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Ji C, Ding L, Jia F, Zhang Z, Long C. Integrated Transcriptome Analysis Reveals Molecular Subtypes and ceRNA Networks in Multiple Sclerosis. Degener Neurol Neuromuscul Dis 2024; 14:115-130. [PMID: 39723345 PMCID: PMC11669277 DOI: 10.2147/dnnd.s491211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Accepted: 12/10/2024] [Indexed: 12/28/2024] Open
Abstract
Aim Multiple sclerosis (MS) is a chronic autoimmune disease affecting the central nervous system (CNS). While extensively studied, its molecular subtypes and mechanisms remain poorly understood, hindering the identification of effective therapeutic targets. Methods We used ConsensusClusterPlus to analyze transcriptome data from 215 MS patient samples, identifying distinct molecular subtypes. Differential expression analysis and variability assessments were conducted to further characterize these subtypes. Additionally, circular RNAs (circRNAs) and microRNAs (miRNAs) were screened for potential ceRNA interactions. Results Three molecular subtypes were identified: MS-FCRL1 (C1), MS-BTG1 (C2), and MS-RPL38 (C3). Each subtype was involved in key MS-related pathways (as annotated by KEGG), but the core genes regulating these pathways differed significantly among the subtypes. Subtype C3 exhibited neurodegenerative pathway enrichment, increased immune activity, and immune cell infiltration, suggesting a more severe disease course. Further analysis revealed 18 differentially expressed circRNAs and 22 miRNAs, with EEF1D and TUBA1A as hub targets in C3. Discussion Differential activation of immune pathways across MS subtypes suggests specific gene expression drives disease heterogeneity. We propose a circ_0045537/miR-196a-5p/TUBA1A axis in subtype C3, modulating microtubule dynamics and worsening MS severity.
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Affiliation(s)
- Caili Ji
- Department of Clinical Laboratory, Jingjiang People’s Hospital Affiliated to Yangzhou University, Taizhou, Jiangsu, 214504, People’s Republic of China
| | - Li Ding
- Department of Clinical Laboratory, Jingjiang People’s Hospital Affiliated to Yangzhou University, Taizhou, Jiangsu, 214504, People’s Republic of China
| | - Fumin Jia
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People’s Republic of China
| | - Zhiyong Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, People’s Republic of China
| | - Cong Long
- Department of Clinical Laboratory, Jingjiang People’s Hospital Affiliated to Yangzhou University, Taizhou, Jiangsu, 214504, People’s Republic of China
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Yang Y, Xie T, Gao P, Han W, Liu Y, Wang Y. Hsa_Circ_002144 Promotes Glycolysis and Immune Escape of Breast Cancer Through miR-326/PKM Axis. Cancer Biother Radiopharm 2024; 39:755-769. [PMID: 38963787 DOI: 10.1089/cbr.2024.0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024] Open
Abstract
Background: Breast cancer is a leading cause of cancer-related deaths in women worldwide, posing a significant threat to female health. Therefore, it is crucial to search for new therapeutic targets and prognostic biomarkers for breast cancer patients. Method: Bioinformatics analysis, quantitative real-time PCR (qRT-PCR), and fluorescence in situ hybridization (FISH) were employed to investigate the expression of hsa_circ_002144 in breast cancer. Transwell assay, Western blotting, and cell viability assay were utilized to assess the impact of hsa_circ_002144 on the proliferation, migration, and invasion of breast cancer cells. Additionally, a mouse model was established to validate its functionality. Flow cytometry, WB analysis, enzyme-linked immunosorbent assay (ELISA), qRT-PCR, exosomes isolation, and co-culture system were employed to elucidate the molecular mechanism underlying macrophage polarization. Result: we have discovered for the first time that hsa_circ_002144 is highly expressed in breast cancer. It affected tumor growth and metastasis and could influence macrophage polarization through the glycolytic pathway. Conclusion: This finding provides a new direction for breast cancer treatment and prognosis assessment.
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Affiliation(s)
- Yong Yang
- College of Basic Medicine, Shaanxi University of Chinese Medicine, Xianyang City, China
| | - Tianhao Xie
- General Surgery, The Affiliated Hospital of Hebei University, Baoding City, China
| | - Peng Gao
- Anesthesiology department, Affiliated hospital of Qingdao university, Qingdao City, China
| | - Weijun Han
- Third Surgery, Baoji traditional Chinese Medicine Hospital in Shaanxi Province, Baoji City, China
| | - Yuhong Liu
- Rheumatology and Immunology Department, The Affiliated Hospital of Yan 'an University, Yan 'an City, China
| | - Yanmei Wang
- School of Nursing and Health, Medical College of Yan 'an University, Yan 'an City, China
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Lou Y, Yan J, Liu Q, Miao M, Shao Y. Biological functions and molecular mechanisms of exosome-derived circular RNAs and their clinical implications in digestive malignancies: the vintage in the bottle. Ann Med 2024; 56:2420861. [PMID: 39484707 PMCID: PMC11536637 DOI: 10.1080/07853890.2024.2420861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Revised: 10/05/2024] [Accepted: 10/11/2024] [Indexed: 11/03/2024] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) are identified as a novel family of endogenous RNA molecules through 'back-splicing' and covalently linked at the 5' and 3' ends. Emerging researches have demonstrated circRNAs are stable and abundant in exosomes called exosomal circRNAs (exo-circRNA). MATERIALS AND METHODS We searched recent studies and references to summary the research progress of exosomal circRNA. RESULTS Recent studies have revealed that exosome-derived circRNAs including exo-CDR1as, exo-circRanGAP1, exo-circIAR play vital roles in cell proliferation and apoptosis, epithelial mesenchymal transition, invasion and metastasis, angiogenesis, immune evasion, cellular crosstalk, cancer cachexia through a variety of biological mechanisms, such as serving as microRNA sponges, interacting with RNA binding proteins, regulating gene transcription, N6-Methyladenosine modification and so on. Due to their characteristics of origin, structure, properties and biological functions, exo-circRNAs are expected to apply in precious diagnosis and prognostic indicators, improving drug and radiation resistance and sensitivity, becoming biological therapeutic targets. CONCLUSION We summarize the update of digestive malignancies associated exo-circRNAs in biogenesis, biological functions, molecular mechanisms, clinical implications, potential applications and experimental technique in order to effectively promote transformation and application in the future.
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Affiliation(s)
- Yuanyan Lou
- Department of Gastroenterology, the First Affiliated Hospital of Ningbo University, Ningbo, China
- Health Science Center, Ningbo University, Ningbo, China
| | - Jianing Yan
- Department of Gastroenterology, the First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Qingqing Liu
- Department of Gastroenterology, the First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Min Miao
- Department of Gastroenterology, the First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Yongfu Shao
- Department of Gastroenterology, the First Affiliated Hospital of Ningbo University, Ningbo, China
- Health Science Center, Ningbo University, Ningbo, China
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Miceli RT, Chen T, Nose Y, Tichkule S, Brown B, Fullard JF, Saulsbury MD, Heyliger SO, Gnjatic S, Kyprianou N, Cordon‐Cardo C, Sahoo S, Taioli E, Roussos P, Stolovitzky G, Gonzalez‐Kozlova E, Dogra N. Extracellular vesicles, RNA sequencing, and bioinformatic analyses: Challenges, solutions, and recommendations. J Extracell Vesicles 2024; 13:e70005. [PMID: 39625409 PMCID: PMC11613500 DOI: 10.1002/jev2.70005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 09/20/2024] [Accepted: 10/07/2024] [Indexed: 12/06/2024] Open
Abstract
Extracellular vesicles (EVs) are heterogeneous entities secreted by cells into their microenvironment and systemic circulation. Circulating EVs carry functional small RNAs and other molecular footprints from their cell of origin, and thus have evident applications in liquid biopsy, therapeutics, and intercellular communication. Yet, the complete transcriptomic landscape of EVs is poorly characterized due to critical limitations including variable protocols used for EV-RNA extraction, quality control, cDNA library preparation, sequencing technologies, and bioinformatic analyses. Consequently, there is a gap in knowledge and the need for a standardized approach in delineating EV-RNAs. Here, we address these gaps by describing the following points by (1) focusing on the large canopy of the EVs and particles (EVPs), which includes, but not limited to - exosomes and other large and small EVs, lipoproteins, exomeres/supermeres, mitochondrial-derived vesicles, RNA binding proteins, and cell-free DNA/RNA/proteins; (2) examining the potential functional roles and biogenesis of EVPs; (3) discussing various transcriptomic methods and technologies used in uncovering the cargoes of EVPs; (4) presenting a comprehensive list of RNA subtypes reported in EVPs; (5) describing different EV-RNA databases and resources specific to EV-RNA species; (6) reviewing established bioinformatics pipelines and novel strategies for reproducible EV transcriptomics analyses; (7) emphasizing the significant need for a gold standard approach in identifying EV-RNAs across studies; (8) and finally, we highlight current challenges, discuss possible solutions, and present recommendations for robust and reproducible analyses of EVP-associated small RNAs. Overall, we seek to provide clarity on the transcriptomics landscape, sequencing technologies, and bioinformatic analyses of EVP-RNAs. Detailed portrayal of the current state of EVP transcriptomics will lead to a better understanding of how the RNA cargo of EVPs can be used in modern and targeted diagnostics and therapeutics. For the inclusion of different particles discussed in this article, we use the terms large/small EVs, non-vesicular extracellular particles (NVEPs), EPs and EVPs as defined in MISEV guidelines by the International Society of Extracellular Vesicles (ISEV).
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Affiliation(s)
- Rebecca T. Miceli
- Department of Pathology, Molecular and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Tzu‐Yi Chen
- Department of Pathology, Molecular and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Yohei Nose
- Department of ImmunologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Oncological SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Swapnil Tichkule
- Department of PsychiatryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Briana Brown
- Department of Pathology, Molecular and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - John F. Fullard
- Department of PsychiatryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Genetics and Genomics SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Center for Disease Neurogenetics, Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Friedman Brain Institute, Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Marilyn D. Saulsbury
- Department of Pharmaceutical Sciences, School of PharmacyHampton UniversityHamptonVirginiaUSA
| | - Simon O. Heyliger
- Department of Pharmaceutical Sciences, School of PharmacyHampton UniversityHamptonVirginiaUSA
| | - Sacha Gnjatic
- Department of ImmunologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Oncological SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Natasha Kyprianou
- Department of Pathology, Molecular and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Oncological SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of UrologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Carlos Cordon‐Cardo
- Department of Pathology, Molecular and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Susmita Sahoo
- Department of MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Emanuela Taioli
- Department of Population Health and ScienceIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Thoracic SurgeryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Panos Roussos
- Department of PsychiatryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Genetics and Genomics SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Center for Disease Neurogenetics, Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Friedman Brain Institute, Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Center for Precision Medicine and Translational TherapeuticsJames J. Peters VA Medicinal CenterBronxNew YorkUSA
- Mental Illness Research Education and Clinical Center (MIRECC)James J. Peters VA Medicinal CenterBronxNew YorkUSA
| | - Gustavo Stolovitzky
- Department of Genetics and Genomics SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Biomedical Data Sciences Hub (Bio‐DaSH), Department of Pathology, NYU Grossman School of MedicineNew YorkNew YorkUSA
| | - Edgar Gonzalez‐Kozlova
- Department of ImmunologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Oncological SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Navneet Dogra
- Department of Pathology, Molecular and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Genetics and Genomics SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Genomics Institute, Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- AI and Human HealthIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
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Yao R, Xu L, Cheng G, Wang Z, Liang R, Pei W, Cao L, Jia Y, Ye H, Hu F, Su Y. Elevated expression of hsa_circ_0000479 in neutrophils correlates with features of systemic lupus erythematosus. Ann Med 2024; 56:2309607. [PMID: 38300888 PMCID: PMC10836484 DOI: 10.1080/07853890.2024.2309607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 01/14/2024] [Indexed: 02/03/2024] Open
Abstract
OBJECTIVE Accumulating evidence suggests that differentially expressed circular RNAs (circRNAs) play critical roles in immune cells of systemic lupus erythematosus (SLE) patients. Hsa_circ_0000479 has been studied in the field of cancer and infection, whereas seldom studied in autoimmune diseases. The aim of this study was to investigate the role and clinical value of neutrophil hsa_circ_0000479 in SLE. METHODS The expression levels of hsa_circ_0000479 in both healthy individuals and SLE patients' neutrophils were detected by qPCR and compared with those in peripheral blood mononuclear cells (PBMCs) . In addition, the correlation of hsa_circ_0000479 levels in neutrophils with the clinical and immunological features of SLE patients was also analysed. RESULTS The expression levels of hsa_circ_0000479 in the patients with SLE were significantly higher in neutrophils than that of PBMCs, and also significantly higher than that in healthy controls (HCs). Moreover, the expression levels of hsa_circ_0000479 in neutrophils were negatively associated with absolute neutrophil count and complement 3 (C3), whereas positively correlated with anti-dsDNA and anti-nucleosome antibodies in SLE. In addition, SLE patients with higher levels of hsa_circ_0000479 demonstrated more several clinical manifestations, including Raynaud's phenomenon, alopecia and leucopenia. CONCLUSIONS Hsa_circ_0000479 is up-regulated in neutrophils of SLE patients, and is also associated with several important laboratory indicators and clinical manifestations, suggesting that hsa_circ_0000479 in neutrophils was one of probable factors involved in the pathogenesis of SLE with potential clinical value.
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Affiliation(s)
- Ranran Yao
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, PR China
| | - Liling Xu
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, PR China
| | - Gong Cheng
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, PR China
| | - Ziye Wang
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, PR China
| | - Ruyu Liang
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, PR China
| | - Wenwen Pei
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, PR China
| | - Lulu Cao
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, PR China
| | - Yuan Jia
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, PR China
| | - Hua Ye
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, PR China
| | - Fanlei Hu
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, PR China
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, PR China
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, PR China
| | - Yin Su
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, PR China
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Li J, Wang X. Functional roles of conserved lncRNAs and circRNAs in eukaryotes. Noncoding RNA Res 2024; 9:1271-1279. [PMID: 39036601 PMCID: PMC11260338 DOI: 10.1016/j.ncrna.2024.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 06/14/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) have emerged as critical regulators in essentially all biological processes across eukaryotes. They exert their functions through chromatin remodeling, transcriptional regulation, interacting with RNA-binding proteins (RBPs), serving as microRNA sponges, etc. Although non-coding RNAs are typically more species-specific than coding RNAs, a number of well-characterized lncRNA (such as XIST and NEAT1) and circRNA (such as CDR1as and ciRS-7) are evolutionarily conserved. The studies on conserved lncRNA and circRNAs across multiple species could facilitate a comprehensive understanding of their roles and mechanisms, thereby overcoming the limitations of single-species studies. In this review, we provide an overview of conserved lncRNAs and circRNAs, and summarize their conserved roles and mechanisms.
