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Kurien BT, Ice JA, Wood R, Pharaoh G, Cavett J, Lewis V, Bhaskaran S, Rasmussen A, Lessard CJ, Farris AD, Sivils KL, Koelsch KA, Van Remmen H, Scofield RH. Mitochondrial Dysfunction and Fatigue in Sjögren's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.598269. [PMID: 38948768 PMCID: PMC11212898 DOI: 10.1101/2024.06.17.598269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Objectives Sjögren's disease (SjD) is a common exocrine disorder typified by chronic inflammation and dryness, but also profound fatigue, suggesting a pathological basis in cellular bioenergetics. In healthy states, damaged or dysfunctional mitochondrial components are broken down and recycled by mitophagy, a specialized form of autophagy. In many autoimmune disorders, however, evidence suggests that dysfunctional mitophagy allows poorly functioning mitochondria to persist and contribute to a cellular milieu with elevated reactive oxygen species. We hypothesized that mitophagic processes are dysregulated in SjD and that dysfunctional mitochondria contribute to overall fatigue. We sought to link fatigue with mitochondrial dysfunction directly in SjD, heretofore unexamined, and further sought to assess the pathogenic extent and implications of dysregulated mitophagy in SjD. Methods We isolated pan T cells via negative selection from the peripheral blood mononuclear cells of 17 SjD and 8 age-matched healthy subjects, all of whom completed fatigue questionnaires prior to phlebotomy. Isolated T cells were analyzed for mitochondrial oxygen consumption rate (OCR) and glycolysis using Seahorse, and linear correlations with fatigue measures were assessed. A mitophagy transcriptional signature in SjD was identified by reanalysis of whole-blood microarray data from 190 SjD and 32 healthy subjects. Differential expression analyses were performed by case/control and subgroup analyses comparing SjD patients by mitophagy transcriptional cluster against healthy subjects followed by bioinformatic interpretation using gene set enrichment analysis. Results Basal OCR, ATP-linked respiration, maximal respiration, and reserve capacity were significantly lower in SjD compared to healthy subjects with no observed differences in non-mitochondrial respiration, basal glycolysis, or glycolytic stress. SjD lymphocytic mitochondria show structural alterations compared to healthy subjects. Fatigue scores related to pain/discomfort in SjD correlated with the altered OCR. Results from subgroup analyses by mitophagic SjD clusters revealed highly variable inter-cluster differentially expressed genes (DEGs) and expanded the number of SjD-associated gene targets by tenfold within the same dataset. Conclusion Mitochondrial dysfunction, associated with fatigue, is a significant problem in SjD and warrants further investigation.
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Liu X, Chen W, Li K, Sheng J. RNA N6-methyladenosine methylation in influenza A virus infection. Front Microbiol 2024; 15:1401997. [PMID: 38957616 PMCID: PMC11217485 DOI: 10.3389/fmicb.2024.1401997] [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: 03/16/2024] [Accepted: 05/30/2024] [Indexed: 07/04/2024] Open
Abstract
Influenza A virus (IAV) is a negative-sense single-stranded RNA virus that causes acute lung injury and acute respiratory distress syndrome, posing a serious threat to both animal and human health. N6-methyladenosine (m6A), a prevalent and abundant post-transcriptional methylation of RNA in eukaryotes, plays a crucial regulatory role in IAV infection by altering viral RNA and cellular transcripts to affect viral infection and the host immune response. This review focuses on the molecular mechanisms underlying m6A modification and its regulatory function in the context of IAV infection and the host immune response. This will provide a better understanding of virus-host interactions and offer insights into potential anti-IAV strategies.
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Affiliation(s)
- Xueer Liu
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Weiqiang Chen
- Department of Neurosurgery, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Kangsheng Li
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Jiangtao Sheng
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong, China
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Zhang X, Li Z, Peng Q, Liu C, Wu Y, Wen Y, Zheng R, Xu C, Tian J, Zheng X, Yan Q, Wang J, Ma J. Epstein-Barr virus suppresses N 6-methyladenosine modification of TLR9 to promote immune evasion. J Biol Chem 2024; 300:107226. [PMID: 38537697 PMCID: PMC11061751 DOI: 10.1016/j.jbc.2024.107226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/08/2024] [Accepted: 03/17/2024] [Indexed: 04/26/2024] Open
Abstract
Epstein-Barr virus (EBV) is a human tumor virus associated with a variety of malignancies, including nasopharyngeal carcinoma, gastric cancers, and B-cell lymphomas. N6-methyladenosine (m6A) modifications modulate a wide range of cellular processes and participate in the regulation of virus-host cell interactions. Here, we discovered that EBV infection downregulates toll-like receptor 9 (TLR9) m6A modification levels and thus inhibits TLR9 expression. TLR9 has multiple m6A modification sites. Knockdown of METTL3, an m6A "writer", decreases TLR9 protein expression by inhibiting its mRNA stability. Mechanistically, Epstein-Barr nuclear antigen 1 increases METTL3 protein degradation via K48-linked ubiquitin-proteasome pathway. Additionally, YTHDF1 was identified as an m6A "reader" of TLR9, enhancing TLR9 expression by promoting mRNA translation in an m6A -dependent manner, which suggests that EBV inhibits TLR9 translation by "hijacking" host m6A modification mechanism. Using the METTL3 inhibitor STM2457 inhibits TLR9-induced B cell proliferation and immunoglobulin secretion, and opposes TLR9-induced immune responses to assist tumor cell immune escape. In clinical lymphoma samples, the expression of METTL3, YTHDF1, and TLR9 was highly correlated with immune cells infiltration. This study reveals a novel mechanism that EBV represses the important innate immunity molecule TLR9 through modulating the host m6A modification system.
