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Guan GF, Fu ZM, Zhang DJ, Guo YY, Guo F, Wan YN, Bai J, Zhao Y. Interferon Gamma Receptor 2 Collaborates With Circular RNA/MicroRNA to Modulate Programmed Cell Death-Ligand 1 Levels in Nasopharyngeal Carcinoma. World J Oncol 2024; 15:929-941. [PMID: 39697423 PMCID: PMC11650609 DOI: 10.14740/wjon1994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Accepted: 12/02/2024] [Indexed: 12/20/2024] Open
Abstract
Background The effectiveness of immune checkpoint therapy highlights the need to understand abnormal programmed cell death protein-1 (PD-1) expression in nasopharyngeal carcinoma (NPC), especially when treatments fail, or resistance develops. Interferon gamma (IFN-γ) signaling is crucial for regulating programmed cell death-ligand 1 (PD-L1) expression. Our study focuses on interferon gamma receptor 2 (IFNGR2), an essential part of the IFN-γ pathway, and its impact on malignant traits in NPC. Methods The expression levels of IFNGR2 and PD-L1 were accessed using quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). To understand the cellular phenotypic effects, small interfering RNA (siRNA)/short hairpin RNA (shRNA) knockdown techniques were used to evaluate cell viability, clonogenic survival, migration and invasion, immunohistochemistry, and tumor formation assays. The relationship between IFNGR2 and microRNAs (miRNAs)/circular RNAs (circRNAs) will be verified using methods such as circRNA stability assay, rescue, and dual-luciferase reporter assay. Results IFNGR2 was significantly overexpressed in NPC, and its expression positively correlated with PD-L1 levels. This overexpression contributed to increased cell proliferation, migration, invasion, clonogenicity, and tumor growth. Additionally, we identified an oncogenic circular RNA, circ_001377, and uncovered a novel mechanism by which upregulation of circ_001377 competitively bound to miR-498-3p. This interaction reduced miR-498-3p's ability to target IFNGR2. As a result, the diminished miR-498-3p led to increased IFNGR2 expression, which subsequently activated the IFN-γ signaling pathway and drove abnormal PD-L1 expression. Conclusions IFNGR2 is an oncogenic factor in NPC. The circ_001377/miR-498-3p interaction drives IFNGR2 upregulation and PD-L1 overexpression, suggesting that targeting this axis could improve therapeutic outcomes.
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Affiliation(s)
- Guo Fang Guan
- Department of Otolaryngology-Head and Neck Surgery, The Second Hospital of Jilin University, Changchun 130041, China
| | - Ze Ming Fu
- Department of Otolaryngology-Head and Neck Surgery, The Second Hospital of Jilin University, Changchun 130041, China
| | - De Jun Zhang
- Department of Otolaryngology-Head and Neck Surgery, The Second Hospital of Jilin University, Changchun 130041, China
| | - Ying Yuan Guo
- Department of Otolaryngology-Head and Neck Surgery, The Second Hospital of Jilin University, Changchun 130041, China
| | - Fang Guo
- Department of Otolaryngology-Head and Neck Surgery, The Second Hospital of Jilin University, Changchun 130041, China
| | - Yi Ning Wan
- Department of Otolaryngology-Head and Neck Surgery, The Second Hospital of Jilin University, Changchun 130041, China
| | - Jie Bai
- Department of Otolaryngology-Head and Neck Surgery, The Second Hospital of Jilin University, Changchun 130041, China
| | - Ying Zhao
- Department of Otolaryngology-Head and Neck Surgery, The Second Hospital of Jilin University, Changchun 130041, China
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102
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Mafi A, Hedayati N, Kahkesh S, Khoshayand S, Alimohammadi M, Farahani N, Hushmandi K. The landscape of circRNAs in gliomas temozolomide resistance: Insights into molecular pathways. Noncoding RNA Res 2024; 9:1178-1189. [PMID: 39022676 PMCID: PMC11250881 DOI: 10.1016/j.ncrna.2024.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/01/2024] [Accepted: 05/20/2024] [Indexed: 07/20/2024] Open
Abstract
As the deadliest type of primary brain tumor, gliomas represent a significant worldwide health concern. Circular RNA (circRNA), a unique non-coding RNA molecule, seems to be one of the most alluring target molecules involved in the pathophysiology of many kinds of cancers. CircRNAs have been identified as prospective targets and biomarkers for the diagnosis and treatment of numerous disorders, particularly malignancies. Recent research has established a clinical link between temozolomide (TMZ) resistance and certain circRNA dysregulations in glioma tumors. CircRNAs may play a therapeutic role in controlling or overcoming TMZ resistance in gliomas and may provide guidance for a novel kind of individualized glioma therapy. To address the biological characteristics of circRNAs and their potential to induce resistance to TMZ, this review has highlighted and summarized the possible roles that circRNAs may play in molecular pathways of drug resistance, including the Ras/Raf/ERK PI3K/Akt signaling pathway and metabolic processes in gliomas.
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Affiliation(s)
- 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
| | - Neda Hedayati
- School of Medicine, Iran University of Medical Science, Tehran, Iran
| | - Samaneh Kahkesh
- Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Sara Khoshayand
- School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mina Alimohammadi
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, 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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103
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Meer E. Role of Noncoding RNAs in Modulating Microglial Phenotype. Glob Med Genet 2024; 11:304-311. [PMID: 39258255 PMCID: PMC11383642 DOI: 10.1055/s-0044-1790283] [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: 09/12/2024] Open
Abstract
Microglia are immunocompetent cells that are present in the retina and central nervous system, and are involved in the development maintenance and immune functions in these systems. Developing from yolk sac-primitive macrophages, they proliferate in the local tissues during the embryonic period without resorting to the production from the hematopoietic stem cells, and are critical in sustaining homeostasis and performing in disease and injury; they have morphological characteristics and distinct phenotypes according to the microenvironment. Microglia are also present in close association with resident cells in the retina where they engage in synapse formation, support normal functions, as well as immune defense. They are involved in the development of numerous neurodegenerative and ophthalmic diseases and act as diversity shields and triggers. Noncoding ribonucleic acids (ncRNAs) refer to RNA molecules synthesized from the mammalian genome, and these do not have protein-coding capacity. These ncRNAs play a role in the regulation of gene expression patterns. ncRNAs have only been recently identified as vastly significant molecules that are involved in the posttranscriptional regulation. Microglia are crucial for brain health and functions and current studies have focused on the effects caused by ncRNA on microglial types. Thus, the aim of the review was to provide an overview of the current knowledge about the regulation of microglial phenotypes by ncRNAs.
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Affiliation(s)
- Eiman Meer
- Department of Biological and Health Sciences, Pak-Austria Fachhochschule Institute of Applied Sciences and Technology, Haripur, Pakistan
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104
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Wu J, Zhao Q, Chen S, Xu H, Zhang R, Cai D, Gao Y, Peng W, Chen X, Yuan S, Li D, Li G, Nan A. NSUN4-mediated m5C modification of circERI3 promotes lung cancer development by altering mitochondrial energy metabolism. Cancer Lett 2024; 605:217266. [PMID: 39332589 DOI: 10.1016/j.canlet.2024.217266] [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: 05/18/2024] [Revised: 09/13/2024] [Accepted: 09/18/2024] [Indexed: 09/29/2024]
Abstract
As a highly important methylation modification, the 5-methyladenosine (m5C) modification can profoundly affect RNAs by regulating their transcription, structure and stability. With the continuous development of high-throughput technology, differentially expressed circular RNAs (circRNAs) have been increasingly discovered, and circRNAs play unique roles in tumorigenesis and development. However, the regulatory mechanism of the m5C modification of circRNAs has not yet been revealed. In this study, circERI3, which is highly expressed in lung cancer tissue and significantly correlated with the clinical progression of lung cancer, was initially identified through differential expression profiling of circRNAs. A combined m5C microarray analysis revealed that circERI3 contains the m5C modification and that the NSUN4-mediated m5C modification of circERI3 can increase its nuclear export. The important function of circERI3 in promoting lung cancer progression in vitro and in vivo was clarified. Moreover, we elucidated the novel mechanism by which circERI3 targets DNA binding protein 1 (DDB1), regulates its ubiquitination, enhances its stability, and in turn promotes the transcription of peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) through DDB1 to affect mitochondrial function and energy metabolism, which ultimately promotes the development of lung cancer. This study not only revealed the reasons for the abnormal distribution of circERI3 in lung cancer tissues from the perspective of methylation and clarified the important role of circERI3 in lung cancer progression but also described a novel mechanism by which circERI3 promotes lung cancer development through mitochondrial energy metabolism, providing new insights for the study of circRNAs in lung cancer.
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Affiliation(s)
- Jiaxi Wu
- School of Public Health, Guangxi Medical University, Nanning 530021, China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Qingyun Zhao
- School of Public Health, Guangxi Medical University, Nanning 530021, China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Sixian Chen
- School of Public Health, Guangxi Medical University, Nanning 530021, China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Haotian Xu
- School of Public Health, Guangxi Medical University, Nanning 530021, China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Ruirui Zhang
- School of Public Health, Guangxi Medical University, Nanning 530021, China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Dunyu Cai
- School of Public Health, Guangxi Medical University, Nanning 530021, China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Yihong Gao
- School of Public Health, Guangxi Medical University, Nanning 530021, China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Wenyi Peng
- School of Public Health, Guangxi Medical University, Nanning 530021, China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Xingcai Chen
- School of Public Health, Guangxi Medical University, Nanning 530021, China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Shengyi Yuan
- School of Public Health, Guangxi Medical University, Nanning 530021, China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Deqing Li
- School of Public Health, Guangxi Medical University, Nanning 530021, China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China
| | - Gang Li
- School of Public Health, Guangxi Medical University, Nanning 530021, China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China.
| | - Aruo Nan
- School of Public Health, Guangxi Medical University, Nanning 530021, China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning, 530021, China.
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105
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Li Q, Yang G, Ren B, Liu X, Tang LQ, Shi Q, Shan G, Wang X. ZC3H14 facilitates backsplicing by binding to exon-intron boundary and 3' UTR. Mol Cell 2024; 84:4314-4333.e9. [PMID: 39461343 DOI: 10.1016/j.molcel.2024.10.001] [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: 02/20/2024] [Revised: 08/02/2024] [Accepted: 10/01/2024] [Indexed: 10/29/2024]
Abstract
Circular RNAs (circRNAs) are natural outputs of eukaryotic transcription and RNA processing and have emerged as critical regulators in physiology and diseases. Although multiple cis-elements and trans-factors are reported to modulate the backsplicing of circRNA biogenesis, most of these regulations play roles in flanking introns of circRNAs. Here, using a genome-wide CRISPR knockout screen, we have identified an evolutionarily conserved RNA-binding protein ZC3H14 in regulating circRNA biogenesis. ZC3H14 binds to 3' and 5' exon-intron boundaries and 3' UTRs of cognate mRNAs to promote circRNA biogenesis through dimerization and the association with spliceosome. Yeast knockout of the ZC3H14 ortholog Nab2 has significantly lower levels of circRNAs. Zc3h14-/- mice exhibit disrupted spermatogenesis and reduced testicular circRNA levels. Additionally, expression levels of human ZC3H14 are associated with non-obstructive azoospermia. Our findings reveal a conserved requirement for ZC3H14 in the modulation of backsplicing and link ZC3H14 and circRNA biogenesis to male fertility.
