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Ye W, Xiang N, Wang Q, Lu Y. Role of circular RNA as competing endogenous RNA in ovarian cancer (Review). Int J Mol Med 2024; 53:41. [PMID: 38456562 DOI: 10.3892/ijmm.2024.5365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/15/2024] [Indexed: 03/09/2024] Open
Abstract
Circular RNA (circRNA), a type of non‑coding RNA, plays a regulatory role in biological processes. The special loop structure of circRNA makes it highly stable and specific in diseased tissues and cells, especially in tumors. Competing endogenous RNAs (ceRNAs) compete for the binding of microRNA (miRNA) at specific binding sites and thus regulate gene expression. ceRNAs play an important role in various diseases and are currently recognized as the most prominent mechanism of action of circRNAs. circRNAs can modulate the proliferation, migration, invasion and apoptosis of tumor cells through the ceRNA mechanism. With further research, circRNAs may serve as novel markers and therapeutic targets for ovarian cancer (OC). In the present review, the research progress of circRNAs as ceRNAs in OC was summarized, focusing on the effects of the circRNA/miRNA/mRNA axis on the biological functions of OC cells through mediating pivotal signaling pathways. The role of circRNAs in the diagnosis, prognostic assessment and treatment of OC was also discussed in the present review.
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Affiliation(s)
- Wanlu Ye
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110003, P.R. China
| | - Nan Xiang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110003, P.R. China
| | - Qing Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110003, P.R. China
| | - Yanming Lu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110003, P.R. China
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Cui YH, Liu CQ, Song XL, Yi WZ, Liu Q, Liu JM, Wu YN, Chen JY, Yang LJ, He HY, Meng J, Pan HW. Integrative Analysis of miRNA and circRNA Expression Profiles and Interaction Network in HSV-1-Infected Primary Corneal Epithelial Cells. Curr Eye Res 2024; 49:368-379. [PMID: 38164922 DOI: 10.1080/02713683.2023.2297345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
PURPOSE Circular RNAs (circRNAs) are products of alternative splicing with roles as competitive endogenous RNAs or microRNA sponges, regulating gene expression and biological processes. However, the involvement of circRNAs in herpes simplex keratitis remains largely unexplored. METHODS This study examines circRNA and miRNA expression profiles in primary human corneal epithelial cells infected with HSV-1, compared to uninfected controls, using microarray analysis. Bioinformatic analysis predicted the potential function of the dysregulated circRNAs and microRNA response elements (MREs) in these circRNAs, forming an interaction network between dysregulated circRNAs and miRNAs. RESULTS A total of 332 circRNAs and 16 miRNAs were upregulated, while 80 circRNAs and six miRNAs were downregulated (fold change ≥2.0 and p < 0.05). Gene ontology (GO) and KEGG pathway analyses were performed on parental genes of dysregulated circRNAs to uncover potential functions in HSV-1 infection. Notably, miR-181b-5p, miR-338-3p, miR-635, and miR-222-3p emerged as pivotal miRNAs interacting with multiple dysregulated circRNAs. CONCLUSIONS This comprehensive study offers insights into differentially expressed circRNAs and miRNAs during HSV-1 infection in corneal epithelial cells, shedding light on circRNA-miRNA interactions' potential role in herpes simplex keratitis pathogenesis.
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Affiliation(s)
- Yu-Hong Cui
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Chao-Qun Liu
- Department of Ophthalmology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Xi-Ling Song
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Wan-Zhao Yi
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Qi Liu
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Jing-Min Liu
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Ya-Ni Wu
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Jian-Ying Chen
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Lv-Jun Yang
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Hui-Ying He
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Jing Meng
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Hong-Wei Pan
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
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Xiao Y, Chen L, Xu Y, Yu R, Lu J, Ke Y, Guo R, Gu T, Yu H, Fang Y, Li Z, Yu J. Circ-ZNF236 mediates stem cells from apical papilla differentiation by regulating LGR4-induced autophagy. Int Endod J 2024; 57:431-450. [PMID: 38240345 DOI: 10.1111/iej.14021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 11/06/2023] [Accepted: 01/03/2024] [Indexed: 03/07/2024]
Abstract
AIM Human stem cells from the apical papilla (SCAPs) are an appealing stem cell source for tissue regeneration engineering. Circular RNAs (circRNAs) are known to exert pivotal regulatory functions in various cell differentiation processes, including osteogenesis of mesenchymal stem cells. However, few studies have shown the potential mechanism of circRNAs in the odonto/osteogenic differentiation of SCAPs. Herein, we identified a novel circRNA, circ-ZNF236 (hsa_circ_0000857) and found that it was remarkably upregulated during the SCAPs committed differentiation. Thus, in this study, we showed the significance of circ-ZNF236 in the odonto/osteogenic differentiation of SCAPs and its underlying regulatory mechanisms. METHODOLOGY The circular structure of circ-ZNF236 was identified via Sanger sequencing, amplification of convergent and divergent primers. The proliferation of SCAPs was detected by CCK-8, flow cytometry analysis and EdU incorporation assay. Western blotting, qRT-PCR, Alkaline phosphatase (ALP) and Alizarin red staining (ARS) were performed to explore the regulatory effect of circ-ZNF236/miR-218-5p/LGR4 axis in the odonto/osteogenic differentiation of SCAPs in vitro. Fluorescence in situ hybridization, as well as dual-luciferase reporting assays, revealed that circ-ZNF236 binds to miR-218-5p. Transmission electron microscopy (TEM) and mRFP-GFP-LC3 lentivirus were performed to detect the activation of autophagy. RESULTS Circ-ZNF236 was identified as a highly stable circRNA with a covalent closed loop structure. Circ-ZNF236 had no detectable influence on cell proliferation but positively regulated SCAPs odonto/osteogenic differentiation. Furthermore, circ-ZNF236 was confirmed as a sponge of miR-218-5p in SCAPs, while miR-218-5p targets LGR4 mRNA at its 3'-UTR. Subsequent rescue experiments revealed that circ-ZNF236 regulates odonto/osteogenic differentiation by miR-218-5p/LGR4 in SCAPs. Importantly, circ-ZNF236 activated autophagy, and the activation of autophagy strengthened the committed differentiation capability of SCAPs. Subsequently, in vivo experiments showed that SCAPs overexpressing circ-ZNF236 promoted bone formation in a rat skull defect model. CONCLUSIONS Circ-ZNF236 could activate autophagy through increasing LGR4 expression, thus positively regulating SCAPs odonto/osteogenic differentiation. Our findings suggested that circ-ZNF236 might represent a novel therapeutic target to prompt the odonto/osteogenic differentiation of SCAPs.
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Affiliation(s)
- Ya Xiao
- Key Laboratory of Oral Diseases of Jiangsu Province and Stomatological Institute of Nanjing Medical University, Nanjing, China
- Endodontic Department, School of Stomatology, Nanjing Medical University, Nanjing, China
| | - Luyao Chen
- Key Laboratory of Oral Diseases of Jiangsu Province and Stomatological Institute of Nanjing Medical University, Nanjing, China
- Endodontic Department, School of Stomatology, Nanjing Medical University, Nanjing, China
| | - Yunlong Xu
- Endodontic Department, Changzhou Stomatological Hospital, Changzhou, Jiangsu, China
| | - Ruiyang Yu
- School of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Jiamin Lu
- Endodontic Department, Changzhou Stomatological Hospital, Changzhou, Jiangsu, China
| | - Yue Ke
- Key Laboratory of Oral Diseases of Jiangsu Province and Stomatological Institute of Nanjing Medical University, Nanjing, China
- Endodontic Department, School of Stomatology, Nanjing Medical University, Nanjing, China
| | - Rong Guo
- Key Laboratory of Oral Diseases of Jiangsu Province and Stomatological Institute of Nanjing Medical University, Nanjing, China
- Endodontic Department, School of Stomatology, Nanjing Medical University, Nanjing, China
| | - Tingjie Gu
- Key Laboratory of Oral Diseases of Jiangsu Province and Stomatological Institute of Nanjing Medical University, Nanjing, China
- Endodontic Department, School of Stomatology, Nanjing Medical University, Nanjing, China
| | - Haowen Yu
- Key Laboratory of Oral Diseases of Jiangsu Province and Stomatological Institute of Nanjing Medical University, Nanjing, China
- Endodontic Department, School of Stomatology, Nanjing Medical University, Nanjing, China
| | - Yuxin Fang
- Key Laboratory of Oral Diseases of Jiangsu Province and Stomatological Institute of Nanjing Medical University, Nanjing, China
- Endodontic Department, School of Stomatology, Nanjing Medical University, Nanjing, China
| | - Zehan Li
- Key Laboratory of Oral Diseases of Jiangsu Province and Stomatological Institute of Nanjing Medical University, Nanjing, China
- Endodontic Department, School of Stomatology, Nanjing Medical University, Nanjing, China
| | - Jinhua Yu
- Endodontic Department, School of Stomatology, Nanjing Medical University, Nanjing, China
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Khalafizadeh A, Hashemizadegan SD, Shokri F, Bakhshinejad B, Jabbari K, Motavaf M, Babashah S. Competitive endogenous RNA networks: Decoding the role of long non-coding RNAs and circular RNAs in colorectal cancer chemoresistance. J Cell Mol Med 2024; 28:e18197. [PMID: 38506091 PMCID: PMC10951891 DOI: 10.1111/jcmm.18197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/17/2023] [Accepted: 02/04/2024] [Indexed: 03/21/2024] Open
Abstract
Colorectal cancer (CRC) is recognized as one of the most common gastrointestinal malignancies across the globe. Despite significant progress in designing novel treatments for CRC, there is a pressing need for more effective therapeutic approaches. Unfortunately, many patients undergoing chemotherapy develop drug resistance, posing a significant challenge for cancer treatment. Non-coding RNAs (ncRNAs) have been found to play crucial roles in CRC development and its response to chemotherapy. However, there are still gaps in our understanding of interactions among various ncRNAs, such as long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs). These ncRNAs can act as either oncogenes or tumour suppressors, affecting numerous biological functions in different cancers including CRC. A class of ncRNA molecules known as competitive endogenous RNAs (ceRNAs) has emerged as a key player in various cellular processes. These molecules form networks through lncRNA/miRNA/mRNA and circRNA/miRNA/mRNA interactions. In CRC, dysregulation of ceRNA networks has been observed across various cellular processes, including proliferation, apoptosis and angiogenesis. These dysregulations are believed to play a significant role in the progression of CRC and, in certain instances, may contribute to the development of chemoresistance. Enriching our knowledge of these dysregulations holds promise for advancing the field of diagnostic and therapeutic modalities for CRC. In this review, we discuss lncRNA- and circRNA-associated ceRNA networks implicated in the emergence and advancement of drug resistance in colorectal carcinogenesis.
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Affiliation(s)
- Ali Khalafizadeh
- Department of Molecular Genetics, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | | | - Fatemeh Shokri
- Research and Development Center of BiotechnologyTarbiat Modares UniversityTehranIran
| | - Babak Bakhshinejad
- Department of Molecular Genetics, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Keyvan Jabbari
- Department of Molecular Genetics, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Mahsa Motavaf
- Department of Molecular Genetics, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Sadegh Babashah
- Department of Molecular Genetics, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
- Research and Development Center of BiotechnologyTarbiat Modares UniversityTehranIran
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Zhang N, Qiu M, Yao S, Zhou H, Zhang H, Jia Y, Li X, Chen X, Li X, Zhou Y, Jiang Y. Circ0087385 promotes DNA damage in benzo(a)pyrene-induced lung cancer development by upregulating CYP1A1. Toxicol Sci 2024; 198:221-232. [PMID: 38310363 DOI: 10.1093/toxsci/kfae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2024] Open
Abstract
Increasing environmental genotoxic chemicals have been shown to induce epigenetic alterations. However, the interaction between genetics and epigenetics in chemical carcinogenesis is still not fully understood. Here, we constructed an in vitro human lung carcinogenesis model (16HBE-T) by treating human bronchial epithelial cells with a typical significant carcinogen benzo(a)pyrene (BaP). We identified a novel circular RNA, circ0087385, which was overexpressed in 16HBE-T and human lung cancer cell lines, as well as in lung cancer tissues and serum exosomes from lung cancer patients. The upregulated circ0087385 after exposure to BaP promoted DNA damage in the early stage of chemical carcinogenesis and affected the cell cycle, proliferation, and apoptosis of the malignantly transformed cells. Overexpression of circ0087385 enhanced the expression of cytochrome P450 1A1 (CYP1A1), which is crucial for metabolically activating BaP. Interfering with circ0087385 or CYP1A1 reduced the levels of ultimate carcinogen benzo(a)pyrene diol epoxide (BPDE) and BPDE-DNA adducts. Interfering with CYP1A1 partially reversed the DNA damage induced by high expression of circ0087385, as well as decreased the level of BPDE and BPDE-DNA adducts. These findings provide novel insights into the interaction between epigenetics and genetics in chemical carcinogenesis which are crucial for understanding the epigenetic and genetic toxicity of chemicals.
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Affiliation(s)
- Nan Zhang
- The Key Laboratory of Advanced Interdisciplinary Studies, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 511436, China
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Miaoyun Qiu
- The Key Laboratory of Advanced Interdisciplinary Studies, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 511436, China
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Shuwei Yao
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Hanyu Zhou
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Han Zhang
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Yangyang Jia
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Xin Li
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Xintong Chen
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Xun Li
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Yun Zhou
- The Key Laboratory of Advanced Interdisciplinary Studies, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 511436, China
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
| | - Yiguo Jiang
- The Key Laboratory of Advanced Interdisciplinary Studies, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 511436, China
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou 511436, China
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Liu L, Hong Y, Ma C, Zhang F, Li Q, Li B, He H, Zhu J, Wang H, Chen L. Circular RNA Gtdc1 Protects Against Offspring Osteoarthritis Induced by Prenatal Prednisone Exposure by Regulating SRSF1-Fn1 Signaling. Adv Sci (Weinh) 2024:e2307442. [PMID: 38520084 DOI: 10.1002/advs.202307442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/21/2024] [Indexed: 03/25/2024]
Abstract
Chondrodysplasia is closely associated with low birth weight and increased susceptibility to osteoarthritis in adulthood. Prenatal prednisone exposure (PPE) can cause low birth weight; however, its effect on offspring cartilage development remains unexplored. Herein, rats are administered clinical doses of prednisone intragastrically on gestational days (GDs) 0-20 and underwent long-distance running during postnatal weeks (PWs) 24-28. Knee cartilage is assayed for quality and related index changes on GD20, PW12, and PW28. In vitro experiments are performed to elucidate the mechanism. PPE decreased cartilage proliferation and matrix synthesis, causing offspring chondrodysplasia. Following long-distance running, the PPE group exhibited more typical osteoarthritis-like changes. Molecular analysis revealed that PPE caused cartilage circRNomics imbalance in which circGtdc1 decreased most significantly and persisted postnatally. Mechanistically, prednisolone reduced circGtdc1 expression and binding with Srsf1 to promote degradation of Srsf1 via K48-linked polyubiquitination. This further inhibited the formation of EDA/B+Fn1 and activation of PI3K/AKT and TGFβ pathways, reducing chondrocyte proliferation and matrix synthesis. Finally, intra-articular injection of offspring with AAV-circGtdc1 ameliorated PPE-induced chondrodysplasia, but this effect is reversed by Srsf1 knockout. Altogether, this study confirms that PPE causes chondrodysplasia and susceptibility to osteoarthritis by altering the circGtdc1-Srsf1-Fn1 axis; in vivo, overexpression of circGtdc1 can represent an effective intervention target for ameliorating PPE-induced chondrodysplasia.
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Affiliation(s)
- Liang Liu
- Department of Orthopedic Surgery, Joint Disease Research Center of Wuhan University, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Yuntian Hong
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Chi Ma
- Department of Orthopedic Surgery, Joint Disease Research Center of Wuhan University, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Fan Zhang
- Department of Orthopedic Surgery, Joint Disease Research Center of Wuhan University, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Qingxian Li
- Department of Orthopedic Surgery, Joint Disease Research Center of Wuhan University, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Bin Li
- Department of Orthopedic Surgery, Joint Disease Research Center of Wuhan University, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China
| | - Hangyuan He
- Department of Orthopedic Surgery, Joint Disease Research Center of Wuhan University, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jiayong Zhu
- Department of Orthopedic Surgery, Joint Disease Research Center of Wuhan University, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Hui Wang
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China
- Department of Pharmacology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Liaobin Chen
- Department of Orthopedic Surgery, Joint Disease Research Center of Wuhan University, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China
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Ren Y, Manoharan T, Liu B, Cheng CZM, En Siew B, Cheong WK, Lee KY, Tan IJW, Lieske B, Tan KK, Chia G. Circular RNA as a source of neoantigens for cancer vaccines. J Immunother Cancer 2024; 12:e008402. [PMID: 38508656 PMCID: PMC10952939 DOI: 10.1136/jitc-2023-008402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND The effectiveness of somatic neoantigen-based immunotherapy is often hindered by the limited number of mutations in tumors with low to moderate mutation burden. Focusing on microsatellite-stable colorectal cancer (CRC), this study investigates the potential of tumor-associated circular RNAs (circRNAs) as an alternative source of neoepitopes in CRC. METHODS Tumor-associated circRNAs in CRC were identified using the MiOncoCirc database and ribo-depletion RNA sequencing of paired clinical normal and tumor samples. Candidate circRNA expression was validated by quantitative real-time PCR (RT-qPCR) using divergent primers. TransCirc database was used for translation prediction. Human leukocyte antigen binding affinity of open reading frames from potentially translatable circRNA was predicted using pVACtools. Strong binders from messenger RNA-encoded proteins were excluded using BlastP. The immunogenicity of the candidate antigens was functionally validated through stimulation of naïve CD8+ T cells against the predicted neoepitopes and subsequent analysis of the T cells through enzyme-linked immunospot (ELISpot) assay, intracellular cytokine staining (ICS) and granzyme B (GZMB) reporter. The cytotoxicity of T cells trained with antigen peptides was further tested using patient-derived organoids. RESULTS We identified a neoepitope from circRAPGEF5 that is upregulated in CRC tumor samples from MiOncoCirc database, and two neoepitopes from circMYH9, which is upregulated across various tumor samples from our matched clinical samples. The translation potential of candidate peptides was supported by Clinical Proteomic Tumor Analysis Consortium database using PepQuery. The candidate peptides elicited antigen-specific T cells response and expansion, evidenced by various assays including ELISpot, ICS and GZMB reporter. Furthermore, T cells trained with circMYH9 peptides were able to specifically target and eliminate tumor-derived organoids but not match normal organoids. This observation underscores the potential of circRNAs as a source of immunogenic neoantigens. Lastly, circMYH9 was enriched in the liquid biopsies of patients with CRC, thus enabling a detection-to-vaccination treatment strategy for patients with CRC. CONCLUSIONS Our findings underscore the feasibility of tumor-associated circRNAs as an alternative source of neoantigens for cancer vaccines targeting tumors with moderate mutation levels.
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Affiliation(s)
- Yi Ren
- Department of Pharmacy, National University of Singapore, Singapore
- NUS iHealthtech, Singapore
| | - Thamizhanban Manoharan
- Department of Pharmacy, National University of Singapore, Singapore
- NUS iHealthtech, Singapore
| | - Beijia Liu
- Department of Pharmacy, National University of Singapore, Singapore
| | - Cyrus Zai Ming Cheng
- Department of Pharmacy, National University of Singapore, Singapore
- NUS iHealthtech, Singapore
| | - Bei En Siew
- Department of Surgery, National University of Singapore, Singapore
- Department of Surgery, National University Hospital, Singapore
| | - Wai-Kit Cheong
- Department of Surgery, National University Hospital, Singapore
| | - Kai Yin Lee
- Department of Surgery, National University Hospital, Singapore
| | - Ian Jse-Wei Tan
- Department of Surgery, National University Hospital, Singapore
| | - Bettina Lieske
- Department of Surgery, National University Hospital, Singapore
| | - Ker-Kan Tan
- Department of Surgery, National University of Singapore, Singapore
- Department of Surgery, National University Hospital, Singapore
| | - Gloryn Chia
- Department of Pharmacy, National University of Singapore, Singapore
- NUS iHealthtech, Singapore
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Liang W, Liu W, Xiong XP, Li JW, Li JL, Perera RJ, Zhou R. The circular RNA circATP8B(2) regulates ROS production and antiviral immunity in Drosophila. Cell Rep 2024; 43:113973. [PMID: 38507406 DOI: 10.1016/j.celrep.2024.113973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/04/2024] [Accepted: 02/29/2024] [Indexed: 03/22/2024] Open
Abstract
We identified and validated a collection of circular RNAs (circRNAs) in Drosophila melanogaster. We show that depletion of the pro-viral circRNA circATP8B(2), but not its linear siblings, compromises viral infection both in cultured Drosophila cells and in vivo. In addition, circATP8B(2) is enriched in the fly gut, and gut-specific depletion of circATP8B(2) attenuates viral replication in an oral infection model. Furthermore, circATP8B(2) depletion results in increased levels of reactive oxygen species (ROS) and enhanced expression of dual oxidase (Duox), which produces ROS. Genetic and pharmacological manipulations of circATP8B(2)-depleted flies that reduce ROS levels rescue the viral replication defects elicited by circATP8B(2) depletion. Mechanistically, circATP8B(2) associates with Duox, and circATP8B(2)-Duox interaction is crucial for circATP8B(2)-mediated modulation of Duox activity. In addition, Gαq, a G protein subunit required for optimal Duox activity, acts downstream of circATP8B(2). We conclude that circATP8B(2) regulates antiviral defense by modulating Duox expression and Duox-dependent ROS production.
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Affiliation(s)
- Weihong Liang
- Departments of Medicine, Biological Chemistry, & Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Johns Hopkins All Children's Hospital, St. Petersburg, FL 33701, USA
| | - Wei Liu
- Departments of Medicine, Biological Chemistry, & Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Johns Hopkins All Children's Hospital, St. Petersburg, FL 33701, USA
| | - Xiao-Peng Xiong
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jennifer W Li
- Department of Medicine, Brown University, Providence, RI 02912, USA
| | - Jian-Liang Li
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; National Institute of Environmental Health Sciences, Durham, NC 27709, USA
| | - Ranjan J Perera
- Departments of Medicine, Biological Chemistry, & Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Johns Hopkins All Children's Hospital, St. Petersburg, FL 33701, USA; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Rui Zhou
- Departments of Medicine, Biological Chemistry, & Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Johns Hopkins All Children's Hospital, St. Petersburg, FL 33701, USA; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
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9
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Heo JI, Ryu J. Exosomal noncoding RNA: A potential therapy for retinal vascular diseases. Mol Ther Nucleic Acids 2024; 35:102128. [PMID: 38356865 PMCID: PMC10865410 DOI: 10.1016/j.omtn.2024.102128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Exosomes are extracellular vesicles that can contain DNA, RNA, proteins, and metabolites. They are secreted by cells and play a regulatory role in various biological responses by mediating cell-to-cell communication. Moreover, exosomes are of interest in developing therapies for retinal vascular disorders because they can deliver various substances to cellular targets. According to recent research, exosomes can be used as a strategy for managing retinal vascular diseases, and they are being investigated for therapeutic purposes in eye conditions, including glaucoma, dry eye syndrome, retinal ischemia, diabetic retinopathy, and age-related macular degeneration. However, the role of exosomal noncoding RNA in retinal vascular diseases is not fully understood. Here, we reviewed the latest research on the biological role of exosomal noncoding RNA in treating retinal vascular diseases. Research has shown that noncoding RNAs, including microRNAs, circular RNAs, and long noncoding RNAs play a significant role in the regulation of retinal vascular diseases. Furthermore, through exosome engineering, the expression of relevant noncoding RNAs in exosomes can be controlled to regulate retinal vascular diseases. Therefore, this review suggests that exosomal noncoding RNA could be considered as a biomarker for diagnosis and as a therapeutic target for treating retinal vascular disease.
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Affiliation(s)
- Jong-Ik Heo
- Vessel-Organ Interaction Research Center, College of Pharmacy, Kyungpook National University, Daegu, South Korea
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, South Korea
| | - Juhee Ryu
- Vessel-Organ Interaction Research Center, College of Pharmacy, Kyungpook National University, Daegu, South Korea
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, South Korea
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10
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Gama-Carvalho M, Tran N. Editorial: Non-coding RNA elements as regulators of host-pathogen interactions. Front Genet 2024; 15:1374636. [PMID: 38510273 PMCID: PMC10952818 DOI: 10.3389/fgene.2024.1374636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/08/2024] [Indexed: 03/22/2024] Open
Affiliation(s)
- Margarida Gama-Carvalho
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Nham Tran
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Ultimo, NSW, Australia
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11
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Babayev M, Silveyra P. Role of circular RNAs in lung cancer. Front Genet 2024; 15:1346119. [PMID: 38501058 PMCID: PMC10944888 DOI: 10.3389/fgene.2024.1346119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/23/2024] [Indexed: 03/20/2024] Open
Abstract
Lung cancer remains a global public health concern with significant research focus on developing better diagnosis/prognosis biomarkers and therapeutical targets. Circular RNAs (circRNAs) are a type of single-stranded RNA molecules that covalently closed and have ubiquitous expression. These molecules have been implicated in a variety of disease mechanisms, including lung cancer, as they exhibit oncogenic or tumor suppressor characteristics. Recent research has shown an important role that circRNAs play at different stages of lung cancer, particularly in lung adenocarcinoma. In this review, we summarize the latest research on circRNAs and their roles within lung cancer diagnosis, as well as on disease mechanisms. We also discuss the knowledge gaps on these topics and possible future research directions.
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Affiliation(s)
| | - Patricia Silveyra
- Department of Environmental and Occupational Health, Indiana University School of Public Health Bloomington, Bloomington, IN, United States
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12
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Yang H, Chen J, Liu S, Xue Y, Li Z, Wang T, Jiao L, An Q, Liu B, Wang J, Zhao H. Exosomes From IgE-Stimulated Mast Cells Aggravate Asthma-Mediated Atherosclerosis Through circRNA CDR1as-Mediated Endothelial Cell Dysfunction in Mice. Arterioscler Thromb Vasc Biol 2024; 44:e99-e115. [PMID: 38235556 DOI: 10.1161/atvbaha.123.319756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
BACKGROUND IgE has been known for mediating endothelial cell dysfunction and mast cell (MC) activation to fuel asthma-aggravated high-fat diet-induced atherosclerosis. However, it remains unclear for the mechanism of asthma-mediated atherosclerosis, especially the potential involvement of IgE in the exacerbation of asthma-mediated atherosclerosis with a standard laboratory diet, and the cross talk between endothelial cells and MCs. METHODS Asthma-mediated atherosclerosis mice models under a standard laboratory diet and FcεR1 knock-out mice were used to determine the role of IgE-FcεR1 signaling in asthma-mediated atherosclerosis, which was assessed by Oil Red O staining and immunohistochemistry. Various in vitro assays including nanoparticle tracking analysis and transmission electron microscopy were used to evaluate exosome characteristics. Immunofluorescence and fluorescent in situ hybridization approaches were used to evaluate the effect and mechanism of MC-secreted exosomes encapsulated circular RNA CDR1as (cerebellar degeneration-related 1 antisense) on endothelial cells in vivo and in vitro. Finally, cohort studies examined the plasma CDR1as levels in patients with atherosclerosis with or without allergies. RESULTS Asthma mice with a standard laboratory diet showed increased atherosclerotic lesions and inflammatory infiltration depending on IgE-FcεR1 signal. FcεR1 knockout mice and blockage of IgE-FcεR1 signaling with IgE monoclonal antibody, omalizumab, all significantly alleviated asthma-mediated atherosclerosis and vascular inflammatory remodeling. Anti-inflammation with dexamethasone and stabilization of MC with cromolyn partially alleviated atherosclerotic lesions and mitigated the inflammatory infiltration in arteries. Mechanistically, IgE stimulation upregulates MC CDR1as expression in exosomes and upregulates the endothelial cell adhesive factors VCAM-1 (vascular cell adhesion molecule-1) and ICAM-1 (intercellular adhesion molecule-1) via the CDR1as-FUS (fused in sarcoma)-phos-p65 axis. Knockdown of CDR1as in vivo significantly decreased the endothelial adhesion function and mitigated asthma-mediated atherosclerosis. Furthermore, a cohort study indicated higher plasma CDR1as levels in patients with atherosclerosis with allergies than in patients with atherosclerosis and healthy controls. CONCLUSIONS Exosomes from IgE-stimulated MCs aggravated atherosclerosis through circular RNA CDR1as-mediated endothelial dysfunction, providing a novel insight into asthma-mediated atherosclerosis and potential diagnostic and therapeutic targets.
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Affiliation(s)
- Hongqin Yang
- Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China (H.Y., J.C., S.L., Y.X., Z.L., J.W., H.Z.)
| | - Junye Chen
- Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China (H.Y., J.C., S.L., Y.X., Z.L., J.W., H.Z.)
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China (J.C., B.L.)
| | - Siyang Liu
- Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China (H.Y., J.C., S.L., Y.X., Z.L., J.W., H.Z.)
| | - Yunfei Xue
- Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China (H.Y., J.C., S.L., Y.X., Z.L., J.W., H.Z.)
| | - Zhiwei Li
- Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China (H.Y., J.C., S.L., Y.X., Z.L., J.W., H.Z.)
| | - Tao Wang
- Department of Neurosurgery and Interventional Neuroradiology, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, National Center for Neurological Disorders, Beijing (T.W., L.J.)
| | - Liqun Jiao
- Department of Neurosurgery and Interventional Neuroradiology, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, National Center for Neurological Disorders, Beijing (T.W., L.J.)
| | - Qi An
- Department of General Surgery, Department of Gastrointestinal Surgery, Beijing Hospital, National Center of Gerontology (Q.A.)
- Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China (Q.A.)
| | - Bao Liu
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China (J.C., B.L.)
| | - Jing Wang
- Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China (H.Y., J.C., S.L., Y.X., Z.L., J.W., H.Z.)
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China (J.W.)
| | - Hongmei Zhao
- Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China (H.Y., J.C., S.L., Y.X., Z.L., J.W., H.Z.)
- State Key Laboratory of Complex, Severe, and Rare Diseases, Beijing, China (H.Z.)
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13
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Zhao Z, Li D, Wang N, Xu L, Weng Y, Zhou W, Pan Y. The identification and functional analysis of CircRNAs in endometrial receptivity of mice with polycystic ovary. Environ Toxicol 2024; 39:1456-1470. [PMID: 37987463 DOI: 10.1002/tox.24052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023]
Abstract
The disorders of endometrial receptivity and ovulatory dysfunction are both significant causes of infertility in patients with polycystic ovary syndrome (PCOS). In this study, we investigated the expression profile and functional implications of circular RNAs (circRNAs) in the endometrial receptivity of PCOS-affected mice. Twenty-four female C57BL/6 mice were divided into PCOS and normal control groups. The PCOS group received subcutaneous DHEA treatment, while the control group remained untreated. Gene chip technology was utilized to analyze circRNA expression in endometrial tissues on the fourth day of gestation with subsequent bioinformatics analyses into circRNA functions. Furthermore, endometrial epithelial cells were used to determine represented circRNA functions. Results showed that the PCOS group exhibited 205 differentially expressed circRNAs, with 147 upregulated and 58 downregulated ones. qRT-PCR confirmed differential expression of circRNAs, including circRNA_38548, circRNA_001686, circRNA_38550, and circRNA_27938. Predicted target genes and a circRNA-miRNA-mRNA regulatory network were constructed. Additionally, four circRNAs (circRNA_38548, circRNA_38550, and circRNA_001686) were identified to contribute to abnormal endometrial receptivity by regulating genes such as Lifr, FOXK1, FOXO1, HOXA10, through interactions with miRNAs. Further research is warranted to elucidate the underlying mechanisms involving these circRNAs.
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Affiliation(s)
- Ziwei Zhao
- Department of Gynaecology and Obstetrics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Dawei Li
- Reproductive Center, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Nan Wang
- Reproductive Center, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Li Xu
- Reproductive Center, Yangzhou Maternal and Child Health Hospital, Yangzhou, China
| | - Yujing Weng
- Reproductive Center, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Weiqin Zhou
- Reproductive Center, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yanping Pan
- Reproductive Center, The First Affiliated Hospital of Soochow University, Suzhou, China
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14
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Liu D, Dong Y, Gao J, Wu Z, Zhang L, Wang B. Role of the circular RNA regulatory network in the pathogenesis of biliary atresia. Exp Ther Med 2024; 27:95. [PMID: 38313582 PMCID: PMC10831818 DOI: 10.3892/etm.2024.12383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 11/13/2023] [Indexed: 02/06/2024] Open
Abstract
Circular RNAs (circRNAs) serve an essential role in the occurrence and development of cholangiocarcinoma, but the expression and function of circRNA in biliary atresia (BA) is not clear. In the present study, circRNA expression profiles were investigated in the liver tissues of patients with BA as well as in the choledochal cyst (CC) tissues of control patients using RNA sequencing. A total of 78 differentially expressed circRNAs (DECs) were identified between the BA and CC tissues. The expression levels of eight circRNAs (hsa_circ_0006137, hsa_circ_0079422, hsa_circ_0007375, hsa_circ_0005597, hsa_circ_0006961, hsa_circ_0081171, hsa_circ_0084665 and hsa_circ_0075828) in the liver tissues of the BA group and control group were measured using reverse transcription-quantitative polymerase chain reaction. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis demonstrated that the identified DECs are involved in a variety of biological processes, including apoptosis and metabolism. In addition, based on the GO and KEGG pathway enrichment analyses, it was revealed that target genes that can be affected by circRNAs regulatory network were enriched in the TGF-β signaling pathway, EGFR tyrosine kinase inhibitor resistance pathway and transcription factor regulation pathway as well as other pathways that may be associated with the pathogenesis of BA. The present study revealed that circRNAs are potentially implicated in the pathogenesis of BA and could help to find promising targets and biomarkers for BA.
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Affiliation(s)
- Dong Liu
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, Guangdong 518000, P.R. China
| | - Yinghui Dong
- Department of Ultrasound, Shenzhen People's Hospital, Shenzhen, Guangdong 518000, P.R. China
| | - Jiahui Gao
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, Guangdong 518000, P.R. China
| | - Zhouguang Wu
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, Guangdong 518000, P.R. China
| | - Lihui Zhang
- Department of Traditional Chinese Medicine, Shenzhen Children's Hospital, Shenzhen, Guangdong 518000, P.R. China
| | - Bin Wang
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, Guangdong 518000, P.R. China
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Li Y, Wang B, Sun W, Kong C, Ding J, Hu F, Li J, Chen X, Lu S. Construction of circ_0071922-miR-15a-5p-mRNA network in intervertebral disc degeneration by RNA-sequencing. JOR Spine 2024; 7:e1275. [PMID: 38222808 PMCID: PMC10782064 DOI: 10.1002/jsp2.1275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/25/2023] [Accepted: 07/19/2023] [Indexed: 01/16/2024] Open
Abstract
Background Low back pain (LBP) is the main factor of global disease burden. Intervertebral disc degeneration (IVDD) has long been known as the leading reason of LBP. Increasing studies have verified that circular RNAs (circRNAs)-microRNAs (miRNAs)-mRNAs network is widely involved in the pathological processes of IVDD. However, no study was made to demonstrate the circRNAs-mediated ferroptosis, oxidative stress, extracellular matrix metabolism, and immune response in IVDD. Methods We collected 3 normal and 3 degenerative nucleus pulposus tissues to conduct RNA-sequencing to identify the key circRNAs and miRNAs in IVDD. Bioinformatics analysis was then conducted to construct circRNAs-miRNAs-mRNAs interaction network associated with ferroptosis, oxidative stress, extracellular matrix metabolism, and immune response. We also performed animal experiments to validate the therapeutic effects of key circRNAs in IVDD. Results We found that circ_0015435 was most obviously upregulated and circ_0071922 was most obviously downregulated in IVDD using RNA-sequencing. Then we observed that hsa-miR-15a-5p was the key downstream of circ_0071922, and hsa-miR-15a-5p was the top upregulated miRNA in IVDD. Bioinformatics analysis was conducted to predict that 56 immunity-related genes, 29 ferroptosis-related genes, 23 oxidative stress-related genes and 8 ECM-related genes are the targets mRNAs of hsa-miR-15a-5p. Then we constructed a ceRNA network encompassing 24 circRNAs, 6 miRNAs, and 101 mRNAs. Additionally, we demonstrated that overexpression of circ_0071922 can alleviate IVDD progression in a rat model. Conclusions The findings of this study suggested that circ_0071922-miR-15a-5p-mRNA signaling network might affect IVDD by modulating the nucleus pulposus cells ferroptosis, oxidative stress, ECM metabolism, and immune response, which is an effective therapeutic targets of IVDD.
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Affiliation(s)
- Yongjin Li
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Baobao Wang
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Wenzhi Sun
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Chao Kong
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Junzhe Ding
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Feng Hu
- Spine Center, Department of Orthopaedics, The First Affiliated Hospital of USTC, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
| | - Jianhua Li
- Department of OrthopedicsTianjin Haihe HospitalTianjinChina
| | - Xiaolong Chen
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Shibao Lu
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
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16
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Ding W, Ding L, Lu Y, Sun W, Wang Y, Wang J, Gao Y, Li M. Circular RNA-circLRP6 protects cardiomyocyte from hypoxia-induced apoptosis by facilitating hnRNPM-mediated expression of FGF-9. FEBS J 2024; 291:1246-1263. [PMID: 38105623 DOI: 10.1111/febs.17038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/30/2023] [Accepted: 12/15/2023] [Indexed: 12/19/2023]
Abstract
Coronary atherosclerosis-induced myocardial ischemia leads to cardiomyocyte apoptosis. The regulatory mechanisms for cardiomyocyte apoptosis have not been fully understood. Circular RNAs are non-coding RNAs which play important roles in heart function maintenance and progression of heart diseases by regulating gene transcription and protein translation. Here, we reported a conserved cardiac circular RNA, which is generated from the second exon of LRP6 and named circLRP62-2 . CircLRP62-2 can protect cardiomyocyte from hypoxia-induced apoptosis. The expression of circLRP62-2 in cardiomyocytes was down-regulated under hypoxia, while forced expression of circLRP62-2 inhibited cell apoptosis. Normally, circLRP62-2 was mainly localized in the nucleus. Under hypoxia, circLRP62-2 is associated with heterogeneous nuclear ribonucleoprotein M (hnRNPM) to be translocated into the cytoplasm. It recruited hnRNPM to fibroblast growth factor 9 (FGF9) mRNA to enhance the expression of FGF9 protein, promoting hypoxia-adaption and viability of cardiomyocytes. In summary, this study uncovers a new inhibitor of apoptosis and reveals a novel anti-apoptotic pathway composed of circLRP62-2 , hnRNPM, and FGF9, which may provide therapeutic targets for coronary heart disease and ischemic myocardial injury.
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Affiliation(s)
- Wei Ding
- The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, China
| | - Lin Ding
- School of Basic Medical Sciences, Qingdao University, China
| | - Yijian Lu
- School of Basic Medical Sciences, Qingdao University, China
| | - Weihan Sun
- School of Basic Medical Sciences, Qingdao University, China
| | - Yu Wang
- School of Basic Medical Sciences, Qingdao University, China
| | - Jianxun Wang
- School of Basic Medical Sciences, Qingdao University, China
| | - Yufang Gao
- The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, China
| | - Mengyang Li
- School of Basic Medical Sciences, Qingdao University, China
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Gao H, Sun M, Gao Z, Song J, Tang D, Liu R. Hsa_circ_0001707 regulates endothelial-mesenchymal transition in esophageal squamous cell carcinoma via miR-203a-3p/Snail2 pathway. Environ Toxicol 2024; 39:1210-1220. [PMID: 37921085 DOI: 10.1002/tox.23998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/02/2023] [Accepted: 10/07/2023] [Indexed: 11/04/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) is a malignant tumor with high mortality and poor prognosis. Despite intensive research focused on tumor suppression, the 5-year survival rate of ESCC is lower than 15%. Therefore, investigate fundamental mechanisms involved in ESCC is on-demand crucial for diagnostics and developing targeted therapeutic drugs. Circular RNAs (circRNAs), as an emerging class of non-coding RNA, have been elucidated that circRNAs participated in regulating a variety of pathological processes and tumorigenesis. Nevertheless, the functional role of circRNAs in the occurrence and development of ESCC remains unclear. We identify a novel circRNA (hsa_circ_0001707), which was highly expressed in ESCC patients' tissues and cell lines. Furthermore, gain- and loss-of-function assays were performed and found that overexpression of hsa_circ_0001707 significantly promote tumor proliferation, metastasis, and invasion. By functioning as a competing endogenous RNA (ceRNA), the dual-luciferase activity assay verified that hsa_circ_0001707 can endogenously bind with miR-203a-3p and regulate its downstream gene Snail2. Rescue assay further confirms that hsa_circ_0001707 downregulation could partially attenuate the facilitation effect of miR-203a-3p, thereby inhibiting the endothelial-mesenchymal transition (EMT) process of ESCC. Our results suggested that hsa_circ_0001707 play an oncogenic role in the pathogenesis of ESCC, which might be a potential biomarker for diagnostics and targeting therapy.
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Affiliation(s)
- Han Gao
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Mingjun Sun
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Zhikui Gao
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Jing Song
- Institute of Nephrology, Zhongda Hospital Southeast University, Nanjing, China
| | - Derong Tang
- Department of Thoracic Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
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Kamali MJ, Salehi M, Mostafavi M, Morovatshoar R, Akbari M, Latifi N, Barzegari O, Ghadimi F, Daraei A. Hijacking and rewiring of host CircRNA/miRNA/mRNA competitive endogenous RNA (ceRNA) regulatory networks by oncoviruses during development of viral cancers. Rev Med Virol 2024; 34:e2530. [PMID: 38517354 DOI: 10.1002/rmv.2530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 03/23/2024]
Abstract
A significant portion of human cancers are caused by oncoviruses (12%-25%). Oncoviruses employ various strategies to promote their replication and induce tumourigenesis in host cells, one of which involves modifying the gene expression patterns of the host cells, leading to the rewiring of genes and resulting in significant changes in cellular processes and signalling pathways. In recent studies, a specific mode of gene regulation known as circular RNA (circRNA)-mediated competing endogenous RNA (ceRNA) networks has emerged as a key player in this context. CircRNAs, a class of non-coding RNA molecules, can interact with other RNA molecules, such as mRNAs and microRNAs (miRNAs), through a process known as ceRNA crosstalk. This interaction occurs when circRNAs, acting as sponges, sequester miRNAs, thereby preventing them from binding to their target mRNAs and modulating their expression. By rewiring the host cell genome, oncoviruses have the ability to manipulate the expression and activity of circRNAs, thereby influencing the ceRNA networks that can profoundly impact cellular processes such as cell proliferation, differentiation, apoptosis, and immune responses. This review focuses on a comprehensive evaluation of the latest findings on the involvement of virus-induced reprogramming of host circRNA-mediated ceRNA networks in the development and pathophysiology of human viral cancers, including cervical cancer, gastric cancer, nasopharyngeal carcinoma, Kaposi's sarcoma, hepatocellular carcinoma, and diffuse large B cell lymphoma. Understanding these mechanisms can improve our knowledge of how oncoviruses contribute to human tumourigenesis and identify potential targets for developing optimised therapies and diagnostic tools for viral cancers.
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Affiliation(s)
- Mohammad Javad Kamali
- Department of Medical Genetics, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Mohammad Salehi
- Department of Medical Genetics, School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mehrnaz Mostafavi
- Department of Physics, Faculty of Allied Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Morovatshoar
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mitra Akbari
- Eye Department, Eye Research Center, Amiralmomenin Hospital, School of Medicine, Guilan University of Medical Science, Rasht, Iran
| | - Narges Latifi
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Omid Barzegari
- Department of Medical Genetics, School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Fatemeh Ghadimi
- Department of Medical Genetics, School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Abdolreza Daraei
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
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Wang Q, Wang H, Zhao X, Han C, Liu C, Li Z, Du T, Sui Y, Zhang X, Zhang J, Xiao Y, Cai G, Meng F. Transcriptome sequencing of circular RNA reveals the involvement of hsa-SCMH1_0001 in the pathogenesis of Parkinson's disease. CNS Neurosci Ther 2024; 30:e14435. [PMID: 37664885 PMCID: PMC10916443 DOI: 10.1111/cns.14435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 08/01/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023] Open
Abstract
BACKGROUND Parkinson's disease (PD) is the second most common neurodegenerative disease. Exosomes are endosome-derived extracellular vesicles that can take part in intercellular communication. Circular RNAs (circRNAs) are noncoding RNAs characterized by covalently closed-loop structures, which perform a crucial function in many diseases. AIM To clarify the expression and function of exosomal circRNSs of PD patients and look for circRNAs that might be related to the pathogenesis of PD. MATERIALS AND METHODS We examined circRNA and mRNA expression profiles in peripheral exosomes from PD patients (n = 23) and healthy controls (n = 15) using next-generation sequencing (NGS) technology, functional annotation, and quantitative polymerase chain reaction. Correlation analysis was performed between the expression levels of the circRNAs and the clinical characteristics of PD patients. The binding miRNAs and target genes were predicted using TargetScanHuman, miRDB, and miRTarBase. The predicted target genes were compared with the differentially expressed mRNAs in sequencing results. RESULTS According to the NGS, 62 upregulated and 37 downregulated circRNAs in the PD group were screened out. Correlation analysis revealed that hsa-SCMH1_0001 has strong clinical relevance. We identified 17 potential binding miRNAs of hsa-SCMH1_0001 with 149 potential target genes. ARID1A and C1orf115 belong to the intersection of the predicted target genes and the differentially expressed mRNAs obtained by sequencing. CONCLUSION This study suggested that hsa-SCMH1_0001 and its target genes ARID1A and C1orf115 are downregulated in PD patients and may be involved in the occurrence of PD.
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Affiliation(s)
- Qiao Wang
- Department of Functional Neurosurgery, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Beijing Key Laboratory of NeurostimulationBeijingChina
- National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijing HospitalBeijingChina
| | - Huizhi Wang
- Department of Functional Neurosurgery, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Beijing Key Laboratory of NeurostimulationBeijingChina
| | - Xuemin Zhao
- Department of Neurophysiology, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
| | - Chunlei Han
- Beijing Key Laboratory of NeurostimulationBeijingChina
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
| | - Chong Liu
- Department of Functional Neurosurgery, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Beijing Key Laboratory of NeurostimulationBeijingChina
| | - Zhibao Li
- Department of Functional Neurosurgery, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Beijing Key Laboratory of NeurostimulationBeijingChina
| | - Tingting Du
- Department of Functional Neurosurgery, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Beijing Key Laboratory of NeurostimulationBeijingChina
| | - Yunpeng Sui
- Department of Functional Neurosurgery, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Beijing Key Laboratory of NeurostimulationBeijingChina
| | - Xin Zhang
- Department of Functional Neurosurgery, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Beijing Key Laboratory of NeurostimulationBeijingChina
| | - Jianguo Zhang
- Department of Functional Neurosurgery, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Beijing Key Laboratory of NeurostimulationBeijingChina
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
| | - Yilei Xiao
- Department of NeurosurgeryLiaocheng People's HospitalLiaochengChina
| | - Guoen Cai
- Department of NeurologyFujian Medical University Union HospitalFuzhouChina
- Fujian Key Laboratory of Molecular Neurology, Institute of Clinical Neurology, Institute of NeuroscienceFujian Medical UniversityFuzhouChina
| | - Fangang Meng
- Department of Functional Neurosurgery, Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina
- Beijing Key Laboratory of NeurostimulationBeijingChina
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
- Chinese Institute for Brain ResearchBeijingChina
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20
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Du C, Waltzer WC, Wilusz JE, Spaliviero M, Darras F, Romanov V. Circular STAG2 RNA Modulates Bladder Cancer Progression via miR-145-5p/TAGLN2 and Is Considered as a Biomarker for Recurrence. Cancers (Basel) 2024; 16:978. [PMID: 38473339 DOI: 10.3390/cancers16050978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/21/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
The current study aimed to elucidate the regulatory mechanisms of the circRNA hsa_circ_0139697 (circSTAG2(16-25)) in BCa and to consider the opportunity of using circSTAG2(16-25) isolated from BCa patient urine as a marker for disease development prediction. The selection of this circRNA was determined by the special role of its parental gene STAG2 in BCa biology. The circRNA hsa_circ_0139697 was chosen from 25 STAG2 circRNAs due to its differential expression in the urine of BCa patients and healthy volunteers. Higher levels of circSTAG2(16-25) were detected in urine samples obtained from patients with recurrent tumors. A higher expression of circSTAG2(16-25) was also detected in more tumorigenic BCa cell lines. The overexpression of circSTAG2(16-25) in BCa cells induced the elevation of proliferation, motility, and invasion. To study the mechanisms of circSTAG2(16-25) activity, we confirmed that circSTAG2(16-25) can bind miR-145-5p in vitro as was predicted by bioinformatic search. miR-145-5p was shown to suppress some genes that promoted BCa progression. One of these genes, TAGLN2, encodes the protein Transgelin 2, which plays a role in BCa cell motility and invasion. Therefore, the possible mechanism of action of circSTAG2(16-25) could be sponging the tumor suppressor miR-145-5p, which results in activation of TAGLN2. In addition, circSTAG2(16-25) might be considered as a potential biomarker for recurrence prediction.
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Affiliation(s)
- Chris Du
- Department of Urology, Renaissance School of Medicine, SUNY at Stony Brook, Stony Brook, NY 11794, USA
| | - Wayne C Waltzer
- Department of Urology, Renaissance School of Medicine, SUNY at Stony Brook, Stony Brook, NY 11794, USA
| | - Jeremy E Wilusz
- Department of Biochemistry & Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Massimiliano Spaliviero
- Department of Urology, Renaissance School of Medicine, SUNY at Stony Brook, Stony Brook, NY 11794, USA
| | - Frank Darras
- Department of Urology, Renaissance School of Medicine, SUNY at Stony Brook, Stony Brook, NY 11794, USA
| | - Victor Romanov
- Department of Urology, Renaissance School of Medicine, SUNY at Stony Brook, Stony Brook, NY 11794, USA
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21
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Muskan M, Abeysinghe P, Cecchin R, Branscome H, Morris KV, Kashanchi F. Therapeutic potential of RNA-enriched extracellular vesicles: The next generation in RNA delivery via biogenic nanoparticles. Mol Ther 2024:S1525-0016(24)00094-7. [PMID: 38414242 DOI: 10.1016/j.ymthe.2024.02.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/21/2024] [Accepted: 02/24/2024] [Indexed: 02/29/2024] Open
Abstract
Exosomes are extracellular vesicles (EVs) (∼50-150 nm) that have emerged as promising vehicles for therapeutic applications and drug delivery. These membrane-bound particles, released by all actively dividing cells, have the ability to transfer effector molecules, including proteins, RNA, and even DNA, from donor cells to recipient cells, thereby modulating cellular responses. RNA-based therapeutics, including microRNAs, messenger RNAs, long non-coding RNAs, and circular RNAs, hold great potential in controlling gene expression and treating a spectrum of medical conditions. RNAs encapsulated in EVs are protected from extracellular degradation, making them attractive for therapeutic applications. Understanding the intricate biology of cargo loading and transfer within EVs is pivotal to unlocking their therapeutic potential. This review discusses the biogenesis and classification of EVs, methods for loading RNA into EVs, their advantages as drug carriers over synthetic-lipid-based systems, and the potential applications in treating neurodegenerative diseases, cancer, and viral infections. Notably, EVs show promise in delivering RNA cargo across the blood-brain barrier and targeting tumor cells, offering a safe and effective approach to RNA-based therapy in these contexts.
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Affiliation(s)
- Muskan Muskan
- School of Pharmacy and Medical Science, Griffith University, Gold Coast Campus, Southport, QLD 4222, Australia
| | - Pevindu Abeysinghe
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, QLD 4059, Australia
| | - Riccardo Cecchin
- School of Pharmacy and Medical Science, Griffith University, Gold Coast Campus, Southport, QLD 4222, Australia
| | - Heather Branscome
- George Mason University, School of Systems Biology, Fairfax, VA 22030, USA
| | - Kevin V Morris
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, QLD 4059, Australia.
| | - Fatah Kashanchi
- George Mason University, School of Systems Biology, Fairfax, VA 22030, USA.
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22
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Xie M, Zhang Y, Yan L, Jin M, Lu X, Yu Q. Peripheral Blood Non-Coding RNA as Biomarker for Schizophrenia: A Review. J Integr Neurosci 2024; 23:42. [PMID: 38419436 DOI: 10.31083/j.jin2302042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/23/2023] [Accepted: 06/09/2023] [Indexed: 03/02/2024] Open
Abstract
Schizophrenia (SCZ) is a complex and heterogeneous neuropsychiatric disorder that lacks objective diagnostic indicators and the pathogenesis remain unclear. Genetic factors may exert a significant impact on the development of the condition. While obtaining brain tissue for biopsy in the course of adjuvant diagnosis of SCZ patients may not be possible, the collection of peripheral blood is more accessible and easier to implement. In recent years, the development and application of RNA sequencing technology has made seeking biomarkers of SCZ becomes more feasible. There is emerging evidence suggesting that certain non-coding RNAs (ncRNA) are distinctly different in the peripheral blood of SCZ patients and healthy controls. Although the mechanisms remain unclear, these aberrantly expressed ncRNAs may be intimately associated with the onset and development of SCZ and may be of great significance for the diagnosis and treatment of SCZ. Therefore, we reviewed the expression of distinct types of ncRNAs that have been found in the peripheral blood of SCZ patients and explored their potential application as diagnostic biomarkers of SCZ. Differentially expressed ncRNAs in the peripheral blood of SCZ patients could not only serve as potential diagnostic biomarkers and therapeutic targets for SCZ but may also have implications for advancing understanding of the molecular mechanisms underlying the development of SCZ and elucidating the complex etiology of SCZ. Early diagnostic biomarkers obtained directly from peripheral blood are of great significance for the timely diagnosis and treatment of SCZ. Our review will enhance the comprehension of molecular mechanisms of SCZ and contribute to the identification of promising ncRNAs in peripheral blood for both diagnosis and therapy of SCZ.
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Affiliation(s)
- Mengtong Xie
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, 130021 Changchun, Jilin, China
| | - Yanchi Zhang
- Department of Psychology, Changchun Sixth Hospital, 130052 Changchun, Jilin, China
| | - Lijuan Yan
- Department of Psychology, Changchun Sixth Hospital, 130052 Changchun, Jilin, China
| | - Mengdi Jin
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, 130021 Changchun, Jilin, China
| | - Xiaoyu Lu
- Innovative Biotechnology Laboratory, Jilin Biological Research Institute, 130012 Changchun, Jilin, China
| | - Qiong Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, 130021 Changchun, Jilin, China
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Fan J, Liao J, Huang Y. Combined bioinformatics and machine learning methodologies reveal prognosis-related ceRNA network and propose ABCA8, CAT, and CXCL12 as independent protective factors against osteosarcoma. ADV CLIN EXP MED 2024; 33:0-0. [PMID: 38315381 DOI: 10.17219/acem/172663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 07/30/2023] [Accepted: 09/20/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND Aberrant circular RNA (circRNA) acts as an oncogene or suppressor during neoplasm initiation and development. However, the functions of most circRNAs in osteosarcoma (OS) remain unclear. OBJECTIVES We aimed to investigate the expression, molecular functions and mechanisms underlying circRNAs in OS. MATERIAL AND METHODS Network interaction, pathway enrichment and regression analyses were performed to determine differentially expressed (DE) circRNAs, microRNAs (miRNAs) and messenger RNAs (mRNAs). We constructed competitive endogenous RcodeNA (ceRNA) networks and integrated patient clinical data to analyze the relationship between the networks and prognosis. The circRNA, miRNA and mRNA data were retrieved from Gene Expression Omnibus (GEO) microarray datasets. A circRNA-miRNA-mRNA interaction network was established and visualized using miRNet. Protein interactions were investigated using STRING and Cytoscape, and hub genes were identified using the MCODE plug-in. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome pathway analyses were performed to determine the DEmRNAs. LIMMA and RobustRankAggreg were used to screen for DERNAs. Node genes in the interaction network were analyzed using least absolute shrinkage and selection operator (LASSO) and Cox regression to obtain OS-related ceRNA networks. RESULTS We identified 9 DEcircRNAs, 243 DEmiRNAs and 211 DEmRNAs. We found that a ceRNA subnetwork, based on 1 circRNA, 1 miRNA and 8 mRNAs, was closely associated with OS prognosis. Integrating the proportional hazards model and survival analysis revealed 3 independent protective factors: adenosine triphosphate (ATP)-binding cassette sub-family A member 8 (ABCA8), catalase (CAT) and C-X-C motif chemokine ligand 12 (CXCL12). CONCLUSIONS Our study provides novel insights into circRNA-related ceRNA networks and identifies potential prognostic biomarkers of OS.
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Affiliation(s)
- Jiaqi Fan
- Department of Orthopaedics, Capital Medical University Affiliated FuXing Hospital, Beijing, China
| | - Jianhong Liao
- Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, China
| | - Yuwen Huang
- Department of Gastrointestinal and Hepatology, Beijing Youan Hospital, Capital Medical University, China
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24
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Nakashima M, Suga N, Ikeda Y, Yoshikawa S, Matsuda S. Circular RNAs, Noncoding RNAs, and N6-methyladenosine Involved in the Development of MAFLD. Noncoding RNA 2024; 10:11. [PMID: 38392966 PMCID: PMC10893449 DOI: 10.3390/ncrna10010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/19/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Noncoding RNAs (ncRNAs), including circular RNAs (circRNAs) and N6-methyladenosine (m6A), have been shown to play a critical role in the development of various diseases including obesity and metabolic disorder-associated fatty liver disease (MAFLD). Obesity is a chronic disease caused by excessive fat accumulation in the body, which has recently become more prevalent and is the foremost risk factor for MAFLD. Causes of obesity may involve the interaction of genetic, behavioral, and social factors. m6A RNA methylation might add a novel inspiration for understanding the development of obesity and MAFLD with post-transcriptional regulation of gene expression. In particular, circRNAs, microRNAs (miRNAs), and m6A might be implicated in the progression of MAFLD. Interestingly, m6A modification can modulate the translation, degradation, and other functions of ncRNAs. miRNAs/circRNAs can also modulate m6A modifications by affecting writers, erasers, and readers. In turn, ncRNAs could modulate the expression of m6A regulators in different ways. However, there is limited evidence on how these ncRNAs and m6A interact to affect the promotion of liver diseases. It seems that m6A can occur in DNA, RNA, and proteins that may be associated with several biological properties. This study provides a mechanistic understanding of the association of m6A modification and ncRNAs with liver diseases, especially for MAFLD. Comprehension of the association between m6A modification and ncRNAs may contribute to the development of treatment tactics for MAFLD.