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Affiliation(s)
- Xiaoyue Zhang
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, China; NHC Key Laboratory of Carcinogenesis, Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, Hunan, China
| | - Zhengshuo Li
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, China; NHC Key Laboratory of Carcinogenesis, Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, Hunan, China
| | - Qiu Peng
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, China; NHC Key Laboratory of Carcinogenesis, Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, Hunan, China
| | - Can Liu
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, China; NHC Key Laboratory of Carcinogenesis, Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, Hunan, China
| | - Yangge Wu
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, China; NHC Key Laboratory of Carcinogenesis, Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, Hunan, China
| | - Yuqing Wen
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, China; NHC Key Laboratory of Carcinogenesis, Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, Hunan, China
| | - Run Zheng
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, China; NHC Key Laboratory of Carcinogenesis, Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, Hunan, China
| | - Chenxiao Xu
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, China; NHC Key Laboratory of Carcinogenesis, Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, Hunan, China
| | - Junrui Tian
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, China; NHC Key Laboratory of Carcinogenesis, Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, Hunan, China
| | - Xiang Zheng
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Qun Yan
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Jia Wang
- Department of Immunology, Changzhi Medical College, Changzhi, Shanxi, China.
| | - Jian Ma
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China; Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, China; NHC Key Laboratory of Carcinogenesis, Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Cancer Metabolism, Changsha, Hunan, China.
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Martínez-López MF, Muslin C, Kyriakidis NC. STINGing Defenses: Unmasking the Mechanisms of DNA Oncovirus-Mediated Immune Escape. Viruses 2024; 16:574. [PMID: 38675916 PMCID: PMC11054469 DOI: 10.3390/v16040574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
DNA oncoviruses represent an intriguing subject due to their involvement in oncogenesis. These viruses have evolved mechanisms to manipulate the host immune response, facilitating their persistence and actively contributing to carcinogenic processes. This paper describes the complex interactions between DNA oncoviruses and the innate immune system, with a particular emphasis on the cGAS-STING pathway. Exploring these interactions highlights that DNA oncoviruses strategically target and subvert this pathway, exploiting its vulnerabilities for their own survival and proliferation within the host. Understanding these interactions lays the foundation for identifying potential therapeutic interventions. Herein, we sought to contribute to the ongoing efforts in advancing our understanding of the innate immune system in oncoviral pathogenesis.
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Affiliation(s)
- Mayra F Martínez-López
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de las Américas, Quito 170503, Ecuador;
| | - Claire Muslin
- One Health Research Group, Faculty of Health Sciences, Universidad de las Américas, Quito 170503, Ecuador;
| | - Nikolaos C. Kyriakidis
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de las Américas, Quito 170503, Ecuador;
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Liu J, Chen L, Guo X, Zhao B, Jiang J. Emerging role of N6-methyladenosine RNA modification in regulation of SARS-CoV-2 infection and virus-host interactions. Biomed Pharmacother 2024; 173:116231. [PMID: 38484561 DOI: 10.1016/j.biopha.2024.116231] [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: 11/28/2023] [Revised: 01/17/2024] [Accepted: 01/29/2024] [Indexed: 03/27/2024] Open
Abstract
Since December 2019, the infection caused by Severe Acute Respiratory Syndrome Coronavirus Type 2 (SARS-CoV-2) has posed an enormous threat to human health security worldwide. Constant mutation of viral genome and varying therapeutic responses of patients infected with this virus prompted efforts to uncover more novel regulators in the pathogenesis. The involvement of N6-methyladenosine, a modified form of RNA, plays a crucial role in viral replication, viral pathogenicity, and intricate signaling pathways connected with immune responses. This review discusses research advances revealing the regulation of the life cycle of SARS-CoV-2 and antiviral responses of host cells by RNA m6A modification, highlights the biological functions of N6-methyladenosine components in SARS-CoV-2 infection and virus-host interactions, and outlines current challenges and future directions for exploring the potential clinical value of m6A modification in COVID-19.
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Affiliation(s)
- Jiayi Liu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Xiangya School of Medicine, Central South University, Changsha 410008, China
| | - Lingli Chen
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xiongmin Guo
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Xiangya School of Medicine, Central South University, Changsha 410008, China
| | - Bingrong Zhao
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Xiangya School of Medicine, Central South University, Changsha 410008, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha 410008, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha 410008, China.
| | - Juan Jiang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Xiangya School of Medicine, Central South University, Changsha 410008, China; Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha 410008, China; Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha 410008, China.
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Chen Y, Jiang Z, Yang Y, Zhang C, Liu H, Wan J. The functions and mechanisms of post-translational modification in protein regulators of RNA methylation: Current status and future perspectives. Int J Biol Macromol 2023; 253:126773. [PMID: 37690652 DOI: 10.1016/j.ijbiomac.2023.126773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
RNA methylation, an epigenetic modification that does not alter gene sequence, may be important to diverse biological processes. Protein regulators of RNA methylation include "writers," "erasers," and "readers," which respectively deposit, remove, and recognize methylated RNA. RNA methylation, particularly N6-methyladenosine (m6A), 5-methylcytosine (m5C), N3-methylcytosine (m3C), N1-methyladenosine (m1A) and N7-methylguanosine (m7G), has been suggested as disease therapeutic targets. Despite advances in the structure and pharmacology of RNA methylation regulators that have improved drug discovery, regulating these proteins by various post-translational modifications (PTMs) has received little attention. PTM modifies protein structure and function, affecting all aspects of normal biology and pathogenesis, including immunology, cell differentiation, DNA damage repair, and tumors. It is becoming evident that RNA methylation regulators are also regulated by diverse PTMs. PTM of RNA methylation regulators induces their covalent linkage to new functional groups, hence modifying their activity and function. Mass spectrometry has identified many PTMs on protein regulators of RNA methylation. In this review, we describe the functions and PTM of protein regulators of RNA methylation and summarize the recent advances in the regulatory mode of human disease and its underlying mechanisms.