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Affiliation(s)
- Jingxin Li
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, The RNA Institute, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (UTSC), Hefei, 230027, Anhui, China
| | - Xiaolin Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, The RNA Institute, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (UTSC), Hefei, 230027, Anhui, China
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Malek Mohammadi M, Rismanchi H, Esmailzadeh S, Farahani A, Hedayati N, Alimohammadi M, Mafi A, Farahani N, Hushmandi K. The emerging role of circular RNAs in cisplatin resistance in ovarian cancer: From molecular mechanism to future potential. Noncoding RNA Res 2024; 9:1280-1291. [PMID: 39040815 PMCID: PMC11261309 DOI: 10.1016/j.ncrna.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/05/2024] [Accepted: 05/19/2024] [Indexed: 07/24/2024] Open
Abstract
Ovarian cancer (OC) is the most common cause of death in female cancers. The prognosis of OC is very poor due to delayed diagnosis and identification of most patients in advanced stages, metastasis, recurrence, and resistance to chemotherapy. As chemotherapy with platinum-based drugs such as cisplatin (DDP) is the main treatment in most OC cases, resistance to DDP is an important obstacle to achieving satisfactory therapeutic efficacy. Consequently, knowing the different molecular mechanisms involved in resistance to DDP is necessary to achieve new therapeutic approaches. According to numerous recent studies, non-coding RNAs (ncRNAs) could regulate proliferation, differentiation, apoptosis, and chemoresistance in many cancers, including OC. Most of these ncRNAs are released by tumor cells into human fluid, allowing them to be used as tools for diagnosis. CircRNAs are ncRNA family members that have a role in the initiation, progression, and chemoresistance regulation of various cancers. In the current study, we investigated the roles of several circRNAs and their signaling pathways on OC progression and also on DDP resistance during chemotherapy.
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Affiliation(s)
| | - Hamidreza Rismanchi
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shakiba Esmailzadeh
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Aryan Farahani
- Student Research Committee, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Neda Hedayati
- School of Medicine, Iran University of Medical Science, Tehran, Iran
| | - Mina Alimohammadi
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Mafi
- Nutrition and Food Security Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Najma Farahani
- Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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Imran M, Altamimi ASA, Babu MA, Goyal K, Kaur I, Kumar S, Sharma N, Kumar MR, Alanazi FJ, Alruwaili AN, Aldhafeeri NA, Ali H. Non-coding RNAs (ncRNAs) as therapeutic targets and biomarkers in oligodendroglioma. Pathol Res Pract 2024; 264:155708. [PMID: 39531874 DOI: 10.1016/j.prp.2024.155708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2024] [Revised: 11/03/2024] [Accepted: 11/05/2024] [Indexed: 11/16/2024]
Abstract
Oligodendrogliomas (ODGs) are neuroepithelial tumors that need personalized treatment plans because of their unique molecular and histological features. Non-coding RNAs form an epigenetic class of molecules that act as the first steps in gene regulation. They consist of microRNAs, long non-coding RNAs, and circular RNAs. These molecules significantly participate in ODG pathogenesis by regulating ODG initiation, progression, and treatment response. This review is designated to analyze the literature and describe the genomic profile of ODGs, the complex actions of ncRNAs in ODGs pathogenesis and treatment, and their roles as appropriate biomarkers and as one of the precision mechanisms action targets, such as antisense oligonucleotides, small interfering RNAs, gene therapy vectors, peptide nucleic acids, and small molecule inhibitors. Overall, ncRNAs considerably alter the pathological spectrum of ODGs by influencing fundamental processes in tumor biology. Applying ncRNAs in a clinical context exhibits promise for enhanced diagnosis and individualized therapeutic interventions. Nevertheless, the delivery efficacy and potential adverse "off-target" sequels retain the main obstacles undermining clinical potential. Continuous research and technological advancements in ncRNAs offer new insights and promising prospects for revolutionizing oligodendroglioma care, leading to better, personalized treatment outcomes.
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Affiliation(s)
- Mohd Imran
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia; Center for Health Research, Northern Border University, Arar, Saudi Arabia
| | | | - M Arockia Babu
- Institute of Pharmaceutical Research, GLA UNIVERSITY, Mathura, UP 281406, India
| | - Kavita Goyal
- Department of Biotechnology, Graphic Era (Deemed to be University), Clement Town, Dehradun 248002, India
| | - Irwanjot Kaur
- Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan 303012, India
| | - Sachin Kumar
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, India.
| | - Naveen Sharma
- Chandigarh Pharmacy College, Chandigarh Group of College, Jhanjeri, Mohali, Punjab 140307, India
| | - M Ravi Kumar
- Department of Chemistry, Raghu Engineering College, Visakhapatnam, Andhra Pradesh 531162, India
| | - Fadiyah Jadid Alanazi
- Center for Health Research, Northern Border University, Arar, Saudi Arabia; Public Health Nursing Department, College of Nursing, Northern Border University, Arar, Saudi Arabia
| | - Abeer Nuwayfi Alruwaili
- Department of Nursing Administration and Education, College of Nursing, Jouf University, Al Jouf City 72388, Saudi Arabia
| | - Nouf Afit Aldhafeeri
- College of Nursing, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia; King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Haider Ali
- Division of Translational Health Research, Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India; Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
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Zharova AMD, Perenkov AD, Vedunova MV. Circular RNAs as multifaceted molecular regulators of vital activity and potential biomarkers of aging. Epigenomics 2024; 16:1465-1475. [PMID: 39589864 PMCID: PMC11622801 DOI: 10.1080/17501911.2024.2430165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2024] [Accepted: 11/06/2024] [Indexed: 11/28/2024] Open
Abstract
Aging presents a significant challenge to health and social care systems due to the increasing proportion of the elderly population. The identification of reliable biomarkers to assess the progression of aging remains an unresolved question. Circular RNAs (circRNAs) are single-stranded covalently closed RNAs. They have been found to regulate various biological processes. CircRNAs are present in human biological fluids, are relatively stable, and accumulate with age, making them promising as biomarkers of aging. Current information on the expression of circRNAs in aging was analyzed using scientific databases. In this review, we have identified key stages in the study of circRNAs during aging and summarized the current understanding of their biogenesis. By focusing on the role of circRNAs in processes that contribute to aging - such as genomic stability, metabolism, cell death, and signaling pathways - we hypothesize that circRNAs may drive the aging process through their age-related accumulation and resultant deregulation. Examples of age-related differential expression of circRNAs in various species, including humans, are provided. This review highlights the importance of finding novel epigenetic biomarkers of aging, beyond the already identified molecules (circFOXO3, circRNA100783, circPVT1), and highlights circRNAs as a potential therapeutic target for the treatment of age-associated diseases.
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Affiliation(s)
- Anna-Maria D. Zharova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Alexey D. Perenkov
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Maria V. Vedunova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
- Biophotonics Center, Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow, Russia
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Krasikova A, Kulikova T, Schelkunov M, Makarova N, Fedotova A, Plotnikov V, Berngardt V, Maslova A, Fedorov A. The first chicken oocyte nucleus whole transcriptomic profile defines the spectrum of maternal mRNA and non-coding RNA genes transcribed by the lampbrush chromosomes. Nucleic Acids Res 2024; 52:12850-12877. [PMID: 39494543 PMCID: PMC11602149 DOI: 10.1093/nar/gkae941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 10/11/2024] [Indexed: 11/05/2024] Open
Abstract
Lampbrush chromosomes, with their unusually high rate of nascent RNA synthesis, provide a valuable model for studying mechanisms of global transcriptome up-regulation. Here, we obtained a whole-genomic profile of transcription along the entire length of all lampbrush chromosomes in the chicken karyotype. With nuclear RNA-seq, we obtained information about a wider set of transcripts, including long non-coding RNAs retained in the nucleus and stable intronic sequence RNAs. For a number of protein-coding genes, we visualized their nascent transcripts on the lateral loops of lampbrush chromosomes by RNA-FISH. The set of genes transcribed on the lampbrush chromosomes is required for basic cellular processes and is characterized by a broad expression pattern. We also present the first high-throughput transcriptome characterization of miRNAs and piRNAs in chicken oocytes at the lampbrush chromosome stage. Major targets of predicted piRNAs include CR1 and long terminal repeat (LTR) containing retrotransposable elements. Transcription of tandem repeat arrays was demonstrated by alignment against the whole telomere-to-telomere chromosome assemblies. We show that transcription of telomere-derived RNAs is initiated at adjacent LTR elements. We conclude that hypertranscription on the lateral loops of giant lampbrush chromosomes is required for synthesizing large amounts of transferred to the embryo maternal RNA for thousands of genes.
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Affiliation(s)
- Alla Krasikova
- Laboratory of Cell Nucleus Structure and Dynamics, Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia
| | - Tatiana Kulikova
- Laboratory of Cell Nucleus Structure and Dynamics, Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia
| | - Mikhail Schelkunov
- Genomics Core Facility, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- Institute for Information Transmission Problems, Moscow, 127051, Russia
| | - Nadezhda Makarova
- Genomics Core Facility, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Anna Fedotova
- Genomics Core Facility, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vladimir Plotnikov
- Laboratory of Cell Nucleus Structure and Dynamics, Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia
| | - Valeria Berngardt
- Laboratory of Cell Nucleus Structure and Dynamics, Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia
| | - Antonina Maslova
- Laboratory of Cell Nucleus Structure and Dynamics, Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia
| | - Anton Fedorov
- Laboratory of Cell Nucleus Structure and Dynamics, Department of Cytology and Histology, Saint-Petersburg State University, Saint-Petersburg, 199034, Russia
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Hu H, Tang J, Wang H, Guo X, Tu C, Li Z. The crosstalk between alternative splicing and circular RNA in cancer: pathogenic insights and therapeutic implications. Cell Mol Biol Lett 2024; 29:142. [PMID: 39550559 PMCID: PMC11568689 DOI: 10.1186/s11658-024-00662-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Accepted: 11/05/2024] [Indexed: 11/18/2024] Open
Abstract
RNA splicing is a fundamental step of gene expression. While constitutive splicing removes introns and joins exons unbiasedly, alternative splicing (AS) selectively determines the assembly of exons and introns to generate RNA variants corresponding to the same transcript. The biogenesis of circular RNAs (circRNAs) is inextricably associated with AS. Back-splicing, the biogenic process of circRNA, is a special form of AS. In cancer, both AS and circRNA deviate from the original track. In the present review, we delve into the intricate interplay between AS and circRNAs in the context of cancer. The relationship between AS and circRNAs is intricate, where AS modulates the biogenesis of circRNAs and circRNAs in return regulate AS events. Beyond that, epigenetic and posttranscriptional modifications concurrently regulate AS and circRNAs. On the basis of this modality, we summarize current knowledge on how splicing factors and other RNA binding proteins regulate circRNA biogenesis, and how circRNAs interact with splicing factors to influence AS events. Specifically, the feedback loop regulation between circRNAs and AS events contributes greatly to oncogenesis and cancer progression. In summary, resolving the crosstalk between AS and circRNA will not only provide better insight into cancer biology but also provoke novel strategies to combat cancer.
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Affiliation(s)
- Hongkun Hu
- Department of Orthopaedics, Hunan Key Laboratory of Tumor Models and Individualized Medicine, Hunan Engineering Research Center of Artificial Intelligence-Based Medical Equipment, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
| | - Jinxin Tang
- Department of Orthopaedics, Hunan Key Laboratory of Tumor Models and Individualized Medicine, Hunan Engineering Research Center of Artificial Intelligence-Based Medical Equipment, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
| | - Hua Wang
- Department of Orthopaedics, Hunan Key Laboratory of Tumor Models and Individualized Medicine, Hunan Engineering Research Center of Artificial Intelligence-Based Medical Equipment, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
| | - Xiaoning Guo
- Department of Orthopaedics, Hunan Key Laboratory of Tumor Models and Individualized Medicine, Hunan Engineering Research Center of Artificial Intelligence-Based Medical Equipment, The Second Xiangya Hospital of Central South University, Changsha, 410011, China.
| | - Chao Tu
- Department of Orthopaedics, Hunan Key Laboratory of Tumor Models and Individualized Medicine, Hunan Engineering Research Center of Artificial Intelligence-Based Medical Equipment, The Second Xiangya Hospital of Central South University, Changsha, 410011, China.
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, 410011, China.
- Hunan Engineering Research Center of Artificial Intelligence-Based Medical Equipment, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China.
| | - Zhihong Li
- Department of Orthopaedics, Hunan Key Laboratory of Tumor Models and Individualized Medicine, Hunan Engineering Research Center of Artificial Intelligence-Based Medical Equipment, The Second Xiangya Hospital of Central South University, Changsha, 410011, China.
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, 410011, China.
- Hunan Engineering Research Center of Artificial Intelligence-Based Medical Equipment, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, China.
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Chen LL, Kim VN. Small and long non-coding RNAs: Past, present, and future. Cell 2024; 187:6451-6485. [PMID: 39547208 DOI: 10.1016/j.cell.2024.10.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Revised: 10/13/2024] [Accepted: 10/15/2024] [Indexed: 11/17/2024]
Abstract
Since the introduction of the central dogma of molecular biology in 1958, various RNA species have been discovered. Messenger RNAs transmit genetic instructions from DNA to make proteins, a process facilitated by housekeeping non-coding RNAs (ncRNAs) such as small nuclear RNAs (snRNAs), ribosomal RNAs (rRNAs), and transfer RNAs (tRNAs). Over the past four decades, a wide array of regulatory ncRNAs have emerged as crucial players in gene regulation. In celebration of Cell's 50th anniversary, this Review explores our current understanding of the most extensively studied regulatory ncRNAs-small RNAs and long non-coding RNAs (lncRNAs)-which have profoundly shaped the field of RNA biology and beyond. While small RNA pathways have been well documented with clearly defined mechanisms, lncRNAs exhibit a greater diversity of mechanisms, many of which remain unknown. This Review covers pivotal events in their discovery, biogenesis pathways, evolutionary traits, action mechanisms, functions, and crosstalks among ncRNAs. We also highlight their roles in pathophysiological contexts and propose future research directions to decipher the unknowns of lncRNAs by leveraging lessons from small RNAs.
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Affiliation(s)
- Ling-Ling Chen
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China; School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; New Cornerstone Science Laboratory, Shenzhen, China.