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Affiliation(s)
- Qiqi 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 (USTC), Hefei 230027, China
| | - Gang Yang
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Bingbing Ren
- Department of Pulmonary and Critical Care Medicine, Regional Medical Center for National Institute of Respiratory Disease, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China
| | - Xu Liu
- 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 (USTC), Hefei 230027, China
| | - Li-Qin Tang
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Qinghua Shi
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230027, China
| | - Ge Shan
- 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 (USTC), Hefei 230027, China; Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science and Technology of China, Hefei 230071, 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 (USTC), Hefei 230027, China.
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106
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Wang Q, Yang Z, Chen X, Yang Y, Jiang K. Noncoding RNA, friend or foe for nephrolithiasis? Front Cell Dev Biol 2024; 12:1457319. [PMID: 39633711 PMCID: PMC11614778 DOI: 10.3389/fcell.2024.1457319] [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: 07/01/2024] [Accepted: 11/08/2024] [Indexed: 12/07/2024] Open
Abstract
Nephrolithiasis is one of the most common diseases in urology, characterized by notable incidence and recurrence rates, leading to significant morbidity and financial burden. Despite its prevalence, the precise mechanisms underlying stone formation remain incompletely understood, thus hindering significant advancements in kidney stone management over the past three decades. Investigating the pivotal biological molecules that govern stone formation has consistently been a challenging and high-priority task. A significant portion of mammalian genomes are transcribed into noncoding RNAs (ncRNAs), which have the ability to modulate gene expression and disease progression. They are thus emerging as a novel target class for diagnostics and pharmaceutical exploration. In recent years, the role of ncRNAs in stone formation has attracted burgeoning attention. They have been found to influence stone formation by regulating ion transportation, oxidative stress injury, inflammation, osteoblastic transformation, autophagy, and pyroptosis. These findings contributes new perspectives on the pathogenesis of nephrolithiasis. To enhance our understanding of the diagnostic and therapeutic potential of nephrolithiasis-associated ncRNAs, we summarized the expression profiles, biological functions, and clinical significance of these ncRNAs in the current review.
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Affiliation(s)
- Qing Wang
- Department of Urology, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Zhenlu Yang
- Department of Radiology, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Xiaolong Chen
- Department of Urology, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Yuanyuan Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Kehua Jiang
- Department of Urology, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
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107
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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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108
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Cao C, Wang C, Dai Q, Zou Q, Wang T. CRBPSA: CircRNA-RBP interaction sites identification using sequence structural attention model. BMC Biol 2024; 22:260. [PMID: 39543602 PMCID: PMC11566611 DOI: 10.1186/s12915-024-02055-0] [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: 07/13/2024] [Accepted: 10/30/2024] [Indexed: 11/17/2024] Open
Abstract
BACKGROUND Due to the ability of circRNA to bind with corresponding RBPs and play a critical role in gene regulation and disease prevention, numerous identification algorithms have been developed. Nevertheless, most of the current mainstream methods primarily capture one-dimensional sequence features through various descriptors, while neglecting the effective extraction of secondary structure features. Moreover, as the number of introduced descriptors increases, the issues of sparsity and ineffective representation also rise, causing a significant burden on computational models and leaving room for improvement in predictive performance. RESULTS Based on this, we focused on capturing the features of secondary structure in sequences and developed a new architecture called CRBPSA, which is based on a sequence-structure attention mechanism. Firstly, a base-pairing matrix is generated by calculating the matching probability between each base, with a Gaussian function introduced as a weight to construct the secondary structure. Then, a Structure_Transformer is employed to extract base-pairing information and spatial positional dependencies, enabling the identification of binding sites through deeper feature extraction. Experimental results using the same set of hyperparameters on 37 circRNA datasets, totaling 671,952 samples, show that the CRBPSA algorithm achieves an average AUC of 99.93%, surpassing all existing prediction methods. CONCLUSIONS CRBPSA is a lightweight and efficient prediction tool for circRNA-RBP, which can capture structural features of sequences with minimal computational resources and accurately predict protein-binding sites. This tool facilitates a deeper understanding of the biological processes and mechanisms underlying circRNA and protein interactions.
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Affiliation(s)
- Chao Cao
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang, China
| | - Chunyu Wang
- Faculty of Computing, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Qi Dai
- College of Life Science and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang, China
| | - Tao Wang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China.
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109
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Li W, Xue X, Li X, Wu X, Zhou P, Xia Y, Zhang J, Zhang M, Zhu F. Ancestral retrovirus envelope protein ERVWE1 upregulates circ_0001810, a potential biomarker for schizophrenia, and induces neuronal mitochondrial dysfunction via activating AK2. Cell Biosci 2024; 14:138. [PMID: 39543767 PMCID: PMC11566632 DOI: 10.1186/s13578-024-01318-1] [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: 04/11/2024] [Accepted: 10/31/2024] [Indexed: 11/17/2024] Open
Abstract
BACKGROUND Increasingly studies highlight the crucial role of the ancestral retrovirus envelope protein ERVWE1 in the pathogenic mechanisms of schizophrenia, a severe psychiatric disorder affecting approximately 1% of the global population. Recent studies also underscore the significance of circular RNAs (circRNAs), crucial for neurogenesis and synaptogenesis, in maintaining neuronal functions. However, the precise relationship between ERVWE1 and circRNAs in the etiology of schizophrenia remains elusive. RESULTS This study observed elevated levels of hsa_circ_0001810 (circ_0001810) in the blood samples of schizophrenia patients, displaying a significant positive correlation with ERVWE1 expression. Interestingly, in vivo studies demonstrated that ERVWE1 upregulated circ_0001810 in neuronal cells. Circ_0001810, acting as a competing endogenous RNA (ceRNA), bound to miR-1197 and facilitated the release of adenylate kinase 2 (AK2). The bioinformatics analysis of the schizophrenia datasets revealed increased levels of AK2 and enrichment of mitochondrial dynamics. Notably, miR-1197 was reduced in schizophrenia patients, while AK2 levels were increased. Additionally, AK2 showed positive correlations with ERVWE1 and circ_0001810. Further studies demonstrated that AK2 led to mitochondrial dysfunction, characterized by loss of intracellular ATP, mitochondrial depolarization, and disruption of mitochondrial dynamics. Our comprehensive investigation suggested that ERVWE1 influenced ATP levels, promoted mitochondrial depolarization, and disrupted mitochondrial dynamics through the circ_0001810/AK2 pathway. CONCLUSIONS Circ_0001810 and AK2 were increased in schizophrenia and positively correlated with ERVWE1. Importantly, ERVWE1 triggered mitochondrial dysfunction through circ_0001810/miR-1197/AK2 pathway. Recent focus on the impact of mitochondrial dynamics on schizophrenia development had led to our discovery of a novel mechanism by which ERVWE1 contributed to the etiology of schizophrenia, particularly through mitochondrial dynamics. Moreover, these findings collectively proposed that circ_0001810 might serve as a potential blood-based biomarker for schizophrenia. Consistent with our previous theories, ERVWE1 is increasingly recognized as a promising therapeutic target for schizophrenia.
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Affiliation(s)
- Wenshi Li
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Science, Wuhan University, Wuhan, 430071, China
| | - Xing Xue
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Science, Wuhan University, Wuhan, 430071, China
| | - Xuhang Li
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Science, Wuhan University, Wuhan, 430071, China
| | - Xiulin Wu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Science, Wuhan University, Wuhan, 430071, China
| | - Ping Zhou
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Science, Wuhan University, Wuhan, 430071, China
| | - Yaru Xia
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Science, Wuhan University, Wuhan, 430071, China
| | - Jiahang Zhang
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Science, Wuhan University, Wuhan, 430071, China
| | - Mengqi Zhang
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Science, Wuhan University, Wuhan, 430071, China
| | - Fan Zhu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Science, Wuhan University, Wuhan, 430071, China.
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110
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Hashmi MATS, Fatima H, Ahmad S, Rehman A, Safdar F. The interplay between epitranscriptomic RNA modifications and neurodegenerative disorders: Mechanistic insights and potential therapeutic strategies. IBRAIN 2024; 10:395-426. [PMID: 39691424 PMCID: PMC11649393 DOI: 10.1002/ibra.12183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 10/16/2024] [Accepted: 10/19/2024] [Indexed: 12/19/2024]
Abstract
Neurodegenerative disorders encompass a group of age-related conditions characterized by the gradual decline in both the structure and functionality of the central nervous system (CNS). RNA modifications, arising from the epitranscriptome or RNA-modifying protein mutations, have recently been observed to contribute significantly to neurodegenerative disorders. Specific modifications like N6-methyladenine (m6A), N1-methyladenine (m1A), 5-methylcytosine (m5C), pseudouridine and adenosine-to-inosine (A-to-I) play key roles, with their regulators serving as crucial therapeutic targets. These epitranscriptomic changes intricately control gene expression, influencing cellular functions and contributing to disease pathology. Dysregulation of RNA metabolism, affecting mRNA processing and noncoding RNA biogenesis, is a central factor in these diseases. This review underscores the complex relationship between RNA modifications and neurodegenerative disorders, emphasizing the influence of RNA modification and the epitranscriptome, exploring the function of RNA modification enzymes in neurodegenerative processes, investigating the functional consequences of RNA modifications within neurodegenerative pathways, and evaluating the potential therapeutic advancements derived from assessing the epitranscriptome.
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Affiliation(s)
| | | | - Sadia Ahmad
- Institute of ZoologyUniversity of PunjabLahorePakistan
| | - Amna Rehman
- Institute of ZoologyUniversity of PunjabLahorePakistan
| | - Fiza Safdar
- Department of BiochemistryUniversity of NarowalNarowalPakistan
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111
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Zhao X, Liu Y, Huang H, Sun Y, Wu F, Jin W. A Simple and Efficient One-Step Synthesis System for Flexible Production of Circular RNA in E. coli. Biomolecules 2024; 14:1416. [PMID: 39595592 PMCID: PMC11592204 DOI: 10.3390/biom14111416] [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: 08/31/2024] [Revised: 11/04/2024] [Accepted: 11/05/2024] [Indexed: 11/28/2024] Open
Abstract
Circular RNA (circRNA) exhibits a higher stability and intracellular half-life than linear RNA and has better potential in the fields of RNA vaccines and RNAi drugs. The current strategies for circRNA preparation have low efficiency, high costs, and high complexity, which significantly limits their applications. In this paper, we propose a one-step synthesis of circRNA based on E. coli. The four RNA sequence lengths of 1700, 1400, 500, and 64 nt were connected to group II intron elements from the surface protein region of Clostridium tetani and then inserted downstream of the T7 promoter in the pET28a plasmid to assist in cyclization. Then, circRNA was produced in HT115, where the yields of pET28-1700, pET28-1400, pET28-500, and pET28-64 were improved to 820, 783, 691, and 460 ng/1 mL, respectively. Consequently, this system could achieve the mass production of circRNA using only a simple E. coli culture and inducible expression. Meanwhile, the overexpressed circRNA and small circular interference RNA (sciRNA) maintained their biological functions in the protein translation and RNAi. Therefore, this simple and efficient one-step synthesis system can be applied to the functional study and preparation of circRNA in the future.