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Affiliation(s)
- Youming Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zuli Jiang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ying Yang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Chenxing Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Hongyang Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Junhu Wan
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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Bhattacharya I, Volety I, Shukla D. OPTN-TBK1 axis and a role for PLK1 in HSV-1 infection. mBio 2023; 14:e0271523. [PMID: 38019030 PMCID: PMC10746225 DOI: 10.1128/mbio.02715-23] [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: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Herpes simplex virus type 1 (HSV-1) is globally prevalent, with latent infections observed in up to 80% of the population. The virus is known for subverting host defense mechanisms and infiltrating the nervous system to establish latency in peripheral ganglia. Multiple stressors can reactivate the virus, and recurrent herpes has been linked to vision loss and neurodegeneration. Identifying critical host factors that limit the spread of HSV-1 and the subsequent establishment of latent infection holds the potential to drive new intervention strategies for eradicating the virus. Numerous pieces of evidence underscore the significance of Tank-binding kinase 1 (TBK1) in restricting HSV-1. Reports have also suggested that phosphorylation of optineurin (OPTN) by TBK1 is required for triggering OPTN-mediated autophagy for HSV degradation. This report adds new insights into the roles of OPTN and TBK1 in HSV-1 infection and provides proof of a TBK1-independent HSV-1 restriction through OPTN. It confirms that TBK1 activation can be substituted by PLK1 to provide protection against HSV-1. In contrast, the activation of OPTN is likely an indispensable host defense mechanism for optimal defense against HSV-1.
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Affiliation(s)
- Ilina Bhattacharya
- Department of Ophthalmology and Visual Sciences, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Ipsita Volety
- Department of Ophthalmology and Visual Sciences, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Deepak Shukla
- Department of Ophthalmology and Visual Sciences, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
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Jing L, Zhou K, Wang Z, Li Y, Fan Y, Liu T, Shan Z, Lin Y. YTHDF1 shapes "cold" tumor and inhibits CD8 + T cells infiltration and function in breast cancer. Exp Cell Res 2023; 432:113778. [PMID: 37741489 DOI: 10.1016/j.yexcr.2023.113778] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/25/2023]
Abstract
While YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) was recognized as a crucial contributor in the development and immune-related regulation of various types of tumors, its function in the immune response of breast cancer has largely remained uninvestigated. Through analysis of public databases, we found YTHDF1 as a highly expressed gene in breast cancers and confirmed this finding in breast cancer cells and clinical specimens from our center. Subsequently, we examined the link between YTHDF1 expression and immune cells and molecules by utilizing immune-related public databases and algorithm. We further validated our findings through cellular and animal experiments, as well as RNA sequencing. YTHDF1 was found highly expressed in tumor tissues of breast cancer, which negatively correlated with patient survival. The downregulation of YTHDF1 promoted the expression of pro-inflammatory markers and improved the anti-cancer ability of immune cells in breast cancer. RNA sequencing analysis revealed that YTHDF1 knockdown resulted in enrichment of differential genes in signal transduction pathways. Additionally, in vitro experiments showed that immune cells had higher cytotoxicity against breast cancer cells with decreased YTHDF1 expression. Moreover, in vivo studies indicated that YTHDF1 promoted breast cancer growth while inhibiting CD8+ T cell infiltration and function. Our study demonstrates that YTHDF1 plays a crucial role in establishing a "cold" tumor microenvironment in breast cancer by inhibiting the release of pro-inflammatory cytokines from cancer cells. As a result, the infiltration and functional differentiation of anti-tumor CD8+ T cells are hindered, ultimately resulting in the immune evasion of breast cancer.
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Affiliation(s)
- Lanyu Jing
- Department of Breast Surgery, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong, China.
| | - Kaiwen Zhou
- Department of Breast Surgery, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong, China.
| | - Zilin Wang
- Department of Breast Surgery, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong, China.
| | - Yuying Li
- Department of Breast Surgery, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong, China.
| | - Yuanjian Fan
- Department of Breast Surgery, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong, China.
| | - Ting Liu
- Department of Breast Surgery, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong, China.
| | - Zhen Shan
- Department of Breast Surgery, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong, China.
| | - Ying Lin
- Department of Breast Surgery, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, Guangdong, China.
