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Fitzsimmons CM, Mandler MD, Lunger JC, Chan D, Maligireddy S, Schmiechen A, Gamage S, Link C, Jenkins L, Chan K, Andresson T, Crooks D, Meier J, Linehan W, Batista P. Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma. NAR Cancer 2024; 6:zcae004. [PMID: 38328795 PMCID: PMC10849186 DOI: 10.1093/narcan/zcae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Metabolic reprogramming is a hallmark of cancer that facilitates changes in many adaptive biological processes. Mutations in the tricarboxylic acid cycle enzyme fumarate hydratase (FH) lead to fumarate accumulation and cause hereditary leiomyomatosis and renal cell cancer (HLRCC). HLRCC is a rare, inherited disease characterized by the development of non-cancerous smooth muscle tumors of the uterus and skin, and an increased risk of an aggressive form of kidney cancer. Fumarate has been shown to inhibit 2-oxoglutarate-dependent dioxygenases (2OGDDs) involved in the hydroxylation of HIF1α, as well as in DNA and histone demethylation. However, the link between fumarate accumulation and changes in RNA post-transcriptional modifications has not been defined. Here, we determine the consequences of fumarate accumulation on the activity of different members of the 2OGDD family targeting RNA modifications. By evaluating multiple RNA modifications in patient-derived HLRCC cell lines, we show that mutation of FH selectively affects the levels of N6-methyladenosine (m6A), while the levels of 5-formylcytosine (f5C) in mitochondrial tRNA are unaffected. This supports the hypothesis of a differential impact of fumarate accumulation on distinct RNA demethylases. The observation that metabolites modulate specific subsets of RNA-modifying enzymes offers new insights into the intersection between metabolism and the epitranscriptome.
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Affiliation(s)
- Christina M Fitzsimmons
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mariana D Mandler
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Judith C Lunger
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dalen Chan
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Siddhardha S Maligireddy
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra C Schmiechen
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Supuni Thalalla Gamage
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Courtney Link
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - King Chan
- Protein Characterization Laboratory, Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pedro J Batista
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Crooks DR, Cawthon GM, Fitzsimmons CM, Perez M, Ricketts CJ, Vocke CD, Yang Y, Middelton L, Nielsen D, Schmidt LS, Tandon M, Merino MJ, Ball MW, Meier JL, Batista PJ, Linehan WM. Cryptic splice mutation in the fumarate hydratase gene in patients with clinical manifestations of Hereditary Leiomyomatosis and Renal Cell Cancer. Hum Mol Genet 2023; 32:3135-3145. [PMID: 37561409 PMCID: PMC10630246 DOI: 10.1093/hmg/ddad131] [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: 07/07/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/11/2023] Open
Abstract
Hereditary leiomyomatosis and renal cell carcinoma (HLRCC) is an autosomal dominant condition characterized by the development of cutaneous and uterine leiomyomas and risk for development of an aggressive form of papillary renal cell cancer. HLRCC is caused by germline inactivating pathogenic variants in the fumarate hydratase (FH) gene, which encodes the enzyme that catalyzes the interconversion of fumarate and L-malate. We utilized enzyme and protein mobility assays to evaluate the FH enzyme in a cohort of patients who showed clinical manifestations of HLRCC but were negative for known pathogenic FH gene variants. FH enzyme activity and protein levels were decreased by 50% or greater in three family members, despite normal FH mRNA expression levels as measured by quantitative PCR. Direct Nanopore RNA sequencing demonstrated 57 base pairs of retained intron sequence between exons 9 and 10 of polyadenylated FH mRNA in these patients, resulting in a truncated FH protein. Genomic sequencing revealed a heterozygous intronic alteration of the FH gene (chr1: 241498239 T/C) resulting in formation of a splice acceptor site near a polypyrimidine tract, and a uterine fibroid obtained from a patient showed loss of heterozygosity at this site. The same intronic FH variant was identified in an unrelated patient who also showed a clinical phenotype of HLRCC. These data demonstrate that careful clinical assessment as well as biochemical characterization of FH enzyme activity, protein expression, direct RNA sequencing, and genomic DNA sequencing of patient-derived cells can identify pathogenic variants outside of the protein coding regions of the FH gene.
