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Feng J, Meng W, Chen L, Zhang X, Markazi A, Yuan W, Huang Y, Gao SJ. N6-Methyladenosine and Reader Protein YTHDF2 Enhance the Innate Immune Response by Mediating DUSP1 mRNA Degradation and Activating Mitogen-Activated Protein Kinases during Bacterial and Viral Infections. mBio 2023; 14:e0334922. [PMID: 36625590 PMCID: PMC9973302 DOI: 10.1128/mbio.03349-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 01/11/2023] Open
Abstract
Mitogen-activated protein kinases (MAPKs) play critical roles in the induction of numerous cytokines, chemokines, and inflammatory mediators that mobilize the immune system to counter pathogenic infections. Dual-specificity phosphatase 1 (DUSP1) is a member of the dual-specificity phosphatases that inactivates MAPKs through a negative-feedback mechanism. Here, we report that in response to viral and bacterial infections, not only the DUSP1 transcript but also its N6-methyladenosine (m6A) levels rapidly increase together with that of the m6A reader protein YTHDF2, resulting in enhanced YTHDF2-mediated DUSP1 transcript degradation. The knockdown of DUSP1 promotes p38 and Jun N-terminal kinase (JNK) phosphorylation and activation, thus increasing the expression of innate immune response genes, including the interleukin-1β (IL-1β), colony-stimulating factor 3 (CSF3), transglutaminase 2 (TGM2), and proto-oncogene tyrosine-protein kinase Src (SRC) genes. Similarly, the knockdown of the m6A eraser ALKBH5 increases the DUSP1 transcript m6A level, resulting in accelerated transcript degradation, the activation of p38 and JNK, and the enhanced expression of IL-1β, CSF3, TGM2, and SRC. These results demonstrate that m6A and the reader protein YTHDF2 orchestrate optimal innate immune responses during viral and bacterial infections by downregulating the expression of a negative regulator, DUSP1, of the p38 and JNK pathways that are central to innate immune responses against pathogenic infections. IMPORTANCE Innate immunity is central to controlling pathogenic infections and maintaining the homeostasis of the host. In this study, we have revealed a novel mechanism regulating innate immune responses during viral and bacterial infections. We have found that N6-methyladenosine (m6A) and the reader protein YTHDF2 regulate dual-specificity phosphatase 1, a negative regulator of the mitogen-activated protein kinases p38 and JNK, to maximize innate immune responses during viral and bacterial infections. These results provide novel insights into the mechanism regulating innate immunity, which could help in the development of novel approaches for controlling pathogenic infections.
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Affiliation(s)
- Jian Feng
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Wen Meng
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Luping Chen
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Xinquan Zhang
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ashley Markazi
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Weiming Yuan
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Yufei Huang
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Electrical and Computer Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Shou-Jiang Gao
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Transcriptome-wide assessment of N6-methyladenosine modification identifies different gene expression and infection-associated pathways in Treponema pallidum-infected macrophage. J Dermatol Sci 2023; 109:108-116. [PMID: 36841722 DOI: 10.1016/j.jdermsci.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 12/18/2022] [Accepted: 02/16/2023] [Indexed: 02/21/2023]
Abstract
BACKGROUND Treponema pallidum (Tp) is a widespread and destructive pathogen that leads to syphilis. As the acknowledged executor of host immunity, macrophage plays vital roles in combating the invasion and migration of Tp. However, the mechanisms of these processes are largely unknown, especially the critical driver genes and associated modifications. OBJECTIVE We aimed to systematically dissect the global N6-methyladenosine (m6A) RNA modification patterns in Tp-infected macrophages. METHODS The RNA of Tp-infected/non-infected macrophage was extracted, followed by mRNA sequencing and methylated RNA immunoprecipitation (MeRIP) sequencing. Bioinformatics analysis was executed by m6A peaks and motifs identification, Gene ontology and signaling pathways analysis of differentially expressed genes, and comprehensive comparison. The m6A levels were measured by RNA Methylation Assay, and m6A modified genes were determined by qPCR. RESULTS Totally, 2623 unique and 3509 common m6A peaks were proved along with related transcripts in Tp-infected macrophages. The common m6A-related genes were enriched in the signals of oxidative stress, cell differentiation, and angiogenesis, while unique genes in those of metabolism, inflammation, and infection. And differentially expressed transcripts revealed various biological processes and pathways associated with catabolic and infection. They also experienced comprehensive analysis due to hyper-/hypo-methylation. And the m6A level of macrophage was elevated, along with qPCR validation of specific genes. CONCLUSION With a particular m6A transcriptome-wide map, our study provides unprecedented insights into the RNA modification of macrophage stimulated by Tp in vitro, which partially differs from other infections and may provide clues to explore the immune process for syphilis.
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Li J, Ding J, Chen M, Chen K, Zou Y, Xu X, Zhang D, Yu X, Ding Z. Transcriptome-wide N6-methyladenosine modification profiling of mRNAs during infection of Newcastle disease virus in chicken macrophages. Virus Res 2023; 323:198993. [PMID: 36326508 PMCID: PMC10194374 DOI: 10.1016/j.virusres.2022.198993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/15/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
N6-methyladenosine (m6A) modification, the most prevalent post-transcriptional modification of eukaryotic mRNAs, is reported to play a crucial role in viral infection. However, the role of m6A modification during Newcastle disease virus (NDV) infection has remained unclear. In this study, we performed MeRIP-seq to investigate the transcriptome-wide m6A methylome and m6A-modified genes in NDV-infected chicken macrophages. A total of 9496 altered peaks were identified, of which 7015 peaks were significantly upregulated across 3320 genes, and 2481 peaks were significantly down-regulated across 1264 genes. Combined analysis of m6A peaks and mRNA expression showed that 1234 mRNAs had significantly altered levels of methylation and expression after NDV infection, and m6A modification tended to have a negative relationship with mRNA expression, suggesting that m6A modification may regulate the process of NDV infection by regulating gene expression, particularly of the genes important in the innate immune response. To the best of our knowledge, this is the first comprehensive characterization of m6A patterns in chicken macrophage mRNA after NDV infection, providing a valuable basis for further exploring the role of m6A modification mechanisms during the course of NDV infection.
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Affiliation(s)
- Jindou Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Jiaxin Ding
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Minghua Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Kainan Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Yinxue Zou
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xiaohong Xu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Di Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xibing Yu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Zhuang Ding
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
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Yu B, Zeng A, Liu H, Yang Z, Fu M. MiR-654-3p, reduced by the excessive ALKBH5, Alleviated the Inflammation in OA by targeting TNFRSF9, the trigger of the NF-κB pathway. Biochem Biophys Res Commun 2022; 634:30-39. [DOI: 10.1016/j.bbrc.2022.09.103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 11/02/2022]
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Shi X, Zhou H, Wei J, Mo W, Li Q, Lv X. The signaling pathways and therapeutic potential of itaconate to alleviate inflammation and oxidative stress in inflammatory diseases. Redox Biol 2022; 58:102553. [PMID: 36459716 PMCID: PMC9713374 DOI: 10.1016/j.redox.2022.102553] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/19/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
Endogenous small molecules are metabolic regulators of cell function. Itaconate is a key molecule that accumulates in cells when the Krebs cycle is disrupted. Itaconate is derived from cis-aconitate decarboxylation by cis-aconitate decarboxylase (ACOD1) in the mitochondrial matrix and is also known as immune-responsive gene 1 (IRG1). Studies have demonstrated that itaconate plays an important role in regulating signal transduction and posttranslational modification through its immunoregulatory activities. Itaconate is also an important bridge among metabolism, inflammation, oxidative stress, and the immune response. This review summarizes the structural characteristics and classical pathways of itaconate, its derivatives, and the compounds that release itaconate. Here, the mechanisms of itaconate action, including its transcriptional regulation of ATF3/IκBζ axis and type I IFN, its protein modification regulation of KEAP1, inflammasome, JAK1/STAT6 pathway, TET2, and TFEB, and succinate dehydrogenase and glycolytic enzyme metabolic action, are presented. Moreover, the roles of itaconate in diseases related to inflammation and oxidative stress induced by autoimmune responses, viruses, sepsis and IRI are discussed in this review. We hope that the information provided in this review will help increase the understanding of cellular immune metabolism and improve the clinical treatment of diseases related to inflammation and oxidative stress.
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Screening and analysis of immune-related genes of Aedes aegypti infected with DENV2. Acta Trop 2022; 236:106698. [PMID: 36162456 DOI: 10.1016/j.actatropica.2022.106698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/17/2022] [Accepted: 09/18/2022] [Indexed: 01/08/2023]
Abstract
Dengue virus type Ⅱ (DENV2) is a primary serotype responsible for the dengue fever epidemic, and Aedes aegypti is the main DENV2 vector. Understanding the Aedes aegypti immune mechanism against DENV2 is the basis for research on immune blockade in mosquitoes. Some preliminary studies lack validation in the literature, so this study was performed to further study and validate the potential target genes to provide a further basis for screening key target genes. We screened 51 genes possibly related to Aedes aegypti infection and immunity from the literature for further verification. First, bioinformatic methods such as GO, KEGG and PPI analysis were used, and then RT-qPCR was used to detect the changes in mRNA expression in the midguts and salivary glands of Aedes aegypti infected with DENV2.Bioinformatic analysis showed that mostly genes of the glucose metabolism pathway and myoprotein were influenced. In salivary glands, the Gst (xa) and Toll (xb) expression levels were significantly correlated with DENV2 load (y, lg[DENV2 RNA copies]), y = -3436xa+0.2287xb+3.8194 (adjusted R2 = 0.5563, F = 9.148, PF = 0.0045). In midguts, DENV2 load was significantly correlated with the relative Fba(R2 = 0.4381, t = 2.497, p < 0.05, df = 8), UcCr(R2 = 0.4072, t = 2.344, p < 0.05, df = 8) and Gbps1(R2 = 0.4678, t = 2.652, p < 0.05, df = 8) expression levels, but multiple regression did not yield significant results. This study shows that genes related to glucose metabolism and muscle proteins contribute to the interaction between Aedes aegypti and dengue virus. It was confirmed that SAAG-4, histone H4, endoplasmin, catalase and other genes are involved in the regulation of DENV2 infection in Aedes aegypti. It was revealed that GST and Toll in salivary glands may have antagonistic effects on the regulation of DENV2 load. Fba, UcCr and Gbps1 in the midgut may increase DENV2 load. These study results further condensed the potential target gene range of the Aedes aegypti immune mechanism against DENV2 infection and provided basic information for research on the Aedes aegypti in vivo blockade strategy against DENV2.
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RNA modifications: importance in immune cell biology and related diseases. Signal Transduct Target Ther 2022; 7:334. [PMID: 36138023 PMCID: PMC9499983 DOI: 10.1038/s41392-022-01175-9] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/23/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
RNA modifications have become hot topics recently. By influencing RNA processes, including generation, transportation, function, and metabolization, they act as critical regulators of cell biology. The immune cell abnormality in human diseases is also a research focus and progressing rapidly these years. Studies have demonstrated that RNA modifications participate in the multiple biological processes of immune cells, including development, differentiation, activation, migration, and polarization, thereby modulating the immune responses and are involved in some immune related diseases. In this review, we present existing knowledge of the biological functions and underlying mechanisms of RNA modifications, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), N7-methylguanosine (m7G), N4-acetylcytosine (ac4C), pseudouridine (Ψ), uridylation, and adenosine-to-inosine (A-to-I) RNA editing, and summarize their critical roles in immune cell biology. Via regulating the biological processes of immune cells, RNA modifications can participate in the pathogenesis of immune related diseases, such as cancers, infection, inflammatory and autoimmune diseases. We further highlight the challenges and future directions based on the existing knowledge. All in all, this review will provide helpful knowledge as well as novel ideas for the researchers in this area.
