1
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Zhang D, Gao J, Zhu Z, Mao Q, Xu Z, Singh PK, Rimayi CC, Moreno-Yruela C, Xu S, Li G, Sin YC, Chen Y, Olsen CA, Snyder NW, Dai L, Li L, Zhao Y. Lysine L-lactylation is the dominant lactylation isomer induced by glycolysis. Nat Chem Biol 2024:10.1038/s41589-024-01680-8. [PMID: 39030363 DOI: 10.1038/s41589-024-01680-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 06/13/2024] [Indexed: 07/21/2024]
Abstract
Lysine L-lactylation (Kl-la) is a novel protein posttranslational modification (PTM) driven by L-lactate. This PTM has three isomers: Kl-la, N-ε-(carboxyethyl)-lysine (Kce) and D-lactyl-lysine (Kd-la), which are often confused in the context of the Warburg effect and nuclear presence. Here we introduce two methods to differentiate these isomers: a chemical derivatization and high-performance liquid chromatography analysis for efficient separation, and isomer-specific antibodies for high-selectivity identification. We demonstrated that Kl-la is the primary lactylation isomer on histones and dynamically regulated by glycolysis, not Kd-la or Kce, which are observed when the glyoxalase system was incomplete. The study also reveals that lactyl-coenzyme A, a precursor in L-lactylation, correlates positively with Kl-la levels. This work not only provides a methodology for distinguishing other PTM isomers, but also highlights Kl-la as the primary responder to glycolysis and the Warburg effect.
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Affiliation(s)
- Di Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
| | - Jinjun Gao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Zhijun Zhu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Qianying Mao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Zhiqiang Xu
- National Clinical Research Center for Geriatrics and General Practice Ward/International Medical Center Ward, General Practice Medical Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Pankaj K Singh
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Center for Metabolic Disease Research, Philadelphia, PA, USA
| | - Cornelius C Rimayi
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Center for Metabolic Disease Research, Philadelphia, PA, USA
| | - Carlos Moreno-Yruela
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Shuling Xu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Gongyu Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
- Research Center for Analytical Science and Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, China
| | - Yi-Cheng Sin
- Department of Biochemistry, Molecular Biology and Biophysics, The University of Minnesota at Twin Cities, Minneapolis, MN, USA
| | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics, The University of Minnesota at Twin Cities, Minneapolis, MN, USA
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nathaniel W Snyder
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Center for Metabolic Disease Research, Philadelphia, PA, USA
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and General Practice Ward/International Medical Center Ward, General Practice Medical Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA.
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2
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Zhang B, Mullmann J, Ludewig AH, Fernandez IR, Bales TR, Weiss RS, Schroeder FC. Acylspermidines are conserved mitochondrial sirtuin-dependent metabolites. Nat Chem Biol 2024; 20:812-822. [PMID: 38167917 DOI: 10.1038/s41589-023-01511-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 11/21/2023] [Indexed: 01/05/2024]
Abstract
Sirtuins are nicotinamide adenine dinucleotide (NAD+)-dependent protein lysine deacylases regulating metabolism and stress responses; however, characterization of the removed acyl groups and their downstream metabolic fates remains incomplete. Here we employed untargeted comparative metabolomics to reinvestigate mitochondrial sirtuin biochemistry. First, we identified N-glutarylspermidines as metabolites downstream of the mitochondrial sirtuin SIR-2.3 in Caenorhabditis elegans and demonstrated that SIR-2.3 functions as a lysine deglutarylase and that N-glutarylspermidines can be derived from O-glutaryl-ADP-ribose. Subsequent targeted analysis of C. elegans, mouse and human metabolomes revealed a chemically diverse range of N-acylspermidines, and formation of N-succinylspermidines and/or N-glutarylspermidines was observed downstream of mammalian mitochondrial sirtuin SIRT5 in two cell lines, consistent with annotated functions of SIRT5. Finally, N-glutarylspermidines were found to adversely affect C. elegans lifespan and mammalian cell proliferation. Our results indicate that N-acylspermidines are conserved metabolites downstream of mitochondrial sirtuins that facilitate annotation of sirtuin enzymatic activities in vivo and may contribute to sirtuin-dependent phenotypes.
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Affiliation(s)
- Bingsen Zhang
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - James Mullmann
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
- Department of Molecular Medicine, Cornell University, Ithaca, NY, USA
| | | | - Irma R Fernandez
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Tyler R Bales
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Robert S Weiss
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Frank C Schroeder
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA.
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
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3
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Lin J, Hou L, Zhao X, Zhong J, Lv Y, Jiang X, Ye B, Qiao Y. Switch of ELF3 and ATF4 transcriptional axis programs the amino acid insufficiency-linked epithelial-to-mesenchymal transition. Mol Ther 2024; 32:1956-1969. [PMID: 38627967 PMCID: PMC11184330 DOI: 10.1016/j.ymthe.2024.04.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 03/19/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) that endows cancer cells with increased invasive and migratory capacity enables cancer dissemination and metastasis. This process is tightly associated with metabolic reprogramming acquired for rewiring cell status and signaling pathways for survival in dietary insufficiency conditions. However, it remains largely unclear how transcription factor (TF)-mediated transcriptional programs are modulated during the EMT process. Here, we reveal that depletion of a key epithelial TF, ELF3 (E74-like factor-3), triggers a transforming growth factor β (TGF-β) signaling activation-like mesenchymal transcriptomic profile and metastatic features linked to the aminoacyl-tRNA biogenesis pathway. Moreover, the transcriptome alterations elicited by ELF3 depletion perfectly resemble an ATF4-dependent weak response to amino acid starvation. Intriguingly, we observe an exclusive enrichment of ELF3 and ATF4 in epithelial and TGF-β-induced or ELF3-depletion-elicited mesenchymal enhancers, respectively, with rare co-binding on altered enhancers. We also find that the upregulation of aminoacyl-tRNA synthetases and some mesenchymal genes upon amino acid deprivation is diminished in ATF4-depleted cells. In sum, the loss of ELF3 binding on epithelial enhancers and the gain of ATF4 binding on the enhancers of mesenchymal factors and amino acid deprivation responsive genes facilitate the loss of epithelial cell features and the gain of TGF-β-signaling-associated mesenchymal signatures, which further promote lung cancer cell metastasis.
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Affiliation(s)
- Jianxiang Lin
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Linjun Hou
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xin Zhao
- Department of Geriatrics, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, China
| | - Jingli Zhong
- College of Life Science, Guangzhou University, Guangzhou 510006, China
| | - Yilv Lv
- Department of Thoracic Surgery, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xiaohua Jiang
- Center for Reproduction and Genetics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, Anhui, China.
| | - Bo Ye
- Department of Thoracic Surgery, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China.
| | - Yunbo Qiao
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China.
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4
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Zhao T, Fan J, Abu-Zaid A, Burley SK, Zheng XS. Nuclear mTOR Signaling Orchestrates Transcriptional Programs Underlying Cellular Growth and Metabolism. Cells 2024; 13:781. [PMID: 38727317 PMCID: PMC11083943 DOI: 10.3390/cells13090781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024] Open
Abstract
mTOR is a central regulator of cell growth and metabolism in response to mitogenic and nutrient signals. Notably, mTOR is not only found in the cytoplasm but also in the nucleus. This review highlights direct involvement of nuclear mTOR in regulating transcription factors, orchestrating epigenetic modifications, and facilitating chromatin remodeling. These effects intricately modulate gene expression programs associated with growth and metabolic processes. Furthermore, the review underscores the importance of nuclear mTOR in mediating the interplay between metabolism and epigenetic modifications. By integrating its functions in nutrient signaling and gene expression related to growth and metabolism, nuclear mTOR emerges as a central hub governing cellular homeostasis, malignant transformation, and cancer progression. Better understanding of nuclear mTOR signaling has the potential to lead to novel therapies against cancer and other growth-related diseases.
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Affiliation(s)
- Tinghan Zhao
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Jialin Fan
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Ahmed Abu-Zaid
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Stephen K. Burley
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - X.F. Steven Zheng
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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5
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Zhu Z, Li S, Yin X, Sun K, Song J, Ren W, Gao L, Zhi K. Review: Protein O-GlcNAcylation regulates DNA damage response: A novel target for cancer therapy. Int J Biol Macromol 2024; 264:130351. [PMID: 38403231 DOI: 10.1016/j.ijbiomac.2024.130351] [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: 01/07/2024] [Revised: 02/02/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
The DNA damage response (DDR) safeguards the stable genetic information inheritance by orchestrating a complex protein network in response to DNA damage. However, this mechanism can often hamper the effectiveness of radiotherapy and DNA-damaging chemotherapy in destroying tumor cells, causing cancer resistance. Inhibiting DDR can significantly improve tumor cell sensitivity to radiotherapy and DNA-damaging chemotherapy. Thus, DDR can be a potential target for cancer treatment. Post-translational modifications (PTMs) of DDR-associated proteins profoundly affect their activity and function by covalently attaching new functional groups. O-GlcNAcylation (O-linked-N-acetylglucosaminylation) is an emerging PTM associated with adding and removing O-linked N-acetylglucosamine to serine and threonine residues of proteins. It acts as a dual sensor for nutrients and stress in the cell and is sensitive to DNA damage. However, the explanation behind the specific role of O-GlcNAcylation in the DDR remains remains to be elucidated. To illustrate the complex relationship between O-GlcNAcylation and DDR, this review systematically describes the role of O-GlcNAcylation in DNA repair, cell cycle, and chromatin. We also discuss the defects of current strategies for targeting O-GlcNAcylation-regulated DDR in cancer therapy and suggest potential directions to address them.
