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Ryan EM, Norinskiy MA, Bracken AK, Lueders EE, Chen X, Fu Q, Anderson ET, Zhang S, Abbasov ME. Activity-Based Acylome Profiling with N-(Cyanomethyl)- N-(phenylsulfonyl)amides for Targeted Lysine Acylation and Post-Translational Control of Protein Function in Cells. J Am Chem Soc 2024; 146:27622-27643. [PMID: 39348182 DOI: 10.1021/jacs.4c09073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Lysine acylations are ubiquitous and structurally diverse post-translational modifications that vastly expand the functional heterogeneity of the human proteome. Hence, the targeted acylation of lysine residues has emerged as a strategic approach to exert biomimetic control over the protein function. However, existing strategies for targeted lysine acylation in cells often rely on genetic intervention, recruitment of endogenous acylation machinery, or nonspecific acylating agents and lack methods to quantify the magnitude of specific acylations on a global level. In this study, we develop activity-based acylome profiling (ABAP), a chemoproteomic strategy that exploits elaborate N-(cyanomethyl)-N-(phenylsulfonyl)amides and lysine-centric probes for site-specific introduction and proteome-wide mapping of posttranslational lysine acylations in human cells. Harnessing this framework, we quantify various artificial acylations and rediscover numerous endogenous lysine acylations. We validate site-specific acetylation of target lysines and establish a structure-activity relationship for N-(cyanomethyl)-N-(phenylsulfonyl)amides in proteins from diverse structural and functional classes. We identify paralog-selective chemical probes that acetylate conserved lysines within interferon-stimulated antiviral RNA-binding proteins, generating de novo proteoforms with obstructed RNA interactions. We further demonstrate that targeted acetylation of a key enzyme in retinoid metabolism engenders a proteoform with a conformational change in the protein structure, leading to a gain-of-function phenotype and reduced drug potency. These findings underscore the versatility of our strategy in biomimetic control over protein function through targeted delivery and global profiling of endogenous and artificial lysine acylations, potentially advancing therapeutic modalities and our understanding of biological processes orchestrated by these post-translational modifications.
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Affiliation(s)
- Elizabeth M Ryan
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Michael A Norinskiy
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Amy K Bracken
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Emma E Lueders
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Xueer Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Qin Fu
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York 14853, United States
| | - Elizabeth T Anderson
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York 14853, United States
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York 14853, United States
| | - Mikail E Abbasov
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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Chen L, Huang L, Gu Y, Li C, Sun P, Xiang Y. Novel post-translational modifications of protein by metabolites with immune responses and immune-related molecules in cancer immunotherapy. Int J Biol Macromol 2024; 277:133883. [PMID: 39033895 DOI: 10.1016/j.ijbiomac.2024.133883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 06/30/2024] [Accepted: 07/13/2024] [Indexed: 07/23/2024]
Abstract
Tumour immunotherapy is an effective and essential treatment for cancer. However, the heterogeneity of tumours and the complex and changeable tumour immune microenvironment (TME) creates many uncertainties in the clinical application of immunotherapy, such as different responses to tumour immunotherapy and significant differences in individual efficacy. It makes anti-tumour immunotherapy face many challenges. Immunometabolism is a critical determinant of immune cell response to specific immune effector molecules, significantly affecting the effects of tumour immunotherapy. It is attributed mainly to the fact that metabolites can regulate the function of immune cells and immune-related molecules through the protein post-translational modifications (PTMs) pathway. This study systematically summarizes a variety of novel protein PTMs including acetylation, propionylation, butyrylation, succinylation, crotonylation, malonylation, glutarylation, 2-hydroxyisobutyrylation, β-hydroxybutyrylation, benzoylation, lactylation and isonicotinylation in the field of tumour immune regulation and immunotherapy. In particular, we elaborate on how different PTMs in the TME can affect the function of immune cells and lead to immune evasion in cancer. Lastly, we highlight the potential treatment with the combined application of target-inhibited protein modification and immune checkpoint inhibitors (ICIs) for improved immunotherapeutic outcomes.
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Affiliation(s)
- Lihua Chen
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China; National Clinical Research Center for Obstetric & Gynecologic Diseases, PR China
| | - Lixiang Huang
- Laboratory of Gynecologic Oncology, Department of Gynecology, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou 350001, Fujian, PR China; Fujian Key Laboratory of Women and Children's Critical Diseases Research, Fuzhou 350001, Fujian, PR China
| | - Yu Gu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China; National Clinical Research Center for Obstetric & Gynecologic Diseases, PR China
| | - Chen Li
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China; National Clinical Research Center for Obstetric & Gynecologic Diseases, PR China
| | - Pengming Sun
- Laboratory of Gynecologic Oncology, Department of Gynecology, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou 350001, Fujian, PR China; Fujian Key Laboratory of Women and Children's Critical Diseases Research, Fuzhou 350001, Fujian, PR China.
| | - Yang Xiang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, PR China; National Clinical Research Center for Obstetric & Gynecologic Diseases, PR China.
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Chen N, Luo J, Zhou T, Shou Y, Du C, Song G, Xu L, Zhao K, Jin Y, Li C, Yu D. Lysine β-hydroxybutyrylation promotes lipid accumulation in alcoholic liver disease. Biochem Pharmacol 2024; 228:115936. [PMID: 38012969 DOI: 10.1016/j.bcp.2023.115936] [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: 09/14/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
Continuous (chronic or sub-chronic) alcohol consumption induces a metabolic byproduct known as ketone bodies, and the accumulation of ketones leads to a life-threatening syndrome called alcoholic ketoacidosis. However, the mechanism underlining the physiological effects of ketone accumulation in alcoholic liver disease (ALD) is still in its infancy. Here, we discovered that mitochondrial acetyl-CoA accumulation was diverted into the ketogenesis pathway in ethanol-fed mice and ethanol-exposed hepatocytes. Unexpectedly, global protein lysine β-hydroxybutyrylation (Kbhb) was induced in response to increased ketogenesis-derived β-hydroxybutyrate (BHB) levels both in hepatocytes and in livers of mice. Focusing on the solute carrier family (SLCs), we found that SLC25A5 presented obvious Kbhb at lysine residues 147 and 166. Kbhb modifications at these two lysine residues stabilized SLC25A5 expression by blocking ubiquitin-proteasome pathway. Subsequent mutation analysis revealed that Kbhb of SLC25A5 at K147 and K166 had site-specific regulatory roles by increasing peroxisome proliferator activated receptor gamma (PPARγ) expression, which further promoting lipogenesis. Additionally, 3-hydroxy-3-methylglutaryl-coenzyme A synthase 2 (HMGCS2), a rate-limiting enzyme for BHB production, was profoundly induced by ethanol exposure, and knockout of Hmgcs2 with CRISPR/Cas9 attenuated SLC25A5 Kbhb. Together, our study demonstrated a widespread Kbhb landscape under ethanol exposure and clarified a physiological effect of Kbhb modification on liver lipid accumulation.
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Affiliation(s)
- Ningning Chen
- School of Public Health, Qingdao University, Qingdao, China
| | - