1
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Jaijyan DK, Yang S, Ramasamy S, Gu A, Zeng M, Subbian S, Tyagi S, Zhu H. Imaging and quantification of human and viral circular RNAs. Nucleic Acids Res 2024; 52:e70. [PMID: 39051561 PMCID: PMC11347131 DOI: 10.1093/nar/gkae583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 06/10/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024] Open
Abstract
We present a robust approach for cellular detection, imaging, localization, and quantification of human and viral encoded circular RNAs (circRNA) using amplified fluorescence in situ hybridization (ampFISH). In this procedure, a pair of hairpin probes bind next to each other at contiguous stretches of sequence and then undergo a conformational reorganization which initiates a target-dependent hybridization chain reaction (HCR) resulting in deposition of an amplified fluorescent signal at the site. By harnessing the capabilities of both ampFISH and single-molecule FISH (smFISH), we selectively identified and imaged circular RNAs and their linear counterparts derived from the human genome, SARS-CoV-2 (an RNA virus), and human cytomegalovirus (HCMV, a DNA virus). Computational image processing facilitated accurate quantification of circular RNA molecules in individual cells. The specificity of ampFISH for circular RNA detection was confirmed through an in situ RNase R treatment that selectively degrades linear RNAs without impacting circular RNAs. The effectiveness of circular RNA detection was further validated by using ampFISH probes with mismatches and probe pairs that do not bind to the continuous sequence in their target RNAs but instead bind at segregated sites. An additional specificity test involved probes against the negative strands of the circular RNA sequence, absent in the cell. Importantly, our technique allows simultaneous detection of circular RNAs and their linear counterparts within the same cell with single molecule sensitivity, enabling explorations of circular RNA biogenesis, subcellular localization, and functions.
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Affiliation(s)
- Dabbu Kumar Jaijyan
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, VA, USA
| | - Shaomin Yang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, China
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Shenzhen Nanshan People's Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Santhamani Ramasamy
- Public Health Research Institute, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark. NJ 07103, USA
| | - Alison Gu
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Mulan Zeng
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Selvakumar Subbian
- Public Health Research Institute, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark. NJ 07103, USA
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark. NJ 07103, USA
- Department of Medicine, New Jersey Medical School, Rutgers University, USA
| | - Hua Zhu
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
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2
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Yang S, Cao D, Jaijyan DK, Wang M, Liu J, Cruz-Cosme R, Wu S, Huang J, Zeng M, Liu X, Sun W, Xiong D, Tang Q, Xiao L, Zhu H. Identification and characterization of Varicella Zoster Virus circular RNA in lytic infection. Nat Commun 2024; 15:4932. [PMID: 38858365 PMCID: PMC11164961 DOI: 10.1038/s41467-024-49112-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 05/17/2024] [Indexed: 06/12/2024] Open
Abstract
This study investigates the role of circular RNAs (circRNAs) in the context of Varicella-Zoster Virus (VZV) lytic infection. We employ two sequencing technologies, short-read sequencing and long-read sequencing, following RNase R treatment on VZV-infected neuroblastoma cells to identify and characterize both cellular and viral circRNAs. Our large scanning analysis identifies and subsequent experiments confirm 200 VZV circRNAs. Moreover, we discover numerous VZV latency-associated transcripts (VLTs)-like circRNAs (circVLTslytic), which contain multiple exons and different isoforms within the same back-splicing breakpoint. To understand the functional significance of these circVLTslytic, we utilize the Bacteria Artificial Chromosome system to disrupt the expression of viral circRNAs in genomic DNA location. We reveal that the sequence flanking circVLTs' 5' splice donor plays a pivotal role as a cis-acting element in the formation of circVLTslytic. The circVLTslytic is dispensable for VZV replication, but the mutation downstream of circVLTslytic exon 5 leads to increased acyclovir sensitivity in VZV infection models. This suggests that circVLTslytic may have a role in modulating the sensitivity to antiviral treatment. The findings shed new insight into the regulation of cellular and viral transcription during VZV lytic infection, emphasizing the intricate interplay between circRNAs and viral processes.