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Yao L, Zhang W, Chen X, Yi M, Jia K. Methyltransferase-like 3 suppresses red spotted grouper nervous necrosis virus and viral hemorrhagic septicemia virus infection by enhancing type I interferon responses in sea perch. FISH & SHELLFISH IMMUNOLOGY 2023; 140:108993. [PMID: 37573969 DOI: 10.1016/j.fsi.2023.108993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/01/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
Methylation at the N6 position of adenosine (m6A) is the most abundant internal mRNA modification in eukaryotes, tightly associating with regulation of viral life circles and immune responses. Here, a methyltransferase-like 3 homolog gene from sea perch (Lateolabrax japonicus), designated LjMETTL3, was cloned and characterized, and its negative role in fish virus pathogenesis was uncovered. The cDNA of LjMETTL3 encoded a 601-amino acid protein with a MT-A70 domain, which shared the closest genetic relationship with Echeneis naucrates METTL3. Spatial expression analysis revealed that LjMETTL3 was more abundant in the immune tissues of sea perch post red spotted grouper nervous necrosis virus (RGNNV) or viral hemorrhagic septicemia virus (VHSV) infection. LjMETTL3 expression was significantly upregulated at 12 and 24 h post RGNNV and VHSV infection in vitro. In addition, ectopic expression of LjMETTL3 inhibited RGNNV and VHSV infection in LJB cells at 12 and 24 h post infection, whereas knockdown of LjMETTL3 led to opposite effects. Furthermore, we found that LjMETTL3 may participate in boosting the type I interferon responses by interacting with TANK-binding kinase. Taken together, these results disclosed the antiviral role of fish METTL3 against RGNNV and VHSV and provided evidence for understanding the potential mechanisms of fish METTL3 in antiviral innate immunity.
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Affiliation(s)
- Lan Yao
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510000, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, China
| | - Wanwan Zhang
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510000, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, China
| | - Xiaoqi Chen
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510000, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, China
| | - Meisheng Yi
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510000, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, China.
| | - Kuntong Jia
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510000, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510000, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, China.
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Kuang M, Zhao Y, Yu H, Li S, Liu T, Chen L, Chen J, Luo Y, Guo X, Wei X, Li Y, Zhang Z, Wang D, You F. XAF1 promotes anti-RNA virus immune responses by regulating chromatin accessibility. SCIENCE ADVANCES 2023; 9:eadg5211. [PMID: 37595039 PMCID: PMC10438455 DOI: 10.1126/sciadv.adg5211] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/20/2023] [Indexed: 08/20/2023]
Abstract
A rapid induction of antiviral genes is critical for eliminating viruses, which requires activated transcription factors and opened chromatins to initiate transcription. However, it remains elusive how the accessibility of specific chromatin is regulated during infection. Here, we found that XAF1 functioned as an epigenetic regulator that liberated repressed chromatin after infection. Upon RNA virus infection, MAVS recruited XAF1 and TBK1. TBK1 phosphorylated XAF1 at serine-252 and promoted its nuclear translocation. XAF1 then interacted with TRIM28 with the guidance of IRF1 to the specific locus of antiviral genes. XAF1 de-SUMOylated TRIM28 through its PHD domain, which led to increased accessibility of the chromatin and robust induction of antiviral genes. XAF1-deficient mice were susceptible to RNA virus due to impaired induction of antiviral genes. Together, XAF1 acts as an epigenetic regulator that promotes the opening of chromatin and activation of antiviral immunity by targeting TRIM28 during infection.
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Affiliation(s)
- Ming Kuang
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, NHC Key Laboratory of Medical Immunology, Peking University Health Science Center, Beijing, China
| | - Yingchi Zhao
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, NHC Key Laboratory of Medical Immunology, Peking University Health Science Center, Beijing, China
| | - Haitao Yu
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, NHC Key Laboratory of Medical Immunology, Peking University Health Science Center, Beijing, China
| | - Siji Li
- Ningbo first hospital, Ningbo hospital Zhejiang university, Ningbo, China
| | - Tianyi Liu
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, NHC Key Laboratory of Medical Immunology, Peking University Health Science Center, Beijing, China
| | - Luoying Chen
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, NHC Key Laboratory of Medical Immunology, Peking University Health Science Center, Beijing, China
| | - Jingxuan Chen
- College of Acupuncture and Massage, Shaanxi University of Chinese Medicine, Xixian New Area, Shaanxi Province 712046, China
- Shaanxi Key Laboratory of Acupuncture and Medicine, Xixian New Area, Shaanxi Province 712046, China
| | - Yujie Luo
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, NHC Key Laboratory of Medical Immunology, Peking University Health Science Center, Beijing, China
| | - Xuefei Guo
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, NHC Key Laboratory of Medical Immunology, Peking University Health Science Center, Beijing, China
| | - Xuemei Wei
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, NHC Key Laboratory of Medical Immunology, Peking University Health Science Center, Beijing, China
| | - Yunfei Li
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, NHC Key Laboratory of Medical Immunology, Peking University Health Science Center, Beijing, China
| | - Zeming Zhang
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, NHC Key Laboratory of Medical Immunology, Peking University Health Science Center, Beijing, China
| | - Dandan Wang
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Artificial Cell Engineering Technology Research Center, Tianjin Institute of Hepatobiliary Disease, Third Central Hospital of Tianjin, 83 Jintang Road, Hedong District, Tianjin 300170, China
| | - Fuping You
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, NHC Key Laboratory of Medical Immunology, Peking University Health Science Center, Beijing, China
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11
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Ribeiro DR, Nunes A, Ribeiro D, Soares AR. The hidden RNA code: implications of the RNA epitranscriptome in the context of viral infections. Front Genet 2023; 14:1245683. [PMID: 37614818 PMCID: PMC10443596 DOI: 10.3389/fgene.2023.1245683] [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: 06/23/2023] [Accepted: 07/19/2023] [Indexed: 08/25/2023] Open
Abstract
Emerging evidence highlights the multifaceted roles of the RNA epitranscriptome during viral infections. By modulating the modification landscape of viral and host RNAs, viruses enhance their propagation and elude host surveillance mechanisms. Here, we discuss how specific RNA modifications, in either host or viral RNA molecules, impact the virus-life cycle and host antiviral responses, highlighting the potential of targeting the RNA epitranscriptome for novel antiviral therapies.