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Affiliation(s)
- Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
| | - Geetha Mariah Cawthon
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
| | - Christina M Fitzsimmons
- RNA Metabolism and Epitranscriptomics Unit, Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - Minervo Perez
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyles St., Frederick, MD 21072, United States
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
| | - Cathy D Vocke
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
| | - Ye Yang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
| | - Lindsay Middelton
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
| | - Debbie Nielsen
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
| | - Laura S Schmidt
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
- Basic Science Program, Frederick National Laboratory for Cancer Research, 1050 Boyles St. Frederick, MD 21701, United States
| | - Mayank Tandon
- CCR Collaborative Bioinformatics Resource (CCBR), Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., 1050 Boyles St., Frederick, MD 21072, United States
| | - Maria J Merino
- Translational Surgical Pathology, Laboratory of Pathology Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, United States
| | - Mark W Ball
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
| | - Jordan L Meier
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyles St., Frederick, MD 21072, United States
| | - Pedro J Batista
- RNA Metabolism and Epitranscriptomics Unit, Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892, United States
| | - William Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Bethesda, MD 20892, United States
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Hooker JP, Parker B, Wright E, Junkers T, Cameron NR. Photoresponsive Emulsion-Templated Porous Materials via Orthogonal Photoclick Chemistry. ACS APPLIED MATERIALS & INTERFACES 2023; 15:11141-11149. [PMID: 36799738 DOI: 10.1021/acsami.2c22546] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The functionalization of emulsion-templated porous polymers (polyHIPEs) utilizing modern and efficient chemistries is an important avenue for tailoring the properties of these scaffolds for specific and specialized applications. Herein, tetrazole photoclick chemistry is utilized for the efficient functionalization of polyHIPEs synthesized from various monomer systems and polymerization chemistries. Using both radical polymerization and thiol-ene polymerization, polyHIPEs with well-defined, interconnected open-cell morphologies are synthesized with tetrazole concentrations ranging from 0 to 5 w/v %, with the pore diameters ranging from 3 to 24 μm. Analyzed by fluorescence spectroscopy, FTIR spectroscopy, and confocal microscopy, spatially controlled functionalization to generate photopatterned fluorescent polyHIPEs is demonstrated via the reaction with residual acrylate and thiol groups. In addition, the scaffolds can be readily functionalized with external dipolarophiles such as acrylates to incorporate a functionality onto the polyHIPE surface. With many functional tetrazoles also reported in the literature, a PEG-tetrazole is also used to explore the photoinduced functionalization of polyHIPEs possessing tunable ratios of thiol and acrylate groups, and the effect on fluorescence, wettability, and biocompatibility is analyzed. Overall, the reaction is shown to be a broadly applicable tool for polyHIPE functionalization with many avenues for further development toward specific applications.
