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Yang H, Mo N, Tong L, Dong J, Fan Z, Jia M, Yue J, Wang Y. Microglia lactylation in relation to central nervous system diseases. Neural Regen Res 2025; 20:29-40. [PMID: 38767474 PMCID: PMC11246148 DOI: 10.4103/nrr.nrr-d-23-00805] [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: 05/15/2023] [Revised: 08/09/2023] [Accepted: 01/08/2024] [Indexed: 05/22/2024] Open
Abstract
The development of neurodegenerative diseases is closely related to the disruption of central nervous system homeostasis. Microglia, as innate immune cells, play important roles in the maintenance of central nervous system homeostasis, injury response, and neurodegenerative diseases. Lactate has been considered a metabolic waste product, but recent studies are revealing ever more of the physiological functions of lactate. Lactylation is an important pathway in lactate function and is involved in glycolysis-related functions, macrophage polarization, neuromodulation, and angiogenesis and has also been implicated in the development of various diseases. This review provides an overview of the lactate metabolic and homeostatic regulatory processes involved in microglia lactylation, histone versus non-histone lactylation, and therapeutic approaches targeting lactate. Finally, we summarize the current research on microglia lactylation in central nervous system diseases. A deeper understanding of the metabolic regulatory mechanisms of microglia lactylation will provide more options for the treatment of central nervous system diseases.
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Affiliation(s)
- Hui Yang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang Province, China
| | - Nan Mo
- Department of Clinical Laboratory, The Fourth Clinical Medical College of Zhejiang University of Traditional Chinese Medicine (Hangzhou First People’s Hospital), Hangzhou, Zhejiang Province, China
| | - Le Tong
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jianhong Dong
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang Province, China
| | - Ziwei Fan
- Department of Orthopedics (Spine Surgery), the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Mengxian Jia
- Department of Orthopedics (Spine Surgery), the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Juanqing Yue
- Department of Pathology, Affiliated Hangzhou First People’s Hospital, Westlake University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Ying Wang
- Department of Clinical Research Center, Affiliated Hangzhou First People’s Hospital, Westlake University School of Medicine, Hangzhou, Zhejiang Province, China
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2
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Yao W, Hu X, Wang X. Crossing epigenetic frontiers: the intersection of novel histone modifications and diseases. Signal Transduct Target Ther 2024; 9:232. [PMID: 39278916 PMCID: PMC11403012 DOI: 10.1038/s41392-024-01918-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/11/2024] [Accepted: 06/30/2024] [Indexed: 09/18/2024] Open
Abstract
Histone post-translational modifications (HPTMs), as one of the core mechanisms of epigenetic regulation, are garnering increasing attention due to their close association with the onset and progression of diseases and their potential as targeted therapeutic agents. Advances in high-throughput molecular tools and the abundance of bioinformatics data have led to the discovery of novel HPTMs which similarly affect gene expression, metabolism, and chromatin structure. Furthermore, a growing body of research has demonstrated that novel histone modifications also play crucial roles in the development and progression of various diseases, including various cancers, cardiovascular diseases, infectious diseases, psychiatric disorders, and reproductive system diseases. This review defines nine novel histone modifications: lactylation, citrullination, crotonylation, succinylation, SUMOylation, propionylation, butyrylation, 2-hydroxyisobutyrylation, and 2-hydroxybutyrylation. It comprehensively introduces the modification processes of these nine novel HPTMs, their roles in transcription, replication, DNA repair and recombination, metabolism, and chromatin structure, as well as their involvement in promoting the occurrence and development of various diseases and their clinical applications as therapeutic targets and potential biomarkers. Moreover, this review provides a detailed overview of novel HPTM inhibitors targeting various targets and their emerging strategies in the treatment of multiple diseases while offering insights into their future development prospects and challenges. Additionally, we briefly introduce novel epigenetic research techniques and their applications in the field of novel HPTM research.
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Affiliation(s)
- Weiyi Yao
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Xinting Hu
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.
- Taishan Scholars Program of Shandong Province, Jinan, Shandong, 250021, China.
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Chakraborty P, Mukherjee C. The interplay of metabolic and epigenetic players in disease development. Biochem Biophys Res Commun 2024; 734:150621. [PMID: 39217811 DOI: 10.1016/j.bbrc.2024.150621] [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: 05/12/2024] [Revised: 08/14/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
Epigenetic modifications and their alterations can cause variation in gene expression patterns which can ultimately affect a healthy individual. Until a few years ago, it was thought that the epigenome affects the transcriptome which can regulate the proteome and the metabolome. Recent studies have shown that the metabolome independently also plays a major role in regulating the epigenome bypassing the need for transcriptomic control. Alternatively, an imbalanced metabolome, stemming from transcriptome abnormalities, can further impact the transcriptome, creating a self-perpetuating cycle of interconnected occurrences. As a result, external factors such as nutrient intake and diet can have a direct impact on the metabolic pools and its reprogramming can change the levels and activity of epigenetic modifiers. Thus, the epigenetic landscape steers toward a diseased condition. In this review, we have discussed how different metabolites and dietary patterns can bring about changes in different arms of the epigenetic machinery such as methylation, acetylation as well as RNA mediated epigenetic mechanisms. We checked for limiting metabolites such as αKG, acetyl-CoA, ATP, NAD+, and FAD, whose abundance levels can lead to common diseases such as cancer, neurodegeneration etc. This gives a clearer picture of how an integrated approach including both epigenetics and metabolomics can be used for therapeutic purposes.
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Affiliation(s)
- Pallavi Chakraborty
- RNABio Lab, Institute of Health Sciences, Presidency University, Kolkata, West Bengal, India; Shiv Nadar Institute of Eminence, Greater Noida, Uttar Pradesh, India
| | - Chandrama Mukherjee
- RNABio Lab, Institute of Health Sciences, Presidency University, Kolkata, West Bengal, India.
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Karri S, Dickinson Q, Jia J, Yang Y, Gan H, Wang Z, Deng Y, Yu C. The role of hexokinases in epigenetic regulation: altered hexokinase expression and chromatin stability in yeast. Epigenetics Chromatin 2024; 17:27. [PMID: 39192292 PMCID: PMC11348520 DOI: 10.1186/s13072-024-00551-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 08/09/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND Human hexokinase 2 (HK2) plays an important role in regulating Warburg effect, which metabolizes glucose to lactate acid even in the presence of ample oxygen and provides intermediate metabolites to support cancer cell proliferation and tumor growth. HK2 overexpression has been observed in various types of cancers and targeting HK2-driven Warburg effect has been suggested as a potential cancer therapeutic strategy. Given that epigenetic enzymes utilize metabolic intermediates as substrates or co-factors to carry out post-translational modification of histones and nucleic acids modifications in cells, we hypothesized that altering HK2 expression could impact the epigenome and, consequently, chromatin stability in yeast. To test this hypothesis, we established genetic models with different yeast hexokinase 2 (HXK2) expression in Saccharomyces cerevisiae yeast cells and investigated the effect of HXK2-dependent metabolism on parental nucleosome transfer, a key DNA replication-coupled epigenetic inheritance process, and chromatin stability. RESULTS By comparing the growth of mutant yeast cells carrying single deletion of hxk1Δ, hxk2Δ, or double-loss of hxk1Δ hxk2Δ to wild-type cells, we firstly confirmed that HXK2 is the dominant HXK in yeast cell growth. Surprisingly, manipulating HXK2 expression in yeast, whether through overexpression or deletion, had only a marginal impact on parental nucleosome assembly, but a noticeable trend with decrease chromatin instability. However, targeting yeast cells with 2-deoxy-D-glucose (2-DG), a clinical glycolysis inhibitor that has been proposed as an anti-cancer treatment, significantly increased chromatin instability. CONCLUSION Our findings suggest that in yeast cells lacking HXK2, alternative HXKs such as HXK1 or glucokinase 1 (GLK1) play a role in supporting glycolysis at a level that adequately maintains epigenomic stability. While our study demonstrated an increase in epigenetic instability with 2-DG treatment, the observed effect seemed to occur dependent on non-glycolytic function of Hxk2. Thus, additional research is needed to identify the molecular mechanism through which 2-DG influences chromatin stability.
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Affiliation(s)
- Srinivasu Karri
- Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
| | - Quinn Dickinson
- Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
| | - Jing Jia
- Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
| | - Yi Yang
- Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
| | - Haiyun Gan
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhiquan Wang
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yibin Deng
- Department of Urology, Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Chuanhe Yu
- Hormel Institute, University of Minnesota, Austin, MN, 55912, USA.
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Zhang F, Cui Y, Zhang T, Yin W. Epigenetic regulation of macrophage activation in chronic obstructive pulmonary disease. Front Immunol 2024; 15:1445372. [PMID: 39206196 PMCID: PMC11349576 DOI: 10.3389/fimmu.2024.1445372] [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: 06/07/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024] Open
Abstract
Macrophages in the innate immune system play a vital role in various lung diseases such as asthma, chronic obstructive pulmonary disease (COPD), acute lung injury and pulmonary fibrosis. Macrophages involved in the process of immunity need to go through a process of activation, including changes in gene expression and cell metabolism. Epigenetic modifications are key factors of macrophage activation including DNA methylation, histone modification and non-coding RNA regulation. Understanding the role and mechanisms of epigenetic regulation of macrophage activation can provide insights into the function of macrophages in lung diseases and help identification of potential therapeutic targets. This review summarizes the latest progress in the epigenetic changes and regulation of macrophages in their development process and in normal physiological states, and the epigenetic regulation of macrophages in COPD as well as the influence of macrophage activation on COPD development.
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Affiliation(s)
- Feng Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University (GMU) - Guangzhou Institutes of Biomedicine and Health (GIBH) Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong, China
| | - Yachao Cui
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University (GMU) - Guangzhou Institutes of Biomedicine and Health (GIBH) Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong, China
| | - Tiejun Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University (GMU) - Guangzhou Institutes of Biomedicine and Health (GIBH) Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
- The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, State Key Laboratory of Respiratory Disease, Guangzhou Medical University Affiliated Qingyuan Hospital, Qingyuan People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wenguang Yin
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University (GMU) - Guangzhou Institutes of Biomedicine and Health (GIBH) Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong, China
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de Jesus Simão J, de Sousa Bispo AF, Plata VTG, Armelin-Correa LM, Alonso-Vale MIC. Fish Oil Supplementation Mitigates High-Fat Diet-Induced Obesity: Exploring Epigenetic Modulation and Genes Associated with Adipose Tissue Dysfunction in Mice. Pharmaceuticals (Basel) 2024; 17:861. [PMID: 39065712 PMCID: PMC11280081 DOI: 10.3390/ph17070861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 06/25/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
This study investigated the effects of fish oil (FO) treatment, particularly enriched with eicosapentaenoic acid (EPA), on obesity induced by a high-fat diet (HFD) in mice. The investigation focused on elucidating the impact of FO on epigenetic modifications in white adipose tissue (WAT) and the involvement of adipose-derived stem cells (ASCs). C57BL/6j mice were divided into two groups: control diet and HFD for 16 weeks. In the last 8 weeks, the HFD group was subdivided into HFD and HFD + FO (treated with FO). WAT was removed for RNA and protein extraction, while ASCs were isolated, cultured, and treated with leptin. All samples were analyzed using functional genomics tools, including PCR-array, RT-PCR, and Western Blot assays. Mice receiving an HFD displayed increased body mass, fat accumulation, and altered gene expression associated with WAT inflammation and dysfunction. FO supplementation attenuated these effects, a potential protective role against HFD-induced obesity. Analysis of H3K27 revealed HFD-induced changes in histone, which were partially reversed by FO treatment. This study further explored leptin signaling in ASCs, suggesting a potential mechanism for ASC dysfunction in the obesity-rich leptin environment of WAT. Overall, FO supplementation demonstrated efficacy in mitigating HFD-induced obesity, influencing epigenetic and molecular pathways, and shedding light on the role of ASCs and leptin signaling in WAT dysfunction associated with obesity.
