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Deng Y, Zhou J, Li HB. The physiological and pathological roles of RNA modifications in T cells. Cell Chem Biol 2024; 31:1578-1592. [PMID: 38986618 DOI: 10.1016/j.chembiol.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/20/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024]
Abstract
RNA molecules undergo dynamic chemical modifications in response to various external or cellular stimuli. Some of those modifications have been demonstrated to post-transcriptionally modulate the RNA transcription, localization, stability, translation, and degradation, ultimately tuning the fate decisions and function of mammalian cells, particularly T cells. As a crucial part of adaptive immunity, T cells play fundamental roles in defending against infections and tumor cells. Recent findings have illuminated the importance of RNA modifications in modulating T cell survival, proliferation, differentiation, and functional activities. Therefore, understanding the epi-transcriptomic control of T cell biology enables a potential avenue for manipulating T cell immunity. This review aims to elucidate the physiological and pathological roles of internal RNA modifications in T cell development, differentiation, and functionality drawn from current literature, with the goal of inspiring new insights for future investigations and providing novel prospects for T cell-based immunotherapy.
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Affiliation(s)
- Yu Deng
- Shanghai Institute of Immunology, 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
| | - Jing Zhou
- Shanghai Institute of Immunology, 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
| | - Hua-Bing Li
- Shanghai Institute of Immunology, 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 Geriatrics, Medical Center on Aging of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Chongqing International Institute for Immunology, Chongqing 401320, China.
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Karmakar A, Kumar U, Prabhu S, Ravindran V, Nagaraju SP, Suryakanth VB, Prabhu MM, Karmakar S. Molecular profiling and therapeutic tailoring to address disease heterogeneity in systemic lupus erythematosus. Clin Exp Med 2024; 24:223. [PMID: 39294397 PMCID: PMC11410857 DOI: 10.1007/s10238-024-01484-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 09/02/2024] [Indexed: 09/20/2024]
Abstract
Systemic lupus erythematosus (SLE) is a chronic, heterogeneous, systemic autoimmune disease characterized by autoantibody production, complement activation, and immune complex deposition. SLE predominantly affects young, middle-aged, and child-bearing women with episodes of flare-up and remission, although it affects males at a much lower frequency (female: male; 7:1 to 15:1). Technological and molecular advancements have helped in patient stratification and improved patient prognosis, morbidity, and treatment regimens overall, impacting quality of life. Despite several attempts to comprehend the pathogenesis of SLE, knowledge about the precise molecular mechanisms underlying this disease is still lacking. The current treatment options for SLE are pragmatic and aim to develop composite biomarkers for daily practice, which necessitates the robust development of novel treatment strategies and drugs targeting specific responsive pathways. In this communication, we review and aim to explore emerging therapeutic modalities, including multiomics-based approaches, rational drug design, and CAR-T-cell-based immunotherapy, for the management of SLE.
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Affiliation(s)
- Abhibroto Karmakar
- Department of General Medicine, Kasturba Medical College, Manipal, Manipal Academy Higher Education, Manipal, India
| | - Uma Kumar
- Department of Rheumatology, All India Institute of Medical Sciences New Delhi, New Delhi, India
| | - Smitha Prabhu
- Department of Dermatology, Kasturba Medical College, Manipal Academy Higher Education, Manipal, India
| | - Vinod Ravindran
- Department of General Medicine, Kasturba Medical College, Manipal, Manipal Academy Higher Education, Manipal, India
- Department of Rheumatology, Centre for Rheumatology, Kozhikode, Kerala, India
| | - Shankar Prasad Nagaraju
- Department of Nephrology, Kasturba Medical College Manipal, Manipal Academy Higher Education, Manipal, India
| | - Varashree Bolar Suryakanth
- Department of Biochemistry, Kasturba Medical College Manipal, Manipal Academy Higher Education, Manipal, India
| | - Mukhyaprana M Prabhu
- Department of General Medicine, Kasturba Medical College, Manipal, Manipal Academy Higher Education, Manipal, India.
| | - Subhradip Karmakar
- Department of Biochemistry, All India Institute of Medical Sciences New Delhi, New Delhi, India.
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Liu D, Kuang Y, Chen S, Li R, Su F, Zhang S, Qiu Q, Lin S, Shen C, Liu Y, Liang L, Wang J, Xu H, Xiao Y. NAT10 promotes synovial aggression by increasing the stability and translation of N4-acetylated PTX3 mRNA in rheumatoid arthritis. Ann Rheum Dis 2024; 83:1118-1131. [PMID: 38724075 DOI: 10.1136/ard-2023-225343] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/22/2024] [Indexed: 08/29/2024]
Abstract
OBJECTIVE Recent studies indicate that N-acetyltransferase 10 (NAT10)-mediated ac4C modification plays unique roles in tumour metastasis and immune infiltration. This study aimed to uncover the role of NAT10-mediated ac4C in fibroblast-like synoviocytes (FLSs) functions and synovial immune cell infiltration in rheumatoid arthritis (RA). METHODS FLSs were obtained from active established patients with RA. Protein expression was determined by western blotting or immunohistochemistry or multiplexed immunohistochemistry. Cell migration was measured using a Boyden chamber. ac4C-RIP-seq combined with RNA-seq was performed to identify potential targets of NAT10. RNA immunoprecipitation was used to validate the interaction between protein and mRNA. NAT10 haploinsufficiency, inhibitor remodelin or intra-articular Adv-NAT10 was used to suppress arthritis in mice with delayed-type hypersensitivity arthritis (DYHA) and collagen II-induced arthritis (CIA) and rats with CIA. RESULTS We found elevated levels of NAT10 and ac4C in FLSs and synovium from patients with RA. NAT10 knockdown or specific inhibitor treatment reduced the migration and invasion of RA FLSs. Increased NAT10 level in the synovium was positively correlated with synovial infiltration of multiple types of immune cells. NAT10 inhibition in vivo attenuated the severity of arthritis in mice with CIA and DTHA, and rats with CIA. Mechanistically, we explored that NAT10 regulated RA FLS functions by promoting stability and translation efficiency of N4-acetylated PTX3 mRNA. PTX3 also regulated RA FLS aggression and is associated with synovial immune cell infiltration. CONCLUSION Our findings uncover the important roles of NAT10-mediated ac4C modification in promoting rheumatoid synovial aggression and inflammation, indicating that NAT10 may be a potential target for the treatment of RA, even other dysregulated FLSs-associated disorders.