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
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Xu D, Liu Y, Liu Q, Li G, Zhang L, Yu C, Liang H, Chen X, Zheng J, Song J. N 6-methyladenosine modification of circular RNA circASH2L suppresses growth and metastasis in hepatocellular carcinoma through regulating hsa-miR-525-3p/MTUS2 axis. J Transl Med 2024; 22:1026. [PMID: 39543614 PMCID: PMC11566831 DOI: 10.1186/s12967-024-05745-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2024] [Accepted: 10/08/2024] [Indexed: 11/17/2024] Open
Abstract
BACKGROUND CircRNAs have been demonstrated to play a crucial role in regulating the growth and progression of various cancers, including hepatocellular carcinoma (HCC). Nevertheless, the circRNA's expression pattern and function in HCC need more investigation. METHODS Bioinformatics techniques were used to identify differentially expressed circRNAs in HCC. CircASH2L expression in HCC tissues was assessed through qRT-PCR and ISH analysis. To assess circASH2L's impact on HCC progression, a variety of experiments were carried out both in vitro and in vivo, such as CCK8, colony formation, EdU assay, flow cytometry, transwell assay, and xenograft mouse model. Various experimental techniques including qRT-PCR, dual luciferase reporter assay, FISH, RNA pull-down, and RIP experiments were utilized to evaluate the relationship between circASH2L, miR-525-3p, and MTUS2. Additionally, experiments were conducted to explore the impact of m6A modification on circASH2L expression, including RNA stability assay, m6A RNA immunoprecipitation assay (MeRIP), and Co-IP experiments. RESULTS We found that circASH2L was downregulated in HCC tissues and the downregulation of circASH2L was significantly correlated with malignant characteristics as well as poor overall survival of patients with HCC. CircASH2L was found to inhibit cells growth, migration and invasion as well as tumorigenesis and metastasis in vivo. Mechanistically, we established that circASH2L directly interacted with miR-525-3p to enhance MTUS2 expression, subsequently leading to tumor suppression. Moreover, the influence of circASH2L on tumor suppression was attenuated by increasing miR-525-3p levels, and MTUS2 was recognized as an essential intermediary in circASH2L-induced tumor suppression. Additionally, N6-methyladenosine (m6A) modification was identified in circASH2L. Our data suggested that METTL3 was responsible for mediating m6A methylation of circASH2L, ultimately regulating circASH2L expression through the promotion of its degradation. These findings collectively highlight the role of circASH2L as a tumor suppressor through a unique circASH2L/miR-525-3p/MTUS2 axis, shedding light on the significance of m6A modification in regulating circASH2L function. CONCLUSION The work emphasizes circASH2L as a promising therapeutic target for treating HCC, offering new insights into the role of circRNAs in HCC development.
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Affiliation(s)
- Dafeng Xu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, People's Republic of China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, People's Republic of China
- Key Laboratory of Organ Transplantation, National Health Commission, Wuhan, People's Republic of China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei, People's Republic of China
| | - Yachong Liu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, People's Republic of China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, People's Republic of China
- Key Laboratory of Organ Transplantation, National Health Commission, Wuhan, People's Republic of China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei, People's Republic of China
| | - Qiumeng Liu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, People's Republic of China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, People's Republic of China
- Key Laboratory of Organ Transplantation, National Health Commission, Wuhan, People's Republic of China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei, People's Republic of China
| | - Ganxun Li
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, People's Republic of China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, People's Republic of China
- Key Laboratory of Organ Transplantation, National Health Commission, Wuhan, People's Republic of China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei, People's Republic of China
| | - Lu Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, People's Republic of China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, People's Republic of China
- Key Laboratory of Organ Transplantation, National Health Commission, Wuhan, People's Republic of China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei, People's Republic of China
| | - Chengpeng Yu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, People's Republic of China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, People's Republic of China
- Key Laboratory of Organ Transplantation, National Health Commission, Wuhan, People's Republic of China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei, People's Republic of China
| | - Huifang Liang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, People's Republic of China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, People's Republic of China
- Key Laboratory of Organ Transplantation, National Health Commission, Wuhan, People's Republic of China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei, People's Republic of China
| | - Xiaoping Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, People's Republic of China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, People's Republic of China
- Key Laboratory of Organ Transplantation, National Health Commission, Wuhan, People's Republic of China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei, People's Republic of China
| | - Jinfang Zheng
- Department of Hepatobiliary and Pancreatic Surgery, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China.
| | - Jia Song
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China.
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, People's Republic of China.
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, People's Republic of China.
- Key Laboratory of Organ Transplantation, National Health Commission, Wuhan, People's Republic of China.
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei, People's Republic of China.
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Yi Q, Ouyang X, Zhong K, Chen Z, Zhu W, Zhu G, Zhong J. circFOXP1: a potential diagnostic and therapeutic target in human diseases. Front Immunol 2024; 15:1489378. [PMID: 39606233 PMCID: PMC11599189 DOI: 10.3389/fimmu.2024.1489378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2024] [Accepted: 10/28/2024] [Indexed: 11/29/2024] Open
Abstract
Circular RNA (circRNA) are a unique class of non-coding RNAs characterized by their covalently closed loop structures, which grant them properties such as stability and conservation. Among these, circFOXP1 has been implicated in various diseases, including cancers, respiratory, skeletal, and cardiovascular disorders. This review systematically examines circFOXP1's role in disease progression, highlighting its involvement in critical biological processes, including cell proliferation, invasion, apoptosis, and autophagy. Mechanistically, circFOXP1 functions through miRNA sponging, protein interactions, and modulation of key signaling pathways such as Wnt and PI3K/AKT. We discuss its potential as a diagnostic and therapeutic target. Our analysis also identifies key unresolved questions, such as the precise regulatory networks involving circFOXP1 and its translation potential, offering pathways for future research.
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Affiliation(s)
- Qiang Yi
- The First Clinical Medical College, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Xinting Ouyang
- The First Clinical Medical College, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Kui Zhong
- The First Clinical Medical College, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Zheng Chen
- The First Clinical Medical College, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Weijian Zhu
- The First Clinical Medical College, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Gangfeng Zhu
- The First Clinical Medical College, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Jinghua Zhong
- Department of Oncology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
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65
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Zhang J. Non-coding RNAs and angiogenesis in cardiovascular diseases: a comprehensive review. Mol Cell Biochem 2024; 479:2921-2953. [PMID: 38306012 DOI: 10.1007/s11010-023-04919-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/18/2023] [Indexed: 02/03/2024]
Abstract
Non-coding RNAs (ncRNAs) have key roles in the etiology of many illnesses, including heart failure, myocardial infarction, stroke, and in physiological processes like angiogenesis. In transcriptional regulatory circuits that control heart growth, signaling, and stress response, as well as remodeling in cardiac disease, ncRNAs have become important players. Studies on ncRNAs and cardiovascular disease have made great progress recently. Here, we go through the functions of non-coding RNAs (ncRNAs) like circular RNAs (circRNAs), and microRNAs (miRNAs) as well as long non-coding RNAs (lncRNAs) in modulating cardiovascular disorders.
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Affiliation(s)
- Jie Zhang
- Medical School, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
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Cai J, Qiu Z, Chi‐Shing Cho W, Liu Z, Chen S, Li H, Chen K, Li Y, Zuo C, Qiu M. Synthetic circRNA therapeutics: innovations, strategies, and future horizons. MedComm (Beijing) 2024; 5:e720. [PMID: 39525953 PMCID: PMC11550093 DOI: 10.1002/mco2.720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 08/18/2024] [Accepted: 08/19/2024] [Indexed: 11/16/2024] Open
Abstract
Small molecule drugs are increasingly emerging as innovative and effective treatments for various diseases, with mRNA therapeutics being a notable representative. The success of COVID-19 vaccines has underscored the transformative potential of mRNA in RNA therapeutics. Within the RNA family, there is another unique type known as circRNA. This single-stranded closed-loop RNA molecule offers notable advantages over mRNA, including enhanced stability and prolonged protein expression, which may significantly impact therapeutic strategies. Furthermore, circRNA plays a pivotal role in the pathogenesis of various diseases, such as cancers, autoimmune disorders, and cardiovascular diseases, making it a promising clinical intervention target. Despite these benefits, the application of circRNA in clinical settings remains underexplored. This review provides a comprehensive overview of the current state of synthetic circRNA therapeutics, focusing on its synthesis, optimization, delivery, and diverse applications. It also addresses the challenges impeding the advancement of circRNA therapeutics from bench to bedside. By summarizing these aspects, the review aims to equip researchers with insights into the ongoing developments and future directions in circRNA therapeutics. Highlighting both the progress and the existing gaps in circRNA research, this review offers valuable perspectives for advancing the field and guiding future investigations.
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Affiliation(s)
- Jingsheng Cai
- Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non‐Small Cell Lung CancerPeking University People's HospitalBeijingChina
- Department of Thoracic SurgeryPeking University People's HospitalBeijingChina
- Institute of Advanced Clinical MedicinePeking UniversityBeijingChina
| | - Zonghao Qiu
- Suzhou CureMed Biopharma Technology Co., Ltd.SuzhouChina
| | | | - Zheng Liu
- Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non‐Small Cell Lung CancerPeking University People's HospitalBeijingChina
- Department of Thoracic SurgeryPeking University People's HospitalBeijingChina
- Institute of Advanced Clinical MedicinePeking UniversityBeijingChina
| | - Shaoyi Chen
- Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non‐Small Cell Lung CancerPeking University People's HospitalBeijingChina
- Department of Thoracic SurgeryPeking University People's HospitalBeijingChina
- Institute of Advanced Clinical MedicinePeking UniversityBeijingChina
| | - Haoran Li
- Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non‐Small Cell Lung CancerPeking University People's HospitalBeijingChina
- Department of Thoracic SurgeryPeking University People's HospitalBeijingChina
- Institute of Advanced Clinical MedicinePeking UniversityBeijingChina
| | - Kezhong Chen
- Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non‐Small Cell Lung CancerPeking University People's HospitalBeijingChina
- Department of Thoracic SurgeryPeking University People's HospitalBeijingChina
- Institute of Advanced Clinical MedicinePeking UniversityBeijingChina
| | - Yun Li
- Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non‐Small Cell Lung CancerPeking University People's HospitalBeijingChina
- Department of Thoracic SurgeryPeking University People's HospitalBeijingChina
| | - Chijian Zuo
- Suzhou CureMed Biopharma Technology Co., Ltd.SuzhouChina
| | - Mantang Qiu
- Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non‐Small Cell Lung CancerPeking University People's HospitalBeijingChina
- Department of Thoracic SurgeryPeking University People's HospitalBeijingChina
- Institute of Advanced Clinical MedicinePeking UniversityBeijingChina
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Hamdy NM, El-Sisi MG, Ibrahim SM, ElNokoudy H, Hady AA, Abd-Ellatef GEF, Sallam AAM, Barakat BM. In silico analysis and comprehensive review of circular-RNA regulatory roles in breast diseases; a step-toward non-coding RNA precision. Pathol Res Pract 2024; 263:155651. [PMID: 39454476 DOI: 10.1016/j.prp.2024.155651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Revised: 10/10/2024] [Accepted: 10/11/2024] [Indexed: 10/28/2024]
Abstract
In the current comprehensive review, we first highlighted circRNAs, which are key ncRNAs. Next, we discussed the relationships among circRNAs and breast cancer subtypes via in silico databases analysis and extensive literature search. CircRNAs, that sponge miRNA axes or act as silencers of oncogenic mRNAs, have been extensively addressed in the context of this review. During BC pathogenesis, the circRNA/microRNA/messenger RNA (mRNA) axis plays a major role in disease growth, progression, and survival/resistance and could be targeted for improved treatment options. This review also aimed to address oncogenic and tumor suppressor mRNAs, which are regulated by various circRNAs in BC. Moreover, we mentioned the relation of different circRNAs with cancer hallmarks, patient survival together with drug resistance. Additionally, we discussed circRNAs as vaccines and biomarkers in BC. Finally, we studied exosomal circRNAs as a hot interesting area in the research. REVIEW SIGNIFICANCE: Via using in silico databases, bioinformatics analysis, and a thorough literature search to first highlight circRNA as a crucial ncRNA and its biogenesis, and then we explored the connection between circRNA and breast illnesses. In the framework of the review, circRNA sponged-miRNAs axis or as silencers to oncogenic mRNAs were extensively discussed. In the pathophysiology of BC, the circular RNA/microRNA/messenger RNA axis is crucial for the propagation of the disease and resistance that may be targeted for more effective treatment options, in order to confront tumor suppressor and oncogenic mRNAs that are presently regulated by circRNAs in BC. For better patient results, we advised further mechanistic research to elucidate additional ncRNA axis that may be targeted for the therapy of BC and for prognosis/ or early diagnosis.
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Affiliation(s)
- Nadia M Hamdy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia, Cairo 11566, Egypt.
| | - Mona G El-Sisi
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia, Cairo 11566, Egypt
| | - Sherine M Ibrahim
- Biochemistry Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Heba ElNokoudy
- Medication Management & Pharmacy Affairs, Egypt Healthcare Authority, Cairo, Egypt
| | - Ahmad A Hady
- Clinical Oncology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Gamal Eldein Fathy Abd-Ellatef
- Therapeutic Chemistry Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, 33 El Bohouth St., Dokki, Giza 12622, Egypt
| | - Al-Aliaa M Sallam
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia, Cairo 11566, Egypt; Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Bassant Mohamed Barakat
- Department of Clinical Pharmacy, Faculty of Pharmacy, Al Baha University, Al Baha 1988, Saudi Arabia; Department of Pharmacology and Toxicology, Faculty of Pharmacy (Girls), Al-Azhar University, Nasr City, Cairo 11651, Egypt
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Wu C, Bao S, Sun H, Chen X, Yang L, Li R, Peng Y. Noncoding RNAs regulating ferroptosis in cardiovascular diseases: novel roles and therapeutic strategies. Mol Cell Biochem 2024; 479:2827-2841. [PMID: 38064139 PMCID: PMC11473578 DOI: 10.1007/s11010-023-04895-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 11/06/2023] [Indexed: 10/15/2024]
Abstract
The morbidity and mortality rates of cardiovascular diseases (CVDs) are increasing; thus, they impose substantial health and economic burdens worldwide, and effective interventions are needed for immediate resolution of this issue. Recent studies have suggested that noncoding RNAs (ncRNAs) play critical roles in the occurrence and development of CVDs and are potential therapeutic targets and novel biomarkers for these diseases. Newly discovered modes of cell death, including necroptosis, pyroptosis, apoptosis, autophagy-dependent cell death and ferroptosis, also play key roles in CVD progression. However, ferroptosis, which differs from the other aforementioned forms of regulated cell death in terms of cell morphology, biochemistry and inhereditability, is a unique iron-dependent mode of nonapoptotic cell death induced by abnormal iron metabolism and excessive accumulation of iron-dependent lipid peroxides and reactive oxygen species (ROS). Increasing evidence has confirmed that ncRNA-mediated ferroptosis is involved in regulating tissue homeostasis and CVD-related pathophysiological conditions, such as cardiac ischemia/reperfusion (I/R) injury, myocardial infarction (MI), atrial fibrillation (AF), cardiomyopathy and heart failure (HF). In this review, we summarize the underlying mechanism of ferroptosis, discuss the pathophysiological effects of ncRNA-mediated ferroptosis in CVDs and provide ideas for effective therapeutic strategies.