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Li M, Cheng W, Zhang L, Zhou C, Peng X, Yu S, Zhang W. Novel Roles of RNA m6A Methylation Regulators in the Occurrence of Alzheimer’s Disease and the Subtype Classification. Int J Mol Sci 2022; 23:ijms231810766. [PMID: 36142676 PMCID: PMC9504232 DOI: 10.3390/ijms231810766] [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: 08/19/2022] [Revised: 09/09/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
Alzheimer’s disease (AD) is one of the most common forms of dementia, closely related to epigenetic factors. N6-methyladenosine (m6A) is the most abundant RNA modification, affecting the pathogenesis and development of neurodegenerative diseases. This study was the first exploration of the combined role of 25 common m6A RNA methylation regulators in AD through the integrated bioinformatics approaches. The 14 m6A regulators related to AD were selected by analyzing differences between AD patients and normal controls. Based on the selected m6A regulators, AD patients could be well classified into two m6A models using consensus clustering. The two clusters of patients had different immune profiles, and m6A regulators were associated with the components of immune cells. Additionally, there were 19 key AD genes obtained by screening differential genes through weighted gene co-expression network and least absolute shrinkage and selection operator regression analysis, which were highly associated with important m6A regulators during the occurrence of AD. More interestingly, NOTCH2 and NME1 could be potential targets for m6A regulation of AD. Taken together, these findings indicate that dysregulation of m6A methylation affects the occurrence of AD and is vital for the subtype classification and immune infiltration of AD.
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Ding C, Xu H, Yu Z, Roulis M, Qu R, Zhou J, Oh J, Crawford J, Gao Y, Jackson R, Sefik E, Li S, Wei Z, Skadow M, Yin Z, Ouyang X, Wang L, Zou Q, Su B, Hu W, Flavell RA, Li HB. RNA m 6A demethylase ALKBH5 regulates the development of γδ T cells. Proc Natl Acad Sci U S A 2022; 119:e2203318119. [PMID: 35939687 PMCID: PMC9388086 DOI: 10.1073/pnas.2203318119] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
γδ T cells are an abundant T cell population at the mucosa and are important in providing immune surveillance as well as maintaining tissue homeostasis. However, despite γδ T cells' origin in the thymus, detailed mechanisms regulating γδ T cell development remain poorly understood. N6-methyladenosine (m6A) represents one of the most common posttranscriptional modifications of messenger RNA (mRNA) in mammalian cells, but whether it plays a role in γδ T cell biology is still unclear. Here, we show that depletion of the m6A demethylase ALKBH5 in lymphocytes specifically induces an expansion of γδ T cells, which confers enhanced protection against gastrointestinal Salmonella typhimurium infection. Mechanistically, loss of ALKBH5 favors the development of γδ T cell precursors by increasing the abundance of m6A RNA modification in thymocytes, which further reduces the expression of several target genes including Notch signaling components Jagged1 and Notch2. As a result, impairment of Jagged1/Notch2 signaling contributes to enhanced proliferation and differentiation of γδ T cell precursors, leading to an expanded mature γδ T cell repertoire. Taken together, our results indicate a checkpoint role of ALKBH5 and m6A modification in the regulation of γδ T cell early development.
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Affiliation(s)
- Chenbo Ding
- aDepartment of Geriatrics, Center for Immune-Related Diseases, Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- bShanghai Jiao Tong University School of Medicine–Yale University Institute for Immune Metabolism, Shanghai 200025, China
| | - Hao Xu
- cDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Zhibin Yu
- aDepartment of Geriatrics, Center for Immune-Related Diseases, Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- bShanghai Jiao Tong University School of Medicine–Yale University Institute for Immune Metabolism, Shanghai 200025, China
| | - Manolis Roulis
- cDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Rihao Qu
- cDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
- dProgram of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520
- eDepartment of Pathology, Yale University School of Medicine, New Haven, CT 06510
| | - Jing Zhou
- aDepartment of Geriatrics, Center for Immune-Related Diseases, Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- bShanghai Jiao Tong University School of Medicine–Yale University Institute for Immune Metabolism, Shanghai 200025, China
| | - Joonseok Oh
- fDepartment of Chemistry, Yale University, New Haven, CT 06520
- gChemical Biology Institute, Yale University, West Haven, CT 06516
| | - Jason Crawford
- fDepartment of Chemistry, Yale University, New Haven, CT 06520
- gChemical Biology Institute, Yale University, West Haven, CT 06516
- hDepartment of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06520
| | - Yimeng Gao
- iSection of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520
- jYale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520
- kYale RNA Center, Yale University School of Medicine, New Haven, CT 06520
| | - Ruaidhrí Jackson
- cDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Esen Sefik
- cDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Simiao Li
- cDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Zheng Wei
- cDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Mathias Skadow
- cDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Zhinan Yin
- lZhuhai Precision Medical Center, Zhuhai People’s Hospital, Jinan University, Zhuhai 519000, Guangdong, China
- mBiomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, Guangdong, China
| | - Xinshou Ouyang
- nSection of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520
| | - Lei Wang
- aDepartment of Geriatrics, Center for Immune-Related Diseases, Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Qiang Zou
- aDepartment of Geriatrics, Center for Immune-Related Diseases, Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Bing Su
- aDepartment of Geriatrics, Center for Immune-Related Diseases, Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- bShanghai Jiao Tong University School of Medicine–Yale University Institute for Immune Metabolism, Shanghai 200025, China
| | - Weiguo Hu
- aDepartment of Geriatrics, Center for Immune-Related Diseases, Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- 2To whom correspondence may be addressed. , , or
| | - Richard A. Flavell
- cDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
- oHHMI, Yale University School of Medicine, New Haven, CT 06520
- 2To whom correspondence may be addressed. , , or
| | - Hua-Bing Li
- aDepartment of Geriatrics, Center for Immune-Related Diseases, Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- bShanghai Jiao Tong University School of Medicine–Yale University Institute for Immune Metabolism, Shanghai 200025, China
- 2To whom correspondence may be addressed. , , or
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Liu Y, Chen C, Wang X, Sun Y, Zhang J, Chen J, Shi Y. An Epigenetic Role of Mitochondria in Cancer. Cells 2022; 11:cells11162518. [PMID: 36010594 PMCID: PMC9406960 DOI: 10.3390/cells11162518] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are not only the main energy supplier but are also the cell metabolic center regulating multiple key metaborates that play pivotal roles in epigenetics regulation. These metabolites include acetyl-CoA, α-ketoglutarate (α-KG), S-adenosyl methionine (SAM), NAD+, and O-linked beta-N-acetylglucosamine (O-GlcNAc), which are the main substrates for DNA methylation and histone post-translation modifications, essential for gene transcriptional regulation and cell fate determination. Tumorigenesis is attributed to many factors, including gene mutations and tumor microenvironment. Mitochondria and epigenetics play essential roles in tumor initiation, evolution, metastasis, and recurrence. Targeting mitochondrial metabolism and epigenetics are promising therapeutic strategies for tumor treatment. In this review, we summarize the roles of mitochondria in key metabolites required for epigenetics modification and in cell fate regulation and discuss the current strategy in cancer therapies via targeting epigenetic modifiers and related enzymes in metabolic regulation. This review is an important contribution to the understanding of the current metabolic-epigenetic-tumorigenesis concept.
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Affiliation(s)
- Yu’e Liu
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Chao Chen
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai 200433, China
| | - Xinye Wang
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yihong Sun
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Jin Zhang
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Juxiang Chen
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai 200433, China
- Correspondence: (J.C.); (Y.S.)
| | - Yufeng Shi
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
- Clinical Center for Brain and Spinal Cord Research, Tongji University, Shanghai 200092, China
- Correspondence: (J.C.); (Y.S.)
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N 6-methyladenosine modification-mediated mRNA metabolism is essential for human pancreatic lineage specification and islet organogenesis. Nat Commun 2022; 13:4148. [PMID: 35851388 PMCID: PMC9293889 DOI: 10.1038/s41467-022-31698-2] [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: 07/23/2021] [Accepted: 06/27/2022] [Indexed: 11/30/2022] Open
Abstract
Pancreatic differentiation from human pluripotent stem cells (hPSCs) provides promising avenues for investigating development and treating diseases. N6-methyladenosine (m6A) is the most prevalent internal messenger RNA (mRNA) modification and plays pivotal roles in regulation of mRNA metabolism, while its functions remain elusive. Here, we profile the dynamic landscapes of m6A transcriptome-wide during pancreatic differentiation. Next, we generate knockout hPSC lines of the major m6A demethylase ALKBH5, and find that ALKBH5 plays significant regulatory roles in pancreatic organogenesis. Mechanistic studies reveal that ALKBH5 deficiency reduces the mRNA stability of key pancreatic transcription factors in an m6A and YTHDF2-dependent manner. We further identify that ALKBH5 cofactor α-ketoglutarate can be applied to enhance differentiation. Collectively, our findings identify ALKBH5 as an essential regulator of pancreatic differentiation and highlight that m6A modification-mediated mRNA metabolism presents an important layer of regulation during cell-fate specification and holds great potentials for translational applications. Ma et al. profile the dynamic landscape of m6A during pancreatic differentiation, and identify ALKBH5 as an essential m6A regulator supporting pancreatic differentiation, indicating a role for m6A-mediated mRNA metabolism in cell-fate specification.
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Liu Y, Song R, Zhao L, Lu Z, Li Y, Zhan X, Lu F, Yang J, Niu Y, Cao X. m 6A demethylase ALKBH5 is required for antibacterial innate defense by intrinsic motivation of neutrophil migration. Signal Transduct Target Ther 2022; 7:194. [PMID: 35764614 PMCID: PMC9240034 DOI: 10.1038/s41392-022-01020-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 12/29/2022] Open
Abstract
Neutrophil migration into the site of infection is necessary for antibacterial innate defense, whereas impaired neutrophil migration may result in excessive inflammation and even sepsis. The neutrophil migration directed by extracellular signals such as chemokines has been extensively studied, yet the intrinsic mechanism for determining neutrophil ability to migrate needs further investigation. N6-methyladenosine (m6A) RNA modification is important in immunity and inflammation, and our preliminary data indicate downregulation of RNA m6A demethylase alkB homolog 5 (ALKBH5) in neutrophils during bacterial infection. Whether m6A modification and ALKBH5 might intrinsically modulate neutrophil innate response remain unknown. Here we report that ALKBH5 is required for antibacterial innate defense by enhancing intrinsic ability of neutrophil migration. We found that deficiency of ALKBH5 increased mortality of mice with polymicrobial sepsis induced by cecal ligation and puncture (CLP), and Alkbh5-deficient CLP mice exhibited higher bacterial burden and massive proinflammatory cytokine production in the peritoneal cavity and blood because of less neutrophil migration. Alkbh5-deficient neutrophils had lower CXCR2 expression, thus exhibiting impaired migration toward chemokine CXCL2. Mechanistically, ALKBH5-mediated m6A demethylation empowered neutrophils with high migration capability through altering the RNA decay, consequently regulating protein expression of its targets, neutrophil migration-related molecules, including increased expression of neutrophil migration-promoting CXCR2 and NLRP12, but decreased expression of neutrophil migration-suppressive PTGER4, TNC, and WNK1. Our findings reveal a previously unknown role of ALKBH5 in imprinting migration-promoting transcriptome signatures in neutrophils and intrinsically promoting neutrophil migration for antibacterial defense, highlighting the potential application of targeting neutrophil m6A modification in controlling bacterial infections.
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Affiliation(s)
- Yang Liu
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, 100005, Beijing, China. .,Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, 300071, Tianjin, China.
| | - Renjie Song
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, 100005, Beijing, China
| | - Lu Zhao
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, 100005, Beijing, China
| | - Zhike Lu
- School of Life Sciences, Westlake University, 310024, Hangzhou, China
| | - Yini Li
- School of Life Sciences, Westlake University, 310024, Hangzhou, China
| | - Xinyi Zhan
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, 100005, Beijing, China
| | - Fengjiao Lu
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, 100005, Beijing, China
| | - Jiang Yang
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, 100005, Beijing, China
| | - Yamei Niu
- Department of Pathology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, 100005, Beijing, China
| | - Xuetao Cao
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, 100005, Beijing, China. .,Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, 300071, Tianjin, China.
