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Wang Y, Li X, Lu W, Li F, Yao L, Liu Z, Shi H, Zhang W, Bai Y. Full-length circRNA sequencing method using low-input RNAs and profiling of circRNAs in MPTP-PD mice on a nanopore platform. Analyst 2024; 149:5118-5130. [PMID: 39240088 DOI: 10.1039/d4an00715h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]
Abstract
Considering the importance of accurate information of full-length (FL) transcripts in functional analysis, researchers prefer to develop new sequencing methods based on third-generation sequencing (TGS) rather than short-read sequencing. Several FL circRNA sequencing strategies have been developed. However, the current methods are inapplicable to low-biomass samples, since a large amount of total RNAs are acquired for circRNA enrichment before library preparation. In this work, we developed an effective method to detect FL circRNAs from a nanogram level (1-100 ng) of total RNAs based on a nanopore platform. Additionally, prior to the library preparation process, we added a series of 24 nt barcodes for each sample to reduce the cost and operating time. Using this method, we profiled circRNA expression in the striatum, hippocampus and cerebral cortex of a Parkinson's disease (PD) mouse model. Over 6% of reads were effective for FL circRNA identification in most datasets. Notably, a reduction in the RNA initial input resulted in a lower correlation between replicates and the detection efficiency for longer circRNA, but the lowest input (1 ng) was able to detect numerous FL circRNAs. Next, we systematically identified over 263 934 circRNAs in PD and healthy mice using the lower-input FL sequencing method, some of which came from 50.52% of PD-associated genes. Moreover, significant changes were observed in the circRNA expression pattern at an isoform level, and high-confidence protein translation evidence was predicted. Overall, we developed an effective method to characterize FL circRNAs from low-input samples and provide a comprehensive insight into the biological function of circRNAs in PD at an isoform level.
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Affiliation(s)
- Ying Wang
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Xiaohan Li
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Wenxiang Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Fuyu Li
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Lingsong Yao
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Zhiyu Liu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Huajuan Shi
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Weizhong Zhang
- Department of Ophthalmology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, China.
| | - Yunfei Bai
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
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2
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Yi Q, Feng J, Lan W, Shi H, Sun W, Sun W. CircRNA and lncRNA-encoded peptide in diseases, an update review. Mol Cancer 2024; 23:214. [PMID: 39343883 PMCID: PMC11441268 DOI: 10.1186/s12943-024-02131-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 09/19/2024] [Indexed: 10/01/2024] Open
Abstract
Non-coding RNAs (ncRNAs), including circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs), are unique RNA molecules widely identified in the eukaryotic genome. Their dysregulation has been discovered and played key roles in the pathogenesis of numerous diseases, including various cancers. Previously considered devoid of protein-coding ability, recent research has revealed that a small number of open reading frames (ORFs) within these ncRNAs endow them with the potential for protein coding. These ncRNAs-derived peptides or proteins have been proven to regulate various physiological and pathological processes through diverse mechanisms. Their emerging roles in disease diagnosis and targeted therapy underscore their potential utility in clinical settings. This comprehensive review aims to provide a systematic overview of proteins or peptides encoded by lncRNAs and circRNAs, elucidate their production and functional mechanisms, and explore their promising applications in cancer diagnosis, disease prediction, and targeted therapy.
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Affiliation(s)
- Qian Yi
- Department of Physiology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, 646099, China
| | - Jianguo Feng
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China.
| | - Weiwu Lan
- Department of Orthopedics, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong, 518035, China
| | - Houyin Shi
- Department of Orthopedics, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000, China
| | - Wei Sun
- Department of Orthopedics, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong, 518035, China.
| | - Weichao Sun
- Department of Orthopedics, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong, 518035, China.
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3
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Deng X, Yu YV, Jin YN. Non-canonical translation in cancer: significance and therapeutic potential of non-canonical ORFs, m 6A-modification, and circular RNAs. Cell Death Discov 2024; 10:412. [PMID: 39333489 PMCID: PMC11437038 DOI: 10.1038/s41420-024-02185-y] [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: 05/12/2024] [Revised: 09/13/2024] [Accepted: 09/18/2024] [Indexed: 09/29/2024] Open
Abstract
Translation is a decoding process that synthesizes proteins from RNA, typically mRNA. The conventional translation process consists of four stages: initiation, elongation, termination, and ribosome recycling. Precise control over the translation mechanism is crucial, as dysregulation in this process is often linked to human diseases such as cancer. Recent discoveries have unveiled translation mechanisms that extend beyond typical well-characterized components like the m7G cap, poly(A)-tail, or translation factors like eIFs. These mechanisms instead utilize atypical elements, such as non-canonical ORF, m6A-modification, and circular RNA, as key components for protein synthesis. Collectively, these mechanisms are classified as non-canonical translations. It is increasingly clear that non-canonical translation mechanisms significantly impact the various regulatory pathways of cancer, including proliferation, tumorigenicity, and the behavior of cancer stem cells. This review explores the involvement of a variety of non-canonical translation mechanisms in cancer biology and provides insights into potential therapeutic strategies for cancer treatment.
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Affiliation(s)
- Xiaoyi Deng
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China
| | - Yanxun V Yu
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, Hubei, China
| | - Youngnam N Jin
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China.
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, Hubei, China.
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Wang X, Nie H, Su M, Wu Y, Pang Q, Zhang Y, He C, Song Y. Serum CircNIPSNAP3A is Associated with Metabolic Disorders, Atherosclerosis and Severity of Coronary Artery Disease in a Chinese Population. TOHOKU J EXP MED 2024; 263:123-131. [PMID: 38569888 DOI: 10.1620/tjem.2024.j023] [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: 04/05/2024]
Abstract
The relationships of serum circNIPSNAP3A and circHIPK3 with metabolic disorders, atherosclerosis and severity of coronary artery disease (CAD) remain to be clarified. Three hundred and thirty-eight subjects were categorized into normal coronary artery, atherosclerosis and CAD groups. Clinical data including anthropometric indexes, medical history, and physiological and biochemical parameters were collected. Serum circNIPSNAP3A and circHIPK3 were determined by quantitative real-time PCR. CAD severity was evaluated by clinical manifestation, electrocardiogram and coronary angiography. Both CAD and atherosclerosis groups had a higher serum level of circNIPSNAP3A than the normal coronary artery group (P < 0.05 for all). The subjects with a high percentage (> 66th percentile) of circNIPSNAP3A had higher mean levels of triglycerides, uric acid and homocysteine, and lower mean levels of high-density lipoprotein cholesterol and apolipoprotein AI than those with a low percentage (< 33rd percentile) of circNIPSNAP3A. Notably, circNIPSNAP3A is significantly and independently associated with CAD, and subjects with a high percentage of circNIPSNAP3A had more diseased coronary branches and a higher incidence of acute coronary syndrome than those with a low percentage of circNIPSNAP3A. Regarding circHIPK3, subjects with a medium or high percentage of circHIPK3 had a lower mean level of apolipoprotein AI than those with a low percentage of circHIPK3, but no significant differences in the incidence and severity of CAD among the < 33rd, 33rd-66th, and > 66th percentiles of circHIPK3 were detected. Serum circNIPSNAP3A is related to cardiovascular risk factors and CAD severity, and may be a potential prognostic marker and/or therapeutic target for CAD.
