block OSCC cell proliferation, cycle progression, migration, invasion, and glycolysis in vitro. In xenograft mouse models, hsa_circ_0020377 silencing might suppress tumor growth. In addition, mechanism research suggested that hsa_circ_0020377 could bind with miR-194-5p and enhance its target gene (KLF7), thereby affecting OSCC development. These results broaden our insights regarding the regulation of OSCC progression via circRNA and act as a reference for future clinical studies in OSCC diagnosis and treatment.

Circular RNA in Retina: A Potential Biomarker and Therapeutic Target

Circular RNA (circRNA) is a newly discovered noncoding RNA, which forms a closed ring with more than 200 bases in length. CircRNA is formed by back splicing of precursor RNA, and its expression abundance in body fluid is up to 10 times that of homologous linear transcripts. Recently, novel activities for circRNA in various diseases have emerged, ranging from cancer therapy and neurodegenerative diseases. Here, we reviewed the literature on the biogenesis of circRNA and its relationship with retinal diseases in recent years. We first described the mechanism, existing form and main function of circRNA. Next, we also pinpoint that circRNA has great value in the diagnosis and treatment of retinal diseases represented by retinoblastoma, retinal degeneration, and diabetic retinopathy. By this review, we hope to explore more possibilities of circRNA in clinical diagnosis and treatment.

DNA Double-Strand Break-Related Competitive Endogenous RNA Network of Noncoding RNA in Bovine Cumulus Cells

(1) Background: DNA double strand breaks (DSBs) are the most serious form of DNA damage that affects oocyte maturation and the physiological state of follicles and ovaries. Non-coding RNAs (ncRNAs) play a crucial role in DNA damage and repair. This study aims to analyze and establish the network of ncRNAs when DSB occurs and provide new ideas for next research on the mechanism of cumulus DSB. (2) Methods: Bovine cumulus cells (CCs) were treated with bleomycin (BLM) to construct a DSB model. We detected the changes of the cell cycle, cell viability, and apoptosis to determine the effect of DSBs on cell biology, and further evaluated the relationship between the transcriptome and competitive endogenous RNA (ceRNA) network and DSBs. (3) Results: BLM increased γH2AX positivity in CCs, disrupted the G1/S phase, and decreased cell viability. Totals of 848 mRNAs, 75 long noncoding RNAs (lncRNAs), 68 circular RNAs (circRNAs), and 71 microRNAs (miRNAs) in 78 groups of lncRNA-miRNA-mRNA regulatory networks, 275 groups of circRNA-miRNA-mRNA regulatory networks, and five groups of lncRNA/circRNA-miRNA-mRNA co-expression regulatory networks were related to DSBs. Most differentially expressed ncRNAs were annotated to cell cycle, p53, PI3K-AKT, and WNT signaling pathways. (4) Conclusions: The ceRNA network helps to understand the effects of DNA DSBs activation and remission on the biological function of CCs.

Protective role of circRNA CCND1 in ulcerative colitis via miR-142-5p/NCOA3 axis

BACKGROUND

Increasing research indicates that circular RNAs (circRNAs) play critical roles in the development of ulcerative colitis (UC). This study aimed to determine the role of circRNA CCND1 in UC bio-progression, which has been shown to be downregulated in UC tissues.

METHODS

Reverse transcription quantitative polymerase chain reaction was used to determine the levels of circRNA CCND1, miR-142-5p, and nuclear receptor coactivator-3 (NCOA3) in UC tissues and in lipopolysaccharide (LPS)-induced Caco-2 cells. Target sites of circRNA CCND1 and miR-142-5p were predicted using StarBase, and TargetScan to forecast potential linkage points of NCOA3 and miR-142-5p, which were confirmed by a double luciferase reporter-gene assay. Cell Counting Kit 8 and flow cytometry assays were performed to assess Caco-2 cell viability and apoptosis. TNF-α, IL-1β, IL-6, and IL-8 were detected using Enzyme-Linked Immunosorbent Assay kits.

RESULTS

CircRNA CCND1 was downregulated in UC clinical samples and LPS-induced Caco-2 cells. In addition, circRNA CCND1 overexpression suppressed LPS-induced apoptosis and inflammatory responses in Caco-2 cells. Dual-luciferase reporter-gene assays showed that miR-142-5p could be linked to circRNA CCND1. Moreover, miR-142-5p was found to be highly expressed in UC, and its silencing inhibited LPS-stimulated Caco-2 cell apoptosis and inflammatory responses. Importantly, NCOA3 was found downstream of miR-142-5p. Overexpression of miR-142-5p reversed the inhibitory effect of circRNA CCND1-plasmid on LPS-stimulated Caco-2 cells, and the effects of miR-142-5p inhibitor were reversed by si-NCOA3.