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Affiliation(s)
- Di Liu
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yu Kuang
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Simin Chen
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ruiru Li
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Fan Su
- Department of Geriatrics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shuoyang Zhang
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Qian Qiu
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shuibin Lin
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Chuyu Shen
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yingli Liu
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Liuqin Liang
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jingnan Wang
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hanshi Xu
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Youjun Xiao
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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Li K, Hong Y, Yu Y, Xie Z, Lv D, Wang C, Xie T, Chen H, Chen Z, Zeng J, Zhao S. NAT10 Promotes Prostate Cancer Growth and Metastasis by Acetylating mRNAs of HMGA1 and KRT8. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310131. [PMID: 38922788 PMCID: PMC11348116 DOI: 10.1002/advs.202310131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/22/2024] [Indexed: 06/28/2024]
Abstract
N4-acetylcytidine (ac4C) is essential for the development and migration of tumor cells. According to earlier research, N-acetyltransferase 10 (NAT10) can increase messenger RNAs (mRNAs) stability by catalyzing the synthesis of ac4C. However, little is known about NAT10 expression and its role in the acetylation modifications in prostate cancer (PCa). Thus, the biological function of NAT10 in PCa is investigated in this study. Compared to paraneoplastic tissues, the expression of NAT10 is significantly higher in PCa. The NAT10 expression is strongly correlated with the pathological grade, clinical stage, Gleason score, T-stage, and N-stage of PCa. NAT10 has the ability to advance the cell cycle and the epithelial-mesenchymal transition (EMT), both of which raise the malignancy of tumor cells. Mechanistically, NAT10 enhance the stability of high mobility group AT-hook 1 (HMGA1) by acetylating its mRNA, thereby promoting cell cycle progression to improve cell proliferation. In addition, NAT10 improve the stability of Keratin 8 (KRT8) by acetylating its mRNA, which promotes the progression of EMT to improve cell migration. This findings provide a potential prognostic or therapeutic target for PCa.
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Affiliation(s)
- Kang‐Jing Li
- Department of UrologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
- Department of UrologyAffiliated Qingyuan HospitalGuangzhou Medical UniversityQingyuan People's HospitalQingyuan511518China
| | - Yaying Hong
- Department of UrologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Yu‐Zhong Yu
- Department of UrologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Zhiyue Xie
- Department of UrologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Dao‐Jun Lv
- Department of UrologyThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
| | - Chong Wang
- Department of UrologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Tao Xie
- Department of UrologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Hong Chen
- Luoyang Key Laboratory of Organic Functional MoleculesCollege of Food and DrugLuoyang Normal UniversityLuoyangHenan471934P. R. China
| | - Zhe‐Sheng Chen
- Department of Pharmaceutical SciencesCollege of Pharmacy and Health SciencesSt. John's UniversityQueensNY11439USA
| | - Jianwen Zeng
- Department of UrologyAffiliated Qingyuan HospitalGuangzhou Medical UniversityQingyuan People's HospitalQingyuan511518China
| | - Shan‐Chao Zhao
- Department of UrologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
- Department of UrologyThe Fifth Affiliated HospitalSouthern Medical UniversityGuangzhou510900China
- Department of UrologyThe Third Affiliated Hospital of Southern Medical UniversityGuangzhou510500China
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Yang R, Yu W, Lin L, Cui Z, Tang J, Li G, Jin M, Gu Y, Lu E. NAT10 promotes osteoclastogenesis in inflammatory bone loss by catalyzing Fos mRNA ac4C modification and upregulating MAPK signaling pathway. J Adv Res 2024:S2090-1232(24)00318-7. [PMID: 39089619 DOI: 10.1016/j.jare.2024.07.031] [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: 03/15/2024] [Revised: 05/14/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024] Open
Abstract
INTRODUCTION Excessive osteoclastogenesis is a key driver of inflammatory bone loss. Suppressing osteoclastogenesis has always been considered essential for the treatment of inflammatory bone loss. N-acetyltransferase 10 (NAT10) is the sole enzyme responsible for N4-acetylcytidine (ac4C) modification of mRNA, and is involved in cell development. However, its role in osteoclastogenesis and inflammatory bone loss remained elusive. OBJECTIVES We aimed to clarify the regulatory mechanism of NAT10 and ac4C modification in osteoclastogenesis and inflammatory bone loss. METHODS NAT10 expression and ac4C modification during osteoclastogenesis were determined by quantitative real-time PCR (qPCR), western blotting, dot blot and immunofluorescent staining, and the effect of NAT10 inhibition on osteoclast differentiation in vitro was measured by the tartrate-resistant acid phosphatase staining, podosome belts staining assay and bone resorption pit assay. Then, acRIP-qPCR and NAT10RIP-qPCR, ac4C site prediction, mRNA decay assay and luciferase reporter assay were performed to further study the underlying mechanisms. At last, mice models of inflammatory bone loss were applied to verify the therapeutic effect of NAT10 inhibition in vivo. RESULTS NAT10 expression was upregulated during osteoclast differentiation and highly expressed in alveolar bone osteoclasts from periodontitis mice. Inhibition of NAT10 notably reduced osteoclast differentiation in vitro, as indicated by great reduction of tartrated resistant acid phosphatse positive multinuclear cells, osteoclast-specific gene expression, F-actin ring formation and bone resorption capacity. Mechanistically, NAT10 catalyzed ac4C modification of Fos (encoding AP-1 component c-Fos) mRNA and maintained its stabilization. Besides, NAT10 promoted MAPK signaling pathway and thereby activated AP-1 (c-Fos/c-Jun) transcription for osteoclastogenesis. Therapeutically, administration of Remodelin, the specific inhibitor of NAT10, remarkably impeded the ligature-induced alveolar bone loss and lipopolysaccharide-induced inflammatory calvarial osteolysis. CONCLUSIONS Our study demonstrated that NAT10-mediated ac4C modification is an important epigenetic regulation of osteoclast differentiation and proposed a promising therapeutic target for inflammatory bone loss.
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Affiliation(s)
- Ruhan Yang
- Department of Stomatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 160 Pujian Road, Shanghai, 200127, China
| | - Weijun Yu
- Department of Stomatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 160 Pujian Road, Shanghai, 200127, China
| | - Lu Lin
- Department of Stomatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 160 Pujian Road, Shanghai, 200127, China
| | - Zhurong Cui
- Department of Stomatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 160 Pujian Road, Shanghai, 200127, China
| | - Jiaqi Tang
- Department of Stomatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 160 Pujian Road, Shanghai, 200127, China
| | - Guanglong Li
- Department of Stomatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 160 Pujian Road, Shanghai, 200127, China
| | - Min Jin
- Department of Stomatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 160 Pujian Road, Shanghai, 200127, China.
| | - Yuting Gu
- Department of Stomatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 160 Pujian Road, Shanghai, 200127, China.
| | - Eryi Lu
- Department of Stomatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 160 Pujian Road, Shanghai, 200127, China.