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Affiliation(s)
- Shaomin Yang
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, 518060, China
| | - Di Cao
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Dabbu Kumar Jaijyan
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ, 070101, USA
| | - Mei Wang
- Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Jian Liu
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, 363000, China
| | - Ruth Cruz-Cosme
- Department of Microbiology, Howard University College of Medicine, 520 W Street NW, Washington, DC, 20059, USA
| | - Songbin Wu
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Jiabin Huang
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Mulan Zeng
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ, 070101, USA
| | - Xiaolian Liu
- Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Wuping Sun
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Donglin Xiong
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, 520 W Street NW, Washington, DC, 20059, USA.
| | - Lizu Xiao
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China.
| | - Hua Zhu
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ, 070101, USA.
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3
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Bhat AA, Gupta G, Goyal A, Thapa R, Almalki WH, Kazmi I, Alzarea SI, Kukreti N, Sekar M, Meenakshi DU, Singh SK, MacLoughlin R, Dua K. Unwinding circular RNA's role in inflammatory pulmonary diseases. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:2567-2588. [PMID: 37917370 DOI: 10.1007/s00210-023-02809-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/20/2023] [Indexed: 11/04/2023]
Abstract
Circular RNAs (circRNAs) have emerged as pivotal regulators of gene expression and cellular processes in various physiological and pathological conditions. In recent years, there has been a growing interest in investigating the role of circRNAs in inflammatory lung diseases, owing to their potential to modulate inflammation-associated pathways and contribute to disease pathogenesis. Inflammatory lung diseases, like asthma, chronic obstructive pulmonary disease (COPD), and COVID-19, pose significant global health challenges. The dysregulation of inflammatory responses demonstrates a pivotal function in advancing these diseases. CircRNAs have been identified as important players in regulating inflammation by functioning as miRNA sponges, engaging with RNA-binding proteins, and participating in intricate ceRNA networks. These interactions enable circRNAs to regulate the manifestation of key inflammatory genes and signaling pathways. Furthermore, emerging evidence suggests that specific circRNAs are differentially expressed in response to inflammatory stimuli and exhibit distinct patterns in various lung diseases. Their involvement in immune cell activation, cytokine production, and tissue remodeling processes underscores their possible capabilities as therapeutic targets and diagnostic biomarkers. Harnessing the knowledge of circRNA-mediated regulation in inflammatory lung diseases could lead to the development of innovative strategies for disease management and intervention. This review summarizes the current understanding of the role of circRNAs in inflammatory lung diseases, focusing on their regulatory mechanisms and functional implications.
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Affiliation(s)
- Asif Ahmad Bhat
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India
| | - Gaurav Gupta
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, 602105, India.
| | - Ahsas Goyal
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, 281406, India
| | - Riya Thapa
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura 302017, Mahal Road, Jaipur, India
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka 72388, Al-Jouf, Saudi Arabia
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun, 248007, India
| | - Mahendran Sekar
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
| | | | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 144411, India
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Ronan MacLoughlin
- Research and Development, Aerogen Limited, IDA Business Park, Galway, Connacht, H91 HE94, Ireland
- School of Pharmacy & Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Leinster, D02 YN77, Ireland
- School of Pharmacy & Pharmaceutical Sciences, Trinity College, Dublin, Leinster, D02 PN40, Ireland
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, 2007, Australia.
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Nemeth K, Bayraktar R, Ferracin M, Calin GA. Non-coding RNAs in disease: from mechanisms to therapeutics. Nat Rev Genet 2024; 25:211-232. [PMID: 37968332 DOI: 10.1038/s41576-023-00662-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2023] [Indexed: 11/17/2023]
Abstract
Non-coding RNAs (ncRNAs) are a heterogeneous group of transcripts that, by definition, are not translated into proteins. Since their discovery, ncRNAs have emerged as important regulators of multiple biological functions across a range of cell types and tissues, and their dysregulation has been implicated in disease. Notably, much research has focused on the link between microRNAs (miRNAs) and human cancers, although other ncRNAs, such as long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), are also emerging as relevant contributors to human disease. In this Review, we summarize our current understanding of the roles of miRNAs, lncRNAs and circRNAs in cancer and other major human diseases, notably cardiovascular, neurological and infectious diseases. Further, we discuss the potential use of ncRNAs as biomarkers of disease and as therapeutic targets.
