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Turgut H, Turanli B, Boz B. DCDA: CircRNA-Disease Association Prediction with Feed-Forward Neural Network and Deep Autoencoder. Interdiscip Sci 2024; 16:91-103. [PMID: 37978116 DOI: 10.1007/s12539-023-00590-y] [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: 03/20/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 11/19/2023]
Abstract
Circular RNA is a single-stranded RNA with a closed-loop structure. In recent years, academic research has revealed that circular RNAs play critical roles in biological processes and are related to human diseases. The discovery of potential circRNAs as disease biomarkers and drug targets is crucial since it can help diagnose diseases in the early stages and be used to treat people. However, in conventional experimental methods, conducting experiments to detect associations between circular RNAs and diseases is time-consuming and costly. To overcome this problem, various computational methodologies are proposed to extract essential features for both circular RNAs and diseases and predict the associations. Studies showed that computational methods successfully predicted performance and made it possible to detect possible highly related circular RNAs for diseases. This study proposes a deep learning-based circRNA-disease association predictor methodology called DCDA, which uses multiple data sources to create circRNA and disease features and reveal hidden feature codings of a circular RNA-disease pair with a deep autoencoder, then predict the relation score of the pair by a deep neural network. Fivefold cross-validation results on the benchmark dataset showed that our model outperforms state-of-the-art prediction methods in the literature with the AUC score of 0.9794.
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Affiliation(s)
- Hacer Turgut
- Computer Engineering Department, Marmara University, 34854, Istanbul, Türkiye.
| | - Beste Turanli
- Bioengineering Department, Marmara University, 34854, Istanbul, Türkiye
| | - Betül Boz
- Computer Engineering Department, Marmara University, 34854, Istanbul, Türkiye.
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2
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Cao QM, Boonchuen P, Chen TC, Lei S, Somboonwiwat K, Sarnow P. Virus-derived circular RNAs populate hepatitis C virus-infected cells. Proc Natl Acad Sci U S A 2024; 121:e2313002121. [PMID: 38319965 PMCID: PMC10873615 DOI: 10.1073/pnas.2313002121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/04/2024] [Indexed: 02/08/2024] Open
Abstract
It is known that pre-mRNAs in eukaryotic cells can be processed to circular RNAs by a backsplicing mechanism. Circular RNAs have great stability and can sequester proteins or small RNAs to exert functions on cellular pathways. Because viruses often exploit host pathways, we explored whether the RNA genome of the cytoplasmic hepatitis C virus is processed to yield virus-derived circRNAs (vcircRNAs). Computational analyses of RNA-seq experiments predicted that the viral RNA genome is fragmented to generate hundreds of vcircRNAs. More than a dozen of them were experimentally verified by rolling-circle amplification. VcircRNAs that contained the viral internal ribosome entry site were found to be translated into proteins that displayed proviral functions. Furthermore, two highly abundant, nontranslated vcircRNAs were shown to enhance viral RNA abundance. These findings argue that novel vcircRNA molecules modulate viral amplification in cells infected by a cytoplasmic RNA virus.
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Affiliation(s)
- Qian M. Cao
- Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA94305
| | - Pakpoom Boonchuen
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Mueang Nakhon Ratchasima30000, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok10330, Thailand
| | - Tzu-Chun Chen
- Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA94305
| | - Shaohua Lei
- Center of Excellence for Leukemia Studies, Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN38105
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN38105
| | - Kunlaya Somboonwiwat
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok10330, Thailand
| | - Peter Sarnow
- Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA94305
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3
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Tan J, Sahaer P, Li H, Han W, Sun H. The expression, function, and network regulation of circDNAJB6 in chicken macrophages under lipopolysaccharide (LPS) stimulation. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 151:105095. [PMID: 37951323 DOI: 10.1016/j.dci.2023.105095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/06/2023] [Accepted: 11/06/2023] [Indexed: 11/13/2023]
Abstract
Circular RNAs (circRNA) originate from back-splicing events that link a downstream 5'splice site to an upstream 3' splice site. Circular RNA has been shown to be involved in gene expression, interacting with microRNA and RNA binding proteins to affect transcription, splicing, translation, and other processes. However, little is known about the potential function of chicken circRNAs that trigger the pathogenesis. In a previous study, a circular RNA DNAJB6 (circDNAJB6) was identified as a typical covalently closed circular RNA that is abundant in chicken macrophages upon bacterial infection. It was identified that circDNAJB6 was formed by reverse splicing of exons 2 to 5 of the DNAJB6 gene by PCR amplification, Sanger sequencing, and RNase R exonuclease treatment. Moreover, circDNAJB6 had ability to exacerbate the lipopolysaccharides (LPS) induced cellular injury via reducing cell viability, increasing NO product and pro-inflammatory cytokines. In addition, bioinformatic analysis showed that five miRNAs were identified to interact with circDNAJB6, potentially targeting 75 genes, which were significantly enriched in the pathways of autophagy-animal and MAPK signaling. This study has provided and broadened a better understanding the function of circDNAJB6, which may exert potential biomarkers and act as potential targets for the treatment of bacterial infection.
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Affiliation(s)
- Jishuang Tan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Paizelaiti Sahaer
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Huan Li
- School of Biological and Chemical Engineering, Yangzhou Polytechnic College, Yangzhou, China
| | - Wei Han
- The Poultry Research Institute of Chinese Academy of Agricultural Sciences, Yangzhou, China
| | - Hongyan Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China; Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China.
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4
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Hong Y, Chen B, Wang C, Gui R, Zhai X, Qian Q, Ren X, Xie X, Jiang C. circPPP2R4 promotes colorectal cancer progression and reduces ROS production through the miR-646/FOXK1 axis. Mol Carcinog 2024; 63:106-119. [PMID: 37750597 DOI: 10.1002/mc.23639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/25/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023]
Abstract
Circular RNAs (circRNAs) play important roles in colorectal cancer (CRC) development and progression. This study aimed to investigate the function and molecular mechanism of circPPP2R4 in CRC. Based on bioinformatic analyses and validation by qRT-PCR, we identified a novel circRNA, circPPP2R4, which was upregulated in CRC tissues. Receiver operating characteristic curve analysis implied a high diagnostic value of circPPP2R4 for CRC. Additionally, high circPPP2R4 levels were positively correlated with advanced clinical stage and lymph node metastasis. Functionally, circPPP2R4 overexpression facilitated CRC cells proliferation, migration and invasion, whereas circPPP2R4 knockdown attenuated the malignant behaviors. In mouse models, circPPP2R4 overexpression remarkably promoted tumor growth and lung metastasis. Mechanistically, a series of experiments containing RIP, RNA pull-down, and dual-luciferase reporter assays revealed the circPPP2R4/miR-646/FOXK1 axis in CRC. Further experiments were conducted to verify that circPPP2R4 reduced reactive oxygen species generation to exert its oncogenic function by sponging miR-646 to upregulate FOXK1 expression. For the first time, we identified the regulatory role of circPPP2R4 in CRC pathogenesis, providing a potential diagnostic biomarker and therapeutic strategy for CRC.
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Affiliation(s)
- Yuntian Hong
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Clinical Center of Intestinal and Colorectal Diseases of Hubei Province, Wuhan, China
- Key Laboratory of Intestinal and Colorectal Diseases of Hubei Province, Wuhan, China
| | - Baoxiang Chen
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Clinical Center of Intestinal and Colorectal Diseases of Hubei Province, Wuhan, China
- Key Laboratory of Intestinal and Colorectal Diseases of Hubei Province, Wuhan, China
| | - Chun Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Rui Gui
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xiang Zhai
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Clinical Center of Intestinal and Colorectal Diseases of Hubei Province, Wuhan, China
- Key Laboratory of Intestinal and Colorectal Diseases of Hubei Province, Wuhan, China
| | - Qun Qian
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Clinical Center of Intestinal and Colorectal Diseases of Hubei Province, Wuhan, China
- Key Laboratory of Intestinal and Colorectal Diseases of Hubei Province, Wuhan, China
| | - Xianghai Ren
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Clinical Center of Intestinal and Colorectal Diseases of Hubei Province, Wuhan, China
- Key Laboratory of Intestinal and Colorectal Diseases of Hubei Province, Wuhan, China
| | - Xiaoyu Xie
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Clinical Center of Intestinal and Colorectal Diseases of Hubei Province, Wuhan, China
- Key Laboratory of Intestinal and Colorectal Diseases of Hubei Province, Wuhan, China
| | - Congqing Jiang
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Clinical Center of Intestinal and Colorectal Diseases of Hubei Province, Wuhan, China
- Key Laboratory of Intestinal and Colorectal Diseases of Hubei Province, Wuhan, China
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5
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Kong P, Tang X, Liu F, Tang X. Astragaloside IV regulates circ_0001615 and miR-873-5p/LASP1 axis to suppress colorectal cancer cell progression. Chem Biol Drug Des 2024; 103:e14423. [PMID: 38230773 DOI: 10.1111/cbdd.14423] [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: 08/21/2023] [Revised: 11/07/2023] [Accepted: 12/04/2023] [Indexed: 01/18/2024]
Abstract
Astragaloside IV (AS-IV) has exhibited pivotal anti-cancer efficacy in multiple types of cancer, including colorectal cancer (CRC). Meanwhile, circular RNA (circRNA) circ_0001615 has been reported to be involved in the malignant development of CRC. Herein, this study is expected to figure out the interaction between circ_0001615 and AS-IV on CRC progression. The 50% inhibition concentration (IC50), proliferation, apoptosis, and migration were detected by Cell Counting Kit-8 (CCK-8), 5-ethynyl-2'-deoxyuridine (EdU), flow cytometry, and wound healing assays. The expression of related proteins was examined by western blot. Circ_0001615, microRNA-873-5p (miR-873-5p), and LIM and SH3 protein 1 (LASP1) levels were detected by real-time quantitative polymerase chain reaction (RT-qPCR). The binding between miR-873-5p and circ_0001615, or LASP1, was predicted by Starbase, followed by verification by dual-luciferase reporter and RNA immunoprecipitation (RIP) assays. The biological role of circ_0001615 and AS-IV on CRC tumor growth was detected by the xenograft tumor model in vivo. According to the IC50 of AS-IV in CRC cells, the 100 ng/mL AS-IV treatment for 24 h was chosen for the following research: Our data confirmed that AS-IV is a beneficial anti-cancer agent in CRC cells. Furthermore, circ_0001615 and LASP1 expression were increased, and miR-873-5p was decreased in CRC patients and cell lines, whereas their expression exhibited an opposite trend in AS-IV-treated cells. Functionally, applying AS-IV might act as a beneficial anti-cancer effect by downregulating circ_0001615 in CRC cells in vitro. Mechanically, circ_0001615 serves as a sponge for miR-873-5p to affect LASP1 expression. In addition, AS-IV inhibited CRC cell growth in vivo by modulating circ_0001615. Overall, AS-IV could mitigate CRC development, at least in part, through the circ_0001615/miR-873-5p/LASP1 axis. These findings support a theoretical basis for an in-depth study of the function of AS-IV and the clinical treatment of CRC.
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Affiliation(s)
- Pengfei Kong
- Department of Anorectal of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of North Sichuan Medical College, Nanchong City, Sichuan, China
| | - Xuemei Tang
- Department of Ultrasound, Affiliated Hospital of North Sichuan Medical College, Nanchong City, China
| | - Fang Liu
- Department of Anorectal of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of North Sichuan Medical College, Nanchong City, Sichuan, China
| | - Xuegui Tang
- Department of Anorectal of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of North Sichuan Medical College, Nanchong City, Sichuan, China
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Zhu Y, Kong D, Wang Z, Li T, Tang T, Peng Y, Hu C, Chao J, Chen H, Chen Y, Guo A. Identification of Differential Circular RNA Expression Profiles and Functional Networks in Human Macrophages Induced by Virulent and Avirulent Mycobacterium tuberculosis Strains. Int J Mol Sci 2023; 24:17561. [PMID: 38139387 PMCID: PMC10744075 DOI: 10.3390/ijms242417561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Circular RNAs (circRNAs) are noncoding RNAs with diverse functions. However, most Mycobacterium tuberculosis (M.tb)-related circRNAs remain undiscovered. In this study, we infected THP-1 cells with virulent and avirulent M.tb strains and then sequenced the cellular circRNAs. Bioinformatic analysis predicted 58,009 circRNAs in all the cells. In total, 2035 differentially expressed circRNAs were identified between the M.tb-infected and uninfected THP-1 cells and 1258 circRNAs were identified in the virulent and avirulent M.tb strains. Further, the top 10 circRNAs were confirmed by Sanger sequencing, among which four circRNAs, namely circSOD2, circCHSY1, circTNFRSF21, and circDHTKD1, which were highly differentially expressed in infected cells compared with those in uninfected cells, were further confirmed by ring formation, specific primers, and RNase R digestion. Next, circRNA-miRNA-mRNA subnetworks were constructed, such as circDHTKD1/miR-660-3p/IL-12B axis. Some of the individual downstream genes, such as miR-660-3p and IL-12B, were previously reported to be associated with cellular defense against pathological processes induced by M.tb infection. Because macrophages are important immune cells and the major host cells of M.tb, these findings provide novel ideas for exploring the M.tb pathogenesis and host defense by focusing on the regulation of circRNAs during M.tb infection.
