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Jabeen S, Ahmed N, Rashid F, Lal N, Kong F, Fu Y, Zhang F. Circular RNAs in tuberculosis and lung cancer. Clin Chim Acta 2024; 561:119810. [PMID: 38866175 DOI: 10.1016/j.cca.2024.119810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 06/08/2024] [Accepted: 06/09/2024] [Indexed: 06/14/2024]
Abstract
This review signifies the role of circular RNAs (circRNAs) in tuberculosis (TB) and lung cancer (LC), focusing on pathogenesis, diagnosis, and treatment. CircRNAs, a newly discovered type of non-coding RNA, have emerged as key regulators of gene expression and promising biomarkers in various bodily fluids due to their stability. The current review discusses circRNA biogenesis, highlighting their RNase-R resistance due to their loop forming structure, making them effective biomarkers. It details their roles in gene regulation, including splicing, transcription control, and miRNA interactions, and their impact on cellular processes and diseases. For LC, the review identifies circRNA dysregulation affecting cell growth, motility, and survival, and their potential as therapeutic targets and biomarkers. In TB, it addresses circRNAs' influence on host anti-TB immune responses, proposing their use as early diagnostic markers. The paper also explores the interplay between TB and LC, emphasizing circRNAs as dual biosignatures, and the necessity for differential diagnosis. It concludes that no single circRNA biomarker is universally applicable for both TB and LC. Ultimately, the review highlights the pivotal role of circRNAs in TB and LC, encouraging further research in biomarker identification and therapeutic development concomitant for both diseases.
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Affiliation(s)
- Sadia Jabeen
- Department of Microbiology, Wu Lien Teh Institute, Harbin Medical University, Harbin 150081, China
| | - Niaz Ahmed
- Department of Microbiology, Wu Lien Teh Institute, Harbin Medical University, Harbin 150081, China
| | - Faiqa Rashid
- Department of Bioinformatics And Biosciences, Capital University Of Science & Technology, Islamabad Expressway, Kahuta Road, Zone-V, Islamabad, Pakistan
| | - Nand Lal
- Department of Physiology, School of Biomedical Sciences, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, 150081, China
| | - Fanhui Kong
- Department of Microbiology, Wu Lien Teh Institute, Harbin Medical University, Harbin 150081, China
| | - Yingmei Fu
- Department of Microbiology, Wu Lien Teh Institute, Harbin Medical University, Harbin 150081, China.
| | - Fengmin Zhang
- Department of Microbiology, Wu Lien Teh Institute, Harbin Medical University, Harbin 150081, China; Heilongjiang Key Laboratory of Immunity and Infection, Harbin 150081, China.
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2
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Rajendran P, Sekar R, Abdallah BM, Fathima JH S, Ali EM, Jayaraman S, Abdelsalam SA, Veeraraghavan V. Epigenetic modulation of long noncoding RNA H19 in oral squamous cell carcinoma-A narrative review. Noncoding RNA Res 2024; 9:602-611. [PMID: 38532798 PMCID: PMC10963247 DOI: 10.1016/j.ncrna.2024.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/16/2024] [Accepted: 01/30/2024] [Indexed: 03/28/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) showed a seemingly increasing incidence in the last decade. In India, despite the use of tobacco decreased rapidly, in the past five years, the incidence pattern of OSCC over gender and age showed a drastic shift. About 51 % of the head and neck cancers are not associated with habits. Studies exploring various contributing factors in the incidence of this malignancy have documented. Recently, the epigenetic factors associated with the induction and progression of OSCC were explored. More than 90 % of the human genome is made up of non-coding transcriptome, which believed to be noises. However, these non-coding RNAs were identified to be the major epigenetic modulators, which raises concern over incidence of carcinoma in non-habit patients. H19 is a long non coding RNA which proved to be an effective biomarker in various carcinoma. Its role in oral squamous cell cancer was not investigated in depth. This review discusses in detail the various epigenetic role of H19 in inducing oral carcinogenesis.
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Affiliation(s)
- Peramaiyan Rajendran
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- COMManD, Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Velappanchavadi, Chennai, 600 077, Tamil Nadu, India
| | - Ramya Sekar
- Department of Oral Pathology & Microbiology, Meenakshi Ammal Dental College & Hospital, Alapakkam Main Road, Maduravoyal, Chennai, 95, TN, India
- COMManD, Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Velappanchavadi, Chennai, 600 077, Tamil Nadu, India
| | - Basem M. Abdallah
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Shazia Fathima JH
- COMManD, Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Velappanchavadi, Chennai, 600 077, Tamil Nadu, India
- Department of Oral Pathology and Microbiology, Ragas Dental College and Hospitals, Chennai, 600119, Tamil Nadu, India
| | - Enas M. Ali
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Cairo, 12613, Egypt
| | - Selvaraj Jayaraman
- COMManD, Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Velappanchavadi, Chennai, 600 077, Tamil Nadu, India
| | - Salaheldin Abdelraouf Abdelsalam
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- Department of Zoology, Faculty of Science, Assiut University, Assiut, 71515, Egypt
| | - Vishnupriya Veeraraghavan
- COMManD, Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Velappanchavadi, Chennai, 600 077, Tamil Nadu, India
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Benitez MBM, Navarro YP, Azuara-Liceaga E, Cruz AT, Flores JV, Lopez-Canovas L. Circular RNAs and the regulation of gene expression in diabetic nephropathy (Review). Int J Mol Med 2024; 53:44. [PMID: 38516776 PMCID: PMC10998718 DOI: 10.3892/ijmm.2024.5368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/14/2024] [Indexed: 03/23/2024] Open
Abstract
Circular RNAs (circRNAs) are non‑coding single‑stranded covalently closed RNA molecules that are considered important as regulators of gene expression at the transcriptional and post‑transcriptional levels. These molecules have been implicated in the initiation and progression of multiple human diseases, ranging from cancer to inflammatory and metabolic diseases, including diabetes mellitus and its vascular complications. The present article aimed to review the current knowledge on the biogenesis and functions of circRNAs, as well as their role in cell processes associated with diabetic nephropathy. In addition, novel potential interactions between circRNAs expressed in renal cells exposed to high‑glucose concentrations and the transcription factors c‑Jun and c‑Fos are reported.
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Affiliation(s)
- Maximo Berto Martinez Benitez
- Postgraduate Program in Genomic Sciences, Science and Technology School, Autonomous University of Mexico City, Mexico City, CP 03100, Mexico
| | - Yussel Pérez Navarro
- Postgraduate Program in Genomic Sciences, Science and Technology School, Autonomous University of Mexico City, Mexico City, CP 03100, Mexico
| | - Elisa Azuara-Liceaga
- Postgraduate Program in Genomic Sciences, Science and Technology School, Autonomous University of Mexico City, Mexico City, CP 03100, Mexico
| | - Angeles Tecalco Cruz
- Postgraduate Program in Genomic Sciences, Science and Technology School, Autonomous University of Mexico City, Mexico City, CP 03100, Mexico
| | - Jesús Valdés Flores
- Biochemistry Department, Center for Research and Advanced Studies, National Polytechnic Institute of Mexico, Mexico City, CP 07360, Mexico
| | - Lilia Lopez-Canovas
- Postgraduate Program in Genomic Sciences, Science and Technology School, Autonomous University of Mexico City, Mexico City, CP 03100, Mexico
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Tang M, Rong Y, Liu S, Wu Z, Ma G, Li X, Cai H. Potential role of lncRNA LOXL1-AS1 in human cancer development: a narrative review. Transl Cancer Res 2024; 13:1997-2011. [PMID: 38737681 PMCID: PMC11082674 DOI: 10.21037/tcr-23-1450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 02/29/2024] [Indexed: 05/14/2024]
Abstract
Background and Objective Long non-coding RNAs (lncRNAs) are a group of non-coding RNAs consisting of more than 200 nucleotides that are widely involved in various physiological and pathobiological processes in the body. LncRNA plays a crucial role in tumorigenesis and development with its unique functions, such as playing a role in a variety of biological processes of malignant tumors as a cancer-promoting factor or a cancer-suppressor factor. Lysyl oxidase-like protein 1-antisense RNA1 (LOXL1-AS1) is a novel functional lncRNA recently reported. This article reviews the current findings on the role of LOXL1-AS1 in cancer, and discusses the potential clinical significance and application prospects, in order to provide a theoretical basis and reference for the clinical diagnosis, treatment and screening of prognostic markers for malignant tumors. Methods The PubMed and Embase databases were searched using the keywords "cancer" or "tumor" or "neoplasm" and "LOXL1-AS1" for publications from 2018 to the present. The English literature was searched, with a focus on relevant articles. These articles validated the role and mechanism of LOXL1-AS1 in different cancers. Key Content and Findings LOXL1-AS1 is a recently reported novel lncRNA, which is abnormally expressed and upregulated in more than ten cancers, and is positively correlated with adverse clinical features and poor prognosis in cancer patients. LOXL1-AS1 competently binds to a variety of microRNAs to regulate the expression of downstream target genes and regulate related signaling pathways, including proliferation, migration, invasion and inhibition of malignant biological behaviors such as apoptosis. Conclusions LOXL1-AS1 is expected to become a novel biomarker for cancer diagnosis and treatment, with great potential as an independent prognostic indicator.
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Affiliation(s)
- Mingzheng Tang
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Lanzhou, China
- National Health Council Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, China
| | - Yao Rong
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Lanzhou, China
- National Health Council Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, China
| | - Songhua Liu
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, China
| | - Zhihang Wu
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
| | - Guorong Ma
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
| | - Xiaofeng Li
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
| | - Hui Cai
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Lanzhou, China
- National Health Council Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, China
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
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Sun H, Yuan X, Zhang N, Luo Z, Zhang L, Li X. Screening of hair follicle telogen-associated circRNAs in sheep and construction of their ceRNA network. Genomics 2024; 116:110818. [PMID: 38431032 DOI: 10.1016/j.ygeno.2024.110818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/08/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Sheep breeds with hair-shedding traits have many advantages over non-shedding sheep breeds, not only because of reduced shearing labor and feeding management costs but also because it reduces in vitro parasites and improves adaptability to summer heat stress. The wool of Dorper sheep naturally sheds in spring due to the periodic growth of hair follicles. CircRNAs primarily regulate the morphogenesis of hair follicles through the ceRNA mechanism. In this study, five 2-year-old Dorper ewes with extreme hair-shedding phenotype (S) and three Dorper ewes with non-shedding (N) phenotype were selected for subsequent analyses. For RNA extraction, skin tissues were collected on 27th September 2019 (S1, N1), 3rd January 2020 (S2, N2), and 17th March 2020 (S3, N3), which were then subjected to RNA-seq. RNA-seq technology revealed 20,185 novel circRNAs in the hair follicles of Dorper sheep. Among them, 1450 circRNAs were differentially expressed (DE). Clustering heatmap and expression pattern analyses were performed on DE circRNAs, which indicated 78 circRNAs with T pattern (Telogen, highly expressed in telogen), and the source genes for candidate circRNAs were further screened by functional enrichment analysis, which identified 13 crucial genes enriched in pathways associated with hair follicle development. Additionally, a ceRNA regulatory network comprising 4 circRNAs, 11 miRNAs, and 13 target genes was constructed. Overall, this study screened circRNAs that may be associated with the telogen phase of hair follicles in sheep, providing a relevant theoretical basis for wool shedding in sheep and for breeding Dorper sheep with automatic wool shedding.
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Affiliation(s)
- Haoran Sun
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, Ningxia, China
| | - Xiaochun Yuan
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, Ningxia, China
| | - Ningyue Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, Ningxia, China
| | - Zhongze Luo
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, Ningxia, China
| | - Liang Zhang
- Ningxia China Animal Husbandry Yilin Livestock Co., Ltd., Yinchuan 750021, Ningxia, China
| | - Xinhai Li
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, Ningxia, China.
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Gerhards K, Becker S, Kuehling J, Lechner M, Bathke J, Willems H, Reiner G. GWAS reveals genomic associations with swine inflammation and necrosis syndrome. Mamm Genome 2023; 34:586-601. [PMID: 37526658 PMCID: PMC10627913 DOI: 10.1007/s00335-023-10011-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/18/2023] [Indexed: 08/02/2023]
Abstract
The recently identified swine inflammation and necrosis syndrome (SINS) occurs in high prevalence from newborn piglets to fattening pigs and resembles an important concern for animal welfare. The primary endogenous syndrome affects the tail, ears, teats, coronary bands, claws and heels. The basis of clinical inflammation and necrosis has been substantiated by histopathology, metabolomic and liver transcriptomic. Considerable variation in SINS scores is evident in offspring of different boars under the same husbandry conditions. The high complexity of metabolic alterations and the influence of the boar led to the hypothesis of a polygenic architecture of SINS. This should be investigated by a genome-wide association study. For this purpose, 27 sows were simultaneously inseminated with mixed semen from two extreme boars. The mixed semen always contained ejaculate from a Pietrain boar classified as extremely SINS susceptible and additionally either the ejaculate from a Pietrain boar classified as SINS stable or from a Duroc boar classified as SINS stable. The 234 piglets were phenotyped on day 3 of life, sampled and genetically assigned to the respective boar. The piglets showed the expected genetic differentiation with respect to SINS susceptibility. The suspected genetic complexity was confirmed both in the number and genome-wide distribution of 221 significantly associated SNPs, and led to 49 candidate genes. As the SNPs were almost exclusively located in noncoding regions, functional nucleotides have not yet been identified. The results suggest that the susceptibility of piglets to SINS depends not only on environmental conditions but also on genomic variation.