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Affiliation(s)
- Jussara de Jesus Simão
- Post-Graduate Program in Chemical Biology, Institute of Environmental Sciences, Chemical and Pharmaceutical, Federal University of São Paulo—UNIFESP, Diadema 09913-030, Brazil; (J.d.J.S.); (A.F.d.S.B.); (V.T.G.P.); (L.M.A.-C.)
| | - Andressa França de Sousa Bispo
- Post-Graduate Program in Chemical Biology, Institute of Environmental Sciences, Chemical and Pharmaceutical, Federal University of São Paulo—UNIFESP, Diadema 09913-030, Brazil; (J.d.J.S.); (A.F.d.S.B.); (V.T.G.P.); (L.M.A.-C.)
| | - Victor Tadeu Gonçalves Plata
- Post-Graduate Program in Chemical Biology, Institute of Environmental Sciences, Chemical and Pharmaceutical, Federal University of São Paulo—UNIFESP, Diadema 09913-030, Brazil; (J.d.J.S.); (A.F.d.S.B.); (V.T.G.P.); (L.M.A.-C.)
| | - Lucia Maria Armelin-Correa
- Post-Graduate Program in Chemical Biology, Institute of Environmental Sciences, Chemical and Pharmaceutical, Federal University of São Paulo—UNIFESP, Diadema 09913-030, Brazil; (J.d.J.S.); (A.F.d.S.B.); (V.T.G.P.); (L.M.A.-C.)
- Department of Biological Sciences, Institute of Environmental Sciences, Chemical and Pharmaceutical, Federal University of São Paulo—UNIFESP, Diadema 09913-030, Brazil
| | - Maria Isabel Cardoso Alonso-Vale
- Post-Graduate Program in Chemical Biology, Institute of Environmental Sciences, Chemical and Pharmaceutical, Federal University of São Paulo—UNIFESP, Diadema 09913-030, Brazil; (J.d.J.S.); (A.F.d.S.B.); (V.T.G.P.); (L.M.A.-C.)
- Department of Biological Sciences, Institute of Environmental Sciences, Chemical and Pharmaceutical, Federal University of São Paulo—UNIFESP, Diadema 09913-030, Brazil
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Zhang T, Zhu Y, Wang X, Chong D, Wang H, Bu D, Zhao M, Fang L, Li C. The characterization of protein lactylation in relation to cardiac metabolic reprogramming in neonatal mouse hearts. J Genet Genomics 2024; 51:735-748. [PMID: 38479452 DOI: 10.1016/j.jgg.2024.02.009] [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: 01/06/2024] [Revised: 02/18/2024] [Accepted: 02/28/2024] [Indexed: 04/23/2024]
Abstract
In mammals, the neonatal heart can regenerate upon injury within a short time after birth, while adults lose this ability. Metabolic reprogramming has been demonstrated to be critical for cardiomyocyte proliferation in the neonatal heart. Here, we reveal that cardiac metabolic reprogramming could be regulated by altering global protein lactylation. By performing 4D label-free proteomics and lysine lactylation (Kla) omics analyses in mouse hearts at postnatal days 1, 5, and 7, 2297 Kla sites from 980 proteins are identified, among which 1262 Kla sites from 409 proteins are quantified. Functional clustering analysis reveals that the proteins with altered Kla sites are mainly involved in metabolic processes. The expression and Kla levels of proteins in glycolysis show a positive correlation while a negative correlation in fatty acid oxidation. Furthermore, we verify the Kla levels of several differentially modified proteins, including ACAT1, ACADL, ACADVL, PFKM, PKM, and NPM1. Overall, our study reports a comprehensive Kla map in the neonatal mouse heart, which will help to understand the regulatory network of metabolic reprogramming and cardiac regeneration.
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Affiliation(s)
- Tongyu Zhang
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, National Resource Center for Mutant Mice, Nanjing, Jiangsu 210093, China
| | - Yingxi Zhu
- State Key Laboratory of Reproductive Medicine and Offspring Health, China International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Gusu School, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xiaochen Wang
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, National Resource Center for Mutant Mice, Nanjing, Jiangsu 210093, China
| | - Danyang Chong
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, National Resource Center for Mutant Mice, Nanjing, Jiangsu 210093, China; State Key Laboratory of Reproductive Medicine and Offspring Health, China International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Gusu School, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Haiquan Wang
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, National Resource Center for Mutant Mice, Nanjing, Jiangsu 210093, China
| | - Dandan Bu
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, National Resource Center for Mutant Mice, Nanjing, Jiangsu 210093, China
| | - Mengfei Zhao
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, National Resource Center for Mutant Mice, Nanjing, Jiangsu 210093, China
| | - Lei Fang
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, National Resource Center for Mutant Mice, Nanjing, Jiangsu 210093, China.
| | - Chaojun Li
- Ministry of Education Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, National Resource Center for Mutant Mice, Nanjing, Jiangsu 210093, China; State Key Laboratory of Reproductive Medicine and Offspring Health, China International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Gusu School, Nanjing Medical University, Nanjing, Jiangsu 211166, China.
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8
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Yu X, Li S. Specific regulation of epigenome landscape by metabolic enzymes and metabolites. Biol Rev Camb Philos Soc 2024; 99:878-900. [PMID: 38174803 DOI: 10.1111/brv.13049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Metabolism includes anabolism and catabolism, which play an essential role in many biological processes. Chromatin modifications are post-translational modifications of histones and nucleic acids that play important roles in regulating chromatin-associated processes such as gene transcription. There is a tight connection between metabolism and chromatin modifications. Many metabolic enzymes and metabolites coordinate cellular activities with alterations in nutrient availability by regulating gene expression through epigenetic mechanisms such as DNA methylation and histone modifications. The dysregulation of gene expression by metabolism and epigenetic modifications may lead to diseases such as diabetes and cancer. Recent studies reveal that metabolic enzymes and metabolites specifically regulate chromatin modifications, including modification types, modification residues and chromatin regions. This specific regulation has been implicated in the development of human diseases, yet the underlying mechanisms are only beginning to be uncovered. In this review, we summarise recent studies of the molecular mechanisms underlying the metabolic regulation of histone and DNA modifications and discuss how they contribute to pathogenesis. We also describe recent developments in technologies used to address the key questions in this field. We hope this will inspire further in-depth investigations of the specific regulatory mechanisms involved, and most importantly will shed lights on the development of more effective disease therapies.
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Affiliation(s)
- Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
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Williams D, Hargrove-Wiley E, Bindeman W, Valent D, Miranda AX, Beckstead J, Fingleton B. Type II Interleukin-4 Receptor Activation in Basal Breast Cancer Cells Promotes Tumor Progression via Metabolic and Epigenetic Modulation. Int J Mol Sci 2024; 25:4647. [PMID: 38731867 PMCID: PMC11083536 DOI: 10.3390/ijms25094647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024] Open
Abstract
Interleukin-4 (IL4) is a Th2 cytokine that can signal through two different receptors, one of which-the type II receptor-is overexpressed by various cancer cells. Previously, we have shown that type II IL4 receptor signaling increases proliferation and metastasis in mouse models of breast cancer, as well as increasing glucose and glutamine metabolism. Here, we expand on those findings to determine mechanistically how IL4 signaling links glucose metabolism and histone acetylation to drive proliferation in the context of triple-negative breast cancer (TNBC). We used a combination of cellular, biochemical, and genomics approaches to interrogate TNBC cell lines, which represent a cancer type where high expression of the type II IL4 receptor is linked to reduced survival. Our results indicate that type II IL4 receptor activation leads to increased glucose uptake, Akt and ACLY activation, and histone acetylation in TNBC cell lines. Inhibition of glucose uptake through the deletion of Glut1 ablates IL4-induced proliferation. Additionally, pharmacological inhibition of histone acetyltransferase P300 attenuates IL4-mediated gene expression and proliferation in vitro. Our work elucidates a role for type II IL4 receptor signaling in promoting TNBC progression, and highlights type II IL4 signaling, as well as histone acetylation, as possible targets for therapy.
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Affiliation(s)
- Demond Williams
- Program in Cancer Biology, Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; (D.W.); (E.H.-W.); (W.B.); (D.V.); (A.X.M.)
| | - Ebony Hargrove-Wiley
- Program in Cancer Biology, Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; (D.W.); (E.H.-W.); (W.B.); (D.V.); (A.X.M.)
| | - Wendy Bindeman
- Program in Cancer Biology, Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; (D.W.); (E.H.-W.); (W.B.); (D.V.); (A.X.M.)
| | - Daniel Valent
- Program in Cancer Biology, Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; (D.W.); (E.H.-W.); (W.B.); (D.V.); (A.X.M.)
| | - Adam X. Miranda
- Program in Cancer Biology, Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; (D.W.); (E.H.-W.); (W.B.); (D.V.); (A.X.M.)
| | - Jacob Beckstead
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA;
| | - Barbara Fingleton
- Program in Cancer Biology, Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; (D.W.); (E.H.-W.); (W.B.); (D.V.); (A.X.M.)
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10
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Yu Y, Zhao F, Yue Y, Zhao Y, Zhou DX. Lysine acetylation of histone acetyltransferase adaptor protein ADA2 is a mechanism of metabolic control of chromatin modification in plants. NATURE PLANTS 2024; 10:439-452. [PMID: 38326652 DOI: 10.1038/s41477-024-01623-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
Abstract
Histone acetylation is a predominant active chromatin mark deposited by histone acetyltransferases (HATs) that transfer the acetyl group from acetyl coenzyme A (acetyl-CoA) to lysine ε-amino groups in histones. GENERAL CONTROL NON-REPRESSED PROTEIN 5 (GCN5) is one of the best-characterized HATs and functions in association with several adaptor proteins such as ADA2 within multiprotein HAT complexes. ADA2-GCN5 interaction increases GCN5 binding to acetyl-CoA and stimulates its HAT activity. It remains unclear whether the HAT activity of GCN5 (which acetylates not only histones but also cellular proteins) is regulated by acetyl-CoA levels, which vary greatly in cells under different metabolic and nutrition conditions. Here we show that the ADA2 protein itself is acetylated by GCN5 in rice cells. Lysine acetylation exposes ADA2 to a specific E3 ubiquitin ligase and reduces its protein stability. In rice plants, ADA2 protein accumulation reversely parallels its lysine acetylation and acetyl-CoA levels, both of which are dynamically regulated under varying growth conditions. Stress-induced ADA2 accumulation could stimulate GCN5 HAT activity to compensate for the reduced acetyl-CoA levels for histone acetylation. These results indicate that ADA2 lysine acetylation that senses cellular acetyl-CoA variations is a mechanism to regulate HAT activity and histone acetylation homeostasis in plants under changing environments.
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Affiliation(s)
- Yue Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Feng Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yaping Yue
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, Orsay, France.
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11
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François CM, Pihl T, Dunoyer de Segonzac M, Hérault C, Hudry B. Metabolic regulation of proteome stability via N-terminal acetylation controls male germline stem cell differentiation and reproduction. Nat Commun 2023; 14:6737. [PMID: 37872135 PMCID: PMC10593830 DOI: 10.1038/s41467-023-42496-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
The molecular mechanisms connecting cellular metabolism with differentiation remain poorly understood. Here, we find that metabolic signals contribute to stem cell differentiation and germline homeostasis during Drosophila melanogaster spermatogenesis. We discovered that external citrate, originating outside the gonad, fuels the production of Acetyl-coenzyme A by germline ATP-citrate lyase (dACLY). We show that this pathway is essential during the final spermatogenic stages, where a high Acetyl-coenzyme A level promotes NatB-dependent N-terminal protein acetylation. Using genetic and biochemical experiments, we establish that N-terminal acetylation shields key target proteins, essential for spermatid differentiation, from proteasomal degradation by the ubiquitin ligase dUBR1. Our work uncovers crosstalk between metabolism and proteome stability that is mediated via protein post-translational modification. We propose that this system coordinates the metabolic state of the organism with gamete production. More broadly, modulation of proteome turnover by circulating metabolites may be a conserved regulatory mechanism to control cell functions.
