Identification and integrated analysis of neuropathic pain-related circular RNA signature

Abstract Background: More and more evidences show that non-coding RNAs are involved in neuropathic pain, however, there are few reports on the regulatory mechanism of competitive endogenous RNA (ceRNA) in neuropathic pain. The purpose of this study is to explore the possible molecular mechanisms of neuropathic pain. Methods: We collected neuropathic pain-related microarray datasets providing expression profile of circular RNAs (circRNAs) and mRNAs from the Gene Expression Omnibus (GEO) and then performed bioinformatics analysis on them. Results: The present study has identified that up-regulated circRNAs primarily regulate the activity of focal adhesion-associated biological processes and down-regulated primarily regulate the activity of metabolic-associated biological processes by means of ceRNAs. Conclusions: Our data suggest that circRNAs may be candidates for pathogenesis in neuropathic pain and may be considered as promising therapeutic targets in the future.

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The effective function of circular RNA in colorectal cancer

Cancer Cell International ◽

10.1186/s12935-021-02196-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Mandana Ameli-Mojarad ◽

Melika Ameli-Mojarad ◽

Mahrooyeh Hadizadeh ◽

Chris Young ◽

Hosna Babini ◽

...

Keyword(s):

Colorectal Cancer ◽

Molecular Mechanisms ◽

Rna Binding ◽

Rna Binding Proteins ◽

Circular Rna ◽

Circular Rnas ◽

Colorectal Tumorigenesis ◽

Non Coding Rnas ◽

Mirna Sponges ◽

Mechanisms Of Development

AbstractColorectal cancer (CRC) is the 3rd most common type of cancer worldwide. Late detection plays role in one-third of annual mortality due to CRC. Therefore, it is essential to find a precise and optimal diagnostic and prognostic biomarker for the identification and treatment of colorectal tumorigenesis. Covalently closed, circular RNAs (circRNAs) are a class of non-coding RNAs, which can have the same function as microRNA (miRNA) sponges, as regulators of splicing and transcription, and as interactors with RNA-binding proteins (RBPs). Therefore, circRNAs have been investigated as specific targets for diagnostic and prognostic detection of CRC. These non-coding RNAs are also linked to metastasis, proliferation, differentiation, migration, angiogenesis, apoptosis, and drug resistance, illustrating the importance of understanding their involvement in the molecular mechanisms of development and progression of CRC. In this review, we present a detailed summary of recent findings relating to the dysregulation of circRNAs and their potential role in CRC.

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Circular RNA Foxo3: A Promising Cancer-Associated Biomarker

Frontiers in Genetics ◽

10.3389/fgene.2021.652995 ◽

2021 ◽

Vol 12 ◽

Author(s):

Tianli Yang ◽

Yang Li ◽

Feng Zhao ◽

Liuhua Zhou ◽

Ruipeng Jia

Keyword(s):

Cancer Diagnosis ◽

Circular Rna ◽

Clinical Applications ◽

Lymphocytic Leukemia ◽

Circular Rnas ◽

Biological Processes ◽

Diagnosis And Prognosis ◽

Forkhead Box ◽

Non Coding Rnas ◽

Downstream Gene Expression

Circular RNAs (circRNAs) are a class of novel non-coding RNAs (ncRNAs). Emerging evidence demonstrates that circRNAs play crucial roles in many biological processes by regulating linear RNA transcription, downstream gene expression and protein or peptide translation. Meanwhile, recent studies have suggested that circRNAs have the potential to be oncogenic or anti-oncogenic and play vital regulatory roles in the initiation and progression of tumors. Circular RNA Forkhead box O3 (circ-Foxo3, hsa_circ_0006404) is encoded by the human FOXO3 gene and is one of the most studied circular RNAs acting as a sponge for potential microRNAs (miRNAs) (Du et al., 2016). Previous studies have reported that circ-Foxo3 is involved in the development and tumorigenesis of a variety of cancers (bladder, gastric, acute lymphocytic leukemia, glioma, etc.). In this review, we summarize the current studies concerning circ-Foxo3 deregulation and the correlative mechanism in various human cancers. We also point out the potential clinical applications of this circRNA as a biomarker for cancer diagnosis and prognosis.