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Affiliation(s)
- Katharina Gerhards
- Department of Veterinary Clinical Sciences, Clinic for Swine, Justus Liebig University Giessen, Frankfurter Strasse 112, 35392, Giessen, Germany
| | - Sabrina Becker
- Department of Veterinary Clinical Sciences, Clinic for Swine, Justus Liebig University Giessen, Frankfurter Strasse 112, 35392, Giessen, Germany
| | - Josef Kuehling
- Department of Veterinary Clinical Sciences, Clinic for Swine, Justus Liebig University Giessen, Frankfurter Strasse 112, 35392, Giessen, Germany
| | | | - Jochen Bathke
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Ludwigstraße 21, 35390, Giessen, Germany
| | - Hermann Willems
- Department of Veterinary Clinical Sciences, Clinic for Swine, Justus Liebig University Giessen, Frankfurter Strasse 112, 35392, Giessen, Germany
| | - Gerald Reiner
- Department of Veterinary Clinical Sciences, Clinic for Swine, Justus Liebig University Giessen, Frankfurter Strasse 112, 35392, Giessen, Germany.
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Zhang LT, Yang YF, Chen XM, Wang SB, Tong GL. IL23R as an indicator of immune infiltration and poor prognosis in intrahepatic cholangiocarcinoma: a bioinformatics analysis. Transl Cancer Res 2023; 12:2461-2476. [PMID: 37969393 PMCID: PMC10643953 DOI: 10.21037/tcr-23-455] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 09/01/2023] [Indexed: 11/17/2023]
Abstract
Background Although the incidence of intrahepatic cholangiocarcinoma (CHOL) is low, the prognosis is very poor. The expression level of interleukin 23 receptor (IL23R) is linked to the occurrence and development of cancers. This study aimed to identify the role of IL23R in CHOL using bioinformatics tools and experimental validation. Methods Circular RNA (circRNA), microRNA (miRNA), and messenger RNA (mRNA) datasets were obtained from the Gene Expression Omnibus (GEO) database, and R software was used for data analysis and visualization. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to conduct functional enrichment analysis, which was verified with gene set enrichment analysis software. Clinical data were obtained from The Cancer Genome Atlas (TCGA), and survival analyses were performed using the DriverDBv3 database and the Gene Expression Profiling Interactive Analysis website. The TIMER2.0 database provided us for immune cell infiltration analysis results of IL23R. Real-time quantitative polymerase chain reaction (RT-qPCR) was used for IL23R expression verification. Results Differentially expressed (DE) mRNAs were enriched in phosphoinositide 3-kinase-serine/threonine kinase signaling pathway, immune-related tumor microenvironment (TME), and amino acid metabolism, etc. In addition, expression of IL23R was associated with immune infiltration-related cells. Furthermore, a circRNA-miRNA-IL23R network and a IL23R protein-protein interaction network were established. Most importantly, IL23R, as a prognostic gene, was found to have a low expression in CHOL. Conclusions A circRNA-miRNA-IL23R network was identified, and it was found that IL23R may be a prognostic and immune-related biomarker in CHOL, which is worthy of further exploration.
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Affiliation(s)
- Lin-Ting Zhang
- Shantou University Medical College, Shantou, China
- Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Cancer Institute of Shenzhen-Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, China
| | - Yi-Fan Yang
- Shantou University Medical College, Shantou, China
- Department of Interventional Radiology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiao-Ming Chen
- Department of Interventional Radiology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Shu-Bin Wang
- Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Cancer Institute of Shenzhen-Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, China
| | - Gang-Ling Tong
- Shantou University Medical College, Shantou, China
- Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Cancer Institute of Shenzhen-Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, China
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Wang K, Wang H, Zhang Q, Liu F. KNOCKDOWN OF CIRC_0001379 ATTENUATES HYPOXIA/REOXYGENATION-INDUCED CARDIOMYOCYTE APOPTOSIS AND INFLAMMATORY RESPONSE BY MIR-98-5P/SOX6 AXIS. Shock 2023; 60:410-418. [PMID: 37493583 DOI: 10.1097/shk.0000000000002178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
ABSTRACT Background: Aberrant expression of circular RNAs (circRNAs) has been revealed to have crucial roles in the pathological processes of cardiovascular disease. Here, this study aimed to investigate the role and mechanism of circ_0001379 in hypoxia/reoxygenation (H/R)-induced cardiomyocyte injury to explore the potential action of circ_0001379 in acute myocardial infarction (AMI). Methods: Levels of genes and proteins were examined by quantitative real-time polymerase chain reaction and western blot. Cell counting kit-8 assay, 5-ethynyl-2'-deoxyuridine assay, and flow cytometry were used to detect cardiomyocyte proliferation and apoptosis, respectively. The activity of IL-1β, IL-6, and TNF-α was determined by ELISA analysis. The target relationship between miR-98-5p and circ_0001379 or SOX6 (SRY-Box Transcription Factor 6) was verified by dual-luciferase reporter and RNA immunoprecipitation assays. Results: Circ_0001379 was highly expressed in AMI mouse model and H/R-induced cardiomyocytes. Functionally, circ_0001379 silencing attenuated H/R-evoked cardiomyocyte apoptosis and inflammatory response. Mechanistically, circ_0001379 functioned as a sponge for miR-98-5p, which directly targeted SOX6. Moreover, circ_0001379 could regulate SOX6 expression via sponging miR-98-5p. Further rescue experiments showed that inhibition of miR-98-5p reversed the protective effects of circ_0001379 silencing on H/R-induced cardiomyocytes. Besides that, miR-98-5p overexpression abolished H/R-evoked cardiomyocyte apoptosis and inflammatory response, while this condition was abated by SOX6. Conclusion: Circ_0001379 silencing protects cardiomyocytes from H/R-induced apoptosis and inflammatory response by miR-98-5p/SOX6 axis, suggesting a novel therapeutic strategy for AMI prevention.
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Affiliation(s)
- Kun Wang
- Department of Cardiovascular Medicine, General Hospital of Tisco (Sixth Hospital of Shanxi Medical University), Taiyuan City, China
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Barbagallo C, Stella M, Ferrara C, Caponnetto A, Battaglia R, Barbagallo D, Di Pietro C, Ragusa M. RNA-RNA competitive interactions: a molecular civil war ruling cell physiology and diseases. EXPLORATION OF MEDICINE 2023:504-540. [DOI: 10.37349/emed.2023.00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/02/2023] [Indexed: 09/02/2023] Open
Abstract
The idea that proteins are the main determining factors in the functioning of cells and organisms, and their dysfunctions are the first cause of pathologies, has been predominant in biology and biomedicine until recently. This protein-centered view was too simplistic and failed to explain the physiological and pathological complexity of the cell. About 80% of the human genome is dynamically and pervasively transcribed, mostly as non-protein-coding RNAs (ncRNAs), which competitively interact with each other and with coding RNAs generating a complex RNA network regulating RNA processing, stability, and translation and, accordingly, fine-tuning the gene expression of the cells. Qualitative and quantitative dysregulations of RNA-RNA interaction networks are strongly involved in the onset and progression of many pathologies, including cancers and degenerative diseases. This review will summarize the RNA species involved in the competitive endogenous RNA network, their mechanisms of action, and involvement in pathological phenotypes. Moreover, it will give an overview of the most advanced experimental and computational methods to dissect and rebuild RNA networks.
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Affiliation(s)
- Cristina Barbagallo
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Michele Stella
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | | | - Angela Caponnetto
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Rosalia Battaglia
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Davide Barbagallo
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Cinzia Di Pietro
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Marco Ragusa
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
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Hoffmann M, Schwartz L, Ciora OA, Trummer N, Willruth LL, Jankowski J, Lee HK, Baumbach J, Furth PA, Hennighausen L, List M. circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging. BIOINFORMATICS ADVANCES 2023; 3:vbad093. [PMID: 37485422 PMCID: PMC10359604 DOI: 10.1093/bioadv/vbad093] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023]
Abstract
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.
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Affiliation(s)
| | | | | | - Nico Trummer
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising D-85354, Germany
| | - Lina-Liv Willruth
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising D-85354, Germany
| | - Jakub Jankowski
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jan Baumbach
- Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Computational BioMedicine Lab, University of Southern Denmark, Odense, Denmark
| | - Priscilla A Furth
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA
| | - Lothar Hennighausen
- Institute for Advanced Study, Technical University of Munich, Garching D-85748, Germany
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Markus List
- To whom correspondence should be addressed. or
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11
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Zhou B, Xue J, Wu R, Meng H, Li R, Mo Z, Zhai H, Chen X, Liu R, Lai G, Chen X, Li T, Zheng S. CREBZF mRNA nanoparticles suppress breast cancer progression through a positive feedback loop boosted by circPAPD4. J Exp Clin Cancer Res 2023; 42:138. [PMID: 37264406 DOI: 10.1186/s13046-023-02701-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/08/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Breast cancer (BC) negatively impacts the health of women worldwide. Circular RNAs (circRNAs) are a group of endogenous RNAs considered essential regulatory factor in BC tumorigenesis and progression. However, the underlying molecular mechanisms of circRNAs remain unclear. METHODS Expression levels of circPAPD4, miR-1269a, CREBZF, and ADAR1 in BC cell lines and tissues were measured using bioinformatics analysis, RT-qPCR, ISH, and IHC. Cell proliferation and apoptosis were measured using CCK8, EdU staining, flow cytometry, and TUNEL assays. Pearson correlation analysis, RNA pull-down, dual-luciferase reporter, and co-immunoprecipitation assays were used to explore the correlation among circPAPD4, miR-1269a, CREBZF, STAT3, and ADAR1. Effects of circPAPD4 overexpression on tumor progression were investigated using in vivo assays. Moreover, CREBZF mRNA delivered by polymeric nanoparticles (CREBZF-mRNA-NPs) was used to examine application value of our findings. RESULTS CircPAPD4 expression was low in BC tissues and cells. Functionally, circPAPD4 inhibited proliferation and promoted apoptosis in vitro and in vivo. Mechanistically, circPAPD4 biogenesis was regulated by ADAR1. And circPAPD4 promoted CREBZF expression by competitively binding to miR-1269a. More importantly, CREBZF promoted circPAPD4 expression by suppressing STAT3 dimerization and ADAR1 expression, revealing a novel positive feedback loop that curbed BC progression. Systematic delivery of CREBZF-mRNA-NPs effectively induced CREBZF expression and activated the positive feedback loop of circPAPD4/miR-1269a/CREBZF/STAT3/ADAR1, which might suppress BC progression in vitro and in vivo. CONCLUSION Our findings firstly illustrated that circPAPD4/miR-1269a/CREBZF/STAT3/ADAR1 positive feedback loop mediated BC progression, and delivering CREBZF mRNA nanoparticles suppressed BC progression in vitro and in vivo, which might provide novel insights into therapeutic strategies for breast cancer.
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Affiliation(s)
- Boxuan Zhou
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330000, China
- Department of Breast Surgery, The First Affiliated Hospital of Gannan Medical University, Gannan Medical University, Ganzhou, 341000, China
| | - Jinhua Xue
- Department of Physiology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, 341000, China
| | - Runxin Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Hongyu Meng
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Ruixi Li
- Department of Hepatobiliary and Pancreatic Surgery, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Zhaohong Mo
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Hang Zhai
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Xianyu Chen
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Rongqiang Liu
- Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Guie Lai
- Department of Breast Surgery, The First Affiliated Hospital of Gannan Medical University, Gannan Medical University, Ganzhou, 341000, China
| | - Xiaohong Chen
- Department of Laboratory, The First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China.
| | - Taiyuan Li
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330000, China.
| | - Shiyang Zheng
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330000, China.
- Department of Head and Neck surgery, Cancer Center of Guangzhou Medical University, Guangzhou, 510060, China.
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12
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Gopikrishnan M, R HC, R G, Ashour HM, Pintus G, Hammad M, Kashyap MK, C GPD, Zayed H. Therapeutic and diagnostic applications of exosomal circRNAs in breast cancer. Funct Integr Genomics 2023; 23:184. [PMID: 37243750 DOI: 10.1007/s10142-023-01083-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/29/2023]
Abstract
Circular RNAs (circRNAs) are regulatory elements that are involved in orchestrating gene expression and protein functions and are implicated in various biological processes including cancer. Notably, breast cancer has a significant mortality rate and is one of the most common malignancies in women. CircRNAs have been demonstrated to contribute to the pathogenesis of breast cancer including its initiation, progression, metastasis, and resistance to drugs. By acting as miRNA sponges, circRNAs can indirectly influence gene expression by disrupting miRNA regulation of their target genes, ultimately altering the course of cancer development and progression. Additionally, circRNAs can interact with proteins and modulate their functions including signaling pathways involved in the initiation and development of cancer. Recently, circRNAs can encode peptides that play a role in the pathophysiology of breast cancer and other diseases and their potential as diagnostic biomarkers and therapeutic targets for various cancers including breast cancer. CircRNAs possess biomarkers that differentiate, such as stability, specificity, and sensitivity, and can be detected in several biological specimens such as blood, saliva, and urine. Moreover, circRNAs play an important role in various cellular processes including cell proliferation, differentiation, and apoptosis, all of which are integral factors in the development and progression of cancer. This review synthesizes the functions of circRNAs in breast cancer, scrutinizing their contributions to the onset and evolution of the disease through their interactions with exosomes and cancer-related intracellular pathways. It also delves into the potential use of circRNA as a biomarker and therapeutic target against breast cancer. It discusses various databases and online tools that offer crucial circRNA information and regulatory networks. Lastly, the challenges and prospects of utilizing circRNAs in clinical settings associated with breast cancer are explored.