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Affiliation(s)
- Charlotte M François
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, 06108, France
| | - Thomas Pihl
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, 06108, France
| | | | - Chloé Hérault
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, 06108, France
| | - Bruno Hudry
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, 06108, France.
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12
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Vardar Acar N, Özgül RK. A big picture of the mitochondria-mediated signals: From mitochondria to organism. Biochem Biophys Res Commun 2023; 678:45-61. [PMID: 37619311 DOI: 10.1016/j.bbrc.2023.08.032] [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: 06/06/2023] [Revised: 08/02/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]
Abstract
Mitochondria, well-known for years as the powerhouse and biosynthetic center of the cell, are dynamic signaling organelles beyond their energy production and biosynthesis functions. The metabolic functions of mitochondria, playing an important role in various biological events both in physiological and stress conditions, transform them into important cellular stress sensors. Mitochondria constantly communicate with the rest of the cell and even from other cells to the organism, transmitting stress signals including oxidative and reductive stress or adaptive signals such as mitohormesis. Mitochondrial signal transduction has a vital function in regulating integrity of human genome, organelles, cells, and ultimately organism.
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Affiliation(s)
- Neşe Vardar Acar
- Department of Pediatric Metabolism, Institute of Child Health, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - R Köksal Özgül
- Department of Pediatric Metabolism, Institute of Child Health, Faculty of Medicine, Hacettepe University, Ankara, Turkey.
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13
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Zhao J, Wang W, Zhang L, Zhang J, Sturmey R, Zhang J. Dynamic metabolism during early mammalian embryogenesis. Development 2023; 150:dev202148. [PMID: 37877936 DOI: 10.1242/dev.202148] [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] [Indexed: 10/26/2023]
Abstract
Dynamic metabolism is exhibited by early mammalian embryos to support changing cell fates during development. It is widely acknowledged that metabolic pathways not only satisfy cellular energetic demands, but also play pivotal roles in the process of cell signalling, gene regulation, cell proliferation and differentiation. Recently, various new technological advances have been made in metabolomics and computational analysis, deepening our understanding of the crucial role of dynamic metabolism during early mammalian embryogenesis. In this Review, we summarize recent studies on oocyte and embryo metabolism and its regulation, with a particular focus on its association with key developmental events such as fertilization, zygote genome activation and cell fate determination. In addition, we discuss the mechanisms of certain metabolites that, in addition to serving as energy sources, contribute to epigenetic modifications.
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Affiliation(s)
- Jing Zhao
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Wenjie Wang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou 310058, China
| | - Ling Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Jia Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou 310058, China
| | - Roger Sturmey
- Biomedical Institute for Multimorbidity, Hull York Medical School, University of Hull, Hull HU6 7RX, UK
| | - Jin Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou 310058, China
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14
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Wartewig T, Daniels J, Schulz M, Hameister E, Joshi A, Park J, Morrish E, Venkatasubramani AV, Cernilogar FM, van Heijster FHA, Hundshammer C, Schneider H, Konstantinidis F, Gabler JV, Klement C, Kurniawan H, Law C, Lee Y, Choi S, Guitart J, Forne I, Giustinani J, Müschen M, Jain S, Weinstock DM, Rad R, Ortonne N, Schilling F, Schotta G, Imhof A, Brenner D, Choi J, Ruland J. PD-1 instructs a tumor-suppressive metabolic program that restricts glycolysis and restrains AP-1 activity in T cell lymphoma. NATURE CANCER 2023; 4:1508-1525. [PMID: 37723306 PMCID: PMC10597841 DOI: 10.1038/s43018-023-00635-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 08/15/2023] [Indexed: 09/20/2023]
Abstract
The PDCD1-encoded immune checkpoint receptor PD-1 is a key tumor suppressor in T cells that is recurrently inactivated in T cell non-Hodgkin lymphomas (T-NHLs). The highest frequencies of PDCD1 deletions are detected in advanced disease, predicting inferior prognosis. However, the tumor-suppressive mechanisms of PD-1 signaling remain unknown. Here, using tractable mouse models for T-NHL and primary patient samples, we demonstrate that PD-1 signaling suppresses T cell malignancy by restricting glycolytic energy and acetyl coenzyme A (CoA) production. In addition, PD-1 inactivation enforces ATP citrate lyase (ACLY) activity, which generates extramitochondrial acetyl-CoA for histone acetylation to enable hyperactivity of activating protein 1 (AP-1) transcription factors. Conversely, pharmacological ACLY inhibition impedes aberrant AP-1 signaling in PD-1-deficient T-NHLs and is toxic to these cancers. Our data uncover genotype-specific vulnerabilities in PDCD1-mutated T-NHL and identify PD-1 as regulator of AP-1 activity.
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Affiliation(s)
- Tim Wartewig
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- Center of Molecular and Cellular Oncology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Jay Daniels
- Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Miriam Schulz
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Erik Hameister
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Abhinav Joshi
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Joonhee Park
- Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Emma Morrish
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Anuroop V Venkatasubramani
- Protein Analysis Unit, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Martinsried, Germany
| | - Filippo M Cernilogar
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Martinsried, Germany
| | - Frits H A van Heijster
- Department of Nuclear Medicine, School of Medicine, Technical University of Munich, Munich, Germany
| | - Christian Hundshammer
- Department of Nuclear Medicine, School of Medicine, Technical University of Munich, Munich, Germany
| | - Heike Schneider
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Filippos Konstantinidis
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Judith V Gabler
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Christine Klement
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Henry Kurniawan
- Experimental and Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Immunology and Genetics, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Calvin Law
- Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Yujin Lee
- Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Sara Choi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Joan Guitart
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Ignasi Forne
- Protein Analysis Unit, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Martinsried, Germany
| | - Jérôme Giustinani
- Institut Mondor de Recherche Biomédicale, Inserm U955, Paris-Est Créteil University, Créteil, France
| | - Markus Müschen
- Center of Molecular and Cellular Oncology, Yale School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, Yale University, New Haven, CT, USA
| | - Salvia Jain
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - David M Weinstock
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Merck Research Laboratories, Boston, MA, USA
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Medicine II, School of Medicine, Technical University of Munich, Munich, Germany
| | - Nicolas Ortonne
- Institut Mondor de Recherche Biomédicale, Inserm U955, Paris-Est Créteil University, Créteil, France
- Pathology Department, AP-HP Inserm U955, Henri Mondor Hospital, Créteil, France
| | - Franz Schilling
- Department of Nuclear Medicine, School of Medicine, Technical University of Munich, Munich, Germany
| | - Gunnar Schotta
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Martinsried, Germany
| | - Axel Imhof
- Protein Analysis Unit, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Martinsried, Germany
| | - Dirk Brenner
- Experimental and Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Immunology and Genetics, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, Odense, Denmark
| | - Jaehyuk Choi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
- Center for Genetic Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
- Center for Human Immunobiology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
| | - Jürgen Ruland
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany.
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.
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15
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Li J, Richmond B, Cluntun AA, Bia R, Walsh MA, Shaw K, Symons JD, Franklin S, Rutter J, Funai K, Shaw RM, Hong T. Cardiac gene therapy treats diabetic cardiomyopathy and lowers blood glucose. JCI Insight 2023; 8:e166713. [PMID: 37639557 PMCID: PMC10561727 DOI: 10.1172/jci.insight.166713] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 08/15/2023] [Indexed: 08/31/2023] Open
Abstract
Diabetic cardiomyopathy, an increasingly global epidemic and a major cause of heart failure with preserved ejection fraction (HFpEF), is associated with hyperglycemia, insulin resistance, and intracardiomyocyte calcium mishandling. Here we identify that, in db/db mice with type 2 diabetes-induced HFpEF, abnormal remodeling of cardiomyocyte transverse-tubule microdomains occurs with downregulation of the membrane scaffolding protein cardiac bridging integrator 1 (cBIN1). Transduction of cBIN1 by AAV9 gene therapy can restore transverse-tubule microdomains to normalize intracellular distribution of calcium-handling proteins and, surprisingly, glucose transporter 4 (GLUT4). Cardiac proteomics revealed that AAV9-cBIN1 normalized components of calcium handling and GLUT4 translocation machineries. Functional studies further identified that AAV9-cBIN1 normalized insulin-dependent glucose uptake in diabetic cardiomyocytes. Phenotypically, AAV9-cBIN1 rescued cardiac lusitropy, improved exercise intolerance, and ameliorated hyperglycemia in diabetic mice. Restoration of transverse-tubule microdomains can improve cardiac function in the setting of diabetic cardiomyopathy and can also improve systemic glycemic control.
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Affiliation(s)
- Jing Li
- Department of Pharmacology and Toxicology, College of Pharmacy
- Nora Eccles Harrison Cardiovascular Research and Training Institute
| | | | | | - Ryan Bia
- Nora Eccles Harrison Cardiovascular Research and Training Institute
| | - Maureen A. Walsh
- College of Health, Department of Nutrition and Integrative Physiology, Program in Molecular Medicine
| | - Kikuyo Shaw
- Department of Pharmacology and Toxicology, College of Pharmacy
| | - J. David Symons
- College of Health, Department of Nutrition and Integrative Physiology, Program in Molecular Medicine
- Diabetes & Metabolism Research Center, and
| | - Sarah Franklin
- Nora Eccles Harrison Cardiovascular Research and Training Institute
| | - Jared Rutter
- Department of Biochemistry
- College of Health, Department of Nutrition and Integrative Physiology, Program in Molecular Medicine
- Diabetes & Metabolism Research Center, and
- Howard Hughes Medical Institute, University of Utah, Salt Lake City, Utah, USA
| | - Katsuhiko Funai
- College of Health, Department of Nutrition and Integrative Physiology, Program in Molecular Medicine
- Diabetes & Metabolism Research Center, and
| | - Robin M. Shaw
- Nora Eccles Harrison Cardiovascular Research and Training Institute
| | - TingTing Hong
- Department of Pharmacology and Toxicology, College of Pharmacy
- Nora Eccles Harrison Cardiovascular Research and Training Institute
- Howard Hughes Medical Institute, University of Utah, Salt Lake City, Utah, USA
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16
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Li AM, He B, Karagiannis D, Li Y, Jiang H, Srinivasan P, Ramirez Y, Zhou MN, Curtis C, Gruber JJ, Lu C, Rankin EB, Ye J. Serine starvation silences estrogen receptor signaling through histone hypoacetylation. Proc Natl Acad Sci U S A 2023; 120:e2302489120. [PMID: 37695911 PMCID: PMC10515173 DOI: 10.1073/pnas.2302489120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 08/07/2023] [Indexed: 09/13/2023] Open
Abstract
Loss of estrogen receptor (ER) pathway activity promotes breast cancer progression, yet how this occurs remains poorly understood. Here, we show that serine starvation, a metabolic stress often found in breast cancer, represses estrogen receptor alpha (ERα) signaling by reprogramming glucose metabolism and epigenetics. Using isotope tracing and time-resolved metabolomic analyses, we demonstrate that serine is required to maintain glucose flux through glycolysis and the TCA cycle to support acetyl-CoA generation for histone acetylation. Consequently, limiting serine depletes histone H3 lysine 27 acetylation (H3K27ac), particularly at the promoter region of ER pathway genes including the gene encoding ERα, ESR1. Mechanistically, serine starvation impairs acetyl-CoA-dependent gene expression by inhibiting the entry of glycolytic carbon into the TCA cycle and down-regulating the mitochondrial citrate exporter SLC25A1, a critical enzyme in the production of nucleocytosolic acetyl-CoA from glucose. Consistent with this model, total H3K27ac and ERα expression are suppressed by SLC25A1 inhibition and restored by acetate, an alternate source of acetyl-CoA, in serine-free conditions. We thus uncover an unexpected role for serine in sustaining ER signaling through the regulation of acetyl-CoA metabolism.