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Affiliation(s)
- Kinga Nemeth
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Recep Bayraktar
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Manuela Ferracin
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy.
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.
| | - George A Calin
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The RNA Interference and Non-coding RNA Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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5
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Koonin EV. Circular RNAs from linear viral RNA genomes: A distinct dimension in the virus world. Proc Natl Acad Sci U S A 2024; 121:e2401335121. [PMID: 38349885 PMCID: PMC10895248 DOI: 10.1073/pnas.2401335121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024] Open
Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD20894
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Cao QM, Boonchuen P, Chen TC, Lei S, Somboonwiwat K, Sarnow P. Virus-derived circular RNAs populate hepatitis C virus-infected cells. Proc Natl Acad Sci U S A 2024; 121:e2313002121. [PMID: 38319965 PMCID: PMC10873615 DOI: 10.1073/pnas.2313002121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/04/2024] [Indexed: 02/08/2024] Open
Abstract
It is known that pre-mRNAs in eukaryotic cells can be processed to circular RNAs by a backsplicing mechanism. Circular RNAs have great stability and can sequester proteins or small RNAs to exert functions on cellular pathways. Because viruses often exploit host pathways, we explored whether the RNA genome of the cytoplasmic hepatitis C virus is processed to yield virus-derived circRNAs (vcircRNAs). Computational analyses of RNA-seq experiments predicted that the viral RNA genome is fragmented to generate hundreds of vcircRNAs. More than a dozen of them were experimentally verified by rolling-circle amplification. VcircRNAs that contained the viral internal ribosome entry site were found to be translated into proteins that displayed proviral functions. Furthermore, two highly abundant, nontranslated vcircRNAs were shown to enhance viral RNA abundance. These findings argue that novel vcircRNA molecules modulate viral amplification in cells infected by a cytoplasmic RNA virus.
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Affiliation(s)
- Qian M. Cao
- Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA94305
| | - Pakpoom Boonchuen
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Mueang Nakhon Ratchasima30000, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok10330, Thailand
| | - Tzu-Chun Chen
- Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA94305
| | - Shaohua Lei
- Center of Excellence for Leukemia Studies, Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN38105
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN38105
| | - Kunlaya Somboonwiwat
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok10330, Thailand
| | - Peter Sarnow
- Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA94305
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7
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Sberna G, Maggi F, Amendola A. Virus-Encoded Circular RNAs: Role and Significance in Viral Infections. Int J Mol Sci 2023; 24:16547. [PMID: 38003737 PMCID: PMC10671809 DOI: 10.3390/ijms242216547] [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: 10/31/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 11/26/2023] Open
Abstract
Circular RNAs (circRNAs) have been the focus of intense scientific research to understand their biogenesis, mechanisms of action and regulatory functions. CircRNAs are single stranded, covalently closed RNA molecules lacking the 5'-terminal cap and the 3'-terminal polyadenine chain, characteristics that make them very stable and resistant. Synthesised by both cells and viruses, in the past circRNAs were considered to have no precise function. Today, increasing evidence shows that circRNAs are ubiquitous, some of them are tissue- and cell-specific, and critical in multiple regulatory processes (i.e., infections, inflammation, oncogenesis, gene expression). Moreover, circRNAs are emerging as important biomarkers of viral infection and disease progression. In this review, we provided an updated overview of current understanding of virus-encoded and cellular-encoded circRNAs and their involvement in cellular pathways during viral infection.
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Affiliation(s)
| | | | - Alessandra Amendola
- Laboratory of Virology and Biosafety Laboratories, National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00149 Rome, Italy; (G.S.)