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Affiliation(s)
| | | | | | | | - Satoru Matsuda
- Department of Food Science and Nutrition, Nara Women’s University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
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25
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Zhou Z, Zhang J, Zheng X, Pan Z, Zhao F, Gao Y. CIRI-Deep Enables Single-Cell and Spatial Transcriptomic Analysis of Circular RNAs with Deep Learning. Adv Sci (Weinh) 2024:e2308115. [PMID: 38308181 DOI: 10.1002/advs.202308115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Circular RNAs (circRNAs) are a crucial yet relatively unexplored class of transcripts known for their tissue- and cell-type-specific expression patterns. Despite the advances in single-cell and spatial transcriptomics, these technologies face difficulties in effectively profiling circRNAs due to inherent limitations in circRNA sequencing efficiency. To address this gap, a deep learning model, CIRI-deep, is presented for comprehensive prediction of circRNA regulation on diverse types of RNA-seq data. CIRI-deep is trained on an extensive dataset of 25 million high-confidence circRNA regulation events and achieved high performances on both test and leave-out data, ensuring its accuracy in inferring differential events from RNA-seq data. It is demonstrated that CIRI-deep and its adapted version enable various circRNA analyses, including cluster- or region-specific circRNA detection, BSJ ratio map visualization, and trans and cis feature importance evaluation. Collectively, CIRI-deep's adaptability extends to all major types of RNA-seq datasets including single-cell and spatial transcriptomic data, which will undoubtedly broaden the horizons of circRNA research.
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Affiliation(s)
- Zihan Zhou
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinyang Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Xin Zheng
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhicheng Pan
- Center for Computational Biology Flatiron Institute, New York, 10010, USA
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuan Gao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
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26
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Xu Y, Han J, Zhang X, Zhang X, Song J, Gao Z, Qian H, Jin J, Liang Z. Exosomal circRNAs in gastrointestinal cancer: Role in occurrence, development, diagnosis and clinical application (Review). Oncol Rep 2024; 51:19. [PMID: 38099408 PMCID: PMC10777447 DOI: 10.3892/or.2023.8678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/27/2023] [Indexed: 12/18/2023] Open
Abstract
Gastrointestinal cancer is frequently detected at an advanced stage and has an undesirable prognosis due to the absence of efficient and precise biomarkers and therapeutic targets. Exosomes are small, living‑cell‑derived vesicles that serve a critical role in facilitating intercellular communication by transporting molecules from donor cells to receiver cells. circular RNAs (circRNAs) are mis‑expressed in a variety of diseases, including gastrointestinal cancer, and are promising as diagnostic biomarkers and tumor therapeutic targets for gastrointestinal cancer. The main features of exosomes and circRNAs are discussed in the present review, along with research on the biological function of exosomal circRNAs in the development and progression of gastrointestinal cancer. It also assesses the advantages and disadvantages of implementing these findings in clinical applications.
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Affiliation(s)
- Yumeng Xu
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu 213017, P.R. China
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Jiayi Han
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Xuan Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Xinyi Zhang
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu 213017, P.R. China
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Jiajia Song
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu 213017, P.R. China
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Zihan Gao
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu 213017, P.R. China
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Hui Qian
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu 213017, P.R. China
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
| | - Jianhua Jin
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu 213017, P.R. China
| | - Zhaofeng Liang
- Wujin Institute of Molecular Diagnostics and Precision Cancer Medicine of Jiangsu University, Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu 213017, P.R. China
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
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Xie Q, Ma Y, Ren Z, Gu T, Jiang Z. Circular RNA: A new expectation for cardiovascular diseases. J Cell Biochem 2024; 125:e30512. [PMID: 38098251 DOI: 10.1002/jcb.30512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/14/2023] [Accepted: 11/30/2023] [Indexed: 01/30/2024]
Abstract
Circular RNA (circRNA) is a class of RNA with the 5' and 3' ends connected covalently to form a closed loop structure and characterized by high stability, conserved sequences and tissue specificity, which is caused by special reverse splicing methods. Currently, it has become a hot spot for research. With the discovery of its powerful regulatory functions and roles, the molecular mechanisms and future value of circRNA in participating in and regulating biological and pathological processes are becoming increasingly apparent. Among them is the increasing prevalence of cardiovascular diseases (CVDs). Many studies have elucidated that circRNA plays a crucial role in the development and progression of CVDs. Therefore, circRNA shows its advantages and brilliant expectations in the field of CVDs. In this review, we describe the biogenesis, bioinformatics detection and function of circRNA and discuss the role of circRNA and its effects on CVDs, including atherosclerosis, myocardial infarction, cardiac hypertrophy and heart failure, myocardial fibrosis, cardiac senescence, pulmonary hypertension, and diabetic cardiomyopathy by different mechanisms. That shows circRNA advantages and brilliant expectations in the field of CVDs.
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Affiliation(s)
- Qiao Xie
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Yun Ma
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Zhong Ren
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Tianhe Gu
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Zhisheng Jiang
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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28
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Jiang J, Luo Z, Zhang HL, Qiu ZJ, Huang C. [ Circular RNA-Encoded Proteins in Gastrointestinal Cancer:A Review]. Zhongguo Yi Xue Ke Xue Yuan Xue Bao 2024; 46:72-81. [PMID: 38433635 DOI: 10.3881/j.issn.1000-503x.15498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
Circular RNAs(CircRNAs)are a class of non-coding RNAs with a covalently closed-loop structure,high stability,and tissue specificity,with the production mechanisms different from linear RNAs.Recent studies have discovered that some CircRNAs can encode proteins via cap-independent translation mechanisms such as internal ribosome entry site,N6-methyladenosine,and rolling loop translation.The encoded proteins regulate homologous linear proteins or downstream signaling pathways via protein bait or other mechanisms,thereby exerting biological functions.Studies have shown that CircRNAs play a role in various diseases,especially in tumor progression,proliferation,invasion,and metastasis and immune regulation.Therefore,by elucidating the expression and roles of proteins encoded by CircRNAs in tumorigenesis and development,this paper is expected to provide new tumor markers and potential targets for tumor diagnosis and treatment.
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Affiliation(s)
- Jie Jiang
- Department of Gastrointestinal Surgery,Shanghai General Hospital,Shanghai Jiaotong University School of Medicine,Shanghai 200080,China
| | - Zai Luo
- Department of Gastrointestinal Surgery,Shanghai General Hospital,Shanghai Jiaotong University School of Medicine,Shanghai 200080,China
| | - Hao-Liang Zhang
- Department of Gastrointestinal Surgery,Shanghai General Hospital,Shanghai Jiaotong University School of Medicine,Shanghai 200080,China
| | - Zheng-Jun Qiu
- Department of Gastrointestinal Surgery,Shanghai General Hospital,Shanghai Jiaotong University School of Medicine,Shanghai 200080,China
| | - Chen Huang
- Department of Gastrointestinal Surgery,Shanghai General Hospital,Shanghai Jiaotong University School of Medicine,Shanghai 200080,China
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Yoshitomi R, Kumazoe M, Lee KW, Marugame Y, Fujimura Y, Tachibana H. Regulatory effect of Epigallocatechin-3-O-gallate on circular RNA expression in mouse liver. J Nutr Biochem 2024; 124:109506. [PMID: 37890708 DOI: 10.1016/j.jnutbio.2023.109506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 10/22/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Abstract
There are few studies on the connection between food components and circular RNA (circRNA), a type of noncoding RNA that is significant for living organisms. (-)-Epigallocatechin-3-O-gallate (EGCG) has been reported to have various biological effects, and elucidation of the molecular mechanism is important for clarifying the functionality of EGCG. In the current study, we looked at how EGCG regulates the expression of circRNA in the liver, which expresses a lot of circRNAs. Mice were given EGCG (10 mg/kg b.w.) orally for one week before circRNA microarray testing was done on their livers. The microarray analysis revealed that mice treated with EGCG had altered expression of 35 circRNAs in their livers. To clarify the function of mmu_circRNA_011775, one of the circRNAs upregulated by EGCG, mouse liver cells after the mmu_circRNA_011775 expression vector was transfected into NMuLi cells, next-generation sequencing (NGS) was used to analyze the gene expression. NGS analysis shows that the expression of the genes responsible for liver fibrosis and inflammation. Gene ontology (GO) analysis showed that mmu_circRNA_011775 changed the meaning of GO terms associated with the cardiovascular system. In the microarray, EGCG altered 35 genes expression. Among them, pre-ribosomal RNA-derived circRNA mmu_circRNA_011775 regulated the expression of various genes related to liver fibrosis and cardiovascular system.
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Affiliation(s)
- Ren Yoshitomi
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Motofumi Kumazoe
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Kwan-Woo Lee
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yuki Marugame
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yoshinori Fujimura
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Hirofumi Tachibana
- Division of Applied Biological Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.
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30
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Zhang Y, Tao K, Ding L, Zhao Y. Assessing biomarkers for post-surgical wound healing: A meta-analysis of exosome-based CircRNA in breast cancer recovery. Int Wound J 2024; 21:e14723. [PMID: 38379248 PMCID: PMC10830351 DOI: 10.1111/iwj.14723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/07/2024] [Accepted: 01/13/2024] [Indexed: 02/22/2024] Open
Abstract
To evaluate the diagnostic potential of exosome-based circular RNAs (circRNAs) as biomarkers for wound healing in patients after breast cancer surgery, we conducted a comprehensive meta-analysis of studies that measured exosome-based circRNA levels in breast cancer patients post-surgery. Data sources included several biomedical databases up to April 2023. Two independent reviewers extracted the data and assessed study quality. Sensitivity, specificity and diagnostic odds ratios were synthesized using random-effects model with subgroup analyses performed based on study characteristics. Seventeen studies met the inclusion criteria, encompassing a total of 1234 patients. The pooled sensitivity and specificity of exosome-based circRNA for detecting wound healing complications were 0.85 (95% CI: 0.77-0.91) and 0.83 (95% CI: 0.78-0.88), respectively. The area under the summary receiver operating characteristic (SROC) curve was 0.90, indicating high diagnostic accuracy. Subgroup analyses revealed that diagnostic performance was consistent across studies of different geographic regions and sample types but indicated potential variability related to patient age and study design. Exosome-based circRNA profiles exhibited the high diagnostic accuracy for monitoring wound healing in breast cancer post-operative care. These findings supported the potential utility of circRNA as non-invasive biomarkers for post-surgical recovery. However, variability among studies suggested the need for standardized protocols in biomarker measurement. Future research should focus on longitudinal studies to validate the prognostic value of these biomarkers and investigate their role in personalized patient management.
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Affiliation(s)
- Yunsuo Zhang
- Department of Breast SurgeryThe Fourth People's Hospital of ZhenjiangZhenjiangChina
| | - Kai Tao
- Department of Breast SurgeryThe Fourth People's Hospital of ZhenjiangZhenjiangChina
| | - Lachun Ding
- Department of InformationThe Fourth People's Hospital of ZhenjiangZhenjiangChina
| | - Yi Zhao
- Department of Breast SurgeryThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
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Bao H, Li J, Zhao Q, Yang Q, Xu Y. Circular RNAs in Breast Cancer: An Update. Biomolecules 2024; 14:158. [PMID: 38397395 PMCID: PMC10887059 DOI: 10.3390/biom14020158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/14/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Breast cancer (BC), characterized by high heterogeneity, is the most commonly reported malignancy among females across the globe. Every year, many BC patients die owing to delayed diagnosis and treatment. Increasing researches have indicated that aberrantly expressed circular RNAs (circRNAs) are implicated in the tumorigenesis and progression of various tumors, including BC. Hence, this article provides a summary of the biogenesis and functions of circRNAs, as well as an examination of how circRNAs regulate the progression of BC. Moreover, circRNAs have aroused incremental attention as potential diagnostic and prognostic biomarkers for BC. Exosomes enriched with circRNAs can be secreted into the tumor microenvironment to mediate intercellular communication, affecting the progression of BC. Detecting the expression levels of exosomal circRNAs may provide reference for BC diagnosis and prognosis prediction. Illuminating insights into the earlier diagnosis and better treatment regimens of BC will be potentially available following elucidation of deeper regulatory mechanisms of circRNAs in this malignancy.
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Affiliation(s)
- Haolin Bao
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Jiehan Li
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Qihang Zhao
- Department of Mammary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Qingling Yang
- Anhui Province Key Laboratory of Cancer Translational Medicine, Bengbu Medical University, Bengbu 233030, China
| | - Yi Xu
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150086, China
- Anhui Province Key Laboratory of Cancer Translational Medicine, Bengbu Medical University, Bengbu 233030, China
- State Key Laboratory of Oncology in South China, Cancer Center of Sun Yat-Sen University, Guangzhou 510060, China
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai 201318, China
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
- Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
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32
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Kong K, Ding X, Wang Y, Xu S, Li G, Wang X, Zhang M, Ni Y, Xu G. Circular RNA expression profile and functional analysis of circUvrag in light-induced photoreceptor degeneration. Clin Exp Ophthalmol 2024. [PMID: 38282307 DOI: 10.1111/ceo.14355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 11/18/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND Circular RNAs (circRNAs) are implicated in retinal pathophysiology; however, their expression profiles and functions in photoreceptor apoptosis are largely unknown. We explored circRNA-expression profiles and circUvrag (host gene: Uvrag, ultraviolet radiation resistance associated gene) function in light-induced photoreceptor apoptosis. METHODS Sprague-Dawley rats and 661 W photoreceptor cells were exposed to blue light to establish light-induced photoreceptor degeneration. Differentially expressed circRNAs were identified using microarrays. Potential functions of dysregulated circRNAs were analysed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. CircUvrag expression and localization were evaluated using quantitative RT-PCR and fluorescence in situ hybridization, respectively. CircUvrag overexpression and knockdown were induced using a plasmid and a small interfering RNA, respectively, and retinal function and structure were assessed using scotopic electroretinography, haematoxylin-eosin staining, and TUNEL staining. Microglial migration was assessed using IBA1 immunostaining. The apoptosis ratio of photoreceptor cells in vitro was detected using flow cytometry. RESULTS We identified 764 differentially expressed circRNAs, which were potentially related with the development of retinal structures, including neurons, dendrites, and synapses, and might participate in nervous-system pathophysiology. Light exposure enriched circUvrag in the cytoplasm of photoreceptors in the outer nuclear layer (ONL). CircUvrag knockdown decreased photoreceptor apoptosis and microglial migration to the ONL after light exposure, preserving ONL thickness and a-wave amplitude. In vitro, circUvrag knockdown inhibited photoreceptor apoptosis, although circUvrag overexpression slightly promoted photoreceptor apoptosis. CONCLUSIONS CircUvrag knockdown attenuated light-induced photoreceptor apoptosis, and might be a potential target in retinal degeneration.