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Affiliation(s)
- Albert M Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305
| | - Bo He
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Dimitris Karagiannis
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032
| | - Yang Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Haowen Jiang
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Preethi Srinivasan
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Yaniel Ramirez
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Meng-Ning Zhou
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Christina Curtis
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Joshua J Gruber
- Department of Internal Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75235
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032
| | - Erinn B Rankin
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Jiangbin Ye
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305
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17
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Geffen Y, Anand S, Akiyama Y, Yaron TM, Song Y, Johnson JL, Govindan A, Babur Ö, Li Y, Huntsman E, Wang LB, Birger C, Heiman DI, Zhang Q, Miller M, Maruvka YE, Haradhvala NJ, Calinawan A, Belkin S, Kerelsky A, Clauser KR, Krug K, Satpathy S, Payne SH, Mani DR, Gillette MA, Dhanasekaran SM, Thiagarajan M, Mesri M, Rodriguez H, Robles AI, Carr SA, Lazar AJ, Aguet F, Cantley LC, Ding L, Getz G. Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation. Cell 2023; 186:3945-3967.e26. [PMID: 37582358 PMCID: PMC10680287 DOI: 10.1016/j.cell.2023.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 01/06/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023]
Abstract
Post-translational modifications (PTMs) play key roles in regulating cell signaling and physiology in both normal and cancer cells. Advances in mass spectrometry enable high-throughput, accurate, and sensitive measurement of PTM levels to better understand their role, prevalence, and crosstalk. Here, we analyze the largest collection of proteogenomics data from 1,110 patients with PTM profiles across 11 cancer types (10 from the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium [CPTAC]). Our study reveals pan-cancer patterns of changes in protein acetylation and phosphorylation involved in hallmark cancer processes. These patterns revealed subsets of tumors, from different cancer types, including those with dysregulated DNA repair driven by phosphorylation, altered metabolic regulation associated with immune response driven by acetylation, affected kinase specificity by crosstalk between acetylation and phosphorylation, and modified histone regulation. Overall, this resource highlights the rich biology governed by PTMs and exposes potential new therapeutic avenues.
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Affiliation(s)
- Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Shankara Anand
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Yo Akiyama
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Tomer M Yaron
- Weill Cornell Medical College, Meyer Cancer Center, New York, NY 10021, USA
| | - Yizhe Song
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jared L Johnson
- Weill Cornell Medical College, Meyer Cancer Center, New York, NY 10021, USA
| | - Akshay Govindan
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Özgün Babur
- Department of Computer Science, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Yize Li
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Emily Huntsman
- Weill Cornell Medical College, Meyer Cancer Center, New York, NY 10021, USA
| | - Liang-Bo Wang
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chet Birger
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - David I Heiman
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Qing Zhang
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Mendy Miller
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Yosef E Maruvka
- Biotechnology and Food Engineering, Lokey Center for Life Science and Engineering, Technion, Israel Institute of Technology, Haifa, Israel
| | - Nicholas J Haradhvala
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Anna Calinawan
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Saveliy Belkin
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Alexander Kerelsky
- Weill Cornell Medical College, Meyer Cancer Center, New York, NY 10021, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Alexander J Lazar
- Departments of Pathology & Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - François Aguet
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Lewis C Cantley
- Weill Cornell Medical College, Meyer Cancer Center, New York, NY 10021, USA.
| | - Li Ding
- Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
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18
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Huang L, Wang Q, Gu S, Cao N. Integrated metabolic and epigenetic mechanisms in cardiomyocyte proliferation. J Mol Cell Cardiol 2023; 181:79-88. [PMID: 37331466 DOI: 10.1016/j.yjmcc.2023.06.002] [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: 12/30/2022] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 06/20/2023]
Abstract
Heart disease continues to be the leading cause of mortality worldwide, primarily attributed to the restricted regenerative potential of the adult human heart following injury. In contrast to their adult counterparts, many neonatal mammals can spontaneously regenerate their myocardium in the first few days of life via extensive proliferation of the pre-existing cardiomyocytes. Reasons for the decline in regenerative capacity during postnatal development, and how to control it, remain largely unexplored. Accumulated evidence suggests that the preservation of regenerative potential depends on a conducive metabolic state in the embryonic and neonatal heart. Along with the postnatal increase in oxygenation and workload, the mammalian heart undergoes a metabolic transition, shifting its primary metabolic substrate from glucose to fatty acids shortly after birth for energy advantage. This metabolic switch causes cardiomyocyte cell-cycle arrest, which is widely regarded as a key mechanism for the loss of regenerative capacity. Beyond energy provision, emerging studies have suggested a link between this intracellular metabolism dynamics and postnatal epigenetic remodeling of the mammalian heart that reshapes the expression of many genes important for cardiomyocyte proliferation and cardiac regeneration, since many epigenetic enzymes utilize kinds of metabolites as obligate cofactors or substrates. This review summarizes the current state of knowledge of metabolism and metabolite-mediated epigenetic modifications in cardiomyocyte proliferation, with a particular focus on highlighting the potential therapeutic targets that hold promise to treat human heart failure via metabolic and epigenetic regulations.
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Affiliation(s)
- Liying Huang
- Zhongshan School of Medicine and the Seventh Affiliated Hospital, Sun Yat-Sen University, Guangdong 510080, China; Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangdong 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangdong 510080, China
| | - Qiyuan Wang
- Zhongshan School of Medicine and the Seventh Affiliated Hospital, Sun Yat-Sen University, Guangdong 510080, China; Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangdong 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangdong 510080, China
| | - Shanshan Gu
- Zhongshan School of Medicine and the Seventh Affiliated Hospital, Sun Yat-Sen University, Guangdong 510080, China; Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangdong 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangdong 510080, China
| | - Nan Cao
- Zhongshan School of Medicine and the Seventh Affiliated Hospital, Sun Yat-Sen University, Guangdong 510080, China; Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangdong 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangdong 510080, China.
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19
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Soukar I, Amarasinghe A, Pile LA. Coordination of cross-talk between metabolism and epigenetic regulation by the SIN3 complex. Enzymes 2023; 53:33-68. [PMID: 37748836 DOI: 10.1016/bs.enz.2023.06.001] [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] [Indexed: 09/27/2023]
Abstract
Post-translational modifications of histone proteins control the expression of genes. Metabolites from central and one-carbon metabolism act as donor moieties to modify histones and regulate gene expression. Thus, histone modification and gene regulation are connected to the metabolite status of the cell. Histone modifiers, such as the SIN3 complex, regulate genes involved in proliferation and metabolism. The SIN3 complex contains a histone deacetylase and a histone demethylase, which regulate the chromatin landscape and gene expression. In this chapter, we review the cross-talk between metabolic pathways that produce donor moieties, and epigenetic complexes regulating proliferation and metabolic genes. This cross-talk between gene regulation and metabolism is tightly controlled, and disruption of this cross-talk leads to metabolic diseases. We discuss promising therapeutics that directly regulate histone modifiers, and can affect the metabolic status of the cell, alleviating some metabolic diseases.
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Affiliation(s)
- Imad Soukar
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Anjalie Amarasinghe
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States.
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20
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Wu H, Huang H, Zhao Y. Interplay between metabolic reprogramming and post-translational modifications: from glycolysis to lactylation. Front Immunol 2023; 14:1211221. [PMID: 37457701 PMCID: PMC10338923 DOI: 10.3389/fimmu.2023.1211221] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
Cellular metabolism plays a critical role in determining the fate and function of cells. Metabolic reprogramming and its byproducts have a complex impact on cellular activities. In quiescent T cells, oxidative phosphorylation (OXPHOS) is the primary pathway for survival. However, upon antigen activation, T cells undergo rapid metabolic reprogramming, characterized by an elevation in both glycolysis and OXPHOS. While both pathways are induced, the balance predominantly shifts towards glycolysis, enabling T cells to rapidly proliferate and enhance their functionality, representing the most distinctive signature during activation. Metabolic processes generate various small molecules resulting from enzyme-catalyzed reactions, which also modulate protein function and exert regulatory control. Notably, recent studies have revealed the direct modification of histones, known as lactylation, by lactate derived from glycolysis. This lactylation process influences gene transcription and adds a novel variable to the regulation of gene expression. Protein lactylation has been identified as an essential mechanism by which lactate exerts its diverse functions, contributing to crucial biological processes such as uterine remodeling, tumor proliferation, neural system regulation, and metabolic regulation. This review focuses on the metabolic reprogramming of T cells, explores the interplay between lactate and the immune system, highlights the impact of lactylation on cellular function, and elucidates the intersection of metabolic reprogramming and epigenetics.
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Affiliation(s)
- Hengwei Wu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, People's Government of Zhejiang Province, Hangzhou, Zhejiang, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
| | - He Huang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, People's Government of Zhejiang Province, Hangzhou, Zhejiang, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
| | - Yanmin Zhao
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, People's Government of Zhejiang Province, Hangzhou, Zhejiang, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
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21
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Tarasenko T, Banerjee P, Gomez-Rodriguez J, Gildea D, Zhang S, Wolfsberg T, Jenkins L, McGuire P. Pyruvate dehydrogenase complex integrates the metabolome and epigenome in CD8+ memory T cell differentiation in vitro. RESEARCH SQUARE 2023:rs.3.rs-2838359. [PMID: 37215014 PMCID: PMC10197744 DOI: 10.21203/rs.3.rs-2838359/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Modulation of metabolic flux through pyruvate dehydrogenase complex (PDC) plays an important role in T cell activation and differentiation. PDC sits at the transition between glycolysis and the tricarboxylic acid cycle and is a major producer of acetyl-CoA, marking it as a potential metabolic and epigenetic node To understand the role of pyruvate dehydrogenase complex in T cell differentiation, we generated mice deficient in T cell pyruvate dehydrogenase E1A (Pdha) subunit using a CD4-cre recombinase-based strategy. Herein, we show that genetic ablation of PDC activity in T cells (TPdh-/-) leads to marked perturbations in glycolysis, the tricarboxylic acid cycle, and OXPHOS. TPdh-/- T cells became dependent upon substrate level phosphorylation via glycolysis, secondary to depressed OXPHOS. Due to the block of PDC activity, histone acetylation was also reduced, including H3K27, a critical site for CD8+ TM differentiation. Transcriptional and functional profiling revealed abnormal CD8+ TM differentiation in vitro. Collectively, our data indicate that PDC integrates the metabolome and epigenome in CD8+ memory T cell differentiation. Targeting this metabolic and epigenetic node can have widespread ramifications on cellular function.
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22
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Podyacheva E, Toropova Y. The Role of NAD+, SIRTs Interactions in Stimulating and Counteracting Carcinogenesis. Int J Mol Sci 2023; 24:ijms24097925. [PMID: 37175631 PMCID: PMC10178434 DOI: 10.3390/ijms24097925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
The World Health Organization has identified oncological diseases as one of the most serious health concerns of the current century. Current research on oncogenesis is focused on the molecular mechanisms of energy-biochemical reprogramming in cancer cell metabolism, including processes contributing to the Warburg effect and the pro-oncogenic and anti-oncogenic roles of sirtuins (SIRTs) and poly-(ADP-ribose) polymerases (PARPs). However, a clear understanding of the interaction between NAD+, SIRTs in cancer development, as well as their effects on carcinogenesis, has not been established, and literature data vary greatly. This work aims to provide a summary and structure of the available information on NAD+, SIRTs interactions in both stimulating and countering carcinogenesis, and to discuss potential approaches for pharmacological modulation of these interactions to achieve an anticancer effect.