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Affiliation(s)
- Zhuang Zhu
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Shaoming Li
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Xiaopeng Yin
- Department of Oral and Maxillofacial Surgery, Central Laboratory of Jinan Stamotological Hospital, Jinan Key Laboratory of Oral Tissue Regeneration, Jinan 250001, Shandong Province, China
| | - Kai Sun
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Jianzhong Song
- Department of Oral and Maxilloafacial Surgery, People's Hospital of Rizhao, Rizhao, Shandong, China
| | - Wenhao Ren
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Ling Gao
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Key Lab of Oral Clinical Medicine, the Affiliated Hospital of Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Keqian Zhi
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Key Lab of Oral Clinical Medicine, the Affiliated Hospital of Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
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6
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Mitchener M, Begley TJ, Dedon PC. Molecular Coping Mechanisms: Reprogramming tRNAs To Regulate Codon-Biased Translation of Stress Response Proteins. Acc Chem Res 2023; 56:3504-3514. [PMID: 37992267 PMCID: PMC10702489 DOI: 10.1021/acs.accounts.3c00572] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 11/24/2023]
Abstract
As part of the classic central dogma of molecular biology, transfer RNAs (tRNAs) are integral to protein translation as the adaptor molecules that link the genetic code in messenger RNA (mRNA) to the amino acids in the growing peptide chain. tRNA function is complicated by the existence of 61 codons to specify 20 amino acids, with most amino acids coded by two or more synonymous codons. Further, there are often fewer tRNAs with unique anticodons than there are synonymous codons for an amino acid, with a single anticodon able to decode several codons by "wobbling" of the base pairs arising between the third base of the codon and the first position on the anticodon. The complications introduced by synonymous codons and wobble base pairing began to resolve in the 1960s with the discovery of dozens of chemical modifications of the ribonucleotides in tRNA, which, by analogy to the epigenome, are now collectively referred to as the epitranscriptome for not changing the genetic code inherent to all RNA sequences. tRNA modifications were found to stabilize codon-anticodon interactions, prevent misinitiation of translation, and promote translational fidelity, among other functions, with modification deficiencies causing pathological phenotypes. This led to hypotheses that modification-dependent tRNA decoding efficiencies might play regulatory roles in cells. However, it was only with the advent of systems biology and convergent "omic" technologies that the higher level function of synonymous codons and tRNA modifications began to emerge.Here, we describe our laboratories' discovery of tRNA reprogramming and codon-biased translation as a mechanism linking tRNA modifications and synonymous codon usage to regulation of gene expression at the level of translation. Taking a historical approach, we recount how we discovered that the 8-10 modifications in each tRNA molecule undergo unique reprogramming in response to cellular stresses to promote translation of mRNA transcripts with unique codon usage patterns. These modification tunable transcripts (MoTTs) are enriched with specific codons that are differentially decoded by modified tRNAs and that fall into functional families of genes encoding proteins necessary to survive the specific stress. By developing and applying systems-level technologies, we showed that cells lacking specific tRNA modifications are sensitized to certain cellular stresses by mistranslation of proteins, disruption of mitochondrial function, and failure to translate critical stress response proteins. In essence, tRNA reprogramming serves as a cellular coping strategy, enabling rapid translation of proteins required for stress-specific cell response programs. Notably, this phenomenon has now been characterized in all organisms from viruses to humans and in response to all types of environmental changes. We also elaborate on recent findings that cancer cells hijack this mechanism to promote their own growth, metastasis, and chemotherapeutic resistance. We close by discussing how understanding of codon-biased translation in various systems can be exploited to develop new therapeutics and biomanufacturing processes.
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Affiliation(s)
- Michelle
M. Mitchener
- Antimicrobial
Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602, Singapore
| | - Thomas J. Begley
- Department
of Biological Sciences, University at Albany, Albany, New York 12222, United States
- RNA
Institute, University at Albany, Albany, New York 12222, United States
| | - Peter C. Dedon
- Antimicrobial
Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602, Singapore
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
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7
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Zhang L, Shi X, Qiu H, Liu S, Yang T, Li X, Liu X. Protein modification by short-chain fatty acid metabolites in sepsis: a comprehensive review. Front Immunol 2023; 14:1171834. [PMID: 37869005 PMCID: PMC10587562 DOI: 10.3389/fimmu.2023.1171834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/15/2023] [Indexed: 10/24/2023] Open
Abstract
Sepsis is a major life-threatening syndrome of organ dysfunction caused by a dysregulated host response due to infection. Dysregulated immunometabolism is fundamental to the onset of sepsis. Particularly, short-chain fatty acids (SCFAs) are gut microbes derived metabolites serving to drive the communication between gut microbes and the immune system, thereby exerting a profound influence on the pathophysiology of sepsis. Protein post-translational modifications (PTMs) have emerged as key players in shaping protein function, offering novel insights into the intricate connections between metabolism and phenotype regulation that characterize sepsis. Accumulating evidence from recent studies suggests that SCFAs can mediate various PTM-dependent mechanisms, modulating protein activity and influencing cellular signaling events in sepsis. This comprehensive review discusses the roles of SCFAs metabolism in sepsis associated inflammatory and immunosuppressive disorders while highlights recent advancements in SCFAs-mediated lysine acylation modifications, such as substrate supplement and enzyme regulation, which may provide new pharmacological targets for the treatment of sepsis.
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Affiliation(s)
- Liang Zhang
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing, China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, China
| | - Xinhui Shi
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing, China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, China
| | - Hongmei Qiu
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing, China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, China
| | - Sijia Liu
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing, China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, China
| | - Ting Yang
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing, China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, China
| | - Xiaoli Li
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing, China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, China
| | - Xin Liu
- Medical Research Center, Southwest Hospital, Third Military Medical University, Chongqing, China
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8
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Snyder NW, Meier JL. Metabolic regulation of epigenetic drug resistance. Nat Chem Biol 2023; 19:1174-1175. [PMID: 37127755 DOI: 10.1038/s41589-023-01323-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Affiliation(s)
- Nathaniel W Snyder
- Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA.
| | - Jordan L Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA.
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9
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An YJ, Jo S, Kim JM, Kim HS, Kim HY, Jeon SM, Han D, Yook JI, Kang KW, Park S. Lactate as a major epigenetic carbon source for histone acetylation via nuclear LDH metabolism. Exp Mol Med 2023; 55:2238-2247. [PMID: 37779146 PMCID: PMC10618192 DOI: 10.1038/s12276-023-01095-w] [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: 12/23/2022] [Revised: 06/19/2023] [Accepted: 07/06/2023] [Indexed: 10/03/2023] Open
Abstract
Histone acetylation involves the transfer of two-carbon units to the nucleus that are embedded in low-concentration metabolites. We found that lactate, a high-concentration metabolic byproduct, can be a major carbon source for histone acetylation through oxidation-dependent metabolism. Both in cells and in purified nuclei, 13C3-lactate carbons are incorporated into histone H4 (maximum incorporation: ~60%). In the purified nucleus, this process depends on nucleus-localized lactate dehydrogenase (LDHA), knockout (KO) of which abrogates incorporation. Heterologous expression of nucleus-localized LDHA reverses the KO effect. Lactate itself increases histone acetylation, whereas inhibition of LDHA reduces acetylation. In vitro and in vivo settings exhibit different lactate incorporation patterns, suggesting an influence on the microenvironment. Higher nuclear LDHA localization is observed in pancreatic cancer than in normal tissues, showing disease relevance. Overall, lactate and nuclear LDHA can be major structural and regulatory players in the metabolism-epigenetics axis controlled by the cell's own status or the environmental status.
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Affiliation(s)
- Yong Jin An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Korea
| | - Sihyang Jo
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Korea
| | - Jin-Mo Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Korea
| | - Han Sun Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Korea
| | - Hyun Young Kim
- College of Pharmacy, Seoul National University, Seoul, 08826, Korea
| | - Sang-Min Jeon
- College of Pharmacy, Seoul National University, Seoul, 08826, Korea
- College of Pharmacy and Institute of Pharmaceutical Science and Technology, Ajou University, Gyeonggi-do, 16499, Korea
| | - Dawool Han
- Department of Oral Pathology, Oral Cancer Research Institute, Yonsei University College of Dentistry, Seoul, 03722, Korea
| | - Jong In Yook
- Department of Oral Pathology, Oral Cancer Research Institute, Yonsei University College of Dentistry, Seoul, 03722, Korea
| | - Keon Wook Kang
- College of Pharmacy, Seoul National University, Seoul, 08826, Korea
| | - Sunghyouk Park
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Korea.
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10
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Kitamura N, Galligan JJ. A global view of the human post-translational modification landscape. Biochem J 2023; 480:1241-1265. [PMID: 37610048 PMCID: PMC10586784 DOI: 10.1042/bcj20220251] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023]
Abstract
Post-translational modifications (PTMs) provide a rapid response to stimuli, finely tuning metabolism and gene expression and maintain homeostasis. Advances in mass spectrometry over the past two decades have significantly expanded the list of known PTMs in biology and as instrumentation continues to improve, this list will surely grow. While many PTMs have been studied in detail (e.g. phosphorylation, acetylation), the vast majority lack defined mechanisms for their regulation and impact on cell fate. In this review, we will highlight the field of PTM research as it currently stands, discussing the mechanisms that dictate site specificity, analytical methods for their detection and study, and the chemical tools that can be leveraged to define PTM regulation. In addition, we will highlight the approaches needed to discover and validate novel PTMs. Lastly, this review will provide a starting point for those interested in PTM biology, providing a comprehensive list of PTMs and what is known regarding their regulation and metabolic origins.