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Liang S, Liu S, Song J, Lin Q, Zhao S, Li S, Li J, Liang S, Wang J. HMCDA: a novel method based on the heterogeneous graph neural network and metapath for circRNA-disease associations prediction. BMC Bioinformatics 2023; 24:335. [PMID: 37697297 PMCID: PMC10494331 DOI: 10.1186/s12859-023-05441-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/08/2023] [Indexed: 09/13/2023] Open
Abstract
Circular RNA (CircRNA) is a type of non-coding RNAs in which both ends are covalently linked. Researchers have demonstrated that many circRNAs can act as biomarkers of diseases. However, traditional experimental methods for circRNA-disease associations identification are labor-intensive. In this work, we propose a novel method based on the heterogeneous graph neural network and metapaths for circRNA-disease associations prediction termed as HMCDA. First, a heterogeneous graph consisting of circRNA-disease associations, circRNA-miRNA associations, miRNA-disease associations and disease-disease associations are constructed. Then, six metapaths are defined and generated according to the biomedical pathways. Afterwards, the entity content transformation, intra-metapath and inter-metapath aggregation are implemented to learn the embeddings of circRNA and disease entities. Finally, the learned embeddings are used to predict novel circRNA-disase associations. In particular, the result of extensive experiments demonstrates that HMCDA outperforms four state-of-the-art models in fivefold cross validation. In addition, our case study indicates that HMCDA has the ability to identify novel circRNA-disease associations.
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Affiliation(s)
- Shiyang Liang
- Department of Gastroenterology, Tangdu Hospital, Air Force Medical University, Xinsi Road, Xi'an, China
- Department of Internal Medicine, The No. 944 Hospital of Joint Logistic Support Force of PLA, Xiongguan Road, Jiuquan, China
| | - Siwei Liu
- Department of Machine Learning, Mohamed bin Zayed University of Artificial Intelligence, Abu Dhabi, United Arab Emirates
| | - Junliang Song
- Department of Gastroenterology, Tangdu Hospital, Air Force Medical University, Xinsi Road, Xi'an, China
| | - Qiang Lin
- Department of Gastroenterology, Tangdu Hospital, Air Force Medical University, Xinsi Road, Xi'an, China
| | - Shihong Zhao
- Department of Respiratory Medicine, Tangdu Hospital, Air Force Medical University, Xinsi Road, Xi'an, China
| | - Shuaixin Li
- Department of Gastroenterology, Tangdu Hospital, Air Force Medical University, Xinsi Road, Xi'an, China
| | - Jiahui Li
- Department of Gastroenterology, Tangdu Hospital, Air Force Medical University, Xinsi Road, Xi'an, China
| | - Shangsong Liang
- Department of Machine Learning, Mohamed bin Zayed University of Artificial Intelligence, Abu Dhabi, United Arab Emirates
| | - Jingjie Wang
- Department of Gastroenterology, Tangdu Hospital, Air Force Medical University, Xinsi Road, Xi'an, China.
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Zeng J, Cao D, Yang S, Jaijyan DK, Liu X, Wu S, Cruz-Cosme R, Tang Q, Zhu H. Insights into the Transcriptome of Human Cytomegalovirus: A Comprehensive Review. Viruses 2023; 15:1703. [PMID: 37632045 PMCID: PMC10458407 DOI: 10.3390/v15081703] [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: 07/12/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Human cytomegalovirus (HCMV) is a widespread pathogen that poses significant risks to immunocompromised individuals. Its genome spans over 230 kbp and potentially encodes over 200 open-reading frames. The HCMV transcriptome consists of various types of RNAs, including messenger RNAs (mRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs), with emerging insights into their biological functions. HCMV mRNAs are involved in crucial viral processes, such as viral replication, transcription, and translation regulation, as well as immune modulation and other effects on host cells. Additionally, four lncRNAs (RNA1.2, RNA2.7, RNA4.9, and RNA5.0) have been identified in HCMV, which play important roles in lytic replication like bypassing acute antiviral responses, promoting cell movement and viral spread, and maintaining HCMV latency. CircRNAs have gained attention for their important and diverse biological functions, including association with different diseases, acting as microRNA sponges, regulating parental gene expression, and serving as translation templates. Remarkably, HCMV encodes miRNAs which play critical roles in silencing human genes and other functions. This review gives an overview of human cytomegalovirus and current research on the HCMV transcriptome during lytic and latent infection.