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63
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Wu L, Quan W, Zhang Y, Wang M, Ou X, Mao S, Sun D, Yang Q, Wu Y, Wei Y, Jia R, Chen S, Zhu D, Liu M, Zhao X, Zhang S, Huang J, Gao Q, Tian B, Cheng A. Attenuated Duck Hepatitis A Virus Infection Is Associated With High mRNA Maintenance in Duckling Liver via m6A Modification. Front Immunol 2022; 13:839677. [PMID: 35757688 PMCID: PMC9218207 DOI: 10.3389/fimmu.2022.839677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/05/2022] [Indexed: 11/15/2022] Open
Abstract
Host translation is generally modulated by viral infection, including duck hepatitis A virus (DHAV) infection. Previously, we reported that cellular protein synthesis in a cell model of duck embryo fibroblasts is significantly inhibited by DHAV infection but not viral proteins, suggesting that an important viral-host interaction occurs at the translational level. In this study, we aim to further understand the impact of DHAV virulence on cellular N6-methyladenosine (m6A) modification, which is essential to a wide variety of RNA biological processes, such as mRNA stabilization and translation. Using m6A antibody-based immunoprecipitation, m6A-seq, and LC–MS/MS, we observed that m6A-modified mRNA exists in both virulent and attenuated DHAV-infected duckling livers. Importantly, m6A levels in mRNA were much higher in attenuated DHAV-infected livers compared with virulent DHAV-infected livers, suggesting virulence-dependent regulation of m6A modification. Analysis of modification motifs indicated that GAAGAAG is the most enriched motif. Combined m6A-seq and RNA-seq data analysis indicated a generally positive correlation between m6A and mRNA expression levels in DHAV-infected duckling livers. GO analysis of genes with decreased or increased m6A levels showed that these genes were enriched in various terms, including oxidation–reduction processes and antiviral immune responses. Collectively, our work reveals DHAV virulence-dependent coordination between m6A modification and mRNA expression in duckling livers.
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Affiliation(s)
- Liping Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Weili Quan
- ABLife BioBigData Institute, Wuhan, China
| | - Yi Zhang
- ABLife BioBigData Institute, Wuhan, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yaxun Wei
- Center for Genome Analysis, ABLife, Inc., Wuhan, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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64
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Zhang Y, Gao LX, Wang W, Zhang T, Dong FY, Ding WP. M 6 A Demethylase FTO Regulates Cisplatin Resistance of Gastric Cancer by Modulating Autophagy Activation via ULK1. Cancer Sci 2022; 113:3085-3096. [PMID: 35730319 PMCID: PMC9459343 DOI: 10.1111/cas.15469] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/03/2022] [Accepted: 06/13/2022] [Indexed: 11/30/2022] Open
Abstract
Drug resistance is an important factor for treatment failure of gastric cancer. N6‐methyladenosine (m6A) is the predominant mRNA internal modification in eukaryotes. The roles of m6A modification in drug resistance of gastric cancer remains unclear. In the present study, the m6A methylated RNA level was significantly decreased while the expression of m6A demethylase fat mass and obesity‐associated protein (FTO) was obviously elevated in cisplatin‐resistant (SGC‐7901/DDP) gastric cancer cells. Knockdown of FTO reversed cisplatin resistance of SGC‐7901/DDP cells both in vitro and in vivo, which was attributed to the inhibition of Unc‐51‐like kinase 1 (ULK1)‐mediated autophagy. Mechanistically, ULK1 expression was regulated in an FTO‐m6A‐dependent and YTHDF2‐mediated manner. Collectively, our findings indicate that the FTO/ULK1 axis exerts crucial roles in cisplatin resistance of gastric cancer.
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Affiliation(s)
- Yan Zhang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, China.,Department of Gastroenterology, The First Aflliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu, China
| | - Ling-Xi Gao
- Department of Gastroenterology, The First Aflliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu, China
| | - Wen Wang
- Department of Gastroenterology, The First Aflliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu, China
| | - Teng Zhang
- Department of Gastroenterology, The First Aflliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu, China
| | - Fang-Yi Dong
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wen-Ping Ding
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, China.,Department of Radiotherapy, The First Aflliated Hospital of Wannan Medical College, Yijishan Hospital, Wuhu, China
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65
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Dendritic cells in systemic lupus erythematosus: From pathogenesis to therapeutic applications. J Autoimmun 2022; 132:102856. [DOI: 10.1016/j.jaut.2022.102856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 06/15/2022] [Indexed: 11/18/2022]
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66
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Li ZX, Zheng ZQ, Yang PY, Lin L, Zhou GQ, Lv JW, Zhang LL, Chen F, Li YQ, Wu CF, Li F, Ma J, Liu N, Sun Y. WTAP-mediated m 6A modification of lncRNA DIAPH1-AS1 enhances its stability to facilitate nasopharyngeal carcinoma growth and metastasis. Cell Death Differ 2022; 29:1137-1151. [PMID: 34999731 DOI: 10.1038/s41418-021-00905-w] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
As the most predominant RNA epigenetic regulation in eukaryotic cells, N6-methyladenosine (m6A) plays a critical role in human tumorigenesis and cancer progression. However, the biological function and molecular mechanism of m6A regulation in naso-pharyngeal carcinoma (NPC) remain elusive. Here, we showed that Wilms' tumor 1-associating protein (WTAP) expression was apparently upregulated in NPC, and increased WTAP was associated with poor prognosis. WTAP upregulated in NPC was fine-tuned by KAT3A-mediated H3K27 acetylation. Functionally, WTAP was required for the growth and metastasis of NPC. Mechanistically, lncRNA DIAPH1-AS1 was identified as a bona fide m6A target of WTAP. WTAP-mediated m6A modification of DIAPH1-AS1 enhanced its stability relying on the m6A reader IGF2BP2-dependent pathway. Furthermore, DIAPH1-AS1 acted as a molecular adaptor that promoted MTDH-LASP1 complex formation and upregulated LASP1 expression, ultimately facilitating NPC growth and metastasis. Thus, WTAP-mediated DIAPH1-AS1 m6A methylation is required for NPC tumorigenesis and metastasis.
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Affiliation(s)
- Zhi-Xuan Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 510060, Guangzhou, P.R. China
| | - Zi-Qi Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 510060, Guangzhou, P.R. China
| | - Pan-Yang Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 510060, Guangzhou, P.R. China
| | - Li Lin
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 510060, Guangzhou, P.R. China
| | - Guan-Qun Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 510060, Guangzhou, P.R. China
| | - Jia-Wei Lv
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 510060, Guangzhou, P.R. China
| | - Lu-Lu Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, 510060, Guangzhou, P.R. China
| | - FoPing Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 510060, Guangzhou, P.R. China
| | - Ying-Qin Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 510060, Guangzhou, P.R. China
| | - Chen-Fei Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 510060, Guangzhou, P.R. China
| | - Feng Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 510060, Guangzhou, P.R. China
| | - Jun Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 510060, Guangzhou, P.R. China
| | - Na Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 510060, Guangzhou, P.R. China.
| | - Ying Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 510060, Guangzhou, P.R. China.
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67
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Li P, Liu Y, Song R, Zhao L, Yang J, Lu F, Cao X. RNA 2 '-O-Methyltransferase Fibrillarin Facilitates Virus Entry Into Macrophages Through Inhibiting Type I Interferon Response. Front Immunol 2022; 13:793582. [PMID: 35464456 PMCID: PMC9021640 DOI: 10.3389/fimmu.2022.793582] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 03/15/2022] [Indexed: 11/17/2022] Open
Abstract
Type I interferons (IFN-I) play crucial roles in antiviral immune responses through inducing multiple antiviral interferon stimulated genes (ISGs). RNA modifications are emerging as critical post-transcriptional regulators of gene expression programs, which affect diverse biological processes. 2’-O-methylation (Nm) is one of the most common types of RNA modifications found in several kinds of RNA. However, the function and underlying mechanism of Nm modification in regulating viral infection and innate immunity are largely unknown. Here we found that 2’-O-methyladenosine (Am) on poly A+ RNA was increased in virus infected-macrophages. Functional screening identified RNA 2’-O-methyltransferase Fibrillarin (FBL) in facilitating viral infection. Down-regulation of FBL inhibited viral infection through blocking virus entry into macrophages. Furthermore, knockdown of FBL could reduce viral entry by increasing ISGs expression through IFN-I signaling. These results indicated that FBL-mediated Nm modifications of RNA may avoid the innate immune recognition, thereby maintain immune homeostasis. Once FBL is down-regulated, the decreased Nm modifications of RNA in macrophages may act as “non-self” RNA and be recognized by RNA sensor interferon induced with helicase C domain 1 (MDA5), leading to innate immune activation by inducing the expression of IFN-I and ISGs. Therefore, our finding reveals a new role of FBL and its mediated RNA Nm modifications in facilitating viral infection and inhibiting innate immune response, adding mechanistic insight to the RNA modifications in infection and immunity.
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Affiliation(s)
- Panpan Li
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yang Liu
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Renjie Song
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Lu Zhao
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiang Yang
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Fengjiao Lu
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xuetao Cao
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Institute of Immunology, College of Life Sciences, Nankai University, Tianjin, China
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68
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Li Z, Teng M, Jiang Y, Zhang L, Luo X, Liao Y, Yang B. YTHDF1 Negatively Regulates Treponema pallidum-Induced Inflammation in THP-1 Macrophages by Promoting SOCS3 Translation in an m6A-Dependent Manner. Front Immunol 2022; 13:857727. [PMID: 35444649 PMCID: PMC9013966 DOI: 10.3389/fimmu.2022.857727] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
Background Previous studies have confirmed that the bacterium Treponema pallidum (TP) or its proteins provide signals to macrophages that induce an inflammatory response; however, little is known about the negative regulation of this macrophage-mediated inflammatory response during syphilis infection or the underlying mechanism. Recent evidence suggests the role of the RNA modification, N6-adenosine methylation (m6A), in regulating the inflammatory response and pathogen-host cell interactions. Therefore, we hypothesized that m6A plays a role in the regulation of the inflammatory response in macrophages exposed to TP. Methods We first assessed m6A levels in TP-infected macrophages differentiated from the human monocyte cell line THP-1. The binding and interaction between the m6A "writer" methyltransferase-like 3 (METTL3) or the m6A "reader" YT521-B homology (YTH) domain-containing protein YTHDF1 and the suppressor of cytokine signaling 3 (SOCS3), as a major regulator of the inflammatory response, were explored in differentiated TP-infected THP-1 cells as well as in secondary syphilitic lesions from patients. The mechanisms by which YTHDF1 and SOCS3 regulate the inflammatory response in macrophages were assessed. Results and Conclusion After macrophages were stimulated by TP, YTHDF1 was upregulated in the cells. YTHDF1 was also upregulated in the syphilitic lesions compared to adjacent tissue in patients. YTHDF1 recognizes and binds to the m6A methylation site of SOCS3 mRNA, consequently promoting its translation, thereby inhibiting the JAK2/STAT3 pathway, and reducing the secretion of inflammatory factors, which results in anti-inflammatory regulation. This study provides the first demonstration of the role of m6A methylation in the pathological process of syphilis and further offers new insight into the pathogenesis of TP infection.