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Affiliation(s)
- Xue Wang
- Central Laboratory, Clinical Medical College and Affiliated Hospital of Chengdu University
| | - Haiyan Nie
- Clinical Medical College of Chengdu University
| | - Mi Su
- Functional Science Laboratory, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University
| | - Yang Wu
- Clinical Medical College of Chengdu University
| | | | - Youjin Zhang
- Central Laboratory, Clinical Medical College and Affiliated Hospital of Chengdu University
| | - Chuan He
- Department of Cardiology, Clinical Medical College and Affiliated Hospital of Chengdu University
| | - Yongyan Song
- Central Laboratory, Clinical Medical College and Affiliated Hospital of Chengdu University
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5
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Wang C, Wang Q, Xu G, Sun Z, Zhang D, Ma C, Li Y, Wen D, Zhang X, Cong B. Circular RNA expression profiles and functional predication after restraint stress in the amygdala of rats. Front Mol Neurosci 2024; 17:1381098. [PMID: 38685915 PMCID: PMC11056511 DOI: 10.3389/fnmol.2024.1381098] [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: 02/02/2024] [Accepted: 04/04/2024] [Indexed: 05/02/2024] Open
Abstract
Prolonged or repeated exposure to stress elevates the risk of various psychological diseases, many of which are characterized by central nervous system dysfunction. Recent studies have demonstrated that circular RNAs (circRNAs) are highly abundant in the mammalian brain. Although their precise expression and function remain unknown, they have been hypothesized to regulate transcriptional and post-transcriptional gene expression. In this investigation, we comprehensively analyzed whether restraint stress for 2 days altered the circRNA expression profile in the amygdala of male rats. The impact of restraint stress on behavior was evaluated using an elevated plus maze and open field test. Serum corticosterone levels were measured using an enzyme-linked immunosorbent assay. A total of 10,670 circRNAs were identified using RNA sequencing. Ten circRNAs were validated by reverse transcription and quantitative polymerase chain reaction analysis. Gene ontology and Kyoto encyclopedia of genes and genomes pathway analyzes supported the notion that genes associated with differentially expressed circRNAs are primarily implicated in neuronal activity and neurotransmitter transport. Moreover, the three differentially expressed circRNAs showed high specificity in the amygdala. Overall, these findings indicate that differentially expressed circRNAs are highly enriched in the amygdala and offer a potential direction for further research on restraint stress.
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Affiliation(s)
- Chuan Wang
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Hebei Medical University, Shijiazhuang, China
| | - Qian Wang
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Hebei Medical University, Shijiazhuang, China
| | - Guangming Xu
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Hebei Medical University, Shijiazhuang, China
- Department of Forensic Medicine, The National Police University for Criminal Justice, Baoding, China
| | - Zhaoling Sun
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Hebei Medical University, Shijiazhuang, China
| | - Dong Zhang
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Hebei Medical University, Shijiazhuang, China
- College of Integrative Medicine, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Chunling Ma
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Hebei Medical University, Shijiazhuang, China
| | - Yingmin Li
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Hebei Medical University, Shijiazhuang, China
| | - Di Wen
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Hebei Medical University, Shijiazhuang, China
| | - Xiaojing Zhang
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Hebei Medical University, Shijiazhuang, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Hebei Medical University, Shijiazhuang, China
- Hainan Tropical Forensic Medicine Academician Workstation, Haikou, China
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Xiao F, He Z, Wang S, Li J, Fan X, Yan T, Yang M, Yang D. Regulatory mechanism of circular RNAs in neurodegenerative diseases. CNS Neurosci Ther 2024; 30:e14499. [PMID: 37864389 PMCID: PMC11017410 DOI: 10.1111/cns.14499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 08/24/2023] [Accepted: 10/02/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Neurodegenerative disease is a collective term for a category of diseases that are caused by neuronal dysfunction, such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS). Circular RNAs (circRNAs) are a class of non-coding RNAs without the 3' cap and 5' poly(A) and are linked by covalent bonds. CircRNAs are highly expressed in brain neurons and can regulate the pathological process of neurodegenerative diseases by affecting the levels of various deposition proteins. AIMS This review is aiming to suggest that the majority of circRNAs influence neurodegenerative pathologies mainly by affecting the abnormal deposition of proteins in neurodegenerative diseases. METHODS We systematically summarized the pathological features of neurodegenerative diseases and the regulatory mechanisms of circRNAs in various types of neurodegenerative diseases. RESULTS Neurodegenerative disease main features include intercellular ubiquitin-proteasome system abnormalities, changes in cytoskeletal proteins, and the continuous deposition of insoluble protein fragments and inclusion bodies in the cytoplasm or nucleus, resulting in impairment of the normal physiological processes of the neuronal system. CircRNAs have multiple mechanisms, such as acting as microRNA sponges, binding to proteins, and regulating transcription. CircRNAs, which are highly stable molecules, are expected to be potential biomarkers for the pathological detection of neurodegenerative diseases such as AD and PD. CONCLUSIONS In this review, we describe the regulatory roles and mechanisms of circRNAs in neurodegenerative diseases and aim to employ circRNAs as biomarkers for the diagnosis and treatment of neurodegenerative diseases.
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Affiliation(s)
- Feng Xiao
- College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduChina
| | - Zhi He
- College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Siqi Wang
- College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduChina
| | - Jiamei Li
- College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduChina
| | - Xiaolan Fan
- College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduChina
| | - Taiming Yan
- College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Mingyao Yang
- College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduChina
| | - Deying Yang
- College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan ProvinceSichuan Agricultural UniversityChengduChina
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Zhang B, Zhang H, Wang Z, Cao H, Zhang N, Dai Z, Liang X, Peng Y, Wen J, Zhang X, Zhang L, Luo P, Zhang J, Liu Z, Cheng Q, Peng R. The regulatory role and clinical application prospects of circRNA in the occurrence and development of CNS tumors. CNS Neurosci Ther 2024; 30:e14500. [PMID: 37953502 PMCID: PMC11017455 DOI: 10.1111/cns.14500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/20/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Central nervous system (CNS) tumors originate from the spinal cord or brain. The study showed that even with aggressive treatment, malignant CNS tumors have high mortality rates. However, CNS tumor risk factors and molecular mechanisms have not been verified. Due to the reasons mentioned above, diagnosis and treatment of CNS tumors in clinical practice are currently fraught with difficulties. Circular RNAs (circRNAs), single-stranded ncRNAs with covalently closed continuous structures, are essential to CNS tumor development. Growing evidence has proved the numeral critical biological functions of circRNAs for disease progression: sponging to miRNAs, regulating gene transcription and splicing, interacting with proteins, encoding proteins/peptides, and expressing in exosomes. AIMS This review aims to summarize current progress regarding the molecular mechanism of circRNA in CNS tumors and to explore the possibilities of clinical application based on circRNA in CNS tumors. METHODS We have summarized studies of circRNA in CNS tumors in Pubmed. RESULTS This review summarized their connection with CNS tumors and their functions, biogenesis, and biological properties. Furthermore, we introduced current advances in clinical RNA-related technologies. Then we discussed the diagnostic and therapeutic potential (especially for immunotherapy, chemotherapy, and radiotherapy) of circRNA in CNS tumors in the context of the recent advanced research and application of RNA in clinics. CONCLUSIONS CircRNA are increasingly proven to participate in decveloping CNS tumors. An in-depth study of the causal mechanisms of circRNAs in CNS tomor progression will ultimately advance their implementation in the clinic and developing new strategies for preventing and treating CNS tumors.