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Affiliation(s)
- Janine Zeng
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Di Cao
- Department of Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Shaomin Yang
- Department of Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Dabbu Kumar Jaijyan
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Xiaolian Liu
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Songbin Wu
- Department of Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Ruth Cruz-Cosme
- Department of Microbiology, Howard University College of Medicine, 520 W Street NW, Washington, DC 20059, USA
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, 520 W Street NW, Washington, DC 20059, USA
| | - Hua Zhu
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
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10
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Maarouf M, Wang L, Wang Y, Rai KR, Chen Y, Fang M, Chen JL. Functional Involvement of circRNAs in the Innate Immune Responses to Viral Infection. Viruses 2023; 15:1697. [PMID: 37632040 PMCID: PMC10458642 DOI: 10.3390/v15081697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Effective viral clearance requires fine-tuned immune responses to minimize undesirable inflammatory responses. Circular RNAs (circRNAs) are a class of non-coding RNAs that are abundant and highly stable, formed by backsplicing pre-mRNAs, and expressed ubiquitously in eukaryotic cells, emerging as critical regulators of a plethora of signaling pathways. Recent progress in high-throughput sequencing has enabled a better understanding of the physiological and pathophysiological functions of circRNAs, overcoming the obstacle of the sequence overlap between circRNAs and their linear cognate mRNAs. Some viruses also encode circRNAs implicated in viral replication or disease progression. There is increasing evidence that viral infections dysregulate circRNA expression and that the altered expression of circRNAs is critical in regulating viral infection and replication. circRNAs were shown to regulate gene expression via microRNA and protein sponging or via encoding small polypeptides. Recent studies have also highlighted the potential role of circRNAs as promising diagnostic and prognostic biomarkers, RNA vaccines and antiviral therapy candidates due to their higher stability and lower immunogenicity. This review presents an up-to-date summary of the mechanistic involvement of circRNAs in innate immunity against viral infections, the current understanding of their regulatory roles, and the suggested applications.
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Affiliation(s)
- Mohamed Maarouf
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China;
- Department of Virology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Lulu Wang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- Fujian Province Joint Laboratory of Animal Pathogen Prevention and Control of the “Belt and Road”, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yiming Wang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- Fujian Province Joint Laboratory of Animal Pathogen Prevention and Control of the “Belt and Road”, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kul Raj Rai
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- Fujian Province Joint Laboratory of Animal Pathogen Prevention and Control of the “Belt and Road”, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Department of Microbiology, ShiGan International College of Science and Technology/ShiGan Health Foundation, Narayangopal Chowk, Kathmandu 44600, Nepal
| | - Yuhai Chen
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China;
| | - Min Fang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China;
| | - Ji-Long Chen
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- Fujian Province Joint Laboratory of Animal Pathogen Prevention and Control of the “Belt and Road”, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Gu A, Jaijyan DK, Yang S, Zeng M, Pei S, Zhu H. Functions of Circular RNA in Human Diseases and Illnesses. Noncoding RNA 2023; 9:38. [PMID: 37489458 PMCID: PMC10366867 DOI: 10.3390/ncrna9040038] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/26/2023] Open
Abstract
Circular RNAs (circRNAs) represent single-stranded RNA species that contain covalently closed 3' and 5' ends that provide them more stability than linear RNA, which has free ends. Emerging evidence indicates that circRNAs perform essential functions in many DNA viruses, including coronaviruses, Epstein-Barr viruses, cytomegalovirus, and Kaposi sarcoma viruses. Recent studies have confirmed that circRNAs are present in viruses, including DNA and RNA viruses, and play various important functions such as evading host immune response, disease pathogenesis, protein translation, miRNA sponges, regulating cell proliferation, and virus replication. Studies have confirmed that circRNAs can be biological signatures or pathological markers for autoimmune diseases, neurological diseases, and cancers. However, our understanding of circRNAs in DNA and RNA viruses is still limited, and functional evaluation of viral and host circRNAs is essential to completely understand their biological functions. In the present review, we describe the metabolism and cellular roles of circRNA, including its roles in various diseases and viral and cellular circRNA functions. Circular RNAs are found to interact with RNA, proteins, and DNA, and thus can modulate cellular processes, including translation, transcription, splicing, and other functions. Circular RNAs interfere with various signaling pathways and take part in vital functions in various biological, physiological, cellular, and pathophysiological processes. We also summarize recent evidence demonstrating cellular and viral circRNA's roles in DNA and RNA viruses in this growing field of research.