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Affiliation(s)
- Yifan Zhu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (T.L.)
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Delai Kong
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (T.L.)
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zijian Wang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (T.L.)
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ting Li
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (T.L.)
| | - Tian Tang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (T.L.)
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongchong Peng
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (T.L.)
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Changmin Hu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (T.L.)
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jin Chao
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, Institute of Infection and Inflammation, Medical College, China Three Gorges University, Yichang 443002, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (T.L.)
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingyu Chen
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (T.L.)
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Aizhen Guo
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (T.L.)
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, International Research Center for Animal Disease, Ministry of Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Xue L, Wang B, Zhu J, He Q, Huang F, Wang W, Tao L, Wang Y, Xu N, Yang N, Jin L, Zhang H, Gao N, Lei K, Zhang Y, Xiong C, Lei J, Zhang T, Geng Y, Li M. Profiling of differentially expressed circRNAs and functional prediction in peripheral blood mononuclear cells from patients with rheumatoid arthritis. Ann Med 2023; 55:175-189. [PMID: 36661308 PMCID: PMC9870011 DOI: 10.1080/07853890.2022.2156596] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) is a chronic autoimmune disease associated with an increased risk of death, but its underlying mechanisms are not fully understood. Circular RNAs (circRNAs) have recently been implicated in various biological processes. The aim of this study was to investigate the key circRNAs related to RA. METHODS A microarray assay was used to identify the differentially expressed circRNAs (DEcircRNAs) in peripheral blood mononuclear cells (PBMCs) from patients with RA compared to patients with osteoarthritis (OA) and healthy controls. Then, quantitative real-time PCR was applied to verify the DEcircRNAs, and correlations between the levels of DEcircRNAs and laboratory indices were analysed. We also performed extensive bioinformatic analyses including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genome (KEGG) pathway and potential circRNA-miRNA-mRNA network analyses to predict the function of these DEcircRNAs. RESULTS A total of 35,342 and 6146 DEcircRNAs were detected in RA patients compared to controls and OA patients, respectively. Nine out of the DEcircRNAs in RA were validated by real-time PCR. There were correlations between the levels of DEcircRNAs and some of the laboratory indices. GO analyses revealed that these DEcircRNAs in RA were closely related to cellular protein metabolic processes, gene expression, the immune system, cell cycle, posttranslational protein modification and collagen formation. Functional annotation of host genes of these DEcircRNAs was implicated in several significantly enriched pathways, including metabolic pathways, ECM-receptor interaction, the PI3K-Akt signalling pathway, the AMPK signalling pathway, leukocyte transendothelial migration, platelet activation and the cAMP signalling pathway, which might be responsible for the pathophysiology of RA. CONCLUSIONS The findings of this study may help to elucidate the role of circRNAs in the specific mechanism underlying RA.Key messagesMicroarray assays showed that a total of 35,342 and 6146 DEcircRNAs were detected in RA patients compared to controls and OA patients, respectively.Nine out of the DEcircRNAs in RA were validated by real-time PCR, and the levels of the DEcircRNAs were related to some of the laboratory indices.GO analyses revealed that the DEcircRNAs in RA were closely related to cellular protein metabolic processes, gene expression, the immune system, etc.Functional annotation of host genes of the DEcircRNAs in RA was implicated in several significantly enriched pathways, including metabolic pathways, ECM-receptor interaction, the PI3K-Akt signalling pathway, etc.
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Affiliation(s)
- Li Xue
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center for Endemic Disease of Shaanxi Province, Xi'an, China
| | - Biao Wang
- Department of Immunology and Pathogenic Biology, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jianhong Zhu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center for Endemic Disease of Shaanxi Province, Xi'an, China
| | - Qian He
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Fang Huang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Wei Wang
- Department of Bone and Joint Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Li Tao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yan Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Nan Xu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ni Yang
- Emergency Department, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Li Jin
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Hua Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ning Gao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ke Lei
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yanping Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Chaoliang Xiong
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jing Lei
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ting Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yan Geng
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,National Local Joint Engineering Research Centre of Biodiagnostics and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ming Li
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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8
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Mao Y, Zhao K, Chen N, Fu Q, Zhou Y, Kong C, Li P, Yang C. A 2-decade bibliometric analysis of epigenetics of cardiovascular disease: from past to present. Clin Epigenetics 2023; 15:184. [PMID: 38007493 PMCID: PMC10676610 DOI: 10.1186/s13148-023-01603-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 11/14/2023] [Indexed: 11/27/2023] Open
Abstract
BACKGROUND Cardiovascular disease (CVD) remains a major health killer worldwide, and the role of epigenetic regulation in CVD has been widely studied in recent decades. Herein, we perform a bibliometric study to decipher how research topics in this field have evolved during the past 2 decades. RESULTS Publications on epigenetics in CVD produced during the period 2000-2022 were retrieved from the Web of Science Core Collection (WoSCC). We utilized Bibliometrix to build a science map of the publications and applied VOSviewer and CiteSpace to assess co-authorship, co-citation, co-occurrence, and bibliographic coupling. In total, 27,762 publications were included for bibliometric analysis. The yearly amount of publications experienced exponential growth. The top 3 most influential countries were China, the United States, and Germany, while the most cited institutions were Nanjing Medical University, Harbin Medical University, and Shanghai Jiao Tong University. Four major research trends were identified: (a) epigenetic mechanisms of CVD; (b) epigenetics-based therapies for CVD; (c) epigenetic profiles of specific CVDs; and (d) epigenetic biomarkers for CVD diagnosis/prediction. The latest and most important research topics, including "nlrp3 inflammasome", "myocardial injury", and "reperfusion injury", were determined by detecting citation bursts of co-occurring keywords. The most cited reference was a review of the current knowledge about how miRNAs recognize target genes and modulate their expression and function. CONCLUSIONS The number and impact of global publications on epigenetics in CVD have expanded rapidly over time. Our findings may provide insights into the epigenetic basis of CVD pathogenesis, diagnosis, and treatment.
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Affiliation(s)
- Yukang Mao
- Department of Cardiology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215000, Jiangsu, China
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China
| | - Kun Zhao
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China
| | - Nannan Chen
- Department of Cardiology, Yangpu Hospital, Tongji University School of Medicine, 450 Tengyue Road, Shanghai, 200090, China
| | - Qiangqiang Fu
- Department of General Practice, Clinical Research Center for General Practice, Yangpu Hospital, Tongji University School of Medicine, Shanghai, 200090, China
| | - Yimeng Zhou
- Department of Cardiology, Yangpu Hospital, Tongji University School of Medicine, 450 Tengyue Road, Shanghai, 200090, China
| | - Chuiyu Kong
- Department of Cardio-Thoracic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
- Institute of Cardiothoracic Vascular Disease, Nanjing University, Nanjing, China.
| | - Peng Li
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China.
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China.
| | - Chuanxi Yang
- Department of Cardiology, Yangpu Hospital, Tongji University School of Medicine, 450 Tengyue Road, Shanghai, 200090, China.
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9
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Shen Q, Gong W, Pan X, Cai J, Jiang Y, He M, Zhao S, Li Y, Yuan X, Li J. Comprehensive Analysis of CircRNA Expression Profiles in Multiple Tissues of Pigs. Int J Mol Sci 2023; 24:16205. [PMID: 38003395 PMCID: PMC10671760 DOI: 10.3390/ijms242216205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs with diverse functions, and previous studies have reported that circRNAs are involved in the growth and development of pigs. However, studies about porcine circRNAs over the past few years have focused on a limited number of tissues. Based on 215 publicly available RNA sequencing (RNA-seq) samples, we conducted a comprehensive analysis of circRNAs in nine pig tissues, namely, the gallbladder, heart, liver, longissimus dorsi, lung, ovary, pituitary, skeletal muscle, and spleen. Here, we identified a total of 82,528 circRNAs and discovered 3818 novel circRNAs that were not reported in the CircAtlas database. Moreover, we obtained 492 housekeeping circRNAs and 3489 tissue-specific circRNAs. The housekeeping circRNAs were enriched in signaling pathways regulating basic biological tissue activities, such as chromatin remodeling, nuclear-transcribed mRNA catabolic process, and protein methylation. The tissue-specific circRNAs were enriched in signaling pathways related to tissue-specific functions, such as muscle system process in skeletal muscle, cilium organization in pituitary, and cortical cytoskeleton in ovary. Through weighted gene co-expression network analysis, we identified 14 modules comprising 1377 hub circRNAs. Additionally, we explored circRNA-miRNA-mRNA networks to elucidate the interaction relationships between tissue-specific circRNAs and tissue-specific genes. Furthermore, our conservation analysis revealed that 19.29% of circRNAs in pigs shared homologous positions with their counterparts in humans. In summary, this extensive profiling of housekeeping, tissue-specific, and co-expressed circRNAs provides valuable insights into understanding the molecular mechanisms of pig transcriptional expression, ultimately deepening our understanding of genetic and biological processes.
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Affiliation(s)
- Qingpeng Shen
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Wentao Gong
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Xiangchun Pan
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Jiali Cai
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Yao Jiang
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA 6149, Australia
| | - Mingran He
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Shanghui Zhao
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Yipeng Li
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Xiaolong Yuan
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Jiaqi Li
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
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10
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Cai YJ, Huang W, Zhu LY, Lin YX, Huang CF, Yang WF, Zhou JL, Dong JD, Zhou WH, Qin QW, Sun HY. Identification of circRNAs and circRNA-mRNA network of Epinephelus coioides during Singapore grouper iridovirus infection. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109113. [PMID: 37788751 DOI: 10.1016/j.fsi.2023.109113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/19/2023] [Accepted: 09/24/2023] [Indexed: 10/05/2023]
Abstract
Circular RNA (circRNA), one of the important non-coding RNA molecules with a closed-loop structure, plays a key regulatory role in cell processing. In this study, circRNAs of Epinephelus coioides, an important marine cultured fish in China, were isolated and characterized, and the network of circRNAs and mRNA was explored during Singapore grouper iridovirus (SGIV) infection, one of the most important double stranded DNA virus pathogens of marine fish. 10 g of raw data was obtained by high-throughput sequencing, and 2599 circRNAs were classified. During SGIV infection, 123 and 37 circRNAs occurred differential expression in spleen and spleen cells, indicating that circRNAs would be involved in the viral infection. GO annotation and KEGG demonstrated that circRNAs could target E. coioides genes to regulate cell activity and the activation of immune factors. The results provide some insights into the circRNAs mediated immune regulatory network during bony fish virus infection.
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Affiliation(s)
- Yi-Jie Cai
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, 511450, Guangdong Province, PR China
| | - Wei Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, 511450, Guangdong Province, PR China
| | - Liang-Yuan Zhu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Yun-Xiang Lin
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Cui-Fen Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Wen-Feng Yang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Jia-Lin Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Jun-De Dong
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Wei-Hua Zhou
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Qi-Wei Qin
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, 511450, Guangdong Province, PR China.
| | - Hong-Yan Sun
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China; Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, 511450, Guangdong Province, PR China.
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11
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Ayyildiz D, Bergonzoni G, Monziani A, Tripathi T, Döring J, Kerschbamer E, Di Leva F, Pennati E, Donini L, Kovalenko M, Zasso J, Conti L, Wheeler VC, Dieterich C, Piazza S, Dassi E, Biagioli M. CAG repeat expansion in the Huntington's disease gene shapes linear and circular RNAs biogenesis. PLoS Genet 2023; 19:e1010988. [PMID: 37831730 PMCID: PMC10617732 DOI: 10.1371/journal.pgen.1010988] [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: 03/06/2022] [Revised: 10/31/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
Alternative splicing (AS) appears to be altered in Huntington's disease (HD), but its significance for early, pre-symptomatic disease stages has not been inspected. Here, taking advantage of Htt CAG knock-in mouse in vitro and in vivo models, we demonstrate a correlation between Htt CAG repeat length and increased aberrant linear AS, specifically affecting neural progenitors and, in vivo, the striatum prior to overt behavioral phenotypes stages. Remarkably, a significant proportion (36%) of the aberrantly spliced isoforms are not-functional and meant to non-sense mediated decay (NMD). The expanded Htt CAG repeats further reflect on a previously neglected, global impairment of back-splicing, leading to decreased circular RNAs production in neural progenitors. Integrative transcriptomic analyses unveil a network of transcriptionally altered micro-RNAs and RNA-binding proteins (Celf, hnRNPs, Ptbp, Srsf, Upf1, Ythd2) which might influence the AS machinery, primarily in neural cells. We suggest that this unbalanced expression of linear and circular RNAs might alter neural fitness, contributing to HD pathogenesis.