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Affiliation(s)
- Kangjie Kong
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Xinyi Ding
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Yingchao Wang
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Sisi Xu
- Department of Ophthalmology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Gang Li
- Research Center, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Xin Wang
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Meng Zhang
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Yingqin Ni
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Gezhi Xu
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
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Gutierrez-Camino A, Caron M, Richer C, Fuchs C, Illarregi U, Poncelet L, St-Onge P, Bataille AR, Tremblay-Dauphinais P, Lopez-Lopez E, Camos M, Ramirez-Orellana M, Astigarraga I, Lécuyer É, Bourque G, Martin-Guerrero I, Sinnett D. CircRNAome of Childhood Acute Lymphoblastic Leukemia: Deciphering Subtype-Specific Expression Profiles and Involvement in TCF3::PBX1 ALL. Int J Mol Sci 2024; 25:1477. [PMID: 38338754 PMCID: PMC10855129 DOI: 10.3390/ijms25031477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/12/2024] Open
Abstract
Childhood B-cell acute lymphoblastic leukemia (B-ALL) is a heterogeneous disease comprising multiple molecular subgroups with subtype-specific expression profiles. Recently, a new type of ncRNA, termed circular RNA (circRNA), has emerged as a promising biomarker in cancer, but little is known about their role in childhood B-ALL. Here, through RNA-seq analysis in 105 childhood B-ALL patients comprising six genetic subtypes and seven B-cell controls from two independent cohorts we demonstrated that circRNAs properly stratified B-ALL subtypes. By differential expression analysis of each subtype vs. controls, 156 overexpressed and 134 underexpressed circRNAs were identified consistently in at least one subtype, most of them with subtype-specific expression. TCF3::PBX1 subtype was the one with the highest number of unique and overexpressed circRNAs, and the circRNA signature could effectively discriminate new patients with TCF3::PBX1 subtype from others. Our results indicated that NUDT21, an RNA-binding protein (RBP) involved in circRNA biogenesis, may contribute to this circRNA enrichment in TCF3::PBX1 ALL. Further functional characterization using the CRISPR-Cas13d system demonstrated that circBARD1, overexpressed in TCF3::PBX1 patients and regulated by NUDT21, might be involved in leukemogenesis through the activation of p38 via hsa-miR-153-5p. Our results suggest that circRNAs could play a role in the pathogenesis of childhood B-ALL.
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Affiliation(s)
- Angela Gutierrez-Camino
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Maxime Caron
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada;
| | - Chantal Richer
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Claire Fuchs
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - 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; (U.I.); (I.M.-G.)
| | - Lucas Poncelet
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Pascal St-Onge
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Alain R. Bataille
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Pascal Tremblay-Dauphinais
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - 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, Biobizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Mireia Camos
- Hematology Laboratory, Sant Joan de Déu Research Institute, Esplugues de Llobregat, 08950 Barcelona, Spain;
| | - Manuel Ramirez-Orellana
- Department of Pediatric Hematology and Oncology, Niño Jesús University Hospital, 28009 Madrid, Spain;
| | - Itziar Astigarraga
- Pediatric Oncology Group, Biobizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Department of Pediatrics, Cruces University Hospital, 48903 Barakaldo, Spain
| | - Éric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada;
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC H3C 3J7, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada;
| | - 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; (U.I.); (I.M.-G.)
- Pediatric Oncology Group, Biobizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Daniel Sinnett
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
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Unti MJ, Jaffrey SR. Highly efficient cellular expression of circular mRNA enables prolonged protein expression. Cell Chem Biol 2024; 31:163-176.e5. [PMID: 37883972 PMCID: PMC10841545 DOI: 10.1016/j.chembiol.2023.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/25/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023]
Abstract
A major problem with mRNA therapeutics is that mRNA is usually degraded within a few hours after entering the cytosol. New approaches for in vitro synthesis of circular mRNA have allowed increased levels and duration of protein synthesis from mRNA therapeutics due to the long half-life of circular mRNA. However, it remains difficult to genetically encode circular mRNAs in mammalian cells. Here, we describe the adaptation of the Tornado (Twister-optimized RNA for durable overexpression) system to achieve in-cell synthesis of circular mRNAs. We screen different promoters and internal ribosomal entry sites (IRESs) and identify combinations that result in high levels of circular mRNA and protein expression. We show that these circular mRNAs can be packaged into virus-like particles (VLPs), thus enabling prolonged protein expression. Overall, these data describe a platform for synthesis of circular mRNAs and how these circular mRNAs can improve VLP therapeutics.
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Affiliation(s)
- Mildred J Unti
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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35
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Tan X, Zhang J, Dong J, Huang M, Zhou Z, Wang D. Novel Insights into the Circadian Rhythms Based on Long Noncoding and Circular RNA Profiling. Int J Mol Sci 2024; 25:1161. [PMID: 38256234 PMCID: PMC10816401 DOI: 10.3390/ijms25021161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/07/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Circadian rhythm disorders pose major risks to human health and animal production activity, and the hypothalamus is the center of circadian rhythm regulation. However, the epigenetic regulation of circadian rhythm based on farm animal models has been poorly investigated. We collected chicken hypothalamus samples at seven time points in one light/dark cycle and performed long noncoding RNA (lncRNA), circular RNA (circRNA), and mRNA sequencing to detect biomarkers associated with circadian rhythm. We enhanced the comprehensive expression profiling of ncRNAs and mRNAs in the hypothalamus and found two gene sets (circadian rhythm and retinal metabolism) associated with the light/dark cycle. Noncoding RNA networks with circadian expression patterns were identified by differential expression and circadian analysis was provided that included 38 lncRNAs, 15 circRNAs, and 200 candidate genes. Three lncRNAs (ENSGALT00000098661, ENSGALT00000100816, and MSTRG.16980.1) and one circRNA (novel_circ_010168) in the ncRNA-mRNA regulatory network were identified as key molecules influencing circadian rhythm by regulating AOX1 in retinal metabolism. These ncRNAs were predicted to be related to pernicious anemia, gonadal, eye disease and other disorders in humans. Together, the findings of this study provide insights into the epigenetic mechanisms of circadian rhythm and reveal AOX1 as a promising target of circadian rhythm regulation.
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Affiliation(s)
| | | | | | | | | | - Deqian Wang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.T.)
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Chen M, Kang L, Zhang T, Zheng J, Chen D, Shao D, Li Z, Li B, Wei J, Qiu Y, Feng X, Ma Z, Liu K. Circular RNA network plays a potential antiviral role in the early stage of JEV infection in mouse brain. Front Microbiol 2024; 14:1165378. [PMID: 38249464 PMCID: PMC10797004 DOI: 10.3389/fmicb.2023.1165378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Japanese encephalitis is one of the most important insect-borne infectious disease with public health concern. The virus can break the blood-brain barrier and cause death or long-term sequela in infected humans or animals. Viral encephalitis is an important clinical feature of JEV infection. In recent studies, CircRNAs and related ceRNAs data illustrated the regulative role in many aspects of biological process and disease duration. It is believed that CircRNA regulates JEV infection in a ceRNA-dependent mechanism. In this study, brain tissues of experimental mice were sequenced and analysised. 61 differentially expressed circRNAs, 172 differentially expressed miRNAs and 706 differentially expressed mRNAs were identified by RNA-Sequencing and statistical analysis. CX3CR1 was determined as a key host factor impact JEV infection by microRNA interference measurement. CX3CR1 interaction network indicated circStrbp/miR709/CX3CR1 as a functional regulation axis. Further sequencing in BV2 cell shown CX3CR1 is a special target of miR-709 only during JEV infection. In summary, our study presented a new ceRNA pathway that impact JEV infection in vivo and in vitro, which could be a therapeutic target to fight against JEV.
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Affiliation(s)
- Mengli Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
- Key Laboratory of Animal Disease Diagnostic and Immunology, Department of Veterinary Medicine College, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Lei Kang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
- Key Laboratory of Animal Disease Diagnostic and Immunology, Department of Veterinary Medicine College, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Tong Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Jiayang Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Dishi Chen
- Sichuan Animal Disease Prevention and Control Center, Chengdu, China
| | - Donghua Shao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Zongjie Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Beibei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Xiuli Feng
- Key Laboratory of Animal Disease Diagnostic and Immunology, Department of Veterinary Medicine College, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
| | - Ke Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China
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Wei Y, Wei H, Tian C, Wu Q, Li D, Huang C, Zhang G, Chen R, Wang N, Li Y, Li B, Chu XM. The Transcriptome Analysis of Circular RNAs between the Doxorubicin-Induced Cardiomyocytes and Bone Marrow Mesenchymal Stem Cells-Derived Exosomes Treated Ones. Comb Chem High Throughput Screen 2024; 27:CCHTS-EPUB-137002. [PMID: 38305398 DOI: 10.2174/0113862073261891231115072310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/10/2023] [Accepted: 09/21/2023] [Indexed: 02/03/2024]
Abstract
AIM To analyze the sequencing results of circular RNAs (circRNAs) in cardiomyocytes between the doxorubicin (DOX)-injured group and exosomes treatment group. Moreover, to offer potential circRNAs possibly secreted by exosomes mediating the therapeutic effect on DOXinduced cardiotoxicity for further study. MATERIALS & METHODS The DOX-injured group (DOX group) of cardiomyocytes was treated with DOX, while an exosomes-treated group of injured cardiomyocytes were cocultured with bone marrow mesenchymal stem cells (BMSC)-derived exosomes (BEC group). The high-throughput sequencing of circRNAs was conducted after the extraction of RNA from cardiomyocytes. The differential expression of circRNA was analyzed after identifying the number, expression, and conservative of circRNAs. Then, the target genes of differentially expressed circRNAs were predicted based on the targetscan and Miranda database. Next, the GO and KEGG enrichment analyses of target genes of circRNAs were performed. The crucial signaling pathways participating in the therapeutic process were identified. Finally, a real-time quantitative polymerase chain reaction experiment was conducted to verify the results obtained by sequencing. RESULTS Thirty-two circRNAs are differentially expressed between the two groups, of which twenty-three circRNAs were elevated in the exosomes-treated group (BEC group). The GO analysis shows that target genes of differentially expressed circRNAs are mainly enriched in the intracellular signalactivity, regulation of nucleic acid-templated transcription, Golgi-related activity, and GTPase activator activity. The KEGG analysis displays that they were involved in the autophagy biological process and NOD-like receptor signaling pathway. The verification experiment suggested that mmu_circ_0000425 (ID: 116324210) was both decreased in the DOX group and elevated in BEC group, which was consistent with the result of sequencing. CONCLUSION mmu_circ_0000425 in exosomes derived from bone marrow mesenchymal stem cells (BMSC) may have a therapeutic role in alleviating doxorubicin-induced cardiotoxicity (DIC).
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Affiliation(s)
- Yanhuan Wei
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
- Department of Emergency Medicine, Rizhao People's Hospital, Rizhao, China
| | - Haixia Wei
- Qingdao Chengyang People's Hospital, Qingdao, China
| | - Chao Tian
- Hepatopancreatobiliary Center, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Qinchao Wu
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Daisong Li
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chao Huang
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Guoliang Zhang
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ruolan Chen
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ni Wang
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yonghong Li
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Bing Li
- Department of Genetics, Basic Medicine School, Qingdao University, Qingdao, China
- Department of Hematology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xian-Ming Chu
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
- Department of Cardiology, The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao, China
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Shen J, Jin X, Hao Z, Wang J, Hu J, Liu X, Li S, Zhao F, Li M, Zhao Z, Shi B, Ren C. Identification and screening of circular RNAs during adipogenic differentiation of ovine preadipocyte by RNA-seq. J Anim Sci 2024; 102:skae042. [PMID: 38364365 PMCID: PMC10939429 DOI: 10.1093/jas/skae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs that play important roles in preadipocyte differentiation and adipogenesis. However, little is known about genome-wide identification, expression profile, and function of circRNAs in sheep. To investigate the role of circRNAs during ovine adipogenic differentiation, the subcutaneous adipose tissue of Tibetan rams was collected in June 2022. Subsequently, the preadipocytes were immediately isolated from collected adipose tissue and then induced to begin differentiation. The adipocytes samples cultured on days 0, 2, and 8 of preadipocytes differentiation were used to perform RNA sequencing (RNA-seq) analysis to construct the expression profiles of circRNAs. Subsequently, the function of differentially expressed circRNAs was investigated by performing the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of their parent genes. Finally, a circRNAs-miRNAs-mRNAs network involved in adipogenic differentiation was been analyzed. As a result, a total of 6,449 candidate circRNAs were identified in ovine preadipocytes. Of these circRNAs identified, 63 candidate circRNAs were differentially expressed among the three differentiation stages and their parent genes were mainly enriched in acetyl-CoA metabolic process, positive regulation of lipid biosynthetic process, positive regulation of steroid biosynthetic process, and focal adhesion pathway (P < 0.05). Based on a circRNAs-miRNAs-mRNAs regulatory network constructed, circ_004977, circ_006132 and circ_003788 were found to function as competing endogenous RNAs (ceRNAs) to regulate ovine preadipocyte differentiation and lipid metabolism. The results provide an improved understanding of functions and molecular mechanisms of circRNAs underlying ovine adipogenesis in sheep.
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Affiliation(s)
- Jiyuan Shen
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiayang Jin
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhiyun Hao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Fangfang Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Mingna Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhidong Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Bingang Shi
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Chunyan Ren
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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Mazziotta C, Badiale G, Cervellera CF, Tognon M, Martini F, Rotondo JC. Regulatory mechanisms of circular RNAs during human mesenchymal stem cell osteogenic differentiation. Theranostics 2024; 14:143-158. [PMID: 38164139 PMCID: PMC10750202 DOI: 10.7150/thno.89066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/01/2023] [Indexed: 01/03/2024] Open
Abstract
Human osteogenic differentiation is a complex and well-orchestrated process which involves a plethora of molecular players and cellular processes. A growing number of studies have underlined that circular RNAs (circRNAs) play an important regulatory role during human osteogenic differentiation. CircRNAs are single-stranded, covalently closed non-coding RNA molecules that are acquiring increased attention as epigenetic regulators of gene expression. Given their intrinsic high conformational stability, abundance, and specificity, circRNAs can undertake various biological activities in order to regulate multiple cellular processes, including osteogenic differentiation. The most recent evidence indicates that circRNAs control human osteogenesis by preventing the inhibitory activity of miRNAs on their downstream target genes, using a competitive endogenous RNA mechanism. The aim of this review is to draw attention to the currently known regulatory mechanisms of circRNAs during human osteogenic differentiation. Specifically, we provide an understanding of recent advances in research conducted on various human mesenchymal stem cell types that underlined the importance of circRNAs in regulating osteogenesis. A comprehensive understanding of the underlying regulatory mechanisms of circRNA in osteogenesis will improve knowledge on the molecular processes of bone growth, resulting in the potential development of novel preclinical and clinical studies and the discovery of novel diagnostic and therapeutic tools for bone disorders.