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Affiliation(s)
- Mohanraj Gopikrishnan
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India
| | - Hephzibah Cathryn R
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India
| | - Gnanasambandan R
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India
| | - Hossam M Ashour
- Department of Integrative Biology, College of Arts and Sciences, University of South Florida, St. Petersburg, Florida, 33701, USA
| | - Gianfranco Pintus
- Department of Biomedical Sciences, University of Sassari, 07100, Sassari, Italy
| | - Mohamed Hammad
- Department of Stem Cell Biology and Regenerative Medicine, City of Hope Beckman Research Institute, Duarte, California, USA
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Manesar (Gurugram), Panchgaon, Haryana (HR), 122413, India
- Clinical Biosamples & Research Services (CBRS), Noida, Uttar Pradesh, 201301, India
| | - George Priya Doss C
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India.
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, 2713, Doha, Qatar.
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13
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Han Z, Mou Z, Jing Y, Jiang R, Sun T. CircSmox knockdown alleviates PC12 cell apoptosis and inflammation in spinal cord injury by miR-340-5p/Smurf1 axis. Immun Inflamm Dis 2023; 11:e824. [PMID: 37102659 PMCID: PMC10091371 DOI: 10.1002/iid3.824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/27/2022] [Accepted: 03/09/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Spinal cord injury (SCI) is a traumatic central nervous system disorder that leads to irreversible neurological dysfunction. Emerging evidence has shown that differentially expressed circular RNAs (circRNAs) after SCI is closely associated with the pathophysiological process. Herein, the potential function of circRNA spermine oxidase (circSmox) in functional recovery after SCI was investigated. METHODS Differentiated PC12 cells stimulated with lipopolysaccharide (LPS) were employed as an in vitro model for neurotoxicity research. Levels of genes and proteins were detected by quantitative real-time PCR and Western blot analysis. Cell viability and apoptosis were determined by CCK-8 assay and flow cytometry. Western blot analysis was used to detect the protein level of apoptosis-related markers. The levels of interleukin (IL)-1β, IL-6, IL-8, and tumor necrosis factor (TNF)-α. Dual-luciferase reporter, RIP, and pull-down assays were used to confirm the target relationship between miR-340-5p and circSmox or Smurf1 (SMAD Specific E3 Ubiquitin Protein Ligase 1). RESULTS LPS elevated the levels of circSmox and Smurf1, but decreased the levels of miR-340-5p in PC12 cells in a dose-dependent manner. Functionally, circSmox silencing alleviated LPS-induced apoptosis and inflammation in PC12 cells in vitro. Mechanistically, circSmox directly sponged miR-340-5p, which targeted Smurf1. Rescue experiments showed that miR-340-5p inhibition attenuated the neuroprotective effect of circSmox siRNA in PC12 cells. Moreover, miR-340-5p suppressed LPS-triggered neurotoxicity in PC12 cells, which was reversed by Smurf1 overexpression. CONCLUSION CircSmox enhances LPS-induced apoptosis and inflammation via miR-340-5p/Smurf1 axis, providing an exciting view of the potential involvement of circSmox in SCI pathogenesis.
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Affiliation(s)
- Ziyin Han
- Department of Traumatic Orthopedics, Yantaishan Hospital, Yantai, China
| | - Zufang Mou
- Department of Nosocomial Infection, Yantaishan Hospital, Yantai, China
| | - Yulong Jing
- Department of Traumatic Orthopedics, Yantaishan Hospital, Yantai, China
| | - Rong Jiang
- Department of Physiology, Binzhou Medical University, Binzhou, China
| | - Tao Sun
- Department of Traumatic Orthopedics, Yantaishan Hospital, Yantai, China
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Jagtap U, Anderson ES, Slack FJ. The Emerging Value of Circular Noncoding RNA Research in Cancer Diagnosis and Treatment. Cancer Res 2023; 83:809-813. [PMID: 36919419 PMCID: PMC10020866 DOI: 10.1158/0008-5472.can-22-3014] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/29/2022] [Accepted: 01/03/2023] [Indexed: 03/16/2023]
Abstract
Circular RNAs (circRNA) are a recently described class of RNA molecules that have attracted substantial attention as new components of disease mechanisms and as potential biomarkers in multiple diseases, including cancer. CircRNAs are often highly conserved and exhibit developmental stage- and disease-specific expression. Several studies have reported circRNA expression patterns that are associated with specific cancer types and with patient prognosis. Here, we overview the active registered clinical trials that investigate the value of circRNAs as cancer biomarkers and discuss the potential of circRNAs in clinical cancer care. Taken together, circRNAs are actively being investigated as diagnostic, predictive, and prognostic biomarkers, and their potential to serve as therapeutic intervention points motivates ongoing translational and clinical research.
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Affiliation(s)
- Urmila Jagtap
- Department of Pathology, Center of Life Sciences, Beth Israel Deaconess Medical Center, Boston, Massachusetts, 02115, USA
- HMS Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Erik S. Anderson
- HMS Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, 02115, USA
| | - Frank J. Slack
- Department of Pathology, Center of Life Sciences, Beth Israel Deaconess Medical Center, Boston, Massachusetts, 02115, USA
- HMS Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, 02115, USA
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15
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Hoffmann M, Schwartz L, Ciora OA, Trummer N, Willruth LL, Jankowski J, Lee HK, Baumbach J, Furth P, Hennighausen L, List M. circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.19.524495. [PMID: 36789427 PMCID: PMC9928029 DOI: 10.1101/2023.01.19.524495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
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 back-splicing 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 distinct ratio of the binding site length. 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 Bioinformatics online.
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Affiliation(s)
- Markus Hoffmann
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany,Institute for Advanced Study (Lichtenbergstrasse 2a, D-85748 Garching, Germany), Technical University of Munich, Germany,National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America,corresponding authors Contact:;
| | - Leon Schwartz
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Octavia-Andreea Ciora
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Nico Trummer
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Lina-Liv Willruth
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Jakub Jankowski
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Hye Kyung Lee
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Jan Baumbach
- Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany,Computational BioMedicine Lab, University of Southern Denmark, Odense, Denmark
| | - Priscilla Furth
- Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA
| | - Lothar Hennighausen
- Institute for Advanced Study (Lichtenbergstrasse 2a, D-85748 Garching, Germany), Technical University of Munich, Germany,National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Markus List
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany,corresponding authors Contact:;
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16
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Nishita-Hiresha V, Varsha R, Jayasuriya R, Ramkumar KM. The role of circRNA-miRNA-mRNA interaction network in endothelial dysfunction. Gene 2023; 851:146950. [DOI: 10.1016/j.gene.2022.146950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/24/2022] [Accepted: 10/03/2022] [Indexed: 11/27/2022]
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17
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Zhou J, Liu L, Wu P, Zhao L, Wu Y. Identification and characterization of non-coding RNA networks in infected macrophages revealing the pathogenesis of F. nucleatum-associated diseases. BMC Genomics 2022; 23:826. [PMID: 36513974 DOI: 10.1186/s12864-022-09052-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND F. nucleatum, as an important periodontal pathogen, is not only closely associated with the development of periodontitis, but also implicated in systemic diseases. Macrophages may act as an important mediator in the pathogenic process of F. nucleatum infection. As non-coding RNAs (ncRNAs) have attracted extensive attention as important epigenetic regulatory mechanisms recently, we focus on the competing endogenous RNA (ceRNA) regulatory networks to elucidate the pathogenesis of F. nucleatum-associated diseases. RESULTS We screen abnormally expressed mRNAs, miRNAs, lncRNAs and circRNAs in macrophages after F. nucleatum infection via the whole transcriptome sequencing technology, including 375 mRNAs, 5 miRNAs, 64 lncRNAs, and 180 circRNAs. The accuracy of RNA-seq and microRNA-seq result was further verified by qRT-PCR analysis. GO and KEGG analysis show that the differentially expressed genes were mainly involved in MAPK pathway, Toll-like receptor pathway, NF-κB pathway and apoptosis. KEGG disease analysis reveals that they were closely involved in immune system diseases, cardiovascular disease, cancers, inflammatory bowel disease (IBD) et al. We constructed the underlying lncRNA/circRNA-miRNA-mRNA networks to understand their interaction based on the correlation analysis between the differentially expressed RNAs, and then screen the core non-coding RNAs. In which, AKT2 is controlled by hsa_circ_0078617, hsa_circ_0069227, hsa_circ_0084089, lncRNA NUP210, lncRNA ABCB9, lncRNA DIXDC1, lncRNA ATXN1 and lncRNA XLOC_237387 through miR-150-5p; hsa_circ_0001165, hsa_circ_0008460, hsa_circ_0001118, lncRNA XLOC_237387 and lncRNA ATXN1 were identified as the ceRNAs of hsa-miR-146a-3p and thereby indirectly modulating the expression of MITF. CONCLUSIONS Our data identified promising candidate ncRNAs responsible for regulating immune response in the F. nucleatum-associated diseases, offering new insights regarding the pathogenic mechanism of this pathogen.
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Affiliation(s)
- Jieyu Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Lin Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Peiyao Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Lei Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China. .,Department of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
| | - Yafei Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China. .,Department of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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18
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Wu B, Sun Y, Hou J. CircMED12L Protects Against Hydrogen Peroxide-induced Apoptotic and Oxidative Injury in Human Lens Epithelial Cells by miR-34a-5p/ALCAM axis. Curr Eye Res 2022; 47:1631-1640. [PMID: 36218352 DOI: 10.1080/02713683.2022.2134427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
PURPOSE Cataract is the leading cause of visual impairment and reversible blindness. Despite advances in surgical removal of cataracts, cataract continues to be a leading public-health issue due to the complications after surgery. Circular RNAs (circRNAs) have been showed to be implicated in the pathophysiology of age-related cataract (ARC). Herein, this work elucidated the role and mechanism of circMED12L in the process of ARC. METHODS Human lens epithelial cells (HLECs) were exposed to hydrogen peroxide (H2O2) in experimental groups. Levels of genes and proteins were measured by qRT-PCR and western blotting. Cell growth was evaluated by Cell Counting Kit-8 (CCK-8) assay and flow cytometry, respectively. The oxidative stress was assessed by detecting the activity of malondialdehyde, catalase, and superoxide dismutase. The interaction between miR-34a-5p and circMED12L or ALCAM (activated leukocyte cell adhesion molecule) was validated using dual-luciferase reporter and RNA immunoprecipitation assays. RESULTS CircMED12L expression was lower in the lens epithelium of ARC patients and H2O2-induced HLECs compared with the normal individuals and untreated cells. Functionally, forced expression of circMED12L could alleviate H2O2-induced viability inhibition, as well as apoptotic and oxidative injury in HLECs. Mechanistically, circMED12L/miR-34a-5p/ALCAM constituted a feedback loop in HLECs. MiR-34a-5p was increased, while ALCAM was decreased in ARC patients and H2O2-induced HLECs. High expression of miR-34a-5p reversed the protective effects of circMED12L on HLECs under H2O2 treatment. Besides, inhibition of miR-34a-5p could repress H2O2-induced apoptotic and oxidative injury in HLECs, which were abolished by subsequent ALCAM knockdown. CONCLUSION Overexpression of circMED12L could protect against H2O2-induced apoptosis and oxidative stress in HLECs by miR-34a-5p/ALCAM axis.
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Affiliation(s)
- Baohua Wu
- Department of Ophthalmology, Lanzhou Purui Ophthalmology Hospital, Lanzhou, China
| | - Yan Sun
- Department of Ophthalmology, Lanzhou Purui Ophthalmology Hospital, Lanzhou, China.,Department of Ophthalmology, Gansu Rehabilitation Center Hospital, Lanzhou, China.,Clinical School of Traditional Chinese, Gansu University of Chinese Medicine, Lanzhou, China
| | - Jingmei Hou
- Department of Ophthalmology, Lanzhou Purui Ophthalmology Hospital, Lanzhou, China.,Department of Ophthalmology, Gansu Rehabilitation Center Hospital, Lanzhou, China
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19
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Ali MK, Schimmel K, Zhao L, Chen CK, Dua K, Nicolls MR, Spiekerkoetter E. The role of circular RNAs in pulmonary hypertension. Eur Respir J 2022; 60:2200012. [PMID: 35680145 PMCID: PMC10361089 DOI: 10.1183/13993003.00012-2022] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 05/18/2022] [Indexed: 12/14/2022]
Abstract
Circular RNAs (circRNAs) are endogenous, covalently circularised, non-protein-coding RNAs generated from back-splicing. Most circRNAs are very stable, highly conserved, and expressed in a tissue-, cell- and developmental stage-specific manner. circRNAs play a significant role in various biological processes, such as regulation of gene expression and protein translation via sponging of microRNAs and binding with RNA-binding proteins. circRNAs have become a topic of great interest in research due to their close link with the development of various diseases. Their high stability, conservation and abundance in body fluids make them promising biomarkers for many diseases. A growing body of evidence suggests that aberrant expression of circRNAs and their targets plays a crucial role in pulmonary vascular remodelling and pulmonary arterial hypertension (group 1) as well as other forms (groups 3 and 4) of pulmonary hypertension (PH). Here we discuss the roles and molecular mechanisms of circRNAs in the pathogenesis of pulmonary vascular remodelling and PH. We also highlight the therapeutic and biomarker potential of circRNAs in PH.