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Affiliation(s)
- Dilara Ayyildiz
- Bioinformatic facility, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
- Biomedical Sciences and Biotechnology, University of Udine, Udine, Italy
| | - Guendalina Bergonzoni
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Alan Monziani
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Takshashila Tripathi
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Jessica Döring
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Emanuela Kerschbamer
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Francesca Di Leva
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Elia Pennati
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Luisa Donini
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Marina Kovalenko
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jacopo Zasso
- Laboratory of Stem Cell Biology, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Luciano Conti
- Laboratory of Stem Cell Biology, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Vanessa C. Wheeler
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Neurology Harvard Medical School, Boston, Massachusetts, United States of America
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Silvano Piazza
- Bioinformatic facility, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Marta Biagioli
- NeuroEpigenetics laboratory, Department of Cellular, Computational and Integrative Biology, CIBIO, University of Trento, Trento, Italy
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12
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Martinez de Estibariz I, Jakjimovska A, Illarregi U, Martin-Guerrero I, Gutiérrez-Camino A, Lopez-Lopez E, Bilbao-Aldaiturriaga N. The Role of the Dysregulation of Long Non-Coding and Circular RNA Expression in Medulloblastoma: A Systematic Review. Cancers (Basel) 2023; 15:4686. [PMID: 37835380 PMCID: PMC10571996 DOI: 10.3390/cancers15194686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023] Open
Abstract
Medulloblastoma (MB) is the most common malignant brain tumor in childhood. Although recent multi-omic studies have led to advances in MB classification, there is still room for improvement with regard to treatment response and survival. Therefore, identification of new and less invasive biomarkers is needed to refine the diagnostic process and to develop more personalized treatment strategies. In this context, non-coding RNAs (ncRNAs) could be useful biomarkers for MB. In this article, we reviewed the role of two types of ncRNAs, long non-coding (lncRNAs) and circular RNAs (circRNAs), as biomarkers for the diagnosis, subgroup classification, and prognosis of MB. We also reviewed potential candidates with specific functions and mechanisms of action in the disease. We performed a search in PubMed and Scopus using the terms ("long non coding RNAs" OR "lncRNAs") and ("circular RNAs" OR "circRNAs") AND "medulloblastoma" to identify biomarker discovery or functional studies evaluating the effects of these ncRNAs in MB. A total of 26 articles met the inclusion criteria. Among the lncRNAs, the tumorigenic effects of the upregulated lnc-IRX3-80 and lnc-LRRC47-78 were the most studied in MB. Among the circRNAs, the upregulation of circSKA3 and its functional impact in MB cell lines were the most consistent results, so this circRNA could be considered a potential biomarker in MB. Additional validation is required for many deregulated lncRNAs and circRNAs; therefore, further studies are warranted.
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Affiliation(s)
- Ivan Martinez de Estibariz
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (I.M.d.E.); (U.I.); (I.M.-G.)
| | - Anastasija Jakjimovska
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
| | - Unai Illarregi
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (I.M.d.E.); (U.I.); (I.M.-G.)
| | - Idoia Martin-Guerrero
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (I.M.d.E.); (U.I.); (I.M.-G.)
- Pediatric Oncology Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Angela Gutiérrez-Camino
- Pediatric Oncology Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Elixabet Lopez-Lopez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
- Pediatric Oncology Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Nerea Bilbao-Aldaiturriaga
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
- Pediatric Oncology Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
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13
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Wang MN, Xie XJ, You ZH, Wong L, Li LP, Chen ZH. Combining K Nearest Neighbor With Nonnegative Matrix Factorization for Predicting Circrna-Disease Associations. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:2610-2618. [PMID: 35675235 DOI: 10.1109/tcbb.2022.3180903] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Accumulating evidences show that circular RNAs (circRNAs) play an important role in regulating gene expression, and involve in many complex human diseases. Identifying associations of circRNA with disease helps to understand the pathogenesis, treatment and diagnosis of complex diseases. Since inferring circRNA-disease associations by biological experiments is costly and time-consuming, there is an urgently need to develop a computational model to identify the association between them. In this paper, we proposed a novel method named KNN-NMF, which combines K nearest neighbors with nonnegative matrix factorization to infer associations between circRNA and disease (KNN-NMF). Frist, we compute the Gaussian Interaction Profile (GIP) kernel similarity of circRNA and disease, the semantic similarity of disease, respectively. Then, the circRNA-disease new interaction profiles are established using weight K nearest neighbors to reduce the false negative association impact on prediction performance. Finally, Nonnegative Matrix Factorization is implemented to predict associations of circRNA with disease. The experiment results indicate that the prediction performance of KNN-NMF outperforms the competing methods under five-fold cross-validation. Moreover, case studies of two common diseases further show that KNN-NMF can identify potential circRNA-disease associations effectively.
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14
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Wu Q, Deng Z, Zhang W, Pan X, Choi KS, Zuo Y, Shen HB, Yu DJ. MLNGCF: circRNA-disease associations prediction with multilayer attention neural graph-based collaborative filtering. Bioinformatics 2023; 39:btad499. [PMID: 37561093 PMCID: PMC10457666 DOI: 10.1093/bioinformatics/btad499] [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: 05/17/2023] [Revised: 06/17/2023] [Accepted: 08/09/2023] [Indexed: 08/11/2023] Open
Abstract
MOTIVATION CircRNAs play a critical regulatory role in physiological processes, and the abnormal expression of circRNAs can mediate the processes of diseases. Therefore, exploring circRNAs-disease associations is gradually becoming an important area of research. Due to the high cost of validating circRNA-disease associations using traditional wet-lab experiments, novel computational methods based on machine learning are gaining more and more attention in this field. However, current computational methods suffer to insufficient consideration of latent features in circRNA-disease interactions. RESULTS In this study, a multilayer attention neural graph-based collaborative filtering (MLNGCF) is proposed. MLNGCF first enhances multiple biological information with autoencoder as the initial features of circRNAs and diseases. Then, by constructing a central network of different diseases and circRNAs, a multilayer cooperative attention-based message propagation is performed on the central network to obtain the high-order features of circRNAs and diseases. A neural network-based collaborative filtering is constructed to predict the unknown circRNA-disease associations and update the model parameters. Experiments on the benchmark datasets demonstrate that MLNGCF outperforms state-of-the-art methods, and the prediction results are supported by the literature in the case studies. AVAILABILITY AND IMPLEMENTATION The source codes and benchmark datasets of MLNGCF are available at https://github.com/ABard0/MLNGCF.
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Affiliation(s)
- Qunzhuo Wu
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China
| | - Zhaohong Deng
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China
| | - Wei Zhang
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China
| | - Xiaoyong Pan
- Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai, China
| | - Kup-Sze Choi
- The Centre for Smart Health, The Hong Kong Polytechnic University, Hong Kong
| | - Yun Zuo
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai, China
| | - Dong-Jun Yu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, China
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15
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Yu F, Duan Y, Liu C, Huang H, Xiao X, He Z. Extracellular vesicles in atherosclerosis and vascular calcification: the versatile non-coding RNAs from endothelial cells and vascular smooth muscle cells. Front Med (Lausanne) 2023; 10:1193660. [PMID: 37469665 PMCID: PMC10352799 DOI: 10.3389/fmed.2023.1193660] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/12/2023] [Indexed: 07/21/2023] Open
Abstract
Atherosclerosis (AS) is characterized by the accumulation of lipids, fibrous elements, and calcification in the innermost layers of arteries. Vascular calcification (VC), the deposition of calcium and phosphate within the arterial wall, is an important characteristic of AS natural history. However, medial arterial calcification (MAC) differs from intimal calcification and cannot simply be explained as the consequence of AS. Endothelial cells (ECs) and vascular smooth muscle cells (VSMCs) are directly involved in AS and VC processes. Understanding the communication between ECs and VSMCs is critical in revealing mechanisms underlying AS and VC. Extracellular vesicles (EVs) are found as intercellular messengers in kinds of physiological processes and pathological progression. Non-coding RNAs (ncRNAs) encapsulated in EVs are involved in AS and VC, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). The effects of ncRNAs have not been comprehensively understood, especially encapsulated in EVs. Some ncRNAs have demonstrated significant roles in AS and VC, but it remains unclear the functions of the majority ncRNAs detected in EVs. In this review, we summarize ncRNAs encapsulated in EC-EVs and VSMC-EVs, and the signaling pathways that are involved in AS and VC.
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Affiliation(s)
- Fengyi Yu
- Department of Nephrology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Yingjie Duan
- Department of Nephrology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Chongmei Liu
- Department of Pathology, Yueyang People's Hospital, Yueyang, Hunan, China
| | - Hong Huang
- Hengyang Medical School, The First Affiliated Hospital, Institute of Clinical Medicine, University of South China, Hengyang, Hunan, China
| | - Xiangcheng Xiao
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhangxiu He
- Department of Nephrology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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16
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Xiong H, Huang G, Zhu Y, Chen R, Zuo L, Liu H. Circ-SHPRH in human cancers: a systematic review and meta-analysis. Front Cell Dev Biol 2023; 11:1182900. [PMID: 37305675 PMCID: PMC10248025 DOI: 10.3389/fcell.2023.1182900] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/16/2023] [Indexed: 06/13/2023] Open
Abstract
Circular RNA (circRNA) molecules are noncoding RNAs with ring-like structures formed by covalent bonds and are characterized by no 5'caps or 3'polyadenylated tails. Increasing evidence shows that circRNAs may play an important role in tumorigenesis and cancer metastasis. Circ-SHPRH originates from exons 26-29 of the SHPRH gene, and it is closely associated with human cancers. We searched PubMed, Web of Science, and Embase databases for relevant literatures until 24 December 2022. Eighteen research papers were included in this review, and 11 papers were selected for meta-analysis after screening. Three eligible published studies about circ-SHPRH were enrolled based on their tumor diagnosis aspect, 7 eligible published studies were related to overall survival (OS), and 3 eligible published studies were related to tumor grade. Many studies have shown that circ-SHPRH acts as a miRNA sponge or encodes a protein to regulate downstream genes or signal pathways, and exerts specific biological functions that affect the proliferation, invasion, and apoptosis of cancer cells. Meta-analysis showed that patients with high expression of circ-SHPRH had better OS (HR = 0.53, 95% CI 0.38-0.74, p-value <0.05) and lower TNM stage (HR = 0.33, 95% CI 0.18-0.62, p-value = 0.001). In addition, circ-SHPRH has potential diagnostic value (AUC = 0.8357). This review will help enrich our understanding of the role and mechanism of circ-SHPRH in human cancers. Circ-SHPRH has the potential to be a novel diagnostic and prognostic biomarker for various solid cancers.
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Affiliation(s)
- Hong Xiong
- Laboratory of Urology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Gaozhen Huang
- Laboratory of Urology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Yi Zhu
- Laboratory of Urology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Ruiqi Chen
- Laboratory of Urology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Ling Zuo
- Department of Traditional Chinese Medicine, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Hongwei Liu
- Laboratory of Urology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
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17
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Moura SR, Fernandes MJ, Santos SG, Almeida MI. Circular RNAs: Promising Targets in Osteoporosis. Curr Osteoporos Rep 2023; 21:289-302. [PMID: 37119447 PMCID: PMC10169890 DOI: 10.1007/s11914-023-00786-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/21/2023] [Indexed: 05/01/2023]
Abstract
PURPOSE OF REVIEW Circular RNAs (circRNAs) are RNA transcripts derived from fragments of pre-messenger RNAs through a back-splicing process. An advantage that rises from their circular covalently closed conformation is their high stability, when compared with their linear counterparts. The current review focuses on the emerging roles of circRNAs in osteoporosis, including in osteogenic differentiation and osteoclastogenesis. Their potential as osteoporosis biomarkers will also be discussed. RECENT FINDINGS Although firstly described as non-coding, some of these single-stranded RNAs were recently reported to possess protein-coding capacity. On the other hand, the circRNAs exhibit cell and tissue-specific patterns at the transcriptome level in eukaryotes and are regulated throughout the development or disease progression. Even though thousands of these circular transcripts are listed and annotated, only a limited number of studies describe their biological role in bone processes. Recent evidence indicates inhibitory activator roles in both osteoblasts and osteoclasts differentiation and function. Latest screenings in the blood, plasma, or serum of osteoporosis patients support the potential for circRNA signature to be used as biomarkers in osteoporosis, but further validation is required. While intense research into circRNAs has been detailing their biological roles, there remains a need for standardization and further research to fulfil the future potential of this emerging and highly promising class of regulatory molecules.