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Li F, Zhang J, Li K, Peng Y, Zhang H, Xu Y, Yu Y, Zhang Y, Liu Z, Wang Y, Huang L, Zhou F. GANSamples-ac4C: Enhancing ac4C site prediction via generative adversarial networks and transfer learning. Anal Biochem 2024; 689:115495. [PMID: 38431142 DOI: 10.1016/j.ab.2024.115495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 03/05/2024]
Abstract
RNA modification, N4-acetylcytidine (ac4C), is enzymatically catalyzed by N-acetyltransferase 10 (NAT10) and plays an essential role across tRNA, rRNA, and mRNA. It influences various cellular functions, including mRNA stability and rRNA biosynthesis. Wet-lab detection of ac4C modification sites is highly resource-intensive and costly. Therefore, various machine learning and deep learning techniques have been employed for computational detection of ac4C modification sites. The known ac4C modification sites are limited for training an accurate and stable prediction model. This study introduces GANSamples-ac4C, a novel framework that synergizes transfer learning and generative adversarial network (GAN) to generate synthetic RNA sequences to train a better ac4C modification site prediction model. Comparative analysis reveals that GANSamples-ac4C outperforms existing state-of-the-art methods in identifying ac4C sites. Moreover, our result underscores the potential of synthetic data in mitigating the issue of data scarcity for biological sequence prediction tasks. Another major advantage of GANSamples-ac4C is its interpretable decision logic. Multi-faceted interpretability analyses detect key regions in the ac4C sequences influencing the discriminating decision between positive and negative samples, a pronounced enrichment of G in this region, and ac4C-associated motifs. These findings may offer novel insights for ac4C research. The GANSamples-ac4C framework and its source code are publicly accessible at http://www.healthinformaticslab.org/supp/.
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Affiliation(s)
- Fei Li
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, and College of Computer Science and Technology, Jilin University, Changchun, Jilin, 130012, China
| | - Jiale Zhang
- College of Software, Jilin University, Changchun, Jilin, 130012, China
| | - Kewei Li
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, and College of Computer Science and Technology, Jilin University, Changchun, Jilin, 130012, China.
| | - Yu Peng
- College of Software, Jilin University, Changchun, Jilin, 130012, China
| | - Haotian Zhang
- College of Software, Jilin University, Changchun, Jilin, 130012, China
| | - Yiping Xu
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, and College of Computer Science and Technology, Jilin University, Changchun, Jilin, 130012, China
| | - Yue Yu
- College of Software, Jilin University, Changchun, Jilin, 130012, China
| | - Yuteng Zhang
- College of Software, Jilin University, Changchun, Jilin, 130012, China
| | - Zewen Liu
- College of Software, Jilin University, Changchun, Jilin, 130012, China
| | - Ying Wang
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, and College of Computer Science and Technology, Jilin University, Changchun, Jilin, 130012, China
| | - Lan Huang
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, and College of Computer Science and Technology, Jilin University, Changchun, Jilin, 130012, China
| | - Fengfeng Zhou
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, and College of Computer Science and Technology, Jilin University, Changchun, Jilin, 130012, China; School of Biology and Engineering, Guizhou Medical University, Guiyang, 550025, Guizhou, China.
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Li L, Xia X, Yang T, Sun Y, Liu X, Xu W, Lu M, Cui D, Wu Y. RNA methylation: A potential therapeutic target in autoimmune disease. Int Rev Immunol 2024; 43:160-177. [PMID: 37975549 DOI: 10.1080/08830185.2023.2280544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Autoimmune diseases such as rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and inflammatory bowel disease (IBD) are caused by the body's immune response to autoantigens. The pathogenesis of autoimmune diseases is unclear. Numerous studies have demonstrated that RNA methylation plays a key role in disease progression, which is essential for post-transcriptional regulation and has gradually become a broad regulatory mechanism that controls gene expression in various physiological processes, including RNA nuclear output, translation, splicing, and noncoding RNA processing. Here, we outline the writers, erasers, and readers of RNA methylation, including N6-methyladenosine (m6A), 2'-O-methylation (Nm), 2'-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), 5-methylcytidine (m5C) and N7-methylguanosine (m7G). As the role of RNA methylation modifications in the immune system and diseases is explained, the potential treatment value of these modifications has also been demonstrated. This review reports the relationship between RNA methylation and autoimmune diseases, highlighting the need for future research into the therapeutic potential of RNA modifications.
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Affiliation(s)
- Lele Li
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xiaoping Xia
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Tian Yang
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Yuchao Sun
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xueke Liu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Wei Xu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Mei Lu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Dawei Cui
- The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingping Wu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
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Beiki H, Sturgill D, Arango D, Relier S, Schiffers S, Oberdoerffer S. Detection of ac4C in human mRNA is preserved upon data reassessment. Mol Cell 2024; 84:1611-1625.e3. [PMID: 38640896 PMCID: PMC11353019 DOI: 10.1016/j.molcel.2024.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/19/2023] [Accepted: 03/18/2024] [Indexed: 04/21/2024]
Abstract
We recently reported the distribution of N4-acetylcytidine (ac4C) in HeLa mRNA at base resolution through chemical reduction and the induction of C:T mismatches in sequencing (RedaC:T-seq). Our results contradicted an earlier report from Schwartz and colleagues utilizing a similar method termed ac4C-seq. Here, we revisit both datasets and reaffirm our findings. Through RedaC:T-seq reanalysis, we establish a low basal error rate at unmodified nucleotides that is not skewed to any specific mismatch type and a prominent increase in C:T substitutions as the dominant mismatch type in both treated wild-type replicates, with a high degree of reproducibility across replicates. In contrast, through ac4C-seq reanalysis, we uncover significant data quality issues including insufficient depth, with one wild-type replicate yielding 2.7 million reads, inconsistencies in reduction efficiencies between replicates, and an overall increase in mismatches involving thymine that could obscure ac4C detection. These analyses bolster the detection of ac4C in HeLa mRNA through RedaC:T-seq.
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Affiliation(s)
- Hamid Beiki
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Daniel Arango
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sebastien Relier
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sarah Schiffers
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shalini Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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Luo Q, Zhu J, Wang S, Fu P, Fu B, Huang Z, Li J. Decreased expression of NAT10 in peripheral blood mononuclear cells from new-onset ankylosing spondylitis and its clinical significance. Arthritis Res Ther 2024; 26:7. [PMID: 38167491 PMCID: PMC10759761 DOI: 10.1186/s13075-023-03250-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND NAT10 is the firstly recognized RNA acetyltransferase that participates in multiple cellular biological processes and human disease. However, the role of N-acetyltransferase 10 (NAT10) in ankylosing spondylitis (AS) is still poorly elaborated. METHODS Fifty-six patients with New-Onset AS, 52 healthy controls (HC), 20 patients with rheumatoid arthritis (RA) and 16 patients with systemic lupus erythematosus (SLE) were recruited from The First Afliated Hospital of Nanchang University, and their clinical characteristics were recorded. The expression level of NAT10 in peripheral blood mononuclear cell (PBMC) was examined using reverse transcription-quantitative PCR analysis. The correlations between the expression level of NAT10 in the New-Onset AS patients and disease activity of AS were examined, and receiver operating characteristic (ROC) curves were built to evaluate predictive value in AS. Univariate analysis and multivariate regression analysis were used to analyze the risk factors and construct predictive model. RESULTS The mRNA expressions of NAT10 in PBMC from new-onset AS patients were significantly low and there were negative correlation between mRNA NAT10 and ASDAS-CRP, BASDIA in new-onset AS patients. ROC analysis suggested that mRNA NAT10 has value in distinguishing new-onset AS patients from HC, RA and SLE. Furthermore, a novel predictive model based on mRNA NAT10 and neutrophil percentages (N%) was constructed for distinguishing new-onset AS patients from HC (AUC = 0.880, sensitivity = 84.62%, specificity = 76.92%) and the predictive model correlated with the activity of new-onset AS. Furthermore, the predictive model could distinguish new-onset AS patients from RA and SLE (AUC = 0.661, sensitivity = 90.38%, specificity = 47.22%). Moreover, the potential predictive value of the combination of predictive model-HLA-B27 for AS vs. HC with a sensitivity of 92.86% (39/42), a specificity of 100.00% (52/52) and an accuracy of 96.81% (91/94) was superior to that of HLA-B27, which in turn had a sensitivity of 84.44% (38/45), a specificity of 100.00% (52/52) and an accuracy of 92.78% (90/97). CONCLUSION The present study suggested that the decreased mRNA NAT10 may play a role in AS pathogenesis and predictive model based on mRNA NAT10 and N% act as bioindicator for forecast and progression of diseases.