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Affiliation(s)
- Naoya Kitamura
- Department of Pharmacology and College of Pharmacy, University of Arizona, Tucson, Arizona 85721, U.S.A
| | - James J. Galligan
- Department of Pharmacology and College of Pharmacy, University of Arizona, Tucson, Arizona 85721, U.S.A
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11
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Apiz Saab JJ, Dzierozynski LN, Jonker PB, AminiTabrizi R, Shah H, Menjivar RE, Scott AJ, Nwosu ZC, Zhu Z, Chen RN, Oh M, Sheehan C, Wahl DR, Pasca di Magliano M, Lyssiotis CA, Macleod KF, Weber CR, Muir A. Pancreatic tumors exhibit myeloid-driven amino acid stress and upregulate arginine biosynthesis. eLife 2023; 12:e81289. [PMID: 37254839 PMCID: PMC10260022 DOI: 10.7554/elife.81289] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 05/25/2023] [Indexed: 06/01/2023] Open
Abstract
Nutrient stress in the tumor microenvironment requires cancer cells to adopt adaptive metabolic programs for survival and proliferation. Therefore, knowledge of microenvironmental nutrient levels and how cancer cells cope with such nutrition is critical to understand the metabolism underpinning cancer cell biology. Previously, we performed quantitative metabolomics of the interstitial fluid (the local perfusate) of murine pancreatic ductal adenocarcinoma (PDAC) tumors to comprehensively characterize nutrient availability in the microenvironment of these tumors. Here, we develop Tumor Interstitial Fluid Medium (TIFM), a cell culture medium that contains nutrient levels representative of the PDAC microenvironment, enabling us to study PDAC metabolism ex vivo under physiological nutrient conditions. We show that PDAC cells cultured in TIFM adopt a cellular state closer to that of PDAC cells present in tumors compared to standard culture models. Further, using the TIFM model, we found arginine biosynthesis is active in PDAC and allows PDAC cells to maintain levels of this amino acid despite microenvironmental arginine depletion. We also show that myeloid derived arginase activity is largely responsible for the low levels of arginine in PDAC tumors. Altogether, these data indicate that nutrient availability in tumors is an important determinant of cancer cell metabolism and behavior, and cell culture models that incorporate physiological nutrient availability have improved fidelity to in vivo systems and enable the discovery of novel cancer metabolic phenotypes.
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Affiliation(s)
- Juan J Apiz Saab
- Ben May Department for Cancer Research, University of ChicagoChicagoUnited States
| | | | - Patrick B Jonker
- Ben May Department for Cancer Research, University of ChicagoChicagoUnited States
| | - Roya AminiTabrizi
- Metabolomics Platform, Comprehensive Cancer Center, University of ChicagoChicagoUnited States
| | - Hardik Shah
- Metabolomics Platform, Comprehensive Cancer Center, University of ChicagoChicagoUnited States
| | - Rosa Elena Menjivar
- Cellular and Molecular Biology Program, University of Michigan-Ann ArborAnn ArborUnited States
| | - Andrew J Scott
- Department of Radiation Oncology, University of MichiganAnn ArborUnited States
| | - Zeribe C Nwosu
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Zhou Zhu
- Ben May Department for Cancer Research, University of ChicagoChicagoUnited States
| | - Riona N Chen
- Ben May Department for Cancer Research, University of ChicagoChicagoUnited States
| | - Moses Oh
- Ben May Department for Cancer Research, University of ChicagoChicagoUnited States
| | - Colin Sheehan
- Ben May Department for Cancer Research, University of ChicagoChicagoUnited States
| | - Daniel R Wahl
- Department of Radiation Oncology, University of MichiganAnn ArborUnited States
| | | | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Kay F Macleod
- Ben May Department for Cancer Research, University of ChicagoChicagoUnited States
| | | | - Alexander Muir
- Ben May Department for Cancer Research, University of ChicagoChicagoUnited States
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12
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Gao J, Sheng X, Du J, Zhang D, Han C, Chen Y, Wang C, Zhao Y. Identification of 113 new histone marks by CHiMA, a tailored database search strategy. SCIENCE ADVANCES 2023; 9:eadf1416. [PMID: 37018393 PMCID: PMC10075957 DOI: 10.1126/sciadv.adf1416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/03/2023] [Indexed: 06/19/2023]
Abstract
Shotgun proteomics has been widely used to identify histone marks. Conventional database search methods rely on the "target-decoy" strategy to calculate the false discovery rate (FDR) and distinguish true peptide-spectrum matches (PSMs) from false ones. This strategy has a caveat of inaccurate FDR caused by the small data size of histone marks. To address this challenge, we developed a tailored database search strategy, named "Comprehensive Histone Mark Analysis (CHiMA)." Instead of target-decoy-based FDR, this method uses "50% matched fragment ions" as the key criterion to identify high-confidence PSMs. CHiMA identified twice as many histone modification sites as the conventional method in benchmark datasets. Reanalysis of our previous proteomics data using CHiMA led to the identification of 113 new histone marks for four types of lysine acylations, almost doubling the number of previously reported marks. This tool not only offers a valuable approach for identifying histone modifications but also greatly expands the repertoire of histone marks.
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Affiliation(s)
- Jinjun Gao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Xinlei Sheng
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Jianfeng Du
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Di Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Peking–Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Chang Han
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics, The University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA
| | - Chu Wang
- Peking–Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Synthetic and Functional Biomolecules Center; Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
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13
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Wei W, Zhang J, Xu Z, Liu Z, Huang C, Cheng K, Meng L, Matsuda Y, Hao Q, Zhang H, Sun H. Universal Strategy to Develop Fluorogenic Probes for Lysine Deacylase/Demethylase Activity and Application in Discriminating Demethylation States. ACS Sens 2023; 8:28-39. [PMID: 36602906 DOI: 10.1021/acssensors.2c01345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Dynamically controlling the post-translational modification of the ε-amino groups of lysine residues is critical for regulating many cellular events. Increasing studies have revealed that many important diseases, including cancer and neurological disorders, are associated with the malfunction of lysine deacylases and demethylases. Developing fluorescent probes that are capable of detecting lysine deacylase and demethylase activity is highly useful for interrogating their roles in epigenetic regulation and diseases. Due to the distinct substrate recognition of these epigenetic eraser enzymes, designing a universal strategy for detecting their activity poses substantial difficulty. Moreover, designing activity-based probes for differentiating their demethylation states is even more challenging and still remains largely unexplored. Herein, we report a universal strategy to construct probes that can detect the enzymatic activity of epigenetic "erasers" through NBD-based long-distance intramolecular reactions. The probes can be easily prepared by installing the O-NBD group at the C-terminal residue of specific peptide substrates by click chemistry. Based on this strategy, detecting the activity of lysine deacetylase, desuccinylase, or demethylase with superior sensitivity and selectivity has been successfully achieved through single-step probe development. Furthermore, the demethylase probe based on this strategy is capable of distinguishing different demethylation states by both absorption and fluorescence lifetime readout. We envision that these newly developed probes will provide powerful tools to facilitate drug discovery in epigenetics in the future.
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Affiliation(s)
- Wenyu Wei
- Department of Chemistry and COSADAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong999077, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen518057, China
| | - Jie Zhang
- Department of Chemistry and COSADAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong999077, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen518057, China
| | - Zhiqiang Xu
- Department of Chemistry and COSADAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong999077, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen518057, China
| | - Zhiyang Liu
- Department of Chemistry and COSADAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong999077, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen518057, China
| | - Chen Huang
- Department of Chemistry and COSADAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong999077, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen518057, China
| | - Ke Cheng
- Department of Chemistry and COSADAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong999077, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen518057, China
| | - Lingkuan Meng
- Department of Chemistry and COSADAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong999077, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen518057, China
| | - Yudai Matsuda
- Department of Chemistry and COSADAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong999077, China
| | - Quan Hao
- Department of Physiology, University of Hong Kong, Pok Fu Lam, Hong Kong999077, China
| | - Huatang Zhang
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, Guangdong510006, China
| | - Hongyan Sun
- Department of Chemistry and COSADAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong999077, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen518057, China
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14
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Dietary regulation in health and disease. Signal Transduct Target Ther 2022; 7:252. [PMID: 35871218 PMCID: PMC9308782 DOI: 10.1038/s41392-022-01104-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/21/2022] [Accepted: 07/04/2022] [Indexed: 02/08/2023] Open
Abstract
Nutriments have been deemed to impact all physiopathologic processes. Recent evidences in molecular medicine and clinical trials have demonstrated that adequate nutrition treatments are the golden criterion for extending healthspan and delaying ageing in various species such as yeast, drosophila, rodent, primate and human. It emerges to develop the precision-nutrition therapeutics to slow age-related biological processes and treat diverse diseases. However, the nutritive advantages frequently diversify among individuals as well as organs and tissues, which brings challenges in this field. In this review, we summarize the different forms of dietary interventions extensively prescribed for healthspan improvement and disease treatment in pre-clinical or clinical. We discuss the nutrient-mediated mechanisms including metabolic regulators, nutritive metabolism pathways, epigenetic mechanisms and circadian clocks. Comparably, we describe diet-responsive effectors by which dietary interventions influence the endocrinic, immunological, microbial and neural states responsible for improving health and preventing multiple diseases in humans. Furthermore, we expatiate diverse patterns of dietotheroapies, including different fasting, calorie-restricted diet, ketogenic diet, high-fibre diet, plants-based diet, protein restriction diet or diet with specific reduction in amino acids or microelements, potentially affecting the health and morbid states. Altogether, we emphasize the profound nutritional therapy, and highlight the crosstalk among explored mechanisms and critical factors to develop individualized therapeutic approaches and predictors.
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15
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Zhang Z, Lin J, Liu Z, Tian G, Li XM, Jing Y, Li X, Li XD. Photo-Cross-Linking To Delineate Epigenetic Interactome. J Am Chem Soc 2022; 144:20979-20997. [DOI: 10.1021/jacs.2c06135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zhuoyuan Zhang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jianwei Lin
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Gaofei Tian
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiao-Meng Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yihang Jing
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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16
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Abstract
The analogy of mitochondria as powerhouses has expired. Mitochondria are living, dynamic, maternally inherited, energy-transforming, biosynthetic, and signaling organelles that actively transduce biological information. We argue that mitochondria are the processor of the cell, and together with the nucleus and other organelles they constitute the mitochondrial information processing system (MIPS). In a three-step process, mitochondria (1) sense and respond to both endogenous and environmental inputs through morphological and functional remodeling; (2) integrate information through dynamic, network-based physical interactions and diffusion mechanisms; and (3) produce output signals that tune the functions of other organelles and systemically regulate physiology. This input-to-output transformation allows mitochondria to transduce metabolic, biochemical, neuroendocrine, and other local or systemic signals that enhance organismal adaptation. An explicit focus on mitochondrial signal transduction emphasizes the role of communication in mitochondrial biology. This framework also opens new avenues to understand how mitochondria mediate inter-organ processes underlying human health.