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Affiliation(s)
- Bo Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Hao Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- Department of Neurosurgery, The Second Affiliated HospitalChongqing Medical UniversityChongqingChina
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- MRC Centre for Regenerative Medicine, Institute for Regeneration and RepairUniversity of EdinburghEdinburghUK
| | - Hui Cao
- Department of Psychiatry, The School of Clinical MedicineHunan University of Chinese MedicineChangshaChina
| | - Nan Zhang
- College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Xisong Liang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Yun Peng
- Teaching and Research Section of Clinical NursingXiangya Hospital of Central South UniversityChangshaChina
- Department of Geriatrics, Xiangya HospitalCentral South UniversityChangshaChina
| | - Jie Wen
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Xun Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Liyang Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Peng Luo
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Jian Zhang
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Zaoqu Liu
- Department of Interventional RadiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Quan Cheng
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Renjun Peng
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
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Zhou M, Li S, Huang C. Physiological and pathological functions of circular RNAs in the nervous system. Neural Regen Res 2024; 19:342-349. [PMID: 37488888 PMCID: PMC10503630 DOI: 10.4103/1673-5374.379017] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/20/2023] [Accepted: 05/29/2023] [Indexed: 07/26/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of covalently closed single-stranded RNAs that are expressed during the development of specific cells and tissues. CircRNAs play crucial roles in physiological and pathological processes by sponging microRNAs, modulating gene transcription, controlling the activity of certain RNA-binding proteins, and producing functional peptides. A key focus of research at present is the functionality of circRNAs in the nervous system and several advances have emerged over the last 2 years. However, the precise role of circRNAs in the nervous system has yet to be comprehensively reviewed. In this review, we first summarize the recently described roles of circRNAs in brain development, maturity, and aging. Then, we focus on the involvement of circRNAs in various diseases of the central nervous system, such as brain cancer, chronic neurodegenerative diseases, acute injuries of the nervous system, and neuropathic pain. A better understanding of the functionality of circRNAs will help us to develop potential diagnostic, prognostic, and therapeutic strategies to treat diseases of the nervous system.
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Affiliation(s)
- Min Zhou
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Shi Li
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, China
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Lindner G, Takenaka K, Santucci K, Gao Y, Janitz M. Protein-coding circular RNAs - mechanism, detection, and their role in cancer and neurodegenerative diseases. Biochem Biophys Res Commun 2023; 678:68-77. [PMID: 37619313 DOI: 10.1016/j.bbrc.2023.08.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/04/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]
Abstract
Circular RNAs (circRNAs) are a unique class of non-coding RNAs and were originally thought to have no protein-coding potential due to their lack of a 5' cap and 3' poly(A) tail. However, recent studies have challenged this notion and revealed that some circRNAs have protein-coding potential. They have emerged as a key area of interest in cancer and neurodegeneration research as recent studies have identified several circRNAs that can produce functional proteins with important roles in cancer progression. The protein-coding potential of circRNAs is determined by the presence of an open reading frame (ORF) within the circular structure that can encode a protein. In some cases, the ORF can be translated into a functional protein despite the lack of traditional mRNA features. While the protein-coding potential of most circRNAs remains unclear, several studies have identified specific circRNAs that can produce functional proteins. Understanding the protein-coding potential of circRNAs is important for unravelling their biological functions and potential roles in disease. Our review provides comprehensive coverage of recent advances in the field of circRNA protein-coding capacity and its impact on cancer and neurodegenerative diseases pathogenesis and progression.
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Affiliation(s)
- Grace Lindner
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Konii Takenaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Kristina Santucci
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Yulan Gao
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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10
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Hwang JY, Kook TL, Paulus SM, Park JW. Translation of Circular RNAs: Functions of Translated Products and Related Bioinformatics Approaches. Curr Bioinform 2023; 19:3-13. [PMID: 38500957 PMCID: PMC10947221 DOI: 10.2174/1574893618666230505101059] [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: 11/23/2022] [Revised: 03/09/2023] [Accepted: 03/16/2023] [Indexed: 03/20/2024]
Abstract
Over the past two decades, studies have discovered a special form of alternative splicing (AS) that produces a circular form of RNA. This stands in contrast to normal AS, which produces a linear form of RNA. Although these circRNAs have garnered considerable attention in the scientific community for their biogenesis and functions, the focus of these studies has been on the regulatory role of circRNAs with the assumption that circRNAs are non-coding. As non-coding RNAs, they may regulate mRNA transcription, tumor initiation, and translation by sponging miRNAs and RNA-binding proteins (RBPs). In addition to these regulatory roles of circRNAs, however, recent studies have provided strong evidence for their translation. The translation of circRNAs is expected to have an important role in promoting cancer cell growth and activating molecular pathways related to cancer development. In some cases, the translation of circRNAs is shown to be efficiently driven by an internal ribosome entry site (IRES). The development of a computational tool for identifying and characterizing the translation of circRNAs using high-throughput sequencing and IRES increases identifiable proteins translated from circRNAs. In turn, it has a substantial impact on helping researchers understand the functional role of proteins derived from circRNAs. New web resources for aggregating, cataloging, and visualizing translational information of circRNAs derived from previous studies have been developed. In this paper, general concepts of circRNA, circRNA biogenesis, translation of circRNA, and existing circRNA tools and databases are summarized to provide new insight into circRNA studies.
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Affiliation(s)
- Jae Yeon Hwang
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA
| | - Tae Lim Kook
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA
| | - Sydney M. Paulus
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA
| | - Juw Won Park
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA
- CIEHS Biostatistics and Informatics Facility Core, University of Louisville, Louisville, KY 40292, USA
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11
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Shi X, Liao S, Bi Z, Liu J, Li H, Feng C. Newly discovered circRNAs encoding proteins: recent progress. Front Genet 2023; 14:1264606. [PMID: 37829278 PMCID: PMC10565661 DOI: 10.3389/fgene.2023.1264606] [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: 07/21/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023] Open
Abstract
Circular RNA (circRNA) is a special class of noncoding RNA molecules and the latest research hotspot in the field of RNA. CircRNA molecules have a closed loop structure, which is not affected by RNA exonuclease and has the characteristics of more stable expression. Previous studies have shown that circRNA molecules are rich in microRNA (miRNA) binding sites and act as miRNA sponges in cells. By interacting with miRNAs associated with tumors and other diseases, circRNAs play an important regulatory role. However, circRNAs have recently been found to have small open reading frames that enable them to encode peptides/proteins. These proteins have been reported to play an important role in the mechanism of regulation of a variety of diseases and have great potential in the diagnosis and treatment of diseases. In this review, we summarize the mechanism of action of the newly discovered circRNA-coding proteins since 2022 and briefly describe their research process. In addition, we also discuss the prediction model of the functional sites and encoded proteins of circRNAs, which provides a potential idea for future research on circRNAs.
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Affiliation(s)
- Xiaotong Shi
- Department of Obstetrics and Gynecology, Beijing Chao-yang Hospital of Capital Medical University, Beijing, China
- Department of Orthopedics, The First Hospital of Jilin University, Changchun, China
| | - Shiyu Liao
- Department of Orthopedics, The First Hospital of Jilin University, Changchun, China
| | - Zhiguo Bi
- Department of Orthopedics, The First Hospital of Jilin University, Changchun, China
| | - Jianguo Liu
- Department of Orthopedics, The First Hospital of Jilin University, Changchun, China
| | - Hua Li
- Department of Obstetrics and Gynecology, Beijing Chao-yang Hospital of Capital Medical University, Beijing, China
| | - Chunyang Feng
- Department of Obstetrics and Gynecology, Beijing Chao-yang Hospital of Capital Medical University, Beijing, China
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12
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Crudele F, Bianchi N, Terrazzan A, Ancona P, Frassoldati A, Gasparini P, D'Adamo AP, Papaioannou D, Garzon R, Wójcicka A, Gaj P, Jażdżewski K, Palatini J, Volinia S. Circular RNAs Could Encode Unique Proteins and Affect Cancer Pathways. BIOLOGY 2023; 12:biology12040493. [PMID: 37106694 PMCID: PMC10135897 DOI: 10.3390/biology12040493] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023]
Abstract
circRNAs constitute a novel class of RNA, generally considered as non-coding RNAs; nonetheless, their coding potential has been under scrutiny. In this work, we systematically explored the predicted proteins of more than 160,000 circRNAs detected by exome capture RNA-sequencing and collected in the MiOncoCirc pan-cancer compendium, including normal and cancer samples from different types of tissues. For the functional evaluation, we compared their primary structure and domain composition with those derived from the same linear mRNAs. Among the 4362 circRNAs potentially encoding proteins with a unique primary structure and 1179 encoding proteins with a novel domain composition, 183 were differentially expressed in cancer. In particular, eight were associated with prognosis in acute myeloid leukemia. The functional classification of the dysregulated circRNA-encoded polypeptides showed an enrichment in the heme and cancer signaling, DNA-binding, and phosphorylation processes, and disclosed the roles of some circRNA-based effectors in cancer.