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Affiliation(s)
- Sara Reis Moura
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Maria João Fernandes
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Susana G Santos
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal.
| | - Maria Inês Almeida
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
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Ren Y, Pan K, Wang Y, Zhang S, Wang Y, Zhou X, Dan H, Chen Q, Ji N, Li J. circFANCA accelerates the malignant process of OSCC by modulating miR-34a/PA28γ signaling. Biochem Biophys Res Commun 2023; 665:45-54. [PMID: 37148744 DOI: 10.1016/j.bbrc.2023.04.084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 04/24/2023] [Indexed: 05/08/2023]
Abstract
OBJECTIVES To investigate the upstream regulatory molecules of proteasomal activator 28γ (PA28γ), and explore its specific regulatory mechanism and potential clinical significance in OSCC. MATERIALS AND METHODS qPCR was used to examine miR-34a, circFANCA and PSME3 expression. Western blotting was adopted to detect PA28γ expression. Transwell experiments were conducted to evaluate OSCC cell migration and invasion ability. FISH was used to evaluate the subcellular localization of circFANCA and miR-34a, and RNA pull-down verified the interaction between them. The expression of circFANCA and miR-34a in clinical cohorts was assessed by ISH, and the results were subjected to survival analysis using Kaplan-Meier analysis. RESULTS Here, we proved that miR-34a expression is lower in highly aggressive OSCC tissues and cell lines. Notably, miR-34a can downregulate PA28γ expression and inhibit OSCC invasion and migration. Next, we confirmed that circFANCA promoted OSCC cell metastatic ability by sponging miR-34a. Importantly, interfering with miR-34a rescued the malignant progression of OSCC induced by silencing circFANCA. Finally, clinical data showed lower miR-34a expression and higher circFANCA expression were associated with poor prognosis in OSCC patients. CONCLUSION The circFANCA/miR-34a/PA28γ axis facilitates the metastasis of OSCC, and circFANCA and miR-34a have potential to serve as prognostic markers for OSCC patients.
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Affiliation(s)
- Yuan Ren
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, PR China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Keran Pan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Ying Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Shiyu Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Yimei Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Xikun Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - HongXia Dan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Ning Ji
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, PR China.
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Abbas MN, Kausar S, Gul I, Li J, Yu H, Dong M, Cui H. The Potential Biological Roles of Circular RNAs in the Immune Systems of Insects to Pathogen Invasion. Genes (Basel) 2023; 14:genes14040895. [PMID: 37107653 PMCID: PMC10137924 DOI: 10.3390/genes14040895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/08/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Circular RNAs (circRNAs) are a newly discovered class of endogenously expressed non-coding RNAs (ncRNAs). They are highly stable, covalently closed molecules that frequently exhibit tissue-specific expression in eukaryotes. A small number of circRNAs are abundant and have been remarkably conserved throughout evolution. Numerous circRNAs are known to play important biological roles by acting as microRNAs (miRNAs) or protein inhibitors ('sponges'), by regulating the function of proteins, or by being translated themselves. CircRNAs have distinct cellular functions due to structural and production differences from mRNAs. Recent advances highlight the importance of characterizing circRNAs and their targets in a variety of insect species in order to fully understand how they contribute to the immune responses of these insects. Here, we focus on the recent advances in our understanding of the biogenesis of circRNAs, regulation of their abundance, and biological roles, such as serving as templates for translation and in the regulation of signaling pathways. We also discuss the emerging roles of circRNAs in regulating immune responses to various microbial pathogens. Furthermore, we describe the functions of circRNAs encoded by microbial pathogens that play in their hosts.
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Affiliation(s)
- Muhammad Nadeem Abbas
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
| | - Saima Kausar
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
| | - Isma Gul
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
| | - Jisheng Li
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
| | - Huijuan Yu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
| | - Mengyao Dong
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
| | - Hongjuan Cui
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
- Jinfeng Laboratory, Chongqing 401329, China
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20
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Gao YC, Jiang NN, Qin XJ, Jiang H, Wei LB, Gao JR. High-throughput data on circular RNA reveal novel insights into chronic glomerulonephritis. Genes Genomics 2023; 45:475-490. [PMID: 36264417 DOI: 10.1007/s13258-022-01320-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/27/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Circular RNAs (circRNAs), a unique novel type of RNA, have been widely reported to be involved in physiologic and pathologic processes in humans. However, the exact molecular pathogenesis of circRNAs in chronic glomerulonephritis (CGN) is far from clear. OBJECTIVE This paper aims to evaluate the specific expression profile of circRNAs in renal cortex tissues from Adriamycin-induced CGN rats. METHODS CircRNAs were screened in renal cortex tissues from 3 CGN rats and 3 control rats by using high-throughput sequencing (HTS). Then, 4 circRNAs were selected randomly for verification by quantitative real-time polymerase chain reaction (qRT-PCR). In addition, the differentially expressed (DE) circRNAs were analyzed by bioinformatics methods. RESULTS In total, 31 significantly DE circRNAs were identified, which revealed their potential roles in CGN; in particular, we found that 4 confirmed altered circRNAs (rno-circ-RNAs 689, 3217, 1327, and 5001) might play important roles in the development of CGN. CONCLUSION This study reveals a cluster of circRNAs that are DE in Adriamycin-induced CGN rats, which brings us closer to understanding the pathogenic mechanisms and may provide new potential targets for clinical treatment.
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Affiliation(s)
- Ya-Chen Gao
- Department of Nephrology, The First Affiliated Hospital of Anhui University of Chinese Medicine, 117 Meishan Road, Hefei, China
| | - Nan-Nan Jiang
- College of Pharmacy, Anhui University of Chinese Medicine, 103 Meishan Road, Hefei, China
| | - Xiu-Juan Qin
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, 117 Meishan Road, Hefei, 230031, China
| | - Hui Jiang
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, 117 Meishan Road, Hefei, 230031, China
| | - Liang-Bing Wei
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, 117 Meishan Road, Hefei, 230031, China
| | - Jia-Rong Gao
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, 117 Meishan Road, Hefei, 230031, China.
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21
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Tong Y, Zhang S, Riddle S, Song R, Yue D. Circular RNAs in the Origin of Developmental Lung Disease: Promising Diagnostic and Therapeutic Biomarkers. Biomolecules 2023; 13:biom13030533. [PMID: 36979468 PMCID: PMC10046088 DOI: 10.3390/biom13030533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/11/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023] Open
Abstract
Circular RNA (circRNA) is a newly discovered noncoding RNA that regulates gene transcription, binds to RNA-related proteins, and encodes protein microRNAs (miRNAs). The development of molecular biomarkers such as circRNAs holds great promise in the diagnosis and prognosis of clinical disorders. Importantly, circRNA-mediated maternal-fetus risk factors including environmental (high altitude), maternal (preeclampsia, smoking, and chorioamnionitis), placental, and fetal (preterm birth and low birth weight) factors are the early origins and likely to contribute to the occurrence and progression of developmental and pediatric cardiopulmonary disorders. Although studies of circRNAs in normal cardiopulmonary development and developmental diseases have just begun, some studies have revealed their expression patterns. Here, we provide an overview of circRNAs’ biogenesis and biological functions. Furthermore, this review aims to emphasize the importance of circRNAs in maternal-fetus risk factors. Likewise, the potential biomarker and therapeutic target of circRNAs in developmental and pediatric lung diseases are explored.
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Affiliation(s)
- Yajie Tong
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Shuqing Zhang
- School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Suzette Riddle
- Cardiovascular Pulmonary Research Laboratories, Departments of Pediatrics and Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Rui Song
- Lawrence D. Longo MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
- Correspondence: (R.S.); (D.Y.); Tel.: +01-909-558-4325 (R.S.); +86-24-9661551125 (D.Y.)
| | - Dongmei Yue
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Correspondence: (R.S.); (D.Y.); Tel.: +01-909-558-4325 (R.S.); +86-24-9661551125 (D.Y.)
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22
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Chen YF, Xu AP. Circular RNA circDLG1 (has_circ_0068706) functions as an oncogene in nonsmall cell lung cancer through regulating AKT/mTOR signaling and direct binding to miR-144. Kaohsiung J Med Sci 2023; 39:446-457. [PMID: 36876724 DOI: 10.1002/kjm2.12662] [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: 09/02/2022] [Revised: 12/09/2022] [Accepted: 12/22/2022] [Indexed: 03/07/2023] Open
Abstract
Nonsmall cell lung cancer (NSCLC) is a major subtype of lung cancer, causing substantial cancer-related deaths worldwide. However, the molecular basis of NSCLC development and progression remains understudied. Recently, a circular RNA, circDLG1, has been implicated in carcinogenesis and cancer metastasis. Yet, how circDLG1 affects NSCLC progression has not been reported. Here this study aims to elucidate the role of circDLG1 in NSCLC. First, we found that circDLG1 was significantly upregulated in both the GEO dataset and NSCLC tissues. Next, we silenced the expression of circDLG1 in NSCLC cell lines. Knockdown of circDLG1 upregulated miR-144 and downregulated Protein kinase B (AKT)/mechanistic target of rapamycin (mTOR), resulting in suppression of the proliferation activity and metastasis ability of NSCLC. In addition, circDLG1 knockdown significantly decreased the expression of the mesenchymal markers, proliferating cell nuclear antigen (PCNA), and N-cadherin, while increasing the expression level of E-cadherin. In conclusion, we demonstrate that circDLG1 promotes the pathogenesis and progression of NSCLC by regulating the miR-144/AKT/mTOR signaling axis, providing potential diagnostic and therapeutic targets for designing innovative treatment strategies.
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Affiliation(s)
- Yong-Feng Chen
- Department of Respiratory and Critical Care, Tongxiang First People's Hospital, Tongxiang, People's Republic of China
| | - Ai-Ping Xu
- Department of Respiratory and Critical Care, Tongxiang First People's Hospital, Tongxiang, People's Republic of China
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23
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Long Q, Lv B, Jiang S, Lin J. The Landscape of Circular RNAs in Cardiovascular Diseases. Int J Mol Sci 2023; 24:ijms24054571. [PMID: 36902000 PMCID: PMC10003248 DOI: 10.3390/ijms24054571] [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: 01/24/2023] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023] Open
Abstract
Cardiovascular disease (CVD) remains the leading cause of mortality globally. Circular RNAs (circRNAs) have attracted extensive attention for their roles in the physiological and pathological processes of various cardiovascular diseases (CVDs). In this review, we briefly describe the current understanding of circRNA biogenesis and functions and summarize recent significant findings regarding the roles of circRNAs in CVDs. These results provide a new theoretical basis for diagnosing and treating CVDs.
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Affiliation(s)
- Qi Long
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Bingjie Lv
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Shijiu Jiang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jibin Lin
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Correspondence:
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24
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Zhou J, Qiu C, Tang X, Wan R, Wu Z, Zou D, Wang W, Luo Y, Liu T. Investigation of the clinicopathological and prognostic role of circMTO1 in multiple cancers. Expert Rev Mol Diagn 2023; 23:159-170. [PMID: 36734331 DOI: 10.1080/14737159.2023.2177102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE To observe the prognostic value of circular RNA mitochondrial tRNA translation optimization 1 (circMTO1) in human tumors. METHODS We searched multiple databases for related reports published before November 01, 2021. The OR/HR and 95% CI were extracted to explore the correlation between circMTO1 expression and clinicopathological features in various cancers. The stability of the results from meta-analysis was estimated via sensitivity analysis. We adopted Begg's funnel plots and Egger's test to appraise the potential bias of publication. Subgroup analysis for overall survival (OS) were also performed. RESULTS 11 studies containing 1383 patients and 4 articles including 536 patients were enrolled. We found that low expression status of circMTO1 was significantly related to big tumor size (OR=2.11, 95% CI: 1.26-3.56, P<0.05), poor differentiation tumors (OR=2.09, 95% CI: 1.46-2.98, P<0.05), OS (HR=2.02, 95% CI: 1.63-2.50, P<0.05), disease-free survival (DFS) (HR=1.83, 95% CI: 1.27-2.56, P<0.05) of cancers. Subgroup analysis indicated that low expression status of circMTO1 was correlated with OS, regardless of analysis method, cut-off value, case number and NOS score. CONCLUSIONS The low expression of circMTO1 may predict big tumor size, poor differentiation and worse outcome of cancer, presenting that circMTO1 may be a useful biomarker for prognosis of tumors.