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Affiliation(s)
- Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA; New York State Psychiatric Institute, New York, NY 10032, USA.
| | - Orian S Shirihai
- Department of Medicine, Endocrinology, and Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Metabolism Theme, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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17
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Mitchener MM, Muir TW. Oncohistones: Exposing the nuances and vulnerabilities of epigenetic regulation. Mol Cell 2022; 82:2925-2938. [PMID: 35985302 PMCID: PMC9482148 DOI: 10.1016/j.molcel.2022.07.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/20/2022] [Accepted: 07/14/2022] [Indexed: 12/19/2022]
Abstract
Work over the last decade has uncovered a new layer of epigenetic dysregulation. It is now appreciated that somatic missense mutations in histones, the packaging agents of genomic DNA, are often associated with human pathologies, especially cancer. Although some of these "oncohistone" mutations are thought to be key drivers of cancer, the impacts of the majority of them on disease onset and progression remain to be elucidated. Here, we survey this rapidly expanding research field with particular emphasis on how histone mutants, even at low dosage, can corrupt chromatin states. This work is unveiling the remarkable intricacies of epigenetic control mechanisms. Throughout, we highlight how studies of oncohistones have leveraged, and in some cases fueled, the advances in our ability to manipulate and interrogate chromatin at the molecular level.
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Affiliation(s)
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
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18
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Sun Y, Chen Y, Xu Y, Zhang Y, Lu M, Li M, Zhou L, Peng T. Genetic encoding of ε- N-L-lactyllysine for detecting delactylase activity in living cells. Chem Commun (Camb) 2022; 58:8544-8547. [PMID: 35815577 DOI: 10.1039/d2cc02643k] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Lysine ε-N-L-lactylation is a newly discovered post-translational modification. Herein we present the genetic encoding of ε-N-L-lactyllysine in bacterial and mammalian cells, allowing the preparation of site-specifically ε-N-L-lactylated recombinant proteins and the construction of fluorescent and luminescent probes for detecting delactylases in living cells. Using these probes, we demonstrate sirtuin 1 as a potential delactylase for non-histone proteins.
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Affiliation(s)
- Yanan Sun
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Yanchi Chen
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Yaxin Xu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Yuqing Zhang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Minghao Lu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Manjia Li
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Liyan Zhou
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Tao Peng
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China. .,Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, 518132, China
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19
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Dai SK, Liu PP, Li X, Jiao LF, Teng ZQ, Liu CM. Dynamic profiling and functional interpretation of histone lysine crotonylation and lactylation during neural development. Development 2022; 149:276044. [DOI: 10.1242/dev.200049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 06/16/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Metabolites such as crotonyl-CoA and lactyl-CoA influence gene expression by covalently modifying histones, known as histone lysine crotonylation (Kcr) and lysine lactylation (Kla). However, the existence patterns, dynamic changes, biological functions and associations of these modifications with histone lysine acetylation and gene expression during mammalian development remain largely unknown. Here, we find that histone Kcr and Kla are widely distributed in the brain and undergo global changes during neural development. By profiling the genome-wide dynamics of H3K9ac, H3K9cr and H3K18la in combination with ATAC and RNA sequencing, we reveal that these marks are tightly correlated with chromatin state and gene expression, and extensively involved in transcriptome remodeling to promote cell-fate transitions in the developing telencephalon. Importantly, we demonstrate that global Kcr and Kla levels are not the consequence of transcription and identify the histone deacetylases (HDACs) 1-3 as novel ‘erasers’ of H3K18la. Using P19 cells as an induced neural differentiation system, we find that HDAC1-3 inhibition by MS-275 pre-activates neuronal transcriptional programs by stimulating multiple histone lysine acylations simultaneously. These findings suggest that histone Kcr and Kla play crucial roles in the epigenetic regulation of neural development.
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Affiliation(s)
- Shang-Kun Dai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences 1 , Beijing 100101 , China
- Savaid Medical School, University of Chinese Academy of Sciences 2 , Beijing 100049 , China
- School of Life Sciences and Medicine, Shandong University of Technology 3 , Zibo 255049 , China
| | - Pei-Pei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences 1 , Beijing 100101 , China
- Savaid Medical School, University of Chinese Academy of Sciences 2 , Beijing 100049 , China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences 4 , Beijing 100101 , China
- Beijing Institute for Stem Cell and Regenerative Medicine 5 , Beijing 100101 , China
| | - Xiao Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences 1 , Beijing 100101 , China
- Savaid Medical School, University of Chinese Academy of Sciences 2 , Beijing 100049 , China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences 4 , Beijing 100101 , China
- Beijing Institute for Stem Cell and Regenerative Medicine 5 , Beijing 100101 , China
| | - Lin-Fei Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences 1 , Beijing 100101 , China
- Savaid Medical School, University of Chinese Academy of Sciences 2 , Beijing 100049 , China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences 4 , Beijing 100101 , China
- Beijing Institute for Stem Cell and Regenerative Medicine 5 , Beijing 100101 , China
| | - Zhao-Qian Teng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences 1 , Beijing 100101 , China
- Savaid Medical School, University of Chinese Academy of Sciences 2 , Beijing 100049 , China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences 4 , Beijing 100101 , China
- Beijing Institute for Stem Cell and Regenerative Medicine 5 , Beijing 100101 , China
| | - Chang-Mei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences 1 , Beijing 100101 , China
- Savaid Medical School, University of Chinese Academy of Sciences 2 , Beijing 100049 , China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences 4 , Beijing 100101 , China
- Beijing Institute for Stem Cell and Regenerative Medicine 5 , Beijing 100101 , China
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20
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Ferrara AL, Liotti A, Pezone A, De Rosa V. Therapeutic opportunities to modulate immune tolerance through the metabolism-chromatin axis. Trends Endocrinol Metab 2022; 33:507-521. [PMID: 35508518 DOI: 10.1016/j.tem.2022.04.002] [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: 02/16/2022] [Revised: 03/30/2022] [Accepted: 04/05/2022] [Indexed: 11/17/2022]
Abstract
The ability of the immune system to discriminate external stimuli from self-components - namely immune tolerance - occurs through a coordinated cascade of events involving a dense network of immune cells. Among them, CD4+CD25+ T regulatory cells are crucial to balance immune homeostasis and function. Growing evidence supports the notion that energy metabolites can dictate T cell fate and function via epigenetic modifications, which affect gene expression without altering the DNA sequence. Moreover, changes in cellular metabolism couple with activation of immune pathways and epigenetic remodeling to finely tune the balance between T cell activation and tolerance. This Review summarizes these aspects and critically evaluates novel possibilities for developing therapeutic strategies to modulate immune tolerance through metabolism via epigenetic drugs.
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Affiliation(s)
- Anne Lise Ferrara
- Dipartimento di Scienze Mediche Traslazionali, Università di Napoli "Federico II", 80131 Napoli, Italy; Istituto per l'Endocrinologia e l'Oncologia Sperimentale, Consiglio Nazionale delle Ricerche (IEOS-CNR), 80131 Napoli, Italy
| | - Antonietta Liotti
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale, Consiglio Nazionale delle Ricerche (IEOS-CNR), 80131 Napoli, Italy
| | - Antonio Pezone
- Dipartimento di Biologia, Università di Napoli "Federico II", 80131 Napoli, Italy.
| | - Veronica De Rosa
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale, Consiglio Nazionale delle Ricerche (IEOS-CNR), 80131 Napoli, Italy.
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21
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Nian F, Qian Y, Xu F, Yang M, Wang H, Zhang Z. LDHA promotes osteoblast differentiation through histone lactylation. Biochem Biophys Res Commun 2022; 615:31-35. [DOI: 10.1016/j.bbrc.2022.05.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/07/2022] [Accepted: 05/10/2022] [Indexed: 11/02/2022]
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22
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Moreno-Yruela C, Bæk M, Monda F, Olsen CA. Chiral Posttranslational Modification to Lysine ε-Amino Groups. Acc Chem Res 2022; 55:1456-1466. [PMID: 35500056 DOI: 10.1021/acs.accounts.2c00115] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
ConspectusThe sophistication of proteomic analysis has revealed that protein lysine residues are posttranslationally modified by a variety of acyl groups. Protein lysine acetylation regulates metabolism, gene expression, and microtubule formation and has been extensively studied; however, the understanding of the biological significance of other acyl posttranslational modifications (PTMs) is still in its infancy. The acylation of lysine residues is mediated either by acyltransferase "writer" enzymes or by nonenzymatic mechanisms and hydrolase enzymes, termed "erasers", that cleave various acyl PTMs to reverse the modified state. We have studied the human lysine deacylase enzymes, comprising the 11 Zn2+-dependent histone deacetylases (HDACs) and the 7 NAD+-consuming sirtuins (SIRTs), over the past decade. We have thus developed selective inhibitors and molecular probes and have studied the acyl substrate scope of each enzyme using chemically synthesized peptide substrates and photo-cross-linking probes. Recently, we have turned our attention to PTMs containing a stereogenic center, such as ε-N-β-hydroxybutyryllysine (Kbhb) and ε-N-lactyllysine (Kla), that each comprise a pair of mirror image stereoisomers as modifications. Both modifications are found on histones, where they affect gene transcription in response to specific metabolic states, and they are found on cytosolic and mitochondrial enzymes involved in fatty acid oxidation (Kbhb) and glycolysis (Kla), respectively. Thus, chiral modifications to lysine side chains give rise to two distinct diastereomeric products, with separate metabolic origins and potentially different activities exhibited by writer and eraser enzymes. Lysine l-lactylation originates from l-lactate, a major energy carrier produced from pyruvate after glycolysis, and it is highly induced by metabolic states such as the Warburg effect. l-Lactate can possibly be activated by acyl-coenzyme A (CoA) synthetases and transferred to lysine residues by histone acetyltransferases such as p300. d-Lactylation, on the other hand, arises primarily from a nonenzymatic reaction with d-lactylglutathione, an intermediate in the glyoxalase pathway. In addition to their distinct origin, we found that both K(l-la) and K(d-la) modifications are erased by HDACs with different catalytic efficiencies. Also, K(l-bhb) and K(d-bhb) arise from different metabolites but depend on interconnected metabolic pathways, and the two stereoisomers of ε-N-3-hydroxy-3-methylglutaryllysine (Khmg) originate from a single precursor that may then be regulated differently by eraser enzymes. Distinguishing between the individual stereoisomers of PTMs is therefore of crucial importance. In the present Account, we will (1) revisit the long-standing evidence for the distinct production and dynamics of enantiomeric forms of chiral metabolites that serve as ε-N-acyllysine PTMs and (2) highlight the outstanding questions that arise from the recent literature on chiral lysine PTMs resulting from these metabolites.