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Affiliation(s)
- Md Khadem Ali
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University, Stanford, CA, USA
| | - Katharina Schimmel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University, Stanford, CA, USA
| | - Lan Zhao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University, Stanford, CA, USA
| | - Chun-Kan Chen
- Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, Australia
- Australian Research Centre in Complementary and Integrative Medicine, Faculty of Health, University of Technology Sydney, Ultimo, Australia
| | - Mark R Nicolls
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University, Stanford, CA, USA
| | - Edda Spiekerkoetter
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University, Stanford, CA, USA
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20
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Teekas L, Sharma S, Vijay N. Lineage-specific protein repeat expansions and contractions reveal malleable regions of immune genes. Genes Immun 2022; 23:218-234. [PMID: 36203090 DOI: 10.1038/s41435-022-00186-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 01/07/2023]
Abstract
Functional diversification, a higher evolutionary rate, and intense positive selection help a limited number of immune genes interact with many pathogens. Repeats in protein-coding regions are a well-known source of functional diversification, adaptive variation, and evolutionary novelty in a short time. Repeats play a crucial role in biochemical functions like functional diversification of transcription regulation, protein kinases, cell adhesion, signaling pathways, morphogenesis, DNA repair, recombination, and RNA processing. Repeat length variation can change the associated protein's interaction, efficacy, and overall protein network. Repeats have an intrinsic unstable nature and can potentially evolve rapidly and expedite the acquisition of complex phenotypic traits and functions. Because of their ability to generate rapid, adaptive variations over short evolutionary distances, repeats are considered "tuning knobs." Repeat length variation in specific genes, like RUNX2 and ALX4, is associated with morphological and physiological changes across vertebrates. Here we study repeat length variation as a potent source of species-specific immune diversification across several clades of tetrapods. Moreover, we provide a clade-wise comprehensive list of immune genes with repeat types for future studies of morphological/evolutionary changes within species groups. We observe significant repeat length variation of FASLG and C1QC in Rodentia and Primates' contrasting species groups, respectively.
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Affiliation(s)
- Lokdeep Teekas
- Department of Biological Sciences, Computational Evolutionary Genomics Lab, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Sandhya Sharma
- Department of Biological Sciences, Computational Evolutionary Genomics Lab, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Nagarjun Vijay
- Department of Biological Sciences, Computational Evolutionary Genomics Lab, IISER Bhopal, Bhauri, Madhya Pradesh, India.
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21
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Zhao F, Zhang X, Pei X, Yang D, Han M. Deregulated Expression of Circular RNAs Is Associated with Immune Evasion and Leukemia Relapse after Allogeneic Hematopoietic Stem Cell Transplantation. Genes (Basel) 2022; 13:1986. [PMID: 36360223 PMCID: PMC9689715 DOI: 10.3390/genes13111986] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) are a novel class of epigenetic regulators that participate in leukemogenesis. However, their roles in leukemia relapse after transplantation remain unclear. METHODS We defined the circRNAs profile of the bone-marrow-enriched CD34+ cells from ten acute myeloid leukemia (AML) patients after transplantation (five relapse [RE] and five continuous complete remission [CR]) and four healthy controls (HCs) by RNA-seq. Differentially expressed circRNAs were validated using real-time quantitative polymerase chain reaction (RT-qPCR) in an independent cohort of six AML patients with pairwise samples at diagnosis and at relapse and six controls. RESULTS The bioinformatics analysis revealed a distinct circRNAs profile in relapse patients compared with controls (CR or HCs), while there was no significant difference between CR and HCs. Functional enrichment analysis demonstrated that mRNAs co-expressed with identified circRNAs were primarily involved in immune-related pathways, including the T cell receptor signaling pathway and lymphocyte differentiation. Moreover, we performed a protein-protein interaction network based on the immune-related genes and annotated 20 hub genes. The abnormal expression of hub genes was responsible for impairing T cell co-stimulation and activation, thus contributing to the immune escape of relapse blasts. We further constructed competing endogenous RNAs (ceRNA) regulatory networks based on immune-related genes and identified 10 key circRNAs that are associated with immune evasion. Six candidate circRNAs and their associated miRNA/mRNAs in the ceRNA network were randomly selected to be validated in another set by RT-qPCR. CONCLUSIONS CircRNAs dysregulation may be involved in the immune evasion of relapse blasts and is associated with AML relapse. Our results identify several promising biomarkers and might provide novel insights into the biology of AML relapse post-transplantation.
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22
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Liang Q, Fu J, Wang X, Liu L, Xiao W, Gao Y, Yang L, Yu H, Xueru X, Zikun T, Huang S, Han X, Qian L, Zhou Y.
circS100A11
enhances M2a macrophage activation and lung inflammation in children with asthma. Allergy 2022. [DOI: 10.1111/all.15515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/13/2022] [Accepted: 08/10/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Qiuyan Liang
- Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University Shanghai China
- National Health Commission (NHC) Key Laboratory of Neonatal Diseases Fudan University Shanghai China
| | - Jinrong Fu
- Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University Shanghai China
- Department of General Medicine, Children’s Hospital of Fudan University Shanghai China
| | - Xiang Wang
- Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University Shanghai China
- National Health Commission (NHC) Key Laboratory of Neonatal Diseases Fudan University Shanghai China
| | - Lijuan Liu
- Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University Shanghai China
- Department of Respiratory Medicine, Children’s Hospital of Fudan University Shanghai China
| | - Wenfeng Xiao
- Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University Shanghai China
- National Health Commission (NHC) Key Laboratory of Neonatal Diseases Fudan University Shanghai China
| | - Yajing Gao
- Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University Shanghai China
- National Health Commission (NHC) Key Laboratory of Neonatal Diseases Fudan University Shanghai China
| | - Lan Yang
- Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University Shanghai China
- National Health Commission (NHC) Key Laboratory of Neonatal Diseases Fudan University Shanghai China
| | - Hongmiao Yu
- Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University Shanghai China
- National Health Commission (NHC) Key Laboratory of Neonatal Diseases Fudan University Shanghai China
| | - Xie Xueru
- Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University Shanghai China
- National Health Commission (NHC) Key Laboratory of Neonatal Diseases Fudan University Shanghai China
| | - Tu Zikun
- Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University Shanghai China
- National Health Commission (NHC) Key Laboratory of Neonatal Diseases Fudan University Shanghai China
| | - Saihua Huang
- Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University Shanghai China
- National Health Commission (NHC) Key Laboratory of Neonatal Diseases Fudan University Shanghai China
| | - Xiao Han
- Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University Shanghai China
- National Health Commission (NHC) Key Laboratory of Neonatal Diseases Fudan University Shanghai China
| | - Liling Qian
- Department of Respiratory Medicine, Children’s Hospital of Fudan University Shanghai China
| | - Yufeng Zhou
- Institute of Pediatrics, Children’s Hospital of Fudan University, National Children’s Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, International Co‐laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University Shanghai China
- National Health Commission (NHC) Key Laboratory of Neonatal Diseases Fudan University Shanghai China
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23
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Bagheri Moghaddam M, Maleki M, Oveisee M, Bagheri Moghaddam M, Arabian M, Malakootian M. Circular RNAs: New Players in Cardiomyopathy. Genes (Basel) 2022; 13:genes13091537. [PMID: 36140705 PMCID: PMC9498503 DOI: 10.3390/genes13091537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Cardiomyopathies comprise a heterogeneous group of cardiac diseases identified by myocardium disorders and diminished cardiac function. They often lead to heart failure or heart transplantation and constitute one of the principal causes of morbidity and mortality worldwide. Circular RNAs (circRNAs) are a novel type of noncoding RNAs. They are covalently closed and single-stranded and derived from the exons and introns of genes by alternative splicing. This specific structure renders them resistant to exonuclease digestion. Many recent studies have demonstrated that circRNAs are highly abundant and conserved and can play central roles in biological functions such as microRNA (miRNA) sponging, splicing, and transcription regulation. Emerging evidence indicates that circRNAs can play significant roles in cardiovascular diseases, including cardiomyopathies. In this review, we briefly describe the current understanding regarding the classification, nomenclature, characteristics, and function of circRNAs and report recent significant findings concerning the roles of circRNAs in cardiomyopathies. Furthermore, we discuss the clinical application potential of circRNAs as the therapeutic targets and diagnostic biomarkers of cardiomyopathies.
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Affiliation(s)
- Maedeh Bagheri Moghaddam
- Molecular Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 141171311, Iran
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran 1995614331, Iran
| | - Majid Maleki
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran 1995614331, Iran
| | - Maziar Oveisee
- School of Medicine, Bam University of Medical Sciences, Bam 7661771967, Iran
| | - Mahrokh Bagheri Moghaddam
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran 1995614331, Iran
| | - Maedeh Arabian
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran 1995614331, Iran
| | - Mahshid Malakootian
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran 1995614331, Iran
- Correspondence: ; Tel.: +98-2123923033; Fax: +98-2122663213
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24
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Zhang Y, Jiao Z, Chen M, Shen B, Shuai Z. Roles of Non-Coding RNAs in Primary Biliary Cholangitis. Front Mol Biosci 2022; 9:915993. [PMID: 35874606 PMCID: PMC9305664 DOI: 10.3389/fmolb.2022.915993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Primary biliary cholangitis (PBC) is an autoimmune-mediated chronic cholestatic liver disease, fatigue, and skin itching are the most common clinical symptoms. Its main pathological feature is the progressive damage and destruction of bile duct epithelial cells. Non-coding RNA (NcRNA, mainly including microRNA, long non-coding RNA and circular RNA) plays a role in the pathological and biological processes of various diseases, especially autoimmune diseases. Many validated ncRNAs are expected to be biomarkers for the diagnosis or treatment of PBC. This review will elucidate the pathogenesis of PBC and help to identify potential ncRNA biomarkers for PBC.
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Affiliation(s)
- Yaqin Zhang
- Department of Rheumatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ziying Jiao
- Department of Physiology, School of Basic Medicine of Anhui Medical University, Hefei, China
| | - Mingwei Chen
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Bing Shen
- Department of Physiology, School of Basic Medicine of Anhui Medical University, Hefei, China
| | - Zongwen Shuai
- Department of Rheumatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- *Correspondence: Zongwen Shuai,
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25
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Gu J, Su C, Huang F, Zhao Y, Li J. Past, Present and Future: The Relationship Between Circular RNA and Immunity. Front Immunol 2022; 13:894707. [PMID: 35693804 PMCID: PMC9174805 DOI: 10.3389/fimmu.2022.894707] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/28/2022] [Indexed: 12/21/2022] Open
Abstract
The immune system has evolved since the birth of humans. However, immune-related diseases have not yet been overcome due to the lack of expected indicators and targeting specificity of current medical technology, subjecting patients to very uncomfortable physical and mental experiences and high medical costs. Therefore, the requirements for treatments with higher specificity and indicative ability are raised. Fortunately, the discovery of and continuous research investigating circular RNAs (circRNAs) represent a promising method among numerous methods. Although circRNAs wear regarded as metabolic wastes when discovered, as a type of noncoding RNA (ncRNA) with a ring structure and wide distribution range in the human body, circRNAs shine brilliantly in medical research by virtue of their special nature and structure-determined functions, such as high stability, wide distribution, high detection sensitivity, acceptable reproducibility and individual differences. Based on research investigating the role of circRNAs in immunity, we systematically discuss the hotspots of the roles of circRNAs in immune-related diseases, including expression profile analyses, potential biomarker research, ncRNA axis/network construction, impacts on phenotypes, therapeutic target seeking, maintenance of nucleic acid stability and protein binding research. In addition, we summarize the current situation of and problems associated with circRNAs in immune research, highlight the applications and prospects of circRNAs in the treatment of immune-related diseases, and provide new insight into future directions and new strategies for laboratory research and clinical applications.
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Affiliation(s)
- Junjie Gu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chongying Su
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Fei Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuwei Zhao
- Chengdu Blood Center, Blood Research Laboratory, Chengdu, China
- *Correspondence: Jing Li, ; Yuwei Zhao,
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Jing Li, ; Yuwei Zhao,
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26
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Peng H, Xing J, Wang X, Ding X, Tang X, Zou J, Wang S, Liu Y. Circular RNA circNUP214 Modulates the T Helper 17 Cell Response in Patients With Rheumatoid Arthritis. Front Immunol 2022; 13:885896. [PMID: 35686126 PMCID: PMC9170918 DOI: 10.3389/fimmu.2022.885896] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/25/2022] [Indexed: 12/05/2022] Open
Abstract
Circular RNAs (circRNAs) are important transcriptional regulators of genome expression that participate in the pathogenesis of human diseases. Mechanistically, circRNAs, as competitive endogenous RNAs (ceRNAs), can sponge microRNAs (miRNAs) with miRNA response elements. A previous study identified that hsa_circ_0089172 (circNUP214) is abnormally expressed in Hashimoto's thyroiditis. However, the role of circNUP214 in rheumatoid arthritis (RA) remains unclear. In total, 28 RA patients and 28 healthy controls were enrolled in this study. We found that circNUP214 is an abundant and stable circRNA in RA patients that can potentially differentiate RA patients from healthy subjects. Additionally, the elevated levels of IL-23R positively correlated with circNUP214 expression. The knockdown of circNUP214 resulted in the reduction of IL-23R at both transcriptional and translational levels in human CD4+ T cells. The proportion of circulating Th17 cells and the transcript levels of IL-17A were increased in RA patients and were both positively correlated with IL-23R expression. Moreover, positive correlations between the transcript levels of circNUP214 and the percentage of Th17 cells and the transcript levels of IL-17A were observed in RA patients. The downregulation of circNUP214 decreased the proportion of Th17 cells and the transcript levels of IL-17A in vitro. Furthermore, circNUP214 functioned as a ceRNA for miR-125a-3p in RA patients. Taken together, our results indicate that elevated levels of circNUP214 contribute to the Th17 cell response in RA patients.