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Affiliation(s)
- Zhijia Li
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Muzhou Teng
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Yinbo Jiang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Litian Zhang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Xi Luo
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Yuhui Liao
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Bin Yang
- Dermatology Hospital, Southern Medical University, Guangzhou, China
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69
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Liu Y, Wang H, Shao M, Jin Y, Liao B. The functional role of OGDH for maintaining mitochondrial respiration and identity of primed human embryonic stem cells. Biochem Biophys Res Commun 2022; 612:30-36. [DOI: 10.1016/j.bbrc.2022.04.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/13/2022] [Indexed: 11/02/2022]
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70
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Song D, Shyh-Chang N. An RNA methylation code to regulate protein translation and cell fate. Cell Prolif 2022; 55:e13224. [PMID: 35355346 PMCID: PMC9136488 DOI: 10.1111/cpr.13224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/28/2022] [Accepted: 03/06/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Dan Song
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Ng Shyh-Chang
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
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71
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Zhuo R, Xu M, Wang X, Zhou B, Wu X, Leone V, Chang EB, Zhong X. The regulatory role of N 6 -methyladenosine modification in the interaction between host and microbes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1725. [PMID: 35301791 DOI: 10.1002/wrna.1725] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/21/2022] [Accepted: 02/21/2022] [Indexed: 01/02/2023]
Abstract
N6 -methyladenosine (m6 A) is the most prevalent posttranscriptional modification in eukaryotic mRNAs. Dynamic and reversible m6 A modification regulates gene expression to control cellular processes and diverse biological functions. Growing evidence indicated that m6 A modification is involved in the homeostasis of host and microbes (mostly viruses and bacteria). Disturbance of m6 A modification affects the life cycles of viruses and bacteria, however, these microbes could in turn change host m6 A modification leading to human disease including autoimmune diseases and cancer. Thus, we raise the concept that m6 A could be a "messenger" molecule to participate in the interactions between host and microbes. In this review, we summarize the regulatory mechanisms of m6 A modification on viruses and commensal microbiota, highlight the roles of m6 A methylation in the interaction of host and microbes, and finally discuss drugs development targeting m6 A modification. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Ruhao Zhuo
- Joint International Research Laboratory of Animal Health & Food Safety, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Menghui Xu
- Joint International Research Laboratory of Animal Health & Food Safety, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaoyun Wang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Bin Zhou
- Joint International Research Laboratory of Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xin Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Vanessa Leone
- Department of Animal Biologics and Metabolism, University of Wisconsin, Madison, Wisconsin, USA.,Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Eugene B Chang
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Xiang Zhong
- Joint International Research Laboratory of Animal Health & Food Safety, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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72
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Host Cells Actively Resist Porcine Reproductive and Respiratory Syndrome Virus Infection via the IRF8-MicroRNA-10a-SRP14 Regulatory Pathway. J Virol 2022; 96:e0000322. [PMID: 35293774 DOI: 10.1128/jvi.00003-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRNAs) play an important role in the virus-host interaction. Our previous work has indicated that the expression level of miR-10a increased in porcine alveolar macrophages (PAMs) during porcine reproductive and respiratory syndrome virus (PRRSV) infection and further inhibited viral replication through downregulates the expression of host molecule signal-recognition particle 14 (SRP14) protein. However, the molecular mechanism of miR-10a increased after PRRSV infection remains unknown. In the present study, transcription factor interferon regulatory factor 8 (IRF8) was identified as a negative regulator of miR-10a. PRRSV infection decreases the expression level of IRF8 in PAMs, leading to upregulating miR-10a expression to play an anti-PRRSV role. Meanwhile, this work first proved that IRF8 promoted PRRSV replication in an miR-10a-dependent manner. Further, we explained that SRP14, the target gene of miR-10a, promotes the synthesis of the PRRSV genome by interacting with the viral components Nsp2, thus facilitating PRRSV replication. In conclusion, we identified a novel IRF8-miR-10a-SRP14 regulatory pathway against PRRSV infection, which provides new insights into virus-host interactions and suggests potential new antiviral strategies to control PRRSV. IMPORTANCE Porcine reproductive and respiratory syndrome virus (PRRSV) has rapidly spread to the global pig industry and caused incalculable economic damage since first discovered in the 1980s. However, conventional vaccines do not provide satisfactory protection. Understanding the molecular mechanisms of host resistance to PRRSV infection is necessary to develop safe and effective strategies to control PRRSV. During viral infection, miRNAs play vital roles in regulating the expression of viral or host genes at the posttranscriptional level. The significance of our study is that we revealed the transcriptional regulation mechanism of the antiviral molecule miR-10a after PRRSV infection. Moreover, our research also explained the mechanism of host molecule SRP14, the target gene of miR-10a regulating PRRSV replication. Thus, we report a novel regulatory pathway of IRF8-miR-10a-SRP14 against PRRSV infection, which provides new insights into virus-host interactions and suggests potential new control measures for future PRRSV outbreaks.
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73
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Global profiling reveals common and distinct N6-methyladenosine (m6A) regulation of innate immune responses during bacterial and viral infections. Cell Death Dis 2022; 13:234. [PMID: 35288544 PMCID: PMC8921188 DOI: 10.1038/s41419-022-04681-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/11/2022] [Accepted: 02/18/2022] [Indexed: 12/15/2022]
Abstract
N6-methyladenosine (m6A) is a dynamic post-transcriptional RNA modification influencing all aspects of mRNA biology. While m6A modifications during numerous viral infections have been described, the role of m6A in innate immune response remains unclear. Here, we examined cellular m6A epitranscriptomes during infections of Pseudomonas aeruginosa and herpes simplex virus type 1 (HSV-1), and lipopolysaccharide (LPS) stimulation to identify m6A-regulated innate immune response genes. We showed that a significant portion of cellular genes including many innate immune response genes underwent m6A modifications in 5'UTR and 3'UTR. We identified common and distinct m6A-modified genes under different stimulating conditions. Significantly, the expression of a subset of innate immune response genes was positively correlated with m6A level. Importantly, we identified genes that had significant enrichments of m6A peaks during P. aeruginosa infection following knockdown of m6A "eraser" ALKBH5, confirming the regulation of these genes by m6A and ALKBH5. Among them, we confirmed the association of m6A modification with gene expression in immune response genes TNFAIP3, IFIT1, IFIT2 and IFIH1. Taken together, our results revealed the vital role of m6A in regulating innate immunity against bacterial and viral infections. These works also provided rich resources for the scientific community.
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Control of animal virus replication by RNA adenosine methylation. Adv Virus Res 2022; 112:87-114. [PMID: 35840182 DOI: 10.1016/bs.aivir.2022.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Methylation at the N6-position of either adenosine (m6A) or 2'-O-methyladenosine (m6Am) represents two of the most abundant internal modifications of coding and non-coding RNAs, influencing their maturation, stability and function. Additionally, although less abundant and less well-studied, monomethylation at the N1-position (m1A) can have profound effects on RNA folding. It has been known for several decades that RNAs produced by both DNA and RNA viruses can be m6A/m6Am modified and the list continues to broaden through advances in detection technologies and identification of the relevant methyltransferases. Recent studies have uncovered varied mechanisms used by viruses to manipulate the m6A pathway in particular, either to enhance virus replication or to antagonize host antiviral defenses. As such, RNA modifications represent an important frontier of exploration in the broader realm of virus-host interactions, and this new knowledge already suggests exciting opportunities for therapeutic intervention. In this review we summarize the principal mechanisms by which m6A/m6Am can promote or hinder viral replication, describe how the pathway is actively manipulated by biomedically important viruses, and highlight some remaining gaps in understanding how adenosine methylation of RNA controls viral replication and pathogenesis.
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Li G, Luo R, Zhang W, He S, Wang B, Liang H, Song Y, Ke W, Shi Y, Feng X, Zhao K, Wu X, Zhang Y, Wang K, Yang C. m6A hypomethylation of DNMT3B regulated by ALKBH5 promotes intervertebral disc degeneration via E4F1 deficiency. Clin Transl Med 2022; 12:e765. [PMID: 35340126 PMCID: PMC8957938 DOI: 10.1002/ctm2.765] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The intervertebral disc (IVD) degeneration is the leading cause of low back pain, which accounts for a main cause of disability. N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNAs and is involved in various diseases and cellular processes by modulating mRNA fate. However, the critical role of m6A regulation in IVD degeneration remains unclear. Nucleus pulposus cell (NPC) senescence is critical for the progression of IVD degeneration. Here, we uncovered the role and explored the regulatory mechanism of m6A in NPC senescence during IVD degeneration. METHODS Identification of NPC senescence during IVD degeneration was based on the analysis of tissue samples and the cellular model. ALKBH5 upregulation inducing cellular senescence was confirmed by functional experiments in vivo and in vitro. ChIP-qPCR and DNA-Pulldown were used to reveal increased ALKBH5 was regulated by KDM4A-mediated H3K9me3. Furthermore, Me-RIP-seq was performed to identify m6A hypomethylation of DNMT3B transcripts in senescent NPCs. Stability analysis showed that DNMT3B expression was enhanced for less YTHDF2 recognition and increased DNMT3B promoted NPC senescence and IVD degeneration via E4F1 methylation by in vivo and in vitro analyses. RESULTS Expression of ALKBH5 is enhanced during IVD degeneration and NPC senescence, due to decreased KDM4A-mediated H3K9me3 modification. Functionally, ALKBH5 causes NPC senescence by demethylating DNMT3B transcripts and in turn promoting its expression via less YTHDF2 recognition and following degradation due to transcript hypomethylation in vitro and in vivo. Increased DNMT3B promotes the development of IVD degeneration and NPC senescence, mechanistically by methylating CpG islands of E4F1 at the promoter region and thus restraining its transcription and expression. CONCLUSIONS Collectively, our findings reveal an epigenetic interplay mechanism in NPC senescence and IVD degeneration, presenting a critical pro-senescence role of ALKBH5 and m6A hypomethylation, highlighting the therapeutic potential of targeting the m6A/DNMT3B/E4F1 axis for treating IVD degeneration.
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Affiliation(s)
- Gaocai Li
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Rongjin Luo
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Weifeng Zhang
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Shujie He
- Department of Cardiology, Union Hospital, and Key Laboratory of Biological Targeted Therapy of the Ministry of EducationTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Bingjin Wang
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Huaizhen Liang
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yu Song
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Wencan Ke
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yunsong Shi
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Xiaobo Feng
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Kangcheng Zhao
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Xinghuo Wu
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yukun Zhang
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Kun Wang
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Cao Yang
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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76
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Chen J, Wei X, Wang X, Liu T, Zhao Y, Chen L, Luo Y, Du H, Li Y, Liu T, Cao L, Zhou Z, Zhang Z, Liang L, Li L, Yan X, Zhang X, Deng X, Yang G, Yin P, Hao J, Yin Z, You F. TBK1-METTL3 axis facilitates antiviral immunity. Cell Rep 2022; 38:110373. [PMID: 35172162 DOI: 10.1016/j.celrep.2022.110373] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 11/30/2021] [Accepted: 01/21/2022] [Indexed: 02/09/2023] Open
Abstract
mRNA m6A modification is heavily involved in modulation of immune responses. However, its function in antiviral immunity is controversial, and how immune responses regulate m6A modification remains elusive. We here find TBK1, a key kinase of antiviral pathways, phosphorylates the core m6A methyltransferase METTL3 at serine 67. The phosphorylated METTL3 interacts with the translational complex, which is required for enhancing protein translation, thus facilitating antiviral responses. TBK1 also promotes METTL3 activation and m6A modification to stabilize IRF3 mRNA. Type I interferon (IFN) induction is severely impaired in METTL3-deficient cells. Mettl3fl/fl-lyz2-Cre mice are more susceptible to influenza A virus (IAV)-induced lethality than control mice. Consistently, Ythdf1-/- mice show higher mortality than wild-type mice due to decreased IRF3 expression and subsequently attenuated IFN production. Together, we demonstrate that innate signals activate METTL3 via TBK1, and METTL3-mediated m6A modification secures antiviral immunity by promoting mRNA stability and protein translation.
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Affiliation(s)
- Jingxuan 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 100191, China; College of Acupuncture & Massage, Shaanxi University of Chinese Medicine, Xixian New Area, Shaanxi Province 712046, 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 100191, China
| | - Xiao Wang
- 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 100191, China
| | - Tong Liu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, 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 100191, 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 100191, 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 100191, China
| | - Hongqiang Du
- 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 100191, 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 100191, China
| | - Tongtong 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 100191, China
| | - Lili Cao
- 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 100191, China
| | - Zhe Zhou
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, 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 100191, China
| | - Ling Liang
- Institute of Systems Biomedicine, Department of Biochemistry and Biophysics, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lu Li
- College of Acupuncture & Massage, Shaanxi University of Chinese Medicine, Xixian New Area, Shaanxi Province 712046, China
| | - Xuhui Yan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuehui Zhang
- Department of Dental Materials, National Engineering Laboratory for Digital and Material Technology of Stomatology & NMPA Key Laboratory for Dental Materials, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - Xuliang Deng
- Department of Dental Materials, National Engineering Laboratory for Digital and Material Technology of Stomatology & NMPA Key Laboratory for Dental Materials, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - Guang Yang
- Departments of Parasitology and Public Health and Preventive Medicine, School of Medicine, Jinan University, No. 601, Huangpu Avenue West, Guangzhou, Guangdong 510632, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianlei Hao
- Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, Guangdong 519000, China; The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, Guangdong 510632, China
| | - Zhinan Yin
- Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, Guangdong 519000, China; The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, Guangdong 510632, 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 100191, China.