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Affiliation(s)
- Carlos Moreno-Yruela
- Center for Biopharmaceuticals & Department of Drug Design of Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Michael Bæk
- Center for Biopharmaceuticals & Department of Drug Design of Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Fabrizio Monda
- Center for Biopharmaceuticals & Department of Drug Design of Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Christian A. Olsen
- Center for Biopharmaceuticals & Department of Drug Design of Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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23
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Yamaguchi K, Chen X, Oji A, Hiratani I, Defossez PA. Large-Scale Chromatin Rearrangements in Cancer. Cancers (Basel) 2022; 14:cancers14102384. [PMID: 35625988 PMCID: PMC9139990 DOI: 10.3390/cancers14102384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Cancers have many genetic mutations such as nucleotide changes, deletions, amplifications, and chromosome gains or losses. Some of these genetic alterations directly contribute to the initiation and progression of tumors. In parallel to these genetic changes, cancer cells acquire modifications to their chromatin landscape, i.e., to the marks that are carried by DNA and the histone proteins it is associated with. These “epimutations” have consequences for gene expression and genome stability, and also contribute to tumoral initiation and progression. Some of these chromatin changes are very local, affecting just one or a few genes. In contrast, some chromatin alterations observed in cancer are more widespread and affect a large part of the genome. In this review, we present different types of large-scale chromatin rearrangements in cancer, explain how they may occur, and why they are relevant for cancer diagnosis and treatment. Abstract Epigenetic abnormalities are extremely widespread in cancer. Some of them are mere consequences of transformation, but some actively contribute to cancer initiation and progression; they provide powerful new biological markers, as well as new targets for therapies. In this review, we examine the recent literature and focus on one particular aspect of epigenome deregulation: large-scale chromatin changes, causing global changes of DNA methylation or histone modifications. After a brief overview of the one-dimension (1D) and three-dimension (3D) epigenome in healthy cells and of its homeostasis mechanisms, we use selected examples to describe how many different events (mutations, changes in metabolism, and infections) can cause profound changes to the epigenome and fuel cancer. We then present the consequences for therapies and briefly discuss the role of single-cell approaches for the future progress of the field.
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Affiliation(s)
- Kosuke Yamaguchi
- UMR7216 Epigenetics and Cell Fate, Université Paris Cité, CNRS, F-75006 Paris, France; (K.Y.); (X.C.)
| | - Xiaoying Chen
- UMR7216 Epigenetics and Cell Fate, Université Paris Cité, CNRS, F-75006 Paris, France; (K.Y.); (X.C.)
| | - Asami Oji
- RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), Kobe 650-0047, Japan; (A.O.); (I.H.)
| | - Ichiro Hiratani
- RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), Kobe 650-0047, Japan; (A.O.); (I.H.)
| | - Pierre-Antoine Defossez
- UMR7216 Epigenetics and Cell Fate, Université Paris Cité, CNRS, F-75006 Paris, France; (K.Y.); (X.C.)
- Correspondence: ; Tel.: +33-157278916
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24
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Zhu S, Wang Q. Metabolic control of oocyte development. Biol Reprod 2022; 107:54-61. [PMID: 35470861 DOI: 10.1093/biolre/ioac082] [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: 12/08/2021] [Revised: 03/19/2022] [Accepted: 04/18/2022] [Indexed: 11/12/2022] Open
Abstract
Well balanced and timed metabolism is essential for oocyte development. The effects of extrinsic nutrients on oocyte maturation have been widely reported. In contrast, intrinsic control of oogenesis by intracellular metabolites and metabolic enzymes has received little attention. The comprehensive characterization of metabolic patterns could lead to more complete understanding of regulatory mechanisms underlying oocyte development. A cell's metabolic state is integrated with epigenetic regulation. Epigenetic modifications in germ cells are therefore sensitive to parental environmental exposures. Nevertheless, direct genetic evidence for metabolites involvement in epigenetic establishment during oocyte development is still lacking. Moreover, metabolic disorder-induced epigenetic perturbations during oogenesis might mediate the inter/transgenerational effects of environmental insults. The molecular mechanisms responsible for this deserve further investigation. Here, we summarize the findings on metabolic regulation in oocyte maturation, and how it contributes to oocyte epigenetic modification. Finally, we propose a mouse model that metabolic disorder in oocyte serves as a potential factor mediating the maternal environment effects on offspring health.
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Affiliation(s)
- Shuai Zhu
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Qiang Wang
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing 211166, China.,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
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25
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Wang ZA, Whedon SD, Wu M, Wang S, Brown EA, Anmangandla A, Regan L, Lee K, Du J, Hong JY, Fairall L, Kay T, Lin H, Zhao Y, Schwabe JWR, Cole PA. Histone H2B Deacylation Selectivity: Exploring Chromatin's Dark Matter with an Engineered Sortase. J Am Chem Soc 2022; 144:3360-3364. [PMID: 35175758 PMCID: PMC8895396 DOI: 10.1021/jacs.1c13555] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We describe a new method to produce histone H2B by semisynthesis with an engineered sortase transpeptidase. N-Terminal tail site-specifically modified acetylated, lactylated, and β-hydroxybutyrylated histone H2Bs were incorporated into nucleosomes and investigated as substrates of histone deacetylase (HDAC) complexes and sirtuins. A wide range of rates and site-specificities were observed by these enzyme forms suggesting distinct biological roles in regulating chromatin structure and epigenetics.
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Affiliation(s)
- Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Samuel D Whedon
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Mingxuan Wu
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Siyu Wang
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Edward A Brown
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Ananya Anmangandla
- Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Liam Regan
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jianfeng Du
- The Ben May Department for Cancer Research, Chicago, Illinois 60637, United States
| | - Jun Young Hong
- Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Louise Fairall
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Taylor Kay
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Hening Lin
- Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Yingming Zhao
- The Ben May Department for Cancer Research, Chicago, Illinois 60637, United States
| | - John W R Schwabe
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
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26
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Moreno-Yruela C, Zhang D, Wei W, Bæk M, Liu W, Gao J, Danková D, Nielsen AL, Bolding JE, Yang L, Jameson ST, Wong J, Olsen CA, Zhao Y. Class I histone deacetylases (HDAC1-3) are histone lysine delactylases. SCIENCE ADVANCES 2022; 8:eabi6696. [PMID: 35044827 PMCID: PMC8769552 DOI: 10.1126/sciadv.abi6696] [Citation(s) in RCA: 156] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 11/25/2021] [Indexed: 05/22/2023]
Abstract
Lysine L-lactylation [K(L-la)] is a newly discovered histone mark stimulated under conditions of high glycolysis, such as the Warburg effect. K(L-la) is associated with functions that are different from the widely studied histone acetylation. While K(L-la) can be introduced by the acetyltransferase p300, histone delactylases enzymes remained unknown. Here, we report the systematic evaluation of zinc- and nicotinamide adenine dinucleotide–dependent histone deacetylases (HDACs) for their ability to cleave ε-N-L-lactyllysine marks. Our screens identified HDAC1–3 and SIRT1–3 as delactylases in vitro. HDAC1–3 show robust activity toward not only K(L-la) but also K(D-la) and diverse short-chain acyl modifications. We further confirmed the de-L-lactylase activity of HDACs 1 and 3 in cells. Together, these data suggest that histone lactylation is installed and removed by regulatory enzymes as opposed to spontaneous chemical reactivity. Our results therefore represent an important step toward full characterization of this pathway’s regulatory elements.
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Affiliation(s)
- Carlos Moreno-Yruela
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Di Zhang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Wei Wei
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Michael Bæk
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Wenchao Liu
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Jinjun Gao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Daniela Danková
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Alexander L. Nielsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Julie E. Bolding
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Lu Yang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Samuel T. Jameson
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Christian A. Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
- Corresponding author. (Y.Z.); (C.A.O.)
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
- Corresponding author. (Y.Z.); (C.A.O.)
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27
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Charidemou E, Tsiarli MA, Theophanous A, Yilmaz V, Pitsouli C, Strati K, Griffin JL, Kirmizis A. Histone acetyltransferase NAA40 modulates acetyl-CoA levels and lipid synthesis. BMC Biol 2022; 20:22. [PMID: 35057804 PMCID: PMC8781613 DOI: 10.1186/s12915-021-01225-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 12/30/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Epigenetic regulation relies on the activity of enzymes that use sentinel metabolites as cofactors to modify DNA or histone proteins. Thus, fluctuations in cellular metabolite levels have been reported to affect chromatin modifications. However, whether epigenetic modifiers also affect the levels of these metabolites and thereby impinge on downstream metabolic pathways remains largely unknown. Here, we tested this notion by investigating the function of N-alpha-acetyltransferase 40 (NAA40), the enzyme responsible for N-terminal acetylation of histones H2A and H4, which has been previously implicated with metabolic-associated conditions such as age-dependent hepatic steatosis and calorie-restriction-mediated longevity. RESULTS Using metabolomic and lipidomic approaches, we found that depletion of NAA40 in murine hepatocytes leads to significant increase in intracellular acetyl-CoA levels, which associates with enhanced lipid synthesis demonstrated by upregulation in de novo lipogenesis genes as well as increased levels of diglycerides and triglycerides. Consistently, the increase in these lipid species coincide with the accumulation of cytoplasmic lipid droplets and impaired insulin signalling indicated by decreased glucose uptake. However, the effect of NAA40 on lipid droplet formation is independent of insulin. In addition, the induction in lipid synthesis is replicated in vivo in the Drosophila melanogaster larval fat body. Finally, supporting our results, we find a strong association of NAA40 expression with insulin sensitivity in obese patients. CONCLUSIONS Overall, our findings demonstrate that NAA40 affects the levels of cellular acetyl-CoA, thereby impacting lipid synthesis and insulin signalling. This study reveals a novel path through which histone-modifying enzymes influence cellular metabolism with potential implications in metabolic disorders.
