101
|
Iaiza A, Mazzanti G, Goeman F, Cesaro B, Cortile C, Corleone G, Tito C, Liccardo F, De Angelis L, Petrozza V, Masciarelli S, Blandino G, Fanciulli M, Fatica A, Fontemaggi G, Fazi F. WTAP and m 6A-modified circRNAs modulation during stress response in acute myeloid leukemia progenitor cells. Cell Mol Life Sci 2024; 81:276. [PMID: 38909325 PMCID: PMC11335200 DOI: 10.1007/s00018-024-05299-9] [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: 03/23/2024] [Revised: 05/19/2024] [Accepted: 05/27/2024] [Indexed: 06/24/2024]
Abstract
N6-methyladenosine (m6A) is one of the most prevalent and conserved RNA modifications. It controls several biological processes, including the biogenesis and function of circular RNAs (circRNAs), which are a class of covalently closed-single stranded RNAs. Several studies have revealed that proteotoxic stress response induction could be a relevant anticancer therapy in Acute Myeloid Leukemia (AML). Furthermore, a strong molecular interaction between the m6A mRNA modification factors and the suppression of the proteotoxic stress response has emerged. Since the proteasome inhibition leading to the imbalance in protein homeostasis is strictly linked to the stress response induction, we investigated the role of Bortezomib (Btz) on m6A regulation and in particular its impact on the modulation of m6A-modified circRNAs expression. Here, we show that treating AML cells with Btz downregulated the expression of the m6A regulator WTAP at translational level, mainly because of increased oxidative stress. Indeed, Btz treatment promoted oxidative stress, with ROS generation and HMOX-1 activation and administration of the reducing agent N-acetylcysteine restored WTAP expression. Additionally, we identified m6A-modified circRNAs modulated by Btz treatment, including circHIPK3, which is implicated in protein folding and oxidative stress regulation. These results highlight the intricate molecular networks involved in oxidative and ER stress induction in AML cells following proteotoxic stress response, laying the groundwork for future therapeutic strategies targeting these pathways.
Collapse
MESH Headings
- Humans
- RNA, Circular/genetics
- RNA, Circular/metabolism
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/drug therapy
- Adenosine/analogs & derivatives
- Adenosine/metabolism
- Adenosine/pharmacology
- Oxidative Stress/drug effects
- Bortezomib/pharmacology
- Cell Line, Tumor
- Reactive Oxygen Species/metabolism
- RNA Splicing Factors/metabolism
- RNA Splicing Factors/genetics
- Cell Cycle Proteins/metabolism
- Cell Cycle Proteins/genetics
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/drug effects
- Neoplastic Stem Cells/pathology
- Heme Oxygenase-1/metabolism
- Heme Oxygenase-1/genetics
- Protein Serine-Threonine Kinases
- Intracellular Signaling Peptides and Proteins
Collapse
Affiliation(s)
- Alessia Iaiza
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro, 5, 00185, Rome, Italy
| | - Gilla Mazzanti
- Section of Histology and Medical Embryology, Department of Anatomical, Histological, Forensic Medicine and Orthopedics Sciences, Sapienza University of Rome, Via A. Scarpa, 14-16, 00161, Rome, Italy
| | - Frauke Goeman
- SAFU, Department of Research, Diagnosis and Innovative Technologies, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Bianca Cesaro
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro, 5, 00185, Rome, Italy
| | - Clelia Cortile
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro, 5, 00185, Rome, Italy
- SAFU, Department of Research, Diagnosis and Innovative Technologies, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giacomo Corleone
- SAFU, Department of Research, Diagnosis and Innovative Technologies, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Claudia Tito
- Section of Histology and Medical Embryology, Department of Anatomical, Histological, Forensic Medicine and Orthopedics Sciences, Sapienza University of Rome, Via A. Scarpa, 14-16, 00161, Rome, Italy
| | - Francesca Liccardo
- Section of Histology and Medical Embryology, Department of Anatomical, Histological, Forensic Medicine and Orthopedics Sciences, Sapienza University of Rome, Via A. Scarpa, 14-16, 00161, Rome, Italy
| | - Luciana De Angelis
- Section of Histology and Medical Embryology, Department of Anatomical, Histological, Forensic Medicine and Orthopedics Sciences, Sapienza University of Rome, Via A. Scarpa, 14-16, 00161, Rome, Italy
| | - Vincenzo Petrozza
- Department of Medico-Surgical Science and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | - Silvia Masciarelli
- Section of Histology and Medical Embryology, Department of Anatomical, Histological, Forensic Medicine and Orthopedics Sciences, Sapienza University of Rome, Via A. Scarpa, 14-16, 00161, Rome, Italy
| | - Giovanni Blandino
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Maurizio Fanciulli
- SAFU, Department of Research, Diagnosis and Innovative Technologies, Translational Research Area, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro, 5, 00185, Rome, Italy.
| | - Giulia Fontemaggi
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy.
| | - Francesco Fazi
- Section of Histology and Medical Embryology, Department of Anatomical, Histological, Forensic Medicine and Orthopedics Sciences, Sapienza University of Rome, Via A. Scarpa, 14-16, 00161, Rome, Italy.
| |
Collapse
|
102
|
Li S, Tan X, He Z, Jiang L, Li Y, Yang L, Hoffmann AA, Zhao C, Fang J, Ji R. Transcriptome-wide N 6-methyladenosine profiling reveals growth-defense trade-offs in the response of rice to brown planthopper (Nilaparvata lugens) infestation. PEST MANAGEMENT SCIENCE 2024. [PMID: 39031631 DOI: 10.1002/ps.8265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/08/2024] [Accepted: 06/06/2024] [Indexed: 07/22/2024]
Abstract
BACKGROUND N6-Methyladenosine (m6A) is a common messenger RNA (mRNA) modification that affects various physiological processes in stress responses. However, the role of m6A modifications in plants responses to herbivore stress remains unclear. RESULTS Here, we found that an infestation of brown planthopper (Nilaparvata lugens) female adults enhanced the resistance of rice to N. lugens. The m6A methylome analysis of N. lugens-infested and uninfested rice samples was performed to explore the interaction between rice and N. lugens. The m6A methylation mainly occurred in genes that were actively expressed in rice following N. lugens infestation, while an analysis of the whole-genomic mRNA distribution of m6A showed that N. lugens infestation caused an overall decrease in the number of m6A methylation sites across the chromosomes. The m6A methylation of genes involved in the m6A modification machinery and several defense-related phytohormones (jasmonic acid and salicylic acid) pathways was increased in N. lugens-infested rice compared to that in uninfested rice. In contrast, m6A modification levels of growth-related phytohormone (auxin and gibberellin) biosynthesis-related genes were significantly attenuated during N. lugens infestation, accompanied by the down-regulated expression of these transcripts, indicating that rice growth was restricted during N. lugens attack to rapidly optimize resource allocation for plant defense. Integrative analysis of the differential patterns of m6A methylation and the corresponding transcripts showed a positive correlation between m6A methylation and transcriptional regulation. CONCLUSION The m6A modification is an important strategy for regulating the expression of genes involved in rice defense and growth during rice-N. lugens interactions. These findings provide new ideas for formulating strategies to control herbivorous pests. © 2024 Society of Chemical Industry.
Collapse
Affiliation(s)
- Shuai Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Xinyang Tan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhen He
- School of Plant Protection, Yangzhou University, Yangzhou, China
| | - Lei Jiang
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yali Li
- Wuhan Benagen Technology Company Limited, Wuhan, China
| | - Liu Yang
- Wuhan Benagen Technology Company Limited, Wuhan, China
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Australia
| | - Chunqing Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jichao Fang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Rui Ji
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
- School of Life Sciences, Anhui Normal University/Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui, China
| |
Collapse
|
103
|
Jin H, Chen Y, Zhang D, Lin J, Huang S, Wu X, Deng W, Huang J, Yao Y. YTHDF2 favors protumoral macrophage polarization and implies poor survival outcomes in triple negative breast cancer. iScience 2024; 27:109902. [PMID: 38812540 PMCID: PMC11134561 DOI: 10.1016/j.isci.2024.109902] [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: 12/24/2023] [Revised: 03/11/2024] [Accepted: 05/01/2024] [Indexed: 05/31/2024] Open
Abstract
Patients with triple-negative breast cancer (TNBC) frequently experience resistance to chemotherapy, leading to recurrence. The approach of optimizing anti-tumoral immunological effect is promising in overcoming such resistance, given the heterogeneity and lack of biomarkers in TNBC. In this study, we focused on YTHDF2, an N6-methyladenosine (m6A) RNA-reader protein, in macrophages, one of the most abundant intra-tumoral immune cells. Using single-cell sequencing and ex vivo experiments, we discovered that YTHDF2 significantly promotes pro-tumoral phenotype polarization of macrophages and is closely associated with down-regulated antigen-presentation signaling to other immune cells in TNBC. The in vitro deprivation of YTHDF2 favors anti-tumoral effect. Expressions of multiple transcription factors, especially SPI1, were consistently observed in YTHDF2-high macrophages, providing potential therapeutic targets for new strategies. In conclusion, YTHDF2 in macrophages appears to promote pro-tumoral effects while suppressing immune activity, indicating the treatment targeting YTHDF2 or its transcription factors could be a promising strategy for chemoresistant TNBC.
Collapse
Affiliation(s)
- Hao Jin
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province 510120, China
| | - Yue Chen
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province 510120, China
| | - Dongbo Zhang
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province 510120, China
| | - Junfan Lin
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province 510120, China
| | - Songyin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province 510120, China
| | - Xiaohua Wu
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province 510120, China
| | - Wen Deng
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province 510120, China
| | - Jiandong Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong Province 518055, China
- Clinical Oncology Center, Shenzhen Key Laboratory for Cancer Metastasis and Personalized Therapy, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Yandan Yao
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province 510120, China
- Shenshan Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Shanwei, Guangdong Province 516621, China
- Guangdong Provincial Key Laboratory of Cancer Pathogenesis and Precision Diagnosis and Treatment, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Shanwei, Guangdong Province 516621, China
| |
Collapse
|
104
|
Li Y, Yi Y, Gao X, Wang X, Zhao D, Wang R, Zhang LS, Gao B, Zhang Y, Zhang L, Cao Q, Chen K. 2'-O-methylation at internal sites on mRNA promotes mRNA stability. Mol Cell 2024; 84:2320-2336.e6. [PMID: 38906115 PMCID: PMC11196006 DOI: 10.1016/j.molcel.2024.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/13/2024] [Accepted: 04/17/2024] [Indexed: 06/23/2024]
Abstract
2'-O-methylation (Nm) is a prominent RNA modification well known in noncoding RNAs and more recently also found at many mRNA internal sites. However, their function and base-resolution stoichiometry remain underexplored. Here, we investigate the transcriptome-wide effect of internal site Nm on mRNA stability. Combining nanopore sequencing with our developed machine learning method, NanoNm, we identify thousands of Nm sites on mRNAs with a single-base resolution. We observe a positive effect of FBL-mediated Nm modification on mRNA stability and expression level. Elevated FBL expression in cancer cells is associated with increased expression levels for 2'-O-methylated mRNAs of cancer pathways, implying the role of FBL in post-transcriptional regulation. Lastly, we find that FBL-mediated 2'-O-methylation connects to widespread 3' UTR shortening, a mechanism that globally increases RNA stability. Collectively, we demonstrate that FBL-mediated Nm modifications at mRNA internal sites regulate gene expression by enhancing mRNA stability.
Collapse
Affiliation(s)
- Yanqiang Li
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Yang Yi
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Xinlei Gao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Xin Wang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Dongyu Zhao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Rui Wang
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Li-Sheng Zhang
- Department of Chemistry, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China; Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, Chicago, IL, USA
| | - Boyang Gao
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, Chicago, IL, USA
| | - Yadong Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Qi Cao
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Boston, MA, USA; Prostate Cancer Program, Dana-Farber/Harvard Cancer Center, Boston, MA, USA.
| |
Collapse
|
105
|
Zhang H, Tang Y, Zhou Y, Wang Y, Si H, Li L, Tang B. DNAzyme-RCA-based colorimetric and lateral flow dipstick assays for the point-of-care testing of exosomal m5C-miRNA-21. Chem Sci 2024; 15:9345-9352. [PMID: 38903234 PMCID: PMC11186332 DOI: 10.1039/d4sc02648a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/03/2024] [Indexed: 06/22/2024] Open
Abstract
Methylation of microRNAs (miRNAs) is a post-transcriptional modification that affects miRNA activity by altering the specificity of miRNAs to target mRNAs. Abnormal methylation of miRNAs in cancer suggests their potential as a tumor marker. However, the traditional methylated miRNA detection mainly includes mass spectrometry, sequencing and others; complex procedures and reliance on large instruments greatly limit their application in point-of-care testing (POCT). Based on this, we developed DNAzyme-RCA-based gold nanoparticle (AuNP) colorimetric and lateral flow dipstick (LFD) assays to achieve convenient detection of exosomal 5-methylcytosine miRNA-21 (m5C-miRNA-21) for the first time. The two assays achieved specific recognition and linear amplification of m5C-miRNA-21 through the DNAzyme triggered RCA reaction and color output with low background interference through AuNP aggregation induced by base complementary pairing. The lowest concentration of m5C-miRNA-21 visible to the naked eye of the two assays can reach 1 pM and 0.1 pM, respectively. Detection of exosomal m5C-miRNA-21 in clinical blood samples showed that the expression level of m5C-miRNA-21 in colorectal cancer patients was significantly higher than that in healthy individuals. This approach not only demonstrates a new strategy for the detection of colorectal cancer but also provides a reference for the development of novel diagnostic tools for other miRNA methylation-related diseases.