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Wu R, Kang R, Tang D. Mitochondrial ACOD1/IRG1 in infection and sterile inflammation. JOURNAL OF INTENSIVE MEDICINE 2022; 2:78-88. [PMID: 36789185 PMCID: PMC9924012 DOI: 10.1016/j.jointm.2022.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/31/2021] [Accepted: 01/12/2022] [Indexed: 12/15/2022]
Abstract
Immunometabolism is a dynamic process involving the interplay of metabolism and immune response in health and diseases. Increasing evidence suggests that impaired immunometabolism contributes to infectious and inflammatory diseases. In particular, the mitochondrial enzyme aconitate decarboxylase 1 (ACOD1, best known as immunoresponsive gene 1 [IRG1]) is upregulated under various inflammatory conditions and serves as a pivotal regulator of immunometabolism involved in itaconate production, macrophage polarization, inflammasome activation, and oxidative stress. Consequently, the activation of the ACOD1 pathway is implicated in regulating the pathogenic process of sepsis and septic shock, which are part of a clinical syndrome of life-threatening organ failure caused by a dysregulated host response to pathogen infection. In this review, we discuss the latest research advances in ACOD1 expression and function, with particular attention to how the ACOD1-itaconate pathway affects infection and sterile inflammation diseases. These new insights may give us a deeper understanding of the role of immunometabolism in innate immunity.
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Affiliation(s)
- Runliu Wu
- Department of Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, Texas 75390, USA,Corresponding author: Daolin Tang, Department of Surgery, UT Southwestern Medical Center, Dallas, Texas 75390, USA.
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Liu R, Ou L, Sheng B, Hao P, Li P, Yang X, Xue G, Zhu L, Luo Y, Zhang P, Yang P, Li H, Feng DD. Mixed-weight Neural Bagging for Detecting m6A Modifications in SARS-CoV-2 RNA Sequencing. IEEE Trans Biomed Eng 2022; 69:2557-2568. [PMID: 35148261 PMCID: PMC9599617 DOI: 10.1109/tbme.2022.3150420] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Objective: The m6A modification is the most common ribonucleic acid (RNA) modification, playing a role in prompting the virus's gene mutation and protein structure changes in the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Nanopore single-molecule direct RNA sequencing (DRS) provides data support for RNA modification detection, which can preserve the potential \documentclass[12pt]{minimal}
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}{}$m^6A$\end{document} signature compared to second-generation sequencing. However, due to insufficient DRS data, there is a lack of methods to find m6A RNA modifications in DRS. Our purpose is to identify \documentclass[12pt]{minimal}
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}{}$m^6A$\end{document} modifications in DRS precisely. Methods: We present a methodology for identifying \documentclass[12pt]{minimal}
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}{}$m^6A$\end{document} modifications that incorporated mapping and extracted features from DRS data. To detect \documentclass[12pt]{minimal}
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}{}$m^6A$\end{document} modifications, we introduce an ensemble method called mixed-weight neural bagging (MWNB), trained with 5-base RNA synthetic DRS containing modified and unmodified \documentclass[12pt]{minimal}
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}{}$m^6A$\end{document}. Results: Our MWNB model achieved the highest classification accuracy of 97.85% and AUC of 0.9968. Additionally, we applied the MWNB model to the COVID-19 dataset; the experiment results reveal a strong association with biomedical experiments. Conclusion: Our strategy enables the prediction of \documentclass[12pt]{minimal}
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}{}$m^6A$\end{document} modifications using DRS data and completes the identification of \documentclass[12pt]{minimal}
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}{}$m^6A$\end{document} modifications on the SARS-CoV-2. Significance: The Corona Virus Disease 2019 (COVID-19) outbreak has significantly influence, caused by the SARS-CoV-2. An RNA modification called \documentclass[12pt]{minimal}
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}{}$m^6A$\end{document} is connected with viral infections. The appearance of \documentclass[12pt]{minimal}
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}{}$m^6A$\end{document} modifications related to several essential proteins affects proteins’ structure and function. Therefore, finding the location and number of \documentclass[12pt]{minimal}
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}{}$m^6A$\end{document} RNA modifications is crucial for subsequent analysis of the protein expression profile.
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79
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Burgess HM, Vink EI, Mohr I. Minding the message: tactics controlling RNA decay, modification, and translation in virus-infected cells. Genes Dev 2022; 36:108-132. [PMID: 35193946 PMCID: PMC8887129 DOI: 10.1101/gad.349276.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
With their categorical requirement for host ribosomes to translate mRNA, viruses provide a wealth of genetically tractable models to investigate how gene expression is remodeled post-transcriptionally by infection-triggered biological stress. By co-opting and subverting cellular pathways that control mRNA decay, modification, and translation, the global landscape of post-transcriptional processes is swiftly reshaped by virus-encoded factors. Concurrent host cell-intrinsic countermeasures likewise conscript post-transcriptional strategies to mobilize critical innate immune defenses. Here we review strategies and mechanisms that control mRNA decay, modification, and translation in animal virus-infected cells. Besides settling infection outcomes, post-transcriptional gene regulation in virus-infected cells epitomizes fundamental physiological stress responses in health and disease.
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Affiliation(s)
- Hannah M Burgess
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Elizabeth I Vink
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA.,Laura and Isaac Perlmutter Cancer Institute, New York University School of Medicine, New York, New York 10016, USA
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80
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Wang A, Tao W, Tong J, Gao J, Wang J, Hou G, Qian C, Zhang G, Li R, Wang D, Ren X, Zhang K, Ding S, Flavell RA, Li H, Pan W, Zhu S. m6A modifications regulate intestinal immunity and rotavirus infection. eLife 2022; 11:73628. [PMID: 35098923 PMCID: PMC8860440 DOI: 10.7554/elife.73628] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 01/28/2022] [Indexed: 12/02/2022] Open
Abstract
N6-methyladenosine (m6A) is an abundant mRNA modification and affects many biological processes. However, how m6A levels are regulated during physiological or pathological processes such as virus infections, and the in vivo function of m6A in the intestinal immune defense against virus infections are largely unknown. Here, we uncover a novel antiviral function of m6A modification during rotavirus (RV) infection in small bowel intestinal epithelial cells (IECs). We found that rotavirus infection induced global m6A modifications on mRNA transcripts by down-regulating the m6a eraser ALKBH5. Mice lacking the m6A writer enzymes METTL3 in IECs (Mettl3ΔIEC) were resistant to RV infection and showed increased expression of interferons (IFNs) and IFN-stimulated genes (ISGs). Using RNA-sequencing and m6A RNA immuno-precipitation (RIP)-sequencing, we identified IRF7, a master regulator of IFN responses, as one of the primary m6A targets during virus infection. In the absence of METTL3, IECs showed increased Irf7 mRNA stability and enhanced type I and III IFN expression. Deficiency in IRF7 attenuated the elevated expression of IFNs and ISGs and restored susceptibility to RV infection in Mettl3ΔIEC mice. Moreover, the global m6A modification on mRNA transcripts declined with age in mice, with a significant drop from 2 weeks to 3 weeks post birth, which likely has broad implications for the development of intestinal immune system against enteric viruses early in life. Collectively, we demonstrated a novel host m6A-IRF7-IFN antiviral signaling cascade that restricts rotavirus infection in vivo.
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Affiliation(s)
- Anmin Wang
- Department of Digestive Disease, University of Science and Technology of China, Hefei, China
| | - Wanyiin Tao
- Department of Digestive Disease, University of Science and Technology of China, Hefei, China
| | - Jiyu Tong
- Department of Microbiology and Immunology, Shanghai Jiao Tong University, Shanghai, China
| | - Juanzi Gao
- Department of Digestive Disease, University of Science and Technology of China, Hefei, China
| | - Jinghao Wang
- Department of Digestive Disease, University of Science and Technology of China, Hefei, China
| | - Gaopeng Hou
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, United States
| | - Chen Qian
- Department of Digestive Disease, University of Science and Technology of China, Hefei, China
| | - Guorong Zhang
- Department of Digestive Disease, University of Science and Technology of China, Hefei, China
| | - Runzhi Li
- Department of Digestive Disease, University of Science and Technology of China, Hefei, China
| | - Decai Wang
- Department of Digestive Disease, University of Science and Technology of China, Hefei, China
| | - Xingxing Ren
- Department of Digestive Disease, University of Science and Technology of China, Hefei, China
| | - Kaiguang Zhang
- Department of Digestive Disease, University of Science and Technology of China, Hefei, China
| | - Siyuan Ding
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, United States
| | - Richard A Flavell
- Department of Immunobiology, Yale University, New Haven, United States
| | - Huabing Li
- Department of Microbiology and Immunology, Shanghai Jiao Tong University, Shanghai, China
| | - Wen Pan
- Department of Digestive Disease, University of Science and Technology of China, Hefei, China
| | - Shu Zhu
- Institute of Immunology, University of Science and Technology of China, Hefei, China
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81
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Wang S, Lv W, Li T, Zhang S, Wang H, Li X, Wang L, Ma D, Zang Y, Shen J, Xu Y, Wei W. Dynamic regulation and functions of mRNA m6A modification. Cancer Cell Int 2022; 22:48. [PMID: 35093087 PMCID: PMC8800407 DOI: 10.1186/s12935-022-02452-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/03/2022] [Indexed: 12/27/2022] Open
Abstract
AbstractN6-Methyladenosine (m6A), the most abundant internal modification associated with eukaryotic mRNAs, has emerged as a dynamic regulatory mechanism controlling the expression of genes involved in many physiological activities by affecting various steps of mRNA metabolism, including splicing, export, translation, and stability. Here, we review the general role of m6A, highlighting recent advances related to the three major types enzymes that determine the level of m6A modification (i.e., writers, erasers, and readers) and the regulatory mechanism by which m6A influences multiple stages of RNA metabolism. This review clarifies the close connection and interaction between m6A modification and nuclear gene expression, and provides key background information for further studies of its roles in numerous physiological and pathophysiological processes. Among them, perhaps the most eye-catching process is tumorigenesis. Clarifying the molecular mechanism of tumorigenesis, development and metastasis in various tissues of the human body is conducive to curbing out-of-control cell activities from the root and providing a new strategy for human beings to defeat tumors.
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82
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Nie K, Yi J, Yang Y, Deng M, Yang Y, Wang T, Chen X, Zhang Z, Wang X. A Broad m6A Modification Landscape in Inflammatory Bowel Disease. Front Cell Dev Biol 2022; 9:782636. [PMID: 35127705 PMCID: PMC8809481 DOI: 10.3389/fcell.2021.782636] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022] Open
Abstract
Background and Aims: N6-Methyladenosine (m6A) is the most common post-transcriptional modification on eukaryotic mRNA, affecting the mRNA’s fate. The role of m6A regulation in inflammatory bowel disease is unclear. Here, we investigated the m6A landscape in inflammatory bowel diseases (IBD). Methods: Eleven human IBD microarray datasets were recruited from the Gene Expression Omnibus database and four were selected as discovery cohorts. An RNA-seq dataset from the Inflammatory Bowel Disease Multi’omics Database was used as a validation cohort. m6A regulators were measured in volunteers’ colonic samples. Consensus clustering and immune scoring were used to estimate the characteristics of m6A regulation in IBD. m6A-related characteristics of different sub-phenotypes, sample sources, and biological therapeutic responses were determined using seven independent datasets. Results: m6A modification involves methyltransferases (writers), demethylases (erasers), and methylation-reading proteins (readers). A wide interaction exists between m6A regulators and IBD risk genes. The IBD risk loci can also be modified by m6A modifications in the public m6A sequencing data. Furthermore, m6A regulators displayed extensive differential expression in four independent discovery cohorts that share common differential genes (IGF2BP2, HNRNPA2B1, ZCCHC4, and EIF3I). In the validated cohort and enrolled volunteers’ colonic biopsy samples, the differential m6A regulators were reconfirmed. Two clusters of consensus clustering exhibit different immune phenotypes. m6A-modified positions exist in the core IBD immune cytokines. Another set of IBD datasets revealed m6A-related differences across clinical phenotypes, biological samples, and therapeutic response subgroups in IBD patients. Conclusion: Regulation of m6A methylation is widely involved in IBD occurrence and development. m6A modifications in risk variants, core cytokines, immune cells, and other proteins may deeply influence the pathophysiology and clinical phenotypes. Further studies are needed to determine its role in IBD.