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Affiliation(s)
- Ekaterina Podyacheva
- Almazov National Medical Research Centre, Ministry of Health of the Russian Federation, 197341 Saint-Petersburg, Russia
| | - Yana Toropova
- Almazov National Medical Research Centre, Ministry of Health of the Russian Federation, 197341 Saint-Petersburg, Russia
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23
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Wortham M, Liu F, Harrington AR, Fleischman JY, Wallace M, Mulas F, Mallick M, Vinckier NK, Cross BR, Chiou J, Patel NA, Sui Y, McGrail C, Jun Y, Wang G, Jhala US, Schüle R, Shirihai OS, Huising MO, Gaulton KJ, Metallo CM, Sander M. Nutrient regulation of the islet epigenome controls adaptive insulin secretion. J Clin Invest 2023; 133:e165208. [PMID: 36821378 PMCID: PMC10104905 DOI: 10.1172/jci165208] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 02/14/2023] [Indexed: 02/24/2023] Open
Abstract
Adaptation of the islet β cell insulin-secretory response to changing insulin demand is critical for blood glucose homeostasis, yet the mechanisms underlying this adaptation are unknown. Here, we have shown that nutrient-stimulated histone acetylation plays a key role in adapting insulin secretion through regulation of genes involved in β cell nutrient sensing and metabolism. Nutrient regulation of the epigenome occurred at sites occupied by the chromatin-modifying enzyme lysine-specific demethylase 1 (Lsd1) in islets. β Cell-specific deletion of Lsd1 led to insulin hypersecretion, aberrant expression of nutrient-response genes, and histone hyperacetylation. Islets from mice adapted to chronically increased insulin demand exhibited shared epigenetic and transcriptional changes. Moreover, we found that genetic variants associated with type 2 diabetes were enriched at LSD1-bound sites in human islets, suggesting that interpretation of nutrient signals is genetically determined and clinically relevant. Overall, these studies revealed that adaptive insulin secretion involves Lsd1-mediated coupling of nutrient state to regulation of the islet epigenome.
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Affiliation(s)
- Matthew Wortham
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Fenfen Liu
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Austin R. Harrington
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Johanna Y. Fleischman
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Martina Wallace
- Department of Bioengineering, UCSD, La Jolla, California, USA
| | - Francesca Mulas
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Medhavi Mallick
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Nicholas K. Vinckier
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Benjamin R. Cross
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Joshua Chiou
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Nisha A. Patel
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Yinghui Sui
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Carolyn McGrail
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Yesl Jun
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Gaowei Wang
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Ulupi S. Jhala
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | - Roland Schüle
- Department of Urology, University of Freiburg Medical Center, Freiburg, Germany
| | - Orian S. Shirihai
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Mark O. Huising
- Department of Neurobiology, Physiology and Behavior, College of Biological Sciences, and Physiology and Membrane Biology, School of Medicine, UCD, Davis, California, USA
| | - Kyle J. Gaulton
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
| | | | - Maike Sander
- Departments of Pediatrics and Cellular & Molecular Medicine, Pediatric Diabetes Research Center and
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24
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Marcucci F, Rumio C. On the Role of Glycolysis in Early Tumorigenesis-Permissive and Executioner Effects. Cells 2023; 12:cells12081124. [PMID: 37190033 DOI: 10.3390/cells12081124] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/26/2023] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
Reprogramming energy production from mitochondrial respiration to glycolysis is now considered a hallmark of cancer. When tumors grow beyond a certain size they give rise to changes in their microenvironment (e.g., hypoxia, mechanical stress) that are conducive to the upregulation of glycolysis. Over the years, however, it has become clear that glycolysis can also associate with the earliest steps of tumorigenesis. Thus, many of the oncoproteins most commonly involved in tumor initiation and progression upregulate glycolysis. Moreover, in recent years, considerable evidence has been reported suggesting that upregulated glycolysis itself, through its enzymes and/or metabolites, may play a causative role in tumorigenesis, either by acting itself as an oncogenic stimulus or by facilitating the appearance of oncogenic mutations. In fact, several changes induced by upregulated glycolysis have been shown to be involved in tumor initiation and early tumorigenesis: glycolysis-induced chromatin remodeling, inhibition of premature senescence and induction of proliferation, effects on DNA repair, O-linked N-acetylglucosamine modification of target proteins, antiapoptotic effects, induction of epithelial-mesenchymal transition or autophagy, and induction of angiogenesis. In this article we summarize the evidence that upregulated glycolysis is involved in tumor initiation and, in the following, we propose a mechanistic model aimed at explaining how upregulated glycolysis may play such a role.
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Affiliation(s)
- Fabrizio Marcucci
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Trentacoste 2, 20134 Milan, Italy
| | - Cristiano Rumio
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Trentacoste 2, 20134 Milan, Italy
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25
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Minic Z, Li Y, Hüttmann N, Uppal GK, D’Mello R, Berezovski MV. Lysine Acetylome of Breast Cancer-Derived Small Extracellular Vesicles Reveals Specific Acetylation Patterns for Metabolic Enzymes. Biomedicines 2023; 11:biomedicines11041076. [PMID: 37189694 DOI: 10.3390/biomedicines11041076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/20/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Cancer-derived small extracellular vesicles have been proposed as promising potential biomarkers for diagnosis and prognosis of breast cancer (BC). We performed a proteomic study of lysine acetylation of breast cancer-derived small extracellular vesicles (sEVs) to understand the potential role of the aberrant acetylated proteins in the biology of invasive ductal carcinoma and triple-negative BC. Three cell lines were used as models for this study: MCF10A (non-metastatic), MCF7 (estrogen and progesterone receptor-positive, metastatic) and MDA-MB-231 (triple-negative, highly metastatic). For a comprehensive protein acetylation analysis of the sEVs derived from each cell line, acetylated peptides were enriched using the anti-acetyl-lysine antibody, followed by LC-MS/MS analysis. In total, there were 118 lysine-acetylated peptides, of which 22, 58 and 82 have been identified in MCF10A, MCF7 and MDA-MB-231 cell lines, respectively. These acetylated peptides were mapped to 60 distinct proteins and mainly identified proteins involved in metabolic pathways. Among the acetylated proteins identified in cancer-derived sEVs from MCF7 and MDA-MB-231 cell lines are proteins associated with the glycolysis pathway, annexins and histones. Five acetylated enzymes from the glycolytic pathway, present only in cancer-derived sEVs, were validated. These include aldolase (ALDOA), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase (PGK1), enolase (ENO) and pyruvate kinase M1/2 (PKM). For three of these enzymes (ALDOA, PGK1 and ENO) the specific enzymatic activity was significantly higher in MDA-MB-231 when compared with MCF10A-derived sEVs. This study reveals that sEVs contain acetylated glycolytic metabolic enzymes that could be interesting potential candidates for early BC diagnostics.
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Affiliation(s)
- Zoran Minic
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Yingxi Li
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Nico Hüttmann
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Gurcharan K. Uppal
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Rochelle D’Mello
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Maxim V. Berezovski
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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26
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Watowich MB, Gilbert MR, Larion M. T cell exhaustion in malignant gliomas. Trends Cancer 2023; 9:270-292. [PMID: 36681605 PMCID: PMC10038906 DOI: 10.1016/j.trecan.2022.12.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 01/21/2023]
Abstract
Despite advances in understanding tumor biology, malignant gliomas remain incurable. While immunotherapy has improved outcomes in other cancer types, comparable efficacy has not yet been demonstrated for primary cancers of the central nervous system (CNS). T cell exhaustion, defined as a progressive decrease in effector function, sustained expression of inhibitory receptors, metabolic dysfunction, and distinct epigenetic and transcriptional alterations, contributes to the failure of immunotherapy in the CNS. Herein, we describe recent advances in understanding the drivers of T cell exhaustion in the glioma microenvironment. We discuss the extrinsic and intrinsic factors that contribute to exhaustion and highlight potential avenues for reversing this phenotype. Our ability to directly target specific immunosuppressive drivers in brain cancers would be a major advance in immunotherapy.
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Affiliation(s)
- Matthew B Watowich
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mioara Larion
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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27
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Berg JA, Zhou Y, Ouyang Y, Cluntun AA, Waller TC, Conway ME, Nowinski SM, Van Ry T, George I, Cox JE, Wang B, Rutter J. Metaboverse enables automated discovery and visualization of diverse metabolic regulatory patterns. Nat Cell Biol 2023; 25:616-625. [PMID: 37012464 PMCID: PMC10104781 DOI: 10.1038/s41556-023-01117-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 02/24/2023] [Indexed: 04/05/2023]
Abstract
Metabolism is intertwined with various cellular processes, including controlling cell fate, influencing tumorigenesis, participating in stress responses and more. Metabolism is a complex, interdependent network, and local perturbations can have indirect effects that are pervasive across the metabolic network. Current analytical and technical limitations have long created a bottleneck in metabolic data interpretation. To address these shortcomings, we developed Metaboverse, a user-friendly tool to facilitate data exploration and hypothesis generation. Here we introduce algorithms that leverage the metabolic network to extract complex reaction patterns from data. To minimize the impact of missing measurements within the network, we introduce methods that enable pattern recognition across multiple reactions. Using Metaboverse, we identify a previously undescribed metabolite signature that correlated with survival outcomes in early stage lung adenocarcinoma patients. Using a yeast model, we identify metabolic responses suggesting an adaptive role of citrate homeostasis during mitochondrial dysfunction facilitated by the citrate transporter, Ctp1. We demonstrate that Metaboverse augments the user's ability to extract meaningful patterns from multi-omics datasets to develop actionable hypotheses.
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Affiliation(s)
- Jordan A Berg
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
- Altos Labs, Redwood City, CA, USA.
| | - Youjia Zhou
- School of Computing, University of Utah, Salt Lake City, UT, USA
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA
| | - Yeyun Ouyang
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
- Altos Labs, Redwood City, CA, USA
| | - Ahmad A Cluntun
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - T Cameron Waller
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Megan E Conway
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Sara M Nowinski
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Tyler Van Ry
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
- Metabolomics Core Facility, University of Utah, Salt Lake City, UT, USA
- College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
| | - Ian George
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - James E Cox
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
- Metabolomics Core Facility, University of Utah, Salt Lake City, UT, USA
- Diabetes & Metabolism Research Center, University of Utah, Salt Lake City, UT, USA
| | - Bei Wang
- School of Computing, University of Utah, Salt Lake City, UT, USA
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA
| | - Jared Rutter
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
- Diabetes & Metabolism Research Center, University of Utah, Salt Lake City, UT, USA.
- Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA.
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28
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Zhang K, Sowers ML, Cherryhomes EI, Singh VK, Mishra A, Restrepo BI, Khan A, Jagannath C. Sirtuin-dependent metabolic and epigenetic regulation of macrophages during tuberculosis. Front Immunol 2023; 14:1121495. [PMID: 36993975 PMCID: PMC10040548 DOI: 10.3389/fimmu.2023.1121495] [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: 12/11/2022] [Accepted: 02/01/2023] [Indexed: 03/14/2023] Open
Abstract
Macrophages are the preeminent phagocytic cells which control multiple infections. Tuberculosis a leading cause of death in mankind and the causative organism Mycobacterium tuberculosis (MTB) infects and persists in macrophages. Macrophages use reactive oxygen and nitrogen species (ROS/RNS) and autophagy to kill and degrade microbes including MTB. Glucose metabolism regulates the macrophage-mediated antimicrobial mechanisms. Whereas glucose is essential for the growth of cells in immune cells, glucose metabolism and its downsteam metabolic pathways generate key mediators which are essential co-substrates for post-translational modifications of histone proteins, which in turn, epigenetically regulate gene expression. Herein, we describe the role of sirtuins which are NAD+-dependent histone histone/protein deacetylases during the epigenetic regulation of autophagy, the production of ROS/RNS, acetyl-CoA, NAD+, and S-adenosine methionine (SAM), and illustrate the cross-talk between immunometabolism and epigenetics on macrophage activation. We highlight sirtuins as emerging therapeutic targets for modifying immunometabolism to alter macrophage phenotype and antimicrobial function.