Collapse
Affiliation(s)
- Hao Zhang
- Department College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University Jinan 250014 P. R. China
| | - Yue Tang
- Department of Emergency Medicine, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University Jinan 250014 P. R. China
| | - Yingshun Zhou
- Department College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University Jinan 250014 P. R. China
| | - Yiguo Wang
- First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital Jinan 250014 P. R. China
| | - Haibin Si
- Department College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University Jinan 250014 P. R. China
| | - Lu Li
- Department College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University Jinan 250014 P. R. China
| | - Bo Tang
- Department College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University Jinan 250014 P. R. China
- Laoshan Laboratory Qingdao 266237 P. R. China
| |
Collapse
|
106
|
Liu X, Chen W, Li K, Sheng J. RNA N6-methyladenosine methylation in influenza A virus infection. Front Microbiol 2024; 15:1401997. [PMID: 38957616 PMCID: PMC11217485 DOI: 10.3389/fmicb.2024.1401997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 05/30/2024] [Indexed: 07/04/2024] Open
Abstract
Influenza A virus (IAV) is a negative-sense single-stranded RNA virus that causes acute lung injury and acute respiratory distress syndrome, posing a serious threat to both animal and human health. N6-methyladenosine (m6A), a prevalent and abundant post-transcriptional methylation of RNA in eukaryotes, plays a crucial regulatory role in IAV infection by altering viral RNA and cellular transcripts to affect viral infection and the host immune response. This review focuses on the molecular mechanisms underlying m6A modification and its regulatory function in the context of IAV infection and the host immune response. This will provide a better understanding of virus-host interactions and offer insights into potential anti-IAV strategies.
Collapse
Affiliation(s)
- Xueer Liu
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Weiqiang Chen
- Department of Neurosurgery, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Kangsheng Li
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Jiangtao Sheng
- Department of Microbiology and Immunology, Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong, China
| |
Collapse
|
107
|
Ning K, Zhao J, Feng Z, Park SY, McFarlin S, Cheng F, Yan Z, Wang J, Qiu J. N6-methyladenosine modification of a parvovirus-encoded small noncoding RNA facilitates viral DNA replication through recruiting Y-family DNA polymerases. Proc Natl Acad Sci U S A 2024; 121:e2320782121. [PMID: 38875150 PMCID: PMC11194592 DOI: 10.1073/pnas.2320782121] [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: 11/27/2023] [Accepted: 05/14/2024] [Indexed: 06/16/2024] Open
Abstract
Human bocavirus 1 (HBoV1) is a human parvovirus that causes lower respiratory tract infections in young children. It contains a single-stranded (ss) DNA genome of ~5.5 kb that encodes a small noncoding RNA of 140 nucleotides known as bocavirus-encoded small RNA (BocaSR), in addition to viral proteins. Here, we determined the secondary structure of BocaSR in vivo by using DMS-MaPseq. Our findings reveal that BocaSR undergoes N6-methyladenosine (m6A) modification at multiple sites, which is critical for viral DNA replication in both dividing HEK293 cells and nondividing cells of the human airway epithelium. Mechanistically, we found that m6A-modified BocaSR serves as a mediator for recruiting Y-family DNA repair DNA polymerase (Pol) η and Pol κ likely through a direct interaction between BocaSR and the viral DNA replication origin at the right terminus of the viral genome. Thus, this report represents direct involvement of a viral small noncoding RNA in viral DNA replication through m6A modification.
Collapse
Affiliation(s)
- Kang Ning
- Department of Microbiology, Molecular Genetics and Immunology, University of KansasMedical Center, Kansas City, KS66160
| | - Junxing Zhao
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS66045
- Section of Genetic Medicine, Department of Medicine, Biological Sciences Division, University of Chicago, Chicago, IL60637
| | - Zehua Feng
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA52242
| | - Soo Yeun Park
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA52242
| | - Shane McFarlin
- Department of Microbiology, Molecular Genetics and Immunology, University of KansasMedical Center, Kansas City, KS66160
| | - Fang Cheng
- Department of Microbiology, Molecular Genetics and Immunology, University of KansasMedical Center, Kansas City, KS66160
| | - Ziying Yan
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA52242
| | - Jingxin Wang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS66045
- Section of Genetic Medicine, Department of Medicine, Biological Sciences Division, University of Chicago, Chicago, IL60637
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of KansasMedical Center, Kansas City, KS66160
| |
Collapse
|
108
|
Wang J, Gao W, Yu H, Xu Y, Bai C, Cong Q, Zhu Y. Research Progress on the Role of Epigenetic Methylation Modification in Hepatocellular Carcinoma. J Hepatocell Carcinoma 2024; 11:1143-1156. [PMID: 38911291 PMCID: PMC11192199 DOI: 10.2147/jhc.s458734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/30/2024] [Indexed: 06/25/2024] Open
Abstract
Hepatocellular carcinoma (HCC) stands as the prevailing form of primary liver cancer, characterized by a poor prognosis and high mortality rate. A pivotal factor in HCC tumorigenesis is epigenetics, specifically the regulation of gene expression through methylation. This process relies significantly on the action of proteins that modify methylation, including methyltransferases, their associated binding proteins, and demethylases. These proteins are crucial regulators, orchestrating the methylation process by regulating enzymes and their corresponding binding proteins. This orchestration facilitates the reading, binding, detection, and catalysis of gene methylation sites. Methylation ences the development, prolisignificantly influferation, invasion, and prognosis of HCC. Furthermore, methylation modification and its regulatory mechanisms activate distinct biological characteristics in HCC cancer stem cells, such as inducing cancer-like differentiation of stem cells. They also influence the tumor microenvironment (TME) in HCC, modulate immune responses, affect chemotherapy resistance in HCC patients, and contribute to HCC progression through signaling pathway feedback. Given the essential role of methylation in genetic information, it holds promise as a potential tool for the early detection of HCC and as a target to improve drug resistance and promote apoptosis in HCC cells.
Collapse
Affiliation(s)
- Jing Wang
- Infectious Department, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, People’s Republic of China
| | - Wenyue Gao
- Infectious Department, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, People’s Republic of China
| | - Hongbo Yu
- Infectious Department, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, People’s Republic of China
| | - Yuting Xu
- Infectious Department, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, People’s Republic of China
| | - Changchuan Bai
- Internal Department of Chinese Medicine, Dalian Hospital of Traditional Chinese Medicine, Dalian, Liaoning, 116013, People’s Republic of China
| | - Qingwei Cong
- Infectious Department, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, People’s Republic of China
| | - Ying Zhu
- Infectious Department, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, People’s Republic of China
| |
Collapse
|
109
|
Liu ZH, Xia Y, Ai S, Wang HL. Health risks of Bisphenol-A exposure: From Wnt signaling perspective. ENVIRONMENTAL RESEARCH 2024; 251:118752. [PMID: 38513750 DOI: 10.1016/j.envres.2024.118752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
Human beings are routinely exposed to chronic and low dose of Bisphenols (BPs) due to their widely pervasiveness in the environment. BPs hold similar chemical structures to 17β-estradiol (E2) and thyroid hormone, thus posing threats to human health by rendering the endocrine system dysfunctional. Among BPs, Bisphenol-A (BPA) is the best-known and extensively studied endocrine disrupting compound (EDC). BPA possesses multisystem toxicity, including reproductive toxicity, neurotoxicity, hepatoxicity and nephrotoxicity. Particularly, the central nervous system (CNS), especially the developing one, is vulnerable to BPA exposure. This review describes our current knowledge of BPA toxicity and the related molecular mechanisms, with an emphasis on the role of Wnt signaling in the related processes. We also discuss the role of oxidative stress, endocrine signaling and epigenetics in the regulation of Wnt signaling by BPA exposure. In summary, dysfunction of Wnt signaling plays a key role in BPA toxicity and thus can be a potential target to alleviate EDCs induced damage to organisms.
Collapse
Affiliation(s)
- Zhi-Hua Liu
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, Anhui 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
| | - Yanzhou Xia
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, Anhui 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
| | - Shu Ai
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, Anhui 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
| | - Hui-Li Wang
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, Anhui 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China.
| |
Collapse
|
110
|
Wu J, Huang H, Yang W, Xue T, Wang W, Zheng GD. TRPM4 mRNA stabilization by METTL3-mediated m6A modification promotes calcific aortic valve inflammation. Heliyon 2024; 10:e31871. [PMID: 38868032 PMCID: PMC11167295 DOI: 10.1016/j.heliyon.2024.e31871] [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: 01/04/2024] [Revised: 04/22/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024] Open
Abstract
Background Transient receptor potential melastatin 4 (TRPM4) affects immune responses by regulating calcium homeostasis, but its role in calcific aortic valve inflammation remains unclear. This study aimed to assess the expression and function of TRPM4 in patients with or without calcific aortic valve disease (CAVD). Methods The mRNA and protein expression levels of TRPM4 and related factors in calcified and noncalcified tissues were measured using qRT-PCR and Western blot. The proteins interacting with TRPM4 were confirmed by RNA pull-down and RNA immunoprecipitation assays. Dual-Luciferase Reporter Assay was performed to confirm the m6A site of TRPM4. Results The mRNA expression levels of TRPM4, TLR4, IL-6, MCP-1, TNF-α, and NF-κB p65 were significantly higher in calcified aortic valve tissues than in noncalcified tissues, and TRPM4 was significantly positively correlated with inflammation-related factors. The protein expression level of TRPM4, TLR4 and NF-κB p65 were significantly higher in calcified aortic valve tissues than in noncalcified tissues. N6-methyladenosine (m6A) modification of TRPM4 mRNA by METTL3-YTHDF1 up-regulated its expression in CAVD. And TRPM4 promoted the level of inflammation via activation of the JNK-MAPK signaling pathway, after knockdown TRPM4, the production of proinflammatory cytokines was significantly suppressed. Conclusion The results indicate the pivotal role of TRPM4 in CAVD and highlight METTL3-mediated m6A modification of TRPM4 in promoting inflammation through JNK-MAPK signaling pathway. This work provides potential therapeutic strategy to impede inflammation in CAVD.
Collapse
Affiliation(s)
- Jianguo Wu
- Department of Cardiac and Macrovascular Surgery, Central People's Hospital of Zhanjiang, Guangdong province, China
| | - Haozong Huang
- Department of Cardiac and Macrovascular Surgery, Central People's Hospital of Zhanjiang, Guangdong province, China
| | - Wenkai Yang
- Department of Cardiac and Macrovascular Surgery, Central People's Hospital of Zhanjiang, Guangdong province, China
| | - Tufeng Xue
- Department of Cardiac and Macrovascular Surgery, Central People's Hospital of Zhanjiang, Guangdong province, China
| | - Wenjuan Wang
- Department of Cardiac and Macrovascular Surgery, Central People's Hospital of Zhanjiang, Guangdong province, China
| | - Guang-Di Zheng
- Department of Cardiac and Macrovascular Surgery, Central People's Hospital of Zhanjiang, Guangdong province, China
| |
Collapse
|
111
|
Lin X, Zhang J, Wu Z, Shi Y, Chen M, Li M, Hu H, Tian K, Lv X, Li C, Liu Y, Gao X, Yang Q, Chen K, Zhu A. Involvement of autophagy in mesaconitine-induced neurotoxicity in HT22 cells revealed through integrated transcriptomic, proteomic, and m6A epitranscriptomic profiling. Front Pharmacol 2024; 15:1393717. [PMID: 38939838 PMCID: PMC11208636 DOI: 10.3389/fphar.2024.1393717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/20/2024] [Indexed: 06/29/2024] Open
Abstract
Background: Mesaconitine (MA), a diester-diterpenoid alkaloid extracted from the medicinal herb Aconitum carmichaelii, is commonly used to treat various diseases. Previous studies have indicated the potent toxicity of aconitum despite its pharmacological activities, with limited understanding of its effects on the nervous system and the underlying mechanisms. Methods: HT22 cells and zebrafish were used to investigate the neurotoxic effects of MA both in vitro and in vivo, employing multi-omics techniques to explore the potential mechanisms of toxicity. Results: Our results demonstrated that treatment with MA induces neurotoxicity in zebrafish and HT22 cells. Subsequent analysis revealed that MA induced oxidative stress, as well as structural and functional damage to mitochondria in HT22 cells, accompanied by an upregulation of mRNA and protein expression related to autophagic and lysosomal pathways. Furthermore, methylated RNA immunoprecipitation sequencing (MeRIP-seq) showed a correlation between the expression of autophagy-related genes and N6-methyladenosine (m6A) modification following MA treatment. In addition, we identified METTL14 as a potential regulator of m6A methylation in HT22 cells after exposure to MA. Conclusion: Our study has contributed to a thorough mechanistic elucidation of the neurotoxic effects caused by MA, and has provided valuable insights for optimizing the rational utilization of traditional Chinese medicine formulations containing aconitum in clinical practice.