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Affiliation(s)
- Changyong Wu
- Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Suli Bao
- Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Huang Sun
- Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiaocui Chen
- Department of Gastroenterology, Affiliated Hospital of Panzhihua University, Panzhihua, China
| | - Lu Yang
- Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ruijie Li
- Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming, China.
| | - Yunzhu Peng
- Department of Cardiology, the First Affiliated Hospital of Kunming Medical University, Kunming, China.
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Gao Y, Lin H, Tang T, Wang Y, Chen W, Li L. Circular RNAs in programmed cell death: Regulation mechanisms and potential clinical applications in cancer: A review. Int J Biol Macromol 2024; 280:135659. [PMID: 39288849 DOI: 10.1016/j.ijbiomac.2024.135659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Revised: 09/10/2024] [Accepted: 09/12/2024] [Indexed: 09/19/2024]
Abstract
Circular RNAs (circRNAs) are a novel class of non-coding RNAs with covalently closed structures formed by reverse splicing of precursor mRNAs. The widespread expression of circRNAs across species has been revealed by high-throughput sequencing and bioinformatics approaches, indicating their unique properties and diverse functions including acting as microRNA sponges and interacting with RNA-binding proteins. Programmed cell death (PCD), encompassing various forms such as apoptosis, necroptosis, pyroptosis, autophagy, and ferroptosis, is an essential process for maintaining normal development and homeostasis in the human body by eliminating damaged, infected, and aging cells. Many studies have demonstrated that circRNAs play crucial roles in tumourigenesis and development by regulating PCD in tumor cells, showing that circRNAs have the potential to be biomarkers and therapeutic targets in cancer. This review aims to comprehensively summarize the intricate associations between circRNAs and diverse PCD pathways in tumor cells, which play crucial roles in cancer development. Additionally, this review provides a detailed overview of the underlying mechanisms by which circRNAs modulate various forms of PCD for the first time. The ultimate objective is to offer valuable insights into the potential clinical significance of developing novel strategies based on circRNAs and PCD for cancer diagnosis, prognosis, and treatment.
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Affiliation(s)
- Yudi Gao
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Hong Lin
- Department of Pharmacy, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Tiantian Tang
- Department of Pharmacy, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Yuanqiang Wang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China.
| | - Wanyi Chen
- Department of Pharmacy, Chongqing University Cancer Hospital, Chongqing, 400030, China.
| | - Lixian Li
- Department of Pharmacy, Chongqing University Cancer Hospital, Chongqing, 400030, China.
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70
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Wang H, Gao Y, Bai J, Liu H, Li Y, Zhang J, Ma C, Zhao X, Zhang L, Wan K, Zhu D. CircLMBR1 inhibits phenotypic transformation of hypoxia-induced pulmonary artery smooth muscle via the splicing factor PUF60. Eur J Pharmacol 2024; 980:176855. [PMID: 39059570 DOI: 10.1016/j.ejphar.2024.176855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/04/2024] [Accepted: 07/24/2024] [Indexed: 07/28/2024]
Abstract
Phenotypic transformation of pulmonary artery smooth muscle cells (PASMCs) contributes to vascular remodeling in hypoxic pulmonary hypertension (PH). Recent studies have suggested that circular RNAs (circRNAs) may play important roles in the vascular remodeling of hypoxia-induced PH. However, whether circRNAs cause pulmonary vascular remodeling by regulating the phenotypic transformation in PH has not been investigated. Microarray and RT-qPCR analysis identified that circLMBR1, a novel circRNA, decreased in mouse lung tissues of the hypoxia-SU5416 PH model, as well as in human PASMCs and mouse PASMCs exposed to hypoxia. Overexpression of circLMBR1 in the Semaxinib (SU5416) mouse model ameliorated hypoxia-induced PH and vascular remodeling in the lungs. Notably, circLMBR1 was mainly distributed in the nucleus and bound to the splicing factor PUF60. CircLMBR1 suppressed the phenotypic transformation of human PASMCs and vascular remodeling by inhibiting PUF60 expression. Furthermore, we identified U2AF65 as the downstream regulatory factor of PUF60. U2AF65 directly interacted with the pre-mRNA of the contractile phenotype marker smooth muscle protein 22-α (SM22α) and inhibited its splicing. Meanwhile, hypoxia exposure increased the formation of the PUF60-U2AF65 complex, thereby inhibiting SM22α production and inducing the transition of human PASMCs from a contractile phenotype to a synthetic phenotype. Overall, our results verified the important role of circLMBR1 in the pathological process of PH. We also proposed a new circLMBR1/PUF60-U2AF65/pre-SM22α pathway that could regulate the phenotypic transformation and proliferation of human PASMCs. This study may provide new perspectives for the diagnosis and treatment of PH.
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MESH Headings
- Pulmonary Artery/metabolism
- Pulmonary Artery/pathology
- Pulmonary Artery/drug effects
- Animals
- Humans
- Mice
- Vascular Remodeling/drug effects
- Vascular Remodeling/genetics
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/drug effects
- Myocytes, Smooth Muscle/pathology
- Phenotype
- RNA, Circular/genetics
- RNA, Circular/metabolism
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Muscle, Smooth, Vascular/drug effects
- Male
- Splicing Factor U2AF/genetics
- Splicing Factor U2AF/metabolism
- Hypertension, Pulmonary/metabolism
- Hypertension, Pulmonary/pathology
- Hypertension, Pulmonary/genetics
- Hypoxia/metabolism
- Hypoxia/genetics
- Mice, Inbred C57BL
- Cell Hypoxia
- Indoles/pharmacology
- Pyrroles
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Affiliation(s)
- Hongdan Wang
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Pharmacy, Harbin Medical University, Harbin, 150081, PR China
| | - Yupei Gao
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Pharmacy, Harbin Medical University, Harbin, 150081, PR China
| | - June Bai
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Pharmacy, Harbin Medical University, Harbin, 150081, PR China
| | - Huiyu Liu
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Pharmacy, Harbin Medical University, Harbin, 150081, PR China
| | - Yiying Li
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Pharmacy, Harbin Medical University, Harbin, 150081, PR China
| | - Junting Zhang
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Pharmacy, Harbin Medical University, Harbin, 150081, PR China
| | - Cui Ma
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Medical Laboratory Science and Technology, Harbin Medical University (Daqing), Daqing, 163319, PR China
| | - Xijuan Zhao
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Medical Laboratory Science and Technology, Harbin Medical University (Daqing), Daqing, 163319, PR China
| | - Lixin Zhang
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Medical Laboratory Science and Technology, Harbin Medical University (Daqing), Daqing, 163319, PR China
| | - Kuiyu Wan
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China
| | - Daling Zhu
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Pharmacy, Harbin Medical University, Harbin, 150081, PR China; Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, Harbin, 150081, PR China.
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71
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Figueroa-Angulo EE, Puente-Rivera J, Perez-Navarro YF, Condado EM, Álvarez-Sánchez ME. Epigenetic alteration in cervical cancer induced by human papillomavirus. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 390:25-66. [PMID: 39864896 DOI: 10.1016/bs.ircmb.2024.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
Abstract
The critical role of a subset of Human Papillomavirus in cervical cancer has been widely acknowledged and studied. Despite progress in our understanding of the viral molecular mechanisms of pathogenesis, knowledge of how infection with HPV oncogenic variants progresses from latent infection to incurable cancer has not been completely elucidated. In this paper we reviewed the relationship between HPV infection and epigenetic mechanisms such as histone acetylation and deacetylation, DNA methylation and non-coding RNAs associated with this infection and the carcinogenic process.
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Affiliation(s)
- Elisa-Elvira Figueroa-Angulo
- Licenciatura en Ciencias Genómicas, Laboratorio de Patogénesis Celular y Molecular Humana y Veterinaria, Universidad Autónoma de la Ciudad de la México, Ciudad de México, México
| | - Jonathan Puente-Rivera
- División de Investigación, Hospital Juárez De México, Ciudad de México, México; Posgrado en Ciencias Genómicas, Laboratorio de Patogenesis Celular y Molecular Humana y Veterinaria, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
| | - Yussel Fernando Perez-Navarro
- Posgrado en Ciencias Genómicas, Laboratorio de Patogenesis Celular y Molecular Humana y Veterinaria, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
| | - Edgar Mendieta Condado
- Laboratorio Estatal de Salud Pública, Secretaría de Salud de Jalisco, Guadalajara, Jalisco, México
| | - María-Elizbeth Álvarez-Sánchez
- Posgrado en Ciencias Genómicas, Laboratorio de Patogenesis Celular y Molecular Humana y Veterinaria, Universidad Autónoma de la Ciudad de México, Ciudad de México, México.
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72
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Liu CX, Yang L, Chen LL. Dynamic conformation: Marching toward circular RNA function and application. Mol Cell 2024; 84:3596-3609. [PMID: 39366349 DOI: 10.1016/j.molcel.2024.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/01/2024] [Accepted: 08/15/2024] [Indexed: 10/06/2024]
Abstract
Circular RNA is a group of covalently closed, single-stranded transcripts with unique biogenesis, stability, and conformation that play distinct roles in modulating cellular functions and also possess a great potential for developing circular RNA-based therapies. Importantly, due to its circular conformation, circular RNA generates distinct intramolecular base pairing that is different from the linear transcript. In this perspective, we review how circular RNA conformation can affect its turnover and modes of action, as well as what factors can modulate circular RNA conformation. We also discuss how understanding circular RNA conformation can facilitate learning about their functions as well as the remaining technological issues to further address their conformation. These efforts will ultimately inform the design of circular RNA-based platforms for biomedical applications.
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Affiliation(s)
- Chu-Xiao Liu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ling-Ling Chen
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China; New Cornerstone Science Laboratory, Shenzhen, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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73
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Jiang H, Xu Y, Tong Y, Zhang D, Zhou R. IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation. PLoS Comput Biol 2024; 20:e1012293. [PMID: 39466881 PMCID: PMC11542809 DOI: 10.1371/journal.pcbi.1012293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 11/07/2024] [Accepted: 10/12/2024] [Indexed: 10/30/2024] Open
Abstract
As an emerging class of RNA molecules, circular RNAs play pivotal roles in various biological processes, thereby determining their three-dimensional (3D) structure is crucial for a deep understanding of their biological significances. Similar to linear RNAs, the development of computational methods for circular RNA 3D structure prediction is challenging, especially considering the inherent flexibility and potentially long length of circular RNAs. Here, we introduce an extension of our previous IsRNA2 model, named IsRNAcirc, to enable circular RNA 3D structure predictions through coarse-grained molecular dynamics simulations. The workflow of IsRNAcirc consists of four main steps, including input preparation, end closure, structure prediction, and model refinement. Our results demonstrate that IsRNAcirc can provide reasonable 3D structure predictions for circular RNAs, which significantly reduce the locally irrational elements contained in the initial input. Moreover, for a validation test set comprising 34 circular RNAs, our IsRNAcirc can generate 3D models with better scores than the template-based 3dRNA method. These findings demonstrate that our IsRNAcirc method is a promising tool to explore the structural details along with intricate interactions of circular RNAs.
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Affiliation(s)
- Haolin Jiang
- College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yulian Xu
- College of Life Sciences, China Jiliang University, Hangzhou, China
- China Jiliang University—Aoming (Hangzhou) Biomedical Co., Ltd. Joint Laboratory, Hangzhou, China
| | - Yunguang Tong
- College of Life Sciences, China Jiliang University, Hangzhou, China
- Aoming (Hangzhou) Biomedical Co., Ltd., Hangzhou, China
| | - Dong Zhang
- College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ruhong Zhou
- College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou, Zhejiang, China
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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74
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Hejazian SM, Rahbar Saadat Y, Hosseiniyan Khatibi SM, Farnood F, Farzamikia N, Hejazian SS, Batoumchi S, Shoja MM, Zununi Vahed S, Ardalan M. Circular RNAs as novel biomarkers in glomerular diseases. Arch Physiol Biochem 2024; 130:568-580. [PMID: 37194131 DOI: 10.1080/13813455.2023.2212328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/18/2023]
Abstract
Circular RNAs (circRNAs) regulate gene expression and biological procedures by controlling target genes or downstream pathways by sponging their related miRNA (s). Three types of circRNAs have been identified; exonic circRNAs (ecircRNAs), intronic RNAs (ciRNAs), and exon-intron circRNAs (ElciRNAs). It is clarified that altered levels of circRNAs have dynamic pathological and physiological functions in kidney diseases. Evidence suggests that circRNAs can be considered novel diagnostic biomarkers and therapeutic targets for renal diseases. Glomerulonephritis (GN) is a general term used to refer to a wide range of glomerular diseases. GN is an important cause of chronic kidney diseases. Here, we review the biogenesis of circRNAs, and their molecular and physiological functions in the kidney. Moreover, the dysregulated expression of circRNAs and their biological functions are discussed in primary and secondary glomerulonephritis. Moreover, diagnostic and therapeutic values of circRNAs in distinguishing or treating different types of GN are highlighted.