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Affiliation(s)
- Xiayang Zhao
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (X.Z.); (Y.L.); (H.H.); (F.W.)
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine, Zhejiang Sci-Tech University, Shaoxing 312366, China;
| | - Yiqing Liu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (X.Z.); (Y.L.); (H.H.); (F.W.)
| | - Huanhui Huang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (X.Z.); (Y.L.); (H.H.); (F.W.)
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine, Zhejiang Sci-Tech University, Shaoxing 312366, China;
| | - Yue Sun
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine, Zhejiang Sci-Tech University, Shaoxing 312366, China;
| | - Fangli Wu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (X.Z.); (Y.L.); (H.H.); (F.W.)
| | - Weibo Jin
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; (X.Z.); (Y.L.); (H.H.); (F.W.)
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine, Zhejiang Sci-Tech University, Shaoxing 312366, China;
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112
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Li Z, Sarker B, Zhao F, Zhou T, Zhang J, Xu C. COL: a method for identifying putatively functional circular RNAs. J Genet Genomics 2024; 51:1338-1341. [PMID: 39218058 PMCID: PMC11645182 DOI: 10.1016/j.jgg.2024.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2024] [Revised: 08/27/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Affiliation(s)
- Zheng Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bandhan Sarker
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fengyu Zhao
- Department of Statistics, George Washington University, Washington, DC 20052, USA
| | - Tianjiao Zhou
- Department of Otorhinolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Chuan Xu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China.
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113
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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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114
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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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115
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Sun W, Ren C, Xu J, Zhang P. SAGCN: Using Graph Convolutional Network With Subgraph-Aware for circRNA-Drug Sensitivity Identification. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024; 21:1765-1774. [PMID: 38885113 DOI: 10.1109/tcbb.2024.3415058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Circular RNAs (circRNAs) play a significant role in cancer development and therapy resistance. There is substantial evidence indicating that the expression of circRNAs affects the sensitivity of cells to drugs. Identifying circRNAs-drug sensitivity association (CDA) is helpful for disease treatment and drug discovery. However, the identification of CDA through conventional biological experiments is both time-consuming and costly. Therefore, it is urgent to develop computational methods to predict CDA. In this study, we propose a new computational method, the subgraph-aware graph convolutional network (SAGCN), for predicting CDA. SAGCN first constructs a heterogeneous network composed of circRNA similarity network, drug similarity network, and circRNA-drug bipartite network. Then, a subgraph extractor is proposed to learn the latent subgraph structure of the heterogeneous network using a graph convolutional network. The extractor can capture 1-hop and 2-hop information and then a fusing attention mechanism is designed to integrate them adaptively. Simultaneously, a novel subgraph-aware attention mechanism is proposed to detect intrinsic subgraph structure. The final node feature representation is obtained to make the CDA prediction. Experimental results demonstrate that SAGCN obtained an average AUC of 0.9120 and AUPR of 0.8693, exceeding the performance of the most advanced models under 10-fold cross-validation. Case studies have demonstrated the potential of SAGCN in identifying associations between circRNA and drug sensitivity.
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116
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Liu C, Yang P, Wang X, Xiang B, E G, Huang Y. Candidate circRNAs related to skeletal muscle development in Dazu black goats. Anim Biotechnol 2024; 35:2286609. [PMID: 38032316 DOI: 10.1080/10495398.2023.2286609] [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: 12/01/2023]
Abstract
Circular RNA (CircRNA), as a classical noncoding RNA, has been proven to regulate skeletal muscle development (SMD). However, the molecular genetic basis of circRNA regulation in muscle cells remains unclear. In this study, the expression patterns of circRNAs in the longissimus dorsi muscle at embryonic day 75 and postnatal day 1 in DBGs were investigated to identify the key circRNAs that play an important role in SMD in goats. A total of 140 significantly and differentially expressed circRNAs (DEcircRNAs) were identified among the groups at different developmental stages. Among the 116 host genes (HGs) of DEcircRNAs, 76 were significantly and differentially expressed, which was confirmed by previous RNA_seq data. Furthermore, the expression pattern of 10 DEcircRNAs with RT-qPCR was verified, which showed 80% concordance rate with that of RNA_seq datasets. Moreover, the authenticity of seven randomly selected DEcircRNAs was verified by PCR Sanger sequencing. Based on the functional annotation results, among the 76 significantly and differentially expressed HGs, 74 were enriched in 845 GO terms, whereas 35 were annotated to 85 KEGG pathways. The results of this study could provide a comprehensive understanding of the genetic basis of circRNAs involved in SMD and muscle growth.
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Affiliation(s)
- Chengli Liu
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Pu Yang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Xiao Wang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Baiju Xiang
- Chongqing Academy of Animal Sciences, Chongqing, China
| | - Guangxin E
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Yongfu Huang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
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117
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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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118
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Jiang W, Wang Y, He W, Wang P, Meng P, Zhang S. CircCOCH plays a critical role in Hepatocellular carcinoma through modulating miR-450a and activating PI3K/mTOR pathway. Transl Oncol 2024; 49:102090. [PMID: 39181116 PMCID: PMC11388191 DOI: 10.1016/j.tranon.2024.102090] [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: 10/12/2023] [Revised: 07/29/2024] [Accepted: 08/11/2024] [Indexed: 08/27/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a primary liver cancer with high pathogenicity and extremely poor prognosis. The role of circular RNAs (circRNAs) in HCC carcinogenesis and progression remains to be determined. Based on the analysis of HCC-related databases, as well as the expression analysis and identification of 25 HCC patient tissues and HCC cell lines, we found that the hsa_circ_0031431 (circCOCH) is significantly highly expressed in HCC tissues and cell lines. High circCOCH expression is associated with enhanced tumor proliferation and metastasis, and knocking down circCOCH can inhibit the growth of HCC in vivo and in vitro. Mechanistic studies show that circCOCH upregulates the expression of epidermal growth factor receptor (EGFR) through sponge miR-450a, thereby activating the Phosphoinositide 3-kinases (PI3Ks) cell pathway to promote HCC proliferation and metastasis. Futhermore, we found that IGF2BP3 mediates the biogenesis of circCOCH. The present study provides innovative insights into the role of circRNAs in the etiology of HCC carcinogenesis and might serve as a new promising therapeutic target for HCC.
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Affiliation(s)
- Weiwei Jiang
- School of Medicine, Shangqiu Institute of Technology, Shangqiu, China
| | - Yan Wang
- Shangqiu Medical College, Shangqiu, China
| | - Wanli He
- School of Medicine, Shangqiu Institute of Technology, Shangqiu, China
| | - Peng Wang
- School of nursing and health, Zhengzhou University, Zhengzhou, China
| | - Peng Meng
- Department of Obstetrics and Gynecology, Xijing Hospital Affiliated to the Fourth Military Medical University, Xi'an, Shaanxi, China.
| | - Shanfeng Zhang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China.
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119
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Fang L, Zhu Z, Han M, Li S, Kong X, Yang L. Unlocking the potential of extracellular vesicle circRNAs in breast cancer: From molecular mechanisms to therapeutic horizons. Biomed Pharmacother 2024; 180:117480. [PMID: 39357330 DOI: 10.1016/j.biopha.2024.117480] [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: 07/30/2024] [Revised: 09/17/2024] [Accepted: 09/20/2024] [Indexed: 10/04/2024] Open
Abstract
Breast cancer remains the leading cause of cancer-related morbidity and mortality among women worldwide, underscoring the urgent need for novel diagnostic and therapeutic strategies. This review explores the emerging roles of circular RNAs (circRNAs) within extracellular vesicles (exosomes) in breast cancer. circRNAs, known for their stability and tissue-specific expression, are aberrantly expressed in breast cancer and regulate critical cellular processes such as proliferation, migration, and apoptosis, positioning them as promising biomarkers. Exosomes facilitate intercellular communication by delivering circRNAs, reflecting the physiological and pathological state of their source cells. This review highlights the multifaceted roles of exosomal circRNAs in promoting tumor growth, metastasis, and drug resistance through their modulation of tumor metabolism, the tumor microenvironment, and immune responses. In particular, we emphasize their contributions to chemotherapy resistance and their potential as both diagnostic markers and therapeutic targets. By synthesizing current research, this review provides novel insights into the clinical applications of exosomal circRNAs, offering a foundation for future studies aimed at improving breast cancer management through non-invasive diagnostics and targeted therapies.
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Affiliation(s)
- Lijuan Fang
- Department of Laboratory Medicine, Hangzhou Ninth People's Hospital, Hangzhou, Zhejaing Province 311200, China
| | - Zehua Zhu
- Department of Laboratory Medicine, Hangzhou Ninth People's Hospital, Hangzhou, Zhejaing Province 311200, China
| | - Mingyue Han
- Department of Laboratory Medicine, Hangzhou Ninth People's Hospital, Hangzhou, Zhejaing Province 311200, China
| | - Shaojie Li
- Department of Laboratory Medicine, Hangzhou Ninth People's Hospital, Hangzhou, Zhejaing Province 311200, China
| | - Xiangyi Kong
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Lusen Yang
- Department of Laboratory Medicine, Hangzhou Ninth People's Hospital, Hangzhou, Zhejaing Province 311200, China.
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120
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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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121
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Lu P, Wu J, Zhang W. Identifying circRNA-disease association based on relational graph attention network and hypergraph attention network. Anal Biochem 2024; 694:115628. [PMID: 39069246 DOI: 10.1016/j.ab.2024.115628] [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: 05/20/2024] [Revised: 07/11/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
In recent years, with the in-depth study of circRNA, scholars have begun to discover a synergistic relationship between circRNA and microorganisms. Traditional wet lab experiments in biology require expensive financial, material, and human resources to investigate the relationship between circRNA and diseases. Therefore, we propose a new predictive model for inferring the association between circRNA and diseases, called HAGACDA. Specifically, we first aggregate the unique features of circRNA and diseases themselves through singular value decomposition, Pearson similarity, and the biological information characteristics of circRNA and diseases. Utilizing the competitive relationships between miRNA and other microorganisms, we construct a circRNA-miRNA-disease multi-source heterogeneous network. Subsequently, we use a relational graph attention network to aggregate features based on the structural connections between different nodes. To address the inherent limitations in capturing high-order patterns in edge sets, we integrate a hypergraph attention network to extract features of circRNA and diseases. Finally, association prediction scores for node pairs are obtained through a multilayer perceptron. We conducted a comprehensive analysis of the model, including comparative experiments and case studies. Experimental results demonstrate that our model accurately predicts the association between circRNA and diseases.