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Affiliation(s)
- Jordan P Hooker
- Polymer Reaction Design Group, School of Chemistry, Monash University, 19 Rainforest Walk, Clayton, Victoria 3800, Australia
- Department of Materials Science and Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Bradyn Parker
- Department of Materials Science and Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Elise Wright
- Department of Materials Science and Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Tanja Junkers
- Polymer Reaction Design Group, School of Chemistry, Monash University, 19 Rainforest Walk, Clayton, Victoria 3800, Australia
| | - Neil R Cameron
- Department of Materials Science and Engineering, Monash University, Clayton, Victoria 3800, Australia
- School of Engineering, University of Warwick, Coventry CV4 7AL, U.K
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Deepthi A, Acharjee N, Sruthi S, Meenakshy C. An overview of nitrile imine based [3+2] cycloadditions over half a decade. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Abstract
The merging of click chemistry with discrete photochemical processes has led to the creation of a new class of click reactions, collectively known as photoclick chemistry. These light-triggered click reactions allow the synthesis of diverse organic structures in a rapid and precise manner under mild conditions. Because light offers unparalleled spatiotemporal control over the generation of the reactive intermediates, photoclick chemistry has become an indispensable tool for a wide range of spatially addressable applications including surface functionalization, polymer conjugation and cross-linking, and biomolecular labeling in the native cellular environment. Over the past decade, a growing number of photoclick reactions have been developed, especially those based on the 1,3-dipolar cycloadditions and Diels-Alder reactions owing to their excellent reaction kinetics, selectivity, and biocompatibility. This review summarizes the recent advances in the development of photoclick reactions and their applications in chemical biology and materials science. A particular emphasis is placed on the historical contexts and mechanistic insights into each of the selected reactions. The in-depth discussion presented here should stimulate further development of the field, including the design of new photoactivation modalities, the continuous expansion of λ-orthogonal tandem photoclick chemistry, and the innovative use of these unique tools in bioconjugation and nanomaterial synthesis.
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Affiliation(s)
- Gangam Srikanth Kumar
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
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Scinto SL, Bilodeau DA, Hincapie R, Lee W, Nguyen SS, Xu M, am Ende CW, Finn MG, Lang K, Lin Q, Pezacki JP, Prescher JA, Robillard MS, Fox JM. Bioorthogonal chemistry. NATURE REVIEWS. METHODS PRIMERS 2021; 1:30. [PMID: 34585143 PMCID: PMC8469592 DOI: 10.1038/s43586-021-00028-z] [Citation(s) in RCA: 158] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/05/2021] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemistry represents a class of high-yielding chemical reactions that proceed rapidly and selectively in biological environments without side reactions towards endogenous functional groups. Rooted in the principles of physical organic chemistry, bioorthogonal reactions are intrinsically selective transformations not commonly found in biology. Key reactions include native chemical ligation and the Staudinger ligation, copper-catalysed azide-alkyne cycloaddition, strain-promoted [3 + 2] reactions, tetrazine ligation, metal-catalysed coupling reactions, oxime and hydrazone ligations as well as photoinducible bioorthogonal reactions. Bioorthogonal chemistry has significant overlap with the broader field of 'click chemistry' - high-yielding reactions that are wide in scope and simple to perform, as recently exemplified by sulfuryl fluoride exchange chemistry. The underlying mechanisms of these transformations and their optimal conditions are described in this Primer, followed by discussion of how bioorthogonal chemistry has become essential to the fields of biomedical imaging, medicinal chemistry, protein synthesis, polymer science, materials science and surface science. The applications of bioorthogonal chemistry are diverse and include genetic code expansion and metabolic engineering, drug target identification, antibody-drug conjugation and drug delivery. This Primer describes standards for reproducibility and data deposition, outlines how current limitations are driving new research directions and discusses new opportunities for applying bioorthogonal chemistry to emerging problems in biology and biomedicine.