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Affiliation(s)
| | | | | | - Farahnoosh Farnood
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Negin Farzamikia
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyyed Sina Hejazian
- Neurosciences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sepideh Batoumchi
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammadali M Shoja
- College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA
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75
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Wismayer R, Matthews R, Whalley C, Kiwanuka J, Kakembo FE, Thorn S, Wabinga H, Odida M, Tomlinson I. Determination of the frequency and distribution of APC, PIK3CA, and SMAD4 gene mutations in Ugandan patients with colorectal cancer. BMC Cancer 2024; 24:1212. [PMID: 39350061 PMCID: PMC11440721 DOI: 10.1186/s12885-024-12967-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 09/19/2024] [Indexed: 10/04/2024] Open
Abstract
Uganda is a developing low-income country with a low incidence of colorectal cancer, which is steadily increasing. Ugandan colorectal cancer (CRC) patients are young and present with advanced-stage disease. In our population, there is a scarcity of genetic oncological studies, therefore, we investigated the mutational status of CRC tissues, focusing in particular on the adenomatous polyposis coli (APC), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), and SMAD4 genes. Our objective was to determine whether there were any differences between other populations and Ugandan patients. We performed next-generation sequencing on the extracted DNA from formalin-fixed paraffin-embedded adenocarcinoma samples from 127 patients (mean (SD) age: 54.9 (16.0) years; male:female sex ratio: 1.2:1). Most tumours were located in the rectum 56 (44.1%), 14 (11%) tumours were high grade, and 96 (75.6%) were moderate grade CRC. Stage III + IV CRC tumours were found in 109 (85.8%) patients. We identified 48 variants of APC, including 9 novel APC mutations that were all pathogenic or deleterious. For PIK3CA, we found 19 variants, of which 9 were deleterious or pathogenic. Four PIK3CA novel pathogenic or deleterious variants were included (c.1397C > G, c.2399_2400insA, c.2621G > C, c.2632C > G). Three SMAD4 variants were reported, including two pathogenic or deleterious variants (c.1268G > T, c.556dupC) and one tolerant (c.563A > C) variant. One novel SMAD4 deleterious mutation (c.1268G > T) was reported. In conclusion, we provide clinicopathological information and new genetic variation data pertinent to CRC in Uganda.
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Affiliation(s)
- Richard Wismayer
- Department of Surgery, Masaka Regional Referral Hospital, Masaka, Uganda.
- Department of Surgery, Faculty of Health Sciences, Equator University of Science and Technology, Masaka, Uganda.
- Department of Surgery, Faculty of Health Sciences, Habib Medical School, IUIU University, Kampala, Uganda.
- Department of Pathology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda.
- Institute of Genetics and Cancer, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK.
| | - Rosie Matthews
- Institute of Genetics and Cancer, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - Celina Whalley
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Julius Kiwanuka
- Department of Epidemiology and Biostatistics, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Fredrick Elishama Kakembo
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
- African Centre of Excellence in Bioinformatics and Data Intensive Sciences, Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Steve Thorn
- Institute of Genetics and Cancer, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Henry Wabinga
- Department of Pathology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Michael Odida
- Department of Pathology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
- Department of Pathology, Faculty of Medicine, Gulu University, Gulu, Uganda
| | - Ian Tomlinson
- Institute of Genetics and Cancer, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
- Department of Oncology, University of Oxford, Oxford, UK
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76
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Yi Q, Feng J, Lan W, Shi H, Sun W, Sun W. CircRNA and lncRNA-encoded peptide in diseases, an update review. Mol Cancer 2024; 23:214. [PMID: 39343883 PMCID: PMC11441268 DOI: 10.1186/s12943-024-02131-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 09/19/2024] [Indexed: 10/01/2024] Open
Abstract
Non-coding RNAs (ncRNAs), including circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs), are unique RNA molecules widely identified in the eukaryotic genome. Their dysregulation has been discovered and played key roles in the pathogenesis of numerous diseases, including various cancers. Previously considered devoid of protein-coding ability, recent research has revealed that a small number of open reading frames (ORFs) within these ncRNAs endow them with the potential for protein coding. These ncRNAs-derived peptides or proteins have been proven to regulate various physiological and pathological processes through diverse mechanisms. Their emerging roles in disease diagnosis and targeted therapy underscore their potential utility in clinical settings. This comprehensive review aims to provide a systematic overview of proteins or peptides encoded by lncRNAs and circRNAs, elucidate their production and functional mechanisms, and explore their promising applications in cancer diagnosis, disease prediction, and targeted therapy.
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Affiliation(s)
- Qian Yi
- Department of Physiology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, 646099, China
| | - Jianguo Feng
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.
| | - Weiwu Lan
- Department of Orthopedics, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong, 518035, China
| | - Houyin Shi
- Department of Orthopedics, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000, China
| | - Wei Sun
- Department of Orthopedics, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong, 518035, China.
| | - Weichao Sun
- Department of Orthopedics, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong, 518035, China.
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77
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Jiang M, Bai H, Fang S, Zhou C, Shen W, Gong Z. CircLIFRSA/miR-1305/PTEN axis attenuates malignant cellular processes in non-small cell lung cancer by regulating AKT phosphorylation. Mol Cancer 2024; 23:208. [PMID: 39342185 PMCID: PMC11438201 DOI: 10.1186/s12943-024-02120-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 09/10/2024] [Indexed: 10/01/2024] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) is typically diagnosed at advanced stages, which limits the effectiveness of therapeutic interventions. The present study aimed to explore the role of the newly identified circLIFRSA in the PTEN/AKT signaling pathway and its involvement in the malignant processes of NSCLC. METHODS CircLIFRSA expression was identified through microarray analysis, and its levels in NSCLC samples were quantified by RT-qPCR. The impact of circLIFRSA on cell growth, proliferation, apoptosis, and cell cycle were evaluated by MTT assay, colony formation assay, and flow cytometry. Additionally, Western blotting was employed to analyze the expression of PTEN and phosphorylated AKT (pAKT) in NSCLC cells. RESULTS The expression of circLIFRSA was found to be significantly reduced in NSCLC cells and tissues. This downregulation correlated with various clinicopathological characteristics and indicated its potential as an early diagnostic biomarker for NSCLC. Importantly, circLIFRSA was shown to inhibit cell growth and proliferation while promoting apoptosis in NSCLC cells. Mechanically, circLIFRSA was found to attenuate the malignant processes of NSCLC cells via the miR-1305/PTEN axis and the suppression of AKT phosphorylation. CONCLUSIONS These findings indicate that circLIFRSA/miR-1305/PTEN axis attenuates malignant processes by regulating AKT phosphorylation, and provide new insights into the potential of circLIFRSA as a biomarker for early diagnosis and as a promising therapeutic target in NSCLC.
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Affiliation(s)
- Meina Jiang
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Huihui Bai
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Shuai Fang
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Chengwei Zhou
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, 315020, China
| | - Weiyu Shen
- Department of Thoracic Surgery, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, 315040, China
| | - Zhaohui Gong
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, School of Basic Medical Sciences, Health Science Center, Ningbo University, Ningbo, Zhejiang, 315211, China.
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, 315020, China.
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78
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Long BY, Wang Y, Hao SH, Shi G. Molecular significance of circRNAs in malignant lymphoproliferative disorders: pathogenesis and novel biomarkers or therapeutic targets. Am J Cancer Res 2024; 14:4633-4651. [PMID: 39417189 PMCID: PMC11477815 DOI: 10.62347/kmwb5164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 09/22/2024] [Indexed: 10/19/2024] Open
Abstract
Recent studies have shown that circular RNAs (CircRNAs) have the novel functions and molecular mechanisms in the pathogenesis of malignant diseases. CircRNAs have been found to be associated with the occurrence and development of lymphoproliferative diseases, impacting on lymphocyte proliferation. This article provides a review of the pathogenesis of circRNAs in malignant lymphoproliferative disorders, focusing on conditions such as acute lymphocytic leukemia (ALL), chronic lymphocytic leukemia (CLL), and lymphoma. Additionally, it discusses the potential value of circRNAs as novel biomarkers or therapeutic targets in these disorders.
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Affiliation(s)
- Bo-Yang Long
- Department of Oncology and Hematology, The Second Hospital of Jilin UniversityChangchun, Jilin, China
| | - Yan Wang
- Department of Hematology, The Affiliated Yantai Yuhuangding Hospital of Qingdao UniversityYantai, Shandong, China
| | - Shu-Hong Hao
- Department of Oncology and Hematology, The Second Hospital of Jilin UniversityChangchun, Jilin, China
| | - Guang Shi
- Department of Oncology and Hematology, The Second Hospital of Jilin UniversityChangchun, Jilin, China
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Yuan H, Liao X, Hu D, Guan D, Tian M. Back to the Origin: Mechanisms of circRNA-Directed Regulation of Host Genes in Human Disease. Noncoding RNA 2024; 10:49. [PMID: 39452835 PMCID: PMC11510700 DOI: 10.3390/ncrna10050049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 09/14/2024] [Accepted: 09/17/2024] [Indexed: 10/26/2024] Open
Abstract
Circular RNAs (circRNAs) have been shown to be pivotal regulators in various human diseases by participating in gene splicing, acting as microRNA (miRNA) sponges, interacting with RNA-binding proteins (RBPs), and translating into short peptides. As the back-splicing products of pre-mRNAs, many circRNAs can modulate the expression of their host genes through transcriptional, post-transcriptional, translational, and post-translational control via interaction with other molecules. This review provides a detailed summary of these regulatory mechanisms based on the class of molecules that they interact with, which encompass DNA, mRNA, miRNA, and RBPs. The co-expression of circRNAs with their parental gene productions (including linear counterparts and proteins) provides potential diagnostic biomarkers for multiple diseases. Meanwhile, the different regulatory mechanisms by which circRNAs act on their host genes via interaction with other molecules constitute complex regulatory networks, which also provide noticeable clues for therapeutic strategies against diseases. Future research should explore whether these proven mechanisms can play a similar role in other types of disease and clarify further details about the cross-talk between circRNAs and host genes. In addition, the regulatory relationship between circRNAs and their host genes in circRNA circularization, degradation, and cellular localization should receive further attention.
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Affiliation(s)
- Haomiao Yuan
- Center of Forensic Investigation, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang 110122, China;
- Liaoning Province Key Laboratory of Forensic Bio-Evidence Science, No. 77 Puhe Road, Shenyang North New Area, Shenyang 110122, China
- Department of Forensic Pathology, School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang 110122, China
| | - Xizhou Liao
- Department of Forensic Genetic and Biology, School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang 110122, China; (X.L.); (D.H.)
| | - Ding Hu
- Department of Forensic Genetic and Biology, School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang 110122, China; (X.L.); (D.H.)
| | - Dawei Guan
- Center of Forensic Investigation, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang 110122, China;
- Liaoning Province Key Laboratory of Forensic Bio-Evidence Science, No. 77 Puhe Road, Shenyang North New Area, Shenyang 110122, China
- Department of Forensic Pathology, School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang 110122, China
| | - Meihui Tian
- Center of Forensic Investigation, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang 110122, China;
- Liaoning Province Key Laboratory of Forensic Bio-Evidence Science, No. 77 Puhe Road, Shenyang North New Area, Shenyang 110122, China
- Department of Forensic Genetic and Biology, School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang 110122, China; (X.L.); (D.H.)
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80
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Dong X, Chen Q, Du H, Qiu L. 2,3,7,8-Tetrachlorodibenzo-p-Dioxin Suppresses Mesenchymal Cell Proliferation and Migration Through miR-214-3p in Cleft Palate. Cleft Palate Craniofac J 2024:10556656241286314. [PMID: 39314083 DOI: 10.1177/10556656241286314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/25/2024] Open
Abstract
OBJECTIVE The aetiology of CL/P is complicated, with both genetic and environmental factors. This study aimed to investigate the association between TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) exposure and changes in the expression of miR-214-3p in the context of cleft palate. DESIGN In this study, we established a fetal mouse cleft palate model using TCDD and differentially expressed miRNAs were analysed by microarray analysis and verified by qRT-PCR. Finally, we demonstrated the effects of TCDD and microRNAs on the proliferation and migration of mesenchymal cells by using CCK8, EDU, Transwell, and wound-healing assays. RESULTS Our findings revealed significant upregulation of miRNAs such as miR-214-3p, miR-296-5p, and miR-33-5p in the TCDD intervention group, while miRNAs like miR-92a-3p, miR-126a-3p, and miR-411-5p were significantly downregulated. Notably, qRT-PCR testing confirmed a significant difference in miR-214-3P expression. Further investigations involved the overexpression of miR-214-3p, reducing cell proliferation and migration in primary mouse embryonic palatal mesenchymal (MEPM) cells. CONCLUSIONS These results are consistent with the finding that TCDD suppresses palatal mesenchymal cell proliferation and migration through miR-214-3p. In conclusion, miR-214-3p probably plays a role in TCDD-induced cleft palates in mice.
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Affiliation(s)
- Xiaobo Dong
- Department of Burn and Plastic Surgery, Children's Hospital of Chongqing Medical University, National Clinical Research Centre for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Chongqing 404000, P.R. China
| | - Qiang Chen
- Department of Burn and Plastic Surgery, Children's Hospital of Chongqing Medical University, National Clinical Research Centre for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Chongqing 404000, P.R. China
- Department of Paediatrics Surgery, Chongqing University Three Gorges Hospital, Chongqing 404000 P.R. China
| | - Haojuan Du
- Chongqing Key Laboratory of Pediatrics, Chongqing 404000, P.R. China
| | - Lin Qiu
- Department of Burn and Plastic Surgery, Children's Hospital of Chongqing Medical University, National Clinical Research Centre for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Chongqing 404000, P.R. China
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81
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Liu XY, Tong JF, Li MY, Li LF, Cai WW, Li JQ, Wang LH, Sun MJ. Progress in application of cyclic single-stranded nucleic acids. J Biotechnol 2024; 393:140-148. [PMID: 39067578 DOI: 10.1016/j.jbiotec.2024.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 07/21/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
Cyclic nucleic acids are biologically stable against nucleic acid exonucleases due to the absence of 5' and 3' termini. Studies of cyclic nucleic acids mainly focus on cyclic single-stranded nucleic acids. Cyclic single-stranded nucleic acids are further divided into circular RNA (circRNA) and circular single-stranded DNA (cssDNA). The synthesis methods of circRNA include lasso-driven cyclization, intron-paired cyclization, intron cyclization, intron complementary pairing-driven cyclization, RNA-binding protein-driven cyclization, and artificial synthesis depending on the source. Its main role is to participate in gene expression and the treatment of some diseases. Circular single-stranded DNA is mainly synthesized by chemical ligation, template-directed enzyme ligation, and new techniques for the efficient preparation of DNA single loops and topologies based on CircLigase. It is mainly used in rolling circle amplification (RCA) technology and in the bioprotection of circular aptamers and second messengers. This review focuses on the types, synthesis methods, and applications of cyclic single-stranded nucleic acids, providing a reference for further research on cyclic single-stranded nucleic acids.