Collapse
Affiliation(s)
- Xiaohuang Lin
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Jian Zhang
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Zekai Wu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yuan Shi
- State Key Laboratory of Mariculture Breeding, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mengting Chen
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Maodong Li
- Shenzhen Bay Laboratory, Institute of Systems and Physical Biology, Shenzhen, China
| | - Hong Hu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Kun Tian
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Xiaoqi Lv
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, Peking University Genome Editing Research Center, College of Life Sciences, Peking University, Beijing, China
| | - Chutao Li
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yang Liu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Xinyue Gao
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Qiaomei Yang
- Department of Gynecology, Fujian Maternity and Child Health Hospital (Fujian Obstetrics and Gynecology Hospital), Fuzhou, China
| | - Kunqi Chen
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - An Zhu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| |
Collapse
|
112
|
Chokkalla AK, Arruri V, Mehta SL, Vemuganti R. Loss of Epitranscriptomic Modification N 6-Methyladenosine (m 6A) Reader YTHDF1 Exacerbates Ischemic Brain Injury in a Sexually Dimorphic Manner. Transl Stroke Res 2024:10.1007/s12975-024-01267-4. [PMID: 38869772 DOI: 10.1007/s12975-024-01267-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/28/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]
Abstract
N6-Methyladenosine (m6A) is a neuronal-enriched, reversible post-transcriptional modification that regulates RNA metabolism. The m6A-modified RNAs recruit various m6A-binding proteins that act as readers. Differential m6A methylation patterns are implicated in ischemic brain damage, yet the precise role of m6A readers in propagating post-stroke m6A signaling remains unclear. We presently evaluated the functional significance of the brain-enriched m6A reader YTHDF1, in post-stroke pathophysiology. Focal cerebral ischemia significantly increased YTHDF1 mRNA and protein expression in adult mice of both sexes. YTHDF1-/- male, but not female, mice subjected to transient middle cerebral artery occlusion (MCAO) showed worsened motor function recovery and increased infarction compared to sex-matched YTHDF1+/+ mice. YTHDF1-/- male, but not female, mice subjected to transient MCAO also showed significantly perturbed expression of genes related to inflammation, and increased infiltration of peripheral immune cells into the peri-infarct cortex, compared with sex-matched YTHDF1+/+ mice. Thus, this study demonstrates a sexual dimorphism of YTHDF1 in regulating post-ischemic inflammation and pathophysiology. Hence, post-stroke epitranscriptomic regulation might be sex-dependent.
Collapse
Affiliation(s)
- Anil K Chokkalla
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, 53792, USA
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin, Madison, WI, USA
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Vijay Arruri
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, 53792, USA
| | - Suresh L Mehta
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, 53792, USA
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, 53792, USA.
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin, Madison, WI, USA.
- William S. Middleton Memorial Veteran Administration Hospital, Madison, WI, USA.
| |
Collapse
|
113
|
Baquero-Pérez B, Bortoletto E, Rosani U, Delgado-Tejedor A, Medina R, Novoa EM, Venier P, Díez J. Elucidation of the Epitranscriptomic RNA Modification Landscape of Chikungunya Virus. Viruses 2024; 16:945. [PMID: 38932237 PMCID: PMC11209572 DOI: 10.3390/v16060945] [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: 05/02/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
The genomes of positive-sense (+) single-stranded RNA (ssRNA) viruses are believed to be subjected to a wide range of RNA modifications. In this study, we focused on the chikungunya virus (CHIKV) as a model (+) ssRNA virus to study the landscape of viral RNA modification in infected human cells. Among the 32 distinct RNA modifications analysed by mass spectrometry, inosine was found enriched in the genomic CHIKV RNA. However, orthogonal validation by Illumina RNA-seq analyses did not identify any inosine modification along the CHIKV RNA genome. Moreover, CHIKV infection did not alter the expression of ADAR1 isoforms, the enzymes that catalyse the adenosine to inosine conversion. Together, this study highlights the importance of a multidisciplinary approach to assess the presence of RNA modifications in viral RNA genomes.
Collapse
Affiliation(s)
- Belinda Baquero-Pérez
- Molecular Virology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Enrico Bortoletto
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; (E.B.); (U.R.)
| | - Umberto Rosani
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; (E.B.); (U.R.)
| | - Anna Delgado-Tejedor
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; (A.D.-T.); (R.M.); (E.M.N.)
| | - Rebeca Medina
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; (A.D.-T.); (R.M.); (E.M.N.)
| | - Eva Maria Novoa
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; (A.D.-T.); (R.M.); (E.M.N.)
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Paola Venier
- Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy; (E.B.); (U.R.)
| | - Juana Díez
- Molecular Virology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| |
Collapse
|
114
|
Wang G, Li H, Ye C, He K, Liu S, Jiang B, Ge R, Gao B, Wei J, Zhao Y, Li A, Zhang D, Zhang J, He C. Quantitative profiling of m 6A at single base resolution across the life cycle of rice and Arabidopsis. Nat Commun 2024; 15:4881. [PMID: 38849358 PMCID: PMC11161662 DOI: 10.1038/s41467-024-48941-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/13/2024] [Indexed: 06/09/2024] Open
Abstract
N6-methyladenosine (m6A) plays critical roles in regulating mRNA metabolism. However, comprehensive m6A methylomes in different plant tissues with single-base precision have yet to be reported. Here, we present transcriptome-wide m6A maps at single-base resolution in different tissues of rice and Arabidopsis using m6A-SAC-seq. Our analysis uncovers a total of 205,691 m6A sites distributed across 22,574 genes in rice, and 188,282 m6A sites across 19,984 genes in Arabidopsis. The evolutionarily conserved m6A sites in rice and Arabidopsis ortholog gene pairs are involved in controlling tissue development, photosynthesis and stress response. We observe an overall mRNA stabilization effect by 3' UTR m6A sites in certain plant tissues. Like in mammals, a positive correlation between the m6A level and the length of internal exons is also observed in plant mRNA, except for the last exon. Our data suggest an active m6A deposition process occurring near the stop codon in plant mRNA. In addition, the MTA-installed plant mRNA m6A sites correlate with both translation promotion and translation suppression, depicting a more complicated regulatory picture. Our results therefore provide in-depth resources for relating single-base resolution m6A sites with functions in plants and uncover a suppression-activation model controlling m6A biogenesis across species.
Collapse
Affiliation(s)
- Guanqun Wang
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA
| | - Haoxuan Li
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA
| | - Chang Ye
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA
| | - Kayla He
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Shun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA
| | - Bochen Jiang
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA
| | - Ruiqi Ge
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Boyang Gao
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA
| | - Jiangbo Wei
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Chemistry and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yutao Zhao
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Aixuan Li
- Department of Biology, Hong Kong Baptist University and School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Di Zhang
- Department of Biology, Hong Kong Baptist University and School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University and School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA.
| |
Collapse
|
115
|
Klein P, Petrić Howe M, Harley J, Crook H, Esteban Serna S, Roumeliotis TI, Choudhary JS, Chakrabarti AM, Luisier R, Patani R, Ramos A. m6a methylation orchestrates IMP1 regulation of microtubules during human neuronal differentiation. Nat Commun 2024; 15:4819. [PMID: 38844464 PMCID: PMC11156911 DOI: 10.1038/s41467-024-49139-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 05/21/2024] [Indexed: 06/09/2024] Open
Abstract
Neuronal differentiation requires building a complex intracellular architecture, and therefore the coordinated regulation of defined sets of genes. RNA-binding proteins (RBPs) play a key role in this regulation. However, while their action on individual mRNAs has been explored in depth, the mechanisms used to coordinate gene expression programs shaping neuronal morphology are poorly understood. To address this, we studied how the paradigmatic RBP IMP1 (IGF2BP1), an essential developmental factor, selects and regulates its RNA targets during the human neuronal differentiation. We perform a combination of system-wide and molecular analyses, revealing that IMP1 developmentally transitions to and directly regulates the expression of mRNAs encoding essential regulators of the microtubule network, a key component of neuronal morphology. Furthermore, we show that m6A methylation drives the selection of specific IMP1 mRNA targets and their protein expression during the developmental transition from neural precursors to neurons, providing a molecular principle for the onset of target selectivity.
Collapse
Affiliation(s)
- Pierre Klein
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6XA, UK
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Marija Petrić Howe
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Jasmine Harley
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Harry Crook
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sofia Esteban Serna
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6XA, UK
| | - Theodoros I Roumeliotis
- Functional Proteomics team, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Jyoti S Choudhary
- Functional Proteomics team, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Anob M Chakrabarti
- RNA Networks Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Raphaëlle Luisier
- Idiap Research Institute, Martigny, 1920, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Rickie Patani
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.
| | - Andres Ramos
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6XA, UK.
| |
Collapse
|
116
|
Li S, Tan XY, He Z, Shen C, Li YL, Qin L, Zhao CQ, Luo GH, Fang JC, Ji R. The dynamics of N 6-methyladenine RNA modification in resistant and susceptible rice varieties responding to rice stem borer damage. INSECT SCIENCE 2024. [PMID: 38831720 DOI: 10.1111/1744-7917.13401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 06/05/2024]
Abstract
N6-methyladenosine (m6A) is the most prevalent modification in cellular RNA which orchestrates diverse physiological and pathological processes during stress response. However, the differential m6A modifications that cope with herbivore stress in resistant and susceptible crop varieties remain unclear. Here, we found that rice stem borer (RSB) larvae grew better on indica rice (e.g., MH63, IR64, Nanjing 11) than on japonica rice varieties (e.g., Nipponbare, Zhonghua 11, Xiushui 11). Then, transcriptome-wide m6A profiling of representative resistant (Nipponbare) and susceptible (MH63) rice varieties were performed using a nanopore direct RNA sequencing approach, to reveal variety-specific m6A modifications against RSB. Upon RSB infestation, m6A methylation occurred in actively expressed genes in Nipponbare and MH63, but the number of methylation sites decreased across rice chromosomes. Integrative analysis showed that m6A methylation levels were closely associated with transcriptional regulation. Genes involved in herbivorous resistance related to mitogen-activated protein kinase, jasmonic acid (JA), and terpenoid biosynthesis pathways, as well as JA-mediated trypsin protease inhibitors, were heavily methylated by m6A, and their expression was more pronounced in RSB-infested Nipponbare than in RSB-infested MH63, which may have contributed to RSB resistance in Nipponbare. Therefore, dynamics of m6A modifications act as the main regulatory strategy for expression of genes involved in plant-insect interactions, which is attributed to differential responses of resistant and susceptible rice varieties to RSB infestation. These findings could contribute to developing molecular breeding strategies for controlling herbivorous pests.
Collapse
Affiliation(s)
- Shuai Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Xin-Yang Tan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhen He
- School of Plant Protection, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Chen Shen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ya-Li Li
- Wuhan Benagen Technology Company Limited, Wuhan, China
| | - Lang Qin
- School of Plant Protection, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Chun-Qing Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Guang-Hua Luo
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Ji-Chao Fang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huaian, Jiangsu Province, China
| | - Rui Ji
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huaian, Jiangsu Province, China
- School of Life Sciences, Anhui Normal University/Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Wuhu, Anhui Province, China
| |
Collapse
|
117
|
Kunoh S, Nakashima H, Nakashima K. Epigenetic Regulation of Neural Stem Cells in Developmental and Adult Stages. EPIGENOMES 2024; 8:22. [PMID: 38920623 PMCID: PMC11203245 DOI: 10.3390/epigenomes8020022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/18/2024] [Accepted: 05/31/2024] [Indexed: 06/27/2024] Open
Abstract
The development of the nervous system is regulated by numerous intracellular molecules and cellular signals that interact temporally and spatially with the extracellular microenvironment. The three major cell types in the brain, i.e., neurons and two types of glial cells (astrocytes and oligodendrocytes), are generated from common multipotent neural stem cells (NSCs) throughout life. However, NSCs do not have this multipotentiality from the beginning. During cortical development, NSCs sequentially obtain abilities to differentiate into neurons and glial cells in response to combinations of spatiotemporally modulated cell-intrinsic epigenetic alterations and extrinsic factors. After the completion of brain development, a limited population of NSCs remains in the adult brain and continues to produce neurons (adult neurogenesis), thus contributing to learning and memory. Many biological aspects of brain development and adult neurogenesis are regulated by epigenetic changes via behavioral control of NSCs. Epigenetic dysregulation has also been implicated in the pathogenesis of various brain diseases. Here, we present recent advances in the epigenetic regulation of NSC behavior and its dysregulation in brain disorders.
Collapse
Affiliation(s)
| | - Hideyuki Nakashima
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan;
| | - Kinichi Nakashima
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan;
| |
Collapse
|
118
|
Goebel GL, Giannino N, Lampe P, Qiu X, Schloßhauer JL, Imig J, Sievers S, Wu P. Profiling Cellular Morphological Changes Induced by Dual-Targeting PROTACs of Aurora Kinase and RNA-Binding Protein YTHDF2. Chembiochem 2024:e202400183. [PMID: 38837838 DOI: 10.1002/cbic.202400183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/02/2024] [Accepted: 06/04/2024] [Indexed: 06/07/2024]
Abstract
Proteolysis targeting chimeras (PROTACs) are new chemical modalities that degrade proteins of interest, including established kinase targets and emerging RNA-binding proteins (RBPs). Whereas diverse sets of biochemical, biophysical and cellular assays are available for the evaluation and optimizations of PROTACs in understanding the involved ubiquitin-proteasome-mediated degradation mechanism and the structure-degradation relationship, a phenotypic method profiling the cellular morphological changes is rarely used. In this study, first, we reported the only examples of PROTACs degrading the mRNA-binding protein YTHDF2 via screening of multikinase PROTACs. Second, we reported the profiling of cellular morphological changes of the dual kinase- and RBP-targeting PROTACs using the unbiased cell painting assay (CPA). The CPA analysis revealed the high biosimilarity with the established aurora kinase cluster and annotated aurora kinase inhibitors, which reflected the association between YTHDF2 and the aurora kinase signaling network. Broadly, the results demonstrated that the cell painting assay can be a straightforward and powerful approach to evaluate PROTACs. Complementary to the existing biochemical, biophysical and cellular assays, CPA provided a new perspective in characterizing PROTACs at the cellular morphology.