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Affiliation(s)
- PengLi Lu
- School of Computer and Communication, Lanzhou University of Technology, Lanzhou, 730050, Gansu, PR China.
| | - Jinkai Wu
- School of Computer and Communication, Lanzhou University of Technology, Lanzhou, 730050, Gansu, PR China
| | - Wenqi Zhang
- School of Computer and Communication, Lanzhou University of Technology, Lanzhou, 730050, Gansu, PR China
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Yuan Z, Huang S, Jin X, Li S. Circular RNAs in Cardiovascular Diseases: Molecular Mechanisms, Therapeutic Advances, and Innovations. Genes (Basel) 2024; 15:1423. [PMID: 39596623 PMCID: PMC11593509 DOI: 10.3390/genes15111423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Revised: 10/28/2024] [Accepted: 10/29/2024] [Indexed: 11/29/2024] Open
Abstract
Circular RNAs (circRNAs) have emerged as promising therapeutic targets due to their unique covalently closed-loop structures and their regulatory roles in gene expression. Despite their potential, challenges in circRNA-based therapies include ensuring stability, tissue specificity, and efficient intracellular delivery. This review explores the implications of circRNAs in cardiovascular diseases (CVDs), providing an overview of their biogenesis, molecular mechanisms, and roles in disease pathology. In addition to discussing molecular features, this review highlights therapeutic advances, including small-molecule drugs targeting circRNAs, synthetic circRNA sponges, and innovations in drug delivery systems that enhance the effectiveness of these therapies. Finally, current challenges and future directions are addressed, emphasizing the need for continued research to fully unlock the therapeutic potential of circRNA-based strategies in cardiovascular medicine.
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Affiliation(s)
- Zheng Yuan
- College of Science, China University of Petroleum-Beijing, Beijing 102249, China
| | - Shaoyuan Huang
- School of Medicine, Nankai University, Tianjin 300071, China; (S.H.); (X.J.)
| | - Xin Jin
- School of Medicine, Nankai University, Tianjin 300071, China; (S.H.); (X.J.)
| | - Shanshan Li
- School of Medicine, Nankai University, Tianjin 300071, China; (S.H.); (X.J.)
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123
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Yang Y, Cheng H. Emerging Roles of ncRNAs in Type 2 Diabetes Mellitus: From Mechanisms to Drug Discovery. Biomolecules 2024; 14:1364. [PMID: 39595541 PMCID: PMC11592034 DOI: 10.3390/biom14111364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 10/23/2024] [Accepted: 10/26/2024] [Indexed: 11/28/2024] Open
Abstract
Type 2 diabetes mellitus (T2DM), a high-incidence chronic metabolic disorder, has emerged as a global health issue, where most patients need lifelong medication. Gaining insights into molecular mechanisms involved in T2DM development is expected to provide novel strategies for clinical prevention and treatment. Growing evidence validates that non-coding RNAs (ncRNAs) including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) function as crucial regulators in multiple biological processes of T2DM, inspiring various potential targets and drug candidates. In this review, we summarize the current understanding of ncRNA roles in T2DM and discuss the potential use of ncRNAs as targets and active molecules for drug discovery.
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Affiliation(s)
- Yue Yang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Hao Cheng
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
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Wang L, Zheng G, Yang Y, Wu J, Du Y, Chen J, Liu C, Liu Y, Zhang B, Zhang H, Deng X, Lian L. Rolling-Translated circRUNX2.2 Promotes Lymphoma Cell Proliferation and Cycle Transition in Marek's Disease Model. Int J Mol Sci 2024; 25:11486. [PMID: 39519039 PMCID: PMC11545863 DOI: 10.3390/ijms252111486] [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: 09/12/2024] [Revised: 10/18/2024] [Accepted: 10/23/2024] [Indexed: 11/16/2024] Open
Abstract
Marek's disease (MD), an immunosuppressive disease induced by the Marek's disease virus (MDV), is regarded as an ideal model for lymphoma research to elucidate oncogenic and anti-oncogene genes. Using this model, we found that circRUNX2.2, derived from exon 6 of RUNX2, was significantly upregulated in MDV-infected tumorous spleens. In this study, we deeply analyzed the potential role of circRUNX2.2 in lymphoma cells. An open reading frame (ORF) in circRUNX2.2 with no stop codon was predicted, and small peptides (named circRUNX2.2-rt) presenting multiple ladder-like bands with different molecular weights encoded by circRUNX2.2 were detected via Western blotting assay. The polysome fraction assay reconfirmed the translation ability of circRUNX2.2, which could be detected in polysome fractions. Subsequent analysis verified that it translated in a rolling circle manner, rather than being assisted by the internal ribosome entry site (IRES) or m6A-mediated mechanism. Furthermore, we found that circRUNX2.2-rt was potently induced in MSB1 cells treated with sodium butyrate (NaB), which reactivated MDV and forced the MDV transition from the latent to reactivation phase. During this phase, MDV particles were clearly observed by electron microscopy, and the viral gene pp38 was also significantly upregulated. A biological function study showed that circRUNX2.2-rt promoted cell proliferation and cell cycle transition from the S to G2 phase and inhibited the apoptosis of MSB1. Further immunoprecipitation and mass spectrometry assays showed that 168 proteins potentially interacting with circRUNX2.2-rt were involved in multiple pathways related to cell cycle regulation, which proved that circRUNX2.2-rt could bind or recruit proteins to mediate the cell cycle.
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Affiliation(s)
- Lulu Wang
- Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing 100193, China
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Gang Zheng
- Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing 100193, China
| | - Yuqin Yang
- Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing 100193, China
| | - Junfeng Wu
- Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing 100193, China
| | - Yushuang Du
- Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing 100193, China
| | - Jiahua Chen
- Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing 100193, China
| | - Changjun Liu
- Division of Avian Infectious Diseases, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Yongzhen Liu
- Division of Avian Infectious Diseases, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Bo Zhang
- Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing 100193, China
| | - Hao Zhang
- Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing 100193, China
| | - Xuemei Deng
- Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing 100193, China
| | - Ling Lian
- Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing 100193, China
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125
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Yin A, Chen L, Zhou B, Cai YD. CMAGN: circRNA-miRNA association prediction based on graph attention auto-encoder and network consistency projection. BMC Bioinformatics 2024; 25:336. [PMID: 39449126 PMCID: PMC11515630 DOI: 10.1186/s12859-024-05959-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 10/16/2024] [Indexed: 10/26/2024] Open
Abstract
BACKGROUND As noncoding RNAs, circular RNAs (circRNAs) can act as microRNA (miRNA) sponges due to their abundant miRNA binding sites, allowing them to regulate gene expression and influence disease development. Accurately identifying circRNA-miRNA associations (CMAs) is helpful to understand complex disease mechanisms. Given that biological experiments are time consuming and labor intensive, alternative computational methods to predict CMAs are urgently needed. RESULTS This study proposes a novel computational model named CMAGN, which incorporates several advanced computational methods, for predicting CMAs. First, similarity networks for circRNAs and miRNAs are constructed according to their sequences. Graph attention autoencoder is then applied to these networks to generate the first representations of circRNAs and miRNAs. The second representations of circRNAs and miRNAs are obtained from the CMA network via node2vec. The similarity networks of circRNAs and miRNAs are reconstructed on the basis of these new representations. Finally, network consistency projection is applied to the reconstructed similarity networks and the CMA network to generate a recommendation matrix. CONCLUSION Five-fold cross-validation of CMAGN reveals that the area under ROC and PR curves exceed 0.96 on two widely used CMA datasets, outperforming several existing models. Additional tests elaborate the reasonability of the architecture of CMAGN and uncover its strengths and weaknesses.
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Affiliation(s)
- Anhui Yin
- College of Information Engineering, Shanghai Maritime University, Shanghai, 201306, People's Republic of China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, 201306, People's Republic of China.
| | - Bo Zhou
- Institute of Wound Prevention and Treatment, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
- School of Basic Medical Sciences, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, 200444, People's Republic of China.
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126
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Sun X, Feng P, Chen H, Ji Z, Zhuang L, Zhu T, Ji G, Wang J. Hsa_circ_0048764 facilitates the progression of non-small cell lung cancer by targeting miR-1178-3p/HMGA1 axis. Cell Signal 2024; 125:111484. [PMID: 39461578 DOI: 10.1016/j.cellsig.2024.111484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 09/30/2024] [Accepted: 10/23/2024] [Indexed: 10/29/2024]
Abstract
Non-small cell lung cancer (NSCLC) remains a highly lethal disease, with a lack of fully established biomarkers and therapies. Circular RNAs (circRNAs) have emerged as powerful regulators of gene expression in multiple cancers. The role of circRNAs in NSCLC progression is still not well understood. In this study, GEO database analysis and qRT-PCR results revealed that hsa_circ_0048764 (circ_0048764) was overexpressed in NSCLC tissues and associated with poorer overall survival in patients with NSCLC. Functional assays demonstrated that silencing circ_0048764 inhibited NSCLC cell proliferation and metastasis. Bioinformatics analysis identified miR-1178-3p as having complementary binding sites with circ_0048764, a finding further validated by the dual-luciferase reporter assay. Additionally, predictions from the Starbase3.0 database, along with cellular experiments, revealed that miR-1178-3p regulates HMGA1 expression in NSCLC. Taken together, our findings suggest that circ_0048764 promotes NSCLC progression by enhancing HMGA1 expression through sponging miR-1178-3p, offering potential therapeutic targets for NSCLC treatment.
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Affiliation(s)
- Xing Sun
- Department of Respiratory Medicine, Shanghai Shibei Hospital, No. 4500 Gonghe New Road, Shanghai 200436, China
| | - Ping Feng
- Department of Gastroenterology, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, No. 1279 Sanmen Road, Shanghai 200434, China
| | - Haihua Chen
- Department of Respiratory Medicine, Shanghai Shibei Hospital, No. 4500 Gonghe New Road, Shanghai 200436, China
| | - Zhijuan Ji
- Department of Respiratory Medicine, Shanghai Shibei Hospital, No. 4500 Gonghe New Road, Shanghai 200436, China
| | - Lanmei Zhuang
- Department of Respiratory Medicine, Shanghai Shibei Hospital, No. 4500 Gonghe New Road, Shanghai 200436, China
| | - Ting Zhu
- Department of Respiratory Medicine, Shanghai Gonghui Hospital, No. 450 Wenshui Road, Shanghai 200040, China
| | - Guangling Ji
- Department of Respiratory Medicine, Shanghai Shibei Hospital, No. 4500 Gonghe New Road, Shanghai 200436, China
| | - Jin Wang
- Department of Respiratory Medicine, Shanghai Shibei Hospital, No. 4500 Gonghe New Road, Shanghai 200436, China.