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Affiliation(s)
- Huiyong Peng
- Department of Laboratory Medicine, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang Medical School of Nanjing Medical University, Zhenjiang, China
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jie Xing
- Department of Laboratory Medicine, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang Medical School of Nanjing Medical University, Zhenjiang, China
| | - Xuehua Wang
- Department of Endocrinology, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Xiangmei Ding
- Department of Endocrinology, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang Medical School of Nanjing Medical University, Zhenjiang, China
| | - Xinyi Tang
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Junli Zou
- Department of Endocrinology, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang Medical School of Nanjing Medical University, Zhenjiang, China
| | - Shengjun Wang
- Department of Laboratory Medicine, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang Medical School of Nanjing Medical University, Zhenjiang, China
| | - Yingzhao Liu
- Department of Endocrinology, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang Medical School of Nanjing Medical University, Zhenjiang, China
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Circ_NNT suppresses the apoptosis and inflammation in glucose-induced human retinal pigment epithelium by regulating miR-320b/TIMP3 axis in diabetic retinopathy. Clin Immunol 2022; 238:109023. [PMID: 35477026 DOI: 10.1016/j.clim.2022.109023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/08/2022] [Accepted: 04/20/2022] [Indexed: 11/23/2022]
Abstract
BACKGROUND Diabetic retinopathy (DR) is a frequent complication of diabetes. Recent reports have showed that circular RNAs (circRNAs) play important roles in DR progression. Herein, the aim of this study was to explore the role and molecular mechanism of circ_NNT in DR process. METHODS Human retinal pigment epithelial cells ARPE-19 were treated with high glucose (HG) in experimental group. The expression of circ_NNT, miR-320b, and TIMP3 (TIMP Metallopeptidase Inhibitor 3) were determined using quantitative real-time polymerase chain reaction and Western blot. In vitro experiments were conducted by 5-ethynyl-2'-deoxyuridine (EdU) assay, MTT assay, flow cytometry, Western blot, and ELISA. The binding interaction was confirmed using dual-luciferase reporter and pull-down assays. RESULTS HG stimulation led to a decrease of circ_NNT and TIMP3 expression, and an increase of miR-320b expression in ARPE-19 cells. Functionally, circ_NNT up-regulation reversed HG-evoked apoptosis and inflammation in ARPE-19 cells. Mechanistically, circ_NNT acted as a sponge for miR-320b to elevate TIMP3 expression. Further rescue experiments showed that miR-320b elevation attenuated the protective effects of circ_NNT on HG-induced ARPE-19 cells. Moreover, inhibition of miR-320b protected ARPE-19 cells against HG-evoked apoptosis and inflammation, which were abolished by TIMP3 knockdown. CONCLUSION Circ_NNT protected ARPE-19 cells against HG-evoked apoptosis and inflammation via elevating TIMP3 through sequestering miR-320b, indicating that up-regulation of circ_NNT might contribute to the inhibition of DR process.
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28
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Wang J, Wu X, Kang Y, Zhang L, Niu H, Qu J, Wang Y, Ji D, Li Y. Integrative analysis of circRNAs from Yangtze River Delta white goat neck skin tissue by high-throughput sequencing (circRNA-seq). Anim Genet 2022; 53:405-415. [PMID: 35383992 DOI: 10.1111/age.13198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/16/2022] [Accepted: 03/22/2022] [Indexed: 01/22/2023]
Abstract
The Yangtze River Delta white goat is a unique goat species that can produce superior-quality brush hair. The formation of this brush hair is controlled by a series of critical genes and related signaling pathways. Circular RNAs (circRNAs), are ubiquitous endogenous non-coding RNAs that regulate many biological and physiological processes in mammals. However, little is known about the potential regulatory role of circRNAs on superior-quality brush hair formation in Yangtze River Delta white goat. In this study, high-throughput sequencing technology was used to only detect circRNAs in the neck skin tissue of normal-quality goats (NHQs) and superior-quality goats (HQs). A total of 61 803 circRNAs were identified and 32 of them were differentially expressed in the NHQ group vs. the HQ group. Functional enrichment analysis showed that the source gene of differentially expressed circRNAs (DE-circRNAs) was enriched mostly in platelet activation and the focal adhesion signal pathway. Action mechanism analysis revealed that DE-circRNAs could sponge to many identified miRNAs, including miR-31, miR-125b, miR-let-7a and miR-149-5p, which have important roles in goat hair follicle stem cell growth, hair follicle development and morphogenesis. Altogether, our findings provide a valuable basis for studying circRNAs involved in superior-quality brush hair traits and meanwhile advance our understanding of circRNA complex regulation mechanisms in Yangtze River Delta white goat skin hair follicle development.
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Affiliation(s)
- Jian Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Animal Genetics and Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Xi Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yan Kang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Liuming Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Haoyuan Niu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jingwen Qu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yanhu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Dejun Ji
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Animal Genetics and Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Yongjun Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory of Animal Genetics and Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou, China
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Biernacki T, Kokas Z, Sandi D, Füvesi J, Fricska-Nagy Z, Faragó P, Kincses TZ, Klivényi P, Bencsik K, Vécsei L. Emerging Biomarkers of Multiple Sclerosis in the Blood and the CSF: A Focus on Neurofilaments and Therapeutic Considerations. Int J Mol Sci 2022; 23:ijms23063383. [PMID: 35328802 PMCID: PMC8951485 DOI: 10.3390/ijms23063383] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/12/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Multiple Sclerosis (MS) is the most common immune-mediated chronic neurodegenerative disease of the central nervous system (CNS) affecting young people. This is due to the permanent disability, cognitive impairment, and the enormous detrimental impact MS can exert on a patient's health-related quality of life. It is of great importance to recognise it in time and commence adequate treatment at an early stage. The currently used disease-modifying therapies (DMT) aim to reduce disease activity and thus halt disability development, which in current clinical practice are monitored by clinical and imaging parameters but not by biomarkers found in blood and/or the cerebrospinal fluid (CSF). Both clinical and radiological measures routinely used to monitor disease activity lack information on the fundamental pathophysiological features and mechanisms of MS. Furthermore, they lag behind the disease process itself. By the time a clinical relapse becomes evident or a new lesion appears on the MRI scan, potentially irreversible damage has already occurred in the CNS. In recent years, several biomarkers that previously have been linked to other neurological and immunological diseases have received increased attention in MS. Additionally, other novel, potential biomarkers with prognostic and diagnostic properties have been detected in the CSF and blood of MS patients. AREAS COVERED In this review, we summarise the most up-to-date knowledge and research conducted on the already known and most promising new biomarker candidates found in the CSF and blood of MS patients. DISCUSSION the current diagnostic criteria of MS relies on three pillars: MRI imaging, clinical events, and the presence of oligoclonal bands in the CSF (which was reinstated into the diagnostic criteria by the most recent revision). Even though the most recent McDonald criteria made the diagnosis of MS faster than the prior iteration, it is still not an infallible diagnostic toolset, especially at the very early stage of the clinically isolated syndrome. Together with the gold standard MRI and clinical measures, ancillary blood and CSF biomarkers may not just improve diagnostic accuracy and speed but very well may become agents to monitor therapeutic efficacy and make even more personalised treatment in MS a reality in the near future. The major disadvantage of these biomarkers in the past has been the need to obtain CSF to measure them. However, the recent advances in extremely sensitive immunoassays made their measurement possible from peripheral blood even when present only in minuscule concentrations. This should mark the beginning of a new biomarker research and utilisation era in MS.
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Affiliation(s)
- Tamás Biernacki
- Albert Szent-Györgyi Clinical Centre, Department of Neurology, Faculty of General Medicine, University of Szeged, 6725 Szeged, Hungary; (T.B.); (Z.K.); (D.S.); (J.F.); (Z.F.-N.); (P.F.); (T.Z.K.); (P.K.); (K.B.)
| | - Zsófia Kokas
- Albert Szent-Györgyi Clinical Centre, Department of Neurology, Faculty of General Medicine, University of Szeged, 6725 Szeged, Hungary; (T.B.); (Z.K.); (D.S.); (J.F.); (Z.F.-N.); (P.F.); (T.Z.K.); (P.K.); (K.B.)
| | - Dániel Sandi
- Albert Szent-Györgyi Clinical Centre, Department of Neurology, Faculty of General Medicine, University of Szeged, 6725 Szeged, Hungary; (T.B.); (Z.K.); (D.S.); (J.F.); (Z.F.-N.); (P.F.); (T.Z.K.); (P.K.); (K.B.)
| | - Judit Füvesi
- Albert Szent-Györgyi Clinical Centre, Department of Neurology, Faculty of General Medicine, University of Szeged, 6725 Szeged, Hungary; (T.B.); (Z.K.); (D.S.); (J.F.); (Z.F.-N.); (P.F.); (T.Z.K.); (P.K.); (K.B.)
| | - Zsanett Fricska-Nagy
- Albert Szent-Györgyi Clinical Centre, Department of Neurology, Faculty of General Medicine, University of Szeged, 6725 Szeged, Hungary; (T.B.); (Z.K.); (D.S.); (J.F.); (Z.F.-N.); (P.F.); (T.Z.K.); (P.K.); (K.B.)
| | - Péter Faragó
- Albert Szent-Györgyi Clinical Centre, Department of Neurology, Faculty of General Medicine, University of Szeged, 6725 Szeged, Hungary; (T.B.); (Z.K.); (D.S.); (J.F.); (Z.F.-N.); (P.F.); (T.Z.K.); (P.K.); (K.B.)
| | - Tamás Zsigmond Kincses
- Albert Szent-Györgyi Clinical Centre, Department of Neurology, Faculty of General Medicine, University of Szeged, 6725 Szeged, Hungary; (T.B.); (Z.K.); (D.S.); (J.F.); (Z.F.-N.); (P.F.); (T.Z.K.); (P.K.); (K.B.)
- Albert Szent-Györgyi Clinical Centre, Department of Radiology, Albert Szent-Györgyi Faculty of Medicine, University of Szeged, 6725 Szeged, Hungary
| | - Péter Klivényi
- Albert Szent-Györgyi Clinical Centre, Department of Neurology, Faculty of General Medicine, University of Szeged, 6725 Szeged, Hungary; (T.B.); (Z.K.); (D.S.); (J.F.); (Z.F.-N.); (P.F.); (T.Z.K.); (P.K.); (K.B.)
| | - Krisztina Bencsik
- Albert Szent-Györgyi Clinical Centre, Department of Neurology, Faculty of General Medicine, University of Szeged, 6725 Szeged, Hungary; (T.B.); (Z.K.); (D.S.); (J.F.); (Z.F.-N.); (P.F.); (T.Z.K.); (P.K.); (K.B.)
| | - László Vécsei
- Albert Szent-Györgyi Clinical Centre, Department of Neurology, Faculty of General Medicine, University of Szeged, 6725 Szeged, Hungary; (T.B.); (Z.K.); (D.S.); (J.F.); (Z.F.-N.); (P.F.); (T.Z.K.); (P.K.); (K.B.)
- MTA-SZTE Neuroscience Research Group, University of Szeged, 6725 Szeged, Hungary
- Correspondence: ; Tel.: +36-62-545-356; Fax: +36-62-545-597
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Ou R, Lu S, Wang L, Wang Y, Lv M, Li T, Xu Y, Lu J, Ge RS. Circular RNA circLMO1 Suppresses Cervical Cancer Growth and Metastasis by Triggering miR-4291/ACSL4-Mediated Ferroptosis. Front Oncol 2022; 12:858598. [PMID: 35321435 PMCID: PMC8936435 DOI: 10.3389/fonc.2022.858598] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/14/2022] [Indexed: 12/24/2022] Open
Abstract
Background A number of studies have demonstrated that circular RNA (circRNA) plays a critical role in tumorigenesis and tumor progression. However, the biological effects of most circRNAs on cervical cancer remain unclear. Hsa_circ_0021087 (thereafter named circLMO1) is a circRNA generated from the circularization of exon 2 and exon 3 of LIM Domain Only 1 (LMO1) and first identified as a tumor suppressor in gastric cancer. We aimed to identify the role of circLMO1 in cervical cancer progression. Methods CircLMO1 was verified through qPCR and Sanger sequencing. The biological role of circLMO1 in regulating cervical cancer growth and metastasis was investigated both in vitro and in the nude mouse xenograft tumor model. The dual luciferase reporter assay and rescue experiment were conducted to evaluate the interactions among circLMO1, microRNA (miR)-4291, and acyl-CoA synthetase long chain family member 4 (ACSL4). The role of circLMO1 in regulating ferroptosis was assessed by analyzing lipid reactive oxygen species (ROS), and malonyl dialdehyde (MDA), and glutathione (GSH) content. Results The level of circLMO1 was down-regulated in cervical cancer tissues and was associated with the International Federation of Gynecology and Obstetrics (FIGO) staging. Functionally, circLMO1 overexpression inhibited cervical cancer growth and metastasis both in vitro and in vivo, whereas circLMO1 depletion promoted cervical cancer cell proliferation and invasion. Mechanistically, circLMO1 acted as a competing endogenous RNA (ceRNA) by sponging miR-4192 to repress target gene ACSL4. CircLMO1 promoted cervical cancer cell ferroptosis through up-regulating ACSL4 expression. Overexpression of miR-4291 or knockdown of ACSL4 reversed the effect of circLMO1 on facilitating ferroptosis and repressing cervical cancer cell proliferation and invasion. Conclusion CircLMO1 acted as a tumor suppressor of cervical cancer by regulating miR-4291/ACSL4-mediated ferroptosis, and could be a promising biomarker for the clinical management of cervical cancer.