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Hsa_circ_0000673 is down-regulated in gastric cancer and inhibits the proliferation and invasion of tumor cells by targetting miR-532-5p

Bioscience Reports ◽

10.1042/bsr20180538 ◽

2018 ◽

Vol 38 (5) ◽

Cited By ~ 18

Author(s):

Peng Chang ◽

Furong Wang ◽

Yumin Li

Keyword(s):

Gastric Cancer ◽

Molecular Mechanisms ◽

Circular Rnas ◽

Biological Processes ◽

Biological Functions ◽

Mirna Sponge ◽

New Class ◽

Non Coding Rnas ◽

Proliferation And Invasion

Circular RNAs (circRNAs), a new class of endogenous non-coding RNAs, have recently been known to play critical roles in various cellular biological processes, including tumorigenesis, in which they act as an miRNA sponge that regulates gene expression. Thus, revealing the functions of circRNAs in carcinogenesis and cancer development has been of great interest. However, their expression and functions in gastric cancer (GC) development are still largely unknown. Therefore, the present study aimed to identify novel deregulated circRNAs in GC and reveal their biological functions and molecular mechanisms in GC. Quantitative real-time PCR (qRT-PCR) was performed to measure the expression levels of circRNAs in GC tissues, cell lines, and plasma. The MTT assay, colony formation assay, transwell assay, and tumor xenografts in vivo were used to evaluate the effects of circRNAs on the proliferation and invasion of GC. The abovementioned methods coupled with Western blotting were used to investigate the molecular mechanisms. The current study showed that hsa_circ_0000673 was significantly down-regulated in GC. Overexpression of hsa_circ_0000673 inhibited the proliferation and invasion of GC cells. In contrast, hsa_circ_0000673 down-regulation promoted the proliferation and invasion of GC cells. Further studies revealed that hsa_circ_0000673 targetted miR-532-5p and up-regulated the expression of RUNX3. The present study showed that hsa_circ_0000673 was decreased in GC and it exerted tumor-suppressing effects by targetting miR-532-5p and up-regulating RUNX3 expression level. Hsa_circ_0000673 may be a promising diagnosis biomarker and therapeutic target in GC.

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The Roles of circMTO1 in Cancer

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.656258 ◽

2021 ◽

Vol 9 ◽

Author(s):

Wei Liu ◽

Yuanyuan Xiong ◽

Renhua Wan ◽

Renfeng Shan ◽

Jianfeng Li ◽

...

Keyword(s):

Molecular Mechanisms ◽

Malignant Tumors ◽

Circular Rna ◽

Circular Rnas ◽

Biological Functions ◽

Future Prospects ◽

Mitochondrial Trna ◽

Cellular Context ◽

Non Coding Rnas ◽

Translation Optimization

Circular RNAs (circRNAs) are a recently discovered type of covalently-closed circular non-coding RNAs, mainly formed by non-sequential back-splicing of precursor mRNAs (pre-mRNAs). Recent studies have demonstrated that circRNAs can have either oncogenic or tumor-suppressor roles depending on the cellular context. CircRNA mitochondrial tRNA translation optimization 1 (circMTO1), a recently reported circular RNA originating from exons of MTO1 located on chromosome 6q13, was proved to be abnormally expressed in many malignant tumors, such as hepatocellular carcinoma, gastric carcinoma and colorectal cancer, resulting in tumor initiation and progression. However, there are no reviews focusing on the roles of circMTO1 in cancer. Here, we first summarize the main biological characteristics of circMTO1, and then focus on its biological functions and the possible underlying molecular mechanisms. Finally, we summarize the roles of circMTO1 in cancer and discuss future prospects in this area of research.

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Radio-Susceptibility of Nasopharyngeal Carcinoma: Focus on Epstein- Barr Virus, MicroRNAs, Long Non-Coding RNAs and Circular RNAs

Current Molecular Pharmacology ◽

10.2174/1874467213666191227104646 ◽

2020 ◽

Vol 13 (3) ◽

pp. 192-205 ◽

Cited By ~ 2

Author(s):

Fanghong Lei ◽

Tongda Lei ◽

Yun Huang ◽

Mingxiu Yang ◽

Mingchu Liao ◽

...

Keyword(s):

Nasopharyngeal Carcinoma ◽

Regulatory Networks ◽

Epstein Barr Virus ◽

Molecular Mechanisms ◽

Acquired Resistance ◽

Treatment Strategies ◽

Circular Rnas ◽

Barr Virus ◽

Non Coding Rnas ◽

Epstein Barr

Nasopharyngeal carcinoma (NPC) is a type of head and neck cancer. As a neoplastic disorder, NPC is a highly malignant squamous cell carcinoma that is derived from the nasopharyngeal epithelium. NPC is radiosensitive; radiotherapy or radiotherapy combining with chemotherapy are the main treatment strategies. However, both modalities are usually accompanied by complications and acquired resistance to radiotherapy is a significant impediment to effective NPC therapy. Therefore, there is an urgent need to discover effective radio-sensitization and radio-resistance biomarkers for NPC. Recent studies have shown that Epstein-Barr virus (EBV)-encoded products, microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), which share several common signaling pathways, can function in radio-related NPC cells or tissues. Understanding these interconnected regulatory networks will reveal the details of NPC radiation sensitivity and resistance. In this review, we discuss and summarize the specific molecular mechanisms of NPC radio-sensitization and radio-resistance, focusing on EBV-encoded products, miRNAs, lncRNAs and circRNAs. This will provide a foundation for the discovery of more accurate, effective and specific markers related to NPC radiotherapy. EBVencoded products, miRNAs, lncRNAs and circRNAs have emerged as crucial molecules mediating the radio-susceptibility of NPC. This understanding will improve the clinical application of markers and inform the development of novel therapeutics for NPC.

