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Han G, Lin Q, Yi J, Lyu Q, Ma Q, Qiao L. MazF-rolling circle amplification combined MALDI-TOF MS for site-specific detection of N 6-methyladenosine RNA. Anal Chim Acta 2024; 1303:342532. [PMID: 38609270 DOI: 10.1016/j.aca.2024.342532] [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: 07/07/2023] [Revised: 03/11/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024]
Abstract
N6-methyladenosine (m6A) is one of the most abundant chemical modifications in RNA and has vital significance in cellular processes and tumor development. However, the accurate analysis of site-specific m6A modification remains a challenge. In this work, a MazF endoribonuclease activated rolling circle amplification (MazF-RCA) combined MALDI-TOF MS assay is developed for the detection of site-specific m6A-RNA. MazF endoribonuclease can specifically cleave the ACA motif, leaving methylated (m6A)CA motif intact. The intact methylated RNA can then be amplified through rolling circle amplification, and the generated reporter oligonucleotides are detected by MALDI-TOF MS. The assay exhibits good quantification ability, presenting a wide linear range (100 fM to 10 nM) with the limit-of-detection lower than 100 fM. Additionally, the assay can accurately detect methylated RNA in the presence of large amount of non-methylated RNA with a relative abundance of methylated RNA down to 0.5%. The developed assay was further applied to detect m6A-RNA spiked in MCF-7 cell RNA extracts, with the recovery rates in the range of 90.64-106.93%. The present assay provides a novel platform for the analysis of site-specific m6A-RNA at high specificity and sensitivity, which can promote the study of RNA methylation in clinical and biomedical research.
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Affiliation(s)
- Guobin Han
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai, 200000, China; Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Qiuyuan Lin
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai, 200000, China
| | - Jia Yi
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai, 200000, China
| | - Qian Lyu
- Bioyong Technologics, Inc., Beijing, 100176, China
| | - Qingwei Ma
- Bioyong Technologics, Inc., Beijing, 100176, China
| | - Liang Qiao
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai, 200000, China.
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Kundu A, Brinkley GJ, Nam H, Karki S, Kirkman R, Pandit M, Shim E, Widden H, Liu J, Heidarian Y, Mahmoudzadeh NH, Fitt AJ, Absher D, Ding HF, Crossman DK, Placzek WJ, Locasale JW, Rakheja D, McConathy JE, Ramachandran R, Bae S, Tennessen JM, Sudarshan S. l-2-Hydroxyglutarate remodeling of the epigenome and epitranscriptome creates a metabolic vulnerability in kidney cancer models. J Clin Invest 2024; 134:e171294. [PMID: 38743486 PMCID: PMC11213505 DOI: 10.1172/jci171294] [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: 04/17/2023] [Accepted: 05/07/2024] [Indexed: 05/16/2024] Open
Abstract
Tumor cells are known to undergo considerable metabolic reprogramming to meet their unique demands and drive tumor growth. At the same time, this reprogramming may come at a cost with resultant metabolic vulnerabilities. The small molecule l-2-hydroxyglutarate (l-2HG) is elevated in the most common histology of renal cancer. Similarly to other oncometabolites, l-2HG has the potential to profoundly impact gene expression. Here, we demonstrate that l-2HG remodels amino acid metabolism in renal cancer cells through combined effects on histone methylation and RNA N6-methyladenosine. The combined effects of l-2HG result in a metabolic liability that renders tumors cells reliant on exogenous serine to support proliferation, redox homeostasis, and tumor growth. In concert with these data, high-l-2HG kidney cancers demonstrate reduced expression of multiple serine biosynthetic enzymes. Collectively, our data indicate that high-l-2HG renal tumors could be specifically targeted by strategies that limit serine availability to tumors.