CONCLUSION

CircRNA CCND1 is involved in UC development by dampening miR-142-5p function, and may represent a novel approach for treating UC patients.

Advances in targeting of miR‑10‑associated lncRNAs/circRNAs for the management of cancer (Review)

With advancements in sequencing technologies, an increasing number of aberrantly expressed long-non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) have been identified in various types of cancer. lncRNAs and circRNAs are now well-established tumor-influencing factors in cancer, driving not only tumor proliferation and invasion, but also cancer progression, drug resistance and metastatic recurrence. The majority of lncRNAs and circRNAs influence cancer progression by targeting microRNAs (miRNAs/miRs). miR-10a and miR-10b, key members of the miR-10 family, have been shown to play important regulatory roles in cell proliferation, differentiation to cancer progression, and development. Manual evaluation and grouping according to different types of competing endogenous RNA and tumor was performed. The review outlined the current state of knowledge on the regulation of miR-10 family-related lncRNAs and circRNAs. The involvement of lncRNAs and circRNAs in the biogenesis, maturation and function of malignant tumors through the miR-10 family, and the key gene targets and signaling cascades that lncRNAs and circRNAs regulate through the miR-10 family were summarized. Based on the findings of this review, it can be hypothesized that lncRNAs and circRNAs targeting the miR-10 family may serve as diagnostic/prognostic markers and/or therapeutic targets for the management of cancer.

Epidemiology and outcomes of hyponatremia in patients with COVID-19-A territory-wide study in Hong Kong

Background

Hyponatremia is common in COVID-19, but its epidemiology and impact on clinical outcomes in relation to different variants, especially the Omicron variant, requires further clarification.

Methods

This was a territory-wide retrospective study to investigate the epidemiology and outcomes of COVID-19 patients with hyponatremia from January 1, 2020 to March 31, 2022 in Hong Kong. The primary outcome was 30-day mortality of patients with COVID-19 and hyponatremia at presentation. Secondary outcomes included rate of hospitalization, intensive care unit (ICU) hospitalization, overall duration of hospitalization, and duration of ICU hospitalization.

Results

A total of 53,415 COVID-19 patients were included for analysis, of which 14,545 (27.2%) had hyponatremia at presentation. 9813 (67.5%), 2821 (19.4%), and 1911 (13.1%) had mild (130 to <135 mmol/L), moderate (125 to <130 mmol/L), and severe hyponatremia (<125 mmol/L) at presentation respectively. Age, male sex, diabetes, active malignancy, white cell count, serum creatinine, hypoalbuminemia, C-reactive protein, and viral loads were independent predictors for hyponatremia in COVID-19 patients (P < 0.001, for all). Hyponatremic patients had increased 30-day mortality (9.7 vs. 5.7%, P < 0.001), prolonged hospitalization (11.9 ± 15.1 days vs. 11.5 ± 12.1 days, P < 0.001), and more ICU admissions (7.0% vs. 3.3%, P < 0.001). Patients diagnosed during the "fifth wave" Omicron BA.2 outbreak had 2.29-fold risk (95% CI 2.02-2.59, P < 0.001) of presenting with hyponatremia compared to other waves.

Conclusion

Hyponatremia is common among COVID-19 patients, and may serve as a prognostic indicator for unfavorable outcomes and increased healthcare utilization in the evolving COVID-19 outbreak.

Identification, biogenesis, function, and mechanism of action of circular RNAs in plants

Circular RNAs (circRNAs) are a class of single-stranded, closed RNA molecules with unique functions that are ubiquitously expressed in all eukaryotes. The biogenesis of circRNAs is regulated by specific cis-acting elements and trans-acting factors in humans and animals. circRNAs mainly exert their biological functions by acting as microRNA sponges, forming R-loops, interacting with RNA-binding proteins, or being translated into polypeptides or proteins in human and animal cells. Genome-wide identification of circRNAs has been performed in multiple plant species, and the results suggest that circRNAs are abundant and ubiquitously expressed in plants. There is emerging compelling evidence to suggest that circRNAs play essential roles during plant growth and development as well as in the responses to biotic and abiotic stress. However, compared with recent advances in human and animal systems, the roles of most circRNAs in plants are unclear at present. Here we review the identification, biogenesis, function, and mechanism of action of plant circRNAs, which will provide a fundamental understanding of the characteristics and complexity of circRNAs in plants.