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DEBKS: A Tool to Detect Differentially Expressed Circular RNA

10.1101/2020.10.14.336982 ◽

2020 ◽

Author(s):

Zelin Liu ◽

Huiru Ding ◽

Jianqi She ◽

Chunhua Chen ◽

Weiguang Zhang ◽

...

Keyword(s):

Open Source ◽

Rna Sequencing ◽

Open Source Software ◽

Simulated Data ◽

Circular Rna ◽

Host Gene ◽

Circular Rnas ◽

Biological Processes ◽

Rna Seq ◽

Disease Pathogenesis

AbstractCircular RNAs (circRNAs) are involved in various biological processes and in disease pathogenesis. However, only a small number of functional circRNAs have been identified among hundreds of thousands of circRNA species, partly because most current methods are based on circular junction counts and overlook the fact that circRNA is formed from the host gene by back-splicing (BS). To distinguish between expression originating from BS and that from the host gene, we present DEBKS, a software program to streamline the discovery of differential BS between two rRNA-depleted RNA sequencing (RNA-seq) sample groups. By applying real and simulated data and employing RT-qPCR for validation, we demonstrate that DEBKS is efficient and accurate in detecting circRNAs with differential BS events between paired and unpaired sample groups. DEBKS is available at https://github.com/yangence/DEBKS as open-source software.

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Identification of Potential Biomarkers and Pathways in Neonatal Hypoxic-Ischemic Brain Injury: Based on Bioinformatics Technology

10.21203/rs.3.rs-777916/v1 ◽

2021 ◽

Author(s):

Shangbin Li ◽

Shuangshuang Li ◽

Qian Zhao ◽

Jiayu Huang ◽

Jinfeng Meng ◽

...

Keyword(s):

Signaling Pathways ◽

Gene Expression Omnibus ◽

Biological Processes ◽

Ischemic Brain ◽

Protein Protein Interaction ◽

Immune Mediated ◽

Disability Rate ◽

Potential Biomarker ◽

Microarray Datasets ◽

Cerebral Cortex Tissue

Abstract Background Neonatal hypoxic-ischemic brain damage (HIBD) is one of the most common serious diseases in newborns, with a high mortality and disability rate. This study aims to use the bioinformatics analysis to identify potential hematologic/immune systems tissue-specific genes and related signaling pathways neonatal HIBD.Methods Microarray datasets in HIBD were downloaded from the Gene Expression Omnibus database, and DEGs were identified by R software.Enrichment analyses were performed and protein–protein interaction networks were constructed to understand the functions and enriched pathways of DEGs and to identify central genes and key modules. Results In the cerebral cortex tissue with HIBD, 2598 DEGs were identified, including 2362 up-regulated and 236 down-regulated DEGs. In the blood with HIBD, 1442 DEGs were identified, including 540 up-regulated and 902 down-regulated DEGs. The results of biological processes and KEGG enrichment were very similar in DEGs of the two kinds of tissues, and both involved inflammation, immunity and apoptosis. The common DEGs of the two kinds of tissues also showed similar results in biological processes and KEGG enrichment.and four hematologic/immune system tissues specifically expressed potential biomarker genes were confirmed through a variety of methods, which were verified by GEO datasets and published experimental research. Conclusion The DEGs of HIBD including the potential peripheral biomarkers TYROBP, ITGAM, EGR1 and HMOX1, which may play a role in the pathogenesis of HIBD through inflammation and immune-mediated signaling pathways.

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EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments

Nucleic Acids Research ◽

10.1093/nar/gkaa1076 ◽

2020 ◽

Vol 49 (D1) ◽

pp. D86-D91

Author(s):

Bailing Zhou ◽

Baohua Ji ◽

Kui Liu ◽

Guodong Hu ◽

Fei Wang ◽

...