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Affiliation(s)
- Evelina Charidemou
- Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - Maria A Tsiarli
- Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - Andria Theophanous
- Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - Vural Yilmaz
- Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - Chrysoula Pitsouli
- Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - Katerina Strati
- Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - Julian L Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, CB2 1GA, UK
- Hammersmith Campus, UK Dementia Research Institute at Imperial College, Burlington Danes Building, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Section of Biomolecular Medicine, Department of Metabolism, Division of Systems Medicine, Digestion and Reproduction, The Sir Alexander Fleming Building, Exhibition Road, South Kensington, Imperial College London, London, SW7 2AZ, UK
| | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus.
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28
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Shvedunova M, Akhtar A. Modulation of cellular processes by histone and non-histone protein acetylation. Nat Rev Mol Cell Biol 2022; 23:329-349. [PMID: 35042977 DOI: 10.1038/s41580-021-00441-y] [Citation(s) in RCA: 269] [Impact Index Per Article: 134.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2021] [Indexed: 12/12/2022]
Abstract
Lysine acetylation is a widespread and versatile protein post-translational modification. Lysine acetyltransferases and lysine deacetylases catalyse the addition or removal, respectively, of acetyl groups at both histone and non-histone targets. In this Review, we discuss several features of acetylation and deacetylation, including their diversity of targets, rapid turnover, exquisite sensitivity to the concentrations of the cofactors acetyl-CoA, acyl-CoA and NAD+, and tight interplay with metabolism. Histone acetylation and non-histone protein acetylation influence a myriad of cellular and physiological processes, including transcription, phase separation, autophagy, mitosis, differentiation and neural function. The activity of lysine acetyltransferases and lysine deacetylases can, in turn, be regulated by metabolic states, diet and specific small molecules. Histone acetylation has also recently been shown to mediate cellular memory. These features enable acetylation to integrate the cellular state with transcriptional output and cell-fate decisions.
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Affiliation(s)
- Maria Shvedunova
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
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29
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Unconventional metabolites in chromatin regulation. Biosci Rep 2022; 42:230604. [PMID: 34988581 PMCID: PMC8777195 DOI: 10.1042/bsr20211558] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 11/17/2022] Open
Abstract
Chromatin, the complex of DNA and histone proteins, serves as a main integrator of cellular signals. Increasing evidence links cellular functional to chromatin state. Indeed, different metabolites are emerging as modulators of chromatin function and structure. Alterations in chromatin state are decisive for regulating all aspects of genome function and ultimately have the potential to produce phenotypic changes. Several metabolites such as acetyl-CoA, S-adenosylmethionine (SAM) or adenosine triphosphate (ATP) have now been well characterized as main substrates or cofactors of chromatin-modifying enzymes. However, there are other metabolites that can directly interact with chromatin influencing its state or that modulate the properties of chromatin regulatory factors. Also, there is a growing list of atypical enzymatic and nonenzymatic chromatin modifications that originate from different cellular pathways that have not been in the limelight of chromatin research. Here, we summarize different properties and functions of uncommon regulatory molecules originating from intermediate metabolism of lipids, carbohydrates and amino acids. Based on the various modes of action on chromatin and the plethora of putative, so far not described chromatin-regulating metabolites, we propose that there are more links between cellular functional state and chromatin regulation to be discovered. We hypothesize that these connections could provide interesting starting points for interfering with cellular epigenetic states at a molecular level.
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30
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Histone lysine methacrylation is a dynamic post-translational modification regulated by HAT1 and SIRT2. Cell Discov 2021; 7:122. [PMID: 34961760 PMCID: PMC8712513 DOI: 10.1038/s41421-021-00344-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 09/13/2021] [Indexed: 02/05/2023] Open
Abstract
Histone lysine crotonylation is a posttranslational modification with demonstrated functions in transcriptional regulation. Here we report the discovery of a new type of histone posttranslational modification, lysine methacrylation (Kmea), corresponding to a structural isomer of crotonyllysine. We validate the identity of this modification using diverse chemical approaches and further confirm the occurrence of this type of histone mark by pan specific and site-specific anti-methacryllysine antibodies. In total, we identify 27 Kmea modified histone sites in HeLa cells using affinity enrichment with a pan Kmea antibody and mass spectrometry. Subsequent biochemical studies show that histone Kmea is a dynamic mark, which is controlled by HAT1 as a methacryltransferase and SIRT2 as a de-methacrylase. Altogether, these investigations uncover a new type of enzyme-catalyzed histone modification and suggest that methacrylyl-CoA generating metabolism is part of a growing number of epigenome-associated metabolic pathways.
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31
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Tauc M, Cougnon M, Carcy R, Melis N, Hauet T, Pellerin L, Blondeau N, Pisani DF. The eukaryotic initiation factor 5A (eIF5A1), the molecule, mechanisms and recent insights into the pathophysiological roles. Cell Biosci 2021; 11:219. [PMID: 34952646 PMCID: PMC8705083 DOI: 10.1186/s13578-021-00733-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/14/2021] [Indexed: 11/29/2022] Open
Abstract
Since the demonstration of its involvement in cell proliferation, the eukaryotic initiation factor 5A (eIF5A) has been studied principally in relation to the development and progression of cancers in which the isoform A2 is mainly expressed. However, an increasing number of studies report that the isoform A1, which is ubiquitously expressed in normal cells, exhibits novel molecular features that reveal its new relationships between cellular functions and organ homeostasis. At a first glance, eIF5A can be regarded, among other things, as a factor implicated in the initiation of translation. Nevertheless, at least three specificities: (1) its extreme conservation between species, including plants, throughout evolution, (2) its very special and unique post-translational modification through the activating-hypusination process, and finally (3) its close relationship with the polyamine pathway, suggest that the role of eIF5A in living beings remains to be uncovered. In fact, and beyond its involvement in facilitating the translation of proteins containing polyproline residues, eIF5A is implicated in various physiological processes including ischemic tolerance, metabolic adaptation, aging, development, and immune cell differentiation. These newly discovered physiological properties open up huge opportunities in the clinic for pathologies such as, for example, the ones in which the oxygen supply is disrupted. In this latter case, organ transplantation, myocardial infarction or stroke are concerned, and the current literature defines eIF5A as a new drug target with a high level of potential benefit for patients with these diseases or injuries. Moreover, the recent use of genomic and transcriptomic association along with metadata studies also revealed the implication of eIF5A in genetic diseases. Thus, this review provides an overview of eIF5A from its molecular mechanism of action to its physiological roles and the clinical possibilities that have been recently reported in the literature.
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Affiliation(s)
- Michel Tauc
- LP2M, CNRS, Université Côte d'Azur, Nice, France. .,Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France. .,Laboratoire de Physiomédecine Moléculaire, UMR7370, Faculté de Médecine, CNRS, Université Côte d'Azur, 28 Avenue de Valombrose, 06107, Nice Cedex, France.
| | - Marc Cougnon
- LP2M, CNRS, Université Côte d'Azur, Nice, France.,Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
| | - Romain Carcy
- Service de Réanimation Polyvalente et Service de Réanimation des Urgences Vitales, CHU Nice, Hôpital Pasteur 2, Nice, France
| | - Nicolas Melis
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Thierry Hauet
- INSERM, IRTOMIT, CHU de Poitiers, Université de Poitiers, La Milétrie, Poitiers, France
| | - Luc Pellerin
- INSERM, IRTOMIT, CHU de Poitiers, Université de Poitiers, La Milétrie, Poitiers, France
| | - Nicolas Blondeau
- Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France.,IPMC, CNRS, Université Côte d'Azur, Valbonne, France
| | - Didier F Pisani
- LP2M, CNRS, Université Côte d'Azur, Nice, France.,Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
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32
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Valentino T, Figueiredo VC, Mobley CB, McCarthy JJ, Vechetti IJ. Evidence of myomiR regulation of the pentose phosphate pathway during mechanical load-induced hypertrophy. Physiol Rep 2021; 9:e15137. [PMID: 34889054 PMCID: PMC8661100 DOI: 10.14814/phy2.15137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/13/2021] [Accepted: 11/10/2021] [Indexed: 12/29/2022] Open
Abstract
Many of the molecular and cellular mechanisms discovered to regulate skeletal muscle hypertrophy were first identified using the rodent synergist ablation model. This model reveals the intrinsic capability and necessary pathways of skeletal muscle growth in response to mechanical overload (MOV). Reminiscent of the rapid cellular growth observed with cancer, we hypothesized that in response to MOV, skeletal muscle would undergo metabolic programming to sustain increased demands to support hypertrophy. To test this hypothesis, we analyzed the gene expression of specific metabolic pathways taken from transcriptomic microarray data of a MOV time course. We found an upregulation of genes involved in the oxidative branch of the pentose phosphate pathways (PPP) and mitochondrial branch of the folate cycle suggesting an increase in the production of NADPH. In addition, we sought to determine the potential role of skeletal muscle-enriched microRNA (myomiRs) and satellite cells in the regulation of the metabolic pathways that changed during MOV. We observed an inverse pattern in gene expression between muscle-enriched myomiR-1 and its known target gene glucose-6-phosphate dehydrogenase, G6pdx, suggesting myomiR regulation of PPP activation in response to MOV. Satellite cell fusion had a significant but modest impact on PPP gene expression. These transcriptomic findings suggest the robust muscle hypertrophy induced by MOV requires enhanced redox metabolism via PPP production of NADPH which is potentially regulated by a myomiR network.