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127
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Silenzi V, D'Ambra E, Santini T, D'Uva S, Setti A, Salvi N, Nicoletti C, Scarfò R, Cordella F, Mongiardi B, Cavezza D, Liessi N, Ferrucci L, Ragozzino D, Armirotti A, Di Angelantonio S, De Leonibus E, Bozzoni I, Morlando M. A tripartite circRNA/mRNA/miRNA interaction regulates glutamatergic signaling in the mouse brain. Cell Rep 2024; 43:114766. [PMID: 39321023 DOI: 10.1016/j.celrep.2024.114766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 08/06/2024] [Accepted: 08/30/2024] [Indexed: 09/27/2024] Open
Abstract
Functional studies of circular RNAs (circRNAs) began quite recently, and few data exist on their function in vivo. Here, we have generated a knockout (KO) mouse model to study circDlc1(2), a circRNA highly expressed in the prefrontal cortex and striatum. The loss of circDlc1(2) led to the upregulation of glutamatergic-response-associated genes in the striatal tissue, enhanced excitatory synaptic transmission in neuronal cultures, and hyperactivity and increased stereotypies in mice. Mechanistically, we found that circDlc1(2) physically interacts with some mRNAs, associated with glutamate receptor signaling (gluRNAs), and with miR-130b-5p, a translational regulator of these transcripts. Notably, differently from canonical microRNA (miRNA) "sponges," circDlc1(2) synergizes with miR-130b-5p to repress gluRNA expression. We found that circDlc1(2) is required to spatially control miR-130b-5p localization at synaptic regions where gluRNA is localized, indicating a different layer of regulation where circRNAs ensure robust control of gene expression via the correct subcellular compartmentalization of functionally linked interacting partners.
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Affiliation(s)
- Valentina Silenzi
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Eleonora D'Ambra
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy; Center for Life Nano- & Neuro-Science@Sapienza of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Tiziana Santini
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Sara D'Uva
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy; Center for Life Nano- & Neuro-Science@Sapienza of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Adriano Setti
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Nicolò Salvi
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Carmine Nicoletti
- Department of Anatomical, Histological, Forensic Medicine and Orthopedic Sciences, Section of Histology and Embryology, Sapienza University of Rome, 00161 Rome, Italy
| | - Rebecca Scarfò
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Federica Cordella
- Center for Life Nano- & Neuro-Science@Sapienza of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy; Department of Physiology and Pharmacology, Sapienza University of Rome, 00185 Rome, Italy
| | - Brunella Mongiardi
- Institute of Biochemistry and Cell Biology, CNR, Monterotondo, 00015 Rome, Italy; Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, 80078 Naples, Italy
| | - Diletta Cavezza
- Institute of Biochemistry and Cell Biology, CNR, Monterotondo, 00015 Rome, Italy; Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, 80078 Naples, Italy
| | - Nara Liessi
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Laura Ferrucci
- Department of Physiology and Pharmacology, Sapienza University of Rome, 00185 Rome, Italy
| | - Davide Ragozzino
- Department of Physiology and Pharmacology, Sapienza University of Rome, 00185 Rome, Italy; IRCCS Santa Lucia Foundation, 00179 Rome, Italy
| | - Andrea Armirotti
- Analytical Chemistry Facility, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Silvia Di Angelantonio
- Center for Life Nano- & Neuro-Science@Sapienza of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy; Department of Physiology and Pharmacology, Sapienza University of Rome, 00185 Rome, Italy; D-Tails srl BC, 00165 Rome, Italy
| | - Elvira De Leonibus
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, 80078 Naples, Italy; Institute of Cellular Biology and Neurobiology "ABT", CNR, Monterotondo, 00015 Rome, Italy
| | - Irene Bozzoni
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy; Center for Life Nano- & Neuro-Science@Sapienza of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy.
| | - Mariangela Morlando
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, 06123 Perugia, Italy.
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128
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Chen Z, Fu S, Shan Y, He Z, Gu J, Wu H, Lin J, Huang Y, Wang H, Lu Y, Ding M. Circ_0001047 inhibits prostate cancer progression and enhances abiraterone sensitivity via miR-122-5p/FKBP5/PHLPP1/AKT axis in vitro. Discov Oncol 2024; 15:569. [PMID: 39419900 PMCID: PMC11486870 DOI: 10.1007/s12672-024-01408-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 10/01/2024] [Indexed: 10/19/2024] Open
Abstract
Prostate cancer (PCa), with high heterogeneity and poor prognosis, is one of the most common malignant tumors in men. Circular RNAs (circRNAs) have been identified in tumor progression and resistance to medication in numerous studies. However, the role of circ_0001047 in PCa is unclear. In this research, we found that circ_0001047 had low expression in PCa cells and tissues and was negatively correlated with testosterone secretion in vivo. Overexpression of circ_0001047 inhibited the proliferation, migration, invasion, and anti-apoptotic abilities of human PCa cells in vitro. Mechanistically, circ_0001047 promoted the expression of FKBP5 through sponge adsorption of miR-122-5p and then inhibited the proliferation, anti-apoptotic migration, and invasion abilities of PCa cells. In addition, overexpression of circ_0001047 enhanced the sensitivity of PCa cells to abiraterone by inhibiting AKT phosphorylation activation through upregulation of FKBP5/PHLPP1. This study revealed a novel mechanism by which circ_0001047 regulates PCa progression and treatment sensitivity via the miR-122-5p/FKBP5/PHLPP1/AKT axis. These findings deepen our comprehension of the molecular mechanisms in latent PCa progression and treatment resistance.
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Affiliation(s)
- Zhenjie Chen
- Yunnan Institute of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
- Zhongshan City People's Hospital, Zhongshan, 528403, China
| | - Shi Fu
- Yunnan Institute of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
| | - Yiqian Shan
- The Sixth People's Hospital of Nansha District, Guangzhou, 511458, China
| | - Zexi He
- Yunnan Institute of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
| | - Jun Gu
- Yunnan Institute of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
| | - Haichao Wu
- Yunnan Institute of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
| | - Jiawei Lin
- Yunnan Institute of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
| | - Yinglong Huang
- Yunnan Institute of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
| | - Haifeng Wang
- Yunnan Institute of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
| | - Yangbai Lu
- Zhongshan City People's Hospital, Zhongshan, 528403, China.
| | - Mingxia Ding
- Yunnan Institute of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650101, China
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129
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Liu D, Wang X, Cui L, Zhang M, Lei K, Aierken N. SPECC1 as a pan-cancer biomarker: unraveling its role in drug sensitivity and resistance mechanisms. Discov Oncol 2024; 15:552. [PMID: 39397181 PMCID: PMC11471742 DOI: 10.1007/s12672-024-01426-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Accepted: 10/04/2024] [Indexed: 10/15/2024] Open
Abstract
Previous studies have shown a relationship between SPECC1 and the prognosis of breast cancer, indicating a potential function for SPECC1 in the initiation and progression of cancer. However, the role played by SPECC1 in other tumors is not yet known. Therefore, we used bioinformatics techniques to conduct a thorough investigation into the possible mechanism of SPECC1 in pan-cancer, analyzing data reported in the literature as well as databases such as GTEx and CCLE, cBioportal, TCGA, and UCSC XENA. Comparing the results with matching normal tissues, the majority of cancers, including pancreatic adenocarcinoma (PAAD) and breast invasive carcinoma (BRCA), exhibited higher levels of SPECC1, while hepatocellular carcinoma (HCC) showed lower expression levels. SPECC1 was also found to be genetically mutated in endometrial cancer, sarcoma, and esophageal cancer. The prognosis of lung adenocarcinoma, kidney papillary cell carcinoma, and breast cancer is highly correlated with dysregulation of SPECC1 expression. This work helps guide clinical therapy by highlighting the sensitivity of tumor-treating medicines and the prognostic importance of SPECC1 in various malignancies. KEGG pathway enrichment analysis revealed focused adhesion, collagen-containing extracellular matrix (collagen), and the primary enrichment domains for SPECC1-related genes. These findings were obtained through gene annotation (GO) examination of SPECC1 expression. Primary mediators of the cytokine-cytokine receptor interaction include PICOC1-associated genes, cell-substrate junction genes, and extracellular matrix containing collagen. PICOC1-associated genes primarily mediate the PI3K-AKT signaling pathway. Drug sensitivity assay showed that SPECC1 high-expressing cell lines were more sensitive to docetaxel, doxorubicin, etc. In conclusion, the current study shows how SPECC1 is expressed in different cancers and how this expression relates to the prognosis of the tumor. It also revealed the mutations and copy number variations of SPECC1 in various tumors and its potential involvement in cellular pathway regulatory networks and cytological processes. This study examines the relationship between immune genes, cellular infiltration, and immunological scores in the tumor microenvironment, which explain the severity of the disease. This study looks at the response of SPEC1 expression to anticancer therapy. Explains the prognostic significance and drug response of SPECC-1.
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Affiliation(s)
- Dongwei Liu
- Department of General Practice, The seventh Affiliated Hospital of sun yat-sen university, Shenzhen, 518107, China
| | - Xidi Wang
- Department of Thyroid and Breast surgery, The seventh Affiliated Hospital of sun yat-sen university, Shenzhen, 518107, China
| | - Lingfei Cui
- Department of Thyroid and Breast surgery, The seventh Affiliated Hospital of sun yat-sen university, Shenzhen, 518107, China
| | - Mingxia Zhang
- Department of Thyroid and Breast surgery, The seventh Affiliated Hospital of sun yat-sen university, Shenzhen, 518107, China
| | - Kefeng Lei
- Department of Thyroid and Breast surgery, The seventh Affiliated Hospital of sun yat-sen university, Shenzhen, 518107, China.
| | - Nijiati Aierken
- Department of Thyroid and Breast surgery, The seventh Affiliated Hospital of sun yat-sen university, Shenzhen, 518107, China.
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130
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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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131
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Chen S, Han J, Wu S, Guo S, Tang Y, Zheng Y, Hu L, Zhang X, Zhang P, Zhang H, Ren G, Gao S. From non-coding RNAs to histone modification: The epigenetic mechanisms in tomato fruit ripening and quality regulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109070. [PMID: 39191041 DOI: 10.1016/j.plaphy.2024.109070] [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: 05/22/2024] [Revised: 07/28/2024] [Accepted: 08/22/2024] [Indexed: 08/29/2024]
Abstract
Ripening is one of the most important stages of fruit development and determines the fruit quality. Various factors play a role in this process, with epigenetic mechanisms emerging as important players. Epigenetic regulation encompasses DNA methylation, histone modifications and variants, chromatin remodeling, RNA modifications, and non-coding RNAs. Over the past decade, studies using tomato as a model have made considerable progress in understanding the impact of epigenetic regulation on fleshy fruit ripening and quality. In this paper, we provide an overview of recent advancements in the epigenetic regulation of tomato fruit ripening and quality regulation, focusing on three main mechanisms: DNA/RNA modifications, non-coding RNAs, and histone modifications. Furthermore, we highlight the unresolved issues and challenges within this research field, offering perspectives for future investigations to drive agricultural innovation.