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Affiliation(s)
- Samuel L. Scinto
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Didier A. Bilodeau
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Robert Hincapie
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Wankyu Lee
- Pfizer Worldwide Research and Development, Cambridge, MA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Sean S. Nguyen
- Department of Chemistry, University of California, Irvine, CA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Minghao Xu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | | | - M. G. Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kathrin Lang
- Department of Chemistry, Technical University of Munich, Garching, Germany
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Jennifer A. Prescher
- Department of Chemistry, University of California, Irvine, CA, USA
- Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
| | | | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
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7
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Gui W, Shen S, Zhuang Z. Photocaged Cell-Permeable Ubiquitin Probe for Temporal Profiling of Deubiquitinating Enzymes. J Am Chem Soc 2020; 142:19493-19501. [PMID: 33141564 DOI: 10.1021/jacs.9b12426] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Photocaged cell-permeable ubiquitin probe holds promise in profiling the activity of cellular deubiquitinating enzymes (DUBs) with the much needed temporal control. Here we report a new photocaged cell-permeable ubiquitin probe that undergoes photoactivation upon 365 nm UV treatment and enables intracellular deubiquitinating enzyme profiling. We used a semisynthetic approach to generate modular ubiquitin-based probe containing a tetrazole-derived warhead at the C-terminus of ubiquitin and employed a cyclic polyarginine cell-penetrating peptide (cR10) conjugated to the N-terminus of ubiquitin via a disulfide linkage to deliver the probe into live cells. Upon 365 nm UV irradiation, the tetrazole group is converted to a nitrilimine intermediate in situ, which reacts with nearby nucleophilic cysteine residue from the DUB active site. The new photocaged cell-permeable probe showed good reactivity toward purified DUBs, including USP2, UCHL1, and UCHL3, upon photoirradiation. The Ub-tetrazole probe was also assessed in HeLa cell lysate and showed robust labeling only upon photoactivation. We further carried out protein profiling in intact HeLa cells using the new photocaged cell-permeable ubiquitin probe and identified DUBs captured by the probe using label-free quantitative (LFQ) mass spectrometry. Importantly, the photocaged cell-permeable ubiquitin probe captured DUBs specifically in respective G1/S and G2/M phases in synchronized HeLa cells. Moreover, using this probe DUBs were profiled at different time points following the release of HeLa cells from G1/S phase. Our results showed that photocaged cell-permeable probe represents a valuable new tool for achieving a better understanding of the cellular functions of DUBs.
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Affiliation(s)
- Weijun Gui
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware 19716, United States
| | - Siqi Shen
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware 19716, United States
| | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware 19716, United States
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Perez M, Bak DW, Bergholtz SE, Crooks DR, Arimilli BS, Yang Y, Weerapana E, Linehan WM, Meier JL. Heterogeneous adaptation of cysteine reactivity to a covalent oncometabolite. J Biol Chem 2020; 295:13410-13418. [PMID: 32820045 DOI: 10.1074/jbc.ac120.014993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/14/2020] [Indexed: 12/11/2022] Open
Abstract
An important context in which metabolism influences tumorigenesis is the genetic cancer syndrome hereditary leiomyomatosis and renal cell carcinoma (HLRCC), a disease in which mutation of the tricarboxylic acid cycle enzyme fumarate hydratase (FH) causes hyperaccumulation of fumarate. This electrophilic oncometabolite can alter gene activity at the level of transcription, via reversible inhibition of epigenetic dioxygenases, as well as posttranslationally, via covalent modification of cysteine residues. To better understand the potential for metabolites to influence posttranslational modifications important to tumorigenesis and cancer cell growth, here we report a chemoproteomic analysis of a kidney-derived HLRCC cell line. Using a general reactivity probe, we generated a data set of proteomic cysteine residues sensitive to the reduction in fumarate levels caused by genetic reintroduction of active FH into HLRCC cell lines. This revealed a broad up-regulation of cysteine reactivity upon FH rescue, which evidence suggests is caused by an approximately equal proportion of transcriptional and posttranslational modification-mediated regulation. Gene ontology analysis highlighted several new targets and pathways potentially modulated by FH mutation. Comparison of the new data set with prior studies highlights considerable heterogeneity in the adaptive response of cysteine-containing proteins in different models of HLRCC. This is consistent with emerging studies indicating the existence of cell- and tissue-specific cysteine-omes, further emphasizing the need for characterization of diverse models. Our analysis provides a resource for understanding the proteomic adaptation to fumarate accumulation and a foundation for future efforts to exploit this knowledge for cancer therapy.