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Affiliation(s)
- Kangling Zhang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, United States
| | - Mark L. Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, United States
| | - Ellie I. Cherryhomes
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, United States
| | - Vipul K. Singh
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, United States
| | - Abhishek Mishra
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, United States
| | - Blanca I. Restrepo
- University of Texas Health Houston, School of Public Health, Brownsville, TX, United States
| | - Arshad Khan
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, United States
| | - Chinnaswamy Jagannath
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, United States
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29
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Hicks KG, Cluntun AA, Schubert HL, Hackett SR, Berg JA, Leonard PG, Ajalla Aleixo MA, Zhou Y, Bott AJ, Salvatore SR, Chang F, Blevins A, Barta P, Tilley S, Leifer A, Guzman A, Arok A, Fogarty S, Winter JM, Ahn HC, Allen KN, Block S, Cardoso IA, Ding J, Dreveny I, Gasper WC, Ho Q, Matsuura A, Palladino MJ, Prajapati S, Sun P, Tittmann K, Tolan DR, Unterlass J, VanDemark AP, Vander Heiden MG, Webb BA, Yun CH, Zhao P, Wang B, Schopfer FJ, Hill CP, Nonato MC, Muller FL, Cox JE, Rutter J. Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase. Science 2023; 379:996-1003. [PMID: 36893255 PMCID: PMC10262665 DOI: 10.1126/science.abm3452] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/07/2023] [Indexed: 03/11/2023]
Abstract
Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS) to identify such interactions. Analysis of 33 enzymes from human carbohydrate metabolism identified 830 protein-metabolite interactions, including known regulators, substrates, and products as well as previously unreported interactions. We functionally validated a subset of interactions, including the isoform-specific inhibition of lactate dehydrogenase by long-chain acyl-coenzyme A. Cell treatment with fatty acids caused a loss of pyruvate-lactate interconversion dependent on lactate dehydrogenase isoform expression. These protein-metabolite interactions may contribute to the dynamic, tissue-specific metabolic flexibility that enables growth and survival in an ever-changing nutrient environment.
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Affiliation(s)
- Kevin G Hicks
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Ahmad A Cluntun
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Heidi L Schubert
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Jordan A Berg
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paul G Leonard
- Core for Biomolecular Structure and Function, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Institute for Applied Cancer Sciences, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mariana A Ajalla Aleixo
- Laboratório de Cristalografia de Proteinas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Youjia Zhou
- School of Computing, University of Utah, Salt Lake City, UT, USA
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA
| | - Alex J Bott
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Sonia R Salvatore
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Fei Chang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Aubrie Blevins
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paige Barta
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Samantha Tilley
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Aaron Leifer
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Andrea Guzman
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Ajak Arok
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Sarah Fogarty
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jacob M Winter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Hee-Chul Ahn
- Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, The Republic of Korea
| | - Karen N Allen
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Samuel Block
- The Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Iara A Cardoso
- Laboratório de Cristalografia de Proteinas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Ingrid Dreveny
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
| | | | - Quinn Ho
- Department of Biology, Boston University, Boston, MA, USA
| | - Atsushi Matsuura
- Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, The Republic of Korea
| | - Michael J Palladino
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sabin Prajapati
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Pengkai Sun
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Kai Tittmann
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dean R Tolan
- Department of Biology, Boston University, Boston, MA, USA
| | - Judith Unterlass
- Department of Oncology and Pathology, Karolinska Institute, Stockholm, Sweden
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew G Vander Heiden
- The Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bradley A Webb
- Department of Biochemistry, West Virginia University, Morgantown, WV, USA
| | - Cai-Hong Yun
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Pengkai Zhao
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Bei Wang
- School of Computing, University of Utah, Salt Lake City, UT, USA
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA
| | - Francisco J Schopfer
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, Pittsburgh, PA, USA
- Pittsburgh Liver Research Center, Pittsburgh, PA, USA
- Center for Metabolism and Mitochondrial Medicine, Pittsburgh, PA, USA
| | - Christopher P Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteinas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Florian L Muller
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James E Cox
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
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Tarasenko TN, Banerjee P, Gomez-Rodriguez J, Gildea D, Zhang S, Wolfsberg T, Jenkins LM, McGuire PJ. Pyruvate dehydrogenase complex integrates the metabolome and epigenome in memory T cell differentiation in vitro. RESEARCH SQUARE 2023:rs.3.rs-2464392. [PMID: 36789409 PMCID: PMC9928058 DOI: 10.21203/rs.3.rs-2464392/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Background Modulation of metabolic flux through pyruvate dehydrogenase complex (PDC) plays an important role in T cell activation and differentiation. PDC sits at the transition between glycolysis and the tricarboxylic acid cycle and is a major producer of acetyl-CoA, marking it as a potential metabolic and epigenetic node. Methods To understand the role of pyruvate dehydrogenase complex in T cell differentiation, we generated mice deficient in T cell pyruvate dehydrogenase E1A (Pdha) subunit using a CD4-cre recombinase-based strategy. To control for the contribution of exogenous metabolites in vivo, we conducted our T cell functional studies in vitro. T cells were differentiated into memory and effector T cells using standardized protocols. Cells were analyzed using stable isotopic tracing studies, metabolomics, RNAseq, ATACseq, ChIPseq and histone proteomics. Results Herein, we show that genetic ablation of PDC activity in T cells (TPdh-/-) leads to marked perturbations in glycolysis, the tricarboxylic acid cycle, and OXPHOS. Due to depressed OXPHOS, TPdh-/-T cells became dependent upon substrate level phosphorylation via glycolysis. Due to the block of PDC activity, histone acetylation was reduced, as were most other types of post translational modifications. Transcriptional and functional profiling revealed abnormal CD8+ memory T cell differentiation in vitro. Conclusions Collectively, our data indicate that PDC integrates the metabolome and epigenome in memory T cell differentiation. Targeting this metabolic and epigenetic node can have widespread ramifications on cellular function.
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Sowers ML, Tang H, Singh VK, Khan A, Mishra A, Restrepo BI, Jagannath C, Zhang K. Multi-OMICs analysis reveals metabolic and epigenetic changes associated with macrophage polarization. J Biol Chem 2022; 298:102418. [PMID: 36030823 PMCID: PMC9525912 DOI: 10.1016/j.jbc.2022.102418] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 12/04/2022] Open
Abstract
Macrophages (MФ) are an essential immune cell for defense and repair that travel to different tissues and adapt based on local stimuli. A critical factor that may govern their polarization is the crosstalk between metabolism and epigenetics. However, simultaneous measurements of metabolites, epigenetics, and proteins (phenotype) have been a major technical challenge. To address this, we have developed a novel triomics approach using mass spectrometry to comprehensively analyze metabolites, proteins, and histone modifications in a single sample. To demonstrate this technique, we investigated the metabolic-epigenetic-phenotype axis following polarization of human blood–derived monocytes into either ‘proinflammatory M1-’ or ‘anti-inflammatory M2-’ MФs. We report here a complex relationship between arginine, tryptophan, glucose, and the citric acid cycle metabolism, protein and histone post-translational modifications, and human macrophage polarization that was previously not described. Surprisingly, M1-MФs had globally reduced histone acetylation levels but high levels of acetylated amino acids. This suggests acetyl-CoA was diverted, in part, toward acetylated amino acids. Consistent with this, stable isotope tracing of glucose revealed reduced usage of acetyl-CoA for histone acetylation in M1-MФs. Furthermore, isotope tracing also revealed MФs uncoupled glycolysis from the tricarboxylic acid cycle, as evidenced by poor isotope enrichment of succinate. M2-MФs had high levels of kynurenine and serotonin, which are reported to have immune-suppressive effects. Kynurenine is upstream of de novo NAD+ metabolism that is a necessary cofactor for Sirtuin-type histone deacetylases. Taken together, we demonstrate a complex interplay between metabolism and epigenetics that may ultimately influence cell phenotype.
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Affiliation(s)
- Mark L Sowers
- Dept. of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX
| | - Hui Tang
- Dept. of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX
| | - Vipul K Singh
- Dept. of Pathology and Genomic Medicine, Center for Molecular and Translational Human Infectious Diseases Research Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX
| | - Arshad Khan
- Dept. of Pathology and Genomic Medicine, Center for Molecular and Translational Human Infectious Diseases Research Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX
| | - Abhishek Mishra
- Dept. of Pathology and Genomic Medicine, Center for Molecular and Translational Human Infectious Diseases Research Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX
| | | | - Chinnaswamy Jagannath
- Dept. of Pathology and Genomic Medicine, Center for Molecular and Translational Human Infectious Diseases Research Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX.
| | - Kangling Zhang
- Dept. of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX.
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32
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Assante G, Chandrasekaran S, Ng S, Tourna A, Chung CH, Isse KA, Banks JL, Soffientini U, Filippi C, Dhawan A, Liu M, Rozen SG, Hoare M, Campbell P, Ballard JWO, Turner N, Morris MJ, Chokshi S, Youngson NA. Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease. Genome Med 2022; 14:67. [PMID: 35739588 PMCID: PMC9219160 DOI: 10.1186/s13073-022-01071-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 06/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The incidence of non-alcoholic fatty liver disease (NAFLD)-associated hepatocellular carcinoma (HCC) is increasing worldwide, but the steps in precancerous hepatocytes which lead to HCC driver mutations are not well understood. Here we provide evidence that metabolically driven histone hyperacetylation in steatotic hepatocytes can increase DNA damage to initiate carcinogenesis. METHODS Global epigenetic state was assessed in liver samples from high-fat diet or high-fructose diet rodent models, as well as in cultured immortalized human hepatocytes (IHH cells). The mechanisms linking steatosis, histone acetylation and DNA damage were investigated by computational metabolic modelling as well as through manipulation of IHH cells with metabolic and epigenetic inhibitors. Chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) and transcriptome (RNA-seq) analyses were performed on IHH cells. Mutation locations and patterns were compared between the IHH cell model and genome sequence data from preneoplastic fatty liver samples from patients with alcohol-related liver disease and NAFLD. RESULTS Genome-wide histone acetylation was increased in steatotic livers of rodents fed high-fructose or high-fat diet. In vitro, steatosis relaxed chromatin and increased DNA damage marker γH2AX, which was reversed by inhibiting acetyl-CoA production. Steatosis-associated acetylation and γH2AX were enriched at gene clusters in telomere-proximal regions which contained HCC tumour suppressors in hepatocytes and human fatty livers. Regions of metabolically driven epigenetic change also had increased levels of DNA mutation in non-cancerous tissue from NAFLD and alcohol-related liver disease patients. Finally, genome-scale network modelling indicated that redox balance could be a key contributor to this mechanism. CONCLUSIONS Abnormal histone hyperacetylation facilitates DNA damage in steatotic hepatocytes and is a potential initiating event in hepatocellular carcinogenesis.