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Affiliation(s)
- Kai Nie
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Jun Yi
- Department of Gastroenterology, The Xiangya Hospital of Central South University, Changsha, China
| | - Yuanyuan Yang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Minzi Deng
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
| | - Yan Yang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Tianyu Wang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xuejie Chen
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Zhaoyu Zhang
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
- Cancer Research Institute, Central South University, Changsha, China
- *Correspondence: Zhaoyu Zhang, ; Xiaoyan Wang,
| | - Xiaoyan Wang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Cancer Research Institute, Central South University, Changsha, China
- *Correspondence: Zhaoyu Zhang, ; Xiaoyan Wang,
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83
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Zhao B, Wang W, Zhao Y, Qiao H, Gao Z, Chuai X. Regulation of Antiviral Immune Response by N 6-Methyladenosine of mRNA. Front Microbiol 2022; 12:789605. [PMID: 34975810 PMCID: PMC8716812 DOI: 10.3389/fmicb.2021.789605] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 10/28/2021] [Indexed: 12/11/2022] Open
Abstract
Host innate and adaptive immune responses play a vital role in clearing infected viruses. Meanwhile, viruses also evolve a series of mechanisms to weaken the host immune responses and evade immune defense. Recently, N6-methyladenosine (m6A), the most prevalent mRNA modification, has been revealed to regulate multiple steps of RNA metabolism, such as mRNA splicing, localization, stabilization, and translation, thus participating in many biological phenomena, including viral infection. In the process of virus–host interaction, the m6A modification that presents on the virus RNA impedes capture by the pattern recognition receptors, and the m6A modification appearing on the host immune-related molecules regulate interferon response, immune cell differentiation, inflammatory cytokine production, and other immune responses induced by viral infection. This review summarizes the research advances about the regulatory role of m6A modification in the innate and adaptive immune responses during viral infections.
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Affiliation(s)
- Baoxin Zhao
- Department of Pathogen Biology, Hebei Medical University, Shijiazhuang, China.,Institute of Medical and Health Science, Hebei Medical University, Shijiazhuang, China
| | - Weijie Wang
- Department of Pathogen Biology, Hebei Medical University, Shijiazhuang, China.,Institute of Medical and Health Science, Hebei Medical University, Shijiazhuang, China
| | - Yan Zhao
- Department of Pathogen Biology, Hebei Medical University, Shijiazhuang, China.,Institute of Medical and Health Science, Hebei Medical University, Shijiazhuang, China
| | - Hongxiu Qiao
- Department of Pathogen Biology, Hebei Medical University, Shijiazhuang, China.,Institute of Medical and Health Science, Hebei Medical University, Shijiazhuang, China
| | - Zhiyun Gao
- Department of Pathogen Biology, Hebei Medical University, Shijiazhuang, China.,Institute of Medical and Health Science, Hebei Medical University, Shijiazhuang, China
| | - Xia Chuai
- Department of Pathogen Biology, Hebei Medical University, Shijiazhuang, China.,Institute of Medical and Health Science, Hebei Medical University, Shijiazhuang, China
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84
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Dubey PK, Patil M, Singh S, Dubey S, Ahuja P, Verma SK, Krishnamurthy P. Increased m6A-RNA methylation and FTO suppression is associated with myocardial inflammation and dysfunction during endotoxemia in mice. Mol Cell Biochem 2022; 477:129-141. [PMID: 34581943 PMCID: PMC8758538 DOI: 10.1007/s11010-021-04267-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/17/2021] [Indexed: 01/03/2023]
Abstract
Endotoxemia triggers life-threatening immune and cardiovascular response that leads to tissue damage, multi-organ failure, and death. The understanding of underlying molecular mechanisms is still evolving. N6-methyladenosine (m6A)-RNA modification plays key regulatory role in numerous biological processes. However, it remains unclear whether endotoxemia alters RNA methylation in the myocardium. In the current study, we investigated the effect of lipopolysaccharide (LPS)-induced endotoxemia on m6A-RNA methylation and its implications on myocardial inflammation and left ventricular (LV) function. Following LPS administration, mice showed increases in m6A-RNA methylation in the myocardium with a corresponding decrease in the expression of fat mass and obesity-associated protein (FTO, an m6A eraser/demethylase). The changes were associated with a significant increase in expression of myocardial inflammatory cytokine genes, such as IL-6, TNF-α, IL-1β, and reduced LV function. Moreover, rat cardiomyoblasts (H9c2) exposed to LPS showed similar changes (with increase in m6A-RNA methylation and inflammatory cytokine genes, whereas downregulation of FTO). Furthermore, methylated RNA immunoprecipitation assay showed hypermethylation and increase in the expression of IL-6 and TNF-α genes in LPS-treated H9c2 cells as compared to untreated cells. Interestingly, FTO knockdown in cardiomyocytes mimicked the above effects. Taken together, these data suggest that endotoxemia-induced m6A methylation might play a critical role in expression of cardiac proinflammatory cytokines, and modulation of m6A methylation might limit myocardial inflammation and dysfunction during endotoxemia.
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Affiliation(s)
- Praveen K Dubey
- Department of Biomedical Engineering, School of Medicine and School of Engineering, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Mallikarjun Patil
- Department of Biomedical Engineering, School of Medicine and School of Engineering, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Sarojini Singh
- Department of Biomedical Engineering, School of Medicine and School of Engineering, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Shubham Dubey
- Department of Biomedical Engineering, School of Medicine and School of Engineering, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Paras Ahuja
- Science and Technology Honors College, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Suresh Kumar Verma
- Division of Cardiovascular Disease, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Prasanna Krishnamurthy
- Department of Biomedical Engineering, School of Medicine and School of Engineering, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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85
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Yu Y, Pan Y, Fan Z, Xu S, Gao Z, Ren Z, Yu J, Li W, Liu F, Gu J, Yuan Y, Du Z. LuHui Derivative, A Novel Compound That Inhibits the Fat Mass and Obesity-Associated (FTO), Alleviates the Inflammatory Response and Injury in Hyperlipidemia-Induced Cardiomyopathy. Front Cell Dev Biol 2021; 9:731365. [PMID: 34881240 PMCID: PMC8647038 DOI: 10.3389/fcell.2021.731365] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 10/25/2021] [Indexed: 12/04/2022] Open
Abstract
Hyperlipidemia is a major risk factor for metabolic disorders and cardiovascular injury. The excessive deposition of saturated fatty acids in the heart leads to chronic cardiac inflammation, which in turn causes myocardial damage and systolic dysfunction. However, the effective suppression of cardiac inflammation has emerged as a new strategy to reduce the impact of hyperlipidemia on cardiovascular disease. In this study, we identified a novel monomer, known as LuHui Derivative (LHD), which reduced the serum levels of total cholesterol (TC), triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), and reduced lipid deposition in cardiomyocytes. In addition, LHD treatment improved cardiac function, reduced hyperlipidemia-induced inflammatory infiltration in cardiomyocytes and suppressed the release of interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α). From a mechanistic perspective, cluster of differentiation 36 (CD36), an important cell surface receptor, was identified as a downstream target following the LHD treatment of palmitic acid-induced inflammation in cardiomyocytes. LHD specifically binds the pocket containing the regulatory sites of RNA methylation in the fat mass and obesity-associated (FTO) protein that is responsible for elevated intracellular m6A levels. Moreover, the overexpression of the N6-methyladenosine (m6A) demethylase FTO markedly increased CD36 expression and suppressed the anti-inflammatory effects of LHD. Conversely, loss-of-function of FTO inhibited palmitic acid-induced cardiac inflammation and altered CD36 expression by diminishing the stability of CD36 mRNA. Overall, our results provide evidence for the crucial role of LHD in fatty acid-induced cardiomyocyte inflammation and present a new strategy for the treatment of hyperlipidemia and its complications.
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Affiliation(s)
- Ying Yu
- Institute of Clinical Pharmacology, The Second Affiliated Hospital of Harbin Medical University (University Key Laboratory of Drug Research, Heilongjiang Province), Harbin, China
| | - Yumiao Pan
- Institute of Clinical Pharmacology, The Second Affiliated Hospital of Harbin Medical University (University Key Laboratory of Drug Research, Heilongjiang Province), Harbin, China
| | - Ziyi Fan
- Institute of Clinical Pharmacology, The Second Affiliated Hospital of Harbin Medical University (University Key Laboratory of Drug Research, Heilongjiang Province), Harbin, China
| | - Silun Xu
- Institute of Clinical Pharmacology, The Second Affiliated Hospital of Harbin Medical University (University Key Laboratory of Drug Research, Heilongjiang Province), Harbin, China
| | - Zhiyuan Gao
- Institute of Clinical Pharmacology, The Second Affiliated Hospital of Harbin Medical University (University Key Laboratory of Drug Research, Heilongjiang Province), Harbin, China
| | - Zijing Ren
- Institute of Clinical Pharmacology, The Second Affiliated Hospital of Harbin Medical University (University Key Laboratory of Drug Research, Heilongjiang Province), Harbin, China
| | - Jie Yu
- Institute of Clinical Pharmacology, The Second Affiliated Hospital of Harbin Medical University (University Key Laboratory of Drug Research, Heilongjiang Province), Harbin, China
| | - Wen Li
- Institute of Clinical Pharmacology, The Second Affiliated Hospital of Harbin Medical University (University Key Laboratory of Drug Research, Heilongjiang Province), Harbin, China
| | - Fangtong Liu
- Institute of Clinical Pharmacology, The Second Affiliated Hospital of Harbin Medical University (University Key Laboratory of Drug Research, Heilongjiang Province), Harbin, China
| | - Jintao Gu
- Institute of Clinical Pharmacology, The Second Affiliated Hospital of Harbin Medical University (University Key Laboratory of Drug Research, Heilongjiang Province), Harbin, China
| | - Ye Yuan
- Institute of Clinical Pharmacology, The Second Affiliated Hospital of Harbin Medical University (University Key Laboratory of Drug Research, Heilongjiang Province), Harbin, China.,Department of Clinical Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Zhimin Du
- Institute of Clinical Pharmacology, The Second Affiliated Hospital of Harbin Medical University (University Key Laboratory of Drug Research, Heilongjiang Province), Harbin, China.,Department of Clinical Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, China.,State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau, China
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86
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Lisy S, Rothamel K, Ascano M. RNA Binding Proteins as Pioneer Determinants of Infection: Protective, Proviral, or Both? Viruses 2021; 13:2172. [PMID: 34834978 PMCID: PMC8625426 DOI: 10.3390/v13112172] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 12/18/2022] Open
Abstract
As the first intracellular host factors that directly interact with the genomes of RNA viruses, RNA binding proteins (RBPs) have a profound impact on the outcome of an infection. Recent discoveries brought about by new methodologies have led to an unprecedented ability to peer into the earliest events between viral RNA and the RBPs that act upon them. These discoveries have sparked a re-evaluation of current paradigms surrounding RBPs and post-transcriptional gene regulation. Here, we highlight questions that have bloomed from the implementation of these novel approaches. Canonical RBPs can impact the fates of both cellular and viral RNA during infection, sometimes in conflicting ways. Noncanonical RBPs, some of which were first characterized via interactions with viral RNA, may encompass physiological roles beyond viral pathogenesis. We discuss how these RBPs might discriminate between an RNA of either cellular or viral origin and thus exert either pro- or antiviral effects-which is a particular challenge as viruses contain mechanisms to mimic molecular features of cellular RNA.
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Affiliation(s)
- Samantha Lisy
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.L.); (K.R.)
| | - Katherine Rothamel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.L.); (K.R.)
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Manuel Ascano
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.L.); (K.R.)