Keyword(s):

Interaction Network ◽

Circular Rnas ◽

Biological Processes ◽

Drug Resistant ◽

Functional Roles ◽

Visual Interaction ◽

Disease Associations ◽

Non Coding Rnas ◽

Central Database ◽

Data Browsing

Abstract Long non-coding RNAs (lncRNAs) play important functional roles in many diverse biological processes. However, not all expressed lncRNAs are functional. Thus, it is necessary to manually collect all experimentally validated functional lncRNAs (EVlncRNA) with their sequences, structures, and functions annotated in a central database. The first release of such a database (EVLncRNAs) was made using the literature prior to 1 May 2016. Since then (till 15 May 2020), 19 245 articles related to lncRNAs have been published. In EVLncRNAs 2.0, these articles were manually examined for a major expansion of the data collected. Specifically, the number of annotated EVlncRNAs, associated diseases, lncRNA-disease associations, and interaction records were increased by 260%, 320%, 484% and 537%, respectively. Moreover, the database has added several new categories: 8 lncRNA structures, 33 exosomal lncRNAs, 188 circular RNAs, and 1079 drug-resistant, chemoresistant, and stress-resistant lncRNAs. All records have checked against known retraction and fake articles. This release also comes with a highly interactive visual interaction network that facilitates users to track the underlying relations among lncRNAs, miRNAs, proteins, genes and other functional elements. Furthermore, it provides links to four new bioinformatics tools with improved data browsing and searching functionality. EVLncRNAs 2.0 is freely available at https://www.sdklab-biophysics-dzu.net/EVLncRNAs2/.

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CircITCH: A Circular RNA With Eminent Roles in the Carcinogenesis

Frontiers in Oncology ◽

10.3389/fonc.2021.774979 ◽

2021 ◽

Vol 11 ◽

Author(s):

Soudeh Ghafouri-Fard ◽

Tayyebeh Khoshbakht ◽

Mohammad Taheri ◽

Elena Jamali

Keyword(s):

Tumor Suppressor ◽

Circular Rna ◽

Circular Rnas ◽

Protein Coding ◽

Comprehensive Review ◽

Ubiquitin Protein Ligase ◽

Single Study ◽

Non Coding Rnas

Circular RNAs (circRNAs) are a group of long non-coding RNAs with enclosed structure generated by back-splicing events. Numerous members of these transcripts have been shown to affect carcinogenesis. Circular RNA itchy E3 ubiquitin protein ligase (circITCH) is a circRNA created from back splicing events in ITCH gene, a protein coding gene on 20q11.22 region. ITCH has a role as a catalyzer for ubiquitination through both proteolytic and non-proteolytic routes. CircITCH is involved in the pathetiology of cancers through regulation of the linear isoform as well as serving as sponge for several microRNAs, namely miR-17, miR-224, miR-214, miR-93-5p, miR-22, miR-7, miR-106a, miR-10a, miR-145, miR-421, miR-224-5p, miR-197 and miR-199a-5p. CircITCH is also involved in the modulation of Wnt/β-catenin and PTEN/PI3K/AKT pathways. Except from a single study in osteosarcoma, circITCH has been found to exert tumor suppressor role in diverse cancers. In the present manuscript, we provided a comprehensive review of investigations that reported function of circITCH in the carcinogenesis.

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The Role of Non-Coding RNAs in the Sorafenib Resistance of Hepatocellular Carcinoma

Frontiers in Oncology ◽

10.3389/fonc.2021.696705 ◽

2021 ◽

Vol 11 ◽

Author(s):

Xinyao Hu ◽

Hua Zhu ◽

Yang Shen ◽

Xiaoyu Zhang ◽

Xiaoqin He ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Molecular Mechanisms ◽

Vital Role ◽

Circular Rnas ◽

First Line ◽

Advanced Hcc ◽

Chemotherapy Agent ◽

Development Of Resistance ◽

Non Coding Rnas

Hepatocellular carcinoma (HCC) is the second most common cause of cancer-related death. Sorafenib is approved by the U.S. Food and Drug Administration to be a first-line chemotherapy agent for patients with advanced HCC. A portion of advanced HCC patients can benefit from the treatment with sorafenib, but many patients ultimately develop sorafenib resistance, leading to a poor prognosis. The molecular mechanisms of sorafenib resistance are sophisticated and indefinite. Notably, non-coding RNAs (ncRNAs), which include long ncRNAs (lncRNAs), microRNAs (miRNAs) and circular RNAs (circRNAs), are critically participated in the occurrence and progression of tumors. Moreover, growing evidence has suggested that ncRNAs are crucial regulators in the development of resistance to sorafenib. Herein, we integrally and systematically summarized the molecular mechanisms and vital role of ncRNAs impact sorafenib resistance of HCC, and ultimately explored the potential clinical administrations of ncRNAs as new prognostic biomarkers and therapeutic targets for HCC.

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