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Affiliation(s)
- Shengbo Chen
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Jiazhen Han
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Shu Wu
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Shangjing Guo
- Qingdao Agricultural University, Qingdao, 266109, China
| | - Yufei Tang
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yujing Zheng
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Lei Hu
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Xingxing Zhang
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Peng Zhang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | | | - Guodong Ren
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Shuai Gao
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China.
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Li S, Zhou Y, Li K, Liu L, Fang M, Gao H. Inhibition of circDGKZ ameliorates myocardial ischemia/reperfusion injury by targeting miR-345-5p/TLR4. ESC Heart Fail 2024; 11:2730-2741. [PMID: 38725137 PMCID: PMC11424286 DOI: 10.1002/ehf2.14809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/25/2024] [Accepted: 04/01/2024] [Indexed: 09/27/2024] Open
Abstract
AIMS This study aims to explore the molecular mechanism of circular RNAs' (circRNAs) potential involvement in myocardial ischaemia-reperfusion injury (MIRI). METHODS AND RESULTS Differently expressed genes in myocardial infarction (MI) were identified by screening the GEO database. Serum was collected from MI patients and healthy volunteers (n = 5 for each group). AC16 cells were cultured and exposed to hypoxia/reperfusion (H/R) treatment for the cell experiments. Then candidate genes were validated in human serum and the H/R model. Quantitative real-time PCR and western blot were used to detect expression of key molecules such as circDGKZ, miR-345-5p, and Toll-like receptor 4 (TLR4), as well as pyroptosis markers such as NOD-like receptor thermal protein domain-associated protein 3 (NLRP3), ASC, C-caspase1, interleukin (IL)-1β, and IL-18. CircDGKZ was positively correlated in human serum (P < 0.05) and in AC16 cells (P < 0.01). Knockdown of circDGKZ inhibited cardiomyocyte pyroptosis and the TLR4/nuclear factor kappa B (NF-κB) signalling pathway (all P < 0.05). A luciferase assay was used to detect the molecule interaction. MiR-345-5p was regulated by circDGKZ and regulated TLR4 in cardiomyocytes both through direct interaction (P < 0.01). The stability and distribution of circRNA or linear RNA were examined by subcellular localization and RNA decay assays. CircDGKZ was stably expressed in cardiomyocytes and mainly distributed in the cytoplasm (P < 0.01). Knockdown of circDGKZ also promoted the degradation of NLRP3 by inducing autophagy (P < 0.05). MIRI rat models were constructed (n = 5 for each group), and the cellular results were further confirmed in rat models (P < 0.05). CONCLUSIONS Knockdown of circDGKZ interrupted pyroptosis and induced autophagy of cardiomyocytes via regulating miR-345-5p/TLR4/NF-κB.
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Affiliation(s)
- Shiliang Li
- Division of Cardiothoracic and Vascular SurgeryTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanHubei ProvinceChina
| | - Yan Zhou
- Department of OtolaryngologyUnion Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanHubei ProvinceChina
| | - KunSheng Li
- Department of Cardiovascular SurgeryThe First Affiliated Hospital of Nanjing Medical UniversityNanjingJiangsu ProvinceChina
| | - Lu Liu
- Department of PharmacyTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanHubei ProvinceChina
| | - Ming Fang
- Health Management CenterUnion Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanHubei ProvinceChina
| | - Hongfeng Gao
- Department of Emergency MedicineWuhan Wuchang Hospital, Wuchang Hospital Affiliated to Wuhan University of Science and TechnologyNo. 116, Yangyuan StreetWuhan430000Hubei ProvinceChina
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133
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Zhang Y, Wu Y, Liu Z, Yang K, Lin H, Xiong K. Non-coding RNAs as potential targets in metformin therapy for cancer. Cancer Cell Int 2024; 24:333. [PMID: 39354464 PMCID: PMC11445969 DOI: 10.1186/s12935-024-03516-w] [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: 05/17/2024] [Accepted: 09/24/2024] [Indexed: 10/03/2024] Open
Abstract
Metformin, a widely used oral hypoglycemic drug, has emerged as a potential therapeutic agent for cancer treatment. While initially known for its role in managing diabetes, accumulating evidence suggests that metformin exhibits anticancer properties through various mechanisms. Several cellular or animal experiments have attempted to elucidate the role of non-coding RNA molecules, including microRNAs and long non-coding RNAs, in mediating the anticancer effects of metformin. The present review summarized the current understanding of the mechanisms by which non-coding RNAs modulate the response to metformin in cancer cells. The regulatory roles of non-coding RNAs, particularly miRNAs, in key cellular processes such as cell proliferation, cell death, angiogenesis, metabolism and epigenetics, and how metformin affects these processes are discussed. This review also highlights the role of lncRNAs in cancer types such as lung adenocarcinoma, breast cancer, and renal cancer, and points out the need for further exploration of the mechanisms by which metformin regulates lncRNAs. In addition, the present review explores the potential advantages of metformin-based therapies over direct delivery of ncRNAs, and this review highlights the mechanisms of non-coding RNA regulation when metformin is combined with other therapies. Overall, the present review provides insights into the molecular mechanisms underlying the anticancer effects of metformin mediated by non-coding RNAs, offering novel opportunities for the development of personalized treatment strategies in cancer patients.
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Affiliation(s)
- Yihan Zhang
- Department of Gastroenterology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330008, Jiangxi, China
- The Second School of Clinical Medicine, Jiangxi Medical College, Nanchang, China
| | - Yunhao Wu
- The Second School of Clinical Medicine, Jiangxi Medical College, Nanchang, China
| | - Zixu Liu
- The First School of Clinical Medicine, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Kangping Yang
- The Second School of Clinical Medicine, Jiangxi Medical College, Nanchang, China
| | - Hui Lin
- Jiangxi Province Key Laboratory of Tumor Pathogenesis and Molecular Pathology, Department of Pathophysiology, School of Basic Medical Sciences, Nanchang, China
| | - Kai Xiong
- Department of Gastroenterology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330008, Jiangxi, China.
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134
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Pourmehran Y, Sadri F, Hosseini SF, Mohammadi Y, Rezaei Z. Exploring the influence of non-coding RNAs on NF-κB signaling pathway regulation in ulcerative colitis. Biomed Pharmacother 2024; 179:117390. [PMID: 39243424 DOI: 10.1016/j.biopha.2024.117390] [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: 06/18/2024] [Revised: 08/20/2024] [Accepted: 08/30/2024] [Indexed: 09/09/2024] Open
Abstract
The gastrointestinal tract is chronically inflamed in ulcerative colitis (UC), which has a complicated etiology involving immunological, environmental, and genetic factors. The inflammatory response that is typical of UC is significantly regulated via the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling pathway. Latest research has displayed that NF-κB signaling is controlled by three main types of non-coding RNAs (ncRNAs): circular RNAs (circRNAs), long non-coding RNAs (lncRNAs), and microRNAs (miRNAs). These ncRNAs can change the expression of key genes within the NF-κB pathway by acting as molecular sponges, transcriptional regulators, and epigenetic modifiers. This review synthesizes current knowledge on the functions by which ncRNAs modulate NF-κB signaling in UC, discusses their potential as biomarkers for disease prognosis and diagnosis, and explores their therapeutic potential. Understanding the intricate interactions between ncRNAs and NF-κB signaling may provide novel insights into UC pathogenesis and targeted therapeutic strategies.
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Affiliation(s)
- Yasaman Pourmehran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Farzad Sadri
- Student Research Committee, Birjand University of Medical Sciences, Birjand, Iran; Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran.
| | - Seyede Fatemeh Hosseini
- Faculty member, Tabas School of Nursing, Birjand University of medical sciences, Birjand, Iran
| | - Yaser Mohammadi
- Department of Biochemistry, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zohreh Rezaei
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran; Department of Biology, University of Sistan and Baluchestan, ZahedanIran.
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135
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Zhou Y, Jian N, Jiang C, Wang J. m 6A modification in non-coding RNAs: Mechanisms and potential therapeutic implications in fibrosis. Biomed Pharmacother 2024; 179:117331. [PMID: 39191030 DOI: 10.1016/j.biopha.2024.117331] [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: 06/11/2024] [Revised: 08/07/2024] [Accepted: 08/21/2024] [Indexed: 08/29/2024] Open
Abstract
N6-methyladenosine (m6A) is one of the most prevalent and reversible forms of RNA methylation, with increasing evidence indicating its critical role in numerous physiological and pathological processes. m6A catalyzes messenger RNA(mRNA) as well as regulatory non-coding RNAs (ncRNAs), such as microRNAs, long non-coding RNAs, and circular RNAs. This modification modulates ncRNA fate and cell functions in various bioprocesses, including ncRNA splicing, maturity, export, and stability. Key m6A regulators, including writers, erasers, and readers, have been reported to modify the ncRNAs involved in fibrogenesis. NcRNAs affect fibrosis progression by targeting m6A regulators. The interactions between m6A and ncRNAs can influence multiple cellular life activities. In this review, we discuss the impact of the interaction between m6A modifications and ncRNAs on the pathological mechanisms of fibrosis, revealing the possibility of these interactions as diagnostic markers and therapeutic targets in fibrosis.
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Affiliation(s)
- Yutong Zhou
- Department of Immunology, Xiangya School of Medicine, Central South University, Changsha 410078, China
| | - Ni Jian
- Department of Immunology, Xiangya School of Medicine, Central South University, Changsha 410078, China
| | - Canhua Jiang
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, Changsha 410078, China
| | - Jie Wang
- Department of Immunology, Xiangya School of Medicine, Central South University, Changsha 410078, China.
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136
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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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137
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Dong C, Yang L, Zhao G. Circ-PGAM1 Enhances Matrine Resistance of Non-Small Cell Lung Cancer via the miR-326/CXCR5 Axis. Cancer Biother Radiopharm 2024; 39:593-599. [PMID: 36576783 DOI: 10.1089/cbr.2022.0039] [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: 12/29/2022] Open
Abstract
Background: Circular RNAs (circ-RNAs) have been demonstrated to influence initiation, drug resistance, and metastasis of tumors. However, the effects of circular-phosphoglycerate mutase 1 (circ-PGAM1) on matrine resistance in nonsmall cell lung cancer (NSCLC) remain unknown. Materials and Methods: The reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to determine gene expression. The terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) and cell colony formation assays were used to evaluate NSCLC apoptosis and cell proliferation after indicated treatments, respectively. Results: circ-PGAM1 was upregulated in human NSCLC cell lines (H1299 and A549) compared with the human normal lung epithelial (BEAS-2B) cells. circ-PGAM1 overexpression reversed the matrine treatment-induced inhibition on proliferation of NSCLC cells (A549 and H1299) and rescued the matrine treatment-stimulated apoptosis of these cells. miR-326 was demonstrated to interact with circ-PGAM1. circ-PGAM1 knockdown enhanced the antitumor effect of matrine on NSCLC cell proliferation and apoptosis, which was reversed by miR-326 inhibition. The authors also identified CXCR5 as a key downstream target of miR-326 in A549 cells. Conclusions: circ-PGAM1 enhances matrine resistance of NSCLC cells through the miR-326/CXCR5 axis. The authors' findings provide new insights into NSCLC-targeted therapy.