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Affiliation(s)
- Chiara Mazziotta
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center for Studies on Gender Medicine - Department of Medical Sciences, University of Ferrara. 64/b, Fossato di Mortara Street. Ferrara, Italy
| | - Giada Badiale
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | | | - Mauro Tognon
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Fernanda Martini
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center for Studies on Gender Medicine - Department of Medical Sciences, University of Ferrara. 64/b, Fossato di Mortara Street. Ferrara, Italy
- Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - John Charles Rotondo
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center for Studies on Gender Medicine - Department of Medical Sciences, University of Ferrara. 64/b, Fossato di Mortara Street. Ferrara, Italy
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Shen M, Wu Y, Li L, Zhang L, Liu G, Wang R. CircMAP3K5 promotes cardiomyocyte apoptosis in diabetic cardiomyopathy by regulating miR-22-3p/DAPK2 Axis. J Diabetes 2024; 16:e13471. [PMID: 37735821 PMCID: PMC10809294 DOI: 10.1111/1753-0407.13471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/24/2023] [Accepted: 08/16/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Diabetic cardiomyopathy (DCM) is one of the serious complications of the accumulated cardiovascular system in the long course of diabetes. To date, there is no effective treatment available for DCM. Circular RNA (circRNA) is a novel r2egulatory RNA that participates in a variety of cardiac pathological processes. However, the regulatory role of circular RNA MAP3K5 (circMAP3K5) in DCM is largely unclear. METHODS AND RESULTS Microarray analysis of DCM rats' heart circular RNAs was performed and the highly species-conserved circRNA mitogen-activated protein kinase kinase kinase 5 (circMAP3K5) was identified, which participates in DCM processes. High glucose-provoked cardiotoxicity leads to the up-regulation of circMAP3K5, which mechanistically contributes to cardiomyocyte cell death. Also, in high glucose-induced H9c2 cardiomyocytes, the level of apoptosis was significantly increased, as well as the expression of circMAP3K5. In contrast, the depletion of circMAP3K5 could reduce high glucose-induced apoptosis in cardiomyocytes. In terms of mechanism, circMAP3K5 acts as a miR-22-3p sponge and miR-22-3p directly target death-associated protein kinase 2 (DAPK2) in H9c2 cardiomyocytes, where in circMAP3K5 upregulates DAPK2 expression by targeting miR-22-3p. Moreover, we also found that miR-22-3p inhibitor and pcDNA DAPK2 could antagonize the protective effects brought by the depletion of circMAP3K5. CONCLUSION CircMAP3K5 is a highly conserved noncoding RNA that is upregulated during DCM process. We concluded that circMAP3K5 promotes high glucose-induced cardiomyocyte apoptosis by regulating the miR-22-3p/DAPK2 axis. The results of this study highlight a novel and translationally important circMAP3K5-based therapeutic approach for DCM.
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Affiliation(s)
- Ming Shen
- Department of Cardiovascular SurgeryThe First Medical Center of PLA General HospitalBeijingChina
- Department of CardiologyThe First Hospital of Hebei Medical UniversityShijiazhuangChina
| | - Yuanbin Wu
- Department of EmergencyThe Seventh Medical Center of PLA General HospitalBeijingChina
| | - Libing Li
- Department of Cardiovascular SurgeryThe First Medical Center of PLA General HospitalBeijingChina
| | - Liyue Zhang
- Department of Cardiovascular SurgeryThe First Medical Center of PLA General HospitalBeijingChina
| | - Gang Liu
- Department of CardiologyThe First Hospital of Hebei Medical UniversityShijiazhuangChina
| | - Rong Wang
- Department of Cardiovascular SurgeryThe First Medical Center of PLA General HospitalBeijingChina
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Li S, Abu Omar A, Greasley A, Wang B, Wang TZ, Chahal S, Thapa RK, Quan D, Skaro A, Liu K, Zheng X. Circular RNA MAP2K2-modified immunosuppressive dendritic cells for preventing alloimmune rejection in organ transplantation. Bioeng Transl Med 2024; 9:e10615. [PMID: 38193111 PMCID: PMC10771550 DOI: 10.1002/btm2.10615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/27/2023] [Accepted: 10/15/2023] [Indexed: 01/10/2024] Open
Abstract
Long-term patient and graft survival has been achieved in organ transplantation but at the expense of toxic side effects that are associated with long-term use of nonspecific immunosuppressive drugs. Discovering new regulators of dendritic cells is the key for development of an ideal treatment to prevent immune rejection. We hypothesized that knockdown of circMAP2K2 induces immunosuppressive DCs and that treatment with circMAP2K2 silenced-DCs can prevent alloimmune rejection. DCs were cultured and transfected with siRNA for circMAP2K2. circMAP2K2 levels were measured by qRT-PCR. DC's maturation and immune function were assessed by flow cytometry and mixed lymphocyte reactions. The function of circMAP2K2 was illustrated by a series of RIP and IP. The therapeutics of engineered DCs was tested in a mouse heart transplantation model. We found that circMAP2K2 was highly expressed in mature DCs. Knockdown of circMAP2K2 reduced expression of MHCII, CD40 and CD80, attenuated the ability of DCs to activate allogeneic naïve T cells, and enhanced CD4+CD25+FOXP3+ regulatory T cells (Treg). circMAP2K2-induced immunosuppressive DCs by interacting with SENP3. Treatment with circMAP2K2-knockdown DCs attenuated alloimmune rejection and prolonged allograft survival in a murine heart transplantation model. The immune suppression induced in vivo was donor-antigen specific. In conclusion, knockdown of circMAP2K2 can induce immunosuppressive DCs which are able to inhibit overactive immune response, highlighting a new promising therapeutic approach for immune disorder diseases.
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Affiliation(s)
- Shuailong Li
- Department of Cardiovascular SurgeryThe Second Norman Bethune Hospital of Jilin UniversityChangchunChina
- Department of Pathology and Laboratory MedicineWestern UniversityLondonOntarioCanada
| | - Amal Abu Omar
- Department of SurgeryWestern UniversityLondonOntarioCanada
| | - Adam Greasley
- Department of Pathology and Laboratory MedicineWestern UniversityLondonOntarioCanada
| | - Bowen Wang
- Department of Cardiovascular SurgeryThe Second Norman Bethune Hospital of Jilin UniversityChangchunChina
- Department of Pathology and Laboratory MedicineWestern UniversityLondonOntarioCanada
| | - Tan Ze Wang
- Department of Pathology and Laboratory MedicineWestern UniversityLondonOntarioCanada
| | - Serina Chahal
- Department of Microbiology and Immunology OncologyWestern UniversityLondonOntarioCanada
| | | | - Douglas Quan
- Department of SurgeryWestern UniversityLondonOntarioCanada
| | - Anton Skaro
- Department of SurgeryWestern UniversityLondonOntarioCanada
| | - Kexiang Liu
- Department of Cardiovascular SurgeryThe Second Norman Bethune Hospital of Jilin UniversityChangchunChina
| | - Xiufen Zheng
- Department of Pathology and Laboratory MedicineWestern UniversityLondonOntarioCanada
- Department of SurgeryWestern UniversityLondonOntarioCanada
- Department of Microbiology and Immunology OncologyWestern UniversityLondonOntarioCanada
- Department of OncologyWestern UniversityLondonOntarioCanada
- Lawson Health Research InstituteLondonOntarioCanada
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Gabryelska MM, Webb ST, Lin H, Gantley L, Kirk K, Liu R, Stringer BW, Conn VM, Conn SJ. Native Circular RNA Pulldown Method to Simultaneously Profile RNA and Protein Interactions. Methods Mol Biol 2024; 2765:299-309. [PMID: 38381346 DOI: 10.1007/978-1-0716-3678-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Circular RNAs (circRNAs) are a widespread, cell-, tissue-, and disease-specific class of largely non-coding RNA transcripts. These single-stranded, covalently-closed transcripts arise through non-canonical splicing of pre-mRNA, a process called back-splicing. Back-splicing results in circRNAs which are distinguishable from their cognate mRNA as they possess a unique sequence of nucleic acids called the backsplice junction (BSJ). CircRNAs have been shown to play key functional roles in various cellular contexts and achieve this through their interaction with other macromolecules, particularly other RNA molecules and proteins. To elucidate the molecular mechanisms underlying circRNA function, it is necessary to identify these interacting partners. Herein, we present an optimized strategy for the simultaneous purification of the circRNA interactome within eukaryotic cells, allowing the identification of both circRNA-RNA and circRNA-protein interactions.
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Affiliation(s)
- Marta M Gabryelska
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Stuart T Webb
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - He Lin
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Laura Gantley
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Kirsty Kirk
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Ryan Liu
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Brett W Stringer
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Vanessa M Conn
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Simon J Conn
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia.
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Qian H, Zhang Z, Tao Z, Xie Y, Yin Y, He W, Zhang L. Association of Circular RNAs levels in blood and Essential Hypertension with Carotid Plaque. Clin Exp Hypertens 2023; 45:2180020. [PMID: 36843004 DOI: 10.1080/10641963.2023.2180020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
BACKGROUND As one of the essential hypertension (EH)-mediated target organ damage, carotid plaque is a crucial subclinical precursor for cardiovascular events. Therefore, it is vital to identify the risk factors and pathogenesis for EH with carotid plaque. METHODS Based on our previous microarray analysis, we selected four circRNAs as the candidate circRNAs and detected their expression levels in blood of 192 subjects (64 healthy controls, 64 EH patients, and 64 EH patients with carotid plaque) by qRT-PCR analysis. The regulatory mechanism of circRNAs involved in carotid plaque was predicted by bioinformatics analysis. RESULTS The level of hsa_circ_0124782 increased significantly and the levels of hsa_circ_0131618 and hsa_circ_0127342 decreased significantly in the EH group and EH with carotid plaque group compared with the control group (P < .05). Functional enrichment analysis showed that three circRNAs might be implicated in pathogenesis for carotid plaque. CONCLUSION Our study revealed the relationship between three circRNAs and carotid plaque, suggesting that they may serve as potential biomarkers for EH with carotid plaque.
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Affiliation(s)
- Haiyan Qian
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China
| | - Zebo Zhang
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China
| | - Zhenbo Tao
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China.,Ningbo Municipal Centre for Disease Control and Prevention, Ningbo, China
| | - Yanqing Xie
- Institute of Geriatrics, the Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
| | - Yueqi Yin
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China
| | - Wenming He
- Institute of Geriatrics, the Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
| | - Lina Zhang
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China.,Institute of Geriatrics, the Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
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Zhang Z, Luo S, Xiao Z, Yin W, Shi X, Chen H, Xie Z, Liu Z, Li X, Zhou Z. Hsa_circRNA_405498 and hsa_circRNA_100033 serve as potential biomarkers for differential diagnosis of type 1 diabetes. J Clin Endocrinol Metab 2023:dgad761. [PMID: 38157408 DOI: 10.1210/clinem/dgad761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/22/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
PURPOSE The role of circular RNAs (circRNAs) in type 1 diabetes (T1D) is largely unknown. We aimed to identify some circRNAs as differential diagnostic biomarkers for T1D to discriminate patients with latent autoimmune diabetes in adults (LADA), and type 2 diabetes (T2D). METHODS The circRNA expression profiles were determined by Arraystar human circRNA microarray in T1D compared to controls (n = 6 each). The differentially expressed circRNAs were validated by RT-qPCR using a validation cohort with 20 T1D and 20 controls. The diagnostic performances of the candidate circRNAs and the clinical parameters were assessed using the logistic least absolute shrinkage and selection operator (LASSO) regression model in a larger cohort with 457 subjects including patients with T1D, T2D and LADA, and controls. RESULTS We identified 110 differentially expressed circular transcripts (53 upregulated and 57 downregulated) in T1D patients compared with controls. Further analysis showed that the levels of hsa_circRNA_405498 and hsa_circRNA_100033 were significantly downregulated in T1D compared to controls (both P < 0.05). Moreover, the expression levels of these two circRNAs showed sequential downregulation from controls, patients with T2D, LADA, to T1D (P < 0.05). The area under the curve (AUC) of receiver operating characteristic (ROC) plots in logistic LASSO regression model showed high diagnostic accuracy for combination model with the two circRNAs and some clinical parameters in discriminating T1D from LADA (AUC = 0.915), T2D (AUC = 0.993), and controls (AUC = 0.992). CONCLUSIONS Our study demonstrated that hsa_circRNA_405498 and hsa_circRNA_100033 are promising novel differential diagnostic biomarkers for T1D.
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Affiliation(s)
- Ziwei Zhang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Shuoming Luo
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Zilin Xiao
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Wenfeng Yin
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Xiajie Shi
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Hongzhi Chen
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Zhenqi Liu
- Division of Endocrinology and Metabolism, Department of Medicine, University of Virginia Health System, Charlottesville, VA, USA
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
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Cieśla M, Darmochwal-Kolarz DA, Kwaśniak K, Pałka A, Kolarz B. Plasma Circular-RNA 0005567 as a Potential Marker of Disease Activity in Rheumatoid Arthritis. Int J Mol Sci 2023; 25:417. [PMID: 38203588 PMCID: PMC10779327 DOI: 10.3390/ijms25010417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Circular RNAs (circRNAs) are noncoding molecules and are generated through back splicing, during which the 5' and 3' ends are covalently joined. Consequently, the lack of free ends makes them stable and resistant to exonucleases, and they become more suitable biomarkers than other noncoding RNAs. The aim of the study was to find an association between selected circRNAs and disease activity in patients with RA. A total of 71 subjects, 45 patients with RA and 26 healthy controls (HCs), were enrolled. In the RA group, 24 patients had high disease activity (DAS-28-ESR > 5.1) and 21 individuals were in remission (DAS-28-ESR ≤ 2.6). The cell line SW982 was used to evaluate the biological function of circ_0005567. The concentration of circ_0005567 in RA patients was elevated compared to HCs (median, 177.5 [lower-upper quartile, 83.13-234.6] vs. 97.83 [42.03-145.4], p = 0.017). Patients with high disease activity had a higher concentration of circ_0005567 than the control group (185.4 [112.72-249.25] vs. 97.83 [42.03-145.4], p = 0.015). In the cell line model, we found an association between circ_0005567 and miR-194-5p concentration and increased expression of mRNAs that may be related to cell proliferation. The plasma concentration of circ_0005567 may be a new potential biomarker associated with disease activity in patients with RA.