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Affiliation(s)
- Rongying Ou
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Rongying Ou, ; Jieqiang Lu, ; Ren-shan Ge,
| | - Shun Lu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Luhui Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yebo Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Mingfen Lv
- Department of Dermatovenerology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Tian Li
- Department of Obstetrics and Gynecology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yunsheng Xu
- Department of Dermatovenerology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jieqiang Lu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Rongying Ou, ; Jieqiang Lu, ; Ren-shan Ge,
| | - Ren-shan Ge
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Rongying Ou, ; Jieqiang Lu, ; Ren-shan Ge,
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31
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Bao Y, Yao Y, Wang Z, Wu S, Jiang X, Ma H. Analysis of mRNA and circRNA Expression Profiles of Bovine Monocyte-Derived Macrophages Infected With Mycobacterium avium subsp. paratuberculosis. Front Microbiol 2022; 12:796922. [PMID: 35046920 PMCID: PMC8761944 DOI: 10.3389/fmicb.2021.796922] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the pathogen of Johne’s disease (paratuberculosis), which mainly causes chronic infectious granulomatous enteritis in ruminants and has brought huge economic losses to animal husbandry. As a specific intracellular pathogen, when MAP invades the body, it is internalized by macrophages where it is able to replicate by inhibition of the phagosome maturation, escaping the host immune system and surviving, which leads to the spread of the disease. More recent studies have shown that circRNA is involved in many pathological and physiological processes of the body as the molecular sponge of miRNA, the scaffold of RNA binding protein and having the characteristic of being able to translate into protein. In this study, the mRNA and circRNA expression profiles of MAP-infected bovine monocyte-macrophages and uninfected bovine cells were analyzed by high-throughput sequencing. A total of 618 differentially expressed mRNA were screened out, including 322 upregulated mRNA and 296 downregulated mRNA. In addition, the analysis of circRNA differential expression profile showed 39 differentially expressed genes including 12 upregulated and 27 downregulated genes. Moreover, differential genes belonging to cytokine activity, chemokine activity, inflammatory reaction, apoptosis, and other functional groups related to macrophage immune response were significantly enriched in Gene Ontology (GO). Multiple signal pathways including NF-κB, MAPK, Toll-like receptor, IL-17, JAK-STAT, and other signaling pathways related to activating macrophage immune response were significantly enriched in Kyoto Encyclopedia of Genes and Genomes (KEGG). In addition, RT-qPCR technology verified the accuracy of the mRNA sequencing results. In this study, we have obtained the transcriptome information of mRNA and circRNA of bovine monocyte-macrophage infected with MAP. These results will provide data support for the further study of mRNA–miRNA–circRNA network and immune escape mechanism of MAP and will enrich the knowledge of the molecular immune mechanisms of Johne’s disease as well.
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Affiliation(s)
- Yanhong Bao
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Yu Yao
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Zi Wang
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, China
| | - Shuiyin Wu
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Xiuyun Jiang
- College of Life Sciences, Jilin Agricultural University, Changchun, China.,College of Life Sciences, Changchun Sci-Tech University, Changchun, China
| | - Hongxia Ma
- College of Animal Medicine, Jilin Agricultural University, Changchun, China.,The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China.,The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Changchun, China
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32
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Liu Q, You B, Meng J, Huang CP, Dong G, Wang R, Chou F, Gao S, Chang C, Yeh S, Xu W. Targeting the androgen receptor to enhance NK cell killing efficacy in bladder cancer by modulating ADAR2/circ_0001005/PD-L1 signaling. Cancer Gene Ther 2022; 29:1988-2000. [PMID: 35915245 PMCID: PMC9750871 DOI: 10.1038/s41417-022-00506-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/18/2022] [Accepted: 07/06/2022] [Indexed: 01/25/2023]
Abstract
Although androgen receptor (AR) can influence bladder cancer (BCa) initiation and progression, its impact on tumor immune escape remains unclear. Here, we found that targeting AR could enhance natural killer (NK) cell tumor-killing efficacy by decreasing PD-L1 expression. Both antiandrogen treatment and AR knockdown effectively reduced membrane PD-LI expression to facilitate NK cell-mediated BCa cell killing by downregulating circ_0001005. Mechanistically, AR upregulated circRNA circ_0001005 expression via the RNA-editing gene ADAR2. circ_0001005 competitively sponged the miRNA miR-200a-3p to promote PD-L1 expression. A preclinical BCa xenograft mouse model further confirmed this newly identified signaling using the small molecule circ_0001005-shRNA to improve NK cell killing of BCa tumor cells. Collectively, these results suggest that targeting the newly identified ADAR2/circ_0001005/miR-200a-3p/PD-L1 pathway to impact antitumor immunity may suppress progression and boost immunotherapeutic efficacy in BCa.
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Affiliation(s)
- Qing Liu
- grid.412463.60000 0004 1762 6325Department of Radiation Oncology, Urology, and Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001 China ,grid.412750.50000 0004 1936 9166Departments of Urology, Pathology, Radiation Oncology, and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642 USA
| | - Bosen You
- grid.412463.60000 0004 1762 6325Department of Radiation Oncology, Urology, and Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001 China ,grid.412750.50000 0004 1936 9166Departments of Urology, Pathology, Radiation Oncology, and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642 USA
| | - Jialin Meng
- grid.412750.50000 0004 1936 9166Departments of Urology, Pathology, Radiation Oncology, and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642 USA
| | - Chi-Ping Huang
- grid.411508.90000 0004 0572 9415Department of Urology, China Medical University/Hospital, Taichung, 404 Taiwan
| | - Guanglu Dong
- grid.412463.60000 0004 1762 6325Department of Radiation Oncology, Urology, and Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001 China
| | - Ronghao Wang
- grid.412750.50000 0004 1936 9166Departments of Urology, Pathology, Radiation Oncology, and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642 USA
| | - Fuju Chou
- grid.412750.50000 0004 1936 9166Departments of Urology, Pathology, Radiation Oncology, and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642 USA
| | - Shan Gao
- grid.412463.60000 0004 1762 6325Department of Radiation Oncology, Urology, and Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001 China
| | - Chawnshang Chang
- grid.412750.50000 0004 1936 9166Departments of Urology, Pathology, Radiation Oncology, and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642 USA ,grid.411508.90000 0004 0572 9415Department of Urology, China Medical University/Hospital, Taichung, 404 Taiwan
| | - Shuyuan Yeh
- grid.412750.50000 0004 1936 9166Departments of Urology, Pathology, Radiation Oncology, and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642 USA
| | - Wanhai Xu
- grid.410736.70000 0001 2204 9268Department of Urology, The 4th Affiliated Hospital of Harbin Medical University, Harbin, 150001 China
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Wen G, Zhou T, Gu W. The potential of using blood circular RNA as liquid biopsy biomarker for human diseases. Protein Cell 2021; 12:911-946. [PMID: 33131025 PMCID: PMC8674396 DOI: 10.1007/s13238-020-00799-3] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/09/2020] [Indexed: 12/14/2022] Open
Abstract
Circular RNA (circRNA) is a novel class of single-stranded RNAs with a closed loop structure. The majority of circRNAs are formed by a back-splicing process in pre-mRNA splicing. Their expression is dynamically regulated and shows spatiotemporal patterns among cell types, tissues and developmental stages. CircRNAs have important biological functions in many physiological processes, and their aberrant expression is implicated in many human diseases. Due to their high stability, circRNAs are becoming promising biomarkers in many human diseases, such as cardiovascular diseases, autoimmune diseases and human cancers. In this review, we focus on the translational potential of using human blood circRNAs as liquid biopsy biomarkers for human diseases. We highlight their abundant expression, essential biological functions and significant correlations to human diseases in various components of peripheral blood, including whole blood, blood cells and extracellular vesicles. In addition, we summarize the current knowledge of blood circRNA biomarkers for disease diagnosis or prognosis.
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Affiliation(s)
- Guoxia Wen
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Tong Zhou
- Department of Physiology and Cell Biology, Reno School of Medicine, University of Nevada, Reno, NV, 89557, USA.
| | - Wanjun Gu
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, 210096, China.
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34
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Su H, Zheng W, Pan J, Lv X, Xin S, Xu T. Circular RNA circSamd4a Regulates Antiviral Immunity in Teleost Fish by Upregulating STING through Sponging miR-29a-3p. THE JOURNAL OF IMMUNOLOGY 2021; 207:2770-2784. [PMID: 34697227 DOI: 10.4049/jimmunol.2100469] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/21/2021] [Indexed: 12/22/2022]
Abstract
Circular RNAs (circRNAs) are a subgroup of endogenous noncoding RNA that is covalently closed rings and widely expressed. In recent years, there is accumulating evidence indicating that circRNAs are a class of important regulators, which play an important role in various biological processes. However, the biological functions and regulation mechanism of circRNAs in lower vertebrates are little known. In this study, we discovered a circRNA Samd4a (circSamd4a) that is related to the antiviral immune response of teleost fish. It can act as a key regulator of the host's antiviral response and play a key role in inhibiting Sininiperca chuatsi rhabdovirus replication. Further studies have shown that circSamd4a may act as a competing endogenous RNA, which can enhance the STING-mediated NF-κB/IRF3 signaling pathway by adsorbing miR-29a-3p, thereby enhancing the antiviral immune response. Therefore, circSamd4a plays an active regulatory role in the antiviral immune response of bony fish. Our research results provide a strong foundation for circular RNA to play a regulatory role in the antiviral immune response of teleost fish.
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Affiliation(s)
- Hui Su
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Weiwei Zheng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Jiajia Pan
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Xing Lv
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Shiying Xin
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; .,Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China; and.,National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
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35
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Ghafouri-Fard S, Khoshbakht T, Taheri M, Jamali E. A Concise Review on the Role of CircPVT1 in Tumorigenesis, Drug Sensitivity, and Cancer Prognosis. Front Oncol 2021; 11:762960. [PMID: 34804965 PMCID: PMC8599443 DOI: 10.3389/fonc.2021.762960] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/15/2021] [Indexed: 12/16/2022] Open
Abstract
CircPVT1 (hsa_circ_0001821) is a cancer-related circular RNA (circRNA) that originated from a genomic locus on chromosome 8q24. This locus has been previously found to encode the oncogenic long non-coding RNA PVT1. Expression of this circRNA has been found to be upregulated in diverse neoplastic conditions. CircPVT1 acts as a sponge for miR-125a, miR-125b, miR-124-3p, miR-30a-5p, miR-205-5p, miR-423-5p, miR-526b, miR-137, miR-145-5p, miR-497, miR-30d/e, miR-455-5p, miR-29a-3p, miR-204-5p, miR-149, miR-106a-5p, miR-377, miR-3666, miR-203, and miR-199a-5p. Moreover, it can regulate the activities of PI3K/AKT, Wnt5a/Ror2, E2F2, and HIF-1α. Upregulation of circPVT1 has been correlated with decreased survival of patients with different cancer types. In the current review, we explain the oncogenic impact of circPVT1 in different tissues based on evidence from in vitro, in vivo, and clinical investigations.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Elena Jamali
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Grimaldi A, Pietropaolo G, Stabile H, Kosta A, Capuano C, Gismondi A, Santoni A, Sciumè G, Fionda C. The Regulatory Activity of Noncoding RNAs in ILCs. Cells 2021; 10:cells10102742. [PMID: 34685721 PMCID: PMC8534545 DOI: 10.3390/cells10102742] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/01/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
Innate lymphoid cells (ILCs) are innate lymphocytes playing essential functions in protection against microbial infections and participate in both homeostatic and pathological contexts, including tissue remodeling, cancer, and inflammatory disorders. A number of lineage-defining transcription factors concurs to establish transcriptional networks which determine the identity and the activity of the distinct ILC subsets. However, the contribution of other regulatory molecules in controlling ILC development and function is also recently emerging. In this regard, noncoding RNAs (ncRNAs) represent key elements of the complex regulatory network of ILC biology and host protection. ncRNAs mostly lack protein-coding potential, but they are endowed with a relevant regulatory activity in immune and nonimmune cells because of their ability to control chromatin structure, RNA stability, and/or protein synthesis. Herein, we summarize recent studies describing how distinct types of ncRNAs, mainly microRNAs, long ncRNAs, and circular RNAs, act in the context of ILC biology. In particular, we comment on how ncRNAs can exert key effects in ILCs by controlling gene expression in a cell- or state-specific manner and how this tunes distinct functional outputs in ILCs.
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Affiliation(s)
- Alessio Grimaldi
- Department of Molecular Medicine, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (A.G.); (G.P.); (H.S.); (A.K.); (A.G.); (A.S.); (G.S.)
| | - Giuseppe Pietropaolo
- Department of Molecular Medicine, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (A.G.); (G.P.); (H.S.); (A.K.); (A.G.); (A.S.); (G.S.)
| | - Helena Stabile
- Department of Molecular Medicine, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (A.G.); (G.P.); (H.S.); (A.K.); (A.G.); (A.S.); (G.S.)
| | - Andrea Kosta
- Department of Molecular Medicine, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (A.G.); (G.P.); (H.S.); (A.K.); (A.G.); (A.S.); (G.S.)
| | - Cristina Capuano
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy;
| | - Angela Gismondi
- Department of Molecular Medicine, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (A.G.); (G.P.); (H.S.); (A.K.); (A.G.); (A.S.); (G.S.)
| | - Angela Santoni
- Department of Molecular Medicine, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (A.G.); (G.P.); (H.S.); (A.K.); (A.G.); (A.S.); (G.S.)
- IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Neuromed, 86077 Pozzilli, Italy
| | - Giuseppe Sciumè
- Department of Molecular Medicine, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (A.G.); (G.P.); (H.S.); (A.K.); (A.G.); (A.S.); (G.S.)
| | - Cinzia Fionda
- Department of Molecular Medicine, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00161 Rome, Italy; (A.G.); (G.P.); (H.S.); (A.K.); (A.G.); (A.S.); (G.S.)
- Correspondence: ; Tel.: +39-0649255118; Fax: +39-0644340632
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Hu X, Wang P, Qu C, Zhang H, Li L. Circular RNA Circ_0000677 promotes cell proliferation by regulating microRNA-106b-5p/CCND1 in non-small cell lung cancer. Bioengineered 2021; 12:6229-6239. [PMID: 34519258 PMCID: PMC8806897 DOI: 10.1080/21655979.2021.1965697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Recently, circular RNAs (circRNAs) have become an intense focus of research and large numbers of circRNAs have been identified, awaiting functional elucidation. Thus, the present study aims to examine the regulation of circRNAs and its molecular mechanism in lung cancer growth. Here, we show that circular RNA circ_0000677 was overexpressed and correlated with poor prognosis in non‐small cell lung cancer (NSCLC) patients. Functionally, circ_0000677 knockdown markedly inhibited proliferation of NSCLC cells by observing of immunofluorescence staining of Ki67, clone formation assay, and xenograft experiments. In mechanism, circ_0000677 acted as a sponge of microRNA-106b and further regulated CCDND1 gene expression in NSCLC cells by dual luciferase activity assay and their expression examination. Taken together, these findings suggest a role for circ_0000677/miR-106b/CCND1 regulation axis in promoting NSCLC growth and progression.