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12
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Zhong Q, Xiao X, Qiu Y, Xu Z, Chen C, Chong B, Zhao X, Hai S, Li S, An Z, Dai L. Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications. MedComm (Beijing) 2023; 4:e261. [PMID: 37143582 PMCID: PMC10152985 DOI: 10.1002/mco2.261] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
Protein posttranslational modifications (PTMs) refer to the breaking or generation of covalent bonds on the backbones or amino acid side chains of proteins and expand the diversity of proteins, which provides the basis for the emergence of organismal complexity. To date, more than 650 types of protein modifications, such as the most well-known phosphorylation, ubiquitination, glycosylation, methylation, SUMOylation, short-chain and long-chain acylation modifications, redox modifications, and irreversible modifications, have been described, and the inventory is still increasing. By changing the protein conformation, localization, activity, stability, charges, and interactions with other biomolecules, PTMs ultimately alter the phenotypes and biological processes of cells. The homeostasis of protein modifications is important to human health. Abnormal PTMs may cause changes in protein properties and loss of protein functions, which are closely related to the occurrence and development of various diseases. In this review, we systematically introduce the characteristics, regulatory mechanisms, and functions of various PTMs in health and diseases. In addition, the therapeutic prospects in various diseases by targeting PTMs and associated regulatory enzymes are also summarized. This work will deepen the understanding of protein modifications in health and diseases and promote the discovery of diagnostic and prognostic markers and drug targets for diseases.
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Affiliation(s)
- Qian Zhong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xina Xiao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Yijie Qiu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhiqiang Xu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Chunyu Chen
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Baochen Chong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xinjun Zhao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shan Hai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shuangqing Li
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhenmei An
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Lunzhi Dai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
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13
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Weiß E, Hennig T, Graßl P, Djakovic L, Whisnant AW, Jürges CS, Koller F, Kluge M, Erhard F, Dölken L, Friedel CC. HSV-1 Infection Induces a Downstream Shift of Promoter-Proximal Pausing for Host Genes. J Virol 2023; 97:e0038123. [PMID: 37093003 PMCID: PMC10231138 DOI: 10.1128/jvi.00381-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/03/2023] [Indexed: 04/25/2023] Open
Abstract
Herpes simplex virus 1 (HSV-1) infection exerts a profound shutoff of host gene expression at multiple levels. Recently, HSV-1 infection was reported to also impact promoter-proximal RNA polymerase II (Pol II) pausing, a key step in the eukaryotic transcription cycle, with decreased and increased Pol II pausing observed for activated and repressed genes, respectively. Here, we demonstrate that HSV-1 infection induces more complex alterations in promoter-proximal pausing than previously suspected for the vast majority of cellular genes. While pausing is generally retained, it is shifted to more downstream and less well-positioned sites for most host genes. The downstream shift of Pol II pausing was established between 1.5 and 3 h of infection, remained stable until at least 6 hours postinfection, and was observed in the absence of ICP22. The shift in Pol II pausing does not result from alternative de novo transcription initiation at downstream sites or read-in transcription originating from disruption of transcription termination of upstream genes. The use of downstream secondary pause sites associated with +1 nucleosomes was previously observed upon negative elongation factor (NELF) depletion. However, downstream shifts of Pol II pausing in HSV-1 infection were much more pronounced than observed upon NELF depletion. Thus, our study reveals a novel aspect in which HSV-1 infection fundamentally reshapes host transcriptional processes, providing new insights into the regulation of promoter-proximal Pol II pausing in eukaryotic cells. IMPORTANCE This study provides a genome-wide analysis of changes in promoter-proximal polymerase II (Pol II) pausing on host genes induced by HSV-1 infection. It shows that standard measures of pausing, i.e., pausing indices, do not properly capture the complex and unsuspected alterations in Pol II pausing occurring in HSV-1 infection. Instead of a reduction of pausing with increased elongation, as suggested by pausing index analysis, HSV-1 infection leads to a shift of pausing to downstream and less well-positioned sites than in uninfected cells for the majority of host genes. Thus, HSV-1 infection fundamentally reshapes a key regulatory step at the beginning of the host transcriptional cycle on a genome-wide scale.
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Affiliation(s)
- Elena Weiß
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Pilar Graßl
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lara Djakovic
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Adam W. Whisnant
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Christopher S. Jürges
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Franziska Koller
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Kluge
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Caroline C. Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
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14
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Yuan W, Hou Y, Wang Q, Lv T, Ren J, Fan L, Cai J, Xiang B, Lin Q, Liao M, Ding C, Chen L, Ren T. Newcastle disease virus activates methylation-related enzymes to reprogram m 6A methylation in infected cells. Vet Microbiol 2023; 281:109747. [PMID: 37080085 DOI: 10.1016/j.vetmic.2023.109747] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/10/2023] [Accepted: 04/15/2023] [Indexed: 04/22/2023]
Abstract
Newcastle disease virus (NDV) is a paramyxovirus with high incidence and transmissibility in birds and is currently being developed for cancer therapy. N6-methyladenosine (m6A) is a common epigenetic modification of RNA. In this study, we aimed to determine whether this modification plays an important role in NDV infection. We found that methylation-related enzymes were activated in NDV-infected cells, and the abundance of m6A notably increased in vivo and in vitro. Further functional experiments showed that m6A methylation negatively regulates NDV infection. Methylated RNA immunoprecipitation sequencing revealed that the m6A-methylated peaks on different functional components of host genes shifted, underwent reprogramming, and were primarily enriched in the coding sequence after NDV infection. The differentially modified genes were mainly enriched in cellular components, as well as autophagy and ubiquitination-mediated proteolysis signaling pathways. Association analysis of RNA sequencing results showed changes in m6A regulated mRNA transcription and revealed that YTHDC1 is a methylation-related enzyme with important catalytic and recognition roles during NDV infection. Additionally, m6A-methylated peaks were detected in the NDV genome, which may be regulated by methylation-related enzymes in the host, subsequently affecting viral replication. Comprehensive analysis of the m6A expression profile after NDV infection indicated that NDV may cause reprogramming of m6A methylation and that m6A plays important roles during infection. Overall, these findings provide insights into the epigenetic etiology and pathogenesis of NDV.