Collapse
Affiliation(s)
- Georg L Goebel
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
| | - Nicole Giannino
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
| | - Philipp Lampe
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Compound Management and Screening Center, Otto-Hahn Str. 15, Dortmund, 44227, Germany
| | - Xiaqiu Qiu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
| | - Jeffrey L Schloßhauer
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
| | - Jochen Imig
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
| | - Sonja Sievers
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Compound Management and Screening Center, Otto-Hahn Str. 15, Dortmund, 44227, Germany
| | - Peng Wu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
| |
Collapse
|
119
|
Wu S, Li F, Mo K, Huang H, Yu Y, Huang Y, Liu J, Li M, Tan J, Lin Z, Han Z, Wang L, Ouyang H. IGF2BP2 Maintains Retinal Pigment Epithelium Homeostasis by Stabilizing PAX6 and OTX2. Invest Ophthalmol Vis Sci 2024; 65:17. [PMID: 38861275 PMCID: PMC11174093 DOI: 10.1167/iovs.65.6.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/15/2024] [Indexed: 06/12/2024] Open
Abstract
Purpose N6-methyladenosine (m6A) methylation is a chemical modification that occurs on RNA molecules, where the hydrogen atom of adenine (A) nucleotides is replaced by a methyl group, forming N6-methyladenosine. This modification is a dynamic and reversible process that plays a crucial role in regulating various biological processes, including RNA stability, transport, translation, and degradation. Currently, there is a lack of research on the role of m6A modifications in maintaining the characteristics of RPE cells. m6A readers play a crucial role in executing the functions of m6A modifications, which prompted our investigation into their regulatory roles in the RPE. Methods Phagocytosis assays, immunofluorescence staining, flow cytometry experiments, β-galactosidase staining, and RNA sequencing (RNA-seq) were conducted to assess the functional and cellular characteristics changes in retinal pigment epithelium (RPE) cells following short-hairpin RNA-mediated knockdown of insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2). RNA-seq and ultraviolet crosslinking immunoprecipitation with high-throughput sequencing (HITS-CLIP) were employed to identify the target genes regulated by IGF2BP2. adeno-associated virus (AAV) subretinal injection was performed in 6- to 8-week-old C57 mice to reduce IGF2BP2 expression in the RPE, and the impact of IGF2BP2 knockdown on mouse visual function was assessed using immunofluorescence, quantitative real-time PCR, optical coherence tomography, and electroretinography. Results IGF2BP2 was found to have a pronounced effect on RPE phagocytosis. Subsequent in-depth exploration revealed that IGF2BP2 modulates the mRNA stability of PAX6 and OTX2, and the loss of IGF2BP2 induces inflammatory and aging phenotypes in RPE cells. IGF2BP2 knockdown impaired RPE function, leading to retinal dysfunction in vivo. Conclusions Our data suggest a crucial role of IGF2BP2 as an m6A reader in maintaining RPE homeostasis by regulating the stability of PAX6 and OTX2, making it a potential target for preventing the occurrence of retinal diseases related to RPE malfunction.
Collapse
Affiliation(s)
- Siqi Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Fuxi Li
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Kunlun Mo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Huaxing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Yankun Yu
- Department of Pathology, The First Affiliated Hospital of Shihezi University, Shihezi, Xinjiang, China
| | - Ying Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Jiafeng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Mingsen Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Jieying Tan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Zesong Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Zhuo Han
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Li Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Hong Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| |
Collapse
|
120
|
Wang S, Yang Y, Jiang X, Zheng X, Wei Q, Dai W, Zhang X. Nurturing gut health: role of m6A RNA methylation in upholding the intestinal barrier. Cell Death Discov 2024; 10:271. [PMID: 38830900 PMCID: PMC11148167 DOI: 10.1038/s41420-024-02043-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/19/2024] [Accepted: 05/22/2024] [Indexed: 06/05/2024] Open
Abstract
The intestinal lumen acts as a critical interface connecting the external environment with the body's internal state. It's essential to prevent the passage of harmful antigens and bacteria while facilitating nutrient and water absorption. The intestinal barriers encompass microbial, mechanical, immunological, and chemical elements, working together to maintain intestinal balance. Numerous studies have associated m6A modification with intestinal homeostasis. This review comprehensively outlines potential mechanisms through which m6A modification could initiate, exacerbate, or sustain barrier damage from an intestinal perspective. The pivotal role of m6A modification in preserving intestinal equilibrium provides new insights, guiding the exploration of m6A modification as a target for optimizing preventive and therapeutic strategies for intestinal homeostasis.
Collapse
Affiliation(s)
| | - Yuzhong Yang
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Xiaohan Jiang
- Department of Pathology, Liuzhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
| | - Xiang Zheng
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Qiufang Wei
- Department of Pathology, Liuzhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
| | - Wenbin Dai
- Department of Pathology, Liuzhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China.
| | - Xuemei Zhang
- Department of Pathology, Liuzhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China.
| |
Collapse
|
121
|
Chen C, Jiang C, Lin T, Hu Y, Wu H, Xiang Q, Yang M, Wang S, Han X, Tao J. Landscape of transcriptome-wide m 6A modification in diabetic liver reveals rewiring of PI3K-Akt signaling after physical exercise. Acta Physiol (Oxf) 2024; 240:e14154. [PMID: 38682314 DOI: 10.1111/apha.14154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 04/04/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024]
Abstract
AIM Type 2 diabetes mellitus (T2DM) is one of the most common diseases, and epigenetic modification N6-methyladenosine (m6A) is essential for transcriptional modulation involved in its development. However, the precise role and landscape of transcriptome-wide m6A alterations in molecular adaptations after physical exercise have yet to be fully elucidated. METHODS Four-week-old male C57BL/6J mice received a high-fat diet (HFD) for 12 weeks to establish a diabetic state, and HFD mice were simultaneously subjected to physical exercise (HFD + EX). The hepatic RNA m6A methylome was examined, the conjoint MeRIP-seq and RNA-seq was performed, and the exercise-modulated genes were confirmed. RESULTS Physical exercise significantly ameliorates liver metabolic disorder and triggers a dynamic change in hepatic RNA m6A. By analyzing the distribution of m6A in transcriptomes, an abundance of m6A throughout mRNA transcripts and a pattern of conserved m6A after physical exercise was identified. It is noteworthy that conjoint MeRIP-seq and RNA-seq data revealed that both differentially methylated genes and differentially expressed genes were enriched in all stages of the PI3K-Akt signaling pathway, in particular the upstream nodes of this pathway, which are considered a valuable therapeutic target for T2DM. Moreover, in vivo and in vitro analyses showed that exercise-mediated methyltransferase Rbm15 positively regulated the expression of two upstream genes (Itga3 and Fgf21) in an m6A-dependent manner. CONCLUSION These findings highlight the pivotal role of the exercise-induced m6A epigenetic network and contribute insights into the intricate epigenetic mechanism underlying insulin signaling.
Collapse
Affiliation(s)
- Cong Chen
- Rehabilitation Industry Institute, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- National-Local Joint Engineering Research Center of Rehabilitation Medicine Technology, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- Fujian Key Laboratory of cognitive rehabilitation, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
| | - Cai Jiang
- Rehabilitation Industry Institute, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
| | - Ting Lin
- Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Yue Hu
- Rehabilitation Industry Institute, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
| | - Huijuan Wu
- Rehabilitation Industry Institute, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
| | - Qing Xiang
- Rehabilitation Industry Institute, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- National-Local Joint Engineering Research Center of Rehabilitation Medicine Technology, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- Fujian Key Laboratory of cognitive rehabilitation, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
| | - Minguang Yang
- Rehabilitation Industry Institute, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- National-Local Joint Engineering Research Center of Rehabilitation Medicine Technology, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- Fujian Key Laboratory of cognitive rehabilitation, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
| | - Sinuo Wang
- Rehabilitation Industry Institute, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
| | - Xiao Han
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Jing Tao
- Rehabilitation Industry Institute, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- National-Local Joint Engineering Research Center of Rehabilitation Medicine Technology, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- Fujian Key Laboratory of cognitive rehabilitation, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
| |
Collapse
|
122
|
Hwang H, Jeon H, Yeo N, Baek D. Big data and deep learning for RNA biology. Exp Mol Med 2024; 56:1293-1321. [PMID: 38871816 PMCID: PMC11263376 DOI: 10.1038/s12276-024-01243-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 06/15/2024] Open
Abstract
The exponential growth of big data in RNA biology (RB) has led to the development of deep learning (DL) models that have driven crucial discoveries. As constantly evidenced by DL studies in other fields, the successful implementation of DL in RB depends heavily on the effective utilization of large-scale datasets from public databases. In achieving this goal, data encoding methods, learning algorithms, and techniques that align well with biological domain knowledge have played pivotal roles. In this review, we provide guiding principles for applying these DL concepts to various problems in RB by demonstrating successful examples and associated methodologies. We also discuss the remaining challenges in developing DL models for RB and suggest strategies to overcome these challenges. Overall, this review aims to illuminate the compelling potential of DL for RB and ways to apply this powerful technology to investigate the intriguing biology of RNA more effectively.
Collapse
Affiliation(s)
- Hyeonseo Hwang
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyeonseong Jeon
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Genome4me Inc., Seoul, Republic of Korea
| | - Nagyeong Yeo
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Daehyun Baek
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
- Genome4me Inc., Seoul, Republic of Korea.
| |
Collapse
|
123
|
Yang H, Wang W, Liu H, Zhang C, Cao Y, Long L, Han X, Wang Y, Yan F, Li G, Zhu M, Jin L, Fan Z. miR615-3p inhibited FBLN1 and osteogenic differentiation of umbilical cord mesenchymal stem cells by associated with YTHDF2 in a m 6A-miRNA interaction manner. Cell Prolif 2024; 57:e13607. [PMID: 38353178 DOI: 10.1111/cpr.13607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/09/2024] [Accepted: 01/27/2024] [Indexed: 06/06/2024] Open
Abstract
To investigate the role and mechanism of FBLN1 in the osteogenic differentiation and bone regeneration by using umbilical cord mesenchymal stem cells (WJCMSCs). We found that FBLN1 promoted osteogenic differentiation of WJCMSCs and WJCMSC-mediated bone regeneration. It was showed that there was an m6A methylation site in 3'UTR of FBLN1 mRNA, and the mutation of the m6A site enhanced the stability of FBLN1 mRNA, subsequently fostering the FBLN1 enhanced osteogenic differentiation of WJCMSCs. YTHDF2 was identified as capable of recognizing and binding to the m6A site, consequently inducing FBLN1 instability and repressed the osteogenic differentiation of WJCMSCs. Meanwhile, miR-615-3p negatively regulated FBLN1 by binding FBLN1 3'UTR and inhibited the osteogenic differentiation of WJCMSCs and WJCMSC-mediated bone regeneration. Then, we discovered miR-615-3p was found to regulate the functions of FBLN1 facilitated by YTHDF2 through an m6A-miRNA regulation mechanism. We demonstrated that FBLN1 is critical for regulating the osteogenic differentiation potentials of WJCMSCs and have identified that miR615-3p mediated the decay of FBLN1 mRNA which facilitated by m6A reading protein YTHDF2. This provided a novel m6A-miRNA epigenetic regulatory pattern for MSC regulation and bone regeneration.
Collapse
Affiliation(s)
- Haoqing Yang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Wanqing Wang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Huina Liu
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Chen Zhang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Yangyang Cao
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Lujue Long
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Xiao Han
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Yuejun Wang
- Department of General Dentistry and Integrated Emergency Dental Care, Beijing Stomatological Hospital, Capital Medical University, Beijing, China
| | - Fei Yan
- Xiangya Stomatological Hospital and School of Stomatology, Central South University, Changsha, China
| | - Guoqing Li
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Mengyuan Zhu
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Luyuan Jin
- Department of General Dentistry and Integrated Emergency Dental Care, Beijing Stomatological Hospital, Capital Medical University, Beijing, China
| | - Zhipeng Fan
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
- Beijing Laboratory of Oral Health, Capital Medical University, Beijing, China
- Research Unit of Tooth Development and Regeneration, Chinese Academy of Medical Sciences, Beijing, China
| |
Collapse
|
124
|
Jiang J, Duan M, Wang Z, Lai Y, Zhang C, Duan C. RNA epigenetics in pulmonary diseases: Insights into methylation modification of lncRNAs in lung cancer. Biomed Pharmacother 2024; 175:116704. [PMID: 38749181 DOI: 10.1016/j.biopha.2024.116704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/26/2024] [Accepted: 05/02/2024] [Indexed: 06/03/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are pivotal controllers of gene expression through epigenetic mechanisms, Methylation, a prominent area of study in epigenetics, significantly impacts cellular processes. Various RNA base methylations, including m6A, m5C, m1A, and 2'-O-methylation, profoundly influence lncRNA folding, interactions, and stability, thereby shaping their functionality. LncRNAs and methylation significantly contribute to tumor development, especially in lung cancer. Their roles encompass cell differentiation, proliferation, the generation of cancer stem cells, and modulation of immune responses. Recent studies have suggested that dysregulation of lncRNA methylation can contribute to lung cancer development. Furthermore, methylation modifications of lncRNAs hold potential for clinical application in lung cancer. Dysregulated lncRNA methylation can promote lung cancer progression and may offer insights into potential biomarker or therapeutic target. This review summarizes the current knowledge of lncRNA methylation in lung cancer and its implications for RNA epigenetics and pulmonary diseases.