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Affiliation(s)
- Anirban Kundu
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Urology, University of Arizona, Tuscon, Arizona, USA
| | - Garrett J. Brinkley
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Hyeyoung Nam
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Suman Karki
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Richard Kirkman
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Madhuparna Pandit
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - EunHee Shim
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Hayley Widden
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Juan Liu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Yasaman Heidarian
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | - Alexander J. Fitt
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - David K. Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - William J. Placzek
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jason W. Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Dinesh Rakheja
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Rekha Ramachandran
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sejong Bae
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Sunil Sudarshan
- Department of Urology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Ensinck I, Sideri T, Modic M, Capitanchik C, Vivori C, Toolan-Kerr P, van Werven FJ. m6A-ELISA, a simple method for quantifying N6-methyladenosine from mRNA populations. RNA (NEW YORK, N.Y.) 2023; 29:705-712. [PMID: 36759126 PMCID: PMC10159001 DOI: 10.1261/rna.079554.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/19/2023] [Indexed: 05/06/2023]
Abstract
N6-methyladenosine (m6A) is a widely studied and abundant RNA modification. The m6A mark regulates the fate of RNAs in various ways, which in turn drives changes in cell physiology, development, and disease pathology. Over the last decade, numerous methods have been developed to map and quantify m6A sites genome-wide through deep sequencing. Alternatively, m6A levels can be quantified from a population of RNAs using techniques such as liquid chromatography-mass spectrometry or thin layer chromatography. However, many methods for quantifying m6A levels involve extensive protocols and specialized data analysis, and often only a few samples can be handled in a single experiment. Here, we developed a simple method for determining relative m6A levels in mRNA populations from various sources based on an enzyme-linked immunosorbent-based assay (m6A-ELISA). We have optimized various steps of m6A-ELISA, such as sample preparation and the background signal resulting from the primary antibody. We validated the method using mRNA populations from budding yeast and mouse embryonic stem cells. The full protocol takes less than a day, requiring only 25 ng of mRNA. The m6A-ELISA protocol is quick, cost-effective, and scalable, making it a valuable tool for determining relative m6A levels in samples from various sources that could be adapted to detect other mRNA modifications.
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Affiliation(s)
- Imke Ensinck
- The Francis Crick Institute, London NW1 1AT, United Kingdom
| | | | - Miha Modic
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Dementia Research Institute at KCL, London SE5 9RX, United Kingdom
- National Institute of Chemistry, SI-1001 Ljubljana, Slovenia
| | | | - Claudia Vivori
- The Francis Crick Institute, London NW1 1AT, United Kingdom
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Cao L, Morgun E, Genardi S, Visvabharathy L, Cui Y, Huang H, Wang CR. METTL14-dependent m 6A modification controls iNKT cell development and function. Cell Rep 2022; 40:111156. [PMID: 35926466 PMCID: PMC9495716 DOI: 10.1016/j.celrep.2022.111156] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/06/2022] [Accepted: 07/13/2022] [Indexed: 11/25/2022] Open
Abstract
N6-methyladenosine (m6A), the most common form of RNA modification, controls CD4+ T cell homeostasis by targeting the IL-7/STAT5/SOCS signaling pathways. The role of m6A modification in unconventional T cell development remains unknown. Using mice with T cell-specific deletion of RNA methyltransferase METTL14 (T-Mettl14−/−), we demonstrate that m6A modification is indispensable for iNKT cell homeostasis. Loss of METTL14-dependent m6A modification leads to the upregulation of apoptosis in double-positive thymocytes, which in turn decreases Vα14-Jα18 gene rearrangements, resulting in drastic reduction of iNKT numbers in the thymus and periphery. Residual T-Mettl14−/− iNKT cells exhibit increased apoptosis, impaired maturation, and decreased responsiveness to IL-2/IL-15 and TCR stimulation. Furthermore, METTL14 knockdown in mature iNKT cells diminishes their cytokine production, correlating with increased Cish expression and decreased TCR signaling. Collectively, our study highlights a critical role for METTL14-dependent-m6A modification in iNKT cell development and function. Cao et al. show that T cell-specific deletion of METTL14, a component of RNA m6A writer complex, leads to severe defects in iNKT cell development, survival, and function. Mechanistically, METTL14-dependent m6A modification controls iNKT cell development in a cell-intrinsic manner by regulating the apoptosis pathway and TCR signaling pathway.