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Affiliation(s)
- Xin Hu
- Department Of Internal Medicine, Nantong Maternity And Child Health Hospital, Nantong, China
| | - Ping Wang
- Department Of Internal Medicine, Nantong Maternity And Child Health Hospital, Nantong, China
| | - Chen Qu
- Department Of Geriatrics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Haibo Zhang
- Department Of Internal Medicine, Nantong Maternity And Child Health Hospital, Nantong, China
| | - Liang Li
- Department Of Emergency Medicine, Shanghai Seventh People's Hospital, Shanghai, China
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Ma J, Meng Q, Zhan J, Wang H, Fan W, Wang Y, Zhang S, Bian H, Zheng F. Paeoniflorin Suppresses Rheumatoid Arthritis Development via Modulating the Circ-FAM120A/miR-671-5p/MDM4 Axis. Inflammation 2021; 44:2309-2322. [PMID: 34423389 DOI: 10.1007/s10753-021-01504-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/21/2021] [Accepted: 06/16/2021] [Indexed: 11/24/2022]
Abstract
Paeoniflorin is an active ingredient derived from Paeonia, which has an anti-inflammatory effect. However, the potential role and basis of paeoniflorin in rheumatoid arthritis (RA) are indistinct. Cell viability, cycle distribution, migration, and invasion were evaluated via Cell Counting Kit-8 (CCK-8), flow cytometry, and transwell assays. The contents of inflammatory cytokines were examined using enzyme-linked immunosorbent assay (ELISA). RNA expression levels were determined via qRT-PCR and western blot. The targeting relationship between miR-671-5p and circ-FAM120A (hsa_circ_0003972) or murine double minute 4 (MDM4) was validated via dual-luciferase reporter assay. Paeoniflorin restrained proliferation, migration, invasion, and inflammation and accelerated cell cycle arrest in RA fibroblast-like synoviocytes (RA-FLSs). Circ-FAM120A was boosted in RA synovial tissues and RA-FLSs. Circ-FAM120A upregulation, miR-671-5p knockdown, or MDM4 augmentation reversed the repressive effect of paeoniflorin on RA-FLS progression. Moreover, paeoniflorin attenuated RA-FLS progression by regulating the circ-FAM120A/miR-671-5p/MDM4 axis. Paeoniflorin inhibited RA-FLS proliferation, mobility, and inflammation and triggered cell cycle arrest via mediating the circ-FAM120A/miR-671-5p/MDM4 pathway.
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Affiliation(s)
- Junfu Ma
- Department of Rheumatology, Henan Province Hospital of Traditional Chinese Medicine (The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine), Henan University of Traditional Chinese Medicine, Henan Province, Zhengzhou City, China
| | - Qingliang Meng
- Department of Rheumatology, Henan Province Hospital of Traditional Chinese Medicine (The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine), Henan University of Traditional Chinese Medicine, Henan Province, Zhengzhou City, China
| | - Junping Zhan
- Department of Rheumatology, Henan Province Hospital of Traditional Chinese Medicine (The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine), Henan University of Traditional Chinese Medicine, Henan Province, Zhengzhou City, China
| | - Huilian Wang
- Department of Rheumatology, Henan Province Hospital of Traditional Chinese Medicine (The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine), Henan University of Traditional Chinese Medicine, Henan Province, Zhengzhou City, China
| | - Wei Fan
- Department of Rheumatology, Henan Province Hospital of Traditional Chinese Medicine (The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine), Henan University of Traditional Chinese Medicine, Henan Province, Zhengzhou City, China
| | - Yanqi Wang
- Henan Province Hospital of Traditional Chinese Medicine (The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine), Henan University of Traditional Chinese Medicine, Henan Province, Zhengzhou City, China
| | - Sudan Zhang
- Henan Province Hospital of Traditional Chinese Medicine (The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine), Henan University of Traditional Chinese Medicine, Henan Province, Zhengzhou City, China
| | - Hua Bian
- Zhang Zhongjing College of Chinese Medicine, Nanyang Institute of Technology, Henan Province, Nanyang City, China
| | - Fuzeng Zheng
- Department of Rheumatology, Henan Province Hospital of Traditional Chinese Medicine (The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine), Henan University of Traditional Chinese Medicine, Henan Province, Zhengzhou City, China. .,Department of Rheumatology, Henan Province Hospital of Traditional Chinese Medicine (The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine), Henan University of Traditional Chinese Medicine, Zhengzhou City, Henan Province, China.
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Zhang Y, Dong X, Hou L, Cao Z, Zhu G, Vongsangnak W, Xu Q, Chen G. Identification of Differentially Expressed Non-coding RNA Networks With Potential Immunoregulatory Roles During Salmonella Enteritidis Infection in Ducks. Front Vet Sci 2021; 8:692501. [PMID: 34222406 PMCID: PMC8242174 DOI: 10.3389/fvets.2021.692501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/20/2021] [Indexed: 01/22/2023] Open
Abstract
Salmonella enterica serovar Enteritidis (S. Enteritidis) is a pathogen that can colonize the preovulatory follicles of poultry, thereby causing both reduced egg production and an elevated risk of foodborne salmonellosis in humans. Although a few studies have revealed S. Enteritidis preferentially invades the granulosa cell layer within these follicles, it can readily persist and proliferate through mechanisms that are not well-understood. In this study, we characterized competing endogenous RNA (ceRNA) regulatory networks within duck granulosa cells following time-course of S. Enteritidis challenge. The 8108 long non-coding RNAs (lncRNAs), 1545 circular RNAs (circRNAs), 542 microRNAs (miRNAs), and 4137 mRNAs (fold change ≥2; P < 0.01) were differentially expressed during S. Enteritidis challenge. Also, eight mRNAs, eight lncRNAs and five circRNAs were selected and the consistent expression trend was found between qRT-PCR detection and RNA-seq. Moreover, the target genes of these differentially expressed ncRNAs (including lncRNAs, circRNAs and miRNAs) were predicted, and significantly enriched in the innate immune response and steroidogenesis pathways. Then, the colocalization and coexpression analyses were conducted to investigate relationships between ncRNAs and mRNAs. The 16 differentially expressed miRNAs targeting 60 differentially expressed mRNAs were identified in granulosa cells at 3 and 6 h post-infection (hpi) and enriched in the MAPK, GnRH, cytokine-cytokine receptor interaction, Toll-like receptor, endocytosis, and oxidative phosphorylation signaling pathways. Additionally, underlying lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA ceRNA networks were then constructed to further understand their interaction during S. Enteritidis infection. Lnc_012227 and novel_circ_0004892 were identified as ceRNAs, which could compete with miR-let-7g-5p and thereby indirectly modulating map3k8 expression to control S. Enteritidis infection. Together, our data thus identified promising candidate ncRNAs responsible for regulating S. Enteritidis infection in the preovulatory follicles of ducks, offering new insights regarding the ovarian transmission of this pathogen.
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Affiliation(s)
- Yu Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
| | - Xiaoqian Dong
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Lie Hou
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Zhengfeng Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Guoqiang Zhu
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Qi Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Guohong Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
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Zhou Y, Yu Z, Wang X, Chen W, Liu Y, Zhang Y, Yin J, Han S. Exosomal circRNAs contribute to intestinal development via the VEGF signalling pathway in human term and preterm colostrum. Aging (Albany NY) 2021; 13:11218-11233. [PMID: 33820870 PMCID: PMC8109075 DOI: 10.18632/aging.202806] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 02/08/2021] [Indexed: 12/21/2022]
Abstract
Human breast milk (HBM) provides essential nutrients for newborn growth and development, and contains a variety of biologically active ingredients that can affect gastrointestinal tract and immune system development in breastfed infants. HBM also contains mRNAs, microRNAs and lncRNAs, most of which are encapsulated in milk-derived exosomes and exhibit various important infant development related biological functions. While previous studies have shown that exosomal circRNAs are involved in the intestinal epithelial cells’ proliferation and repair. However, the effect of HBM exosomal circRNAs on intestinal development is not clear. In this study, we identified 6756 circRNAs both in preterm colostrum (PC) and term colostrum (TC), of which 66 were upregulated, and 42 were downregulated (|fold change>2|, p < 0.05) in PC. Pathway analysis showed that the VEGF signalling pathway was involved, and network analysis revealed that the differentially expressed circRNAs bound various miRNAs. Further analyses showed that has_circRNA_405708 and has_circRNA_104707 were involved in the VEGF signalling pathway, and that they all bound various mirRNAs. Exosomes found in preterm colostrum (PC) and term colostrum (TC) promoted VEGF protein expression and induced the proliferation and migration of small intestinal epithelial cells (FHCs). Exosomal circRNAs found in human colostrum (HC) binding to related miRNAs may regulate VEGF signalling, and intestinal development.
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Affiliation(s)
- Yahui Zhou
- Department of Pediatrics, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, China.,Department of Pediatrics, Fourth Clinical Medicine College, Nanjing Medical University, Nanjing 210029, China
| | - Zhangbin Yu
- Department of Pediatrics, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, China
| | - Xingyun Wang
- Department of Pediatrics, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, China
| | - Wenjuan Chen
- Department of Pediatrics, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, China
| | - Yiwen Liu
- Department of Pediatrics, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, China
| | - Yinghui Zhang
- Department of Pediatrics, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, China
| | - Jing Yin
- Department of Pediatrics, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, China
| | - Shuping Han
- Department of Pediatrics, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, China
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Liu C, Li N, Dai G, Cavdar O, Fang H. A narrative review of circular RNAs as potential biomarkers and therapeutic targets for cardiovascular diseases. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:578. [PMID: 33987276 PMCID: PMC8105802 DOI: 10.21037/atm-20-7929] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/10/2021] [Indexed: 12/31/2022]
Abstract
Circular RNAs (circRNAs), a novel class of non-coding RNA, are produced by back-splicing and were initially considered to be by-products of splicing. In recent years, computational technology and experimental evidence have revealed the tremendous amounts and potential physiological or pathological functions of this novel non-coding RNA species. At present, the roles of circRNAs in neurological diseases, immune diseases, and cancers have come to light. In addition, increasing studies have identified the expression profiles of circRNA in cardiovascular diseases (CVDs) and revealed the involvement of circRNAs in the pathogenesis of CVDs which are the leading cause of mortality and morbidity worldwide, and result in substantial health and financial burden. Despite current improvements in diagnostic and therapeutic approaches, survival and prognosis of CVDs patients remain relatively poor. Due to the involvements of circRNAs in CVDs and their outstanding characteristics of high stability, conservation, and tissue- or developmental-specificity, circRNA-based biomarkers or gene therapy may be effective approaches to reduce CVDs burden. In the review, we systematically summarized the formation mechanisms, functional models, and research approaches of circRNAs, and several circRNAs involved in CVDs. Finally, we proposed that developing circRNAs as biomarkers or circRNA-based therapeutic strategies based on biological or physical materials may be promising to diagnose or treat CVDs in the future.
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Affiliation(s)
- Chi Liu
- Department of Geriatrics Center, Jing’an District Central Hospital of Shanghai, Fudan University, Shanghai, China
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Nan Li
- Department of Geriatrics Center, Jing’an District Central Hospital of Shanghai, Fudan University, Shanghai, China
| | - Guifeng Dai
- Department of Geriatrics Center, Jing’an District Central Hospital of Shanghai, Fudan University, Shanghai, China
| | - Omer Cavdar
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hong Fang
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
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Li T, Luo R, Wang X, Wang H, Zhao X, Guo Y, Jiang H, Ma Y. Unraveling Stage-Dependent Expression Patterns of Circular RNAs and Their Related ceRNA Modulation in Ovine Postnatal Testis Development. Front Cell Dev Biol 2021; 9:627439. [PMID: 33816472 PMCID: PMC8017185 DOI: 10.3389/fcell.2021.627439] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/03/2021] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs (circRNAs) have been shown to function in the reproductive systems including testis. However, their expression, as well as function in testicular development of sheep remain undefined. Herein, we performed RNA sequencing to reveal circRNA temporal expression patterns in testes of Tibetan sheep from different stages of maturation (3M, 3-month-old; 1Y, 1-year-old; 3Y, 3-year-old). A total of 3,982, 414, and 4,060 differentially expressed (DE) circRNAs were uncovered from 3M vs 1Y, 1Y vs 3Y, and 3M vs 3Y, respectively. Functional enrichment assessment indicated that the source genes of DE circRNAs were primarily engaged in spermatogenesis and testicular immune privilege including blood-testis barrier (BTB). We subsequently constructed the core circRNA-miRNA-mRNA interaction network for genes related to testicular function, such as spermatogenesis, germ cell development, BTB, and cell cycle/meiosis. Furthermore, we validated the target associations between either circ_024949, circ_026259 or IGF1, and oar-miR-29b in this network, and revealed their similar expression signatures in developmental testes that they were extensively expressed in germ cells, Leydig cells, and Sertoli cells, thus suggesting their broad functions in the functional maintenance of Leydig cells and Sertoli cells, as well as the development and maturation of male germ cells. Meanwhile, circ_026259 was shown to promote IGF1 expression through inhibition of oar-miR-29b in sheep Sertoli cells. This work gives the first global view for the expression and regulation of circRNAs in sheep testis, which will be helpful for providing new insights into the molecular mechanism of ovine testis function.