Collapse
Affiliation(s)
- Junjie Jiang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China
| | - Minghao Duan
- Department of Public Health Laboratory Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang, 412017, Hunan, People's Republic of China
| | - Zheng Wang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China
| | - Yuwei Lai
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China
| | - Chunfang Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China; Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China
| | - Chaojun Duan
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China; Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Institute of Medical Sciences, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; National Clinical Research Center for Geriatric Disorders, Changsha 410008, Hunan, People's Republic of China.
| |
Collapse
|
125
|
Ma T, Zhang Q, Zhang S, Yue D, Wang F, Ren Y, Zhang H, Wang Y, Wu Y, Liu LE, Yu F. Research progress of human key DNA and RNA methylation-related enzymes assay. Talanta 2024; 273:125872. [PMID: 38471421 DOI: 10.1016/j.talanta.2024.125872] [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: 12/26/2023] [Revised: 02/18/2024] [Accepted: 03/03/2024] [Indexed: 03/14/2024]
Abstract
Gene methylation-related enzymes (GMREs) are disfunction and aberrantly expressed in a variety of cancers, such as lung, gastric, and pancreatic cancers and have important implications for human health. Therefore,it is critical for early diagnosis and therapy of tumor to develop strategies that allow rapid and sensitive quantitative and qualitative detection of GMREs. With the development of modern analytical techniques and the application of various biosensors, there are numerous methods have been developed for analysis of GMREs. Therefore, this paper provides a systematic review of the strategies for level and activity assay of various GMREs including methyltransferases and demethylase. The detection methods mainly involve immunohistochemistry, colorimetry, fluorescence, chemiluminescence, electrochemistry, etc. Then, this review also addresses the coordinated role of various detection probes, novel nanomaterials, and signal amplification methods. The aim is to highlight potential challenges in the present field, to expand the analytical application of GMREs detection strategies, and to meet the urgent need for future disease diagnosis and intervention.
Collapse
Affiliation(s)
- Tiantian Ma
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Qiongwen Zhang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Shuying Zhang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Dan Yue
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fanting Wang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yujie Ren
- School of Information Management, Zhengzhou University, Zhengzhou 450001, China
| | - Hengmiao Zhang
- School of Information Management, Zhengzhou University, Zhengzhou 450001, China
| | - Yinuo Wang
- Zhengzhou Foreign Language School, Zhengzhou 450001, China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Li-E Liu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fei Yu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
| |
Collapse
|
126
|
Yin H, Ju Z, Zhang X, Zuo W, Yang Y, Zheng M, Zhang X, Liu Y, Peng Y, Xing Y, Yang A, Zhang R. Inhibition of METTL3 in macrophages provides protection against intestinal inflammation. Cell Mol Immunol 2024; 21:589-603. [PMID: 38649449 PMCID: PMC11143309 DOI: 10.1038/s41423-024-01156-8] [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: 11/14/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
Inflammatory bowel disease (IBD) is prevalent, and no satisfactory therapeutic options are available because the mechanisms underlying its development are poorly understood. In this study, we discovered that increased expression of methyltransferase-like 3 (METTL3) in macrophages was correlated with the development of colitis and that depletion of METTL3 in macrophages protected mice against dextran sodium sulfate (DSS)-induced colitis. Mechanistic characterization indicated that METTL3 depletion increased the YTHDF3-mediated expression of phosphoglycolate phosphatase (PGP), which resulted in glucose metabolism reprogramming and the suppression of CD4+ T helper 1 (Th1) cell differentiation. Further analysis revealed that glucose metabolism contributed to the ability of METTL3 depletion to ameliorate colitis symptoms. In addition, we developed two potent small molecule METTL3 inhibitors, namely, F039-0002 and 7460-0250, that strongly ameliorated DSS-induced colitis. Overall, our study suggests that METTL3 plays crucial roles in the progression of colitis and highlights the potential of targeting METTL3 to attenuate intestinal inflammation for the treatment of colitis.
Collapse
Affiliation(s)
- Huilong Yin
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- Molecular Immunology and Immunotherapy Laboratory, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
| | - Zhuan Ju
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Immunology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Medical Genetics and Developmental Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Xiang Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Wenjie Zuo
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- Molecular Immunology and Immunotherapy Laboratory, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
| | - Yuhang Yang
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- Molecular Immunology and Immunotherapy Laboratory, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
| | - Minhua Zheng
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Medical Genetics and Developmental Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Xiaofang Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Yuning Liu
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- Molecular Immunology and Immunotherapy Laboratory, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
| | - Yingran Peng
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Ying Xing
- Department of Endocrinology, Xi'an Daxing Hospital, Xi'an, Shaanxi, 710000, China
| | - Angang Yang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Immunology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China.
| | - Rui Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Immunology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China.
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China.
| |
Collapse
|
127
|
Wang Y, Wu Z, He Y, Zeng X, Gu Z, Zhou X, Si W, Chen D. Fat mass and obesity-associated protein regulates RNA methylation associated with spatial cognitive dysfunction after chronic cerebral hypoperfusion. Neuropeptides 2024; 105:102428. [PMID: 38583362 DOI: 10.1016/j.npep.2024.102428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/31/2024] [Accepted: 04/01/2024] [Indexed: 04/09/2024]
Abstract
RNA methylation can epigenetically regulate learning and memory. However, it is unclear whether RNA methylation plays a critical role in the pathophysiology of Vascular dementia (VD). Here, we report that expression of the fat mass and obesity associated gene (FTO), an RNA demethylase, is downregulated in the hippocampus in models of VD. Through prediction and dual-luciferase reporters validation studies, we observed that miRNA-711 was upregulated after VD and could bind to the 3'-untranslated region of FTO mRNA and regulate its expression in vitro. Methylated RNA immunoprecipitation (MeRIP)-qPCR assay and functional study confirmed that Syn1 was an important target gene of FTO. This suggests that FTO is an important regulator of Syn1. FTO upregulation by inhibition of miR-711 in the hippocampus relieves synaptic association protein and synapse deterioration in vivo, whereas FTO downregulation by miR-711 agomir in the hippocampus leads to aggravate the synapse deterioration. FTO upregulation by inhibition of miR-711 relieves cognitive impairment of rats VD model, whereas FTO downregulation by miR-711 deteriorate cognitive impairment. Our findings suggest that FTO is a regulator of a mechanism underlying RNA methylation associated with spatial cognitive dysfunction after chronic cerebral hypoperfusion.
Collapse
Affiliation(s)
- Yanqing Wang
- Department of Anatomy, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zimei Wu
- Department of Orthopedic Surgery, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China; School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yuyang He
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Xiaoying Zeng
- Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Zijuan Gu
- Shenzhen BaoAn District Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Xianxi Zhou
- Department of Anatomy, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wenwen Si
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China.
| | - Dongfeng Chen
- Department of Anatomy, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China.
| |
Collapse
|
128
|
Knight HM, Demirbugen Öz M, PerezGrovas-Saltijeral A. Dysregulation of RNA modification systems in clinical populations with neurocognitive disorders. Neural Regen Res 2024; 19:1256-1261. [PMID: 37905873 DOI: 10.4103/1673-5374.385858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/10/2023] [Indexed: 11/02/2023] Open
Abstract
ABSTRACT The study of modified RNA known as epitranscriptomics has become increasingly relevant in our understanding of disease-modifying mechanisms. Methylation of N6 adenosine (m6A) and C5 cytosine (m5C) bases occur on mRNAs, tRNA, mt-tRNA, and rRNA species as well as non-coding RNAs. With emerging knowledge of RNA binding proteins that act as writer, reader, and eraser effector proteins, comes a new understanding of physiological processes controlled by these systems. Such processes when spatiotemporally disrupted within cellular nanodomains in highly specialized tissues such as the brain, give rise to different forms of disease. In this review, we discuss accumulating evidence that changes in the m6A and m5C methylation systems contribute to neurocognitive disorders. Early studies first identified mutations within FMR1 to cause intellectual disability Fragile X syndromes several years before FMR1 was identified as an m6A RNA reader protein. Subsequently, familial mutations within the m6A writer gene METTL5, m5C writer genes NSUN2, NSUN3, NSUN5, and NSUN6, as well as THOC2 and THOC6 that form a protein complex with the m5C reader protein ALYREF, were recognized to cause intellectual development disorders. Similarly, differences in expression of the m5C writer and reader effector proteins, NSUN6, NSUN7, and ALYREF in brain tissue are indicated in individuals with Alzheimer's disease, individuals with a high neuropathological load or have suffered traumatic brain injury. Likewise, an abundance of m6A reader and anti-reader proteins are reported to change across brain regions in Lewy bodies diseases, Alzheimer's disease, and individuals with high cognitive reserve. m6A-modified RNAs are also reported significantly more abundant in dementia with Lewy bodies brain tissue but significantly reduced in Parkinson's disease tissue, whilst modified RNAs are misplaced within diseased cells, particularly where synapses are located. In parahippocampal brain tissue, m6A modification is enriched in transcripts associated with psychiatric disorders including conditions with clear cognitive deficits. These findings indicate a diverse set of molecular mechanisms are influenced by RNA methylation systems that can cause neuronal and synaptic dysfunction underlying neurocognitive disorders. Targeting these RNA modification systems brings new prospects for neural regenerative therapies.
Collapse
Affiliation(s)
- Helen M Knight
- Division of Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Merve Demirbugen Öz
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Ankara University, Ankara, Turkey
| | | |
Collapse
|
129
|
Zhong X, Zhou Z, Yang G. The Functions of N-methyladenosine (m6A) Modification on HIV-1 mRNA. Cell Biochem Biophys 2024; 82:561-574. [PMID: 38753251 DOI: 10.1007/s12013-024-01280-2] [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] [Accepted: 04/17/2024] [Indexed: 08/25/2024]
Abstract
In recent years, there has been a growing interest in the study of RNA modifications, with some researchers focusing specifically on the connection between these modifications and viruses, as well as the impact they have on viral mRNA and its functionality. The most common type of RNA chemical modification is m6A, which involves the addition of a methyl group covalently to the N6 position of adenosine. It is a widely observed and evolutionarily conserved RNA modification. The regulation of m6A modification primarily involves methyltransferases (writers) and demethylases (erasers) and is mediated by m6A-binding proteins (readers). In HIV-1, m6A sites are predominantly located in the 5' untranslated region (5'UTR) and 3' untranslated region (3'UTR). Additionally, m6A modifications are also present in the RRE RNA of HIV-1. This review provides a detailed account of the effects of these m6A modifications on HIV-1 functionality.
Collapse
Affiliation(s)
- XinYu Zhong
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, 310013, China
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, 310013, China
| | - ZhuJiao Zhou
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, 310013, China
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, 310013, China
| | - Geng Yang
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, 310013, China.
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310013, China.
| |
Collapse
|
130
|
Rabelo-Fernández RJ, Yuen M, Batista PJ. The metabolic baton: conducting the dance of N6-methyladenosine writing and erasing. Curr Opin Genet Dev 2024; 86:102206. [PMID: 38788488 PMCID: PMC11212039 DOI: 10.1016/j.gde.2024.102206] [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: 02/13/2024] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024]
Abstract
The modification N6-methyladenosine (m6A) plays an important role in determining the functional output of gene expression programs. Throughout the transcriptome, the levels of m6A are tightly regulated by the opposing activities of methyltransferases and demethylases, as well as the interaction of modified transcripts with m6A-dependent RNA-binding proteins that modulate transcript stability, often referred to as writers, erasers, and readers. The enzymatic activities of both writers and erasers are tightly linked to the cellular metabolic environment, as these enzymatic reactions rely on metabolism intermediaries as cofactors. In this review, we highlight the examples of intersection between metabolism and m6A-dependent gene regulation and discuss the different contexts where this interaction plays important roles.
Collapse
Affiliation(s)
- Robert J Rabelo-Fernández
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Madeline Yuen
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Pedro J Batista
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
131
|
Huang X, Li Q, Xu Y, Li A, Wang S, Chen Y, Zhang C, Zhang X, Wang H, Lv C, Sun B, Li S, Kang L, Chen B. A neural m 6A pathway regulates behavioral aggregation in migratory locusts. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1242-1254. [PMID: 38478296 DOI: 10.1007/s11427-023-2476-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 10/07/2023] [Indexed: 06/07/2024]
Abstract
RNA N6-methyladenosine (m6A), as the most abundant modification of messenger RNA, can modulate insect behaviors, but its specific roles in aggregation behaviors remain unexplored. Here, we conducted a comprehensive molecular and physiological characterization of the individual components of the methyltransferase and demethylase in the migratory locust Locusta migratoria. Our results demonstrated that METTL3, METTL14 and ALKBH5 were dominantly expressed in the brain and exhibited remarkable responses to crowding or isolation. The individual knockdown of methyltransferases (i.e., METTL3 and METTL14) promoted locust movement and conspecific attraction, whereas ALKBH5 knockdown induced a behavioral shift toward the solitary phase. Furthermore, global transcriptome profiles revealed that m6A modification could regulate the orchestration of gene expression to fine tune the behavioral aggregation of locusts. In summary, our in vivo characterization of the m6A functions in migratory locusts clearly demonstrated the crucial roles of the m6A pathway in effectively modulating aggregation behaviors.