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Affiliation(s)
- Liang Cao
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Searle 3-401, Chicago, IL 60611, USA
| | - Eva Morgun
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Searle 3-401, Chicago, IL 60611, USA
| | - Samantha Genardi
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Searle 3-401, Chicago, IL 60611, USA
| | - Lavanya Visvabharathy
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Searle 3-401, Chicago, IL 60611, USA
| | - Yongyong Cui
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Searle 3-401, Chicago, IL 60611, USA
| | - Haochu Huang
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Chyung-Ru Wang
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Searle 3-401, Chicago, IL 60611, USA.
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Lv D, Gimple RC, Zhong C, Wu Q, Yang K, Prager BC, Godugu B, Qiu Z, Zhao L, Zhang G, Dixit D, Lee D, Shen JZ, Li X, Xie Q, Wang X, Agnihotri S, Rich JN. PDGF signaling inhibits mitophagy in glioblastoma stem cells through N 6-methyladenosine. Dev Cell 2022; 57:1466-1481.e6. [PMID: 35659339 DOI: 10.1016/j.devcel.2022.05.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 01/14/2022] [Accepted: 05/11/2022] [Indexed: 12/13/2022]
Abstract
Dysregulated growth factor receptor pathways, RNA modifications, and metabolism each promote tumor heterogeneity. Here, we demonstrate that platelet-derived growth factor (PDGF) signaling induces N6-methyladenosine (m6A) accumulation in glioblastoma (GBM) stem cells (GSCs) to regulate mitophagy. PDGF ligands stimulate early growth response 1 (EGR1) transcription to induce methyltransferase-like 3 (METTL3) to promote GSC proliferation and self-renewal. Targeting the PDGF-METTL3 axis inhibits mitophagy by regulating m6A modification of optineurin (OPTN). Forced OPTN expression phenocopies PDGF inhibition, and OPTN levels portend longer survival of GBM patients; these results suggest a tumor-suppressive role for OPTN. Pharmacologic targeting of METTL3 augments anti-tumor efficacy of PDGF receptor (PDGFR) and mitophagy inhibitors in vitro and in vivo. Collectively, we define PDGF signaling as an upstream regulator of oncogenic m6A regulation, driving tumor metabolism to promote cancer stem cell maintenance, highlighting PDGF-METTL3-OPTN signaling as a GBM therapeutic target.
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Affiliation(s)
- Deguan Lv
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA 15232, USA; Division of Regenerative Medicine, School of Medicine, University of California San Diego, CA 92037, USA
| | - Ryan C Gimple
- Division of Regenerative Medicine, School of Medicine, University of California San Diego, CA 92037, USA; Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Cuiqing Zhong
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA 15232, USA; Gene Expression Laboratory, Salk Institute for Biological Studies, San Diego, CA 92037, USA
| | - Qiulian Wu
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA 15232, USA
| | - Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Briana C Prager
- Division of Regenerative Medicine, School of Medicine, University of California San Diego, CA 92037, USA; Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Bhaskar Godugu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Zhixin Qiu
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA 15232, USA; Division of Regenerative Medicine, School of Medicine, University of California San Diego, CA 92037, USA
| | - Linjie Zhao
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA 15232, USA; Division of Regenerative Medicine, School of Medicine, University of California San Diego, CA 92037, USA
| | - Guoxin Zhang
- Division of Regenerative Medicine, School of Medicine, University of California San Diego, CA 92037, USA
| | - Deobrat Dixit
- Division of Regenerative Medicine, School of Medicine, University of California San Diego, CA 92037, USA
| | - Derrick Lee
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA 15232, USA; Division of Regenerative Medicine, School of Medicine, University of California San Diego, CA 92037, USA
| | - Jia Z Shen
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA 92037, USA
| | - Xiqing Li
- Division of Regenerative Medicine, School of Medicine, University of California San Diego, CA 92037, USA; Department of Oncology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, Henan 450003, China
| | - Qi Xie
- Division of Regenerative Medicine, School of Medicine, University of California San Diego, CA 92037, USA; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Xiuxing Wang
- Division of Regenerative Medicine, School of Medicine, University of California San Diego, CA 92037, USA; School of Basic Medical Sciences, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Sameer Agnihotri
- Department of Neurological Surgery, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Jeremy N Rich
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA 15232, USA; Division of Regenerative Medicine, School of Medicine, University of California San Diego, CA 92037, USA; Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, USA.
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