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Affiliation(s)
- Francesca Crudele
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Genetics Unit, Institute for Maternal and Child Health, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS) Burlo Garofolo, 34137 Trieste, Italy
| | - Nicoletta Bianchi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Anna Terrazzan
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratory for Advanced Therapy Technologies (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Pietro Ancona
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Antonio Frassoldati
- Department of Oncology, Azienda Ospedaliero-Universitaria St. Anna di Ferrara, 44124 Ferrara, Italy
| | - Paolo Gasparini
- Genetics Unit, Institute for Maternal and Child Health, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS) Burlo Garofolo, 34137 Trieste, Italy
| | - Adamo P D'Adamo
- Genetics Unit, Institute for Maternal and Child Health, Scientific Institute for Research, Hospitalization and Healthcare (IRCCS) Burlo Garofolo, 34137 Trieste, Italy
| | - Dimitrios Papaioannou
- Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, NYU Langone Health, New York, NY 10016, USA
| | - Ramiro Garzon
- Division of Hematology and Hematological Malignancies, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Paweł Gaj
- Warsaw Genomics INC, 01-682 Warszawa, Poland
| | - Krystian Jażdżewski
- Human Cancer Genetics, Biological and Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland
| | - Jeffrey Palatini
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Stefano Volinia
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratory for Advanced Therapy Technologies (LTTA), University of Ferrara, 44121 Ferrara, Italy
- CNBCh, Biological and Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland
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13
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Urdánoz-Casado A, Sánchez-Ruiz de Gordoa J, Robles M, Roldan M, Macías Conde M, Acha B, Blanco-Luquin I, Mendioroz M. circRNA from APP Gene Changes in Alzheimer's Disease Human Brain. Int J Mol Sci 2023; 24:ijms24054308. [PMID: 36901741 PMCID: PMC10002054 DOI: 10.3390/ijms24054308] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/09/2023] [Accepted: 02/18/2023] [Indexed: 02/24/2023] Open
Abstract
Alzheimer's disease (AD) is the most common cause of age-related dementia. Amyloid precursor protein (APP) is the precursor of Aβ peptides, and its role in AD has been widely investigated. Recently, it has been reported that a circular RNA (circRNA) originated from APP gene can serve as a template for Aβ synthesis, postulating it as an alternative pathway for the Aβ biogenesis. Moreover, circRNAs play important roles in brain development and in neurological diseases. Therefore, our aim was to study the expression of a circAPP (hsa_circ_0007556) and its linear cognate in AD human entorhinal cortex, a brain region most vulnerable to AD pathology. First, we confirmed the presence of circAPP (hsa_circ_0007556) in human entorhinal cortex samples using RT-PCR and Sanger sequencing of PCR products. Next, a 0.49-fold decrease in circAPP (hsa_circ_0007556) levels was observed in entorhinal cortex of AD cases compared to controls (p-value < 0.05) by qPCR. In contrast, APP mRNA expression did not show changes in the entorhinal cortex between AD cases and controls (Fold-change = 1.06; p-value = 0.81). A negative correlation was found between Aβ deposits and circAPP (hsa_circ_0007556) and APP expression levels (Rho Spearman = -0.56, p-value < 0.001 and Rho Spearman = -0.44, p-values < 0.001, respectively). Finally, by using bioinformatics tools, 17 miRNAs were predicted to bind circAPP (hsa_circ_0007556), and the functional analysis predicted that they were involved in some pathways, such as the Wnt-signaling pathway (p = 3.32 × 10-6). Long-term potentiation (p = 2.86 × 10-5), among others, is known to be altered in AD. To sum up, we show that circAPP (hsa_circ_0007556) is deregulated in the entorhinal cortex of AD patients. These results add to the notion that circAPP (hsa_circ_0007556) could be playing a role in the pathogenesis of AD disease.
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Affiliation(s)
- Amaya Urdánoz-Casado
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), Universidad Pública de Navarra (UPNA), Pamplona, 31008 Navarra, Spain
| | - Javier Sánchez-Ruiz de Gordoa
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), Universidad Pública de Navarra (UPNA), Pamplona, 31008 Navarra, Spain
- Department of Neurology, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), Pamplona, 31008 Navarra, Spain
| | - Maitane Robles
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), Universidad Pública de Navarra (UPNA), Pamplona, 31008 Navarra, Spain
| | - Miren Roldan
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), Universidad Pública de Navarra (UPNA), Pamplona, 31008 Navarra, Spain
| | - Mónica Macías Conde
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), Universidad Pública de Navarra (UPNA), Pamplona, 31008 Navarra, Spain
- Department of Neurology, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), Pamplona, 31008 Navarra, Spain
| | - Blanca Acha
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), Universidad Pública de Navarra (UPNA), Pamplona, 31008 Navarra, Spain
| | - Idoia Blanco-Luquin
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), Universidad Pública de Navarra (UPNA), Pamplona, 31008 Navarra, Spain
| | - Maite Mendioroz
- Neuroepigenetics Laboratory-Navarrabiomed, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), Universidad Pública de Navarra (UPNA), Pamplona, 31008 Navarra, Spain
- Department of Neurology, Complejo Hospitalario de Navarra-IdiSNA (Navarra Institute for Health Research), Pamplona, 31008 Navarra, Spain
- Correspondence: ; Tel.: +34-848422677
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14
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Yu X, Liu H, Chang N, Fu W, Guo Z, Wang Y. Circular RNAs: New players involved in the regulation of cognition and cognitive diseases. Front Neurosci 2023; 17:1097878. [PMID: 36816112 PMCID: PMC9932922 DOI: 10.3389/fnins.2023.1097878] [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: 11/14/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Circular RNAs (circRNAs), a type of covalently closed endogenous single-stranded RNA, have been regarded as the byproducts of the aberrant splicing of genes without any biological functions. Recently, with the development of high-throughput sequencing and bioinformatics, thousands of circRNAs and their differential biological functions have been identified. Except for the great advances in identifying circRNA roles in tumor progression, diagnosis, and treatment, accumulated evidence shows that circRNAs are enriched in the brain, especially in the synapse, and dynamically change with the development or aging of organisms. Because of the specific roles of synapses in higher-order cognitive functions, circRNAs may not only participate in cognitive functions in normal physiological conditions but also lead to cognition-related diseases after abnormal regulation of their expression or location. Thus, in this review, we summarized the progress of studies looking at the role of circRNA in cognitive function, as well as their involvement in the occurrence, development, prognosis, and treatment of cognitive-related diseases, including autism, depression, and Alzheimer's diseases.
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Affiliation(s)
- Xiaohan Yu
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Haoyu Liu
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Ning Chang
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Weijia Fu
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Zhiwen Guo
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yue Wang
- School of Clinical and Basic Medical Sciences, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China,*Correspondence: Yue Wang,
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15
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Circular RNAs: Non-Canonical Observations on Non-Canonical RNAs. Cells 2023; 12:cells12020323. [PMID: 36672257 PMCID: PMC9856604 DOI: 10.3390/cells12020323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
The existence of circular RNA (circRNA) research in mainstream science can be attributed to the contemporary synergism of big data and keen attention to detail by several research groups worldwide. Since the re-emergence of these non-canonical RNA transcripts, seminal advances have been made in understanding their biogenesis, interactome, and functions in diverse fields and a myriad of human diseases. However, most research outputs to date have focused on the ability of highly stable circRNAs to interact with, and impact signalling through, microRNAs. This is likely to be the result of seminal papers in the field ascribing a few remarkable circRNAs as "miRNA sponges". However, the stoichiometric ratio between the (often-lowly-expressed) circRNA and their (commonly-more-abundant) target is rarely in favour of a biologically relevant and functional consequence of these interactions. It is time for yet another revolution in circRNA research to uncover functions beyond their documented ability to bind miRNAs. This Special Issue aims to highlight non-canonical functions for this non-canonical family of RNA molecules.