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Affiliation(s)
- Alison Gu
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Dabbu Kumar Jaijyan
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Shaomin Yang
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Mulan Zeng
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Shaokai Pei
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Hua Zhu
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
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12
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Yang S, Cruz-Cosme R, Cao D, Zhou H, Wu S, Huang J, Luo Z, Zhu H, Tang Q. Murine Hepatitis Virus Exoribonuclease nsp14 Is Required for the Biogenesis of Viral Circular RNAs. Microbiol Spectr 2023; 11:e0446022. [PMID: 37184400 PMCID: PMC10269776 DOI: 10.1128/spectrum.04460-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Affiliation(s)
- Shaomin Yang
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | | | - Di Cao
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Hong Zhou
- Howard University College of Medicine, Washington, DC, USA
| | - Songbin Wu
- Shenzhen Nanshan People’s Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Jiabin Huang
- Shenzhen Nanshan People’s Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Zhen Luo
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Hua Zhu
- Rutgers University, Newark, New Jersey, USA
| | - Qiyi Tang
- Howard University College of Medicine, Washington, DC, USA
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13
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Gao X, Fang D, Liang Y, Deng X, Chen N, Zeng M, Luo M. Circular RNAs as emerging regulators in COVID-19 pathogenesis and progression. Front Immunol 2022; 13:980231. [PMID: 36439162 PMCID: PMC9681929 DOI: 10.3389/fimmu.2022.980231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), an infectious acute respiratory disease caused by a newly emerging RNA virus, is a still-growing pandemic that has caused more than 6 million deaths globally and has seriously threatened the lives and health of people across the world. Currently, several drugs have been used in the clinical treatment of COVID-19, such as small molecules, neutralizing antibodies, and monoclonal antibodies. In addition, several vaccines have been used to prevent the spread of the pandemic, such as adenovirus vector vaccines, inactivated vaccines, recombinant subunit vaccines, and nucleic acid vaccines. However, the efficacy of vaccines and the onset of adverse reactions vary among individuals. Accumulating evidence has demonstrated that circular RNAs (circRNAs) are crucial regulators of viral infections and antiviral immune responses and are heavily involved in COVID-19 pathologies. During novel coronavirus infection, circRNAs not only directly affect the transcription process and interfere with viral replication but also indirectly regulate biological processes, including virus-host receptor binding and the immune response. Consequently, understanding the expression and function of circRNAs during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection will provide novel insights into the development of circRNA-based methods. In this review, we summarize recent progress on the roles and underlying mechanisms of circRNAs that regulate the inflammatory response, viral replication, immune evasion, and cytokines induced by SARS-CoV-2 infection, and thus highlighting the diagnostic and therapeutic challenges in the treatment of COVID-19 and future research directions.
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Affiliation(s)
- Xiaojun Gao
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, Sichuan, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Dan Fang
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, Sichuan, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Yu Liang
- College of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Traditional Chinese Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Xin Deng
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, Sichuan, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Ni Chen
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, Sichuan, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Min Zeng
- Department of Pharmacy, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Mao Luo
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Drug Discovery Research Center, Southwest Medical University, Luzhou, Sichuan, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
- College of Integrated Traditional Chinese and Western Medicine, Affiliated Hospital of Traditional Chinese Medicine, Southwest Medical University, Luzhou, Sichuan, China
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14
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Rahmani-Kukia N, Abbasi A. New insights on circular RNAs and their potential applications as biomarkers, therapeutic agents, and preventive vaccines in viral infections: with a glance at SARS-CoV-2. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:705-717. [PMID: 35992045 PMCID: PMC9375856 DOI: 10.1016/j.omtn.2022.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The occurrence of viral infections and approaches to handling them are very challenging and require prompt diagnosis and timely treatment. Recently, genomic medicine approaches have come up with the discovery of the competing endogenous RNA (ceRNA) network, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) on the basis of gene silencing. CircRNAs, as a group of non-encoded RNAs, make a loop-like structure by back-splicing through 3′ and 5′ ends. They are stable, abundant, specific, and highly conserved and can be quickly generated at large scales in vitro. CircRNAs have the potential to contribute in several cellular processes in a way that some serve as microRNA sponges, cellular transporters, protein-binding RNAs, transcriptional regulators, and immune system modulators. CircRNAs can even play an important role in modulating antiviral immune responses. In the present review, circRNAs’ biogenesis, function, and biomarker and therapeutic potential as well as their prospective applications as vaccines against viral infections such as SARS-CoV-2 are explained. By considering their unique properties, their potential to be used as novel vaccines, biomarkers, and a therapeutic approach appears possible.