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Affiliation(s)
- Xin-Yang Liu
- Department of Student team, College of Basic Medical Sciences, Naval Medical University, 200433, People's Republic of China
| | - Jian-Fei Tong
- Department of Student team, College of Basic Medical Sciences, Naval Medical University, 200433, People's Republic of China
| | - Ming-Yang Li
- Department of Student team, College of Basic Medical Sciences, Naval Medical University, 200433, People's Republic of China
| | - Lian-Fang Li
- Department of Student team, College of Basic Medical Sciences, Naval Medical University, 200433, People's Republic of China
| | - Wen-Wei Cai
- Department of Student team, College of Basic Medical Sciences, Naval Medical University, 200433, People's Republic of China
| | - Jin-Qian Li
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, 200433, People's Republic of China
| | - Liang-Hua Wang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, 200433, People's Republic of China.
| | - Ming-Juan Sun
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, 200433, People's Republic of China.
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Yadav V, Singh T, Sharma D, Garg VK, Chakraborty P, Ghatak S, Satapathy SR. Unraveling the Regulatory Role of HuR/microRNA Axis in Colorectal Cancer Tumorigenesis. Cancers (Basel) 2024; 16:3183. [PMID: 39335155 PMCID: PMC11430344 DOI: 10.3390/cancers16183183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 09/04/2024] [Accepted: 09/13/2024] [Indexed: 09/30/2024] Open
Abstract
Colorectal cancer (CRC) remains a significant global health burden with high incidence and mortality. MicroRNAs (miRNAs) are small non-protein coding transcripts, conserved throughout evolution, with an important role in CRC tumorigenesis, and are either upregulated or downregulated in various cancers. RNA-binding proteins (RBPs) are known as essential regulators of miRNA activity. Human antigen R (HuR) is a prominent RBP known to drive tumorigenesis with a pivotal role in CRC. In this review, we discuss the regulatory role of the HuR/miRNA axis in CRC. Interestingly, miRNAs can directly target HuR, altering its expression and activity. However, HuR can also stabilize or degrade miRNAs, forming complex feedback loops that either activate or block CRC-associated signaling pathways. Dysregulation of the HuR/miRNA axis contributes to CRC initiation and progression. Additionally, HuR-miRNA regulation by other small non-coding RNAs, circular RNA (circRNAs), or long-non-coding RNAs (lncRNAs) is also explored here. Understanding this HuR-miRNA interplay could reveal novel biomarkers with better diagnostic or prognostic accuracy.
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Affiliation(s)
- Vikas Yadav
- Department of Translational Medicine, Clinical Research Centre, Lund University, 221 00 Malmö, Sweden;
| | - Tejveer Singh
- Translational Oncology Laboratory, Department of Zoology, Hansraj College, University of Delhi, New Delhi 110021, India; (T.S.); (D.S.)
- Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences (INMAS-DRDO), New Delhi 110054, India
| | - Deepika Sharma
- Translational Oncology Laboratory, Department of Zoology, Hansraj College, University of Delhi, New Delhi 110021, India; (T.S.); (D.S.)
| | - Vivek Kumar Garg
- Department of Medical Lab Technology, Chandigarh University, Gharuan, Mohali 140413, Punjab, India;
| | - Payel Chakraborty
- Amity Institute of Biotechnology, Amity University Kolkata, Kolkata 700135, West Bengal, India; (P.C.); (S.G.)
| | - Souvik Ghatak
- Amity Institute of Biotechnology, Amity University Kolkata, Kolkata 700135, West Bengal, India; (P.C.); (S.G.)
| | - Shakti Ranjan Satapathy
- Department of Translational Medicine, Clinical Research Centre, Lund University, 221 00 Malmö, Sweden;
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83
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Xu S, Chen T, Yu J, Wan L, Zhang J, Chen J, Wei W, Li X. Insights into the regulatory role of epigenetics in moyamoya disease: Current advances and future prospectives. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102281. [PMID: 39188306 PMCID: PMC11345382 DOI: 10.1016/j.omtn.2024.102281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Moyamoya disease (MMD) is a progressive steno-occlusive cerebrovascular disorder that predominantly affecting East Asian populations. The intricate interplay of distinct and overlapping mechanisms, including genetic associations such as the RNF213-p.R4810K variant, contributes to the steno-occlusive lesions and moyamoya vessels. However, genetic mutations alone do not fully elucidate the occurrence of MMD, suggesting a potential role for epigenetic factors. Accruing evidence has unveiled the regulatory role of epigenetic markers, including DNA methylation, histone modifications, and non-coding RNAs (ncRNAs), in regulating pivotal cellular and molecular processes implicated in the pathogenesis of MMD by modulating endothelial cells and smooth muscle cells. The profile of these epigenetic markers in cerebral vasculatures and circulation has been determined to identify potential diagnostic biomarkers and therapeutic targets. Furthermore, in vitro studies have demonstrated the multifaceted effects of modulating specific epigenetic markers on MMD pathogenesis. These findings hold great potential for the discovery of novel therapeutic targets, translational studies, and clinical applications. In this review, we comprehensively summarize the current understanding of epigenetic mechanisms, including DNA methylation, histone modifications, and ncRNAs, in the context of MMD. Furthermore, we discuss the potential challenges and opportunities that lie ahead in this rapidly evolving field.
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Affiliation(s)
- Shuangxiang Xu
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Tongyu Chen
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jin Yu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Lei Wan
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jianjian Zhang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jincao Chen
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Wei Wei
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Xiang Li
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430071, China
- Medical Research Institute, Wuhan University, Wuhan 430071, China
- Sino-Italian Ascula Brain Science Joint Laboratory, Wuhan University, Wuhan 430071, China
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84
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Kundu I, Varshney S, Karnati S, Naidu S. The multifaceted roles of circular RNAs in cancer hallmarks: From mechanisms to clinical implications. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102286. [PMID: 39188305 PMCID: PMC11345389 DOI: 10.1016/j.omtn.2024.102286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Circular RNAs (circRNAs) represent a distinct class of covalently closed RNA species lacking conventional 5' to 3' polarity. Derived predominantly from pre-mRNA transcripts of protein-coding genes, circRNAs arise through back-splicing events of exon-exon or exon-intron junctions. They exhibit tissue- and cell-specific expression patterns and play crucial roles in regulating fundamental cellular processes such as cell cycle dynamics, proliferation, apoptosis, and differentiation. CircRNAs modulate gene expression through a plethora of mechanisms at epigenetic, transcriptional, and post-transcriptional levels, and some can even undergo translation into functional proteins. Recently, aberrant expression of circRNAs has emerged as a significant molecular aberration within the intricate regulatory networks governing hallmarks of cancer. The tumor-specific expression patterns and remarkable stability of circRNAs have profound implications for cancer diagnosis, prognosis, and therapy. This review comprehensively explores the multifaceted roles of circRNAs across cancer hallmarks in various tumor types, underscoring their growing significance in cancer diagnosis and therapeutic interventions. It also details strategies for leveraging circRNA-based therapies and discusses the challenges in using circRNAs for cancer management, emphasizing the need for further research to overcome these obstacles.
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Affiliation(s)
- Indira Kundu
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Shivani Varshney
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Srikanth Karnati
- Institute of Anatomy and Cell Biology, University of Würzburg, 97070 Würzburg, Germany
- Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Germany
| | - Srivatsava Naidu
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
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85
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Wu C, Wang X, Li Y, Zhen W, Wang C, Wang X, Xie Z, Xu X, Guo S, Botella JR, Zheng B, Wang W, Song CP, Hu Z. Sequestration of DBR1 to stress granules promotes lariat intronic RNAs accumulation for heat-stress tolerance. Nat Commun 2024; 15:7696. [PMID: 39227617 PMCID: PMC11371829 DOI: 10.1038/s41467-024-52034-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 08/22/2024] [Indexed: 09/05/2024] Open
Abstract
Heat stress (HS) poses a significant challenge to plant survival, necessitating sophisticated molecular mechanisms to maintain cellular homeostasis. Here, we identify SICKLE (SIC) as a key modulator of HS responses in Arabidopsis (Arabidopsis thaliana). SIC is required for the sequestration of RNA DEBRANCHING ENZYME 1 (DBR1), a rate-limiting enzyme of lariat intronic RNA (lariRNA) decay, into stress granules (SGs). The sequestration of DBR1 by SIC enhances the accumulation of lariRNAs, branched circular RNAs derived from excised introns during pre-mRNA splicing, which in turn promote the transcription of their parental genes. Our findings further demonstrate that SIC-mediated DBR1 sequestration in SGs is crucial for plant HS tolerance, as deletion of the N-terminus of SIC (SIC1-244) impairs DBR1 sequestration and compromises plant response to HS. Overall, our study unveils a mechanism of transcriptional regulation in the HS response, where lariRNAs are enriched through DBR1 sequestration, ultimately promoting the transcription of heat stress tolerance genes.
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Affiliation(s)
- Chengyun Wu
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Sanya Institute, Henan University, Sanya, 572025, China
- The National Engineering Lab of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Xingsong Wang
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Yan Li
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Weibo Zhen
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Chunfei Wang
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Xiaoqing Wang
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Zhouli Xie
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Xiumei Xu
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Sanya Institute, Henan University, Sanya, 572025, China
| | - Siyi Guo
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Sanya Institute, Henan University, Sanya, 572025, China
| | - José Ramón Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Wei Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Center for Life Sciences, Beijing, 100871, China
| | - Chun-Peng Song
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
- Sanya Institute, Henan University, Sanya, 572025, China.
| | - Zhubing Hu
- The Zhongzhou Laboratory for Integrative Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
- Sanya Institute, Henan University, Sanya, 572025, China.
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86
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Xu J, Wang Q, Tang X, Feng X, Zhang X, Liu T, Wu F, Wang Q, Feng X, Tang Q, Lisch D, Lu Y. Drought-induced circular RNAs in maize roots: Separating signal from noise. PLANT PHYSIOLOGY 2024; 196:352-367. [PMID: 38669308 DOI: 10.1093/plphys/kiae229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 04/28/2024]
Abstract
Circular RNAs (circRNAs) play an important role in diverse biological processes; however, their origin and functions, especially in plants, remain largely unclear. Here, we used 2 maize (Zea mays) inbred lines, as well as 14 of their derivative recombination inbred lines with different drought sensitivity, to systematically characterize 8,790 circRNAs in maize roots under well-watered (WW) and water-stress (WS) conditions. We found that a diverse set of circRNAs expressed at significantly higher levels under WS. Enhanced expression of circRNAs was associated with longer flanking introns and an enrichment of long interspersed nuclear element retrotransposable elements. The epigenetic marks found at the back-splicing junctions of circRNA-producing genes were markedly different from canonical splicing, characterized by increased levels of H3K36me3/H3K4me1, as well as decreased levels of H3K9Ac/H3K27Ac. We found that genes expressing circRNAs are subject to relaxed selection. The significant enrichment of trait-associated sites along their genic regions suggested that genes giving rise to circRNAs were associated with plant survival rate under drought stress, implying that circRNAs play roles in plant drought responses. Furthermore, we found that overexpression of circMED16, one of the drought-responsive circRNAs, enhances drought tolerance in Arabidopsis (Arabidopsis thaliana). Our results provide a framework for understanding the intricate interplay of epigenetic modifications and how they contribute to the fine-tuning of circRNA expression under drought stress.
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Affiliation(s)
- Jie Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Sichuan Agricultural University, Sichuan 611130, China
| | - Qi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Xin Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Xiaoju Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Xiaoyue Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Tianhong Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Fengkai Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Qingjun Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Xuanjun Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Qi Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Yanli Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
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He Y, Ma L, Zeng X, Xie J, Ning X. Systematic identification and analysis of immune-related circRNAs of Pelteobagrus fulvidraco involved in Aeromonas veronii infection. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 51:101256. [PMID: 38797004 DOI: 10.1016/j.cbd.2024.101256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Abstract
Circular RNA (circRNA) represents a type of newly discovered non-coding RNA, distinguished by its closed loop structure formed through covalent bonds. Recent studies have revealed that circRNAs have crucial influences on host anti-pathogen responses. Yellow catfish (Pelteobagrus fulvidraco), an important aquaculture fish with great economic value, is susceptible to Aeromonas veronii, a common aquatic pathogen that can cause acute death. Here, we reported the first systematic investigation of circRNAs in yellow catfish, especially those associated with A. veronii infection at different time points. A total of 1205 circRNAs were identified, which were generated from 875 parental genes. After infection, 47 circRNAs exhibited differential expression patterns (named DEcirs). The parental genes of these DEcirs were functionally engaged in immune-related processes. Accordingly, seven DEcirs (novel_circ_000226, 278, 401, 522, 736, 843, and 975) and six corresponding parental genes (ADAMTS13, HAMP1, ANG3, APOA1, FGB, and RALGPS1) associated with immunity were obtained, and their expression was confirmed by RT-qPCR. Moreover, we found that these DEcir-gene pairs likely acted through pathways, such as platelet activation, antimicrobial humoral response, and regulation of Ral protein signal transduction, to influence host immune defenses. Additionally, integrated analysis showed that, of the 7 immune-related DEcirs, three targeted 16 miRNAs, which intertwined into circRNA-miRNA networks. These findings revealed that circRNAs, by targeting genes or miRNAs are highly involved in anti-bacterial responses in yellow catfish. Our study comprehensively illustrates the roles of circRNAs in yellow catfish immune defenses. The identified DEcirs and the circRNA-miRNA network will contribute to the further investigations on the molecular mechanisms underlying yellow catfish immune responses.
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Affiliation(s)
- Yongxin He
- College of Marine Science and Engineering, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Lina Ma
- College of Marine Science and Engineering, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Xueyu Zeng
- College of Marine Science and Engineering, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Jingjing Xie
- College of Marine Science and Engineering, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Xianhui Ning
- College of Marine Science and Engineering, Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing Normal University, Nanjing 210023, Jiangsu, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang 222005, China.
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88
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Zhang Z, Gao Z, Fang H, Zhao Y, Xing R. Therapeutic importance and diagnostic function of circRNAs in urological cancers: from metastasis to drug resistance. Cancer Metastasis Rev 2024; 43:867-888. [PMID: 38252399 DOI: 10.1007/s10555-023-10152-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 10/31/2023] [Indexed: 01/23/2024]
Abstract
Circular RNAs (circRNAs) are a member of non-coding RNAs with no ability in encoding proteins and their aberrant dysregulation is observed in cancers. Their closed-loop structure has increased their stability, and they are reliable biomarkers for cancer diagnosis. Urological cancers have been responsible for high mortality and morbidity worldwide, and developing new strategies in their treatment, especially based on gene therapy, is of importance since these malignant diseases do not respond to conventional therapies. In the current review, three important aims are followed. At the first step, the role of circRNAs in increasing or decreasing the progression of urological cancers is discussed, and the double-edged sword function of them is also highlighted. At the second step, the interaction of circRNAs with molecular targets responsible for urological cancer progression is discussed, and their impact on molecular processes such as apoptosis, autophagy, EMT, and MMPs is highlighted. Finally, the use of circRNAs as biomarkers in the diagnosis and prognosis of urological cancer patients is discussed to translate current findings in the clinic for better treatment of patients. Furthermore, since circRNAs can be transferred to tumor via exosomes and the interactions in tumor microenvironment provided by exosomes such as between macrophages and cancer cells is of importance in cancer progression, a separate section has been devoted to the role of exosomal circRNAs in urological tumors.