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Affiliation(s)
- Jian Zhou
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Cheng Qiu
- Department of Orthopaedic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xianzhe Tang
- Department of Orthopedics, Chenzhou No. 1 People's Hospital, Xiangnan University, Chenzhou, Hunan, China
| | - Rongjun Wan
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Respiratory Medicine, National Clinical Research Center for Geriatric Disorders, Xiangya Hospita, Changsha, Hunan, China
| | - Ziyi Wu
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Dazhi Zou
- Department of Spine Surgery, Longhui People's Hospital, Shaoyang, Hunan, China
| | - Wanchun Wang
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yingquan Luo
- Department of General Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Tang Liu
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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Tong X, Zhao X, Dang X, Kou Y, Kou J. circRNA, a novel diagnostic biomarker for coronary heart disease. Front Cardiovasc Med 2023; 10:1070616. [PMID: 36818340 PMCID: PMC9928865 DOI: 10.3389/fcvm.2023.1070616] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/05/2023] [Indexed: 02/04/2023] Open
Abstract
Objective This study aimed to identify the potential diagnostic biomarkers of coronary heart disease (CHD) from exosome-derived circRNA. Methods The microarray data of circRNA derived from the exosomes of patients with CHD and mRNA in acute myocardial infarction was retrieved from exoRBase website and GEO database (GSE61144), respectively, to identify the differentially expressed genes (DEGs). Our findings detected the differentially expressed circRNAs and mRNAs and predicted their correlation with microRNAs using the microRNA target prediction website, thus ascertaining the corresponding circ-microRNA and micro-mRNAs. Then, we performed systematic Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis on the differentially expressed mRNA. Protein-Protein Interactions (PPI) of these DEGs were examined using STRING. The receiver operator characteristic (ROC) curve was used to validate the diagnostic efficacy of circRNA in patients with CHD. Finally, the RNAs identified in this study were verified by quantitative real-time polymerase chain reaction (qRT-PCR). Results A total of 85 differentially expressed circRNAs (4 up-regulated and 81 down-regulated) were identified by screening the circRNAs in exosome of CHD patients. Based on the prediction data of circRNA, mRNA, and the corresponding microRNA, a ceRNA network was constructed, including 7 circRNA nodes, 5 microRNA nodes, and 2 mRNA nodes. Finally, validated by qRT-PCR testing, we found circRNA0001785, circRNA0000973, circRNA0001741, and circRNA0003922 to be the promising candidate for the effective prediction of CHD. These potential diagnostic markers can provide insight for further research on the occurrence of CHD or even acute coronary syndrome (ACS).
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Luo H, Zhu Y, Wang J, Wang Y, Wei L. Comprehensive profile and contrastive analysis of circular RNA expression in cervical squamous carcinoma and adenocarcinoma. PeerJ 2023; 11:e14759. [PMID: 36721776 PMCID: PMC9884480 DOI: 10.7717/peerj.14759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/27/2022] [Indexed: 01/27/2023] Open
Abstract
Background Numerous studies have shown circular RNA (circRNA) dysregulation is associated with the pathogenesis of cervical cancer,particularly in individual carcinoma variants. The aim of this study is to investigate and contrastively analyze the expression pattern of circRNAs in cervical squamous carcinoma and adenocarcinoma mediated by human papillomavirus type 16 (HPV-16). Methods The expression of circRNAs in cervical squamous carcinoma (SCC), adenocarcinoma (ADC) and adenosquamous carcinoma (ASC) tissues, together with the adjacent normal tissues (ANT), was profiled by high-throughput RNA sequencing (RNA-seq). Bioinformatics analysis and quantitative real time polymerase chain reaction (qRT-PCR) validation of the sequencing data were performed. A network of circRNA-miRNA (microRNA)-mRNA was then constructed according to predicted targets and function of candidate circRNAs. Results A total of 11,685 annotated circRNAs were identified in six cervical samples. There were 42 up-regulated and 98 down-regulated circRNAs. 215 circRNAs were up-regulated in SCC but down-regulated circRNAs in ADC, while 50 circRNAs displayed the opposite trend. Function enrichment analysis based on different expressions of circRNAs found that the most enriched pathway in all the three pathologic variants of cervical cancer was the "ubiquitin mediated proteolysis" pathway. Eight key candidate circRNAs derived from this pathway were further validated, and we noticed that several target miRNAs of candidate circRNAs could target the source genes. Based on this we constructed a related competing endogenous RNA (ceRNA) network. Conclusion Through a comprehensive interpretation of differentially expressed circRNAs in different pathologic variants of cervical cancer, this study provides new insights into the process of tumor differentiation mediated by HPV. Our results may help to complement the molecular typing and stem cell theory of cervical cancer.
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Affiliation(s)
- Hongxue Luo
- Department of Gynecology and Obstetrics, Peking University People’Hospital, Peking University, Beijing, China
| | - Yi Zhu
- Department of Gynecology and Obstetrics, Peking University People’Hospital, Peking University, Beijing, China
| | - Jiaqi Wang
- Department of Gynecology and Obstetrics, Peking University People’Hospital, Peking University, Beijing, China
| | - Yue Wang
- Department of Gynecology and Obstetrics, Peking University People’Hospital, Peking University, Beijing, China
| | - Lihui Wei
- Department of Gynecology and Obstetrics, Peking University People’Hospital, Peking University, Beijing, China
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He D, Li Z, Chen Y, Huang M. Circular RNA circ_0029589 promotes ox-LDL-induced endothelial cell injury through regulating RAB22A by serving as a sponge of miR-1197. Clin Hemorheol Microcirc 2023; 83:359-376. [PMID: 36683504 DOI: 10.3233/ch-221657] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND Dysfunction of endothelial cells is now considered a vital contributor to the pathogenesis of atherosclerosis (AS). Moreover, circular RNA (circRNA) circ_0029589 has been found to be involved in the regulation of oxidized low-density lipoprotein (ox-LDL)-induced endothelial cell damage. Nevertheless, its molecular mechanism in ox-LDL-triggered endothelial cell injury is poorly defined. METHODS Human umbilical vein endothelial cells (HUVECs) treated with ox-LDL were applied as cell models of AS. Circ_0029589, microRNA-1197 (miR-1197), and Ras-related protein Rab-22A (RAB22A) expression were detected using real-time quantitative polymerase chain reaction (RT-qPCR). Cell proliferation, apoptosis, angiogenesis, and invasion were detected using 3-(4, 5-dimethyl-2-thiazolyl)-2, 5-diphenyl-2-H-tetrazolium bromide (MTT), 5-ethynyl-2'-deoxyuridine (EdU), flow cytometry, tube formation, and transwell assays. Western blot analysis of Cleaved-caspase-3, B-cell lymphoma-2 related X protein (Bax), and RAB22A. IL-6, IL-1β, and Tumor necrosis factor α (TNF-α) levels were gauged using ELISA kits. Superoxide Dismutase (SOD) activity and Malondiahyde (MDA) level were assessed using special kits. Bioinformatics software predicted the binding between miR-1197 and circ_0029589 or RAB22A, which was proved using dual-luciferase reporter and RNA pull-down assays. RESULTS Circ_0029589 and RAB22A expression were strengthened, and miR-1197 was reduced in ox-LDL-treated HUVECs. Importantly, circ_0029589 silencing ameliorated ox-LDL-triggered HUVEC damage via promoting cell proliferation, tube formation ability, invasion, and repressing cell apoptosis, inflammation, and oxidative stress. Mechanical analysis suggested that circ_0029589 might affect RAB22A content through sponging miR-1197. CONCLUSION Circ_0090231 might protect against ox-LDL-mediated HUVEC injury via the miR-1197/RAB22A axis, which provides a therapeutic strategy for endothelial cell damage of AS.
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Affiliation(s)
- Dequan He
- Department of Cardiology, Heart Center, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Zhiliang Li
- Department of Cardiology, Heart Center, Zhujiang Hospital of Southern Medical University, Guangzhou, China.,Department of Cardiology, Heart Center, South China hospital, Health Science Center, Shenzhen University, Shenzhen, China
| | - Youquan Chen
- Department of Cardiology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ming Huang
- Department of Cardiology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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Integrating Analysis to Identify Differential circRNAs Involved in Goat Endometrial Receptivity. Int J Mol Sci 2023; 24:ijms24021531. [PMID: 36675045 PMCID: PMC9865150 DOI: 10.3390/ijms24021531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/27/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Endometrial receptivity is one of the main factors underlying a successful pregnancy, with reports substantiating the fact that suboptimal endometrial receptivity accounts for two-thirds of early implantation event failures. The association between circRNAs and endometrial receptivity in the goat remains unclear. This study aims to identify potential circRNAs and regulatory mechanisms related to goat endometrial receptivity. Therefore, the endometrial samples on day 16 of pregnancy and day 16 of the estrous cycle were analyzed using high-throughput RNA-seq and bioinformatics. The results show that 4666 circRNAs were identified, including 7 downregulated and 11 upregulated differentially expressed circRNAs (DE-circRNAs). Back-splicing and RNase R resistance verified the identified circRNAs. We predicted the competing endogenous RNA (ceRNA) regulatory mechanism and potential target genes of DE-circRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of these predicted target genes suggest that DE-circRNAs were significantly involved in establishing endometrial receptivity. Furthermore, Sanger sequencing, qPCR, correlation analysis and Fluorescence in Situ Hybridization (FISH) show that circ_MYRF derived from the host gene myelin regulatory factor (MYRF) might regulate the expression of interferon stimulating gene 15 (ISG15), thereby promoting the formation of endometrial receptivity. These novel findings may contribute to a better understanding of the molecular mechanisms regulating endometrial receptivity and promoting the maternal recognition of pregnancy (MRP).
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Ding M, Dai D, Yang W, Geng C, Cui G. Has_circ_0048764 promotes breast cancer progression by sponging miR-578 and regulating HMGA2 expression. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 42:448-463. [PMID: 36617513 DOI: 10.1080/15257770.2022.2155300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Circular RNAs (circRNAs) function as important regulators in the progression of cancers. The role of circRNA_0048764 (circ_0048764) in the development of breast cancer (BC) remains inconclusive. This work investigates the biological function and molecular mechanism of circ_0048764 in BC. METHODS Quantitative real-time PCR (qRT-PCR) was conducted to measure the expression levels of circ_0048764, microRNA-578 (miR-578) and high mobility group AT-hook 2 (HMGA2) mRNA. The viability of BC cells was examined by cell counting kit 8 (CCK-8) assay. Besides, cyclin D1, proliferating cell nuclear antigen (PCNA) and HMGA2 expression levels were detected by western blot. The migrative and invasive capability of BC cells were probed by transwell assay. The relationships between miR-578 and circ_0048764 or HMGA2 3'-UTR were validated by dual-luciferase reporter gene assay. RESULTS Circ_0048764 was highly expressed in BC tissues and cells, which was significantly associated with tumor size (≥2 cm), lymph node status (positive), and higher TNM stage of BC patients. Circ_0048764 depletion suppressed the proliferative, migrative, and invasive abilities of BC cells, which was rescued by transfection of miR-578 inhibitors. The binding sites were verified between circ_0048764 and miR-578. HMGA2 was identified to be a target of miR-578 in BC cells, and circ_0048764 positively regulated HMGA2 expression in BC cells via repressing miR-578. CONCLUSION Circ_0048764 promotes BC cell growth, migration and invasion via absorbing miR-578 and up-regulating HMGA2.
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Affiliation(s)
- Mingjian Ding
- Breast Center, The Fourth Hospital of Hebei Medical University, Shijiangzhuang, Hebei, P.R. China.,Department of Thyroid Mammary Gland, Cangzhou Central Hospital, Cangzhou, Hebei, P.R. China
| | - Dianlu Dai
- Department of Thyroid Mammary Gland, Cangzhou Central Hospital, Cangzhou, Hebei, P.R. China
| | - Wenhua Yang
- Department of Thyroid Mammary Gland, Cangzhou Central Hospital, Cangzhou, Hebei, P.R. China
| | - Cuizhi Geng
- Breast Center, The Fourth Hospital of Hebei Medical University, Shijiangzhuang, Hebei, P.R. China
| | - Guozhong Cui
- Department of Thyroid Mammary Gland, Cangzhou Central Hospital, Cangzhou, Hebei, P.R. China
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Chen X, Ren X, E J, Zhou Y, Bian R. Exosome-transmitted circ IFNGR2 Modulates Ovarian Cancer Metastasis via miR-378/ST5 Axis. Mol Cell Biol 2023; 43:22-42. [PMID: 36720469 PMCID: PMC9937009 DOI: 10.1080/10985549.2022.2160605] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/05/2022] [Indexed: 01/28/2023] Open
Abstract
Cancer-associated fibroblasts (CAFs)-derived exosomes have emerged as a key driver of ovarian cancer (OVCA) tumor progression. The mechanisms behind the specific circular RNA (circRNA) activity encapsulated by CAF-generated exosomes (CAF-exo) requires to be elucidated. Herein, this study selected specific circRNA (hsa_circIFNGR2) molecules and aimed to clarify novel function of CAF-derived exosomal circIFNGR2 on growth, and metastasis of OVCA cells. In this study, we clarified that the exosomes of CAFs originating from human ovarian cancer hindered tumor cell proliferation, metastasis and EMT in vitro. Interestingly, CAFs directly transferred exosomes into OVCA cells to enrich intracellular circIFNGR2 levels. Biologically, activation of exosomal circIFNGR2 blocked cell proliferation, metastasis and EMT. Mechanistically, enhanced circIFNGR2 activated the miR-378/ST5 axis and directly inhibited the malignant evolution of tumor cells. Furthermore, rescue experiments evidenced that circIFNGR2 and ST5 were two essential participants in OVCA, concretely manifested in the co-culture of OVCA cells with exosomes that reversed the effects of intracellular circIFNGR2 and ST5 depletion. Finally, we observed that CAF-exo treatment hindered tumor growth and increased the size and number of metastatic nodules in mice. Our study revealed a previously unknown regulatory pathway whereby CAFs-derived exosomes delivered circIFNGR2 and inhibited the malignant progression of OVCA by circIFNGR2/miR-378/ST5 axis.