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Affiliation(s)
- Caijun Dong
- Department of Thoracic Surgery, Hwamei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Liangwei Yang
- Department of Cardiothoracic Surgery, Hwamei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Guofang Zhao
- Department of Thoracic Surgery, Hwamei Hospital, University of Chinese Academy of Sciences, Ningbo, China
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138
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Wang L, Zheng G, Yuan Y, Wang Z, Wang Q, Sun M, Wu J, Liu C, Liu Y, Zhang B, Zhang H, Yang N, Lian L. circRUNX2.2, highly expressed in Marek's disease tumor tissues, functions in cis to regulate parental gene RUNX2 expression. Poult Sci 2024; 103:104045. [PMID: 39094493 PMCID: PMC11345620 DOI: 10.1016/j.psj.2024.104045] [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: 04/27/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 08/04/2024] Open
Abstract
Marek's disease (MD), an immunosuppression disease induced by Marek's disease virus (MDV), is one of the significant diseases affecting the health and productive performance of poultry. The roles of circular RNAs (circRNAs) in MD development were poorly understood. In this study, we found a circRNA derived from exon 6 of RUNX family transcription factor 2 (RUNX2) gene, named circRUNX2.2, was highly expressed in chicken tumorous spleens (TS) induced by MDV. Through fluorescence in situ hybridization and nuclear-cytoplasmic separation assay, we determined circRUNX2.2 was mainly located in the nucleus. Knockout experiments confirmed that the flanking complementary sequences (RCMs) mediated its circularization. Gain of function assay and dual luciferase reporter gene assay revealed that circRUNX2.2 could promote the expression of RUNX2 via binding with its promoter region. RNA antisense purification assay and mass spectrometry assay showed circRUNX2.2 could recruit proteins such as CHD9 protein. Knocking down CHD9 expression decreased the expression of RUNX2 gene, which confirmed the positive regulation that circRUNX2.2 on RUNX2 expression was probably facilitated via recruiting CHD9 protein. Functional experiments showed that circRUNX2.2 promoted the proliferation of the MD lymphoma-derived chicken cell line, MDCC-MSB1, which confirmed the potential oncogenic role of circRNX2.2 in tumor development. In conclusion, we found that the RUNX2-derived circRUNX2.2 can positively regulate the transcription of the parental gene RUNX2 in a cis-acting manner. The high expression of circRUNX2.2 in MD tumor tissues indicated that it might mediate MD lymphoma progression.
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Affiliation(s)
- Lulu Wang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Gang Zheng
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yiming Yuan
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ziyi Wang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Qinyuan Wang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Meng Sun
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Junfeng Wu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Changjun Liu
- Division of Avian Infectious Diseases, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Yongzhen Liu
- Division of Avian Infectious Diseases, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Bo Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hao Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ning Yang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ling Lian
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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139
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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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140
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Ji M, Yu Q, Yang XZ, Yu X, Wang J, Xiao C, An NA, Han C, Li CY, Ding W. Long-range alternative splicing contributes to neoantigen specificity in glioblastoma. Brief Bioinform 2024; 25:bbae503. [PMID: 39401143 PMCID: PMC11472750 DOI: 10.1093/bib/bbae503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 08/14/2024] [Indexed: 10/17/2024] Open
Abstract
Recent advances in neoantigen research have accelerated the development of immunotherapies for cancers, such as glioblastoma (GBM). Neoantigens resulting from genomic mutations and dysregulated alternative splicing have been studied in GBM. However, these studies have primarily focused on annotated alternatively-spliced transcripts, leaving non-annotated transcripts largely unexplored. Circular ribonucleic acids (circRNAs), abnormally regulated in tumors, are correlated with the presence of non-annotated linear transcripts with exon skipping events. But the extent to which these linear transcripts truly exist and their functions in cancer immunotherapies remain unknown. Here, we found the ubiquitous co-occurrence of circRNA biogenesis and alternative splicing across various tumor types, resulting in large amounts of long-range alternatively-spliced transcripts (LRs). By comparing tumor and healthy tissues, we identified tumor-specific LRs more abundant in GBM than in normal tissues and other tumor types. This may be attributable to the upregulation of the protein quaking in GBM, which is reported to promote circRNA biogenesis. In total, we identified 1057 specific and recurrent LRs in GBM. Through in silico translation prediction and MS-based immunopeptidome analysis, 16 major histocompatibility complex class I-associated peptides were identified as potential immunotherapy targets in GBM. This study revealed long-range alternatively-spliced transcripts specifically upregulated in GBM may serve as recurrent, immunogenic tumor-specific antigens.
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Affiliation(s)
- Mingjun Ji
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Qing Yu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Xin-Zhuang Yang
- Center for Bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine and Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 9 Dongdan Santiao, Dongcheng District, Beijing 100730, China
| | - Xianhong Yu
- Academic Department, Shanghai MobiDrop Co., Ltd., Room 308, Building 1, No. 351 Guoshoujing Road, Shanghai Free Trade Pilot Zone, Shanghai 200000, China
| | - Jiaxin Wang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Chunfu Xiao
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Ni A An
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Chuanhui Han
- School of Basic Medical Sciences, Peking University, No. 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Chuan-Yun Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
- Chinese Institute for Brain Research, No. 26 Science Park Road, Changping District, Beijing 102206, China
- Southwest United Graduate School, 121 Dajie, Wuhua District, Kunming 650092, China
| | - Wanqiu Ding
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
- Bioinformatics Core Facility, Institute of Molecular Medicine, College of Future Technology, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
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141
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He Z, Ji H, Xia B, Cao X, Huang Y, Zhu Q. Invention of circRNA promoting RNA to specifically promote circRNA production. Nucleic Acids Res 2024; 52:e83. [PMID: 39119897 PMCID: PMC11417354 DOI: 10.1093/nar/gkae693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 07/24/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
CircRNA, an essential RNA molecule involved in various biological functions and diseases, often exhibits decreased expression in tumor tissues, playing a role as a tumor suppressor, and suggesting therapeutic potential for cancer. However, current methods for promoting circRNA production are limited. This study introduces a novel approach for enhancing circRNA biogenesis, termed circRNA promoting RNA (cpRNA). CpRNA is designed to complement the flanking sequences of reverse complementary matches (RCMs) within pre-mRNA, thereby facilitating circRNA formation through improved exon circularization. Using a split-GFP reporter system, we demonstrated that cpRNA significantly enhance circGFP production. Optimization identified the best conditions for cpRNA to promote circRNA biogenesis, and these cpRNAs were then used to augment the production of endogenous circRNAs. These results indicate that cpRNAs can specifically increase the production of endogenous circRNAs with RCMs, such as circZKSCAN1 and circSMARCA5 in cancer cells, thereby inhibiting cell proliferation and migration by modulating circRNA-related pathways, showcasing the therapeutic potential of cpRNAs. Mechanistic studies have also shown that cpRNA promotes circRNA biogenesis, in part, by antagonizing the unwinding function of DHX9. Overall, these findings suggest that cpRNA represents a promising strategy for circRNA overexpression, offering a potential treatment for diseases marked by low circRNA levels.
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Affiliation(s)
- Zhilin He
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, Hunan 410013, China
| | - Haofei Ji
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, Hunan 410013, China
| | - Bei Xia
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, Hunan 410013, China
| | - Xiuen Cao
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, Hunan 410013, China
| | - Ying Huang
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, Hunan 410013, China
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, Hunan 410013, China
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142
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Kim J. Circular RNAs: Novel Players in Cancer Mechanisms and Therapeutic Strategies. Int J Mol Sci 2024; 25:10121. [PMID: 39337606 PMCID: PMC11432211 DOI: 10.3390/ijms251810121] [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: 08/14/2024] [Revised: 09/19/2024] [Accepted: 09/19/2024] [Indexed: 09/30/2024] Open
Abstract
Circular RNAs (circRNAs) are a novel class of noncoding RNAs that have emerged as pivotal players in gene regulation. Our understanding of circRNAs has greatly expanded over the last decade, with studies elucidating their biology and exploring their therapeutic applications. In this review, we provide an overview of the current understanding of circRNA biogenesis, outline their mechanisms of action in cancer, and assess their clinical potential as biomarkers. Furthermore, we discuss circRNAs as a potential therapeutic strategy, including recent advances in circRNA production and translation, along with proof-of-concept preclinical studies of cancer vaccines.
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Affiliation(s)
- Jimi Kim
- Department of Life Sciences, Gachon University, Seongnam 13120, Republic of Korea;
- Department of Health Science and Technology, GAIHST, Lee Gil Ya Cancer and Diabetes Institute, Incheon 21999, Republic of Korea
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143
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Wang J, Wang X, Yang C, Li Q, Li D, Du X, Cheng Y, Tian M, Zheng L, Tong Q. circE2F1-encoded peptide inhibits circadian machinery essential for nucleotide biosynthesis and tumor progression via repressing SPIB/E2F1 axis. Int J Biol Macromol 2024; 280:135698. [PMID: 39288851 DOI: 10.1016/j.ijbiomac.2024.135698] [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: 05/21/2024] [Revised: 09/01/2024] [Accepted: 09/13/2024] [Indexed: 09/19/2024]
Abstract
Circadian clock dominates a variety of biological activities, while its roles and regulatory mechanisms in neuroblastoma (NB), a pediatric extracranial malignancy, still remain largely elusive. Herein, through comprehensive analyses of public datasets, E2F transcription factor 1 (E2F1) and its circular RNA (circE2F1)-encoded 99-amino acid peptide (E2F1-99aa) were identified as vital regulators of circadian machinery essential for purine and pyrimidine biosynthesis during NB progression. Mechanistically, through interaction with Spi-B transcription factor (SPIB), E2F1 was transactivated to up-regulate circadian machinery genes (CRY1 and TIMELESS), resulting in relief of CLOCK/BMAL1-repressed transcription of enzymes (DHODH, PAICS, or PPAT) essential for de novo purine and pyrimidine biosynthesis. The biogenesis of circE2F1 was repressed by eukaryotic translation initiation factor 4A3 (EIF4A3), while E2F1-99aa or its truncated peptide competitively bound to SPIB, leading to decrease in SPIB-E2F1 interaction, circadian machinery and nucleotide biosynthetic gene expression, purine or pyrimidine biosynthesis, tumorigenesis, and aggresiveness of NB cells. In clinical NB cases, high EIF4A3, E2F1 or SPIB expression was correlated with low survival possibility of patients, while lower circE2F1 or E2F1-99aa levels were associated with advanced stages and tumor progression. These results indicate that circE2F1-encoded peptide inhibits circadian machinery essential for nucleotide biosynthesis and tumor progression via repressing SPIB/E2F1 axis.