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Affiliation(s)
- Qing Luo
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
- Institute of Infection and Immunity, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
- Nanchang Key Laboratory of Diagnosis of Infectious Diseases, Nanchang, Jiangxi, 330006, China
| | - Juxiang Zhu
- Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Shiqian Wang
- Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Peng Fu
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Biqi Fu
- Department of Rheumatology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Zikun Huang
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China.
- Institute of Infection and Immunity, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China.
- Nanchang Key Laboratory of Diagnosis of Infectious Diseases, Nanchang, Jiangxi, 330006, China.
| | - Junming Li
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China.
- Institute of Infection and Immunity, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China.
- Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Jiangxi, 330006, China.
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10
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Zhang Y, Lei Y, Dong Y, Chen S, Sun S, Zhou F, Zhao Z, Chen B, Wei L, Chen J, Meng Z. Emerging roles of RNA ac4C modification and NAT10 in mammalian development and human diseases. Pharmacol Ther 2024; 253:108576. [PMID: 38065232 DOI: 10.1016/j.pharmthera.2023.108576] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 01/13/2024]
Abstract
RNA ac4C modification is a novel and rare chemical modification observed in mRNA. Traditional biochemical studies had primarily associated ac4C modification with tRNA and rRNA until in 2018, Arango D et al. first reported the presence of ac4C modification on mRNA and demonstrated its critical role in mRNA stability and translation regulation. Furthermore, they established that the ac4C modification on mRNA is mediated by the classical N-acetyltransferase NAT10. Subsequent studies have underscored the essential implications of NAT10 and mRNA ac4C modification across both physiological and pathological regulatory processes. In this review, we aimed to explore the discovery history of RNA ac4C modification, its detection methods, and its regulatory mechanisms in disease and physiological development. We offer a forward-looking examination and discourse concerning the employment of RNA ac4C modification as a prospective therapeutic strategy across diverse diseases. Furthermore, we comprehensively summarize the functions and mechanisms of NAT10 in gene expression regulation and pathogenesis independent of RNA ac4C modification.
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Affiliation(s)
- Yigan Zhang
- Institute of Biomedical Research, Department of Infectious Diseases, Regulatory Mechanism and Targeted Therapy for Liver Cancer Shiyan Key Laboratory, Hubei rovincial Clinical Research Center for Precise Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China
| | - Yumei Lei
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Yanbin Dong
- Institute of Biophysics, Chinese Academy of Sciences, Key Laboratory of Nucleic Acid Biology, Chinese Academy of Sciences, Beijing, China
| | - Shuwen Chen
- School of Biomedical Engineering, Hubei University of Medicine, Shiyan, China
| | - Siyuan Sun
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Fange Zhou
- The First Clinical School of Hubei University of Medicine, Shiyan, China
| | - Zhiwen Zhao
- Department of Emergency Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Bonan Chen
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Lv Wei
- Institute of Biophysics, Chinese Academy of Sciences, Key Laboratory of Nucleic Acid Biology, Chinese Academy of Sciences, Beijing, China.
| | - Juan Chen
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, China.
| | - Zhongji Meng
- Institute of Biomedical Research, Department of Infectious Diseases, Regulatory Mechanism and Targeted Therapy for Liver Cancer Shiyan Key Laboratory, Hubei rovincial Clinical Research Center for Precise Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China.
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11
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Wang M, Cheng R, He H, Han Z, Zhang Y, Wu Q. N 4-acetylcytidine of Nop2 mRNA is required for the transition of morula-to-blastocyst. Cell Mol Life Sci 2023; 80:307. [PMID: 37768430 PMCID: PMC11071819 DOI: 10.1007/s00018-023-04955-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
N-acetyltransferase 10 (NAT10)-mediated N4-acetylcytidine (ac4C) modification is crucial for mRNA stability and translation efficiency, yet the underlying function in mammalian preimplantation embryos remains unclear. Here, we characterized the ac4C modification landscape in mouse early embryos and found that the majority of embryos deficient in ac4C writer-NAT10 failed to develop into normal blastocysts. Through single-cell sequencing, RNA-seq, acetylated RNA immunoprecipitation combined with PCR (acRIP-PCR), and embryonic phenotype monitoring, Nop2 was screened as a target gene of Nat10. Mechanistically, Nat10 knockdown decreases the ac4C modification on Nop2 mRNA and reduces RNA and protein abundance by affecting the mRNA stability of Nop2. Then, depletion of NOP2 may inhibit the translation of transcription factor TEAD4, resulting in defective expression of the downstream lineage-specific gene Cdx2, and ultimately preventing blastomeres from undergoing the trophectoderm (TE) fate. However, exogenous Nop2 mRNA partially reverses this abnormal development. In conclusion, our findings demonstrate that defective ac4C modification of Nop2 mRNA hinders the morula-to-blastocyst transition by influencing the first cell fate decision in mice.
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Affiliation(s)
- Mengyun Wang
- Developmental Biology Laboratory, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Rui Cheng
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Hongjuan He
- Developmental Biology Laboratory, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Zhengbin Han
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Yan Zhang
- Computational Biology Research Center, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China.
| | - Qiong Wu
- Developmental Biology Laboratory, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China.