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16
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Ruan H, Wang PC, Han L. Characterization of circular RNAs with advanced sequencing technologies in human complex diseases. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1759. [PMID: 36164985 DOI: 10.1002/wrna.1759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/09/2022] [Accepted: 08/02/2022] [Indexed: 01/31/2023]
Abstract
Circular RNAs (circRNAs) are one category of non-coding RNAs that do not possess 5' caps and 3' free ends. Instead, they are derived in closed circle forms from pre-mRNAs by a non-canonical splicing mechanism named "back-splicing." CircRNAs were discovered four decades ago, initially called "scrambled exons." Compared to linear RNAs, the expression levels of circRNAs are considerably lower, and it is challenging to identify circRNAs specifically. Thus, the biological relevance of circRNAs has been underappreciated until the advancement of next generation sequencing (NGS) technology. The biological insights of circRNAs, such as their tissue-specific expression patterns, biogenesis factors, and functional effects in complex diseases, namely human cancers, have been extensively explored in the last decade. With the invention of the third generation sequencing (TGS) with longer sequencing reads and newly designed strategies to characterize full-length circRNAs, the panorama of circRNAs in human complex diseases could be further unveiled. In this review, we first introduce the history of circular RNA detection. Next, we describe widely adopted NGS-based methods and the recently established TGS-based approaches capable of characterizing circRNAs in full-length. We then summarize data resources and representative circRNA functional studies related to human complex diseases. In the last section, we reviewed computational tools and discuss the potential advantages of utilizing advanced sequencing approaches to a functional interpretation of full-length circRNAs in complex diseases. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Hang Ruan
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Peng-Cheng Wang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Leng Han
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas, USA.,Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, Texas, USA
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17
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Wu DP, Zhao YD, Yan QQ, Liu LL, Wei YS, Huang JL. Circular RNAs: emerging players in brain aging and neurodegenerative diseases. J Pathol 2023; 259:1-9. [PMID: 36264226 DOI: 10.1002/path.6021] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 10/06/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
Abstract
Brain aging is closely related to neurodegenerative diseases. Circular RNAs (circRNAs) are a type of conserved RNAs with covalently closed continuous loops. Emerging evidence has shown that circRNAs are implicated in the biology of brain aging and the pathology of age-related neurodegenerative diseases. Here, we summarize current studies on circRNAs associated with brain aging and neurodegenerative diseases by discussing their expression features, pathophysiological roles, and mechanisms of action. We also discuss the potential challenges of circRNA-based therapy against brain aging and neurodegenerative diseases, as well as their potential as diagnostic biomarkers of neurodegenerative diseases. The review provides insights into current progress in the functions of circRNAs in the process of brain aging and neurodegenerative diseases. © 2022 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Deng-Pan Wu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Pharmacy School, Xuzhou Medical University, Xuzhou, Jiangsu, PR China.,Department of Pharmacology, Xuzhou Medical University, Xuzhou, Jiangsu, PR China
| | - Yuan-Dan Zhao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Pharmacy School, Xuzhou Medical University, Xuzhou, Jiangsu, PR China
| | - Qiu-Qing Yan
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Pharmacy School, Xuzhou Medical University, Xuzhou, Jiangsu, PR China
| | - Ling-Ling Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Pharmacy School, Xuzhou Medical University, Xuzhou, Jiangsu, PR China
| | - Yan-Su Wei
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Pharmacy School, Xuzhou Medical University, Xuzhou, Jiangsu, PR China
| | - Jin-Lan Huang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Pharmacy School, Xuzhou Medical University, Xuzhou, Jiangsu, PR China.,Department of Pharmacology, Xuzhou Medical University, Xuzhou, Jiangsu, PR China
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18
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Zhou M, Gao X, Zheng X, Luo J. Functions and clinical significance of circular RNAs in acute myeloid leukemia. Front Pharmacol 2022; 13:1010579. [PMID: 36506538 PMCID: PMC9729264 DOI: 10.3389/fphar.2022.1010579] [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: 08/03/2022] [Accepted: 11/08/2022] [Indexed: 11/25/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of covalently closed single-stranded RNA molecules. Four types of circRNAs have been reported in animal cells, and they have typical characteristics in their biogenesis, nuclear export and degradation. Advances in our understanding of the molecular functions of circRNAs in sponging microRNAs, modulating transcription, regulating RNA-binding proteins, as well as encoding proteins have been made very recently. Dysregulated circRNAs are associated with human diseases such as acute myeloid leukemia (AML). In this review, we focus on the recently described mechanisms, role and clinical significance of circRNAs in AML. Although great progress of circRNAs in AML has been achieved, substantial efforts are still required to explore whether circRNAs exert their biological function by other mechanisms such as regulation of gene transcription or serving as translation template in AML. It is also urgent that researchers study the machineries regulating circRNAs fate, the downstream effectors of circRNAs modulatory networks, and the clinical application of circRNAs in AML.
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Affiliation(s)
- Min Zhou
- School of Life Sciences, Chongqing University, Chongqing, China,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China,*Correspondence: Min Zhou, ; Jing Luo,
| | - Xianling Gao
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xin Zheng
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Luo
- Department of Anesthesiology, The First People’s Hospital of Yunnan Province, Kunming, China,Department of Anesthesiology, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China,*Correspondence: Min Zhou, ; Jing Luo,
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19
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Wang J, Zhang H, Wang C, Fu L, Wang Q, Li S, Cong B. Forensic age estimation from human blood using age-related microRNAs and circular RNAs markers. Front Genet 2022; 13:1031806. [PMID: 36506317 PMCID: PMC9732945 DOI: 10.3389/fgene.2022.1031806] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
Aging is a complicated process characterized by progressive and extensive changes in physiological homeostasis at the organismal, tissue, and cellular levels. In modern society, age estimation is essential in a large variety of legal rights and duties. Accumulating evidence suggests roles for microRNAs (miRNAs) and circular RNAs (circRNAs) in regulating numerous processes during aging. Here, we performed circRNA sequencing in two age groups and analyzed microarray data of 171 healthy subjects (17-104 years old) downloaded from Gene Expression Omnibus (GEO) and ArrayExpress databases with integrated bioinformatics methods. A total of 1,403 circular RNAs were differentially expressed between young and old groups, and 141 circular RNAs were expressed exclusively in elderly samples while 10 circular RNAs were expressed only in young subjects. Based on their expression pattern in these two groups, the circular RNAs were categorized into three classes: age-related expression between young and old, age-limited expression-young only, and age-limited expression-old only. Top five expressed circular RNAs among three classes and a total of 18 differentially expressed microRNAs screened from online databases were selected to validate using RT-qPCR tests. An independent set of 200 blood samples (20-80 years old) was used to develop age prediction models based on 15 age-related noncoding RNAs (11 microRNAs and 4 circular RNAs). Different machine learning algorithms for age prediction were applied, including regression tree, bagging, support vector regression (SVR), random forest regression (RFR), and XGBoost. Among them, random forest regression model performed best in both training set (mean absolute error = 3.68 years, r = 0.96) and testing set (MAE = 6.840 years, r = 0.77). Models using one single type of predictors, circular RNAs-only or microRNAs-only, result in bigger errors. Smaller prediction errors were shown in males than females when constructing models according to different-sex separately. Putative microRNA targets (430 genes) were enriched in the cellular senescence pathway and cell homeostasis and cell differentiation regulation, indirectly indicating that the microRNAs screened in our study were correlated with development and aging. This study demonstrates that the noncoding RNA aging clock has potential in predicting chronological age and will be an available biological marker in routine forensic investigation to predict the age of biological samples.