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Affiliation(s)
- Jianqun Wang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Xiaojing Wang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China; Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Chunhui Yang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Qilan Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Dan Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Xinyi Du
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Yang Cheng
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Minxiu Tian
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China
| | - Liduan Zheng
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China.
| | - Qiangsong Tong
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, PR China.
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144
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Guo D, Xu W, Cui T, Rong Q, Wu Q. Protein-coding circular RNA enhances antiviral immunity via JAK/STAT pathway in Drosophila. mBio 2024; 15:e0146924. [PMID: 39158293 PMCID: PMC11389369 DOI: 10.1128/mbio.01469-24] [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: 05/11/2024] [Accepted: 07/11/2024] [Indexed: 08/20/2024] Open
Abstract
RNA interference (RNAi) drives powerful antiviral immunity in plants and animals so that many viruses must express viral suppressor of RNAi (VSR) to establish virulent infection. However, little is known about the immune responses conferring resistance against viruses that have evolved the counter-defensive strategy to suppress antiviral RNAi. In this study, we discover that Drosophila cells infected with Drosophila C virus (DCV), a natural viral pathogen of Drosophila known to harbor a potent VSR, exhibit heightened expression of circular RNA circZfh1. circZfh1 confers virus resistance in the presence of viral suppression of antiviral RNAi. Furthermore, we validate that circZfh1 encodes a 274-amino acid protein, CRAV, essential for its antiviral activity. Notably, CRAV differs from its parental Zfh1 gene in a different reading frame, with the C-terminal 69 amino acids unique to CRAV. Our analysis also reveals the presence of CRAV in species within the melanogaster subgroup, with the C-terminal unique fragment undergoing accelerated evolution. Expression of CRAV upregulates the expression of the cytokine Upd3, which binds to its receptor, stimulating the JAK-STAT pathway and enhancing the immune response to DCV infection. Notably, CRISPR/Cas9 knockout of circZfh1 significantly enhances DCV replication in vitro and in vivo, with circZfh1-knockout adult flies displaying heightened disease susceptibility to DCV. In summary, our findings unveil a Drosophila protein-coding circular RNA that activates an innate immune signaling pathway crucial for virus resistance following the suppression of antiviral RNAi by viruses, thereby elucidating a novel counter-defensive strategy.IMPORTANCEEukaryotic hosts possess a complex, multilayered immune system that guards against pathogen invasion. In fruit flies, RNA interference (RNAi) drives robust antiviral immunity, prompting many viruses to express viral suppressors of RNAi (VSRs) to establish virulent infections. However, little is known about immune responses that confer resistance against viruses with potent VSRs. In this study, we discovered that Drosophila cells infected with Drosophila C virus (DCV), a natural viral pathogen possessing a potent VSR, upregulated the expression of circular RNA circZfh1. circZfh1 exhibits DCV-specific antiviral activity, encoding a 274-amino acid protein, CRAV, crucial for its antiviral effects. As a different reading frame from its parental Zfh1 gene, the C-terminal 69 amino acids are unique to CRAV, undergoing faster evolution. CRAV activates the JAK-STAT pathway, enhancing the immune response to DCV infection. Therefore, our work uncovers a new strategy for suppressing viral counter-defense through protein-coding circular RNA in fruit flies.
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Affiliation(s)
- Dongyang Guo
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, University of Science and Technology of China, Hefei, China
| | - Wen Xu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, University of Science and Technology of China, Hefei, China
| | - Ting Cui
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, University of Science and Technology of China, Hefei, China
| | - Qiqi Rong
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, University of Science and Technology of China, Hefei, China
| | - Qingfa Wu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, University of Science and Technology of China, Hefei, China
- Division of Molecular Medicine, CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei, Anhui, China
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145
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Morandell J, Monziani A, Lazioli M, Donzel D, Döring J, Oss Pegorar C, D'Anzi A, Pellegrini M, Mattiello A, Bortolotti D, Bergonzoni G, Tripathi T, Mattis VB, Kovalenko M, Rosati J, Dieterich C, Dassi E, Wheeler VC, Ellederová Z, Wilusz JE, Viero G, Biagioli M. CircHTT(2,3,4,5,6) - co-evolving with the HTT CAG-repeat tract - modulates Huntington's disease phenotypes. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102234. [PMID: 38974999 PMCID: PMC11225910 DOI: 10.1016/j.omtn.2024.102234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 05/29/2024] [Indexed: 07/09/2024]
Abstract
Circular RNA (circRNA) molecules have critical functions during brain development and in brain-related disorders. Here, we identified and validated a circRNA, circHTT(2,3,4,5,6), stemming from the Huntington's disease (HD) gene locus that is most abundant in the central nervous system (CNS). We uncovered its evolutionary conservation in diverse mammalian species, and a correlation between circHTT(2,3,4,5,6) levels and the length of the CAG-repeat tract in exon-1 of HTT in human and mouse HD model systems. The mouse orthologue, circHtt(2,3,4,5,6), is expressed during embryogenesis, increases during nervous system development, and is aberrantly upregulated in the presence of the expanded CAG tract. While an IRES-like motif was predicted in circH TT (2,3,4,5,6), the circRNA does not appear to be translated in adult mouse brain tissue. Nonetheless, a modest, but consistent fraction of circHtt(2,3,4,5,6) associates with the 40S ribosomal subunit, suggesting a possible role in the regulation of protein translation. Finally, circHtt(2,3,4,5,6) overexpression experiments in HD-relevant STHdh striatal cells revealed its ability to modulate CAG expansion-driven cellular defects in cell-to-substrate adhesion, thus uncovering an unconventional modifier of HD pathology.
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Affiliation(s)
- Jasmin Morandell
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Alan Monziani
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Martina Lazioli
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Deborah Donzel
- Institute of Biophysics Unit at Trento, National Research Council - CNR, 38123 Trento, Italy
| | - Jessica Döring
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Claudio Oss Pegorar
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Angela D'Anzi
- Cellular Reprogramming Unit Fondazione IRCCS, Casa Sollievo Della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, FG, Italy
| | - Miguel Pellegrini
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Andrea Mattiello
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Dalia Bortolotti
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Guendalina Bergonzoni
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Takshashila Tripathi
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Virginia B Mattis
- Board of Governor's Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Marina Kovalenko
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jessica Rosati
- Cellular Reprogramming Unit Fondazione IRCCS, Casa Sollievo Della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, FG, Italy
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Vanessa C Wheeler
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Zdenka Ellederová
- Research Center PIGMOD, Institute of Animal Physiology and Genetics, Czech Academy of Science, 277 21 Libechov, Czech Republic
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gabriella Viero
- Institute of Biophysics Unit at Trento, National Research Council - CNR, 38123 Trento, Italy
| | - Marta Biagioli
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
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146
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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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147
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Siedlecki E, Remiszewski P, Stec R. The Role of circHIPK3 in Tumorigenesis and Its Potential as a Biomarker in Lung Cancer. Cells 2024; 13:1483. [PMID: 39273053 PMCID: PMC11393915 DOI: 10.3390/cells13171483] [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: 07/29/2024] [Revised: 08/27/2024] [Accepted: 08/31/2024] [Indexed: 09/15/2024] Open
Abstract
Lung cancer treatment and detection can be improved by the identification of new biomarkers. Novel approaches in investigating circular RNAs (circRNAs) as biomarkers have yielded promising results. A circRNA molecule circHIPK3 was found to be widely expressed in non-small-cell lung cancer (NSCLC) cells, where it plays a crucial role in lung cancer tumorigenesis. CircHIPK3 promotes lung cancer progression by sponging oncosuppressive miRNAs such as miR-124, miR-381-3p, miR-149, and miR-107, which results in increased cell proliferation, migration, and resistance to therapies. Inhibiting circHIPK3 has been demonstrated to suppress tumour growth and induce apoptosis, which suggests its potential use in the development of new lung cancer treatment strategies targeting circHIPK3-related pathways. As a biomarker, circHIPK3 shows promise for early detection and monitoring of lung cancer. CircHIPK3 increased expression levels in lung cancer cells, and its potential link to metastasis risk highlights its clinical relevance. Given the promising preliminary findings, more clinical trials are needed to validate circHIPK3 efficacy as a biomarker. Moreover, future research should determine if the mechanisms discovered in NSCLC apply to small cell lung cancer (SCLC) to investigate circHIPK3-targeted therapies for SCLC.
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Affiliation(s)
- Eryk Siedlecki
- Department of Oncology, Medical University of Warsaw, 02-097 Warsaw, Poland; (P.R.); (R.S.)
- Faculty of Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Piotr Remiszewski
- Department of Oncology, Medical University of Warsaw, 02-097 Warsaw, Poland; (P.R.); (R.S.)
- Faculty of Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Rafał Stec
- Department of Oncology, Medical University of Warsaw, 02-097 Warsaw, Poland; (P.R.); (R.S.)
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148
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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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149
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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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150
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Wang J, Zhang Y, Li Z. Advancements in Understanding the Role of Circular RNA in Osteosarcoma. Mol Biotechnol 2024; 66:2157-2167. [PMID: 37661210 DOI: 10.1007/s12033-023-00838-4] [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: 02/06/2023] [Accepted: 07/24/2023] [Indexed: 09/05/2023]
Abstract
Osteosarcoma, the most prevalent primary malignant bone tumor and the third most frequent cancer in children and adolescents worldwide, still poses a significant therapeutic challenge. Even though combined chemotherapy and surgical resection have improved survival rates up to 60%, the prognosis for most patients with metastatic osteosarcoma continues to be dismal. The specific pathogenesis and key regulators of tumor invasion and metastasis remain largely elusive. Circular RNAs (circRNAs), novel endogenous non-coding RNA molecules that form covalently closed continuous loops through splicing, play a crucial role in the development, progression, clinical diagnosis, and treatment of various diseases. Recently, an escalating number of circular structures have been identified in osteosarcoma. Understanding their role in osteosarcoma is advantageous for early detection, diagnosis, and treatment of this disease. The primary function of circRNA involves its unique ability to bind specifically to miRNA, although their biological functions also extend to interacting with proteins, regulating gene transcription, and serving as translation templates. In this review, we explore the mechanisms and clinical applications of circRNAs in the pathogenesis and progression of osteosarcoma, with a particular emphasis on the regulatory mechanisms and functions of circRNAs as miRNA sponges in osteosarcoma development.
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Affiliation(s)
- Jin Wang
- Department of Orthopedics, Wuwei People's Hospital, Xuanwu Street, Liangzhou District, Wuwei, Gansu, 730030, People's Republic of China
| | - Yan Zhang
- Department of Outpatient, Liangzhou District Huangyang Hospital, Wuwei, Gansu, 733000, People's Republic of China
| | - Zicai Li
- Department of Orthopedics, Wuwei People's Hospital, Xuanwu Street, Liangzhou District, Wuwei, Gansu, 730030, People's Republic of China.
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