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12
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Zheng N, Liu X, Yang Y, Liu Y, Yan F, Zeng Y, Cheng Y, Wu D, Chen C, Wang X. Regulatory roles of NAT10 in airway epithelial cell function and metabolism in pathological conditions. Cell Biol Toxicol 2023; 39:1237-1256. [PMID: 35877022 DOI: 10.1007/s10565-022-09743-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/20/2022] [Indexed: 12/01/2022]
Abstract
N-acetyltransferase 10 (NAT10), a nuclear acetyltransferase and a member of the GNAT family, plays critical roles in RNA stability and translation processes as well as cell proliferation. Little is known about regulatory effects of NAT10 in lung epithelial cell proliferation. We firstly investigated NTA10 mRNA expression in alveolar epithelial types I and II, basal, ciliated, club, and goblet/mucous epithelia from heathy and patients with chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, lung adenocarcinoma, para-tumor tissue, and systemic sclerosis, respectively. We selected A549 cells for representative of alveolar epithelia or H1299 and H460 cells as airway epithelia with different genetic backgrounds and studied dynamic responses of NAT10-down-regulated epithelia to high temperature, lipopolysaccharide, cigarette smoking extract (CSE), drugs, radiation, and phosphoinositide 3-kinase (PI3K) inhibitors at various doses. We also compared transcriptomic profiles between alveolar and airway epithelia, between cells with or without NAT10 down-regulation, between early and late stages, and between challenges. The present study demonstrated that NAT10 expression increased in human lung epithelia and varied among epithelial types, challenges, and diseases. Knockdown of NAT10 altered epithelial mitochondrial functions, dynamic responses to LPS, CSE, or PI3K inhibitors, and transcriptomic phenomes. NAT10 regulates biological phenomes, and behaviors are more complex and are dependent upon multiple signal pathways. Thus, NAT10-associated signal pathways can be a new alternative for understanding the disease and developing new biomarkers and targets.
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Affiliation(s)
- Nannan Zheng
- Department of Respiratory Medicine, The First Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Xuanqi Liu
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Ying Yang
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Yifei Liu
- Center of Molecular Diagnosis and Therapy, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Furong Yan
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
- Center of Molecular Diagnosis and Therapy, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Yiming Zeng
- Center of Molecular Diagnosis and Therapy, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
| | - Yunfeng Cheng
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Duojiao Wu
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China.
| | - Chengshui Chen
- Department of Respiratory Medicine, The First Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
- Quzhou Hospital of Wenzhou Medical University, Quzhou, Zhejiang Province, China.
| | - Xiangdong Wang
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China.
- Center of Molecular Diagnosis and Therapy, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
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13
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Abstract
Over the past decade, mRNA modifications have emerged as important regulators of gene expression control in cells. Fueled in large part by the development of tools for detecting RNA modifications transcriptome wide, researchers have uncovered a diverse epitranscriptome that serves as an additional layer of gene regulation beyond simple RNA sequence. Here, we review the proteins that write, read, and erase these marks, with a particular focus on the most abundant internal modification, N6-methyladenosine (m6A). We first describe the discovery of the key enzymes that deposit and remove m6A and other modifications and discuss how our understanding of these proteins has shaped our views of modification dynamics. We then review current models for the function of m6A reader proteins and how our knowledge of these proteins has evolved. Finally, we highlight important future directions for the field and discuss key questions that remain unanswered.
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Affiliation(s)
- Mathieu N Flamand
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Matthew Tegowski
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Kate D Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA;
- Department of Neurobiology, Duke University School of Medicine, Durham, North Carolina, USA
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14
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Akhil A, Bansal R, Anupam K, Tandon A, Bhatnagar A. Systemic lupus erythematosus: latest insight into etiopathogenesis. Rheumatol Int 2023:10.1007/s00296-023-05346-x. [PMID: 37226016 DOI: 10.1007/s00296-023-05346-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/15/2023] [Indexed: 05/26/2023]
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disorder of unknown etiology. Multifactorial interaction among various susceptible factors such as environmental, hormonal, and genetic factors makes it more heterogeneous and complex. Genetic and epigenetic modifications have been realized to regulate the immunobiology of lupus through environmental modifications such as diet and nutrition. Although these interactions may vary from population to population, the understanding of these risk factors can enhance the perception of the mechanistic basis of lupus etiology. To recognize the recent advances in lupus, an electronic search was conducted among search engines such as Google Scholar and PubMed, where we found about 30.4% publications of total studies related to genetics and epigenetics, 33.5% publications related to immunobiology and 34% related to environmental factors. These outcomes suggested that management of diet and lifestyle have a direct relationship with the severity of lupus that influence via modulating the complex interaction among genetics and immunobiology. The present review emphasizes the knowledge about the multifactorial interactions between various susceptible factors based on recent advances that will further update the understanding of mechanisms involved in disease pathoetiology. Knowledge of these mechanisms will further assist in the creation of novel diagnostic and therapeutic options.
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Affiliation(s)
- Akhil Akhil
- Department of Biochemistry, BMS-Block II, South Campus, Panjab University, Chandigarh, 160014, India
| | - Rohit Bansal
- Department of Biochemistry, BMS-Block II, South Campus, Panjab University, Chandigarh, 160014, India
| | - Kumari Anupam
- Department of Pathology, Saint Louis University, St. Louis, MO, 63103, USA
| | - Ankit Tandon
- Department of Endocrinology, PGIMER, Chandigarh, 160012, India
| | - Archana Bhatnagar
- Department of Biochemistry, BMS-Block II, South Campus, Panjab University, Chandigarh, 160014, India.
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15
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Chen K, Wu T, Wang D, Li R, Shen X, Zhao T, Ozato K, Li R. Transcriptomics and quantitative proteomics reveal changes after second stimulation of bone marrow-derived macrophages from lupus-prone MRL/lpr mice. Front Immunol 2022; 13:1004232. [PMID: 36341359 PMCID: PMC9627492 DOI: 10.3389/fimmu.2022.1004232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/27/2022] [Indexed: 11/13/2022] Open
Abstract
Innate immune memory can cause the occurrence and exacerbation of autoimmune diseases, and it is as well as being strongly associated with the pathogenesis of systemic lupus erythematosus (SLE), however, the specific mechanism remains to be further studied. We learned that IFN-γ stimulation generated innate immune memory in bone marrow-derived macrophages (BMDMs) and activated memory interferon-stimulated genes (ISGs). This research used IFN-γ and lipopolysaccharide (LPS) to treat BMDMs with lupus-prone MRL/lpr mice and showed that particular memory ISGs were substantially elevated in prestimulated macrophages. In order to identify the differentially expressed genes (DEGs), researchers turned to RNA-seq. GO and KEGG analysis showed that up-regulated DEGs were enriched in defense and innate immune responses, and were related to the expression of pattern recognition receptors (PRRs)-related pathways in macrophages. TMT-based proteome analysis revealed differentially expressed proteins (DEPs) up-regulated in BMDMs were abundant in metabolic pathways such as glucose metabolism. Our study found that after the secondary stimulation of MRL/lpr mice, the expression of PRRs in innate immune cells was changed, and IFN-related pathways were activated to release a large number of ISGs to promote the secondary response. At the same time, related metabolic modes such as glycolysis were enhanced, and epigenetic changes may occur. Therefore, SLE is brought on, maintained, and worsened by a variety of factors that work together to produce innate immune memory.