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Affiliation(s)
- Weifeng Yuan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China; Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Yuechi Hou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China; Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Qingyi Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China; Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Ting Lv
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China; Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Jinlian Ren
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China; Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Lei Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China; Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Juncheng Cai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China; Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Bin Xiang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201 Yunnan, China
| | - Qiuyan Lin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China; Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Ming Liao
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chan Ding
- Shanghai Veterinary Research Institute (SHVRI), Chinese Academy of Agricultural Sciences (CAAS), Shanghai 200241, China
| | - Libin Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China; Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.
| | - Tao Ren
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China; Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.
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15
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Abstract
While epigenetic modifications of DNA and histones play main roles in gene transcription regulation, recently discovered post-transcriptional RNA modifications, known as epitranscriptomic modifications, have been found to have a profound impact on gene expression by regulating RNA stability, localization and decoding efficiency. Importantly, genetic variations or environmental perturbations of epitranscriptome modifiers (that is, writers, erasers and readers) are associated with obesity and metabolic diseases, such as type 2 diabetes. The epitranscriptome is closely coupled to epigenetic signalling, adding complexity to our understanding of gene expression in both health and disease. Moreover, the epitranscriptome in the parental generation can affect organismal phenotypes in the next generation. In this Review, we discuss the relationship between epitranscriptomic modifications and metabolic diseases, their relationship with the epigenome and possible therapeutic strategies.
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Affiliation(s)
- Yoshihiro Matsumura
- Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Fan-Yan Wei
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Japan
| | - Juro Sakai
- Division of Molecular Physiology and Metabolism, Tohoku University Graduate School of Medicine, Sendai, Japan.
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
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16
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Zhang Y, Hu W, Li HB. RNA modification-mediated translational control in immune cells. RNA Biol 2023; 20:603-613. [PMID: 37584554 PMCID: PMC10435004 DOI: 10.1080/15476286.2023.2246256] [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] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/17/2023] Open
Abstract
RNA modifications play a vital role in multiple pathways of mRNA metabolism, and translational regulation is essential for immune cells to promptly respond to stimuli and adapt to the microenvironment. N6-methyladenosine (m6A) methylation, which is the most abundant mRNA modification in eukaryotes, primarily functions in the regulation of RNA splicing and degradation. However, the role of m6Amethylation in translational control and its underlying mechanism remain controversial. The role of m6A methylation in translation regulation in immune cells has received relatively limited attention. In this review, we aim to provide a comprehensive summary of current studies on the translational regulation of m6A modifications and recent advances in understanding the translational control regulated by RNA modifications during the immune response. Furthermore, we envision the possible pathways through which m6A modifications may be involved in the regulation of immune cell function via translational control.
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Affiliation(s)
- Yujuan Zhang
- Department of Geriatrics, Center for Immune-Related Diseases, Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine-Yale University Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiguo Hu
- Department of Geriatrics, Center for Immune-Related Diseases, Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hua-Bing Li
- Department of Geriatrics, Center for Immune-Related Diseases, Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine-Yale University Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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17
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Zhang Z, Zhou H, Ouyang X, Dong Y, Sarapultsev A, Luo S, Hu D. Multifaceted functions of STING in human health and disease: from molecular mechanism to targeted strategy. Signal Transduct Target Ther 2022; 7:394. [PMID: 36550103 PMCID: PMC9780328 DOI: 10.1038/s41392-022-01252-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/25/2022] [Accepted: 11/09/2022] [Indexed: 12/24/2022] Open
Abstract
Since the discovery of Stimulator of Interferon Genes (STING) as an important pivot for cytosolic DNA sensation and interferon (IFN) induction, intensive efforts have been endeavored to clarify the molecular mechanism of its activation, its physiological function as a ubiquitously expressed protein, and to explore its potential as a therapeutic target in a wide range of immune-related diseases. With its orthodox ligand 2'3'-cyclic GMP-AMP (2'3'-cGAMP) and the upstream sensor 2'3'-cGAMP synthase (cGAS) to be found, STING acquires its central functionality in the best-studied signaling cascade, namely the cGAS-STING-IFN pathway. However, recently updated research through structural research, genetic screening, and biochemical assay greatly extends the current knowledge of STING biology. A second ligand pocket was recently discovered in the transmembrane domain for a synthetic agonist. On its downstream outputs, accumulating studies sketch primordial and multifaceted roles of STING beyond its cytokine-inducing function, such as autophagy, cell death, metabolic modulation, endoplasmic reticulum (ER) stress, and RNA virus restriction. Furthermore, with the expansion of the STING interactome, the details of STING trafficking also get clearer. After retrospecting the brief history of viral interference and the milestone events since the discovery of STING, we present a vivid panorama of STING biology taking into account the details of the biochemical assay and structural information, especially its versatile outputs and functions beyond IFN induction. We also summarize the roles of STING in the pathogenesis of various diseases and highlight the development of small-molecular compounds targeting STING for disease treatment in combination with the latest research. Finally, we discuss the open questions imperative to answer.