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Affiliation(s)
- Junyan Wang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang, Hebei, China
| | - Haixia Zhang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang, Hebei, China
| | - Chunyan Wang
- Physical Examination Center of Shijiazhuang First Hospital, Shijiazhuang, Hebei, China
| | - Lihong Fu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang, Hebei, China
| | - Qian Wang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang, Hebei, China
| | - Shujin Li
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang, Hebei, China,*Correspondence: Bin Cong, ; Shujin Li,
| | - Bin Cong
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang, Hebei, China,*Correspondence: Bin Cong, ; Shujin Li,
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20
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2020 Editor’s Choice Articles in the “Cell Nuclei: Function, Transport and Receptors” Section. Cells 2022; 11:cells11172625. [PMID: 36078033 PMCID: PMC9454793 DOI: 10.3390/cells11172625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 11/16/2022] Open
Abstract
In 2020, a total of 106 original research articles, 84 reviews, and 1 other paper were published within the “Cell Nuclei: Function, Transport and Receptors” section [...]
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21
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Circular RNA circPOSTN promotes neovascularization by regulating miR-219a-2-3p/STC1 axis and stimulating the secretion of VEGFA in glioblastoma. Cell Death Dis 2022; 8:349. [PMID: 35927233 PMCID: PMC9352789 DOI: 10.1038/s41420-022-01136-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 11/09/2022]
Abstract
Glioblastoma (GBM), the most malignant type of astrocytic tumor, is one of the deadliest cancers prevalent in adults. Along with tumor growth, patients with GBM generally suffer from extensive cerebral edema and apparent symptoms of intracranial hyper-pressure. Accumulating evidence has demonstrated that circRNA plays a critically important role in tumorigenesis and progression. However, the biological function and the underlying mechanism of circRNA in GBM remain elusive. In this study, by conducting gene expression detection based on 15 pairs of GBM clinical specimens and the normal adjunct tissues, we observed that circPOSTN showed abnormally higher expression in GBM. Both loss-of-function and gain-of-function biological experiments demonstrated that circPOSTN scheduled the proliferation, migration, and neovascularization abilities of GBM cells. Further, fluorescence in situ hybridization (FISH) assay, quantitative RT-PCR, and subcellular separation suggested that circPOSTN was predominately localized in the cytoplasm and may serve as a competing endogenous RNA (ceRNA). CircRNA-miRNA interaction prediction based on online analytical processing, AGO2-RIP assay, biotin labeled RNA pulldown assay, and dual-luciferase reporter assay revealed that circPOSTN sponged miR-219a-2-3p, limited its biological function, and ultimately upregulated their common downstream gene STC1. Finally, by carrying out in vitro and in vivo functional assays, we uncovered a new regulatory axis circPOSTN/miR-219a-2-3p/STC1 that promoted GBM neovascularization by increasing vascular endothelial growth factor A (VEGFA) secretion. Our study underscores the critical role of circPOSTN in GBM progression, providing a novel insight into GBM anti-tumor therapy.
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Profile of TREM2-Derived circRNA and mRNA Variants in the Entorhinal Cortex of Alzheimer’s Disease Patients. Int J Mol Sci 2022; 23:ijms23147682. [PMID: 35887031 PMCID: PMC9320643 DOI: 10.3390/ijms23147682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 02/04/2023] Open
Abstract
Genetic variants in TREM2, a microglia-related gene, are well-known risk factors for Alzheimer’s disease (AD). Here, we report that TREM2 originates from circular RNAs (circRNAs), a novel class of non-coding RNAs characterized by a covalent and stable closed-loop structure. First, divergent primers were designed to amplify circRNAs by RT-PCR, which were further assessed by Sanger sequencing. Then, additional primer sets were used to confirm back-splicing junctions. In addition, HMC3 cells were used to assess the microglial expression of circTREM2s. Three candidate circTREM2s were identified in control and AD human entorhinal samples. One of the circRNAs, circTREM2_1, was consistently amplified by all divergent primer sets in control and AD entorhinal cortex samples as well as in HMC3 cells. In AD cases, a moderate negative correlation (r = −0.434) was found between the global average area of Aβ deposits in the entorhinal cortex and circTREM2_1 expression level. In addition, by bioinformatics tools, a total of 16 miRNAs were predicted to join with circTREM2s. Finally, TREM2 mRNA corresponding to four isoforms was profiled by RT-qPCR. TREM2 mRNA levels were found elevated in entorhinal samples of AD patients with low or intermediate ABC scores compared to controls. To sum up, a novel circRNA derived from the TREM2 gene, circTREM2_1, has been identified in the human entorhinal cortex and TREM2 mRNA expression has been detected to increase in AD compared to controls. Unraveling the molecular genetics of the TREM2 gene may help to better know the innate immune response in AD.
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Yan H, Yan Y, Gao Y, Zhang N, Kumar G, Fang Q, Li Z, Li J, Zhang Y, Song L, Wang J, Sun J, Zhang HT, Ma CG. Transcriptome analysis of fasudil treatment in the APPswe/PSEN1dE9 transgenic (APP/PS1) mice model of Alzheimer's disease. Sci Rep 2022; 12:6625. [PMID: 35459923 PMCID: PMC9033779 DOI: 10.1038/s41598-022-10554-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/30/2022] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is the most common cause of progressive dementia. In the present study, we showed hippocampal tissue transcriptome analysis in APPswe/PSEN1dE9 (APP/PS1, AD model) mice treated with fasudil (ADF) and compared with AD mice treated with saline (ADNS) and wild type mice (WT). The competing endogenous RNA (ceRNA) network was constructed and validated the differential expression of mRNA, lncRNA, miRNA, and circRNA. Our study showed differentially expressed mRNAs (DEMs) between WT and ADNS, while enriched in cell growth and death and nervous system pathways. DEMs between ADNS-ADF were enriched in the nervous system, glycosaminoglycan biosynthesis-keratan sulfate (KS) and Quorum sensing pathways. We validated four genes with RT-PCR, whereas enrichment of Acyl-CoA Synthetase Long Chain Family Member 4 (Acsl4, ENSMUST00000112903) in Quorum sensing pathways, and BTG anti-proliferation factor 1 (Btg1, ENSMUST00000038377) in RNA degradation pathways were conducted. Expression of these two genes were higher in ADNS, but were significantly reduced in ADF. Histone H4 transcription factor (Hinfp, ENSMUST00000216508) orchestrate G1/S transition of mitotic cell cycle and co-expressed with mmu-miR-26a-2-3p-mediated ceRNA and mmu-miR-3065-5p-mediated ceRNA; Wnt family member 4 (Wnt4, ENSMUST00000045747) was enriched in mTOR, Hippo and Wnt signaling pathway. Expression of these two genes were significantly lower in ADNS, and fasudil treatment reverse it. The present studies demonstrated four genes: Acsl4, Btg1, Hinfp, Wnt4 could be potential biomarkers of AD and the targets of fasudil treatment. These results will pave a novel direction for future clinic studies for AD and fasudil treatment.
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Affiliation(s)
- Hailong Yan
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Yuqing Yan
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China. .,The Key Research Laboratory of Benefiting Qi for Acting Blood Circulation, Research Center of Neurobiology, Shanxi University of Chinese Medicine, Jinzhong, 030619, China.
| | - Ye Gao
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Nianping Zhang
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Gajendra Kumar
- Department of Neuroscience, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong
| | - Qingli Fang
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Ziqing Li
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Jiehui Li
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Yuna Zhang
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Lijuan Song
- The Key Research Laboratory of Benefiting Qi for Acting Blood Circulation, Research Center of Neurobiology, Shanxi University of Chinese Medicine, Jinzhong, 030619, China
| | - Jiawei Wang
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Jingxian Sun
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Han-Ting Zhang
- Department of Pharmacology, Qingdao University School of Pharmacy, Qingdao, 266073, China.
| | - Cun-Gen Ma
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China. .,The Key Research Laboratory of Benefiting Qi for Acting Blood Circulation, Research Center of Neurobiology, Shanxi University of Chinese Medicine, Jinzhong, 030619, China.