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Affiliation(s)
- Keyue Chen
- Key Laboratory of Chinese Medicine Rheumatology of Zhejiang Province, School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Tiyun Wu
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Danyan Wang
- Key Laboratory of Chinese Medicine Rheumatology of Zhejiang Province, School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Rong Li
- Key Laboratory of Chinese Medicine Rheumatology of Zhejiang Province, School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiangfeng Shen
- Key Laboratory of Chinese Medicine Rheumatology of Zhejiang Province, School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Ting Zhao
- Key Laboratory of Chinese Medicine Rheumatology of Zhejiang Province, School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Keiko Ozato
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Keiko Ozato, ; Rongqun Li,
| | - Rongqun Li
- Key Laboratory of Chinese Medicine Rheumatology of Zhejiang Province, School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
- *Correspondence: Keiko Ozato, ; Rongqun Li,
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16
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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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17
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Arango D, Sturgill D, Yang R, Kanai T, Bauer P, Roy J, Wang Z, Hosogane M, Schiffers S, Oberdoerffer S. Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine. Mol Cell 2022; 82:2797-2814.e11. [PMID: 35679869 PMCID: PMC9361928 DOI: 10.1016/j.molcel.2022.05.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/14/2022] [Accepted: 05/12/2022] [Indexed: 12/14/2022]
Abstract
mRNA function is influenced by modifications that modulate canonical nucleobase behavior. We show that a single modification mediates distinct impacts on mRNA translation in a position-dependent manner. Although cytidine acetylation (ac4C) within protein-coding sequences stimulates translation, ac4C within 5' UTRs impacts protein synthesis at the level of initiation. 5' UTR acetylation promotes initiation at upstream sequences, competitively inhibiting annotated start codons. Acetylation further directly impedes initiation at optimal AUG contexts: ac4C within AUG-flanking Kozak sequences reduced initiation in base-resolved transcriptome-wide HeLa results and in vitro utilizing substrates with site-specific ac4C incorporation. Cryo-EM of mammalian 80S initiation complexes revealed that ac4C in the -1 position adjacent to an AUG start codon disrupts an interaction between C and hypermodified t6A at nucleotide 37 of the initiator tRNA. These findings demonstrate the impact of RNA modifications on nucleobase function at a molecular level and introduce mRNA acetylation as a factor regulating translation in a location-specific manner.
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Affiliation(s)
- Daniel Arango
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Renbin Yang
- Center for Molecular Microscopy, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA
| | - Tapan Kanai
- Center for Molecular Microscopy, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA
| | - Paulina Bauer
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jyoti Roy
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ziqiu Wang
- Center for Molecular Microscopy, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA
| | - Masaki Hosogane
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sarah Schiffers
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shalini Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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18
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Liu C, Li L, Yang B, Zhao Y, Dong X, Zhu L, Ren X, Huang B, Yue J, Jin L, Zhang H, Wang L. Transcriptome-wide N6-methyladenine methylation in granulosa cells of women with decreased ovarian reserve. BMC Genomics 2022; 23:240. [PMID: 35346019 PMCID: PMC8961905 DOI: 10.1186/s12864-022-08462-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 03/09/2022] [Indexed: 02/07/2023] Open
Abstract
Abstract
Background
The emerging epitranscriptome plays an essential role in female fertility. As the most prevalent internal mRNA modification, N6-methyladenine (m6A) methylation regulate mRNA fate and translational efficiency. However, whether m6A methylation was involved in the aging-related ovarian reserve decline has not been investigated. Herein, we performed m6A transcriptome-wide profiling in the ovarian granulosa cells of younger women (younger group) and older women (older group).
Results
m6A methylation distribution was highly conserved and enriched in the CDS and 3’UTR region. Besides, an increased number of m6A methylated genes were identified in the older group. Bioinformatics analysis indicated that m6A methylated genes were enriched in the FoxO signaling pathway, adherens junction, and regulation of actin cytoskeleton. A total of 435 genes were differently expressed in the older group, moreover, 58 of them were modified by m6A. Several specific genes, including BUB1B, PHC2, TOP2A, DDR2, KLF13, and RYR2 which were differently expressed and modified by m6A, were validated using qRT-PCR and might be involved in the decreased ovarian functions in the aging ovary.
Conclusions
Hence, our finding revealed the transcriptional significance of m6A modifications and provide potential therapeutic targets to promote fertility reservation for aging women.
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19
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Xu J, Gao Z, Liu K, Fan Y, Zhang Z, Xue H, Guo X, Zhang P, Deng L, Wang S, Wang H, Wang Q, Zhao R, Li G. The Non-N 6-Methyladenosine Epitranscriptome Patterns and Characteristics of Tumor Microenvironment Infiltration and Mesenchymal Transition in Glioblastoma. Front Immunol 2022; 12:809808. [PMID: 35154083 PMCID: PMC8825368 DOI: 10.3389/fimmu.2021.809808] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/29/2021] [Indexed: 12/13/2022] Open
Abstract
Background An increasing number of RNA modification types other than N6-methyladenosine (m6A) modification have been detected. Nonetheless, the probable functions of RNA modifications beyond m6A in the tumor microenvironment (TME), mesenchymal (MES) transition, immunotherapy, and drug sensitivity remain unclear. Methods We analyzed the characteristics of 32 non-m6A RNA modification regulators in 539 glioblastoma (GBM) patients and the TME cell infiltration and MES transition patterns. Using principal component analysis, a non-m6A epitranscriptome regulator score (RM score) model was established. We estimated the association between RM score and clinical characteristics, TME status, GBM subtypes, and drug and immunotherapy response. Results Three definite non-m6A RNA modification patterns associated with diverse biological pathways and clinical characteristics were identified. The high RM score group was characterized by a poor prognosis, enhanced immune infiltration, and MES subtype. Further analysis indicated that the high RM score group had a lower tumor mutation burden as well as a weaker response to immunotherapy. The higher RM score group may benefit more from drugs targeting the EGFR and WNT signaling pathways. Conclusion Our study exposed the potential relationship of non-m6A RNA modification regulators with clinical features, TME status, and GBM subtype and clarified its therapeutic value.
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Affiliation(s)
- Jianye Xu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Zijie Gao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Kaining Liu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Yang Fan
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Zongpu Zhang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Hao Xue
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Xing Guo
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Ping Zhang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Lin Deng
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Shaobo Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Huizhi Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Qingtong Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Rongrong Zhao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Gang Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
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Adams DE, Shao WH. Epigenetic Alterations in Immune Cells of Systemic Lupus Erythematosus and Therapeutic Implications. Cells 2022; 11:cells11030506. [PMID: 35159315 PMCID: PMC8834103 DOI: 10.3390/cells11030506] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disorder that is characterized by autoantibody production and dysregulated immune cell activation. Although the exact etiology of SLE remains unknown, genetic, hormonal, and complex environmental factors are known to be critical for pathologic immune activation. In addition to the inherited genetic predisposition, epigenetic processes that do not change the genomic code, such as DNA methylation, histone modification, and noncoding RNAs are increasingly appreciated to play important roles in lupus pathogenesis. We herein focus on the up-to-date findings of lupus-associated epigenetic alterations and their pathophysiology in lupus development. We also summarize the therapeutic potential of the new findings. It is likely that advances in the epigenetic study will help to predict individual disease outcomes, promise diagnostic accuracy, and design new target-directed immunotherapies.