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Affiliation(s)
- Taylor Valentino
- Department of PhysiologyCollege of MedicineLexingtonKentuckyUSA
- Center for Muscle BiologyUniversity of KentuckyLexingtonKentuckyUSA
| | - Vandre C. Figueiredo
- Center for Muscle BiologyUniversity of KentuckyLexingtonKentuckyUSA
- Department of Physical TherapyCollege of Health SciencesUniversity of KentuckyLexingtonKentuckyUSA
| | | | - John J. McCarthy
- Department of PhysiologyCollege of MedicineLexingtonKentuckyUSA
- Center for Muscle BiologyUniversity of KentuckyLexingtonKentuckyUSA
| | - Ivan J. Vechetti
- Department of Nutrition and Health SciencesCollege of Education and Human SciencesUniversity of Nebraska‐LincolnLincolnNebraskaUSA
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33
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Boon R. Metabolic Fuel for Epigenetic: Nuclear Production Meets Local Consumption. Front Genet 2021; 12:768996. [PMID: 34804127 PMCID: PMC8595138 DOI: 10.3389/fgene.2021.768996] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/20/2021] [Indexed: 12/28/2022] Open
Abstract
Epigenetic modifications are responsible for finetuning gene expression profiles to the needs of cells, tissues, and organisms. To rapidly respond to environmental changes, the activity of chromatin modifiers critically depends on the concentration of a handful of metabolites that act as substrates and co-factors. In this way, these enzymes act as metabolic sensors that directly link gene expression to metabolic states. Although metabolites can easily diffuse through the nuclear pore, molecular mechanisms must be in place to regulate epigenetic marker deposition in specific nuclear subdomains or even on single loci. In this review, I explore the possible subcellular sites of metabolite production that influence the epigenome. From the relationship between cytoplasmic metabolism and nuclear metabolite deposition, I converse to the description of a compartmentalized nuclear metabolism. Last, I elaborate on the possibility of metabolic enzymes to operate in phase-separated nuclear microdomains formed by multienzyme and chromatin-bound protein complexes.
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Affiliation(s)
- Ruben Boon
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, United States.,The Broad Institute of Harvard and MIT, Cambridge, MA, United States.,Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
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34
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Leese HJ, McKeegan PJ, Sturmey RG. Amino Acids and the Early Mammalian Embryo: Origin, Fate, Function and Life-Long Legacy. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:9874. [PMID: 34574797 PMCID: PMC8467587 DOI: 10.3390/ijerph18189874] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/27/2021] [Accepted: 08/27/2021] [Indexed: 12/11/2022]
Abstract
Amino acids are now recognised as having multiple cellular functions in addition to their traditional role as constituents of proteins. This is well-illustrated in the early mammalian embryo where amino acids are now known to be involved in intermediary metabolism, as energy substrates, in signal transduction, osmoregulation and as intermediaries in numerous pathways which involve nitrogen metabolism, e.g., the biosynthesis of purines, pyrimidines, creatine and glutathione. The amino acid derivative S-adenosylmethionine has emerged as a universal methylating agent with a fundamental role in epigenetic regulation. Amino acids are now added routinely to preimplantation embryo culture media. This review examines the routes by which amino acids are supplied to the early embryo, focusing on the role of the oviduct epithelium, followed by an outline of their general fate and function within the embryo. Functions specific to individual amino acids are then considered. The importance of amino acids during the preimplantation period for maternal health and that of the conceptus long term, which has come from the developmental origins of health and disease concept of David Barker, is discussed and the review concludes by considering the potential utility of amino acid profiles as diagnostic of embryo health.
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Affiliation(s)
- Henry J. Leese
- Centre for Atherothrombosis and Metabolic Disease, Hull York Medical School, University of Hull, Hull HU6 7RX, UK;
| | - Paul J. McKeegan
- Centre for Anatomical and Human Sciences, Hull York Medical School, University of Hull, Hull HU6 7RX, UK;
| | - Roger G. Sturmey
- Centre for Atherothrombosis and Metabolic Disease, Hull York Medical School, University of Hull, Hull HU6 7RX, UK;
- Division of Developmental Biology and Medicine, The University of Manchester, St Mary’s Hospital, Manchester M13 9WL, UK
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Maksimovic I, David Y. Non-enzymatic Covalent Modifications as a New Chapter in the Histone Code. Trends Biochem Sci 2021; 46:718-730. [PMID: 33965314 PMCID: PMC8364488 DOI: 10.1016/j.tibs.2021.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/26/2021] [Accepted: 04/02/2021] [Indexed: 12/29/2022]
Abstract
The interior of the cell abounds with reactive species that can accumulate as non-enzymatic covalent modifications (NECMs) on biological macromolecules. These adducts interfere with many cellular processes, for example, by altering proteins' surface topology, enzymatic activity, or interactomes. Here, we discuss dynamic NECMs on chromatin, which serves as the cellular blueprint. We first outline the chemistry of NECM formation and then focus on the recently identified effects of their accumulation on chromatin structure and transcriptional output. We next describe the known cellular regulatory mechanisms that prevent or reverse NECM formation. Finally, we discuss recently developed chemical biology platforms for probing and manipulating these NECMs in vitro and in vivo.
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Affiliation(s)
- Igor Maksimovic
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA; Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yael David
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA; Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA; Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
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36
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Iwata R, Vanderhaeghen P. Regulatory roles of mitochondria and metabolism in neurogenesis. Curr Opin Neurobiol 2021; 69:231-240. [PMID: 34171617 PMCID: PMC8415079 DOI: 10.1016/j.conb.2021.05.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 01/14/2023]
Abstract
Neural stem cells (NSCs) undergo massive molecular and cellular changes during neuronal differentiation. These include mitochondria and metabolism remodelling, which were thought to be mostly permissive cues, but recent work indicates that they are causally linked to neurogenesis. Striking remodelling of mitochondria occurs right after mitosis of NSCs, which influences the postmitotic daughter cells towards self-renewal or differentiation. The transitioning to neuronal fate requires metabolic rewiring including increased oxidative phosphorylation activity, which drives transcriptional and epigenetic effects to influence cell fate. Mitochondria metabolic pathways also contribute in an essential way to the regulation of NSC proliferation and self-renewal. The influence of mitochondria and metabolism on neurogenesis is conserved from fly to human systems, but also displays striking differences linked to cell context or species. These new findings have important implications for our understanding of neurodevelopmental diseases and possibly human brain evolution.
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Affiliation(s)
- Ryohei Iwata
- VIB KULeuven Center for Brain & Disease Research, KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, 3000, Belgium; Université Libre de Bruxelles (ULB), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), ULB Neuroscience Institute (UNI), Brussels, 1070, Belgium
| | - Pierre Vanderhaeghen
- VIB KULeuven Center for Brain & Disease Research, KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, 3000, Belgium; Université Libre de Bruxelles (ULB), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), ULB Neuroscience Institute (UNI), Brussels, 1070, Belgium.
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37
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Wang X, Dong Y, Zheng Y, Chen Y. Multiomics metabolic and epigenetics regulatory network in cancer: A systems biology perspective. J Genet Genomics 2021; 48:520-530. [PMID: 34362682 DOI: 10.1016/j.jgg.2021.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022]
Abstract
Genetic, epigenetic, and metabolic alterations are all hallmarks of cancer. However, the epigenome and metabolome are both highly complex and dynamic biological networks in vivo. The interplay between the epigenome and metabolome contributes to a biological system that is responsive to the tumor microenvironment and possesses a wealth of unknown biomarkers and targets of cancer therapy. From this perspective, we first review the state of high-throughput biological data acquisition (i.e. multiomics data) and analysis (i.e. computational tools) and then propose a conceptual in silico metabolic and epigenetic regulatory network (MER-Net) that is based on these current high-throughput methods. The conceptual MER-Net is aimed at linking metabolomic and epigenomic networks through observation of biological processes, omics data acquisition, analysis of network information, and integration with validated database knowledge. Thus, MER-Net could be used to reveal new potential biomarkers and therapeutic targets using deep learning models to integrate and analyze large multiomics networks. We propose that MER-Net can serve as a tool to guide integrated metabolomics and epigenomics research or can be modified to answer other complex biological and clinical questions using multiomics data.
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Affiliation(s)
- Xuezhu Wang
- The State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Yucheng Dong
- The State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Yongchang Zheng
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yang Chen
- The State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China.
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38
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Troelsen KS, Calder EDD, Skwarska A, Sneddon D, Hammond EM, Conway SJ. Zap-Pano: a Photocaged Prodrug of the KDAC Inhibitor Panobinostat. ChemMedChem 2021; 16:3691-3700. [PMID: 34259396 PMCID: PMC9291796 DOI: 10.1002/cmdc.202100403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/02/2021] [Indexed: 01/04/2023]
Abstract
We report the synthesis and biological evaluation of a light‐activated (caged) prodrug of the KDAC inhibitor panobinostat (Zap‐Pano). We demonstrate that addition of the 4,5‐dimethoxy‐2‐nitrobenzyl group to the hydroxamic acid oxygen results in an inactive prodrug. In two cancer cell lines we show that photolysis of this compound releases panobinostat and an unexpected carboxamide analogue of panobinostat. Photolysis of Zap‐Pano causes an increase in H3K9Ac and H3K18Ac, consistent with KDAC inhibition, in an oesophageal cancer cell line (OE21). Irradiation of OE21 cells in the presence of Zap‐Pano results in apoptotic cell death. This compound is a useful research tool, allowing spatial and temporal control over release of panobinostat.
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Affiliation(s)
- Kathrin S Troelsen
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.,Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, OX3 7DQ, UK.,Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Ewen D D Calder
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Anna Skwarska
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Deborah Sneddon
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Ester M Hammond
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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Coppedè F. One-carbon epigenetics and redox biology of neurodegeneration. Free Radic Biol Med 2021; 170:19-33. [PMID: 33307166 DOI: 10.1016/j.freeradbiomed.2020.12.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022]
Abstract
One-carbon metabolism provides the methyl groups for both DNA and histone tail methylation reactions, two of the main epigenetic processes that tightly regulate the chromatin structure and gene expression levels. Several enzymes involved in one-carbon metabolism, as well as several epigenetic enzymes, are regulated by intracellular metabolites and redox cofactors, but their expression levels are in turn regulated by epigenetic modifications, in such a way that metabolism and gene expression reciprocally regulate each other to maintain homeostasis and regulate cell growth, survival, differentiation and response to environmental stimuli. Increasing evidence highlights the contribution of impaired one-carbon metabolism and epigenetic modifications in neurodegeneration. This article provides an overview of DNA and histone tail methylation changes in major neurodegenerative disorders, namely Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis, discussing the contribution of oxidative stress and impaired one-carbon and redox metabolism to their onset and progression.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Via Roma 55, 56126, Pisa, Italy.