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24
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D’Anca M, Buccellato FR, Fenoglio C, Galimberti D. Circular RNAs: Emblematic Players of Neurogenesis and Neurodegeneration. Int J Mol Sci 2022; 23:ijms23084134. [PMID: 35456950 PMCID: PMC9032451 DOI: 10.3390/ijms23084134] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/06/2022] [Indexed: 12/13/2022] Open
Abstract
In the fascinating landscape of non-coding RNAs (ncRNAs), circular RNAs (circRNAs) are peeping out as a new promising and appreciated class of molecules with great potential as diagnostic and prognostic biomarkers. They come from circularization of single-stranded RNA molecules covalently closed and generated through alternative mRNA splicing. Dismissed for many years, similar to aberrant splicing by-products, nowadays, their role has been regained. They are able to regulate the expression of linear mRNA transcripts at different levels acting as miRNA sponges, interacting with ribonucleoproteins or exerting a control on gene expression. On the other hand, being extremely conserved across phyla and stable, cell and tissue specific, mostly abundant than the linear RNAs, it is not surprising that they should have critical biological functions. Curiously, circRNAs are particularly expressed in brain and they build up during aging and age-related diseases. These extraordinary peculiarities make circRNAs potentially suitable as promising molecular biomarkers, especially of aging and neurodegenerative diseases. This review aims to explore new evidence on circRNAs, emphasizing their role in aging and pathogenesis of major neurodegenerative disorders, Alzheimer's disease, frontotemporal dementia, and Parkinson's diseases with a look toward their potential usefulness in biomarker searching.
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Affiliation(s)
- Marianna D’Anca
- Foundation IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy; (F.R.B.); or (C.F.); or (D.G.)
- Correspondence:
| | - Francesca R. Buccellato
- Foundation IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy; (F.R.B.); or (C.F.); or (D.G.)
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy
| | - Chiara Fenoglio
- Foundation IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy; (F.R.B.); or (C.F.); or (D.G.)
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Daniela Galimberti
- Foundation IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy; (F.R.B.); or (C.F.); or (D.G.)
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy
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25
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Wen SY, Qadir J, Yang BB. Circular RNA translation: novel protein isoforms and clinical significance. Trends Mol Med 2022; 28:405-420. [DOI: 10.1016/j.molmed.2022.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 02/07/2023]
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26
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Chen X, Zhou M, Yant L, Huang C. Circular RNA in disease: Basic properties and biomedical relevance. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1723. [PMID: 35194939 DOI: 10.1002/wrna.1723] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/15/2021] [Accepted: 01/31/2022] [Indexed: 12/26/2022]
Abstract
Circular RNAs (circRNAs) represent a class of covalently closed RNA molecules with great diversity in molecular features, functions, and regulatory mechanisms. Emerging advances in our understanding of circRNA biogenesis, nuclear export, and stability control have been made very recently. In particular, novel roles of circRNAs in diverse human diseases are increasingly recognized. Various circRNAs have been found to affect many disease-relevant pathways through a diverse array of mechanisms, including forming R-loops, sponging miRNAs or proteins, and translating functional proteins, resulting in different pathological phenotypes. This recent progress calls for a revised view of circRNAs in diseases threatening the lives and health of humans. In this review, we focus on the recently described functional relevance of disease-associated circRNAs as well as the potential of circRNAs in diverse clinical applications. This article is categorized under: RNA in Disease and Development > RNA in Disease Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Xiaolan Chen
- School of Life Sciences, Chongqing University, Chongqing, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Min Zhou
- School of Life Sciences, Chongqing University, Chongqing, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Levi Yant
- Future Food Beacon of Excellence and School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
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27
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Wang Y, Wu C, Du Y, Li Z, Li M, Hou P, Shen Z, Chu S, Zheng J, Bai J. Expanding uncapped translation and emerging function of circular RNA in carcinomas and noncarcinomas. Mol Cancer 2022; 21:13. [PMID: 34996480 PMCID: PMC8740365 DOI: 10.1186/s12943-021-01484-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/16/2021] [Indexed: 02/07/2023] Open
Abstract
Circular RNAs (circRNAs) are classified as noncoding RNAs because they are devoid of a 5' end cap and a 3' end poly (A) tail necessary for cap-dependent translation. However, increasing numbers of translated circRNAs identified through high-throughput RNA sequencing overlapping with polysome profiling indicate that this rule is being broken. CircRNAs can be translated in cap-independent mechanism, including IRES (internal ribosome entry site)-initiated pattern, MIRES (m6A internal ribosome entry site) -initiated patterns, and rolling translation mechanism (RCA). CircRNA-encoded proteins harbour diverse functions similar to or different from host proteins. In addition, they are linked to the modulation of human disease including carcinomas and noncarcinomas. CircRNA-related translatomics and proteomics have attracted increasing attention. This review discusses the progress and exclusive characteristics of circRNA translation and highlights the latest mechanisms and regulation of circRNA translatomics. Furthermore, we summarize the extensive functions and mechanisms of circRNA-derived proteins in human diseases, which contribute to a better understanding of intricate noncanonical circRNA translatomics and proteomics and their therapeutic potential in human diseases.
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Affiliation(s)
- Yan Wang
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
- Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of Pharmacy, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Chunjie Wu
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
- Department of Pharmacy, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yu Du
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
- Department of Pharmacy, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zhongwei Li
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
| | - Minle Li
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
| | - Pingfu Hou
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
| | - Zhigang Shen
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
| | - Sufang Chu
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China
| | - Junnian Zheng
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.
- Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.
| | - Jin Bai
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.
- Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.
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28
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The neurobiology of non-coding RNAs and Alzheimer's disease pathogenesis: Pathways, mechanisms and translational opportunities. Ageing Res Rev 2021; 71:101425. [PMID: 34384901 DOI: 10.1016/j.arr.2021.101425] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022]
Abstract
In the past two decades, advances in sequencing technology and analysis of the human and mouse genome have led to the discovery of many non-protein-coding RNAs (ncRNAs) including: microRNA, small-interfering RNAs, piwi-associated small RNAs, transfer RNA-derived small RNAs, long-non-coding RNAs and circular RNAs. Compared with healthy controls, levels of some ncRNAs are significantly altered in the central nervous system and blood of patients affected by neurodegenerative disorders like Alzheimer's disease (AD). Although the mechanisms are still not fully elucidated, studies have revealed that these highly conserved ncRNAs are important modulators of gene expression, amyloid-β production, tau phosphorylation, inflammation, synaptic plasticity and neuronal survival, all features considered central to AD pathogenesis. Despite considerable difficulties due to their large heterogeneity, and the complexity of their regulatory pathways, research in this rapidly growing field suggests that ncRNAs hold great potential as biomarkers and therapeutic targets against AD. Herein, we summarize the current knowledge regarding the neurobiology of ncRNA in the context of AD pathophysiology.