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Affiliation(s)
- Zili Zhang
- grid.33199.310000 0004 0368 7223Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022 Wuhan, China
| | - Haifeng Zhou
- grid.33199.310000 0004 0368 7223Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022 Wuhan, China
| | - Xiaohu Ouyang
- grid.33199.310000 0004 0368 7223Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022 Wuhan, China
| | - Yalan Dong
- grid.33199.310000 0004 0368 7223Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022 Wuhan, China
| | - Alexey Sarapultsev
- grid.426536.00000 0004 1760 306XInstitute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia
| | - Shanshan Luo
- grid.33199.310000 0004 0368 7223Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Desheng Hu
- grid.33199.310000 0004 0368 7223Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022 Wuhan, China ,grid.419897.a0000 0004 0369 313XKey Laboratory of Biological Targeted Therapy, The Ministry of Education, 430022 Wuhan, China ,Clinical Research Center of Cancer Immunotherapy, 430022 Hubei Wuhan, China
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18
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Li H, Guo Y, Qi W, Liao M. N 6-methyladenosine modification of viral RNA and its role during the recognition process of RIG-I-like receptors. Front Immunol 2022; 13:1031200. [PMID: 36582239 PMCID: PMC9792670 DOI: 10.3389/fimmu.2022.1031200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/17/2022] [Indexed: 12/15/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant RNA chemical modification in eukaryotes and is also found in the RNAs of many viruses. In recent years, m6A RNA modification has been reported to have a role not only in the replication of numerous viruses but also in the innate immune escape process. In this review, we describe the viruses that contain m6A in their genomes or messenger RNAs (mRNAs), and summarize the effects of m6A on the replication of different viruses. We also discuss how m6A modification helps viral RNAs escape recognition by exogenous RNA sensors, such as retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), during viral invasion. Overall, the goal of our review is to summarize how m6A regulates viral replication and facilitates innate immune escape. Furthermore, we elaborate on the potential of m6A as a novel antiviral target.
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Affiliation(s)
- Huanan Li
- National Avian Influenza Para-Reference Laboratory (Guangzhou), South China Agricultural University, Guangzhou, China,Key Laboratory of Zoonosis, Ministry of Agriculture and Rural Affairs, Guangzhou, China,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou, China,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Yang Guo
- National Avian Influenza Para-Reference Laboratory (Guangzhou), South China Agricultural University, Guangzhou, China,Key Laboratory of Zoonosis, Ministry of Agriculture and Rural Affairs, Guangzhou, China,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou, China,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Wenbao Qi
- National Avian Influenza Para-Reference Laboratory (Guangzhou), South China Agricultural University, Guangzhou, China,Key Laboratory of Zoonosis, Ministry of Agriculture and Rural Affairs, Guangzhou, China,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou, China,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China,*Correspondence: Wenbao Qi, ; Ming Liao,
| | - Ming Liao
- National Avian Influenza Para-Reference Laboratory (Guangzhou), South China Agricultural University, Guangzhou, China,Key Laboratory of Zoonosis, Ministry of Agriculture and Rural Affairs, Guangzhou, China,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou, China,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China,Guangdong Academy of Agricultural Sciences, Guangzhou, China,*Correspondence: Wenbao Qi, ; Ming Liao,
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19
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Ge Z, Ding S. Regulation of cGAS/STING signaling and corresponding immune escape strategies of viruses. Front Cell Infect Microbiol 2022; 12:954581. [PMID: 36189363 PMCID: PMC9516114 DOI: 10.3389/fcimb.2022.954581] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Innate immunity is the first line of defense against invading external pathogens, and pattern recognition receptors (PRRs) are the key receptors that mediate the innate immune response. Nowadays, there are various PRRs in cells that can activate the innate immune response by recognizing pathogen-related molecular patterns (PAMPs). The DNA sensor cGAS, which belongs to the PRRs, plays a crucial role in innate immunity. cGAS detects both foreign and host DNA and generates a second-messenger cGAMP to mediate stimulator of interferon gene (STING)-dependent antiviral responses, thereby exerting an antiviral immune response. However, the process of cGAS/STING signaling is regulated by a wide range of factors. Multiple studies have shown that viruses directly target signal transduction proteins in the cGAS/STING signaling through viral surface proteins to impede innate immunity. It is noteworthy that the virus utilizes these cGAS/STING signaling regulators to evade immune surveillance. Thus, this paper mainly summarized the regulatory mechanism of the cGAS/STING signaling pathway and the immune escape mechanism of the corresponding virus, intending to provide targeted immunotherapy ideas for dealing with specific viral infections in the future.