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He X, Yang Z, Chu XY, Li YX, Zhu B, Huang YX, Wang W, Gao CY, Chen X, Zheng CY, Yang K, Zhang DL. ROR2 downregulation activates the MSX2/NSUN2/p21 regulatory axis and promotes dental pulp stem cell senescence. Stem Cells 2022; 40:290-302. [PMID: 35356984 DOI: 10.1093/stmcls/sxab024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 12/09/2021] [Indexed: 11/13/2022]
Abstract
Abstract
Cellular senescence severely limits the research and the application of dental pulp stem cells (DPSCs). A previous study conducted by our research group revealed a close implication of ROR2 in DPSC senescence, although the mechanism underlying the regulation of ROR2 in DPSCs remains poorly understood so far. In the present study, it was revealed that the expression of the ROR2-interacting transcription factor MSX2 was increased in aging DPSCs. It was demonstrated that the depletion of MSX2 inhibits the senescence of DPSCs and restores their self-renewal capacity, and the simultaneous overexpression of ROR2 enhanced this effect. Moreover, MSX2 knockdown suppressed the transcription of NSUN2, which regulates the expression of p21 by binding to and causing the m5C methylation of the 3'-UTR of p21 mRNA. Interestingly, ROR2 downregulation elevated the levels of MSX2 protein, and not the MSX2 mRNA expression, by reducing the phosphorylation level of MSX2 and inhibiting the RNF34-mediated MSX2 ubiquitination degradation. The results of the present study demonstrated the vital role of the ROR2/MSX2/NSUN2 axis in the regulation of DPSC senescence, thereby revealing a potential target for antagonizing DPSC aging.
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Affiliation(s)
- Xin He
- Department of Orthodontics, Beijing Stomatological Hospital, Capital Medical University School of Stomatology, Capital Medical University, Beijing, China
| | - Zhan Yang
- Molecular Biology Laboratory, Talent and Academic Exchange Center, The Second Hospital of Hebei Medical University, Shijiazhang, China
| | - Xiao-yang Chu
- Department of Stomatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yun-xia Li
- Department of Stomatology, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Biao Zhu
- Department of Stomatology, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yan-xia Huang
- Department of Orthodontics, Beijing Stomatological Hospital, Capital Medical University School of Stomatology, Capital Medical University, Beijing, China
| | - Wei Wang
- Department of Orthodontics, Beijing Stomatological Hospital, Capital Medical University School of Stomatology, Capital Medical University, Beijing, China
| | - Chun-yan Gao
- Department of Orthodontics, Beijing Stomatological Hospital, Capital Medical University School of Stomatology, Capital Medical University, Beijing, China
| | - Xu Chen
- Department of Orthodontics, Beijing Stomatological Hospital, Capital Medical University School of Stomatology, Capital Medical University, Beijing, China
| | - Chun-yan Zheng
- Department of Orthodontics, Beijing Stomatological Hospital, Capital Medical University School of Stomatology, Capital Medical University, Beijing, China
| | - Kai Yang
- Prenatal Diagnosis Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Dong-liang Zhang
- Department of Orthodontics, Beijing Stomatological Hospital, Capital Medical University School of Stomatology, Capital Medical University, Beijing, China
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22
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Lin J, Xiang Y, Huang J, Zeng H, Zeng Y, Liu J, Wu T, Liang Q, Liang X, Li J, Zhou C. NAT10 Maintains OGA mRNA Stability Through ac4C Modification in Regulating Oocyte Maturation. Front Endocrinol (Lausanne) 2022; 13:907286. [PMID: 35937804 PMCID: PMC9352860 DOI: 10.3389/fendo.2022.907286] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/16/2022] [Indexed: 11/17/2022] Open
Abstract
In vitro maturation (IVM) refers to the process of developing immature oocytes into the mature in vitro under the microenvironment analogous to follicle fluid. It is an important technique for patients with polycystic ovary syndrome and, especially, those young patients with the need of fertility preservation. However, as the mechanisms of oocyte maturation have not been fully understood yet, the cultivation efficiency of IVM is not satisfactory. It was confirmed in our previous study that oocyte maturation was impaired after N-acetyltransferase 10 (NAT10) knockdown (KD). In the present study, we further explored the transcriptome alteration of NAT10-depleted oocytes and found that O-GlcNAcase(OGA) was an important target gene for NAT10-mediated ac4C modification in oocyte maturation. NAT10 might regulate OGA stability and expression by suppressing its degradation. To find out whether the influence of NAT10-mediated ac4C on oocyte maturation was mediated by OGA, we further explored the role of OGA in IVM. After knocking down OGA of oocytes, oocyte maturation was inhibited. In addition, as oocytes matured, OGA expression increased and, conversely, O-linked N-acetylglucosamine (O-GlcNAc) level decreased. On the basis of NAT10 KD transcriptome and OGA KD transcriptome data, NAT10-mediated ac4C modification of OGA might play a role through G protein-coupled receptors, molecular transduction, nucleosome DNA binding, and other mechanisms in oocyte maturation. Rsph6a, Gm7788, Gm41780, Trpc7, Gm29036, and Gm47144 were potential downstream genes. In conclusion, NAT10 maintained the stability of OGA transcript by ac4C modification on it, thus positively regulating IVM. Moreover, our study revealed the regulation mechanisms of oocytes maturation and provided reference for improving IVM outcomes. At the same time, the interaction between mRNA ac4C modification and protein O-GlcNAc modification was found for the first time, which enriched the regulation network of oocyte maturation.
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Affiliation(s)
- Jiayu Lin
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yuting Xiang
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Department of Obstetrics and Gynecology, Affiliated Dongguan People’s Hospital, Southern Medical University, Dongguan, China
| | - Jiana Huang
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Haitao Zeng
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yanyan Zeng
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jiawen Liu
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Taibao Wu
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qiqi Liang
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaoyan Liang
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- *Correspondence: Chuanchuan Zhou, ; Jingjie Li, ; Xiaoyan Liang,
| | - Jingjie Li
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- *Correspondence: Chuanchuan Zhou, ; Jingjie Li, ; Xiaoyan Liang,
| | - Chuanchuan Zhou
- Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- *Correspondence: Chuanchuan Zhou, ; Jingjie Li, ; Xiaoyan Liang,
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23
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Zhou W, Wang X, Chang J, Cheng C, Miao C. The molecular structure and biological functions of RNA methylation, with special emphasis on the roles of RNA methylation in autoimmune diseases. Crit Rev Clin Lab Sci 2021; 59:203-218. [PMID: 34775884 DOI: 10.1080/10408363.2021.2002256] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Autoimmune diseases such as rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and systemic vasculitis are caused by the body's immune response to autoantigens. The pathogenesis of autoimmune diseases is complex. RNA methylation is known to play a key role in disease progression as it regulates almost all aspects of RNA processing, including RNA nuclear export, translation, splicing, and noncoding RNA processing. This review summarizes the mechanisms, molecular structures of RNA methylations and their roles in biological functions. Similar to the roles of RNA methylation in cancers, RNA methylation in RA and SLE involves "writers" that deposit methyl groups to form N6-methyladenosine (m6A) and 5-methylcytosine (m5C), "erasers" that remove these modifications, and "readers" that further affect mRNA splicing, export, translation, and degradation. Recent advances in detection methods have identified N1-methyladenosine (m1A), N6,2-O-dimethyladenosine (m6Am), and 7-methylguanosine (m7G) RNA modifications, and their roles in RA and SLE need to be further studied. The relationship between RNA methylation and other autoimmune diseases has not been reported, and the roles and mechanisms of RNA modifications in these diseases need to be explored in the future.