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Affiliation(s)
- Zhibin Zhang
- College of Traditional Chinese Medicine, Chengde Medical College, Chengde, 067000, Hebei, China.
| | - Zhixu Gao
- Chengde Medical College, Chengde, 067000, Hebei, China
| | - Huimin Fang
- Chengde Medical College, Chengde, 067000, Hebei, China
| | - Yutang Zhao
- Chengde Medical College, Chengde, 067000, Hebei, China
| | - Rong Xing
- Chengde Medical College, Chengde, 067000, Hebei, China
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89
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Xu Y, Gao Z, Sun X, Li J, Ozaki T, Shi D, Yu M, Zhu Y. The role of circular RNA during the urological cancer metastasis: exploring regulatory mechanisms and potential therapeutic targets. Cancer Metastasis Rev 2024; 43:1055-1074. [PMID: 38558156 DOI: 10.1007/s10555-024-10182-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/02/2024] [Indexed: 04/04/2024]
Abstract
Metastasis is a major contributor to treatment failure and death in urological cancers, representing an important biomedical challenge at present. Metastases form as a result of cancer cells leaving the primary site, entering the vasculature and lymphatic vessels, and colonizing clones elsewhere in the body. However, the specific regulatory mechanisms of action underlying the metastatic process of urological cancers remain incompletely elucidated. With the deepening of research, circular RNAs (circRNAs) have been found to not only play a significant role in tumor progression and prognosis but also show aberrant expression in various tumor metastases, consequently impacting tumor metastasis through multiple pathways. Therefore, circRNAs are emerging as potential tumor markers and treatment targets. This review summarizes the research progress on elucidating how circRNAs regulate the urological cancer invasion-metastasis cascade response and related processes, as well as their role in immune microenvironment remodeling and circRNA vaccines. This body of work highlights circRNA regulation as an emerging therapeutic target for urological cancers, which should motivate further specific research in this regard.
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Affiliation(s)
- Yan Xu
- Department of Urology, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Zhipeng Gao
- Department of Urology, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Xiaoyu Sun
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110001, China
| | - Jun Li
- Department of Urology, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Toshinori Ozaki
- Laboratory of DNA Damage Signaling, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Du Shi
- Department of Urology, The First Hospital of China Medical University, Shenyang, 110001, China.
| | - Meng Yu
- Department of Laboratory Animal Science, China Medical University, No. 77 Puhe Road, Shenyang, 110122, Liaoning, China.
| | - Yuyan Zhu
- Department of Urology, The First Hospital of China Medical University, Shenyang, 110001, China.
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90
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Conn VM, Chinnaiyan AM, Conn SJ. Circular RNA in cancer. Nat Rev Cancer 2024; 24:597-613. [PMID: 39075222 DOI: 10.1038/s41568-024-00721-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/13/2024] [Indexed: 07/31/2024]
Abstract
Over the past decade, circular RNA (circRNA) research has evolved into a bona fide research field shedding light on the functional consequence of this unique family of RNA molecules in cancer. Although the method of formation and the abundance of circRNAs can differ from their cognate linear mRNA, the spectrum of interacting partners and their resultant cellular functions in oncogenesis are analogous. However, with 10 times more diversity in circRNA variants compared with linear RNA variants, combined with their hyperstability in the cell, circRNAs are equipped to influence every stage of oncogenesis. This is an opportune time to address the breadth of circRNA in cancer focused on their spatiotemporal expression, mutations in biogenesis factors and contemporary functions through each stage of cancer. In this Review, we highlight examples of functional circRNAs in specific cancers, which satisfy critical criteria, including their physical co-association with the target and circRNA abundance at stoichiometrically valid quantities. These considerations are essential to develop strategies for the therapeutic exploitation of circRNAs as biomarkers and targeted anticancer agents.
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Affiliation(s)
- Vanessa M Conn
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, South Australia, Australia
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Simon J Conn
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, South Australia, Australia.
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91
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Xu Z, Guan C, Cheng Z, Zhou H, Qin W, Feng J, Wan M, Zhang Y, Jia C, Shao S, Guo H, Li S, Liu B. Research trends and hotspots of circular RNA in cardiovascular disease: A bibliometric analysis. Noncoding RNA Res 2024; 9:930-944. [PMID: 38680417 PMCID: PMC11047193 DOI: 10.1016/j.ncrna.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 04/03/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
From a global perspective, cardiovascular diseases (CVDs), the leading factor accounting for population mortality, and circRNAs, RNA molecules with stable closed-loop structures, have been proven to be closely related. The latent clinical value and the potential role of circRNAs in CVDs have been attracting increasing, active research interest, but bibliometric studies in this field are still lacking. Thus, in this study, we conducted a bibliometric analysis by using software such as VOSviewer, CiteSpace, Microsoft Excel, and the R package to determine the current research progress and hotspots and ultimately provide an overview of the development trends and future frontiers in this field. In our study, based on our search strategy, a total of 1206 publications published before July 31, 2023 were accessed from the WOSCC database. According to our findings, there is a notable increasing trend in global publications in the field of circRNA in CVDs. China was found to be the dominant country in terms of publication number, but a lack of high-quality articles was a significant fault. A cluster analysis on the co-cited references indicated that dilated cardiomyopathy, AMI, and cardiac hypertrophy are the greatest objects of concern. In contrast, a keywords analysis indicated that high importance has been ascribed to MI, abdominal aortic aneurysm, cell proliferation, and coronary artery diseases.
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Affiliation(s)
- Zehui Xu
- Department of Anatomy, College of Chinese Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Chong Guan
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Ziji Cheng
- Department of Anatomy, College of Chinese Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Houle Zhou
- Department of Anatomy, College of Chinese Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Wanting Qin
- Department of Anatomy, College of Chinese Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Jiaming Feng
- Department of Anatomy, College of Chinese Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Melisandre Wan
- Department of Anatomy, College of Chinese Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yihan Zhang
- Department of Anatomy, College of Chinese Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Chengyao Jia
- Guanghua School of Stomatology, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Shuijin Shao
- Department of Anatomy, College of Chinese Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Haidong Guo
- Department of Anatomy, College of Chinese Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Shaoling Li
- Department of Pathology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, 200433, China
| | - Baonian Liu
- Department of Anatomy, College of Chinese Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
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92
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Wang Y, Zhang J, Yang Y, Liu Z, Sun S, Li R, Zhu H, Li T, Zheng J, Li J, Ma L. Circular RNAs in human diseases. MedComm (Beijing) 2024; 5:e699. [PMID: 39239069 PMCID: PMC11374765 DOI: 10.1002/mco2.699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/25/2024] [Accepted: 07/30/2024] [Indexed: 09/07/2024] Open
Abstract
Circular RNAs (circRNAs) are a unique class of RNA molecules formed through back-splicing rather than linear splicing. As an emerging field in molecular biology, circRNAs have garnered significant attention due to their distinct structure and potential functional implications. A comprehensive understanding of circRNAs' functions and potential clinical applications remains elusive despite accumulating evidence of their involvement in disease pathogenesis. Recent research highlights their significant roles in various human diseases, but comprehensive reviews on their functions and applications remain scarce. This review provides an in-depth examination of circRNAs, focusing first on their involvement in non-neoplastic diseases such as respiratory, endocrine, metabolic, musculoskeletal, cardiovascular, and renal disorders. We then explore their roles in tumors, with particular emphasis on exosomal circular RNAs, which are crucial for cancer initiation, progression, and resistance to treatment. By detailing their biogenesis, functions, and impact on disease mechanisms, this review underscores the potential of circRNAs as diagnostic biomarkers and therapeutic targets. The review not only enhances our understanding of circRNAs' roles in specific diseases and tumor types but also highlights their potential as novel diagnostic and therapeutic tools, thereby paving the way for future clinical investigations and potential therapeutic interventions.
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Affiliation(s)
- Yuanyong Wang
- Department of Thoracic SurgeryTangdu HospitalAir Force Medical UniversityXi'anChina
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education)The First Department of Thoracic SurgeryPeking University Cancer Hospital and InstitutePeking University School of OncologyBeijingChina
| | - Jin Zhang
- Department of Traditional Chinese MedicineTangdu HospitalAir Force Medical UniversityXi'anChina
- Key Laboratory of Integrated Traditional Chinese and Western Medicine Tumor Diagnosis and Treatment in Shaanxi ProvinceXi'anChina
| | - Yuchen Yang
- Department of Traditional Chinese MedicineTangdu HospitalAir Force Medical UniversityXi'anChina
- Key Laboratory of Integrated Traditional Chinese and Western Medicine Tumor Diagnosis and Treatment in Shaanxi ProvinceXi'anChina
| | - Zhuofeng Liu
- Department of Traditional Chinese MedicineThe Third Affiliated Hospital of Xi'an Medical UniversityXi'anChina
| | - Sijia Sun
- Department of Traditional Chinese MedicineTangdu HospitalAir Force Medical UniversityXi'anChina
- Key Laboratory of Integrated Traditional Chinese and Western Medicine Tumor Diagnosis and Treatment in Shaanxi ProvinceXi'anChina
| | - Rui Li
- Department of EpidemiologySchool of Public HealthAir Force Medical UniversityXi'anChina
| | - Hui Zhu
- Department of AnatomyMedical College of Yan'an UniversityYan'anChina
- Institute of Medical ResearchNorthwestern Polytechnical UniversityXi'anChina
| | - Tian Li
- School of Basic MedicineFourth Military Medical UniversityXi'anChina
| | - Jin Zheng
- Department of Traditional Chinese MedicineTangdu HospitalAir Force Medical UniversityXi'anChina
- Key Laboratory of Integrated Traditional Chinese and Western Medicine Tumor Diagnosis and Treatment in Shaanxi ProvinceXi'anChina
| | - Jie Li
- Department of EndocrineXijing 986 HospitalAir Force Medical UniversityXi'anChina
| | - Litian Ma
- Department of Thoracic SurgeryTangdu HospitalAir Force Medical UniversityXi'anChina
- Department of Traditional Chinese MedicineTangdu HospitalAir Force Medical UniversityXi'anChina
- Key Laboratory of Integrated Traditional Chinese and Western Medicine Tumor Diagnosis and Treatment in Shaanxi ProvinceXi'anChina
- Department of GastroenterologyTangdu HospitalAir Force Medical UniversityXi'anChina
- School of MedicineNorthwest UniversityXi'anChina
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93
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Yao J, Xu H, Ferrick-Kiddie EA, Nottingham RM, Wu DC, Ares M, Lambowitz AM. Human cells contain myriad excised linear intron RNAs with links to gene regulation and potential utility as biomarkers. PLoS Genet 2024; 20:e1011416. [PMID: 39325823 PMCID: PMC11460701 DOI: 10.1371/journal.pgen.1011416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 10/08/2024] [Accepted: 09/03/2024] [Indexed: 09/28/2024] Open
Abstract
A previous study using Thermostable Group II Intron Reverse Transcriptase sequencing (TGIRT-seq) found human plasma contains short (≤300 nt) structured full-length excised linear intron (FLEXI) RNAs with potential to serve as blood-based biomarkers. Here, TGIRT-seq identified >9,000 different FLEXI RNAs in human cell lines, including relatively abundant FLEXIs with cell-type-specific expression patterns. Analysis of public CLIP-seq datasets identified 126 RNA-binding proteins (RBPs) that have binding sites within the region corresponding to the FLEXI or overlapping FLEXI splice sites in pre-mRNAs, including 53 RBPs with binding sites for ≥30 different FLEXIs. These included splicing factors, transcription factors, a chromatin remodeling protein, cellular growth regulators, and proteins with cytoplasmic functions. Analysis of ENCODE datasets identified subsets of these RBPs whose knockdown impacted FLEXI host gene mRNA levels or proximate alternative splicing, indicating functional interactions. Hierarchical clustering identified six subsets of RBPs whose FLEXI binding sites were co-enriched in six subsets of functionally related host genes: AGO1-4 and DICER, including but not limited to agotrons or mirtron pre-miRNAs; DKC1, NOLC1, SMNDC1, and AATF (Apoptosis Antagonizing Transcription Factor), including but not limited to snoRNA-encoding FLEXIs; two subsets of alternative splicing factors; and two subsets that included RBPs with cytoplasmic functions (e.g., LARP4, PABPC4, METAP2, and ZNF622) together with regulatory proteins. Cell fractionation experiments showed cytoplasmic enrichment of FLEXI RNAs with binding sites for RBPs with cytoplasmic functions. The subsets of host genes encoding FLEXIs with binding sites for different subsets of RBPs were co-enriched with non-FLEXI other short and long introns with binding sites for the same RBPs, suggesting overarching mechanisms for coordinately regulating expression of functionally related genes. Our findings identify FLEXIs as a previously unrecognized large class of cellular RNAs and provide a comprehensive roadmap for further analyzing their biological functions and the relationship of their RBPs to cellular regulatory mechanisms.
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Affiliation(s)
- Jun Yao
- Departments of Molecular Biosciences and Oncology University of Texas at Austin Austin, Texas, United States of America
| | - Hengyi Xu
- Departments of Molecular Biosciences and Oncology University of Texas at Austin Austin, Texas, United States of America
| | - Elizabeth A. Ferrick-Kiddie
- Departments of Molecular Biosciences and Oncology University of Texas at Austin Austin, Texas, United States of America
| | - Ryan M. Nottingham
- Departments of Molecular Biosciences and Oncology University of Texas at Austin Austin, Texas, United States of America
| | - Douglas C. Wu
- Departments of Molecular Biosciences and Oncology University of Texas at Austin Austin, Texas, United States of America
| | - Manuel Ares
- Department of Molecular, Cell, and Developmental Biology University of California, Santa Cruz, California, United States of America
| | - Alan M. Lambowitz
- Departments of Molecular Biosciences and Oncology University of Texas at Austin Austin, Texas, United States of America
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94
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Tibenda JJ, Wang N, Li N, Dang Y, Zhu Y, Wang X, Zhang Z, Zhao Q. Research progress of circular RNAs in myocardial ischemia. Life Sci 2024; 352:122809. [PMID: 38908786 DOI: 10.1016/j.lfs.2024.122809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 05/18/2024] [Accepted: 06/04/2024] [Indexed: 06/24/2024]
Abstract
Circular RNAs (circRNAs) are a type of single-stranded RNA that forms a covalently closed continuous loop. Its structure, stability, properties, and cell- and tissue-specificity have gained considerable recognition in the research and clinical sectors, as its role has been observed in different diseases, such as cardiovascular diseases, cancers, and central nervous system diseases, etc. Cardiovascular disease is still named as the number one cause of death globally, with myocardial ischemia (MI) accounting for 15 % of mortality annually. A number of circRNAs have been identified and are being studied for their ability to reduce MI by inhibiting the molecular mechanisms associated with myocardial ischemia reperfusion injury, such as inflammation, oxidative stress, autophagy, apoptosis, and so on. CircRNAs play a significant role as crucial regulatory elements at transcriptional levels, regulating different proteins, and at posttranscriptional levels, having interactions with RNA-binding proteins, ribosomal proteins, micro-RNAS, and long non-coding RNAS, making it possible to exert their effects through the circRNA-miRNA-mRNA axis. CircRNAs are a potential novel biomarker and therapeutic target for myocardial ischemia and cardiovascular diseases in general. The purpose of this review is to summarize the relationship, function, and mechanism observed between circRNAs and MI injury, as well as to provide directions for future research and clinical trials.