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Affiliation(s)
- Xiaoping Chen
- Obstetrics and Gynecology Department, Yancheng First People's Hospital, Yancheng, China
| | - Xinping Ren
- Obstetrics and Gynecology Department, Yancheng First People's Hospital, Yancheng, China
| | - Jiaoting E
- Obstetrics and Gynecology Department, Yancheng First People's Hospital, Yancheng, China
| | - Yaqi Zhou
- Obstetrics and Gynecology Department, Yancheng First People's Hospital, Yancheng, China
| | - Rongfang Bian
- Obstetrics and Gynecology Department, Yancheng First People's Hospital, Yancheng, China
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Gao S, Zhang X, Bai W, Wang J, Jiang B. Circ-IGF1R Affects the Progression of Colorectal Cancer by Activating the miR-362-5p/HMGB3-Mediated Wnt/β-Catenin Signal Pathway. Biochem Genet 2022; 61:1210-1229. [DOI: 10.1007/s10528-022-10316-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
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Gareev I, Kudriashov V, Sufianov A, Begliarzade S, Ilyasova T, Liang Y, Beylerli O. The role of long non-coding RNA ANRIL in the development of atherosclerosis. Noncoding RNA Res 2022; 7:212-216. [PMID: 36157350 PMCID: PMC9467859 DOI: 10.1016/j.ncrna.2022.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/22/2022] [Accepted: 09/01/2022] [Indexed: 11/28/2022] Open
Abstract
Atherosclerosis is an important pathological basis of coronary heart disease, and the antisense non-coding RNA in the INK4 locus (ANRIL) is located in the genetically susceptible segment with the strongest correlation with it - the short arm 2 region 1 of chromosome 9 (Chr9p21). ANRIL can produce linear, circular and other transcripts through different transcriptional splicing methods, which can regulate the proliferation and apoptosis of related cells and closely related to the development of atherosclerotic plaques. Linear ANRIL can regulate proliferation of vascular smooth muscle cells (VSMCs) in plaques by chromatin modification, as well as affecting on proliferation and the apoptosis of macrophages at the transcriptional level; circular ANRIL can affect on proliferation and apoptosis of VSMCs by chromatin modification as well as interfering with rRNA maturation. In this review we describe the evolutionary characteristics of ANRIL, the formation and structure of transcripts, and the mechanism by which each transcript regulates the proliferation and apoptosis of vascular cells and then participates in atherosclerosis.
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Affiliation(s)
- Ilgiz Gareev
- Educational and Scientific Institute of Neurosurgery, Рeoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, Moscow, 117198, Russian Federation
| | | | - Albert Sufianov
- Educational and Scientific Institute of Neurosurgery, Рeoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, Moscow, 117198, Russian Federation.,Department of Neurosurgery, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Sema Begliarzade
- Republican Clinical Perinatal Center, Republic of Bashkortostan, 450106, Russia
| | - Tatiana Ilyasova
- Department of Internal Diseases, Bashkir State Medical University, Republic of Bashkortostan, Ufa, 450008, Russia
| | - Yanchao Liang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Ozal Beylerli
- Educational and Scientific Institute of Neurosurgery, Рeoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, Moscow, 117198, Russian Federation
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Bryl R, Piwocka O, Kawka E, Mozdziak P, Kempisty B, Knopik-Skrocka A. Cancer Stem Cells-The Insight into Non-Coding RNAs. Cells 2022; 11:cells11223699. [PMID: 36429127 PMCID: PMC9688207 DOI: 10.3390/cells11223699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
Since their initial identification three decades ago, there has been extensive research regarding cancer stem cells (CSCs). It is important to consider the biology of cancer stem cells with a particular focus on their phenotypic and metabolic plasticity, the most important signaling pathways, and non-coding RNAs (ncRNAs) regulating these cellular entities. Furthermore, the current status of therapeutic approaches against CSCs is an important consideration regarding employing the technology to improve human health. Cancer stem cells have claimed to be one of the most important group of cells for the development of several common cancers as they dictate features, such as resistance to radio- and chemotherapy, metastasis, and secondary tumor formation. Therapies which could target these cells may develop into an effective strategy for tumor eradication and a hope for patients for whom this disease remains uncurable.
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Affiliation(s)
- Rut Bryl
- Section of Regenerative Medicine and Cancer Research, Natural Sciences Club, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Oliwia Piwocka
- Section of Regenerative Medicine and Cancer Research, Natural Sciences Club, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
- Department of Electroradiology, Poznan University of Medical Sciences, 61-701 Poznań, Poland
- Doctoral School, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Emilia Kawka
- Section of Regenerative Medicine and Cancer Research, Natural Sciences Club, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Paul Mozdziak
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Bartosz Kempisty
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA
- Department of Human Morphology and Embryology, Division of Anatomy, Medical University of Wrocław, 50-367 Wroclaw, Poland
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University, 87-100 Torun, Poland
- Correspondence: or
| | - Agnieszka Knopik-Skrocka
- Section of Regenerative Medicine and Cancer Research, Natural Sciences Club, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
- Department of Cell Biology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
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Zheng J, Luo S, Long Y. Bioinformatic analysis and clinical diagnostic value of hsa_circ_0004099 in acute ischemic stroke. PLoS One 2022; 17:e0277832. [PMID: 36399471 PMCID: PMC9674149 DOI: 10.1371/journal.pone.0277832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022] Open
Abstract
This study investigates the expression and effect of hsa_circ_0004099 in acute ischemic stroke (AIS). We conducted a case-controlled study that included 40 patients with AIS within 24 hours and 40 healthy subjects during the same period as a control group. Differentially expressed circular RNAs (circRNAs) were obtained using GEO2R, and the expression of hsa_circ_0004099 was verified using RT-PCR. Correlation analysis of the National Institutes of Health Stroke Scale (NIHSS) disease severity score and ischemic time with hsa_circ_0004099 expression levels was also performed. The receiver operating characteristic (ROC) curve of hsa_circ_0004099 was constructed, and bioinformatic analysis of hsa_circ_0004099 was performed. NIHSS scores negatively correlated with hsa_circ_0004099 levels (P<0.001, r = -0.7053), whereas infarct time was negatively correlated with hsa_circ_0004099 levels (P<0.001, r = -0.5130); hsa_circ_0004099 could benefit clinical diagnosis (area under the curve [AUC]: 0.923 [95% confidence interval [CI]: 0.8680-0.9904]). Kyoto encyclopedia of genes and genomes (KEGG) analysis showed that hsa_circ_0004099 was enriched in several cancer pathways, which were collectively enriched in four genes namely TCF7L2, NRAS, CTNNB1, and KRAS. Eight core proteins were screened using a protein-protein interaction (PPI) network namely SMAD4, HIF1A, CTNNB1, CDKN1B, CDK6, FOXO3, KRAS, and NRAS. hsa_circ_0004099 is a potential clinical diagnostic marker. In addition, the possible role of hsa_circ_0004099 in the pathogenesis of AIS was analyzed using bioinformatics, which provided a new potential molecular target for AIS treatment.
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Affiliation(s)
- Jiqing Zheng
- Deparment of Rehabilitation, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Shuiming Luo
- Deparment of Rehabilitation, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yaobin Long
- Deparment of Rehabilitation, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
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Current Diagnostic Methods and Non-Coding RNAs as Possible Biomarkers in Huntington’s Disease. Genes (Basel) 2022; 13:genes13112017. [PMID: 36360254 PMCID: PMC9689996 DOI: 10.3390/genes13112017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Whether as a cause or a symptom, RNA transcription is recurrently altered in pathologic conditions. This is also true for non-coding RNAs, with regulatory functions in a variety of processes such as differentiation, cell identity and metabolism. In line with their increasingly recognized roles in cellular pathways, RNAs are also currently evaluated as possible disease biomarkers. They could be informative not only to follow disease progression and assess treatment efficacy in clinics, but also to aid in the development of new therapeutic approaches. This is especially important for neurological and genetic disorders, where the administration of appropriate treatment during the disease prodromal stage could significantly delay, if not halt, disease progression. In this review we focus on the current status of biomarkers in Huntington’s Disease (HD), a fatal hereditary and degenerative disease condition. First, we revise the sources and type of wet biomarkers currently in use. Then, we explore the feasibility of different RNA types (miRNA, ncRNA, circRNA) as possible biomarker candidates, discussing potential advantages, disadvantages, sources of origin and the ongoing investigations on this topic.
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36
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Blocking circ_0010235 suppresses acquired paclitaxel resistance of non-small cell lung cancer by sponging miR-512-5p to modulate FAM83F expression. Anticancer Drugs 2022; 33:1024-1034. [DOI: 10.1097/cad.0000000000001388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Liu W, Liang W, Xiong XP, Li JL, Zhou R. A circular RNA Edis-Relish-castor axis regulates neuronal development in Drosophila. PLoS Genet 2022; 18:e1010433. [PMID: 36301831 PMCID: PMC9612563 DOI: 10.1371/journal.pgen.1010433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
Circular RNAs (circRNAs) are a new group of noncoding/regulatory RNAs that are particularly abundant in the nervous system, however, their physiological functions are underexplored. Here we report that the brain-enriched circular RNA Edis (Ect4-derived immune suppressor) plays an essential role in neuronal development in Drosophila. We show that depletion of Edis in vivo causes defects in axonal projection patterns of mushroom body (MB) neurons in the brain, as well as impaired locomotor activity and shortened lifespan of adult flies. In addition, we find that the castor gene, which encodes a transcription factor involved in neurodevelopment, is upregulated in Edis knockdown neurons. Notably, castor overexpression phenocopies Edis knockdown, and reducing castor levels suppresses the neurodevelopmental phenotypes in Edis-depleted neurons. Furthermore, chromatin immunoprecipitation analysis reveals that the transcription factor Relish, which plays a key role in regulating innate immunity signaling, occupies a pair of sites at the castor promoter, and that both sites are required for optimal castor gene activation by either immune challenge or Edis depletion. Lastly, Relish mutation and/or depletion can rescue both the castor gene hyperactivation phenotype and neuronal defects in Edis knockdown animals. We conclude that the circular RNA Edis acts through Relish and castor to regulate neuronal development.
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Affiliation(s)
- Wei Liu
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Cancer and Blood Disorders Institute, Johns Hopkins All Children’s Hospital, St. Petersburg, Florida, United States of America
- Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, Florida, United States of America
| | - Weihong Liang
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Cancer and Blood Disorders Institute, Johns Hopkins All Children’s Hospital, St. Petersburg, Florida, United States of America
- Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, Florida, United States of America
| | - Xiao-Peng Xiong
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Jian-Liang Li
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
- National Institute of Environmental Health Sciences, Durham, North Carolina, United States of America
| | - Rui Zhou
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Cancer and Blood Disorders Institute, Johns Hopkins All Children’s Hospital, St. Petersburg, Florida, United States of America
- Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, Florida, United States of America
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
- * E-mail:
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Li M, Cui L, Zhang J, Wang S, Du M. The Critical Roles of Circular RNAs in Basic Research and Clinical Application of Female Reproductive-Related Diseases. Reprod Sci 2022; 30:1421-1434. [PMID: 36197632 DOI: 10.1007/s43032-022-01070-2] [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: 06/15/2022] [Accepted: 08/23/2022] [Indexed: 10/10/2022]
Abstract
Circular RNAs (circRNAs), produced by precursor mRNAs, are a type of covalently closed circular molecule without 5' caps and 3' polyadenylated tails. Recently, advances in high-throughput sequencing, transcriptomics and bioinformatics, have revealed that circRNAs with specific traits in tissue or cells play emerging roles in both physiological and panthological contexts instead of as simple by-products of transcription. However, bringing circRNAs to the forefront of clinical practice is still a long way off. In this review, we highlight the progress in the formation and function of circRNAs, and how circRNAs work in female reproductive-related diseases, such as recurrent spontaneous abortion, preeclampsia, and endometriosis. We also discussed the clinical potential of circRNAs as biomarkers, and therapeutic agents in female reproductive diseases as well as research controversies, technical issues, and biological knowledge gaps that need to be addressed. This review may instruct future basic research and clinical applications on circRNAs, especially in female reproduction.