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87
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Figueroa F, Vega-Gibson A, Catrileo J, Gaete-Argel A, Riquelme-Barrios S, Alonso-Palomares LA, Tapia LI, Valiente-Echeverría F, Soto-Rifo R, Acevedo ML. N 6 -Methyladenosine Negatively Regulates Human Respiratory Syncytial Virus Replication. Front Cell Dev Biol 2021; 9:739445. [PMID: 34671602 PMCID: PMC8521026 DOI: 10.3389/fcell.2021.739445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification described in eukaryotic mRNA and several viral RNA including human respiratory syncytial virus (HRSV). Here, we evaluated the impact of m6A writers, erasers and readers on HRSV genomic RNA accumulation and inclusion bodies assembly during viral replication. We observed that the METTL3/METTL14 m6A writer complex plays a negative role in HRSV protein synthesis and viral titers, while m6A erasers FTO and ALKBH5 had the opposite effect. We also observed that m6A readers YTHDF1-3 bind to the viral genomic RNA inducing a decrease in its intracellular levels and thus, inhibiting viral replication. Finally, we observed that overexpression of YTHDFs proteins caused a decrease in the size of inclusion bodies (IBs), accompanied by an increase in their number. METTL3 knockdown cells showed an opposite effect indicating that the dynamics of IBs assembly and coalescence are strongly affected by m6A readers in a mechanism dependent on m6A writers. Taken together, our results demonstrated that the m6A modification negatively affects HRSV replication, possibly through a mechanism involving the assembly of inclusion bodies, the main factories of viral genomic RNA synthesis.
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Affiliation(s)
- Fabian Figueroa
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Alonso Vega-Gibson
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Joseline Catrileo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Aracelly Gaete-Argel
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Sebastian Riquelme-Barrios
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Luis Antonio Alonso-Palomares
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Lorena I Tapia
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,Department of Pediatrics and Pediatric Surgery, Hospital Roberto del Río, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Fernando Valiente-Echeverría
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Ricardo Soto-Rifo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile.,HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Monica L Acevedo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
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88
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Si C, Chen C, Guo Y, Kang Q, Sun Z. Effect, Mechanism, and Applications of Coding/Non-coding RNA m6A Modification in Tumor Microenvironment. Front Cell Dev Biol 2021; 9:711815. [PMID: 34660577 PMCID: PMC8514707 DOI: 10.3389/fcell.2021.711815] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/30/2021] [Indexed: 01/07/2023] Open
Abstract
The tumor microenvironment (TME), which includes immune cells, fibroblasts, and other components, is the site of tumor cell growth and metastasis and significantly impacts tumor development. Among them, N6-methyladenosine RNA modifications (m6A RNA modifications) are the most abundant internal modifications in coding and non-coding RNAs, which can significantly influence the cancer process and have potential as biomarkers and potential therapeutic targets for tumor therapy. This manuscript reviews the role of m6A RNA modifications in TME and their application in tumor therapy. To some extent, an in-depth understanding of the relationship between TME and m6A RNA modifications will provide new approaches and ideas for future cancer therapy.
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Affiliation(s)
- Chaohua Si
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Chen Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yaxin Guo
- Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Qiaozhen Kang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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89
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Lan L, Sun YJ, Liu L, Cheng L. A photo-responsive chemical modulation of m 6A RNA demethylase FTO. Chem Commun (Camb) 2021; 57:10548-10551. [PMID: 34553720 DOI: 10.1039/d1cc04091j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The adenine N6-methylation m6A is a crucial modification that is associated with several biological functions. One of the two m6A demethylases FTO has arisen as an attractive target for the development of novel cancer therapies. Here, we describe a new design, synthesis and evaluation of a photo-responsive and selective inhibitor of FTO.
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Affiliation(s)
- Ling Lan
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Ying-Jie Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
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90
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Cross-Talk between Oxidative Stress and m 6A RNA Methylation in Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:6545728. [PMID: 34484567 PMCID: PMC8416400 DOI: 10.1155/2021/6545728] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/03/2021] [Accepted: 08/06/2021] [Indexed: 12/14/2022]
Abstract
Oxidative stress is a state of imbalance between oxidation and antioxidation. Excessive ROS levels are an important factor in tumor development. Damage stimulation and excessive activation of oncogenes cause elevated ROS production in cancer, accompanied by an increase in the antioxidant capacity to retain redox homeostasis in tumor cells at an increased level. Although moderate concentrations of ROS produced in cancer cells contribute to maintaining cell survival and cancer progression, massive ROS accumulation can exert toxicity, leading to cancer cell death. RNA modification is a posttranscriptional control mechanism that regulates gene expression and RNA metabolism, and m6A RNA methylation is the most common type of RNA modification in eukaryotes. m6A modifications can modulate cellular ROS levels through different mechanisms. It is worth noting that ROS signaling also plays a regulatory role in m6A modifications. In this review, we concluded the effects of m6A modification and oxidative stress on tumor biological functions. In particular, we discuss the interplay between oxidative stress and m6A modifications.
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91
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Furuse Y. RNA Modifications in Genomic RNA of Influenza A Virus and the Relationship between RNA Modifications and Viral Infection. Int J Mol Sci 2021; 22:ijms22179127. [PMID: 34502037 PMCID: PMC8431438 DOI: 10.3390/ijms22179127] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/23/2021] [Accepted: 08/23/2021] [Indexed: 02/07/2023] Open
Abstract
Recent studies about the transcriptome-wide presence of RNA modifications have revealed their importance in many cellular functions. Nevertheless, information about RNA modifications in viral RNA is scarce, especially for negative-strand RNA viruses. Here we provide a catalog of RNA modifications including m1A, ac4C, m7G, inosine, and pseudouridine on RNA derived from an influenza A virus infected into A549 cells, as studied by RNA immunoprecipitation followed by deep-sequencing. Possible regions with RNA modifications were found in the negative-strand segments of viral genomic RNA. In addition, our analyses of previously published data revealed that the expression levels of the host factors for RNA modifications were affected by an infection with influenza A virus, and some of the host factors likely have a proviral effect. RNA modification is a novel aspect of host-virus interactions leading to the discovery of previously unrecognized viral pathogenicity mechanisms and has the potential to aid the development of novel antivirals.
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Affiliation(s)
- Yuki Furuse
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan;
- Hakubi Center for Advanced Research, Kyoto University, Kyoto 606-8501, Japan
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92
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Ma S, Yan J, Barr T, Zhang J, Chen Z, Wang LS, Sun JC, Chen J, Caligiuri MA, Yu J. The RNA m6A reader YTHDF2 controls NK cell antitumor and antiviral immunity. J Exp Med 2021; 218:e20210279. [PMID: 34160549 PMCID: PMC8225680 DOI: 10.1084/jem.20210279] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/07/2021] [Accepted: 05/13/2021] [Indexed: 12/13/2022] Open
Abstract
N 6-methyladenosine (m6A) is the most prevalent posttranscriptional modification on RNA. NK cells are the predominant innate lymphoid cells that mediate antiviral and antitumor immunity. However, whether and how m6A modifications affect NK cell immunity remain unknown. Here, we discover that YTHDF2, a well-known m6A reader, is upregulated in NK cells upon activation by cytokines, tumors, and cytomegalovirus infection. Ythdf2 deficiency in NK cells impairs NK cell antitumor and antiviral activity in vivo. YTHDF2 maintains NK cell homeostasis and terminal maturation, correlating with modulating NK cell trafficking and regulating Eomes, respectively. YTHDF2 promotes NK cell effector function and is required for IL-15-mediated NK cell survival and proliferation by forming a STAT5-YTHDF2 positive feedback loop. Transcriptome-wide screening identifies Tardbp to be involved in cell proliferation or survival as a YTHDF2-binding target in NK cells. Collectively, we elucidate the biological roles of m6A modifications in NK cells and highlight a new direction to harness NK cell antitumor immunity.
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Affiliation(s)
- Shoubao Ma
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA
- Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA
| | - Jiazhuo Yan
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA
- Department of Gynecological Radiotherapy, Harbin Medical University Cancer Hospital, Harbin, China
| | - Tasha Barr
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA
| | - Jianying Zhang
- Department of Computational and Quantitative Medicine, City of Hope National Medical Center, Los Angeles, CA
| | - Zhenhua Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Los Angeles, CA
| | - Li-Shu Wang
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Joseph C. Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Los Angeles, CA
- Comprehensive Cancer Center, City of Hope, Los Angeles, CA
| | - Michael A. Caligiuri
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA
- Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA
- Comprehensive Cancer Center, City of Hope, Los Angeles, CA
| | - Jianhua Yu
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA
- Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA
- Comprehensive Cancer Center, City of Hope, Los Angeles, CA
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Los Angeles, CA
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93
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Qin F, Cai B, Zhao J, Zhang L, Zheng Y, Liu B, Gao C. Methyltransferase-Like Protein 14 Attenuates Mitochondrial Antiviral Signaling Protein Expression to Negatively Regulate Antiviral Immunity via N 6 -methyladenosine Modification. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100606. [PMID: 34047074 PMCID: PMC8336497 DOI: 10.1002/advs.202100606] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/15/2021] [Indexed: 05/07/2023]
Abstract
Mitochondrial antiviral signaling (MAVS) protein is the core signaling adaptor in the RNA signaling pathway. Thus, appropriate regulation of MAVS expression is essential for antiviral immunity against RNA virus infection. However, the regulation of MAVS expression at the mRNA level especially at the post transcriptional level is not well-defined. Here, it is reported that the MAVS mRNA undergoes N6 -methyladenosine (m6 A) modification through methyltransferase-like protein 14 (METTL14), which leads to a fast turnover of MAVS mRNA. Knockdown or deficiency of METTL14 increases MAVS mRNA stability, and downstream phosphorylation of TBK1/IRF3 and interferon-β production in response to RNA viruses. Compared to wild-type mice, heterozygotes Mettl14+/- mice better tolerate RNA virus infection. The authors' findings unveil a novel mechanism to regulate the stability of MAVS transcripts post-transcriptionally through m6 A modification.
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Affiliation(s)
- Fei Qin
- Key Laboratory of Infection and Immunity of Shandong Province and Department of ImmunologySchool of Biomedical SciencesShandong UniversityJinanShandong250012P. R. China
| | - Baoshan Cai
- Key Laboratory of Infection and Immunity of Shandong Province and Department of ImmunologySchool of Biomedical SciencesShandong UniversityJinanShandong250012P. R. China
| | - Jian Zhao
- Key Laboratory of Infection and Immunity of Shandong Province and Department of ImmunologySchool of Biomedical SciencesShandong UniversityJinanShandong250012P. R. China
| | - Lei Zhang
- Key Laboratory of Infection and Immunity of Shandong Province and Department of ImmunologySchool of Biomedical SciencesShandong UniversityJinanShandong250012P. R. China
| | - Yi Zheng
- Key Laboratory of Infection and Immunity of Shandong Province and Department of ImmunologySchool of Biomedical SciencesShandong UniversityJinanShandong250012P. R. China
| | - Bingyu Liu
- Key Laboratory of Infection and Immunity of Shandong Province and Department of ImmunologySchool of Biomedical SciencesShandong UniversityJinanShandong250012P. R. China
| | - Chengjiang Gao
- Key Laboratory of Infection and Immunity of Shandong Province and Department of ImmunologySchool of Biomedical SciencesShandong UniversityJinanShandong250012P. R. China
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94
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Zhang W, Qian Y, Jia G. The detection and functions of RNA modification m 6A based on m 6A writers and erasers. J Biol Chem 2021; 297:100973. [PMID: 34280435 PMCID: PMC8350415 DOI: 10.1016/j.jbc.2021.100973] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 12/26/2022] Open
Abstract
N6-methyladenosine (m6A) is the most frequent chemical modification in eukaryotic mRNA and is known to participate in a variety of physiological processes, including cancer progression and viral infection. The reversible and dynamic m6A modification is installed by m6A methyltransferase (writer) enzymes and erased by m6A demethylase (eraser) enzymes. m6A modification recognized by m6A binding proteins (readers) regulates RNA processing and metabolism, leading to downstream biological effects such as promotion of stability and translation or increased degradation. The m6A writers and erasers determine the abundance of m6A modifications and play decisive roles in its distribution and function. In this review, we focused on m6A writers and erasers and present an overview on their known functions and enzymatic molecular mechanisms, showing how they recognize substrates and install or remove m6A modifications. We also summarize the current applications of m6A writers and erasers for m6A detection and highlight the merits and drawbacks of these available methods. Lastly, we describe the biological functions of m6A in cancers and viral infection based on research of m6A writers and erasers and introduce new assays for m6A functionality via programmable m6A editing tools.