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Affiliation(s)
- Gabriella Assante
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Sriram Chandrasekaran
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Center for Bioinformatics and Computational Medicine, Ann Arbor, MI, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Stanley Ng
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Aikaterini Tourna
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Carolina H Chung
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kowsar A Isse
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Jasmine L Banks
- UNSW Sydney, Sydney, Australia
- Cellular Bioenergetics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Ugo Soffientini
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Celine Filippi
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Anil Dhawan
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Mo Liu
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Steven G Rozen
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Matthew Hoare
- CRUK Cambridge Institute, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | | | - J William O Ballard
- Department of Ecology, Environment and Evolution, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia
| | - Nigel Turner
- UNSW Sydney, Sydney, Australia
- Cellular Bioenergetics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | | | - Shilpa Chokshi
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Neil A Youngson
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK.
- King's College London, Faculty of Life Sciences and Medicine, London, UK.
- UNSW Sydney, Sydney, Australia.
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Barrero MJ, Cejas P, Long HW, Ramirez de Molina A. Nutritional Epigenetics in Cancer. Adv Nutr 2022; 13:1748-1761. [PMID: 35421212 PMCID: PMC9526851 DOI: 10.1093/advances/nmac039] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/11/2022] [Accepted: 04/09/2022] [Indexed: 01/28/2023] Open
Abstract
Alterations in the epigenome are well known to affect cancer development and progression. Epigenetics is highly influenced by the environment, including diet, which is a source of metabolic substrates that influence the synthesis of cofactors or substrates for chromatin and RNA modifying enzymes. In addition, plants are a common source of bioactives that can directly modify the activity of these enzymes. Here, we review and discuss the impact of diet on epigenetic mechanisms, including chromatin and RNA regulation, and its potential implications for cancer prevention and treatment.
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Affiliation(s)
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA,Translational Oncology Laboratory, Hospital La Paz Institute for Health Research, Madrid, Spain
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
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Keating ST, El-Osta A. Metaboloepigenetics in cancer, immunity and cardiovascular disease. Cardiovasc Res 2022; 119:357-370. [PMID: 35389425 PMCID: PMC10064843 DOI: 10.1093/cvr/cvac058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/12/2022] [Accepted: 02/02/2022] [Indexed: 11/14/2022] Open
Abstract
The influence of cellular metabolism on epigenetic pathways are well documented but misunderstood. Scientists have long known of the metabolic impact on epigenetic determinants. More often than not, that title role for DNA methylation was portrayed by the metabolite SAM or S-adenosylmethionine. Technically speaking there are many other metabolites that drive epigenetic processes that instruct seemingly distant - yet highly connect pathways - and none more so than our understanding of the cancer epigenome. Recent studies have shown that available energy link the extracellular environment to influence cellular responses. This focused review examines the recent interest in epigenomics and casts cancer, metabolism and immunity in unfamiliar roles - cooperating. There are not only language lessons from cancer research, we have come round to appreciate that reaching into areas previously thought of as too distinct are also object lessons in understanding health and disease. The Warburg effect is one such signature of how glycolysis influences metabolic shift during oncogenesis. That shift in metabolism - now recognised as central to proliferation in cancer biology - influence core enzymes that not only control gene expression but are also central to replication, condensation and the repair of nucleic acid. These nuclear processes rely on metabolism and with glucose at center stage the role of respiration and oxidative metabolism are now synonymous with the mitochondria as the powerhouses of metaboloepigenetics. The emerging evidence for metaboloepigenetics in trained innate immunity has revealed recognisable signalling pathways with antecedent extracellular stimulation. With due consideration to immunometabolism we discuss the striking signalling similarities influencing these core pathways. The immunometabolic-epigenetic axis in cardiovascular disease has deeply etched connections with inflammation and we examine the chromatin template as a carrier of epigenetic indices that determine the expression of genes influencing atherosclerosis and vascular complications of diabetes.
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Affiliation(s)
- Samuel T Keating
- Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Assam El-Osta
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia.,Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia.,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR.,Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, 3/F Lui Che Woo Clinical Sciences Building, 30-32 Ngan Shing Street, Sha Tin, Hong Kong SAR.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR.,University College Copenhagen, Faculty of Health, Department of Technology, Biomedical Laboratory Science, Copenhagen, Denmark
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35
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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: 292] [Impact Index Per Article: 146.0] [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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36
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Wang X, Wang Z, Huang R, Lu Z, Chen X, Huang D. UPP1 Promotes Lung Adenocarcinoma Progression through Epigenetic Regulation of Glycolysis. Aging Dis 2022; 13:1488-1503. [PMID: 36186123 PMCID: PMC9466982 DOI: 10.14336/ad.2022.0218] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/18/2022] [Indexed: 11/01/2022] Open
Affiliation(s)
- Xuan Wang
- Department of Thoracic Surgery Huashan Hospital & Cancer Metastasis Institute, Fudan University, Shanghai 200040, China.
- Correspondence should be addressed to: Dr. Dayu Huang (), Dr. Xiaofeng Chen (); Dr. Xuan Wang ().Department of Thoracic Surgery Huashan Hospital & Cancer Metastasis Institute, Fudan University, Shanghai 200040, China
| | - Zheng Wang
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Renhong Huang
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhouyi Lu
- Department of Thoracic Surgery Huashan Hospital & Cancer Metastasis Institute, Fudan University, Shanghai 200040, China.
| | - Xiaofeng Chen
- Department of Thoracic Surgery Huashan Hospital & Cancer Metastasis Institute, Fudan University, Shanghai 200040, China.
- Correspondence should be addressed to: Dr. Dayu Huang (), Dr. Xiaofeng Chen (); Dr. Xuan Wang ().Department of Thoracic Surgery Huashan Hospital & Cancer Metastasis Institute, Fudan University, Shanghai 200040, China
| | - Dayu Huang
- Department of Thoracic Surgery Huashan Hospital & Cancer Metastasis Institute, Fudan University, Shanghai 200040, China.
- Correspondence should be addressed to: Dr. Dayu Huang (), Dr. Xiaofeng Chen (); Dr. Xuan Wang ().Department of Thoracic Surgery Huashan Hospital & Cancer Metastasis Institute, Fudan University, Shanghai 200040, China
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37
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Morin AL, Win PW, Lin AZ, Castellani CA. Mitochondrial genomic integrity and the nuclear epigenome in health and disease. Front Endocrinol (Lausanne) 2022; 13:1059085. [PMID: 36419771 PMCID: PMC9678080 DOI: 10.3389/fendo.2022.1059085] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022] Open
Abstract
Bidirectional crosstalk between the nuclear and mitochondrial genomes is essential for proper cell functioning. Mitochondrial DNA copy number (mtDNA-CN) and heteroplasmy influence mitochondrial function, which can influence the nuclear genome and contribute to health and disease. Evidence shows that mtDNA-CN and heteroplasmic variation are associated with aging, complex disease, and all-cause mortality. Further, the nuclear epigenome may mediate the effects of mtDNA variation on disease. In this way, mitochondria act as an environmental biosensor translating vital information about the state of the cell to the nuclear genome. Cellular communication between mtDNA variation and the nuclear epigenome can be achieved by modification of metabolites and intermediates of the citric acid cycle and oxidative phosphorylation. These essential molecules (e.g. ATP, acetyl-CoA, ɑ-ketoglutarate and S-adenosylmethionine) act as substrates and cofactors for enzymes involved in epigenetic modifications. The role of mitochondria as an environmental biosensor is emerging as a critical modifier of disease states. Uncovering the mechanisms of these dynamics in disease processes is expected to lead to earlier and improved treatment for a variety of diseases. However, the influence of mtDNA-CN and heteroplasmy variation on mitochondrially-derived epigenome-modifying metabolites and intermediates is poorly understood. This perspective will focus on the relationship between mtDNA-CN, heteroplasmy, and epigenome modifying cofactors and substrates, and the influence of their dynamics on the nuclear epigenome in health and disease.
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Affiliation(s)
- Amanda L. Morin
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Phyo W. Win
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Angela Z. Lin
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Christina A. Castellani
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- *Correspondence: Christina A. Castellani,
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Mondal P, Tiwary N, Sengupta A, Dhang S, Roy S, Das C. Epigenetic Reprogramming of the Glucose Metabolic Pathways by the Chromatin Effectors During Cancer. Subcell Biochem 2022; 100:269-336. [PMID: 36301498 DOI: 10.1007/978-3-031-07634-3_9] [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] [Indexed: 06/16/2023]
Abstract
Glucose metabolism plays a vital role in regulating cellular homeostasis as it acts as the central axis for energy metabolism, alteration in which may lead to serious consequences like metabolic disorders to life-threatening diseases like cancer. Malignant cells, on the other hand, help in tumor progression through abrupt cell proliferation by adapting to the changed metabolic milieu. Metabolic intermediates also vary from normal cells to cancerous ones to help the tumor manifestation. However, metabolic reprogramming is an important phenomenon of cells through which they try to maintain the balance between normal and carcinogenic outcomes. In this process, transcription factors and chromatin modifiers play an essential role to modify the chromatin landscape of important genes related directly or indirectly to metabolism. Our chapter surmises the importance of glucose metabolism and the role of metabolic intermediates in the cell. Also, we summarize the influence of histone effectors in reprogramming the cancer cell metabolism. An interesting aspect of this chapter includes the detailed methods to detect the aberrant metabolic flux, which can be instrumental for the therapeutic regimen of cancer.
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Affiliation(s)
- Payel Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhaba National Institute, Mumbai, India
| | - Niharika Tiwary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Amrita Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Sinjini Dhang
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Siddhartha Roy
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.
- Homi Bhaba National Institute, Mumbai, India.
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Das D, Karthik N, Taneja R. Epigenetic Small-Molecule Modulators Targeting Metabolic Pathways in Cancer. Subcell Biochem 2022; 100:523-555. [PMID: 36301505 DOI: 10.1007/978-3-031-07634-3_16] [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] [Indexed: 06/16/2023]
Abstract
Metabolic deregulation is a key factor in cancer progression. Epigenetic changes and metabolic rewiring are intertwined in cancer. Deregulated epigenetic modifiers cause metabolic aberrations by targeting the expression of metabolic enzymes. Conversely, metabolites and cofactors affect the expression and activity of epigenetic regulators. Small molecules are promising therapeutic approaches to target the epigenetic-metabolomic crosstalk in cancer. Here, we focus on the interplay between metabolic rewiring and epigenetic landscape in the context of tumourigenesis and highlight recent advances in the use of small-molecule drug targets for therapy.
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Affiliation(s)
- Dipanwita Das
- Department of Physiology and Healthy Longevity Translational Research Program Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nandini Karthik
- Department of Physiology and Healthy Longevity Translational Research Program Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Reshma Taneja
- Department of Physiology and Healthy Longevity Translational Research Program Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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40
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Wang G, Han JJ. Connections between metabolism and epigenetic modifications in cancer. MEDICAL REVIEW (BERLIN, GERMANY) 2021; 1:199-221. [PMID: 37724300 PMCID: PMC10388788 DOI: 10.1515/mr-2021-0015] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/19/2021] [Indexed: 09/20/2023]
Abstract
How cells sense and respond to environmental changes is still a key question. It has been identified that cellular metabolism is an important modifier of various epigenetic modifications, such as DNA methylation, histone methylation and acetylation and RNA N6-methyladenosine (m6A) methylation. This closely links the environmental nutrient availability to the maintenance of chromatin structure and gene expression, and is crucial to regulate cellular homeostasis, cell growth and differentiation. Cancer metabolic reprogramming and epigenetic alterations are widely observed, and facilitate cancer development and progression. In cancer cells, oncogenic signaling-driven metabolic reprogramming modifies the epigenetic landscape via changes in the key metabolite levels. In this review, we briefly summarized the current evidence that the abundance of key metabolites, such as S-adenosyl methionine (SAM), acetyl-CoA, α-ketoglutarate (α-KG), 2-hydroxyglutarate (2-HG), uridine diphospho-N-acetylglucosamine (UDP-GlcNAc) and lactate, affected by metabolic reprogramming plays an important role in dynamically regulating epigenetic modifications in cancer. An improved understanding of the roles of metabolic reprogramming in epigenetic regulation can contribute to uncover the underlying mechanisms of metabolic reprogramming in cancer development and identify the potential targets for cancer therapies.