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Affiliation(s)
- Mengdie Li
- NHC Key Lab of Reproduction Regulation, Laboratory for Reproductive Immunology, Hospital of Obstetrics and Gynecology, Shanghai Institute of Planned Parenthood Research), Fudan University Shanghai Medical College, ZhaoZhou Road 413, Shanghai, 200032, China.,Department of Gynecology, Jing'an District Central Hospital, Fudan University, Shanghai, China
| | - LiYuan Cui
- NHC Key Lab of Reproduction Regulation, Laboratory for Reproductive Immunology, Hospital of Obstetrics and Gynecology, Shanghai Institute of Planned Parenthood Research), Fudan University Shanghai Medical College, ZhaoZhou Road 413, Shanghai, 200032, China
| | - Jianping Zhang
- Department of Gynecology, Jing'an District Central Hospital, Fudan University, Shanghai, China
| | - Songcun Wang
- NHC Key Lab of Reproduction Regulation, Laboratory for Reproductive Immunology, Hospital of Obstetrics and Gynecology, Shanghai Institute of Planned Parenthood Research), Fudan University Shanghai Medical College, ZhaoZhou Road 413, Shanghai, 200032, China.
| | - Meirong Du
- NHC Key Lab of Reproduction Regulation, Laboratory for Reproductive Immunology, Hospital of Obstetrics and Gynecology, Shanghai Institute of Planned Parenthood Research), Fudan University Shanghai Medical College, ZhaoZhou Road 413, Shanghai, 200032, China. .,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China. .,State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macau SAR, China.
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Kadkhoda S, Ghafouri-Fard S, Noorbakhsh F, Ravaei S, Darbeheshti F, Amoli MM, Taslimi R, Shakoori A. The importance of regulatory pathway mediated by Circ0001955 in colorectal cancer. Exp Mol Pathol 2022; 128:104819. [PMID: 35914612 DOI: 10.1016/j.yexmp.2022.104819] [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: 06/28/2021] [Revised: 04/10/2022] [Accepted: 07/22/2022] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Colorectal cancer (CRC) has become one of the most common cancers in recent years. Given the importance that non-coding RNAs have recently acquired in various diseases including cancers, we decided to design this study to evaluate the expression levels of circ0001955/miR-145-5p/ONECUT2 axis in CRC. METHODS After bioinformatics analysis of GEO datasets related to CRC, a putative circ0001955/ miR-145-5p/ ONECUT2 pathway was assumed. Then, the expression levels of these genes were measured in 50 CRC samples and adjacent tissues by qRT- PCR. Also, correlation coefficients, receiver operating characteristic (ROC) curves, and correlation between circ0001955 levels with clinicopathological parameters of patients were analyzed. RESULTS Circ0001955 and ONECUT2 were considerably up-regulated, while the expression level of miR-145-5p was decreased in CRC samples compared with adjacent tissues (p < 0.05). Moreover, statistically significant correlations were observed between expression levels of circ0001955, miR-145-5p, and ONECUT2. We did not find any significant correlation between circ0001955 expression and clinicopathological parameters. CONCLUSION Our study showed that circ0001955 is dysregulated in CRC. This finding can open a new window for researchers for a better understanding of the potential pathways involved in CRC pathogenesis and, consequently, to find new treatment pathways.
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Affiliation(s)
- Sepideh Kadkhoda
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farshid Noorbakhsh
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Sima Ravaei
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Farzaneh Darbeheshti
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Medical Genetics Network (MeGeNe), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Mahsa M Amoli
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular -Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Taslimi
- Department of Gastroenterology, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| | - Abbas Shakoori
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Department of Medical Genetics, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran.
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In Silico Identification and Characterization of circRNAs as Potential Virulence-Related miRNA/siRNA Sponges from Entamoeba histolytica and Encystment-Related circRNAs from Entamoeba invadens. Noncoding RNA 2022; 8:ncrna8050065. [PMID: 36287117 PMCID: PMC9607107 DOI: 10.3390/ncrna8050065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/12/2022] [Accepted: 09/19/2022] [Indexed: 11/30/2022] Open
Abstract
Ubiquitous eukaryotic non-coding circular RNAs regulate transcription and translation. We have reported full-length intronic circular RNAs (flicRNAs) in Entamoeba histolytica with esterified 3′ss and 5′ss. Their 5′ss GU-rich elements are essential for their biogenesis and their suggested role in transcription regulation. Here, we explored whether exonic, exonic-intronic, and intergenic circular RNAs are also part of the E. histolytica and E. invadens ncRNA RNAome and investigated their possible functions. Available RNA-Seq libraries were analyzed with the CIRI-full software in search of circular exonic RNAs (circRNAs). The robustness of the analyses was validated using synthetic decoy sequences with bona fide back splice junctions. Differentially expressed (DE) circRNAs, between the virulent HM1:IMSS and the nonvirulent Rahman E. histolytica strains, were identified, and their miRNA sponging potential was analyzed using the intaRNA software. Respectively, 188 and 605 reverse overlapped circRNAs from E. invadens and E. histolytica were identified. The sequence composition of the circRNAs was mostly exonic although different to human circRNAs in other attributes. 416 circRNAs from E. histolytica were virulent-specific and 267 were nonvirulent-specific. Out of the common circRNAs, 32 were DE between strains. Finally, we predicted that 8 of the DE circRNAs could function as sponges of the bioinformatically reported miRNAs in E. histolytica, whose functions are still unknown. Our results extend the E. histolytica RNAome and allow us to devise a hypothesis to test circRNAs/miRNAs/siRNAs interactions in determining the virulent/nonvirulent phenotypes and to explore other regulatory mechanisms during amoebic encystment.
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Sun H, Yang Y, Ma Y, Li N, Tan J, Sun C, Li H. Analysis of circRNA expression in chicken HD11 cells in response to avian pathogenic E.coli. Front Vet Sci 2022; 9:1005899. [PMID: 36187840 PMCID: PMC9521048 DOI: 10.3389/fvets.2022.1005899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022] Open
Abstract
Avian pathogenic E. coli (APEC), one of the widespread zoonotic-pathogen, can cause a series of diseases collectively known as colibacillosis. This disease can cause thousands of million dollars economic loss each year in poultry industry and threaten to human health via meat or egg contamination. However, the detailed molecular mechanism underlying APEC infection is still not fully understood. Circular RNAs, a new type of endogenous noncoding RNA, have been demonstrated to involve in various biological processes. However, it is still not clear whether the circRNAs participate in host response against APEC infection. Herein, we utilized the high-throughput sequence technology to identify the circRNA expression profiles in APEC infected HD11 cells. A total of 49 differentially expressed (DE) circRNAs were detected in the comparison of APEC infected HD11 cells vs. wild type HD11 cells, which were involved in MAPK signaling pathway, Endocytosis, Focal adhesion, mTOR signaling pathway, and VEGF signaling pathway. Specifically, the source genes (BRAF, PPP3CB, BCL2L13, RAB11A, and TSC2) and their corresponding DE circRNAs may play a significant role in APEC infection. Moreover, based on ceRNA regulation, we constructed the circRNA-miRNA network and identified a couple of important regulatory relationship pairs related to APEC infection, including circRAB11A-gga-miR-125b-3p, circRAB11A-gga-miR-1696, and circTSC2-gga-miR-1649-5p. Results indicate that the aforementioned specific circRNAs and circRNA-miRNA network might have important role in regulating host immune response against APEC infection. This study is the first time to investigate the circRNAs expression profile and the biological function of the source genes of the identified DE circRNAs after APEC infection of chicken HD11 cells. These results would contribute to a better understanding of the molecular mechanisms in host response against APEC infection.
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Affiliation(s)
- Hongyan Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
- *Correspondence: Hongyan Sun
| | - Yexin Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yuyi Ma
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Nayin Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jishuang Tan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Changhua Sun
- School of Biological and Chemical Engineering, Yangzhou Polytechnic College, Yangzhou University, Yangzhou, China
| | - Huan Li
- School of Biological and Chemical Engineering, Yangzhou Polytechnic College, Yangzhou University, Yangzhou, China
- Huan Li
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The Pleiotropy of PAX5 Gene Products and Function. Int J Mol Sci 2022; 23:ijms231710095. [PMID: 36077495 PMCID: PMC9456430 DOI: 10.3390/ijms231710095] [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: 07/21/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
PAX5, a member of the Paired Box (PAX) transcription factor family, is an essential factor for B-lineage identity during lymphoid differentiation. Mechanistically, PAX5 controls gene expression profiles, which are pivotal to cellular processes such as viability, proliferation, and differentiation. Given its crucial function in B-cell development, PAX5 aberrant expression also correlates with hallmark cancer processes leading to hematological and other types of cancer lesions. Despite the well-established association of PAX5 in the development, maintenance, and progression of cancer disease, the use of PAX5 as a cancer biomarker or therapeutic target has yet to be implemented. This may be partly due to the assortment of PAX5 expressed products, which layers the complexity of their function and role in various regulatory networks and biological processes. In this review, we provide an overview of the reported data describing PAX5 products, their regulation, and function in cellular processes, cellular biology, and neoplasm.
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Chen T, Li L, Ye B, Chen W, Zheng G, Xie H, Guo Y. Knockdown of hsa_circ_0005699 attenuates inflammation and apoptosis induced by ox-LDL in human umbilical vein endothelial cells through regulation of the miR-450b-5p/NFKB1 axis. Mol Med Rep 2022; 26:290. [PMID: 35904173 PMCID: PMC9366159 DOI: 10.3892/mmr.2022.12806] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/10/2022] [Indexed: 12/03/2022] Open
Abstract
Atherosclerosis (AS) remains the leading cause of mortality throughout the world, and vascular endothelial cell dysfunction is one of the key events leading to this pathology. In recent years, there has been an increased interest in the role of circulating RNAs in various diseases; these noncoding RNAs can regulate gene products by acting as microRNA (miR) sponges. Furthermore, it has been shown that foam cells exhibit high expression levels of hsa_circ_0005699 (circ_0005699); however, to the best of our knowledge, no previous study has investigated the role of circ_0005699 in the regulation of vascular endothelial function. The present study employed human umbilical vein endothelial cells (HUVECs), which have been widely used to study vascular endothelial cell function. In addition, apolipoprotein E (ApoE)-deficient mice were used, which have been shown to rapidly develop AS and are widely used as a model of this disease. Cellular and biochemical techniques were performed, including gene transfection and short hairpin RNA-mediated gene silencing for cell transfection, luciferase reporter gene assay to confirm predicted genes, Cell Counting Kit-8 assay and flow cytometry to assess cell viability and apoptosis, and reverse transcription-quantitative PCR and western blotting for detection of mRNA and protein expression. In the present study, the expression levels of circ_0005699 were increased by oxidized low-density lipoprotein in a time- and dose-dependent manner in HUVECs; this was also associated with increased apoptosis of these cells. In addition, the expression levels of circ_0005699 were elevated, along with increased levels of inflammatory cytokines, in ApoE-deficient mice. An RNA pull-down assay indicated that circ_0005699 can bind miR-450b-5p to decrease its expression, whereas silencing of circ_0005699 resulted in increased expression of miR-450b-5p. In addition, the online bioinformatics tool starBase predicted NFKB1 as a target gene of miR-450b-5p, which was further confirmed by the luciferase reporter gene assay. Notably, knockdown of circ_0005699 resulted in the increased survival of HUVECs, which was associated with decreased protein expression levels of NFKB1 and inflammatory cytokines. By contrast, the effects of circ-0005699 silencing on survival were reversed by miR-450b-5p inhibition or NFKB1 overexpression. In conclusion, knockdown of circ_0005699 may ameliorate endothelial cell injury through regulation of the miR-450b-5P/NFKB1 signaling axis.
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Affiliation(s)
- Tao Chen
- Department of Vascular Surgery, Ganzhou People's Hospital, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi 341000, P.R. China
| | - Lei Li
- Department of Vascular Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116000, P.R. China
| | - Bo Ye
- Department of Vascular Surgery, Ganzhou People's Hospital, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi 341000, P.R. China
| | - Weiqing Chen
- Department of Vascular Surgery, Ganzhou People's Hospital, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi 341000, P.R. China
| | - Guofu Zheng
- Department of Vascular Surgery, Ganzhou People's Hospital, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi 341000, P.R. China
| | - Hailiang Xie
- Department of Vascular Surgery, Ganzhou People's Hospital, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi 341000, P.R. China
| | - Yi Guo
- Department of Vascular Surgery, Ganzhou People's Hospital, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi 341000, P.R. China
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Rahmani-Kukia N, Abbasi A. New insights on circular RNAs and their potential applications as biomarkers, therapeutic agents, and preventive vaccines in viral infections: with a glance at SARS-CoV-2. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:705-717. [PMID: 35992045 PMCID: PMC9375856 DOI: 10.1016/j.omtn.2022.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The occurrence of viral infections and approaches to handling them are very challenging and require prompt diagnosis and timely treatment. Recently, genomic medicine approaches have come up with the discovery of the competing endogenous RNA (ceRNA) network, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) on the basis of gene silencing. CircRNAs, as a group of non-encoded RNAs, make a loop-like structure by back-splicing through 3′ and 5′ ends. They are stable, abundant, specific, and highly conserved and can be quickly generated at large scales in vitro. CircRNAs have the potential to contribute in several cellular processes in a way that some serve as microRNA sponges, cellular transporters, protein-binding RNAs, transcriptional regulators, and immune system modulators. CircRNAs can even play an important role in modulating antiviral immune responses. In the present review, circRNAs’ biogenesis, function, and biomarker and therapeutic potential as well as their prospective applications as vaccines against viral infections such as SARS-CoV-2 are explained. By considering their unique properties, their potential to be used as novel vaccines, biomarkers, and a therapeutic approach appears possible.