Collapse
Affiliation(s)
- Xianliang Huang
- School of Life Science, Institutes of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Qing Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanan Xu
- Institute of Health Sciences, Anhui University, Hefei, 230601, China
| | - Ang Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shanzheng Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yusheng Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chunrui Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xia Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cong Lv
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Baofa Sun
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shaoqin Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Le Kang
- School of Life Science, Institutes of Life Science and Green Development, Hebei University, Baoding, 071002, China.
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Bing Chen
- School of Life Science, Institutes of Life Science and Green Development, Hebei University, Baoding, 071002, China.
| |
Collapse
|
132
|
Wang X, Gan M, Wang Y, Wang S, Lei Y, Wang K, Zhang X, Chen L, Zhao Y, Niu L, Zhang S, Zhu L, Shen L. Comprehensive review on lipid metabolism and RNA methylation: Biological mechanisms, perspectives and challenges. Int J Biol Macromol 2024; 270:132057. [PMID: 38710243 DOI: 10.1016/j.ijbiomac.2024.132057] [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: 03/03/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 05/08/2024]
Abstract
Adipose tissue plays a crucial role in maintaining energy balance, regulating hormones, and promoting metabolic health. To address disorders related to obesity and develop effective therapies, it is essential to have a deep understanding of adipose tissue biology. In recent years, RNA methylation has emerged as a significant epigenetic modification involved in various cellular functions and metabolic pathways. Particularly in the realm of adipogenesis and lipid metabolism, extensive research is ongoing to uncover the mechanisms and functional importance of RNA methylation. Increasing evidence suggests that RNA methylation plays a regulatory role in adipocyte development, metabolism, and lipid utilization across different organs. This comprehensive review aims to provide an overview of common RNA methylation modifications, their occurrences, and regulatory mechanisms, focusing specifically on their intricate connections to fat metabolism. Additionally, we discuss the research methodologies used in studying RNA methylation and highlight relevant databases that can aid researchers in this rapidly advancing field.
Collapse
Affiliation(s)
- Xingyu Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Mailin Gan
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Saihao Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuhang Lei
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Kai Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xin Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lei Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Ye Zhao
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Niu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shunhua Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Zhu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
| | - Linyuan Shen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
| |
Collapse
|
133
|
Guo W, Wang T, Huai Q, Guo L, Wang X, He J. KIAA1429 regulates lung adenocarcinoma proliferation and metastasis through the PI3K/AKT pathway by modulating ARHGAP30 expression. Thorac Cancer 2024; 15:1397-1409. [PMID: 38717936 PMCID: PMC11194123 DOI: 10.1111/1759-7714.15327] [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: 01/19/2024] [Revised: 04/07/2024] [Accepted: 04/23/2024] [Indexed: 06/25/2024] Open
Abstract
BACKGROUND Alterations in epigenetic factors are recognized as key contributors to the emergence of human cancer. The active and reversible alteration of N6-methyladenosine (m6A) RNA is crucial for controlling gene activity and determining cellular destiny. Even with these insights, the triggering of KIAA1429 (also called VIRMA) and its role in lung adenocarcinoma (LUAD) is mostly unclear. As a result, the objective of this study was to elucidate how KIAA1429 contributes to cancer development in LUAD. METHODS This study utilized multiple methods for investigation, encompassing the in vitro functional examination of KIAA1429 in lung adenocarcinoma cells, transcriptome sequencing, methylation RNA immunoprecipitation sequencing (MeRIP-seq), as well as RNA stability tests to ascertain the half-life and stability of the target genes. RESULTS The results indicated that modifying the expression of KIAA1429 regulated the proliferation and metastasis of LUAD. By employing transcriptome sequencing alongside MeRIP-seq analysis, the research pinpointed genes affected by m6A alterations triggered by KIAA1429. In a more detailed manner, it was discovered that KIAA1429 plays a regulatory role in the expression of ARHGAP30. Suppressing KIAA1429 results in reduced m6A levels in the mRNA of the target gene ARHGAP30, boosting its stability and expression, thus inhibiting tumor proliferation and metastasis. CONCLUSION This study revealed the activation mechanism and pivotal function of KIAA1429 in LUAD tumor development, paving the way for molecular-based interventions for LUAD.
Collapse
Affiliation(s)
- Wei Guo
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
- Key Laboratory of Minimally Invasive Therapy Research for Lung CancerChinese Academy of Medical SciencesBeijingChina
| | - Tan Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Qilin Huai
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Lei Guo
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Xiaobing Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| |
Collapse
|
134
|
Huang G, Huang X, Jiang J. Deepm6A-MT: A deep learning-based method for identifying RNA N6-methyladenosine sites in multiple tissues. Methods 2024; 226:1-8. [PMID: 38485031 DOI: 10.1016/j.ymeth.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/20/2024] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent, abundant, and conserved internal modification in the eukaryotic messenger RNA (mRNAs) and plays a crucial role in the cellular process. Although more than ten methods were developed for m6A detection over the past decades, there were rooms left to improve the predictive accuracy and the efficiency. In this paper, we proposed an improved method for predicting m6A modification sites, which was based on bi-directional gated recurrent unit (Bi-GRU) and convolutional neural networks (CNN), called Deepm6A-MT. The Deepm6A-MT has two input channels. One is to use an embedding layer followed by the Bi-GRU and then by the CNN, and another is to use one-hot encoding, dinucleotide one-hot encoding, and nucleotide chemical property codes. We trained and evaluated the Deepm6A-MT both by the 5-fold cross-validation and the independent test. The empirical tests showed that the Deepm6A-MT achieved the state of the art performance. In addition, we also conducted the cross-species and the cross-tissues tests to further verify the Deepm6A-MT for effectiveness and efficiency. Finally, for the convenience of academic research, we deployed the Deepm6A-MT to the web server, which is accessed at the URL http://www.biolscience.cn/Deepm6A-MT/.
Collapse
Affiliation(s)
- Guohua Huang
- School of Information Technology and Administration, Hunan University of Finance and Economics, Changsha, Hunan 410205, China.
| | - Xiaohong Huang
- College of Information Science and Engineering, Shaoyang University, Shaoyang, Hunan 422000, China
| | - Jinyun Jiang
- College of Information Science and Engineering, Shaoyang University, Shaoyang, Hunan 422000, China
| |
Collapse
|
135
|
Mehmood R. Ramifications of m6A Modification on ncRNAs in Cancer. Curr Genomics 2024; 25:158-170. [PMID: 39087001 PMCID: PMC11288162 DOI: 10.2174/0113892029296712240405053201] [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: 12/18/2023] [Revised: 03/12/2024] [Accepted: 03/26/2024] [Indexed: 08/02/2024] Open
Abstract
N6-methyladenosine (m6A) is an RNA modification wherein the N6-position of adenosine is methylated. It is one of the most prevalent internal modifications of RNA and regulates various aspects of RNA metabolism. M6A is deposited by m6A methyltransferases, removed by m6A demethylases, and recognized by reader proteins, which modulate splicing, export, translation, and stability of the modified mRNA. Recent evidence suggests that various classes of non- coding RNAs (ncRNAs), including microRNAs (miRNAs), circular RNAs (circRNAs), and long con-coding RNAs (lncRNAs), are also targeted by this modification. Depending on the ncRNA species, m6A may affect the processing, stability, or localization of these molecules. The m6A- modified ncRNAs are implicated in a number of diseases, including cancer. In this review, the author summarizes the role of m6A modification in the regulation and functions of ncRNAs in tumor development. Moreover, the potential applications in cancer prognosis and therapeutics are discussed.
Collapse
Affiliation(s)
- Rashid Mehmood
- Department of Life Sciences, College of Science and General Studies, Alfaisal University, Riyadh, Kingdom of Saudi Arabia
| |
Collapse
|
136
|
Song M, Zhao J, Zhang C, Jia C, Yang J, Zhao H, Zhai J, Lei B, Tao S, Chen S, Su R, Ma C. PEA-m6A: an ensemble learning framework for accurately predicting N6-methyladenosine modifications in plants. PLANT PHYSIOLOGY 2024; 195:1200-1213. [PMID: 38428981 DOI: 10.1093/plphys/kiae120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 01/11/2024] [Accepted: 02/01/2024] [Indexed: 03/03/2024]
Abstract
N 6-methyladenosine (m6A), which is the mostly prevalent modification in eukaryotic mRNAs, is involved in gene expression regulation and many RNA metabolism processes. Accurate prediction of m6A modification is important for understanding its molecular mechanisms in different biological contexts. However, most existing models have limited range of application and are species-centric. Here we present PEA-m6A, a unified, modularized and parameterized framework that can streamline m6A-Seq data analysis for predicting m6A-modified regions in plant genomes. The PEA-m6A framework builds ensemble learning-based m6A prediction models with statistic-based and deep learning-driven features, achieving superior performance with an improvement of 6.7% to 23.3% in the area under precision-recall curve compared with state-of-the-art regional-scale m6A predictor WeakRM in 12 plant species. Especially, PEA-m6A is capable of leveraging knowledge from pretrained models via transfer learning, representing an innovation in that it can improve prediction accuracy of m6A modifications under small-sample training tasks. PEA-m6A also has a strong capability for generalization, making it suitable for application in within- and cross-species m6A prediction. Overall, this study presents a promising m6A prediction tool, PEA-m6A, with outstanding performance in terms of its accuracy, flexibility, transferability, and generalization ability. PEA-m6A has been packaged using Galaxy and Docker technologies for ease of use and is publicly available at https://github.com/cma2015/PEA-m6A.
Collapse
Affiliation(s)
- Minggui Song
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiawen Zhao
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chujun Zhang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chengchao Jia
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Yang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Haonan Zhao
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jingjing Zhai
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
| | - Beilei Lei
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shiheng Tao
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Siqi Chen
- School of Computer Software, College of Intelligence and Computing, Tianjin University, Tianjin 300072, China
| | - Ran Su
- School of Computer Software, College of Intelligence and Computing, Tianjin University, Tianjin 300072, China
| | - Chuang Ma
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| |
Collapse
|
137
|
Yang W, Zhao Y, Yang Y. Dynamic RNA methylation modifications and their regulatory role in mammalian development and diseases. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2526-2. [PMID: 38833084 DOI: 10.1007/s11427-023-2526-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/15/2023] [Indexed: 06/06/2024]
Abstract
Among over 170 different types of chemical modifications on RNA nucleobases identified so far, RNA methylation is the major type of epitranscriptomic modifications existing on almost all types of RNAs, and has been demonstrated to participate in the entire process of RNA metabolism, including transcription, pre-mRNA alternative splicing and maturation, mRNA nucleus export, mRNA degradation and stabilization, mRNA translation. Attributing to the development of high-throughput detection technologies and the identification of both dynamic regulators and recognition proteins, mechanisms of RNA methylation modification in regulating the normal development of the organism as well as various disease occurrence and developmental abnormalities upon RNA methylation dysregulation have become increasingly clear. Here, we particularly focus on three types of RNA methylations: N6-methylcytosine (m6A), 5-methylcytosine (m5C), and N7-methyladenosine (m7G). We summarize the elements related to their dynamic installment and removal, specific binding proteins, and the development of high-throughput detection technologies. Then, for a comprehensive understanding of their biological significance, we also overview the latest knowledge on the underlying mechanisms and key roles of these three mRNA methylation modifications in gametogenesis, embryonic development, immune system development, as well as disease and tumor progression.
Collapse
Affiliation(s)
- Wenlan Yang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
| | - Yongliang Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
| | - Yungui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- China National Center for Bioinformation, Beijing, 100101, China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408, China.
| |
Collapse
|
138
|
Mansfield KD. RNA Binding by the m6A Methyltransferases METTL16 and METTL3. BIOLOGY 2024; 13:391. [PMID: 38927271 PMCID: PMC11200852 DOI: 10.3390/biology13060391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/10/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024]
Abstract
Methyltransferases are a wide-ranging, yet well-conserved, class of molecules that have been found to modify a wide variety of substrates. Interest in RNA methylation has surged in recent years with the identification of the major eukaryotic mRNA m6A methyltransferase METTL3. METTL16 has also been identified as an RNA m6A methyltransferase; however, much less is known about its targets and actions. Interestingly, in addition to their catalytic activities, both METTL3 and METTL16 also have "methylation-independent" functions, including translational regulation, which have been discovered. However, evidence suggests that METTL16's role as an RNA-binding protein may be more significant than is currently recognized. In this review, we will introduce RNA methylation, specifically m6A, and the enzymes responsible for its deposition. We will discuss the varying roles that these enzymes perform and delve deeper into their RNA targets and possible roles as methylation-independent RNA binding proteins. Finally, we will touch upon the many open questions still remaining.