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Affiliation(s)
- Marek Cieśla
- Institute of Medical Sciences, College of Medical Sciences, University of Rzeszow, 35-959 Rzeszow, Poland; (D.A.D.-K.); (B.K.)
| | - Dorota A. Darmochwal-Kolarz
- Institute of Medical Sciences, College of Medical Sciences, University of Rzeszow, 35-959 Rzeszow, Poland; (D.A.D.-K.); (B.K.)
| | - Konrad Kwaśniak
- Centre for Innovative Research in Medical and Natural Sciences, Medical College of Rzeszów University, 35-310 Rzeszow, Poland
| | - Anna Pałka
- Institute of Medical Sciences, College of Medical Sciences, University of Rzeszow, 35-959 Rzeszow, Poland; (D.A.D.-K.); (B.K.)
| | - Bogdan Kolarz
- Institute of Medical Sciences, College of Medical Sciences, University of Rzeszow, 35-959 Rzeszow, Poland; (D.A.D.-K.); (B.K.)
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Lun J, Guo J, Yu M, Zhang H, Fang J. Circular RNAs in inflammatory bowel disease. Front Immunol 2023; 14:1307985. [PMID: 38187401 PMCID: PMC10771839 DOI: 10.3389/fimmu.2023.1307985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a term encompassing a few chronic inflammatory disorders that leads to damage of the intestinal tract. Although much progress has been made in understanding the pathology of IBD, the precise pathogenesis is not completely understood. Circular RNAs (circRNAs) are single-stranded, covalently closed, endogenous molecules in eukaryotes with a variety of biological functions. CircRNAs have been shown to have regulatory effects in many diseases, such as cancer, cardiovascular disease, and neurological disorders. CircRNAs have also been found to play important roles in IBD, and although they are not sufficiently investigated in the context of IBD, a few circRNAs have been identified as potential biomarkers for the diagnosis and prognosis of IBD and as potential therapeutic targets for IBD. Herein, we survey recent progress in understanding the functions and roles of circRNAs in IBD and discuss their potential clinical applications.
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Affiliation(s)
- Jie Lun
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao Cancer Institute, Qingdao, China
| | - Jing Guo
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao Cancer Institute, Qingdao, China
| | - Mengchao Yu
- Central Laboratories, Qingdao Municipal Hospital, Qingdao, China
| | - Hongwei Zhang
- Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, China
| | - Jing Fang
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao Cancer Institute, Qingdao, China
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Kanarskaya MA, Pyshnyi DV, Lomzov AA. Diversity of Self-Assembled RNA Complexes: From Nanoarchitecture to Nanomachines. Molecules 2023; 29:10. [PMID: 38202593 PMCID: PMC10779776 DOI: 10.3390/molecules29010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
New tool development for various nucleic acid applications is an essential task in RNA nanotechnology. Here, we determined the ability of self-limited complex formation by a pair of oligoribonucleotides carrying two pairwise complementary blocks connected by a linker of different lengths in each chain. The complexes were analyzed using UV melting, gel shift assay analysis, and molecular dynamics (MD) simulations. We have demonstrated the spontaneous formation of various self-limited and concatemer complexes. The linear concatemer complex is formed by a pair of oligomers without a linker in at least one of them. Longer linkers resulted in the formation of circular complexes. The self-limited complexes formation was confirmed using the toehold strand displacement. The MD simulations indicate the reliability of the complexes' structure and demonstrate their dynamics, which increase with the rise of complex size. The linearization of 2D circular complexes into 1D structures and a reverse cyclization process were demonstrated using a toehold-mediated approach. The approach proposed here for the construction and directed modification of the molecularity and shape of complexes will be a valuable tool in RNA nanotechnology, especially for the rational design of therapeutic nucleic acids with high target specificity and the programmable response of the immune system of organisms.
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Affiliation(s)
| | | | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; (M.A.K.); (D.V.P.)
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Woodruff R, Parekh F, Lamb K, Mekkaoui L, Allen C, Smetanova K, Huang J, Williams A, Toledo GS, Lilova K, Roddie C, Sillibourne J, Pule M. Large-scale manufacturing of base-edited chimeric antigen receptor T cells. Mol Ther Methods Clin Dev 2023; 31:101123. [PMID: 37886606 PMCID: PMC10597784 DOI: 10.1016/j.omtm.2023.101123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023]
Abstract
Base editing is a revolutionary gene-editing technique enabling the introduction of point mutations into the genome without generating detrimental DNA double-stranded breaks. Base-editing enzymes are commonly delivered in the form of modified linear messenger RNA (mRNA) that is costly to produce. Here, we address this problem by developing a simple protocol for manufacturing base-edited cells using circular RNA (circRNA), which is less expensive to synthesize. Compared with linear mRNA, higher editing efficiencies were achieved with circRNA, enabling an 8-fold reduction in the amount of RNA required. We used this protocol to manufacture a clinical dose (1 × 108 cells) of base-edited chimeric antigen receptor (CAR) T cells lacking expression of the inhibitory receptor, PD-1. Editing efficiencies of up to 86% were obtained using 0.25 μg circRNA/1 × 106 cells. Increased editing efficiencies with circRNA were attributed to more efficient translation. These results suggest that circRNA, which is less expensive to produce than linear mRNA, is a viable option for reducing the cost of manufacturing base-edited cells at scale.
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Affiliation(s)
- Rosie Woodruff
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | - Farhaan Parekh
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | - Katarina Lamb
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | - Leila Mekkaoui
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | - Christopher Allen
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | | | - Jasmine Huang
- Imperial College London, South Kensington Campus, SW7 2AZ London, UK
| | - Alex Williams
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | | | - Koki Lilova
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | - Claire Roddie
- Deparment of Haematology, Cancer Institute, 72 Huntley Street, WC1E 6BT London, UK
| | - James Sillibourne
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
| | - Martin Pule
- Autolus Therapeutics, The Mediaworks, 191 Wood Lane, W12 7FP London, UK
- Deparment of Haematology, Cancer Institute, 72 Huntley Street, WC1E 6BT London, UK
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Jeong A, Lim Y, Kook T, Kwon DH, Cho YK, Ryu J, Lee YG, Shin S, Choe N, Kim YS, Cho HJ, Kim JC, Choi Y, Lee SJ, Kim HS, Kee HJ, Nam KI, Ahn Y, Jeong MH, Park WJ, Kim YK, Kook H. Circular RNA circSMAD4 regulates cardiac fibrosis by targeting miR-671-5p and FGFR2 in cardiac fibroblasts. Mol Ther Nucleic Acids 2023; 34:102071. [PMID: 38046397 PMCID: PMC10690640 DOI: 10.1016/j.omtn.2023.102071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 10/31/2023] [Indexed: 12/05/2023]
Abstract
Heart failure is a leading cause of death and is often accompanied by activation of quiescent cardiac myofibroblasts, which results in cardiac fibrosis. In this study, we aimed to identify novel circular RNAs that regulate cardiac fibrosis. We applied transverse aortic constriction (TAC) for 1, 4, and 8 weeks in mice. RNA sequencing datasets were obtained from cardiac fibroblasts isolated by use of a Langendorff apparatus and then further processed by use of selection criteria such as differential expression and conservation in species. CircSMAD4 was upregulated by TAC in mice or by transforming growth factor (TGF)-β1 in primarily cultured human cardiac fibroblasts. Delivery of si-circSMAD4 attenuated myofibroblast activation and cardiac fibrosis in mice treated with isoproterenol (ISP). si-circSmad4 significantly reduced cardiac fibrosis and remodeling at 8 weeks. Mechanistically, circSMAD4 acted as a sponge against the microRNA miR-671-5p in a sequence-specific manner. miR-671-5p was downregulated during myofibroblast activation and its mimic form attenuated cardiac fibrosis. miR-671-5p mimic destabilized fibroblast growth factor receptor 2 (FGFR2) mRNA in a sequence-specific manner and interfered with the fibrotic action of FGFR2. The circSMAD4-miR-671-5p-FGFR2 pathway is involved in the differentiation of cardiac myofibroblasts and thereby the development of cardiac fibrosis.
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Affiliation(s)
- Anna Jeong
- Chonnam University Research Institute of Medical Sciences, Hwasun, Jeollanamdo 58128, Republic of Korea
- BioMedical Sciences Graduate Program (BMSGP), Chonnam National University, Hwasun, Jeollanamdo 58128, Republic of Korea
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
- Department of Pharmacology, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
| | - Yongwoon Lim
- Chonnam University Research Institute of Medical Sciences, Hwasun, Jeollanamdo 58128, Republic of Korea
- BioMedical Sciences Graduate Program (BMSGP), Chonnam National University, Hwasun, Jeollanamdo 58128, Republic of Korea
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
- Department of Pharmacology, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
| | - Taewon Kook
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
- College of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Duk-Hwa Kwon
- Chonnam University Research Institute of Medical Sciences, Hwasun, Jeollanamdo 58128, Republic of Korea
- BioMedical Sciences Graduate Program (BMSGP), Chonnam National University, Hwasun, Jeollanamdo 58128, Republic of Korea
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
- Department of Pharmacology, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
| | - Young Kuk Cho
- Department of Pediatrics, Chosun University School of Medicine, Gwangju, Republic of Korea
| | - Juhee Ryu
- Collage of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Yun-Gyeong Lee
- Chonnam University Research Institute of Medical Sciences, Hwasun, Jeollanamdo 58128, Republic of Korea
- BioMedical Sciences Graduate Program (BMSGP), Chonnam National University, Hwasun, Jeollanamdo 58128, Republic of Korea
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
- Department of Pharmacology, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
| | - Sera Shin
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
- Department of Pharmacology, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
| | - Nakwon Choe
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
- Department of Pharmacology, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
| | - Yong Sook Kim
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
- Department of Cardiology, Heart Research Center, Chonnam National University Hospital, Gwangju, Republic of Korea
| | - Hye Jung Cho
- Chonnam University Research Institute of Medical Sciences, Hwasun, Jeollanamdo 58128, Republic of Korea
- Department of Anatomy, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
| | - Jeong Chul Kim
- Department of Surgery, Chonnam National University Hospital, Gwangju, Republic of Korea
| | - Yoonjoo Choi
- Combinatorial Tumor Immunotherapy Medical Research Center, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
| | - Su-Jin Lee
- Biomedical Research Institute, Chonnam National University Hospital, Gwangju, Republic of Korea
| | - Hyung-Seok Kim
- Chonnam University Research Institute of Medical Sciences, Hwasun, Jeollanamdo 58128, Republic of Korea
- BioMedical Sciences Graduate Program (BMSGP), Chonnam National University, Hwasun, Jeollanamdo 58128, Republic of Korea
- Department of Forensic Medicine, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
| | - Hae Jin Kee
- Department of Cardiology, Heart Research Center, Chonnam National University Hospital, Gwangju, Republic of Korea
| | - Kwang-Il Nam
- Chonnam University Research Institute of Medical Sciences, Hwasun, Jeollanamdo 58128, Republic of Korea
- BioMedical Sciences Graduate Program (BMSGP), Chonnam National University, Hwasun, Jeollanamdo 58128, Republic of Korea
- Department of Anatomy, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
| | - Youngkeun Ahn
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
- Department of Cardiology, Heart Research Center, Chonnam National University Hospital, Gwangju, Republic of Korea
| | - Myung Ho Jeong
- Department of Cardiology, Heart Research Center, Chonnam National University Hospital, Gwangju, Republic of Korea
| | - Woo Jin Park
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
- College of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Young-Kook Kim
- Chonnam University Research Institute of Medical Sciences, Hwasun, Jeollanamdo 58128, Republic of Korea
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
- Department of Biochemistry, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
| | - Hyun Kook
- Chonnam University Research Institute of Medical Sciences, Hwasun, Jeollanamdo 58128, Republic of Korea
- BioMedical Sciences Graduate Program (BMSGP), Chonnam National University, Hwasun, Jeollanamdo 58128, Republic of Korea
- Basic Research Laboratory for Vascular Remodeling, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
- Department of Pharmacology, Chonnam National University Medical School, Hwasun, Jeollanamdo 58128, Republic of Korea
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Sun W, Zhou C, Peng C, Yang R, Li M, Geng J, Zhou J, Chen L, Li W. Diagnostic value of plasma circular RNA based on droplet digital polymerase chain reaction in lung adenocarcinoma. Lab Med 2023:lmad101. [PMID: 38048812 DOI: 10.1093/labmed/lmad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Plasma circular (circ)RNAs detected by droplet digital polymerase chain reaction (ddPCR) may be ideal markers for liquid biopsy. However, ddPCR detection of circRNAs in plasma for diagnosis of lung adenocarcinoma has been rarely reported. METHODS An RNA sequencing analysis was performed in plasma from patients with early lung adenocarcinoma and healthy individuals. Droplet digital PCR was used to verify the differentially expressed genes. RESULTS The copy numbers of circle RNALZIC (circLZIC)and circle RNACEP350 (circCEP350) in the plasma of lung adenocarcinoma patients were significantly higher than in plasma of healthy people, and the copy numbers in postoperative plasma of the same patients were significantly lower than those in preoperative plasma. CircLZIC and circCEP350 alone and in combination had diagnostic value in lung adenocarcinoma and early lung adenocarcinoma. CircLZIC and circCEP350 had more binding sites with multiple microRNAs. Their target genes were enriched in several signaling pathways. CONCLUSION The copy numbers of circLZIC and circCEP350 were higher in plasma of lung adenocarcinoma patients than in plasma of healthy controls, significantly correlated with tumor size and TNM stage, and closely related to the occurrence and development of tumors. These circRNAs may serve as molecular markers for the diagnosis of lung adenocarcinoma.
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Affiliation(s)
- Wanying Sun
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- Center for Clinical Medicine of Respiratory Disease (Tumor) in Anhui, Bengbu, China
- Provincial Key Laboratory of Respiratory Disease in Anhui, Bengbu, China
| | - Changming Zhou
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- Center for Clinical Medicine of Respiratory Disease (Tumor) in Anhui, Bengbu, China
- Provincial Key Laboratory of Respiratory Disease in Anhui, Bengbu, China
| | - Caiqiu Peng
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- Center for Clinical Medicine of Respiratory Disease (Tumor) in Anhui, Bengbu, China
- Provincial Key Laboratory of Respiratory Disease in Anhui, Bengbu, China
| | - Ran Yang
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- Center for Clinical Medicine of Respiratory Disease (Tumor) in Anhui, Bengbu, China
- Provincial Key Laboratory of Respiratory Disease in Anhui, Bengbu, China
| | - Mengting Li
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- Center for Clinical Medicine of Respiratory Disease (Tumor) in Anhui, Bengbu, China
- Provincial Key Laboratory of Respiratory Disease in Anhui, Bengbu, China
| | - Jian Geng
- Department of Biochemistry and Molecular Biology, Bengbu Medical College, Bengbu, China
| | - Jihong Zhou
- Department of Biochemistry and Molecular Biology, Bengbu Medical College, Bengbu, China
| | - Liang Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wei Li
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- Center for Clinical Medicine of Respiratory Disease (Tumor) in Anhui, Bengbu, China
- Provincial Key Laboratory of Respiratory Disease in Anhui, Bengbu, China
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