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Cacabelos R, Carrera I, Martínez-Iglesias O, Cacabelos N, Naidoo V. What is the gold standard model for Alzheimer's disease drug discovery and development? Expert Opin Drug Discov 2021; 16:1415-1440. [PMID: 34330186 DOI: 10.1080/17460441.2021.1960502] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Introduction: Alzheimer's disease models (ADMs) are currently used for drug development (DD). More than 20,000 molecules were screened for AD treatment over decades, with only one drug (Aducanumab)FDA-approved over the past 18 years. A revision of pathogenic concepts and ADMs are needed.Areas covered: The authors discuss herein preclinical models including: (i) in vitro models (cell lines, primary neuron cell cultures, iPSC-derived brain cells), (ii) ex vivo models, and (iii) in vivo models (artificial, transgenic, non-transgenic and induced).Expert opinion: The following types of ADMs have been reported: Mouse models (45.08%), Rat models (15.04%), Non-human Primate models (0.76%), Rabbit models (0.46%), Cat models (0.53%), Pig models (0.30%), Guinea pig models (0.15%), Octodon degu models (0.02%), Dog models (0.54%), Drosophila melanogaster models (1.79%), Zebrafish models (0.50%), Caenorhabditis elegans (1.21%), Cell culture models (3.31%), Cholinergic models (8.26%), Neurotoxic models (6.79%), Neuroinflammation models (6.92%), Neurovascular models (7.88%), and Microbiome models (0.45%).No single ADM faithfully reproduces all the pathogenic events in the human AD phenotype spectrum. ADMs should be different for (i) pathogenic studies vs basic DD, and (ii) preventive interventions vs symptomatic treatments. There cannot be an ideal ADM for DD, because AD is a spectrum of syndromes. DD can integrate pathogenic, mechanistic, metabolic, transporter and pleiotropic genes in a multisystem model.
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Affiliation(s)
- Ramón Cacabelos
- Departments of Genomic Medicine, International Center of Neuroscience and Genomic Medicine, EuroEspes Biomedical Research Center, Bergondo, Spain
| | - Iván Carrera
- Health Biotechnology, International Center of Neuroscience and Genomic Medicine, EuroEspes Biomedical Research Center, Bergondo, Spain
| | - Olaia Martínez-Iglesias
- Medical Epigenetics, International Center of Neuroscience and Genomic Medicine, EuroEspes Biomedical Research Center, Bergondo, Spain
| | - Natalia Cacabelos
- Medical Documentation, International Center of Neuroscience and Genomic Medicine, EuroEspes Biomedical Research Center, Bergondo, Spain
| | - Vinogran Naidoo
- Basic Neuroscience, International Center of Neuroscience and Genomic Medicine, EuroEspes Biomedical Research Center, Bergondo, Spain
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30
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Rybak-Wolf A, Plass M. RNA Dynamics in Alzheimer's Disease. Molecules 2021; 26:5113. [PMID: 34500547 PMCID: PMC8433936 DOI: 10.3390/molecules26175113] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 02/06/2023] Open
Abstract
Alzheimer's disease (AD) is the most common age-related neurodegenerative disorder that heavily burdens healthcare systems worldwide. There is a significant requirement to understand the still unknown molecular mechanisms underlying AD. Current evidence shows that two of the major features of AD are transcriptome dysregulation and altered function of RNA binding proteins (RBPs), both of which lead to changes in the expression of different RNA species, including microRNAs (miRNAs), circular RNAs (circRNAs), long non-coding RNAs (lncRNAs), and messenger RNAs (mRNAs). In this review, we will conduct a comprehensive overview of how RNA dynamics are altered in AD and how this leads to the differential expression of both short and long RNA species. We will describe how RBP expression and function are altered in AD and how this impacts the expression of different RNA species. Furthermore, we will also show how changes in the abundance of specific RNA species are linked to the pathology of AD.
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Affiliation(s)
- Agnieszka Rybak-Wolf
- Max Delbrück Center for Molecular Medicine (MDC), Berlin Institute for Medical Systems Biology (BIMSB), 10115 Berlin, Germany
| | - Mireya Plass
- Gene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, 08908 Barcelona, Spain
- Program for Advancing Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L'Hospitalet del Llobregat, 08908 Barcelona, Spain
- Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
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31
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Zhang M, Bian Z. The Emerging Role of Circular RNAs in Alzheimer's Disease and Parkinson's Disease. Front Aging Neurosci 2021; 13:691512. [PMID: 34322012 PMCID: PMC8311738 DOI: 10.3389/fnagi.2021.691512] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/22/2021] [Indexed: 12/27/2022] Open
Abstract
Alzheimer’s disease (AD) and Parkinson’s disease (PD) are two neurodegenerative diseases (NDDs) commonly found in elderly patients that are difficult to diagnose and lack effective treatment. Currently, the available diagnostic methods for these two NDDs do not meet clinical diagnostic expectations. Circular RNAs (circRNAs) are a diverse group of endogenous non-coding RNAs (ncRNAs) found in eukaryotic cells. Emerging studies suggest that altered expression of circRNAs is involved in the pathological processes of NDDs. CircRNAs could also prove to be promising biomarkers for the early diagnosis of NDDs such as AD and PD. Growing evidence has improved our knowledge of the roles of circRNAs in NDDs, which may lead to new therapeutic approaches that target transcription for preventing neurodegeneration. In this review, we describe the formation mechanisms and functions of circRNAs as well as methods of validation. We also discuss the emerging role of circRNAs in the pathophysiology of AD and PD and their potential value as biomarkers and therapeutic targets for AD and PD in the future.
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Affiliation(s)
- Meng Zhang
- Department of Gerontology and Geriatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhigang Bian
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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32
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He AT, Liu J, Li F, Yang BB. Targeting circular RNAs as a therapeutic approach: current strategies and challenges. Signal Transduct Target Ther 2021; 6:185. [PMID: 34016945 PMCID: PMC8137869 DOI: 10.1038/s41392-021-00569-5] [Citation(s) in RCA: 253] [Impact Index Per Article: 84.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/28/2021] [Accepted: 03/16/2021] [Indexed: 02/04/2023] Open
Abstract
Significant progress has been made in circular RNA (circRNA) research in recent years. Increasing evidence suggests that circRNAs play important roles in many cellular processes, and their dysregulation is implicated in the pathogenesis of various diseases. CircRNAs are highly stable and usually expressed in a tissue- or cell type-specific manner. Therefore, they are currently being explored as potential therapeutic targets. Gain-of-function and loss-of-function approaches are typically performed using circRNA expression plasmids and RNA interference-based strategies, respectively. These strategies have limitations that can be mitigated using nanoparticle and exosome delivery systems. Furthermore, recent developments show that the cre-lox system can be used to knockdown circRNAs in a cell-specific manner. While still in the early stages of development, the CRISPR/Cas13 system has shown promise in knocking down circRNAs with high specificity and efficiency. In this review, we describe circRNA properties and functions and highlight their significance in disease. We summarize strategies that can be used to overexpress or knockdown circRNAs as a therapeutic approach. Lastly, we discuss major challenges and propose future directions for the development of circRNA-based therapeutics.
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Affiliation(s)
- Alina T. He
- grid.17063.330000 0001 2157 2938Sunnybrook Research Institute, Toronto, ON Canada
| | - Jinglei Liu
- Department of Bioinformatics, ATCGene Inc, Guangzhou, China
| | - Feiya Li
- grid.17063.330000 0001 2157 2938Sunnybrook Research Institute, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
| | - Burton B. Yang
- grid.17063.330000 0001 2157 2938Sunnybrook Research Institute, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
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33
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Li H, Xie M, Wang Y, Yang L, Xie Z, Wang H. riboCIRC: a comprehensive database of translatable circRNAs. Genome Biol 2021; 22:79. [PMID: 33685493 PMCID: PMC7938571 DOI: 10.1186/s13059-021-02300-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/18/2021] [Indexed: 01/05/2023] Open
Abstract
riboCIRC is a translatome data-oriented circRNA database specifically designed for hosting, exploring, analyzing, and visualizing translatable circRNAs from multi-species. The database provides a comprehensive repository of computationally predicted ribosome-associated circRNAs; a manually curated collection of experimentally verified translated circRNAs; an evaluation of cross-species conservation of translatable circRNAs; a systematic de novo annotation of putative circRNA-encoded peptides, including sequence, structure, and function; and a genome browser to visualize the context-specific occupant footprints of circRNAs. It represents a valuable resource for the circRNA research community and is publicly available at http://www.ribocirc.com .
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Affiliation(s)
- Huihui Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Mingzhe Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yan Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Ludong Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.
| | - Hongwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.
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