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15
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Yang S, Liu X, Wang M, Cao D, Jaijyan DK, Enescu N, Liu J, Wu S, Wang S, Sun W, Xiao L, Gu A, Li Y, Zhou H, Tyagi S, Wu J, Tang Q, Zhu H. Circular RNAs Represent a Novel Class of Human Cytomegalovirus Transcripts. Microbiol Spectr 2022; 10:e0110622. [PMID: 35604147 PMCID: PMC9241847 DOI: 10.1128/spectrum.01106-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 04/26/2022] [Indexed: 01/03/2023] Open
Abstract
Human cytomegalovirus (HCMV) infects a large portion of the human population globally. Several HCMV-derived noncoding RNAs are involved in the regulation of viral gene expression and the virus life cycle. Here, we reported that circRNAs are a new class of HCMV transcripts. We bioinformatically predict 704 candidate circRNAs encoded by the TB40/E strain and 230 encoded by the HAN strain. We also systematically compare circRNA features, including the breakpoint sequence consensus, strand preference, length distribution, and exon numbers between host genome-encoded circRNAs and viral circRNAs, and showed that the unique characteristics of viral circRNAs are correlated with their genome types. Furthermore, we experimentally confirmed 324 back-splice junctions (BSJs) from three HCMV strains, Towne, TB40/E, and Toledo, and identified 4 representative HCMV circRNAs by RNase R treatment. Interestingly, we also showed that HCMV contains alternative back-splicing circRNAs. We developed a new amplified FISH method that allowed us to visualize circRNAs and quantify the number of circRNA molecules in the infected cells. The competitive endogenous RNA network analysis suggests that HCMV circRNAs play important roles in viral DNA synthesis via circRNA-miRNA-mRNA networks. Our findings highlight that circRNAs are an important component of the HCMV transcriptome that may contribute to viral replication and pathogenesis. IMPORTANCE HCMV infects 40% to 100% of the human population globally and may be a life-threatening pathogen in immunocompromised individuals. CircRNA is a family of unique RNA that is the most newly found and remains unknown in many aspects. Our current studies computationally identified HCMV-encoded circRNAs and confirmed the existence of the HCMV circRNAs in the infected cells. We systematically compared the features between host and different viral circRNAs and found that the unique characteristics of circRNAs were correlated with their genome types. We also first reported that HCMV contained alternative back-splicing circRNAs. More importantly, we developed a new amplified FISH method which allowed us for the first time not only to visualize circRNAs but also to quantify the number of circRNA molecules in the infected cells. This work describes a novel component of HCMV transcriptome bringing a new understanding of HCMV biology and disease.
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Affiliation(s)
| | | | - Mei Wang
- Jinan University, Guangzhou, Guangdong, China
| | - Di Cao
- Jinan University, Guangzhou, Guangdong, China
| | - Dabbu Kumar Jaijyan
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Nicole Enescu
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Jian Liu
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, Fujian, China
| | - Songbin Wu
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Shenzhen Nanshan People's Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong, China
| | - Sashuang Wang
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Shenzhen Nanshan People's Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong, China
| | - Wuping Sun
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Shenzhen Nanshan People's Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong, China
| | - Lizu Xiao
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Shenzhen Nanshan People's Hospital, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong, China
| | - Alison Gu
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Yaolan Li
- Jinan University, Guangzhou, Guangdong, China
| | - Hong Zhou
- Department of Microbiology, Howard University College of Medicine, Washington, DC, USA
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Newark, New Jersey, USA
- Department of Medicine, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Jianguo Wu
- Jinan University, Guangzhou, Guangdong, China
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, Washington, DC, USA
| | - Hua Zhu
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
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