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Affiliation(s)
- Wei Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yang Qian
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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95
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Bechara R, Amatya N, Bailey RD, Li Y, Aggor FEY, Li DD, Jawale CV, Coleman BM, Dai N, Gokhale NS, Taylor TC, Horner SM, Poholek AC, Bansal A, Biswas PS, Gaffen SL. The m 6A reader IMP2 directs autoimmune inflammation through an IL-17- and TNFα-dependent C/EBP transcription factor axis. Sci Immunol 2021; 6:eabd1287. [PMID: 34215679 PMCID: PMC8404281 DOI: 10.1126/sciimmunol.abd1287] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 04/02/2021] [Accepted: 06/03/2021] [Indexed: 12/15/2022]
Abstract
Excessive cytokine activity underlies many autoimmune conditions, particularly through the interleukin-17 (IL-17) and tumor necrosis factor-α (TNFα) signaling axis. Both cytokines activate nuclear factor κB, but appropriate induction of downstream effector genes requires coordinated activation of other transcription factors, notably, CCAAT/enhancer binding proteins (C/EBPs). Here, we demonstrate the unexpected involvement of a posttranscriptional "epitranscriptomic" mRNA modification [N6-methyladenosine (m6A)] in regulating C/EBPβ and C/EBPδ in response to IL-17A, as well as IL-17F and TNFα. Prompted by the observation that C/EBPβ/δ-encoding transcripts contain m6A consensus sites, we show that Cebpd and Cebpb mRNAs are subject to m6A modification. Induction of C/EBPs is enhanced by an m6A methylase "writer" and suppressed by a demethylase "eraser." The only m6A "reader" found to be involved in this pathway was IGF2BP2 (IMP2), and IMP2 occupancy of Cebpd and Cebpb mRNA was enhanced by m6A modification. IMP2 facilitated IL-17-mediated Cebpd mRNA stabilization and promoted translation of C/EBPβ/δ in response to IL-17A, IL-17F, and TNFα. RNA sequencing revealed transcriptome-wide IL-17-induced transcripts that are IMP2 influenced, and RNA immunoprecipitation sequencing identified the subset of mRNAs that are directly occupied by IMP2, which included Cebpb and Cebpd Lipocalin-2 (Lcn2), a hallmark of autoimmune kidney injury, was strongly dependent on IL-17, IMP2, and C/EBPβ/δ. Imp2-/- mice were resistant to autoantibody-induced glomerulonephritis (AGN), showing impaired renal expression of C/EBPs and Lcn2 Moreover, IMP2 deletion initiated only after AGN onset ameliorated disease. Thus, posttranscriptional regulation of C/EBPs through m6A/IMP2 represents a previously unidentified paradigm of cytokine-driven autoimmune inflammation.
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Affiliation(s)
- Rami Bechara
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nilesh Amatya
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Rachel D Bailey
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yang Li
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Felix E Y Aggor
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - De-Dong Li
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Chetan V Jawale
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bianca M Coleman
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ning Dai
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Nandan S Gokhale
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Tiffany C Taylor
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Amanda C Poholek
- Division of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anita Bansal
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Partha S Biswas
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sarah L Gaffen
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA.
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96
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Wang X, Ji Y, Feng P, Liu R, Li G, Zheng J, Xue Y, Wei Y, Ji C, Chen D, Li J. The m6A Reader IGF2BP2 Regulates Macrophage Phenotypic Activation and Inflammatory Diseases by Stabilizing TSC1 and PPAR γ. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2100209. [PMID: 34258163 PMCID: PMC8261491 DOI: 10.1002/advs.202100209] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/06/2021] [Indexed: 05/20/2023]
Abstract
Phenotypic polarization of macrophages is regulated by a milieu of cues in the local tissue microenvironment. Currently, little is known about how the intrinsic regulators modulate proinflammatory (M1) versus prohealing (M2) macrophages activation. Here, it is observed that insulin-like growth factor 2 messenger RNA (mRNA)-binding protein 2 (IGF2BP2)-deleted macrophages exhibit enhanced M1 phenotype and promote dextran sulfate sodium induced colitis development. However, the IGF2BP2-/- macrophages are refractory to interleukin-4 (IL-4) induced activation and alleviate cockroach extract induced pulmonary allergic inflammation. Molecular studies indicate that IGF2BP2 switches M1 macrophages to M2 activation by targeting tuberous sclerosis 1 via an N6-methyladenosine (m6A)-dependent manner. Additionally, it is also shown a signal transducer and activators of transcription 6 (STAT6)-high mobility group AT-hook 2-IGF2BP2-peroxisome proliferator activated receptor-γ axis involves in M2 macrophages differentiation. These findings highlight a key role of IGF2BP2 in regulation of macrophages activation and imply a potential therapeutic target of macrophages in the inflammatory diseases.
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Affiliation(s)
- Xia Wang
- Department of PhysiologySchool of Basic Medical SciencesCheeloo College of MedicineShandong UniversityJinanShandong250012China
| | - Yuge Ji
- Department of PhysiologySchool of Basic Medical SciencesCheeloo College of MedicineShandong UniversityJinanShandong250012China
| | - Panpan Feng
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanShandong250012China
| | - Rucheng Liu
- Department of PhysiologySchool of Basic Medical SciencesCheeloo College of MedicineShandong UniversityJinanShandong250012China
| | - Guosheng Li
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanShandong250012China
| | - Junjie Zheng
- Department of PhysiologySchool of Basic Medical SciencesCheeloo College of MedicineShandong UniversityJinanShandong250012China
| | - Yaqiang Xue
- ABLife BioBigData InstituteWuhanHubei430075China
| | - Yaxun Wei
- Center for Genoem AnalysisABLife Inc.WuhanHubei430075China
| | - Chunyan Ji
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanShandong250012China
| | - Dawei Chen
- Laboratory of Medical ChemistryInterdisciplinary Cluster for Applied Genoproteomics (GIGA) Stem CellsUniversity of LiègeCHU, Sart‐TilmanLiège4000Belgium
| | - Jingxin Li
- Department of PhysiologySchool of Basic Medical SciencesCheeloo College of MedicineShandong UniversityJinanShandong250012China
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97
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Feng L, Fan Y, Zhou J, Li S, Zhang X. The RNA demethylase ALKBH5 promotes osteoblast differentiation by modulating Runx2 mRNA stability. FEBS Lett 2021; 595:2007-2014. [PMID: 34105773 DOI: 10.1002/1873-3468.14145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/18/2021] [Accepted: 05/27/2021] [Indexed: 11/06/2022]
Abstract
AlkB homolog 5 (ALKBH5) has been reported as a key m6A demethylase that is involved in development and diseases; however, the function of ALKBH5 in osteogenesis remains unknown. In this study, we report that ALKBH5 mRNA and protein expression were upregulated during osteoblast differentiation and that ALKBH5 knockdown suppressed osteoblast differentiation, mineralization, and the expression of osteogenic biomarkers. Conversely, ALKBH5 overexpression promoted osteogenesis. Moreover, the expression of wild-type ALKBH5, but not the m6A-modified active site mutant ALKBH5, could rescue ALKBH5 knockdown-induced osteogenesis inhibition. Furthermore, knockdown of ALKBH5 significantly impaired the mRNA stability of the transcription factor Runx2, which plays a key role in osteoblast differentiation. Taken together, our results suggest that ALKBH5 promotes osteogenesis through modulating Runx2 mRNA stability.
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Affiliation(s)
- Lingling Feng
- Department of Paediatrics, Affiliated Maternity and Child Health Care Hospital of Nantong University, China
| | - Yunshan Fan
- Department of Orthopedics, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jinjun Zhou
- Department of Paediatrics, Affiliated Maternity and Child Health Care Hospital of Nantong University, China
| | - Shuangshuang Li
- Department of Paediatrics, Affiliated Maternity and Child Health Care Hospital of Nantong University, China
| | - Xiaohua Zhang
- Department of Paediatrics, Affiliated Maternity and Child Health Care Hospital of Nantong University, China
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98
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Zhou J, Zhang X, Hu J, Qu R, Yu Z, Xu H, Chen H, Yan L, Ding C, Zou Q, Ye Y, Wang Z, Flavell RA, Li HB. m 6A demethylase ALKBH5 controls CD4 + T cell pathogenicity and promotes autoimmunity. SCIENCE ADVANCES 2021; 7:7/25/eabg0470. [PMID: 34134995 PMCID: PMC8208713 DOI: 10.1126/sciadv.abg0470] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/30/2021] [Indexed: 05/31/2023]
Abstract
N6-methyladenosine (m6A) modification is dynamically regulated by "writer" and "eraser" enzymes. m6A "writers" have been shown to ensure the homeostasis of CD4+ T cells, but the "erasers" functioning in T cells is poorly understood. Here, we reported that m6A eraser AlkB homolog 5 (ALKBH5), but not FTO, maintains the ability of naïve CD4+ T cells to induce adoptive transfer colitis. In addition, T cell-specific ablation of ALKBH5 confers protection against experimental autoimmune encephalomyelitis. During the induced neuroinflammation, ALKBH5 deficiency increased m6A modification on interferon-γ and C-X-C motif chemokine ligand 2 messenger RNA (mRNA), thus decreasing their mRNA stability and protein expression in CD4+ T cells. These modifications resulted in attenuated CD4+ T cell responses and diminished recruitment of neutrophils into the central nervous system. Our findings reveal an unexpected specific role of ALKBH5 as an m6A eraser in controlling the pathogenicity of CD4+ T cells during autoimmunity.
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Affiliation(s)
- Jing Zhou
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520-8055, USA
| | - Xingli Zhang
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jiajia Hu
- Department of Nuclear Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Rihao Qu
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Zhibin Yu
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hao Xu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520-8055, USA
| | - Huifang Chen
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lichong Yan
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520-8055, USA
| | - Chenbo Ding
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520-8055, USA
| | - Qiang Zou
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Youqiong Ye
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhengting Wang
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520-8055, USA.
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520-8055, USA
| | - Hua-Bing Li
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520-8055, USA
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99
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From A to m 6A: The Emerging Viral Epitranscriptome. Viruses 2021; 13:v13061049. [PMID: 34205979 PMCID: PMC8227502 DOI: 10.3390/v13061049] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 12/18/2022] Open
Abstract
There are over 100 different chemical RNA modifications, collectively known as the epitranscriptome. N6-methyladenosine (m6A) is the most commonly found internal RNA modification in cellular mRNAs where it plays important roles in the regulation of the mRNA structure, stability, translation and nuclear export. This modification is also found in viral RNA genomes and in viral mRNAs derived from both RNA and DNA viruses. A growing body of evidence indicates that m6A modifications play important roles in regulating viral replication by interacting with the cellular m6A machinery. In this review, we will exhaustively detail the current knowledge on m6A modification, with an emphasis on its function in virus biology.
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100
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Wang X, Xia H, Liu S, Cao L, You F. Epigenetic regulation in antiviral innate immunity. Eur J Immunol 2021; 51:1641-1651. [PMID: 33964027 DOI: 10.1002/eji.202048975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/03/2021] [Indexed: 12/24/2022]
Abstract
Emerging life-threatening viruses have posed great challenges to public health. It is now increasingly clear that epigenetics plays a role in shaping host-virus interactions and there is a great need for a more thorough understanding of these intricate interactions through the epigenetic lens, which may represent potential therapeutic opportunities in the clinic. In this review, we highlight the current understanding of the roles of key epigenetic regulators - chromatin remodeling and histone modification - in modulating chromatin openness during host defense against virus. We also discuss how the RNA modification m6A (N6-methyladenosine) affects fundamental aspects of host-virus interactions. We conclude with future directions for uncovering more detailed functions that epigenetic regulation exerts on both host cells and viruses during infection.
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Affiliation(s)
- Xiao Wang
- Department of Immunology, Institute of Systems Biomedicine, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, P. R. China
| | - Huawei Xia
- Department of Immunology, Institute of Systems Biomedicine, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, P. R. China
| | - Shengde Liu
- Department of Gastrointestinal Oncology, Key laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital and Institute, Beijing, P. R. China
| | - Lili Cao
- Department of Immunology, Institute of Systems Biomedicine, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, P. R. China
| | - Fuping You
- Department of Immunology, Institute of Systems Biomedicine, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, P. R. China
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