Collapse
Affiliation(s)
- Kyle D Mansfield
- Biochemistry and Molecular Biology Department, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| |
Collapse
|
139
|
Gu Y, Wei K, Wang J. Phase separation and transcriptional regulation in cancer development. J Biomed Res 2024; 38:307-321. [PMID: 39113127 PMCID: PMC11300516 DOI: 10.7555/jbr.37.20230214] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 08/10/2024] Open
Abstract
Liquid-liquid phase separation, a novel biochemical phenomenon, has been increasingly studied for its medical applications. It underlies the formation of membrane-less organelles and is involved in many cellular and biological processes. During transcriptional regulation, dynamic condensates are formed through interactions between transcriptional elements, such as transcription factors, coactivators, and mediators. Cancer is a disease characterized by uncontrolled cell proliferation, but the precise mechanisms underlying tumorigenesis often remain to be elucidated. Emerging evidence has linked abnormal transcriptional condensates to several diseases, especially cancer, implying that phase separation plays an important role in tumorigenesis. Condensates formed by phase separation may have an effect on gene transcription in tumors. In the present review, we focus on the correlation between phase separation and transcriptional regulation, as well as how this phenomenon contributes to cancer development.
Collapse
Affiliation(s)
- Yan Gu
- Department of Thoracic Surgery, Jiangsu Province Hospital, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Ke Wei
- Department of Thoracic Surgery, Jiangsu Province Hospital, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Jun Wang
- Department of Thoracic Surgery, Jiangsu Province Hospital, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| |
Collapse
|
140
|
Yang K, Zhong Z, Zou J, Liao JY, Chen S, Zhou S, Zhao Y, Li J, Yin D, Huang K, Li Y. Glycolysis and tumor progression promoted by the m 6A writer VIRMA via m 6A-dependent upregulation of STRA6 in pancreatic ductal adenocarcinoma. Cancer Lett 2024; 590:216840. [PMID: 38604311 DOI: 10.1016/j.canlet.2024.216840] [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: 01/22/2024] [Revised: 03/11/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive and lethal malignancies, highlighting the urgent need to elucidate the underlying oncogenic mechanisms. VIRMA is a classic isoform of methyltransferases that participates in epigenetic transcriptomic modification in eukaryotic mRNAs. However, the exact roles of VIRMA in PDAC remain unclear. Here, we identified that VIRMA is highly expressed in PDAC, and histone modifications of the promoter may partly account for this dysregulation. Moreover, VIRMA is closely related to glycolysis and poor prognosis in PDAC. We further determined that STRA6 is a direct downstream target of VIRMA in PDAC by RNA sequencing (RNA-seq) and m6A sequencing (m6A-seq). VIRMA is involved in gene expression regulation via 3' UTR targeting of STRA6 mRNA. Furthermore, the m6A reader IGF2BP2 was shown to critically contribute to the stability of STRA6 mRNA. We describe the role of VIRMA in promoting signaling via the STRA6/STAT3 axis, which results in increased levels of HIF-1α, a key activator of glycolysis. In vivo and in vitro experiments reveal that the VIRMA-STRA6-STAT3-HIF-1α axis plays an instrumental role in glycolysis and tumor progression in PDAC. In conclusion, we demonstrate that VIRMA can increase glycolysis in PDAC by upregulating STRA6, a cell surface membrane protein that stimulates the STAT3 pathway, thereby activating HIF-1α and leading to pancreatic cancer malignancy. Overall, our data strongly suggest that the VIRMA-STRA6-STAT3-HIF-1α axis is a viable therapeutic target in PDAC.
Collapse
Affiliation(s)
- Kege Yang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Ziyi Zhong
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Jinmao Zou
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Jian-You Liao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Shaojie Chen
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Shurui Zhou
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Yue Zhao
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Jiajia Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Department of Nephrology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, P. R. Guangdong, PR China
| | - Dong Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, PR China.
| | - Kaihong Huang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China.
| | - Yaqing Li
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China.
| |
Collapse
|
141
|
Min YH, Shao WX, Hu QS, Xie NB, Zhang S, Feng YQ, Xing XW, Yuan BF. Simultaneous Detection of Adenosine-to-Inosine Editing and N6-Methyladenosine at Identical RNA Sites through Deamination-Assisted Reverse Transcription Stalling. Anal Chem 2024; 96:8730-8739. [PMID: 38743814 DOI: 10.1021/acs.analchem.4c01022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Adenosine-to-inosine (A-to-I) editing and N6-methyladenosine (m6A) modifications are pivotal RNA modifications with widespread functional significance in physiological and pathological processes. Although significant effort has been dedicated to developing methodologies for identifying and quantifying these modifications, traditional approaches have often focused on each modification independently, neglecting the potential co-occurrence of A-to-I editing and m6A modifications at the same adenosine residues. This limitation has constrained our understanding of the intricate regulatory mechanisms governing RNA function and the interplay between different types of RNA modifications. To address this gap, we introduced an innovative technique called deamination-assisted reverse transcription stalling (DARTS), specifically designed for the simultaneous quantification of A-to-I editing and m6A at the same RNA sites. DARTS leverages the selective deamination activity of the engineered TadA-TadA8e protein, which converts adenosine residues to inosine, in combination with the unique property of Bst 2.0 DNA polymerase, which stalls when encountering inosine during reverse transcription. This approach enables the accurate quantification of A-to-I editing, m6A, and unmodified adenosine at identical RNA sites. The DARTS method is remarkable for its ability to directly quantify two distinct types of RNA modifications simultaneously, a capability that has remained largely unexplored in the field of RNA biology. By facilitating a comprehensive analysis of the co-occurrence and interaction between A-to-I editing and m6A modifications, DARTS opens new avenues for exploring the complex regulatory networks modulated by different RNA modifications.
Collapse
Affiliation(s)
- Yi-Hao Min
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Wen-Xuan Shao
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Qiu-Shuang Hu
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan 430071, China
| | - Neng-Bin Xie
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan 430071, China
- Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
| | - Shan Zhang
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Yu-Qi Feng
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Xi-Wen Xing
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Bi-Feng Yuan
- College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University, Wuhan 430071, China
- Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, China
- Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
| |
Collapse
|
142
|
Pomaville M, Chennakesavalu M, Wang P, Jiang Z, Sun HL, Ren P, Borchert R, Gupta V, Ye C, Ge R, Zhu Z, Brodnik M, Zhong Y, Moore K, Salwen H, George RE, Krajewska M, Chlenski A, Applebaum MA, He C, Cohn SL. Small-molecule inhibition of the METTL3/METTL14 complex suppresses neuroblastoma tumor growth and promotes differentiation. Cell Rep 2024; 43:114165. [PMID: 38691450 PMCID: PMC11181463 DOI: 10.1016/j.celrep.2024.114165] [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: 08/08/2023] [Revised: 03/10/2024] [Accepted: 04/12/2024] [Indexed: 05/03/2024] Open
Abstract
The N6-methyladenosine (m6A) RNA modification is an important regulator of gene expression. m6A is deposited by a methyltransferase complex that includes methyltransferase-like 3 (METTL3) and methyltransferase-like 14 (METTL14). High levels of METTL3/METTL14 drive the growth of many types of adult cancer, and METTL3/METTL14 inhibitors are emerging as new anticancer agents. However, little is known about the m6A epitranscriptome or the role of the METTL3/METTL14 complex in neuroblastoma, a common pediatric cancer. Here, we show that METTL3 knockdown or pharmacologic inhibition with the small molecule STM2457 leads to reduced neuroblastoma cell proliferation and increased differentiation. These changes in neuroblastoma phenotype are associated with decreased m6A deposition on transcripts involved in nervous system development and neuronal differentiation, with increased stability of target mRNAs. In preclinical studies, STM2457 treatment suppresses the growth of neuroblastoma tumors in vivo. Together, these results support the potential of METTL3/METTL14 complex inhibition as a therapeutic strategy against neuroblastoma.
Collapse
Affiliation(s)
- Monica Pomaville
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | | | - Pingluan Wang
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Zhiwei Jiang
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Hui-Lung Sun
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Peizhe Ren
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Ryan Borchert
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | - Varsha Gupta
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | - Chang Ye
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Ruiqi Ge
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Zhongyu Zhu
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Mallory Brodnik
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | - Yuhao Zhong
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Kelley Moore
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | - Helen Salwen
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | - Rani E George
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Malgorzata Krajewska
- School of Biochemistry and Cell Biology, Biosciences Institute, University College Cork, Cork, Ireland
| | - Alexandre Chlenski
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | - Mark A Applebaum
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, University of Chicago, Chicago, Il 60637 USA
| | - Susan L Cohn
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA.
| |
Collapse
|
143
|
Guo Y, Chen X, Gan Y, Li Y, Wang R. Targeted i 6A-RNA degradation through sequential Fluorination-Azidation and Click reaction with imidazole-based probes. Bioorg Med Chem Lett 2024; 108:129815. [PMID: 38795737 DOI: 10.1016/j.bmcl.2024.129815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/07/2024] [Accepted: 05/22/2024] [Indexed: 05/28/2024]
Abstract
We report the use of trimethylsilyl azide and Selectfluor to implement a standard protocol targeted at the prenylated nucleic acid known as i6A-RNA. After optimizing the conditions, we applied this method to regulate a wide range of i6A-RNA species using synthetic imidazole-based probes (I-IV). We observed that prenylated nucleic acid plays a crucial role in the cell hemostasis in A549 cell lines.
Collapse
Affiliation(s)
- Yuyang Guo
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Xiaoqian Chen
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Youfang Gan
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yuanyuan Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Rui Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong 518063, China.
| |
Collapse
|
144
|
Pinello N, Song R, Lee Q, Calonne E, Duan KL, Wong E, Tieng J, Mehravar M, Rong B, Lan F, Roediger B, Ma CJ, Yuan BF, Rasko JEJ, Larance M, Ye D, Fuks F, Wong JJL. Dynamic changes in RNA m 6A and 5 hmC influence gene expression programs during macrophage differentiation and polarisation. Cell Mol Life Sci 2024; 81:229. [PMID: 38780787 PMCID: PMC11116364 DOI: 10.1007/s00018-024-05261-9] [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: 02/06/2024] [Revised: 04/27/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024]
Abstract
RNA modifications are essential for the establishment of cellular identity. Although increasing evidence indicates that RNA modifications regulate the innate immune response, their role in monocyte-to-macrophage differentiation and polarisation is unclear. While m6A has been widely studied, other RNA modifications, including 5 hmC, remain poorly characterised. We profiled m6A and 5 hmC epitranscriptomes, transcriptomes, translatomes and proteomes of monocytes and macrophages at rest and pro- and anti-inflammatory states. Transcriptome-wide mapping of m6A and 5 hmC reveals enrichment of m6A and/or 5 hmC on specific categories of transcripts essential for macrophage differentiation. Our analyses indicate that m6A and 5 hmC modifications are present in transcripts with critical functions in pro- and anti-inflammatory macrophages. Notably, we also discover the co-occurrence of m6A and 5 hmC on alternatively-spliced isoforms and/or opposing ends of the untranslated regions (UTR) of mRNAs with key roles in macrophage biology. In specific examples, RNA 5 hmC controls the decay of transcripts independently of m6A. This study provides (i) a comprehensive dataset to interrogate the role of RNA modifications in a plastic system (ii) a resource for exploring different layers of gene expression regulation in the context of human monocyte-to-macrophage differentiation and polarisation, (iii) new insights into RNA modifications as central regulators of effector cells in innate immunity.
Collapse
Affiliation(s)
- Natalia Pinello
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, 11400, Montevideo, Uruguay
| | - Renhua Song
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Quintin Lee
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Kun-Long Duan
- The Molecular and Cell Biology Lab, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Emilie Wong
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Jessica Tieng
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Majid Mehravar
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
| | - Bowen Rong
- Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Fei Lan
- Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Ben Roediger
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Skin Inflammation Group, Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Autoimmunity, Transplantation and Inflammation (ATI) Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Cheng-Jie Ma
- School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Bi-Feng Yuan
- School of Public Health, Wuhan University, Wuhan, 430071, China
| | - John E J Rasko
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Gene and Stem Cell Therapy Program, Centenary Institute, The University of Sydney, Camperdown, 2050, Australia
- Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, NSW, Australia
| | - Mark Larance
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia
- Charles Perkins Centre, School of Medical Sciences, University of Sydney, Sydney, 2006, Australia
| | - Dan Ye
- The Molecular and Cell Biology Lab, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Justin J-L Wong
- Faculty of Medicine and Health, The University of Sydney, Camperdown, 2050, Australia.
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050, Australia.
- Charles Perkins Centre, School of Medical Sciences, University of Sydney, Sydney, 2006, Australia.
| |
Collapse
|
145
|
Lu X, Li D, Lin Z, Gao T, Gong Z, Zhang Y, Wang H, Xia X, Lu F, Song J, Xu G, Jiang J, Ma X, Zou F. HIF-1α-induced expression of the m6A reader YTHDF1 inhibits the ferroptosis of nucleus pulposus cells by promoting SLC7A11 translation. Aging Cell 2024:e14210. [PMID: 38783692 DOI: 10.1111/acel.14210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
The nucleus pulposus is in a hypoxic environment in the human body, and when intervertebral disc degeneration (IVDD) occurs, the hypoxic environment is disrupted. Nucleus pulposus cell (NPC) ferroptosis is one of the causes of IVDD. N6-methyladenosine (m6A) and its reader protein YTHDF1 regulate cellular activities by affecting RNA metabolism. However, the regulation of ferroptosis in NPCs by m6A-modified RNAs under hypoxic conditions has not been as well studied. In this study, through in vitro and in vivo experiments, we explored the underlying mechanism of HIF-1α and YTHDF1 in regulating ferroptosis in NPCs. The results indicated that the overexpression of HIF-1α or YTHDF1 suppressed NPC ferroptosis; conversely, the knockdown of HIF-1α or YTHDF1 increased ferroptosis levels in NPCs. Luciferase reporter assays and chromatin immunoprecipitation demonstrated that HIF-1α regulated YTHDF1 transcription by directly binding to its promoter region. Polysome profiling results showed that YTHDF1 promoted the translation of SLC7A11 and consequently the expression of the anti-ferroptosis protein GPX4 by binding to m6A-modified SLC7A11 mRNA. In conclusion, HIF-1α-induced YTHDF1 expression reduces NPC ferroptosis and delays IVDD by promoting SLC7A11 translation in a m6A-dependent manner.