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Affiliation(s)
- Minervo Perez
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Daniel W Bak
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, USA
| | - Sarah E Bergholtz
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Bhargav Srinivas Arimilli
- Urologic Oncology Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Youfeng Yang
- Urologic Oncology Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA.
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9
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Bergholtz SE, Briney CA, Najera SS, Perez M, Linehan WM, Meier JL. An Oncometabolite Isomer Rapidly Induces a Pathophysiological Protein Modification. ACS Chem Biol 2020; 15:856-861. [PMID: 32250583 DOI: 10.1021/acschembio.0c00044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metabolites regulate protein function via covalent and noncovalent interactions. However, manipulating these interactions in living cells remains a major challenge. Here, we report a chemical strategy for inducing cysteine S-succination, a nonenzymatic post-translational modification derived from the oncometabolite fumarate. Using a combination of antibody-based detection and kinetic assays, we benchmark the in vitro and cellular reactivity of two novel S-succination "agonists," maleate and 2-bromosuccinate. Cellular assays reveal maleate to be a more potent and less toxic inducer of S-succination, which can activate KEAP1-NRF2 signaling in living cells. By enabling the cellular reconstitution of an oncometabolite-protein interaction with physiochemical accuracy and minimal toxicity, this study provides a methodological basis for better understanding the signaling role of metabolites in disease.
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Affiliation(s)
- Sarah E. Bergholtz
- Chemical Biology Laboratory, National Cancer Institute, Frederick Maryland 21702, United States
| | - Chloe A. Briney
- Chemical Biology Laboratory, National Cancer Institute, Frederick Maryland 21702, United States
| | - Susana S. Najera
- Chemical Biology Laboratory, National Cancer Institute, Frederick Maryland 21702, United States
- Urologic Oncology Branch, National Cancer Institute, Bethesda, Maryland, United States
| | - Minervo Perez
- Chemical Biology Laboratory, National Cancer Institute, Frederick Maryland 21702, United States
| | - W. Marston Linehan
- Urologic Oncology Branch, National Cancer Institute, Bethesda, Maryland, United States
| | - Jordan L. Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick Maryland 21702, United States
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10
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Bioorthogonal oncometabolite ligation. Methods Enzymol 2019. [PMID: 31155064 DOI: 10.1016/bs.mie.2019.02.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Dysregulated cellular metabolism is an emerging hallmark of cancer. Improved methods to profile aberrant metabolic activity thus have substantial applications as tools for diagnosis and understanding the biology of malignant tumors. Here we describe the utilization of a bioorthogonal ligation to fluorescently detect the TCA cycle oncometabolite fumarate. This method enables the facile measurement of fumarate hydratase activity in cell and tissue samples, and can be used to detect disruptions in metabolism that underlie the genetic cancer syndrome hereditary leiomyomatosis and renal cell cancer (HLRCC). The current method has substantial utility for sensitive fumarate hydratase activity profiling, and also provides a foundation for future applications in diagnostic detection and imaging of cancer metabolism.
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11
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Kulkarni RA, Montgomery DC, Meier JL. Epigenetic regulation by endogenous metabolite pharmacology. Curr Opin Chem Biol 2019; 51:30-39. [PMID: 30884380 DOI: 10.1016/j.cbpa.2019.02.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 02/07/2023]
Abstract
Altered metabolite levels can drive epigenetic changes critical to development and disease. However, in many cases the specific protein-metabolite interactions that underlie this process remain enigmatic. In this review, we make the case that this fundamental missing information may be discovered by applying the tools of modern drug target validation to study endogenous metabolite pharmacology. We detail examples in which chemical proteomics has been applied to gain new insights into reversible and covalent metabolite signaling mechanisms, using acetyl-CoA and fumarate as case studies. Finally, we provide a brief survey of nascent chemical biology methods whose application to the study of endogenous metabolite pharmacology may further advance the field.
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Affiliation(s)
- Rhushikesh A Kulkarni
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - David C Montgomery
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
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