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45
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Zhu C, Guo A, Sun B, Zhou Z. Comprehensive elaboration of circular RNA in multiple myeloma. Front Pharmacol 2022; 13:971070. [PMID: 36133810 PMCID: PMC9483726 DOI: 10.3389/fphar.2022.971070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/03/2022] [Indexed: 01/17/2023] Open
Abstract
Circular RNAs (circRNAs), a novel category of endogenous non-coding RNAs, are usually well conserved across different species with a covalent closed-loop structure. Existing and emerging evidence confirms that circRNAs can function as regulators of alternative splicing, microRNA and RNA-binding protein sponges and translation, as well as gene transcription. In consideration of their multi-faceted functions, circRNAs are critically involved in hematological malignancies including multiple myeloma (MM). In particular, circRNAs have been found to play vital roles in tumor microenvironment and drug resistance, which may grant them potential roles as biomarkers for MM diagnosis and targeted therapy. In this review, we comprehensively elaborate the current state-of-the-art knowledge of circRNAs in MM, and then focus on their potential as biomarkers in diagnosis and therapy of MM.
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Affiliation(s)
- Chunsheng Zhu
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Aoxiang Guo
- Department of Pharmacy, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Bao Sun
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacy, Central South University, Changsha, China
- National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Zheng Zhou, ; Bao Sun,
| | - Zheng Zhou
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Zheng Zhou, ; Bao Sun,
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46
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He Z, Ma Z, Yang D, Chen Q, He Z, Hu J, Deng F, Zhang Q, He J, Ye L, Chen H, He L, Huang X, Luo W, Yang S, Gu X, Zhang M, Yan T. Circular RNA expression profiles and CircSnd1-miR-135b/c-foxl2 axis analysis in gonadal differentiation of protogynous hermaphroditic ricefield eel Monopterus albus. BMC Genomics 2022; 23:552. [PMID: 35922747 PMCID: PMC9347082 DOI: 10.1186/s12864-022-08783-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The expression and biological functions of circular RNAs (circRNAs) in reproductive organs have been extensively reported. However, it is still unclear whether circRNAs are involved in sex change. To this end, RNA sequencing (RNA-seq) was performed in gonads at 5 sexual stages (ovary, early intersexual stage gonad, middle intersexual stage gonad, late intersexual stage gonad, and testis) of ricefield eel, and the expression profiles and potential functions of circRNAs were studied. RESULTS Seven hundred twenty-one circRNAs were identified, and the expression levels of 10 circRNAs were verified by quantitative real-time PCR (qRT-PCR) and found to be in accordance with the RNA-seq data, suggesting that the RNA-seq data were reliable. Then, the sequence length, category, sequence composition and the relationship between the parent genes of the circRNAs were explored. A total of 147 circRNAs were differentially expressed in the sex change process, and GO and KEGG analyses revealed that some differentially expressed (such as novel_circ_0000659, novel_circ_0004005 and novel_circ_0005865) circRNAs were closely involved in sex change. Furthermore, expression pattern analysis demonstrated that both circSnd1 and foxl2 were downregulated in the process of sex change, which was contrary to mal-miR-135b. Finally, dual-luciferase reporter assay and RNA immunoprecipitation showed that circSnd1 and foxl2 can combine with mal-miR-135b and mal-miR-135c. These data revealed that circSnd1 regulates foxl2 expression in the sex change of ricefield eel by acting as a sponge of mal-miR-135b/c. CONCLUSION Our results are the first to demonstrate that circRNAs have potential effects on sex change in ricefield eel; and circSnd1 could regulate foxl2 expression in the sex change of ricefield eel by acting as a sponge of mal-miR-135b/c. These data will be useful for enhancing our understanding of sequential hermaphroditism and sex change in ricefield eel or other teleosts.
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Affiliation(s)
- Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhijun Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qiqi Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhide He
- Luzhou City Department of Agricultural and Rural Affairs, Luzhou, 646000, Sichuan, China
| | - Jiaxiang Hu
- Sichuan Water Conservancy Vocational College, Chengdu, 611231, Sichuan, China
| | - Faqiang Deng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qian Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jiayang He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lijuan Ye
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Hongjun Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Liang He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaoli Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Wei Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shiyong Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaobin Gu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Liu J, Zhang Z, Zhu W, Shen Y, Gu Y, Zhang X, He L, Du J. CircFBXW4 regulates human trophoblast cell proliferation and invasion via targeting miR-324–3p/TJP1 axis in recurrent spontaneous abortion. Placenta 2022; 126:1-11. [DOI: 10.1016/j.placenta.2022.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/14/2022] [Accepted: 05/26/2022] [Indexed: 12/01/2022]
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Asim MN, Ibrahim MA, Imran Malik M, Dengel A, Ahmed S. Circ-LocNet: A Computational Framework for Circular RNA Sub-Cellular Localization Prediction. Int J Mol Sci 2022; 23:ijms23158221. [PMID: 35897818 PMCID: PMC9329987 DOI: 10.3390/ijms23158221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/15/2022] [Accepted: 07/20/2022] [Indexed: 02/04/2023] Open
Abstract
Circular ribonucleic acids (circRNAs) are novel non-coding RNAs that emanate from alternative splicing of precursor mRNA in reversed order across exons. Despite the abundant presence of circRNAs in human genes and their involvement in diverse physiological processes, the functionality of most circRNAs remains a mystery. Like other non-coding RNAs, sub-cellular localization knowledge of circRNAs has the aptitude to demystify the influence of circRNAs on protein synthesis, degradation, destination, their association with different diseases, and potential for drug development. To date, wet experimental approaches are being used to detect sub-cellular locations of circular RNAs. These approaches help to elucidate the role of circRNAs as protein scaffolds, RNA-binding protein (RBP) sponges, micro-RNA (miRNA) sponges, parental gene expression modifiers, alternative splicing regulators, and transcription regulators. To complement wet-lab experiments, considering the progress made by machine learning approaches for the determination of sub-cellular localization of other non-coding RNAs, the paper in hand develops a computational framework, Circ-LocNet, to precisely detect circRNA sub-cellular localization. Circ-LocNet performs comprehensive extrinsic evaluation of 7 residue frequency-based, residue order and frequency-based, and physio-chemical property-based sequence descriptors using the five most widely used machine learning classifiers. Further, it explores the performance impact of K-order sequence descriptor fusion where it ensembles similar as well dissimilar genres of statistical representation learning approaches to reap the combined benefits. Considering the diversity of statistical representation learning schemes, it assesses the performance of second-order, third-order, and going all the way up to seventh-order sequence descriptor fusion. A comprehensive empirical evaluation of Circ-LocNet over a newly developed benchmark dataset using different settings reveals that standalone residue frequency-based sequence descriptors and tree-based classifiers are more suitable to predict sub-cellular localization of circular RNAs. Further, K-order heterogeneous sequence descriptors fusion in combination with tree-based classifiers most accurately predict sub-cellular localization of circular RNAs. We anticipate this study will act as a rich baseline and push the development of robust computational methodologies for the accurate sub-cellular localization determination of novel circRNAs.
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Affiliation(s)
- Muhammad Nabeel Asim
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
- Correspondence:
| | - Muhammad Ali Ibrahim
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Muhammad Imran Malik
- School of Computer Science & Electrical Engineering, National University of Sciences and Technology, Islamabad 44000, Pakistan;
| | - Andreas Dengel
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- Department of Computer Science, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Sheraz Ahmed
- German Research Center for Artificial Intelligence (DFKI), 67663 Kaiserslautern, Germany; (M.A.I.); (A.D.); (S.A.)
- DeepReader GmbH, Trippstadter Str. 122, 67663 Kaiserslautern, Germany
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Johannsen EB, Just J, Viuff MH, Okholm TLH, Pedersen SB, Meyer Lauritsen K, Trolle C, Pedersen MGB, Chang S, Fedder J, Skakkebæk A, Gravholt CH. Sex chromosome aneuploidies give rise to changes in the circular RNA profile: A circular transcriptome-wide study of Turner and Klinefelter syndrome across different tissues. Front Genet 2022; 13:928874. [PMID: 35938026 PMCID: PMC9355307 DOI: 10.3389/fgene.2022.928874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose: The landscape of circular RNAs (circRNAs), an important class of non-coding RNAs that regulate gene expression, has never been described in human disorders of sex chromosome aneuploidies. We profiled circRNAs in Turner syndrome females (45,X; TS) and Klinefelter syndrome males (47,XXY; KS) to investigate how circRNAs respond to a missing or an extra X chromosome. Methods: Samples of blood, muscle and fat were collected from individuals with TS (n = 33) and KS (n = 22) and from male (n = 16) and female (n = 44) controls. CircRNAs were identified using a combination of circRNA identification pipelines (CIRI2, CIRCexplorer2 and circRNA_finder). Results: Differential expression of circRNAs was observed throughout the genome in TS and KS, in all tissues. The host-genes from which several of these circRNAs were derived, were associated with known phenotypic traits. Furthermore, several differentially expressed circRNAs had the potential to capture micro RNAs that targeted protein-coding genes with altered expression in TS and KS. Conclusion: Sex chromosome aneuploidies introduce changes in the circRNA transcriptome, demonstrating that the genomic changes in these syndromes are more complex than hitherto thought. CircRNAs may help explain some of the genomic and phenotypic traits observed in these syndromes.
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Affiliation(s)
- Emma B. Johannsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Departments of Clinical Medicine, Aarhus University, Aarhus, Denmark
- *Correspondence: Emma B. Johannsen,
| | - Jesper Just
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Departments of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mette H. Viuff
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Trine Line Hauge Okholm
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Otolaryngology-Head and Neck Surgery and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States
| | | | - Katrine Meyer Lauritsen
- Steno Diabetes Center, Aarhus University Hospital, Aarhus, Denmark
- Department of Endocrinology, Aarhus University Hospital, Aarhus, Denmark
| | - Christian Trolle
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Endocrinology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Simon Chang
- Department of Endocrinology, Aarhus University Hospital, Aarhus, Denmark
| | - Jens Fedder
- Centre of Andrology and Fertility Clinic, Department D, Odense University Hospital, Odense, Denmark
- Research Unit of Human Reproduction, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Anne Skakkebæk
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Claus H. Gravholt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Endocrinology, Aarhus University Hospital, Aarhus, Denmark
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50
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A new circular RNA-encoded protein BIRC6-236aa inhibits transmissible gastroenteritis virus (TGEV)-induced mitochondrial dysfunction. J Biol Chem 2022; 298:102280. [PMID: 35863430 PMCID: PMC9400091 DOI: 10.1016/j.jbc.2022.102280] [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: 10/13/2021] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 11/21/2022] Open
Abstract
Transmissible gastroenteritis virus (TGEV), a member of the coronavirus family, is the pathogen responsible for transmissible gastroenteritis, which results in mitochondrial dysfunction in host cells. Previously, we identified 123 differentially expressed circular RNAs (cRNA)from the TGEV-infected porcine intestinal epithelial cell line jejunum 2 (IPEC-J2). Previous bioinformatics analysis suggested that, of these, circBIRC6 had the potential to regulate mitochondrial function. Furthermore, mitochondrial permeability transition, a key step in the process of mitochondrial dysfunction, is known to be caused by abnormal opening of mitochondrial permeability transition pores (mPTPs) regulated by the voltage-dependent anion-selective channel protein 1 (VDAC)–Cyclophilin D (CypD) complex. Therefore, in the present study, we investigated the effects of circBIRC6-2 on mitochondrial dysfunction and opening of mPTPs. We found that TGEV infection reduced circBIRC6-2 levels, which in turn reduced mitochondrial calcium (Ca2+) levels, the decrease of mitochondrial membrane potential, and opening of mPTPs. In addition, we also identified ORFs and internal ribosomal entrance sites within the circBIRC6-2 RNA. We demonstrate circBIRC6-2 encodes a novel protein, BIRC6-236aa, which we show inhibits TGEV-induced opening of mPTPs during TGEV infection. Mechanistically, we identified an interaction between BIRC6-236aa and VDAC1, suggesting that BIRC6-236aa destabilizes the VDAC1–CypD complex. Taken together, the results suggest that the novel protein BIRC6-236aa encoded by cRNA circBIRC6-2 inhibits mPTP opening and subsequent mitochondrial dysfunction by interacting with VDAC1.
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