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40
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Chen AN, Luo Y, Yang YH, Fu JT, Geng XM, Shi JP, Yang J. Lactylation, a Novel Metabolic Reprogramming Code: Current Status and Prospects. Front Immunol 2021; 12:688910. [PMID: 34177945 PMCID: PMC8222712 DOI: 10.3389/fimmu.2021.688910] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/27/2021] [Indexed: 12/15/2022] Open
Abstract
Lactate is an end product of glycolysis. As a critical energy source for mitochondrial respiration, lactate also acts as a precursor of gluconeogenesis and a signaling molecule. We briefly summarize emerging concepts regarding lactate metabolism, such as the lactate shuttle, lactate homeostasis, and lactate-microenvironment interaction. Accumulating evidence indicates that lactate-mediated reprogramming of immune cells and enhancement of cellular plasticity contribute to establishing disease-specific immunity status. However, the mechanisms by which changes in lactate states influence the establishment of diverse functional adaptive states are largely uncharacterized. Posttranslational histone modifications create a code that functions as a key sensor of metabolism and are responsible for transducing metabolic changes into stable gene expression patterns. In this review, we describe the recent advances in a novel lactate-induced histone modification, histone lysine lactylation. These observations support the idea that epigenetic reprogramming-linked lactate input is related to disease state outputs, such as cancer progression and drug resistance.
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Affiliation(s)
- An-Na Chen
- Department of Translational Medicine Center, Affiliated Hospital of Hangzhou Normal University, Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, Hangzhou, China
| | - Yan Luo
- Department of Translational Medicine Center, Affiliated Hospital of Hangzhou Normal University, Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, Hangzhou, China
| | - Yu-Han Yang
- Department of Translational Medicine Center, Affiliated Hospital of Hangzhou Normal University, Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, Hangzhou, China
| | - Jian-Tao Fu
- Department of Translational Medicine Center, Affiliated Hospital of Hangzhou Normal University, Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, Hangzhou, China
| | - Xiu-Mei Geng
- Department of Translational Medicine Center, Affiliated Hospital of Hangzhou Normal University, Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, Hangzhou, China
| | - Jun-Ping Shi
- Department of Translational Medicine Center, Affiliated Hospital of Hangzhou Normal University, Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, Hangzhou, China
| | - Jin Yang
- Department of Translational Medicine Center, Affiliated Hospital of Hangzhou Normal University, Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, Hangzhou, China
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41
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Siklos M, Kubicek S. Therapeutic targeting of chromatin: status and opportunities. FEBS J 2021; 289:1276-1301. [PMID: 33982887 DOI: 10.1111/febs.15966] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/25/2021] [Accepted: 05/10/2021] [Indexed: 12/13/2022]
Abstract
The molecular characterization of mechanisms underlying transcriptional control and epigenetic inheritance since the 1990s has paved the way for the development of targeted therapies that modulate these pathways. In the past two decades, cancer genome sequencing approaches have uncovered a plethora of mutations in chromatin modifying enzymes across tumor types, and systematic genetic screens have identified many of these proteins as specific vulnerabilities in certain cancers. Now is the time when many of these basic and translational efforts start to bear fruit and more and more chromatin-targeting drugs are entering the clinic. At the same time, novel pharmacological approaches harbor the potential to modulate chromatin in unprecedented fashion, thus generating entirely novel opportunities. Here, we review the current status of chromatin targets in oncology and describe a vision for the epigenome-modulating drugs of the future.
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Affiliation(s)
- Marton Siklos
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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42
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Histone modifications centric-regulation in osteogenic differentiation. Cell Death Dis 2021; 7:91. [PMID: 33941771 PMCID: PMC8093204 DOI: 10.1038/s41420-021-00472-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/21/2021] [Accepted: 04/07/2021] [Indexed: 02/03/2023]
Abstract
Histone modification critically contributes to the epigenetic control of gene expression by changing the configuration of chromatin and modifying the access of transcription factors to gene promoters. Recently, we observed that histone acetylation and crotonylation mediated the expression of endocytosis-related genes and tumor-related immune checkpoint genes by regulating the enrichment of signal transducer and activator of transcription 3 on these gene promoters in Alzheimer's disease and tumorigenesis, suggesting that histone modification plays an important role in disease development. Furthermore, studies performed in the past decade revealed that histone modifications affect osteogenic differentiation by regulating the expression of osteogenic marker genes. In this review, we summarize and discuss the histone modification-centric regulation of osteogenic gene expression. This review improves the understanding of the role of histone modifications in osteogenic differentiation and describes its potential as a therapeutic target for osteogenic differentiation-related diseases.
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43
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Low Plasma Citrate Levels and Specific Transcriptional Signatures Associated with Quiescence of CD34 + Progenitors Predict Azacitidine Therapy Failure in MDS/AML Patients. Cancers (Basel) 2021; 13:cancers13092161. [PMID: 33946220 PMCID: PMC8125503 DOI: 10.3390/cancers13092161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/22/2021] [Accepted: 04/28/2021] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Epigenetic drugs, such as azacitidine (AZA), hold promise in the treatment of myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), however, the mechanisms predicting the patients’ response to AZA is not completely understood. Quiescence of hematopoietic CD34+ progenitors has been proposed as a predictive factor for AZA therapy failure in MDS/AML patients, but the interplay between CD34+ cell cycle status and their metabolic signature in a predisposition to AZA (non)responsiveness remains unclear. Our data on patients with MDS or AML with myelodysplasia-related changes (AML-MRC) suggest that AZA-responders have actively cycling CD34+ cells poised for erythro-myeloid differentiation, with high metabolic activity controlling histone acetylation. Conversely, the patients who progressed early on AZA therapy revealed quiescence signature of their CD34+ cells, with signs of reduced metabolically-controlled acetylation of histones needed for transcription-permissive chromatin configuration. Our study delineates plasma citrate levels and CD34+ cells’ transcriptional signatures associated with cycling status and metabolic characteristics as factors predicting the response to AZA monotherapy in MDS/AML-MRC patients. Abstract To better understand the molecular basis of resistance to azacitidine (AZA) therapy in myelodysplastic syndromes (MDS) and acute myeloid leukemia with myelodysplasia-related changes (AML-MRC), we performed RNA sequencing on pre-treatment CD34+ hematopoietic stem/progenitor cells (HSPCs) isolated from 25 MDS/AML-MRC patients of the discovery cohort (10 AZA responders (RD), six stable disease, nine progressive disease (PD) during AZA therapy) and from eight controls. Eleven MDS/AML-MRC samples were also available for analysis of selected metabolites, along with 17 additional samples from an independent validation cohort. Except for two patients, the others did not carry isocitrate dehydrogenase (IDH)1/2 mutations. Transcriptional landscapes of the patients’ HSPCs were comparable to those published previously, including decreased signatures of active cell cycling and DNA damage response in PD compared to RD and controls. In addition, PD-derived HSPCs revealed repressed markers of the tricarboxylic acid cycle, with IDH2 among the top 50 downregulated genes in PD compared to RD. Decreased citrate plasma levels, downregulated expression of the (ATP)-citrate lyase and other transcriptional/metabolic networks indicate metabolism-driven histone modifications in PD HSPCs. Observed histone deacetylation is consistent with transcription-nonpermissive chromatin configuration and quiescence of PD HSPCs. This study highlights the complexity of the molecular network underlying response/resistance to hypomethylating agents.
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Huang H, Zhang D, Weng Y, Delaney K, Tang Z, Yan C, Qi S, Peng C, Cole PA, Roeder RG, Zhao Y. The regulatory enzymes and protein substrates for the lysine β-hydroxybutyrylation pathway. SCIENCE ADVANCES 2021; 7:7/9/eabe2771. [PMID: 33627428 PMCID: PMC7904266 DOI: 10.1126/sciadv.abe2771] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/12/2021] [Indexed: 05/07/2023]
Abstract
Metabolism-mediated epigenetic changes represent an adapted mechanism for cellular signaling, in which lysine acetylation and methylation have been the historical focus of interest. We recently discovered a β-hydroxybutyrate-mediated epigenetic pathway that couples metabolism to gene expression. However, its regulatory enzymes and substrate proteins remain unknown, hindering its functional study. Here, we report that the acyltransferase p300 can catalyze the enzymatic addition of β-hydroxybutyrate to lysine (Kbhb), while histone deacetylase 1 (HDAC1) and HDAC2 enzymatically remove Kbhb. We demonstrate that p300-dependent histone Kbhb can directly mediate in vitro transcription. Moreover, a comprehensive analysis of Kbhb substrates in mammalian cells has identified 3248 Kbhb sites on 1397 substrate proteins. The dependence of histone Kbhb on p300 argues that enzyme-catalyzed acylation is the major mechanism for nuclear Kbhb. Our study thus reveals key regulatory elements for the Kbhb pathway, laying a foundation for studying its roles in diverse cellular processes.
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Affiliation(s)
- He Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Di Zhang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Yejing Weng
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Kyle Delaney
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Zhanyun Tang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Cong Yan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shankang Qi
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Peng
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA.
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Boon R, Silveira GG, Mostoslavsky R. Nuclear metabolism and the regulation of the epigenome. Nat Metab 2020; 2:1190-1203. [PMID: 33046909 DOI: 10.1038/s42255-020-00285-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022]
Abstract
Cellular metabolism has emerged as a major biological node governing cellular behaviour. Metabolic pathways fuel cellular energy needs, providing basic chemical molecules to sustain cellular homeostasis, proliferation and function. Changes in nutrient consumption or availability therefore can result in complete reprogramming of cellular metabolism towards stabilizing core metabolite pools, such as ATP, S-adenosyl methionine, acetyl-CoA, NAD/NADP and α-ketoglutarate. Because these metabolites underlie a variety of essential metabolic reactions, metabolism has evolved to operate in separate subcellular compartments through diversification of metabolic enzyme complexes, oscillating metabolic activity and physical separation of metabolite pools. Given that these same core metabolites are also consumed by chromatin modifiers in the establishment of epigenetic signatures, metabolite consumption on and release from chromatin directly influence cellular metabolism and gene expression. In this Review, we highlight recent studies describing the mechanisms determining nuclear metabolism and governing the redistribution of metabolites between the nuclear and non-nuclear compartments.
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Affiliation(s)
- Ruben Boon
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Giorgia G Silveira
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Raul Mostoslavsky
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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