Collapse
Affiliation(s)
- Xiao Lu
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, China
| | - Dachuan Li
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhidi Lin
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, China
| | - Tian Gao
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhaoyang Gong
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, China
| | - Yuxuan Zhang
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, China
| | - Hongli Wang
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, China
| | - Xinlei Xia
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, China
| | - Feizhou Lu
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, China
| | - Jian Song
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, China
| | - Guangyu Xu
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, China
| | - Jianyuan Jiang
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaosheng Ma
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, China
| | - Fei Zou
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
146
|
Ingelson-Filpula WA, Kadamani KL, Ojaghi M, Pamenter ME, Storey KB. Hypoxia-induced downregulation of RNA m 6A protein machinery in the naked mole-rat heart. Biochimie 2024; 225:125-132. [PMID: 38788827 DOI: 10.1016/j.biochi.2024.05.017] [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: 02/22/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Naked mole-rats, Heterocephalus glaber, are champion hypoxia-tolerant rodents that live under low oxygen conditions in their subterranean burrows. Detrimental effects of low oxygen can be mitigated through metabolic rate depression (MRD), metabolic reorganization, and global downregulation of nonessential cellular processes. Recent research has progressively implicated epigenetic modifications - rapid, reversible changes to gene expression that do not alter the DNA sequence itself - as major players in implementing and maintaining MRD. N6-adenosine (m6A) methylation is the most prevalent mammalian RNA modification and is responsible for pre-mRNA processing and mRNA export from the nucleus. Hence, m6A -mediated conformational changes alter the cellular fate of transcripts. The present study investigated the role of m6A RNA methylation responses to 24 h of hypoxia exposure in H. glaber cardiac tissue. Total protein levels of m6A writers/readers/erasers, m6A demethylase activity, and total m6A quantification were measured under normoxic vs. hypoxic conditions in H. glaber heart. While there was no change in either demethylase activity or total m6A content, many proteins of the m6A pathway were downregulated during hypoxia. Overall, m6A may not be a signature hypoxia-responsive characteristic in H. glaber heart, but downregulation of the protein machinery involved in m6A cycling points to an alternate biological involvement. Further research will explore other forms of RNA modifications and other epigenetic mechanisms to determine the controls on hypoxia endurance in this subterranean mammal.
Collapse
Affiliation(s)
- W Aline Ingelson-Filpula
- Affiliation: Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada, K1S 5B6.
| | - Karen L Kadamani
- Biology Department, University of Ottawa, Marie-Curie Pvt, Ottawa, Ontario, K1N 9A7, Canada
| | - Mohammad Ojaghi
- Biology Department, University of Ottawa, Marie-Curie Pvt, Ottawa, Ontario, K1N 9A7, Canada
| | - Matthew E Pamenter
- Biology Department, University of Ottawa, Marie-Curie Pvt, Ottawa, Ontario, K1N 9A7, Canada; Brain and Mind Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kenneth B Storey
- Affiliation: Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada, K1S 5B6
| |
Collapse
|
147
|
Ye H, Li T, Rigden DJ, Wei Z. m6ACali: machine learning-powered calibration for accurate m6A detection in MeRIP-Seq. Nucleic Acids Res 2024; 52:4830-4842. [PMID: 38634812 PMCID: PMC11109940 DOI: 10.1093/nar/gkae280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 03/18/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024] Open
Abstract
We present m6ACali, a novel machine-learning framework aimed at enhancing the accuracy of N6-methyladenosine (m6A) epitranscriptome profiling by reducing the impact of non-specific antibody enrichment in MeRIP-Seq. The calibration model serves as a genomic feature-based classifier that refines the identification of m6A sites, distinguishing those genuinely present from those that can be detected in in-vitro transcribed (IVT) control experiments. We find that m6ACali effectively identifies non-specific binding peaks reported by exomePeak2 and MACS2 in novel MeRIP-Seq datasets without the need for paired IVT controls. The model interpretation revealed that off-target antibody binding sites commonly occur at short exons and short mRNAs, originating from high read coverage regions that share the motif sequence with true m6A sites. We also reveal that the ML strategy can efficiently adjust differentially methylated peaks and other antibody-dependent, base-resolution m6A detection techniques. As a result, m6ACali offers a promising method for the universal enhancement of m6A profiles generated by MeRIP-Seq experiments, elevating the benchmark for omics-level m6A data integration.
Collapse
Affiliation(s)
- Haokai Ye
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK
| | - Tenglong Li
- Wisdom Lake Academy of Pharmacy, Xi’an Jiaotong-Liverpool University, Suzhou 215123, China
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK
| | - Zhen Wei
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Life Course and Medical Sciences, University of Liverpool, L7 8TX Liverpool, UK
| |
Collapse
|
148
|
Teng C, Song X, Fan C, Man S, Hu Y, Hou Y, Xin T. Breast cancer clinical outcomes and tumor immune microenvironment: cross-dialogue of multiple epigenetic modification profiles. Aging (Albany NY) 2024; 16:8998-9022. [PMID: 38796789 PMCID: PMC11164499 DOI: 10.18632/aging.205853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/29/2024] [Indexed: 05/29/2024]
Abstract
The discovery of RNA methylation alterations associated with cancer holds promise for their utilization as potential biomarkers in cancer diagnosis, prognosis, and prediction. RNA methylation has been found to impact the immunological microenvironment of tumors, but the specific role of methylation-related genes (MRGs), particularly in breast cancer (BC), the most common cancer among women globally, within the tumor microenvironment remains unknown. In this study, we obtained data from TCGA and GEO databases to investigate the expression patterns of MRGs in both genomic and transcriptional domains in BC. By analyzing the data, we identified two distinct genetic groupings that were correlated with clinicopathological characteristics, prognosis, degree of TME cell infiltration, and other abnormalities in MRGs among patients. Subsequently, an MRG model was developed to predict overall survival (OS) and its accuracy was evaluated in BC patients. Additionally, a highly precise nomogram was created to enhance the practical usability of the MRG model. In low-risk groups, we observed lower TBM values and higher TIDE scores. We further explored how MRGs influence a patient's prognosis, clinically significant characteristics, response to therapy, and the TME. These risk signatures have the potential to improve treatment strategies for BC patients and could be applied in future clinical settings. Moreover, they may also be utilized to determine prognosis and biological features in these patients.
Collapse
Affiliation(s)
- Chong Teng
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiaowei Song
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Chengjuan Fan
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Siqi Man
- Oncology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yuanyuan Hu
- Oncology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yifei Hou
- School of Nursing, Harbin Medical University, Harbin, Heilongjiang, China
| | - Tao Xin
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| |
Collapse
|
149
|
Guo F, Fan J, Liu JM, Kong PL, Ren J, Mo JW, Lu CL, Zhong QL, Chen LY, Jiang HT, Zhang C, Wen YL, Gu TT, Li SJ, Fang YY, Pan BX, Gao TM, Cao X. Astrocytic ALKBH5 in stress response contributes to depressive-like behaviors in mice. Nat Commun 2024; 15:4347. [PMID: 38773146 PMCID: PMC11109195 DOI: 10.1038/s41467-024-48730-2] [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: 07/18/2023] [Accepted: 05/07/2024] [Indexed: 05/23/2024] Open
Abstract
Epigenetic mechanisms bridge genetic and environmental factors that contribute to the pathogenesis of major depression disorder (MDD). However, the cellular specificity and sensitivity of environmental stress on brain epitranscriptomics and its impact on depression remain unclear. Here, we found that ALKBH5, an RNA demethylase of N6-methyladenosine (m6A), was increased in MDD patients' blood and depression models. ALKBH5 in astrocytes was more sensitive to stress than that in neurons and endothelial cells. Selective deletion of ALKBH5 in astrocytes, but not in neurons and endothelial cells, produced antidepressant-like behaviors. Astrocytic ALKBH5 in the mPFC regulated depression-related behaviors bidirectionally. Meanwhile, ALKBH5 modulated glutamate transporter-1 (GLT-1) m6A modification and increased the expression of GLT-1 in astrocytes. ALKBH5 astrocyte-specific knockout preserved stress-induced disruption of glutamatergic synaptic transmission, neuronal atrophy and defective Ca2+ activity. Moreover, enhanced m6A modification with S-adenosylmethionine (SAMe) produced antidepressant-like effects. Our findings indicate that astrocytic epitranscriptomics contribute to depressive-like behaviors and that astrocytic ALKBH5 may be a therapeutic target for depression.
Collapse
MESH Headings
- Animals
- Astrocytes/metabolism
- AlkB Homolog 5, RNA Demethylase/metabolism
- AlkB Homolog 5, RNA Demethylase/genetics
- Mice
- Humans
- Depressive Disorder, Major/metabolism
- Depressive Disorder, Major/genetics
- Depressive Disorder, Major/pathology
- Male
- Mice, Knockout
- Female
- Disease Models, Animal
- Mice, Inbred C57BL
- Neurons/metabolism
- Stress, Psychological/metabolism
- Adenosine/analogs & derivatives
- Adenosine/metabolism
- Excitatory Amino Acid Transporter 2/metabolism
- Excitatory Amino Acid Transporter 2/genetics
- Behavior, Animal
- Prefrontal Cortex/metabolism
- Prefrontal Cortex/pathology
- Depression/metabolism
- Depression/genetics
- Adult
- Synaptic Transmission
- Middle Aged
Collapse
Affiliation(s)
- Fang Guo
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jun Fan
- Department of Anesthesia, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, Guangdong, China
| | - Jin-Ming Liu
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Peng-Li Kong
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jing Ren
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jia-Wen Mo
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Cheng-Lin Lu
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Qiu-Ling Zhong
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Liang-Yu Chen
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Hao-Tian Jiang
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Canyuan Zhang
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - You-Lu Wen
- Department of Psychology and Behavior, Guangdong 999 Brain Hospital, Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, Guangdong, P. R. China
| | - Ting-Ting Gu
- Department of Psychology and Behavior, Guangdong 999 Brain Hospital, Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, Guangdong, P. R. China
| | - Shu-Ji Li
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ying-Ying Fang
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Bing-Xing Pan
- Department of Biological Science, School of Life Science, Nanchang University, Nanchang, China
| | - Tian-Ming Gao
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiong Cao
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
- Department of Oncology, Nanfang Hospital, Southern Medical University Guangzhou, Guangdong, P. R. China.
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, P. R. China.
| |
Collapse
|
150
|
Khan D, Ramachandiran I, Vasu K, China A, Khan K, Cumbo F, Halawani D, Terenzi F, Zin I, Long B, Costain G, Blaser S, Carnevale A, Gogonea V, Dutta R, Blankenberg D, Yoon G, Fox PL. Homozygous EPRS1 missense variant causing hypomyelinating leukodystrophy-15 alters variant-distal mRNA m 6A site accessibility. Nat Commun 2024; 15:4284. [PMID: 38769304 PMCID: PMC11106242 DOI: 10.1038/s41467-024-48549-x] [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: 10/15/2023] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
Hypomyelinating leukodystrophy (HLD) is an autosomal recessive disorder characterized by defective central nervous system myelination. Exome sequencing of two siblings with severe cognitive and motor impairment and progressive hypomyelination characteristic of HLD revealed homozygosity for a missense single-nucleotide variant (SNV) in EPRS1 (c.4444 C > A; p.Pro1482Thr), encoding glutamyl-prolyl-tRNA synthetase, consistent with HLD15. Patient lymphoblastoid cell lines express markedly reduced EPRS1 protein due to dual defects in nuclear export and cytoplasmic translation of variant EPRS1 mRNA. Variant mRNA exhibits reduced METTL3 methyltransferase-mediated writing of N6-methyladenosine (m6A) and reduced reading by YTHDC1 and YTHDF1/3 required for efficient mRNA nuclear export and translation, respectively. In contrast to current models, the variant does not alter the sequence of m6A target sites, but instead reduces their accessibility for modification. The defect was rescued by antisense morpholinos predicted to expose m6A sites on target EPRS1 mRNA, or by m6A modification of the mRNA by METTL3-dCas13b, a targeted RNA methylation editor. Our bioinformatic analysis predicts widespread occurrence of SNVs associated with human health and disease that similarly alter accessibility of distal mRNA m6A sites. These results reveal a new RNA-dependent etiologic mechanism by which SNVs can influence gene expression and disease, consequently generating opportunities for personalized, RNA-based therapeutics targeting these disorders.
Collapse
Affiliation(s)
- Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Kommireddy Vasu
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Arnab China
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Fabio Cumbo
- Genomic Medicine Institute, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Dalia Halawani
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Fulvia Terenzi
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Isaac Zin
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
- Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Briana Long
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Gregory Costain
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Susan Blaser
- Department of Diagnostic Imaging, Division of Neuroradiology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Amanda Carnevale
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Valentin Gogonea
- Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Ranjan Dutta
- Department of Neuroscience, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Daniel Blankenberg
- Genomic Medicine Institute, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Grace Yoon
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
- Department of Paediatrics, Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA.
| |
Collapse
|