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Affiliation(s)
- Zhe Ge
- School of Sport, Shenzhen University, Shenzhen, China
| | - Shuzhe Ding
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, Shanghai, China
- *Correspondence: Shuzhe Ding,
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Maimaiti A, Turhon M, Cheng X, Su R, Kadeer K, Axier A, Ailaiti D, Aili Y, Abudusalamu R, Kuerban A, Wang Z, Aisha M. m6A regulator–mediated RNA methylation modification patterns and immune microenvironment infiltration characterization in patients with intracranial aneurysms. Front Neurol 2022; 13:889141. [PMID: 35989938 PMCID: PMC9389407 DOI: 10.3389/fneur.2022.889141] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundThe role of epigenetic modulation in immunity is receiving increased recognition—particularly in the context of RNA N6-methyladenosine (m6A) modifications. Nevertheless, it is still uncertain whether m6A methylation plays a role in the onset and progression of intracranial aneurysms (IAs). This study aimed to establish the function of m6A RNA methylation in IA, as well as its correlation with the immunological microenvironment.MethodsOur study included a total of 97 samples (64 IA, 33 normal) in the training set and 60 samples (44 IA, 16 normal) in the validation set to systematically assess the pattern of RNA modifications mediated by 22 m6A regulators. The effects of m6A modifications on immune microenvironment features, i.e., immune response gene sets, human leukocyte antigen (HLA) genes, and infiltrating immune cells were explored. We employed Lasso, machine learning, and logistic regression for the purpose of identifying an m6A regulator gene signature of IA with external data validation. For the unsupervised clustering analysis of m6A modification patterns in IA, consensus clustering methods were employed. Enrichment analysis was used to assess immune response activity along with other functional pathways. The identification of m6A methylation markers was identified based on a protein–protein interaction network and weighted gene co-expression network analysis.ResultsWe identified an m6A regulator signature of IGFBP2, IGFBP1, IGF2BP2, YTHDF3, ALKBH5, RBM15B, LRPPRC, and ELAVL1, which could easily distinguish individuals with IA from healthy individuals. Unsupervised clustering revealed three m6A modification patterns. Gene enrichment analysis illustrated that the tight junction, p53 pathway, and NOTCH signaling pathway varied significantly in m6A modifier patterns. In addition, the three m6A modification patterns showed significant differences in m6A regulator expression, immune microenvironment, and bio-functional pathways. Furthermore, macrophages, activated T cells, and other immune cells were strongly correlated with m6A regulators. Eight m6A indicators were discovered—each with a statistically significant correlation with IA—suggesting their potential as prognostic biological markers.ConclusionOur study demonstrates that m6A RNA methylation and the immunological microenvironment are both intricately correlated with the onset and progression of IA. The novel insight into patterns of m6A modification offers a foundation for the development of innovative treatment approaches for IA.
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Affiliation(s)
- Aierpati Maimaiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Mirzat Turhon
- Department of Neurointerventional Surgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Department of Neurointerventional Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xiaojiang Cheng
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Riqing Su
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Kaheerman Kadeer
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Aximujiang Axier
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Dilimulati Ailaiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yirizhati Aili
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Rena Abudusalamu
- Department of Neurology, Neurology Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Ajimu Kuerban
- Department of Neurosurgery, The First People's Hospital of Kashgar Prefecture, Kashgar, China
| | - Zengliang Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Zengliang Wang
| | - Maimaitili Aisha
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Maimaitili Aisha
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Mersinoglu B, Cristinelli S, Ciuffi A. The Impact of Epitranscriptomics on Antiviral Innate Immunity. Viruses 2022; 14:v14081666. [PMID: 36016289 PMCID: PMC9412694 DOI: 10.3390/v14081666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
Epitranscriptomics, i.e., chemical modifications of RNA molecules, has proven to be a new layer of modulation and regulation of protein expression, asking for the revisiting of some aspects of cellular biology. At the virological level, epitranscriptomics can thus directly impact the viral life cycle itself, acting on viral or cellular proteins promoting replication, or impacting the innate antiviral response of the host cell, the latter being the focus of the present review.
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RNA m6A modification: Mapping methods, roles, and mechanisms in acute myeloid leukemia. BLOOD SCIENCE 2022; 4:116-124. [DOI: 10.1097/bs9.0000000000000131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/23/2022] [Indexed: 11/26/2022] Open
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Li J, Teng P, Yang F, Ou X, Zhang J, Chen W. Bioinformatics and Screening of a Circular RNA-microRNA-mRNA Regulatory Network Induced by Coxsackievirus Group B5 in Human Rhabdomyosarcoma Cells. Int J Mol Sci 2022; 23:ijms23094628. [PMID: 35563023 PMCID: PMC9101002 DOI: 10.3390/ijms23094628] [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: 03/18/2022] [Revised: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 02/05/2023] Open
Abstract
Hand, foot and mouth disease (HFMD) caused by Coxsackievirus Group B5 (CVB5) is one of the most common herpetic diseases in human infants and children. The pathogenesis of CVB5 remains unknown. Circular RNAs (CircRNAs), as novel noncoding RNAs, have been shown to play a key role in many pathogenic processes in different species; however, their functions during the process of CVB5 infection remain unclear. In the present study, we investigated the expression profiles of circRNAs using RNA sequencing technology in CVB5-infected and mock-infected human rhabdomyosarcoma cells (CVB5 virus that had been isolated from clinical specimens). In addition, several differentially expressed circRNAs were validated by RT-qPCR. Moreover, the innate immune responses related to circRNA-miRNA-mRNA interaction networks were constructed and verified. A total of 5461 circRNAs were identified at different genomic locations in CVB5 infections and controls, of which 235 were differentially expressed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis demonstrated that the differentially expressed circRNAs were principally involved in specific signaling pathways related to ErbB, TNF, and innate immunity. We further predicted that novel_circ_0002006 might act as a molecular sponge for miR-152-3p through the IFN-I pathway to inhibit CVB5 replication, and that novel_circ_0001066 might act as a molecular sponge for miR-29b-3p via the NF-κB pathway and for the inhibition of CVB5 replication. These findings will help to elucidate the biological functions of circRNAs in the progression of CVB5-related HFMD and identify prospective biomarkers and therapeutic targets for this disease.
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