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Affiliation(s)
- Taotao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ruirui Luo
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xia Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Huihui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xingxu Zhao
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Yunxia Guo
- College of Life Science, Hebei Agricultural University, Baoding, China
| | - Haitao Jiang
- Wenshang County Inspection and Testing Center, Jining, China
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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A Highly Conserved Circular RNA circRasGEF1B Enhances Antiviral Immunity by Regulating miR-21-3p/MITA Pathway in Lower Vertebrates. J Virol 2021; 95:JVI.02145-20. [PMID: 33441345 PMCID: PMC8092700 DOI: 10.1128/jvi.02145-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Circular RNAs (circRNAs) represent a class of widespread, diverse, and covalently closed circRNAs that function as microRNA (miRNA) sponges and crucial regulators of gene expression in mammals. However, the regulation and function of circRNAs in lower vertebrates are still unknown. Here, we first discover a highly conserved circRNA termed circRasGEF1B, which displays a high conservation from mammals to fish and serves as key regulator in eliciting antiviral immunity in teleost fish. Results indicate that circRasGEF1B was highly expressed in Siniperca chuatsi rhabdovirus-infected tissues and cells. Functionally, miR-21-3p could inhibit cellular antiviral responses significantly, whereas circRasGEF1B counteract the effects of miR-21-3p. In mechanism, the results demonstrate that circRasGEF1B acts as a competing endogenous RNA (ceRNA) of miR-21-3p to relieve the repressive effect of miR-21-3p on its target MITA, then enhance the innate antiviral responses. Our results not only provide a novel insight into the functions of circRNAs in lower vertebrates, but broaden our understanding of circRNAs in viral infection.IMPORTANCE Siniperca chuatsi rhabdovirus (SCRV) is a typical fish RNA rhabdovirus, which is one of the most significant viral pathogens in teleost fish and can cause severe hemorrhagic septicemia in freshwater and marine fishes. Here, we discovered a highly conserved circRNAs called circRasGEF1B, which acts as a key regulator for innate antiviral responses upon SCRV infection. circRasGEF1B acts as an endogenous sponge of miR-21-3p that downregulates miR-21-3p expression levels. circRasGEF1B is able to bind to miR-21-3p directly and regulates MITA expression. To our knowledge, this report is the first to characterize circRNA-miRNA regulatory networks that exist in lower vertebrates.
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Fang Z, Jiang C, Li S. The Potential Regulatory Roles of Circular RNAs in Tumor Immunology and Immunotherapy. Front Immunol 2021; 11:617583. [PMID: 33613544 PMCID: PMC7886782 DOI: 10.3389/fimmu.2020.617583] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs (circRNAs) are covalently closed RNA molecules in eukaryotes with features of high stability, tissue-specific and cell-specific expression. According to their biogenesis, circRNAs are mainly classified into five types, i.e. exonic circRNAs (EciRNAs), exon-intron circRNAs (EIciRNAs), intronic RNAs (CiRNAs), fusion circRNAs (f-circRNAs), and read-through circRNAs (rt-circRNAs). CircRNAs have been emerging as important non-coding regulatory RNAs in a variety of human cancers. CircRNA4s were revealed to exert regulatory function through multiple mechanisms, such as sponges/decoys of miRNAs and proteins, enhancers of protein functions, protein scaffolds, protein recruitment, or protein translation templates. Furthermore, some circRNAs are intensively associated with immune cells in tumor immune microenvironment (TIME), e.g. circARSP91 and natural killer cells. Through regulating immune checkpoint genes, circRNAs are demonstrated to modulate the immune checkpoint blockade immunotherapy, e.g. circCPA4 could up-regulate PD-L1 expression. In summary, we reviewed the molecular features of circRNAs and mechanisms how they exert functions. We further summarized functional implications of circRNA regulations in tumor immunology and immunotherapy. Further understanding of the regulatory roles of circRNAs in tumor immunology and immunotherapy will benefit tumor treatment.
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Affiliation(s)
- Zhixiao Fang
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunjie Jiang
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Shengli Li
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Azari H, Mousavi P, Karimi E, Sadri F, Zarei M, Rafat M, Shekari M. The expanding role of CDR1-AS in the regulation and development of cancer and human diseases. J Cell Physiol 2021; 236:771-790. [PMID: 32697389 DOI: 10.1002/jcp.29950] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 12/20/2022]
Abstract
CircRNAs are a superabundant and highly conserved group of noncoding RNAs (ncRNAs) that are characterized by their high stability and integrity compared with linear forms of ncRNAs. Recently, their critical role in gene expression regulation has been shown; thus, it is not far-fetched to believe that their abnormal expression can be a cause of different kinds of diseases such as cancer, neurodegenerative, and autoimmune diseases. They can have a function in variety of biological processes such as microRNA (miRNA) sponging, interacting with RNA-binding proteins, or even an ability to translate to proteins. A huge challenge in finding diagnostic biomarkers is finding noninvasive biomarkers that can be detected in human fluids, especially blood samples. CircRNAs are becoming candidate biomarkers for diagnosis and prognosis of these diseases through their ability to transverse from the blood-brain barrier and their broad presence in circulating exosomes. The circRNA for miRNA-7 (ciRS-7) is newly recognized, and acknowledged to being related to human pathology and cancer progression. In this review, we first briefly summarize the latest studies about their characteristics, biogenesis, and their mechanisms of action in the regulation and development of human diseases. Finally, we provide a list of diseases that are linked to one member of this novel class of ncRNAs called ciRS-7.
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Affiliation(s)
- Hanieh Azari
- Department of Medical Genetics, Faculty of Medicine Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Pegah Mousavi
- Department of Medical Genetics, Faculty of Medicine Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Elham Karimi
- Department of Medical Genetics, Faculty of Medicine Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Fatemeh Sadri
- Department of Medical Genetics, Faculty of Medicine Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mahboobeh Zarei
- Department of Medical Genetics, Faculty of Medicine Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Milad Rafat
- Department of Medical Genetics, Faculty of Medicine Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mohammad Shekari
- Department of Medical Genetics, Faculty of Medicine Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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Yin H, Zhang S, Shen M, Zhang Z, Huang H, Zhao Z, Guo X, Wu P. Integrative analysis of circRNA/miRNA/mRNA regulatory network reveals the potential immune function of circRNAs in the Bombyx mori fat body. J Invertebr Pathol 2021; 179:107537. [PMID: 33472087 DOI: 10.1016/j.jip.2021.107537] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/02/2021] [Accepted: 01/04/2021] [Indexed: 02/07/2023]
Abstract
Bombyx mori nucleopolyhedrosis virus (BmNPV) is one of the greatest threats to sustainable development of the sericulture industry. Circular RNA (circRNA), a type of non-coding RNA, has been shown to play important roles in gene expression regulation, immune response, and diseases. The fat body is a tissue with both metabolic and immune functions. To explore the potential immune function of circRNAs, we analyzed differentially expressed (DE)circRNAs, microRNAs(miRNAs), and mRNAs in the B. mori fat body in response to BmNPV infection using high-throughput RNA sequencing. A total of 77 DEcircRNAs, 32 DEmiRNAs, and 730 DEmRNAs that are associated with BmNPV infection were identified. We constructed a DEcircRNA/DEmiRNA/DEmRNA and DEcircRNA/DEmiRNA/BmNPV gene regulatory network and validated the differential expression of circ_0001432 and its corresponding miRNA (miR-2774c and miR-3406-5p) and mRNA (778467 and 101745232) in the network. Tissue-specific expression of circ_0001432 and its expression at different time points were also examined. KEGG pathway analysis of DEmRNAs, target genes of DEmiRNAs, and host genes of DEcircRNAs in the network showed that these genes were enriched in several metabolic pathways and signaling pathways, which could play important roles in insect immune responses. Our results suggest that circRNA could be involved in immune responses of the B. mori fat body and help in understanding the molecular mechanisms underlying silkworm-pathogen interactions.
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Affiliation(s)
- Haotong Yin
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China
| | - Shaolun Zhang
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212018, China
| | - Manman Shen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212018, China
| | - Zhengdong Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212018, China
| | - Haoling Huang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China
| | - Zhimeng Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China
| | - Xijie Guo
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212018, China
| | - Ping Wu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu 212018, China.
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Malmuthuge N, Guan LL. Noncoding RNAs: Regulatory Molecules of Host-Microbiome Crosstalk. Trends Microbiol 2021; 29:713-724. [PMID: 33419590 DOI: 10.1016/j.tim.2020.12.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 12/13/2022]
Abstract
Recent emerging evidence has revealed that regulatory noncoding RNAs (microRNAs, circular RNAs) modulate host-microbe interactions and they have been proposed as potential biomarkers of the host's response to microbiome-linked pathologies such as cancers, obesity, and neurodegenerative diseases. Interactions between microRNAs and circular RNAs, however, increase the complexity of the mechanisms that modulate host-microbe interactions. Current knowledge on these noncoding RNAs (ncRNAs) is mainly generated from well controlled germ-free or knockout (small) animal models. Application of such knowledge to effective modulation outcomes in humans (and livestock) is challenging due to the complex nature of microbiome-linked pathologies in larger outbred animals that constantly interact with the changing environment. This review critically discusses the findings of regulatory noncoding RNAs and their roles in microbiome-linked pathologies in small and large animals and provides insights on their roles as potential therapeutic agents to improve human (and livestock) health.
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Affiliation(s)
- Nilusha Malmuthuge
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, 5403 1 Ave S, Lethbridge, Alberta, Canada T1J 4B1
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5.
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Hao S, Qu R, Hu C, Wang M, Li Y. A Circular RNA Derived from Golgi Glycoprotein 1 mRNA Regulates KRAS Expression and Promotes Colorectal Cancer Progression by Targeting microRNA-622. Onco Targets Ther 2020; 13:12637-12648. [PMID: 33335404 PMCID: PMC7737168 DOI: 10.2147/ott.s284032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 11/29/2020] [Indexed: 01/11/2023] Open
Abstract
Background Circular RNAs (circRNAs) represent a distinct class of non-coding RNAs that have attracted substantial research attention in recent years. We identified a novel circRNA derived from golgi glycoprotein 1 mRNA (circ_GLG1), the role of which is unknown in colorectal cancer (CRC). The purpose of this study was to explore the potential roles and mechanisms of circ_GLG1 in CRC. Materials and Methods Quantitative reverse transcriptase-polymerase chain reaction analysis was performed to quantify circ_GLG1 expression in 40 pairs of CRC tissues and adjacent normal tissues as well as CRC cell lines. DLD1 CRC cells were transfected with a small-interfering RNA against circ_GLG1, after which cell proliferation, viability, invasion, and migration were measured through cell counting kit-8 colony-formation, transwell, and wound-healing assays, respectively. Dual-luciferase reporter assays were performed to explore the binding sites among circ_GLG1, miR-622, and Kirsten rat sarcoma (KRAS) transcripts. KRAS protein expression was detected using Western blot analysis. Results Circ_GLG1 expression was significantly higher in CRC tissues than in adjacent normal tissues. Knocking down circ_GLG1 in DLD1 cells inhibited tumor cell viability, proliferation, invasion, and migration, and these effects were reversed by co-transfecting an miR-622 inhibitor. Circ_GLG1 promoted KRAS expression at both the mRNA and protein levels by acting as an miR-622 sponge. Dual-luciferase reporter assays demonstrated that miR-622 interacted with circ_GLG1 and KRAS mRNA. Conclusion Our study revealed the role of the circ_GLG1–miR-622–KRAS axis in CRC. Moreover, our findings provide insight into the molecular mechanism of circ_GLG1 in CRC and suggest potential new biomarkers for diagnosing this disease.
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Affiliation(s)
- Shuhong Hao
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Rongfeng Qu
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Chunmei Hu
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Min Wang
- Department of General Surgery, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Yarong Li
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin, People's Republic of China
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MiR-5787 Attenuates Macrophages-Mediated Inflammation by Targeting TLR4/NF-κB in Ischemic Cerebral Infarction. Neuromolecular Med 2020; 23:363-370. [DOI: 10.1007/s12017-020-08628-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 10/28/2020] [Indexed: 01/26/2023]
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Li Y, Zhou S, Peng P, Wang X, Du L, Huo Z, Xu B. Emerging role of circular RNA in intervertebral disc degeneration: Knowns and unknowns (Review). Mol Med Rep 2020; 22:3057-3065. [PMID: 32945490 PMCID: PMC7453660 DOI: 10.3892/mmr.2020.11437] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 06/04/2020] [Indexed: 12/13/2022] Open
Abstract
Lower back pain (LBP) is one of the predominant factors contributing to dyskinesia and remains a serious social and economic burden worldwide. Intervertebral disc degeneration (IDD) is the leading cause of LBP; the existing IDD treatments cannot completely prevent IDD. Circular RNAs (circRNAs) are non‑coding RNAs resulting from back‑splicing with unique structural characteristics and functions. Accumulating evidence suggests that circRNAs are involved in the pathological process of IDD and modulate a range of IDD‑related genes or proteins. However, the underlying circRNA‑mediated regulatory mechanisms remain poorly understood. The aim of the present review is to describe the current understanding of circRNA characteristics, classification, biogenesis and function in relation to its specific roles in IDD. Additionally, the limitations on the current knowledge in the field and the future direction of IDD‑related research are also discussed.
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Affiliation(s)
- Yongjin Li
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin 300211, P.R. China
| | - Suzhe Zhou
- Department of General Practice, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, Fujian 361015, P.R. China
| | - Peng Peng
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China
| | - Xuke Wang
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin 300211, P.R. China
- Department of Minimally Invasive Spine Surgery, Luoyang Orthopedic-Traumatological Hospital, Luoyang, Henan 471002, P.R. China
| | - Lilong Du
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin 300211, P.R. China
| | - Zhenxin Huo
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin 300211, P.R. China
| | - Baoshan Xu
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin 300211, P.R. China
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