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Affiliation(s)
- Jonnea Japhet Tibenda
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University, Ningxia, China
| | - Niuniu Wang
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University, Ningxia, China
| | - Nuan Li
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University, Ningxia, China
| | - Yanning Dang
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University, Ningxia, China
| | - Yafei Zhu
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University, Ningxia, China
| | - Xiaobo Wang
- Innovative Institute of Chinese Medicine and Pharmacy/Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Zhengjun Zhang
- Department of Cardiology, General Hospital of Ningxia Medical University, Ningxia, China.
| | - Qipeng Zhao
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University, Ningxia, China.
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95
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Hsu CY, Faisal A, Jumaa SS, Gilmanova NS, Ubaid M, Athab AH, Mirzaei R, Karampoor S. Exploring the impact of circRNAs on cancer glycolysis: Insights into tumor progression and therapeutic strategies. Noncoding RNA Res 2024; 9:970-994. [PMID: 38770106 PMCID: PMC11103225 DOI: 10.1016/j.ncrna.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/18/2024] [Accepted: 05/04/2024] [Indexed: 05/22/2024] Open
Abstract
Cancer cells exhibit altered metabolic pathways, prominently featuring enhanced glycolytic activity to sustain their rapid growth and proliferation. Dysregulation of glycolysis is a well-established hallmark of cancer and contributes to tumor progression and resistance to therapy. Increased glycolysis supplies the energy necessary for increased proliferation and creates an acidic milieu, which in turn encourages tumor cells' infiltration, metastasis, and chemoresistance. Circular RNAs (circRNAs) have emerged as pivotal players in diverse biological processes, including cancer development and metabolic reprogramming. The interplay between circRNAs and glycolysis is explored, illuminating how circRNAs regulate key glycolysis-associated genes and enzymes, thereby influencing tumor metabolic profiles. In this overview, we highlight the mechanisms by which circRNAs regulate glycolytic enzymes and modulate glycolysis. In addition, we discuss the clinical implications of dysregulated circRNAs in cancer glycolysis, including their potential use as diagnostic and prognostic biomarkers. All in all, in this overview, we provide the most recent findings on how circRNAs operate at the molecular level to control glycolysis in various types of cancer, including hepatocellular carcinoma (HCC), prostate cancer (PCa), colorectal cancer (CRC), cervical cancer (CC), glioma, non-small cell lung cancer (NSCLC), breast cancer, and gastric cancer (GC). In conclusion, this review provides a comprehensive overview of the significance of circRNAs in cancer glycolysis, shedding light on their intricate roles in tumor development and presenting innovative therapeutic avenues.
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Affiliation(s)
- Chou-Yi Hsu
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan City, 71710, Taiwan
- Thunderbird School of Global Management, Arizona State University Tempe Campus, Phoenix, Arizona, 85004, USA
| | - Ahmed Faisal
- Department of Pharmacy, Al-Noor University College, Nineveh, Iraq
| | - Sally Salih Jumaa
- College of Pharmacy, National University of Science and Technology, Dhi Qar, Iraq
| | - Nataliya Sergeevna Gilmanova
- Department of Prosthetic Dentistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), Russia, Moscow
| | - Mohammed Ubaid
- Medical Technical College, Al-Farahidi University, Baghdad, Iraq
| | - Aya H. Athab
- Department of Pharmacy, Al-Zahrawi University College, Karbala, Iraq
| | - Rasoul Mirzaei
- Venom & Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sajad Karampoor
- Gastrointestinal & Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran
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96
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Farhadi E, Khomeijani-Farahani M, Nikbakhsh R, Azizan A, Soltani S, Barekati H, Mahmoudi M. The potential role of circular RNAs in regulating p53 in different types of cancers. Pathol Res Pract 2024; 261:155488. [PMID: 39088876 DOI: 10.1016/j.prp.2024.155488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 07/20/2024] [Accepted: 07/24/2024] [Indexed: 08/03/2024]
Abstract
P53 tumor suppressor is a major regulator of various cellular processes and functions. It has been reported that mutation or inactivation of p53 plays a crucial role in tumorigenesis in different types of cancers. Circular RNAs (circRNAs) are single-stranded non-coding RNAs that have significant post-transcriptional effects on the regulation of gene expression in various ways. These molecules can alter the expression and function of multiple genes and proteins. In the present study, we aimed to review circRNAs that regulate the expression, function, and stability of p53 and the possible interactions between these molecules and p53. Considering the importance of p53 in cancer and the network between p53 and circRNAs, future clinical trials targeting these circRNAs as therapeutic agents deserve worthy of attention.
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Affiliation(s)
- Elham Farhadi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran; Research Center for Chronic Inflammatory Diseases, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mohammadreza Khomeijani-Farahani
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran; Students Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Rambod Nikbakhsh
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran; Department of Biology, Faculty of Sciences, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Amin Azizan
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran; Research Center for Chronic Inflammatory Diseases, Tehran University of Medical Sciences, Tehran, Iran
| | - Samaneh Soltani
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Barekati
- School of Nursing & Midwifery, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran; Research Center for Chronic Inflammatory Diseases, Tehran University of Medical Sciences, Tehran, Iran.
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Son CJ, Carnino JM, Lee H, Jin Y. Emerging Roles of Circular RNA in Macrophage Activation and Inflammatory Lung Responses. Cells 2024; 13:1407. [PMID: 39272979 PMCID: PMC11394395 DOI: 10.3390/cells13171407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/20/2024] [Accepted: 08/20/2024] [Indexed: 09/15/2024] Open
Abstract
Circular RNA (circRNA) is a type of single-stranded RNA that forms a covalently closed continuous loop, unlike linear RNA. The expression of circRNAs in mammals is often conserved across species and shows tissue and cell specificity. Some circRNA serve as gene regulators. However, the biological function of most circRNAs is unclear. CircRNA does not have 5' or 3' ends. The unique structure of circRNAs provides them with a much longer half-life and more resistance to RNase R than linear RNAs. Inflammatory lung responses occur in the pathogenesis and recovery of many lung diseases. Macrophages form the first line of host defense/innate immune responses and initiate/mediate lung inflammation. For example, in bacterial pneumonia, upon pro-inflammatory activation, they release early response cytokines/chemokines that recruit neutrophils, macrophages, and lymphocytes to sites of infection and clear pathogens. The functional effects and mechanisms by which circRNAs exert physiological or pathological roles in macrophage activation and lung inflammation remain poorly understood. In this article, we will review the current understanding and progress of circRNA biogenesis, regulation, secretion, and degradation. Furthermore, we will review the current reports on the role of circRNAs in macrophage activation and polarization, as well as in the process of inflammatory lung responses.
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Affiliation(s)
- Chang Jun Son
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, MA 02118, USA; (C.J.S.); (J.M.C.); (H.L.)
| | - Jonathan M. Carnino
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, MA 02118, USA; (C.J.S.); (J.M.C.); (H.L.)
| | - Heedoo Lee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, MA 02118, USA; (C.J.S.); (J.M.C.); (H.L.)
- Department of Biology and Chemistry, Changwon National University, Changwon 51140, Republic of Korea
| | - Yang Jin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, MA 02118, USA; (C.J.S.); (J.M.C.); (H.L.)
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98
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Luongo M, Laurenziello P, Cesta G, Bochicchio AM, Omer LC, Falco G, Milone MR, Cibarelli F, Russi S, Laurino S. The molecular conversations of sarcomas: exosomal non-coding RNAs in tumor's biology and their translational prospects. Mol Cancer 2024; 23:172. [PMID: 39174949 PMCID: PMC11340101 DOI: 10.1186/s12943-024-02083-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 08/13/2024] [Indexed: 08/24/2024] Open
Abstract
Exosomes mediate cell-to-cell crosstalk involving a variety of biomolecules through an intricate signaling network. In recent years, the pivotal role of exosomes and their non-coding RNAs cargo in the development and progression of several cancer types clearly emerged. In particular, tumor bulk and its microenvironment co-evolve through cellular communications where these nanosized extracellular vesicles are among the most relevant actors. Knowledge about the cellular, and molecular mechanisms involved in these communications will pave the way for novel exosome-based delivery of therapeutic RNAs as well as innovative prognostic/diagnostic tools. Despite the valuable therapeutic potential and clinical relevance of exosomes, their role on sarcoma has been vaguely reported because the rarity and high heterogeneity of this type of cancer. Here, we dissected the scientific literature to unravel the multifaceted role of exosomal non-coding RNAs as mediator of cell-to-cell communications in the sarcoma subtypes.
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Affiliation(s)
- Margherita Luongo
- Laboratory of Preclinical and Translational Research, IRCCS CROB Centro di Riferimento Oncologico della Basilicata, Rionero in Vulture (PZ), 85028, Italy
| | - Pasqualina Laurenziello
- Laboratory of Preclinical and Translational Research, IRCCS CROB Centro di Riferimento Oncologico della Basilicata, Rionero in Vulture (PZ), 85028, Italy
| | - Giuseppe Cesta
- Laboratory of Preclinical and Translational Research, IRCCS CROB Centro di Riferimento Oncologico della Basilicata, Rionero in Vulture (PZ), 85028, Italy
| | - Anna Maria Bochicchio
- Experimental Oncology Unit, IRCCS CROB Centro di Riferimento Oncologico della Basilicata, Rionero in Vulture (PZ), 85028, Italy
| | - Ludmila Carmen Omer
- Experimental Oncology Unit, IRCCS CROB Centro di Riferimento Oncologico della Basilicata, Rionero in Vulture (PZ), 85028, Italy
| | - Geppino Falco
- Department of Biology, University of Naples Federico II, Naples, 80126, Italy
| | | | | | - Sabino Russi
- Laboratory of Preclinical and Translational Research, IRCCS CROB Centro di Riferimento Oncologico della Basilicata, Rionero in Vulture (PZ), 85028, Italy.
| | - Simona Laurino
- Laboratory of Preclinical and Translational Research, IRCCS CROB Centro di Riferimento Oncologico della Basilicata, Rionero in Vulture (PZ), 85028, Italy
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99
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Zhang W, Xu C, Yang Z, Zhou J, Peng W, Zhang X, Li H, Qu S, Tao K. Circular RNAs in tumor immunity and immunotherapy. Mol Cancer 2024; 23:171. [PMID: 39169354 PMCID: PMC11337656 DOI: 10.1186/s12943-024-02082-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 08/13/2024] [Indexed: 08/23/2024] Open
Abstract
Circular RNAs (circRNAs) are unique noncoding RNAs that have a closed and stable loop structure generated through backsplicing. Due to their conservation, stability and tissue specificity, circRNAs can potentially be used as diagnostic indicators and therapeutic targets for certain tumors. Many studies have shown that circRNAs can act as microRNA (miRNA) sponges, and engage in interactions with proteins and translation templates to regulate gene expression and signal transduction, thereby participating in the occurrence and development of a variety of malignant tumors. Immunotherapy has revolutionized the treatment of cancer. Early researches have indicated that circRNAs are involved in regulating tumor immune microenvironment and antitumor immunity. CircRNAs may have the potential to be important targets for increasing sensitivity to immunotherapy and expanding the population of patients who benefit from cancer immunotherapy. However, few studies have investigated the correlation between circRNAs and tumor immunity. In this review, we summarize the current researches on circRNAs involved in antitumor immune regulation through different mechanisms and their potential value in increasing immunotherapy efficacy with the goal of providing new targets for cancer immunotherapy.
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Affiliation(s)
- Wenjie Zhang
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Chen Xu
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Zhipeng Yang
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Jingshi Zhou
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Wei Peng
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Xuan Zhang
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Haimin Li
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Shibin Qu
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China.
| | - Kaishan Tao
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China.
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100
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Racca L, Liuzzi E, Comparato S, Giordano G, Pignochino Y. Nanoparticles-Delivered Circular RNA Strategy as a Novel Antitumor Approach. Int J Mol Sci 2024; 25:8934. [PMID: 39201617 PMCID: PMC11354327 DOI: 10.3390/ijms25168934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/18/2024] [Accepted: 08/06/2024] [Indexed: 09/02/2024] Open
Abstract
Anticancer therapy urgently needs the development of novel strategies. An innovative molecular target is represented by circular RNAs (circRNAs), single-strand RNA molecules with the 5' and 3' ends joined, characterized by a high stability. Although circRNA properties and biological functions have only been partially elucidated, their relationship and involvement in the onset and progression of cancer have emerged. Specific targeting of circRNAs may be obtained with antisense oligonucleotides and silencing RNAs. Nanotechnology is at the forefront of research for perfecting their delivery. Continuous efforts have been made to develop novel nanoparticles (NPs) and improve their performance, materials, and properties regarding biocompatibility and targeting capabilities. Applications in various fields, from imaging to gene therapy, have been explored. This review sums up the smart strategies developed to directly target circRNAs with the fruitful application of NPs in this context.
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Affiliation(s)
- Luisa Racca
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (L.R.); (S.C.)
- Center for Translational Research on Allergic and Autoimmune Diseases (CAAD), Università del Piemonte Orientale, 28100 Novara, Italy
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Elisabetta Liuzzi
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands;
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy;
| | - Simona Comparato
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (L.R.); (S.C.)
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy;
| | - Giorgia Giordano
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy;
- Department of Oncology, University of Turin, 10060 Turin, Italy
| | - Ymera Pignochino
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (L.R.); (S.C.)
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy;
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