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Affiliation(s)
- Guangchao Wang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Jingdong J. Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
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41
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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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42
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Verdikt R, Allard P. Metabolo-epigenetics: the interplay of metabolism and epigenetics during early germ cells development. Biol Reprod 2021; 105:616-624. [PMID: 34132770 PMCID: PMC8444669 DOI: 10.1093/biolre/ioab118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/26/2022] Open
Abstract
Metabolites control epigenetic mechanisms, and conversly, cell metabolism is regulated at the epigenetic level in response to changes in the cellular environment. In recent years, this metabolo-epigenetic control of gene expression has been implicated in the regulation of multiple stages of embryonic development. The developmental potency of stem cells and their embryonic counterparts is directly determined by metabolic rewiring. Here, we review the current knowledge on the interplay between epigenetics and metabolism in the specific context of early germ cell development. We explore the implications of metabolic rewiring in primordial germ cells in light of their epigenetic remodeling during cell fate determination. Finally, we discuss the relevance of concerted metabolic and epigenetic regulation of primordial germ cells in the context of mammalian transgenerational epigenetic inheritance.
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Affiliation(s)
- Roxane Verdikt
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Patrick Allard
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
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43
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Lu J, Liang Y, Meng H, Zhang A, Zhao J, Zhang C. Metabolic Controls on Epigenetic Reprogramming in Regulatory T Cells. Front Immunol 2021; 12:728783. [PMID: 34421930 PMCID: PMC8374078 DOI: 10.3389/fimmu.2021.728783] [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: 06/22/2021] [Accepted: 07/23/2021] [Indexed: 01/20/2023] Open
Abstract
Forkhead box protein 3 (Foxp3+)-expressing regulatory T (Treg) cells are a unique CD4+T cell subset that suppresses excessive immune responses. The epigenetic plasticity and metabolic traits of Treg cells are crucial for the acquisition of their phenotypic and functional characteristics. Therefore, alterations to the epigenetics and metabolism affect Treg cell development and function. Recent evidence reveals that altering the metabolic pathways and generation of metabolites can regulate the epigenetics of Treg cells. Specifically, some intermediates of cell metabolism can directly act as substrates or cofactors of epigenetic-modifying enzymes. Here, we describe the metabolic and epigenetic features during Treg cell development, and discuss how metabolites can contribute to epigenetic alterations of Treg cells, which affects Treg cell activation, differentiation, and function.
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Affiliation(s)
- Jingli Lu
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou, China.,Zhengzhou Key Laboratory of Clinical Mass Spectrometry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yan Liang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou, China.,Zhengzhou Key Laboratory of Clinical Mass Spectrometry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haiyang Meng
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou, China.,Zhengzhou Key Laboratory of Clinical Mass Spectrometry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ailing Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou, China.,Zhengzhou Key Laboratory of Clinical Mass Spectrometry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junjie Zhao
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou, China.,Zhengzhou Key Laboratory of Clinical Mass Spectrometry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chengliang Zhang
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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44
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Meng X, Baine JM, Yan T, Wang S. Comprehensive Analysis of Lysine Lactylation in Rice ( Oryza sativa) Grains. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8287-8297. [PMID: 34264677 DOI: 10.1021/acs.jafc.1c00760] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein lysine lactylation is a new post-translational modification (PTM) prevalently found in fungi and mammalian cells that directly stimulates gene transcription and regulates the glycolytic flux. However, lysine lactylation sites and regulations remain largely unexplored, especially in cereal crops. Herein, we report the first global lactylome profile in rice, which effectively identified 638 lysine lactylation sites across 342 proteins in rice grains. Functional annotations demonstrated that lysine lactylation was enriched in proteins associated with central carbon metabolism and protein biosynthesis. We also observed that proteins serving as nutrition reservoirs in rice grains were frequently targeted by lactylation. Homology analyses indicated that lactylation was conserved on both histone and nonhistone proteins across plants, human cells, and fungi. In addition to lactylation, additional types of acylations could co-occur in many proteins at identical lysine residues, indicating potential cross-talks between these modifications. Our study provided a comprehensive profile of protein lysine lactylation in cereal crop grains.
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Affiliation(s)
- Xiaoxi Meng
- Department of Horticultural Science, University of Minnesota, Saint Paul, Minnesota 55108, United States
| | - Jonathan M Baine
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Tingcai Yan
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Shu Wang
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
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45
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Neural crest metabolism: At the crossroads of development and disease. Dev Biol 2021; 475:245-255. [PMID: 33548210 PMCID: PMC10171235 DOI: 10.1016/j.ydbio.2021.01.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/16/2021] [Accepted: 01/29/2021] [Indexed: 02/06/2023]
Abstract
The neural crest is a migratory stem cell population that contributes to various tissues and organs during vertebrate embryonic development. These cells possess remarkable developmental plasticity and give rise to many different cell types, including chondrocytes, osteocytes, peripheral neurons, glia, melanocytes, and smooth muscle cells. Although the genetic mechanisms underlying neural crest development have been extensively studied, many facets of this process remain unexplored. One key aspect of cellular physiology that has gained prominence in the context of embryonic development is metabolic regulation. Recent discoveries in neural crest biology suggest that metabolic regulation may play a central role in the formation, migration, and differentiation of these cells. This possibility is further supported by clinical studies that have demonstrated a high prevalence of neural crest anomalies in babies with congenital metabolic disorders. Here, we examine why neural crest development is prone to metabolic disruption and discuss how carbon metabolism regulates developmental processes like epithelial-to-mesenchymal transition (EMT) and cell migration. Finally, we explore how understanding neural crest metabolism may inform upon the etiology of several congenital birth defects.
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46
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Gregg C. Starvation and Climate Change—How to Constrain Cancer Cell Epigenetic Diversity and Adaptability to Enhance Treatment Efficacy. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.693781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Advanced metastatic cancer is currently not curable and the major barrier to eliminating the disease in patients is the resistance of subpopulations of tumor cells to drug treatments. These resistant subpopulations can arise stochastically among the billions of tumor cells in a patient or emerge over time during therapy due to adaptive mechanisms and the selective pressures of drug therapies. Epigenetic mechanisms play important roles in tumor cell diversity and adaptability, and are regulated by metabolic pathways. Here, I discuss knowledge from ecology, evolution, infectious disease, species extinction, metabolism and epigenetics to synthesize a roadmap to a clinically feasible approach to help homogenize tumor cells and, in combination with drug treatments, drive their extinction. Specifically, cycles of starvation and hyperthermia could help synchronize tumor cells and constrain epigenetic diversity and adaptability by limiting substrates and impairing the activity of chromatin modifying enzymes. Hyperthermia could also help prevent cancer cells from entering dangerous hibernation-like states. I propose steps to a treatment paradigm to help drive cancer extinction that builds on the successes of fasting, hyperthermia and immunotherapy and is achievable in patients. Finally, I highlight the many unknowns, opportunities for discovery and that stochastic gene and allele level epigenetic mechanisms pose a major barrier to cancer extinction that warrants deeper investigation.
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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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48
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A latent subset of human hematopoietic stem cells resists regenerative stress to preserve stemness. Nat Immunol 2021; 22:723-734. [PMID: 33958784 DOI: 10.1038/s41590-021-00925-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/25/2021] [Indexed: 11/09/2022]
Abstract
Continuous supply of immune cells throughout life relies on the delicate balance in the hematopoietic stem cell (HSC) pool between long-term maintenance and meeting the demands of both normal blood production and unexpected stress conditions. Here we identified distinct subsets of human long-term (LT)-HSCs that responded differently to regeneration-mediated stress: an immune checkpoint ligand CD112lo subset that exhibited a transient engraftment restraint (termed latency) before contributing to hematopoietic reconstitution and a primed CD112hi subset that responded rapidly. This functional heterogeneity and CD112 expression are regulated by INKA1 through direct interaction with PAK4 and SIRT1, inducing epigenetic changes and defining an alternative state of LT-HSC quiescence that serves to preserve self-renewal and regenerative capacity upon regeneration-mediated stress. Collectively, our data uncovered the molecular intricacies underlying HSC heterogeneity and self-renewal regulation and point to latency as an orchestrated physiological response that balances blood cell demands with preserving a stem cell reservoir.
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49
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Felix JB, Cox AR, Hartig SM. Acetyl-CoA and Metabolite Fluxes Regulate White Adipose Tissue Expansion. Trends Endocrinol Metab 2021; 32:320-332. [PMID: 33712368 PMCID: PMC8035226 DOI: 10.1016/j.tem.2021.02.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 12/29/2022]
Abstract
White adipose tissue (WAT) depends on coordinated regulation of transcriptional and metabolic pathways to respond to whole-body energy demands. We highlight metabolites that contribute to biosynthetic reactions for WAT expansion. Recent studies have precisely defined how byproducts of carbohydrate and lipid metabolism affect physiological and endocrine functions in adipocytes. We emphasize the critical emerging roles of short-chain fatty acids (SCFAs) and tricarboxylic acid (TCA) cycle metabolites that connect lipogenesis to WAT energy balance and endocrine functions. These insights address how adipocytes use small molecules generated from central carbon metabolism to measure responses to nutritional stress.
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Affiliation(s)
- Jessica B Felix
- Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Aaron R Cox
- Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Sean M Hartig
- Division of Diabetes, Endocrinology, and Metabolism, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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50
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Kelsey MMG. Reconsidering LINE-1's role in cancer: does LINE-1 function as a reporter detecting early cancer-associated epigenetic signatures? EVOLUTION MEDICINE AND PUBLIC HEALTH 2021; 9:78-82. [PMID: 33717489 PMCID: PMC7937435 DOI: 10.1093/emph/eoab004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/17/2021] [Indexed: 11/24/2022]
Abstract
Long interspersed nuclear element-1 (LINE-1 or L1) is the only autonomously active retrotransposon in humans. While L1 has been implicated in several pathologies and the aging process, I present a model which challenges an understanding of L1 as predominantly antagonistic to human health. I hypothesize that L1 serves as a reporter in an early cancer alert system: a tripwire strung throughout the genome poised to trigger p53 and a type I interferon (IFN-1) response when the epigenetic landscape portends cancer. Cell proliferation and a shift to aerobic glycolysis cause dramatic changes in the epigenome which are permissive to L1’s escape from suppression. L1 has several properties which make it particularly apt to fulfill this hypothesized sentinel function. Being present in many copies spread throughout the genome allows it to monitor many regions for epigenetic instability and renders it robust to deactivation by mutation. This proposed cancer alert system would alter the cancer cell fitness landscape discouraging the use of growth-favoring aerobic glycolysis by threatening the activation of tumor-suppressive mechanisms. It also imposes costs on a strategy of non-specific global transcriptional derepression aimed at activating oncogenes. Erroneous activations of this system are predicted to increase the rate of aging, suggesting this represents a case of antagonistic pleiotropy trading prolonged youth for cancer prevention. More research is needed to assess this model. Lay summary: During carcinogenesis the epigenome is remodeled by the Warburg effect and cellular proliferation. These processes globally relax chromatin. This epigenetic environment is permissive to the retrotransposon long interspersed nuclear element-1’s (LINE-1 or L1) escape from suppression. I hypothesize and present evidence for the notion that L1 has been co-opted to serve as a reporter in an early cancer alert system, poised to trigger tumor suppressive mechanisms when the epigenetic landscape portends cancer. This hypothesis describes a potentially major means by which transformation is thwarted early on.
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Affiliation(s)
- Maxfield M G Kelsey
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Corresponding author. Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA. Tel: 1-818-397-5181; E-mail:
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