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Affiliation(s)
- Wanwan Zhou
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Xiao Wang
- Department of Clinical Nursing, School of Nursing, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Jun Chang
- Department of Orthopaedics, Fourth Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Chenglong Cheng
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Chenggui Miao
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China.,Institute of Prevention and Treatment of Rheumatoid Arthritis, Anhui University of Chinese Medicine, Hefei, Anhui, China.,Department of Pharmacy, School of Life and Health Sciences, Anhui University of Science and Technology, Fengyang, Anhui Province, China
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24
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Huang D, Song B, Wei J, Su J, Coenen F, Meng J. Weakly supervised learning of RNA modifications from low-resolution epitranscriptome data. Bioinformatics 2021; 37:i222-i230. [PMID: 34252943 PMCID: PMC8336446 DOI: 10.1093/bioinformatics/btab278] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Motivation Increasing evidence suggests that post-transcriptional ribonucleic acid (RNA) modifications regulate essential biomolecular functions and are related to the pathogenesis of various diseases. Precise identification of RNA modification sites is essential for understanding the regulatory mechanisms of RNAs. To date, many computational approaches for predicting RNA modifications have been developed, most of which were based on strong supervision enabled by base-resolution epitranscriptome data. However, high-resolution data may not be available. Results We propose WeakRM, the first weakly supervised learning framework for predicting RNA modifications from low-resolution epitranscriptome datasets, such as those generated from acRIP-seq and hMeRIP-seq. Evaluations on three independent datasets (corresponding to three different RNA modification types and their respective sequencing technologies) demonstrated the effectiveness of our approach in predicting RNA modifications from low-resolution data. WeakRM outperformed state-of-the-art multi-instance learning methods for genomic sequences, such as WSCNN, which was originally designed for transcription factor binding site prediction. Additionally, our approach captured motifs that are consistent with existing knowledge, and visualization of the predicted modification-containing regions unveiled the potentials of detecting RNA modifications with improved resolution. Availability implementation The source code for the WeakRM algorithm, along with the datasets used, are freely accessible at: https://github.com/daiyun02211/WeakRM Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Daiyun Huang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.,Department of Computer Science, University of Liverpool, Liverpool L69 7ZB, UK
| | - Bowen Song
- Department of Mathematical Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.,Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Jingjue Wei
- Department of Mathematical Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Jionglong Su
- School of AI and Advanced Computing, XJTLU Entrepreneur College (Taicang), Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.,AI University Research Centre, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Frans Coenen
- Department of Computer Science, University of Liverpool, Liverpool L69 7ZB, UK
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.,Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.,AI University Research Centre, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
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25
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Dalhat MH, Altayb HN, Khan MI, Choudhry H. Structural insights of human N-acetyltransferase 10 and identification of its potential novel inhibitors. Sci Rep 2021; 11:6051. [PMID: 33723305 PMCID: PMC7960695 DOI: 10.1038/s41598-021-84908-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/19/2021] [Indexed: 01/31/2023] Open
Abstract
N-acetyltransferase 10 (NAT10), is an acetyltransferase that regulates RNA stability and translation processes. Association of NAT10 with several diseases including cancer, makes it a promising therapeutic target. Remodelin is the only known NAT10 inhibitor, but the structural information related to its binding with NAT10 is still obscure. Here, we predicted the human NAT10 structure using homology modeling that was not available previously and used human NAT10 to identify the novel binding site(s) of Remodelin. The alignment of the modeled human NAT10 showed 24% identity and 37% positivity with crystal structure of tRNA (Met) cytidine acetyltransferase. Molecular docking showed binding of Remodelin with NAT10 in acetyl-CoA binding pocket. Additionally, we screened a library of FDA-approved drugs for the identification of novel inhibitors of NAT10 activity. Binding score showed that four drugs namely, Fosaprepitant (- 11.709), Leucal (- 10.46), Fludarabine (- 10.347) and Dantrolene (- 9.875) bind to NAT10 and have better binding capability when compared with Acetyl-CoA (- 5.691) and Remodelin (- 5.3). Acetyl-CoA, Remodelin, and others exhibit hits for hydrophobic, hydrophilic and hydrogen interactions. Interestingly, Remodelin and others interact with the amino acid residues ILE629, GLY639, GLY641, LEU719, and PHE722 in the Acetyl-CoA binding pocket of NAT10 similar to Acetyl-CoA. Our findings revealed that Fosaprepitant, Leucal, Fludarabine, and Dantrolene are promising molecules that can be tested and developed as potential inhibitors of NAT10 acetyltransferase activity.
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Affiliation(s)
- Mahmood Hassan Dalhat
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Centre for Artificial Intelligence in Precision Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Cancer and Mutagenesis Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Hisham N Altayb
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Centre for Artificial Intelligence in Precision Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Cancer and Mutagenesis Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Mohammad Imran Khan
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Centre for Artificial Intelligence in Precision Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Cancer and Mutagenesis Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Hani Choudhry
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
- Centre for Artificial Intelligence in Precision Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
- Cancer and Mutagenesis Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
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26
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Yang H, Chen Y, Xu W, Shao M, Deng J, Xu S, Gao X, Guan S, Wang J, Xu S, Shuai Z, Pan F. Epigenetics of ankylosing spondylitis: Recent developments. Int J Rheum Dis 2021; 24:487-493. [PMID: 33608999 DOI: 10.1111/1756-185x.14080] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 12/15/2022]
Abstract
Ankylosing spondylitis (AS) is a chronic inflammatory autoimmune disease which mainly affects the spine, sacroiliac joint and peripheral joints. To date, the exact causes and pathogenesis of AS still remain unknown. It is considered that the pathogenesis of AS is associated with genetic, infection, environment, immunity and other factors. Among them, the role of genetic factors in the pathogenesis of AS has been studied most deeply. However, over the past few years, the function of environmental predisposition and epigenetic modification in the pathogenesis of AS has received extensive attention. This paper summarizes the recent progress in the epigenetics of AS, including abnormal epigenetic modifications at AS-associated genomic loci, such as DNA methylation, histone modification, microRNA, and so on. In summary, the findings of this review attempt to explain the role of epigenetic modification in the occurrence and development of AS. Nevertheless, there are still unknown and complicated aspects worth exploring to deepen our understanding of the pathogenesis of AS.
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Affiliation(s)
- Hui Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Yuting Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Wei Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Ming Shao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Jixiang Deng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Shanshan Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Xing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Shiyang Guan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Jinian Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Shengqian Xu
- Department of Rheumatism and Immunity, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zongwen Shuai
- Department of Rheumatism and Immunity, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Faming Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
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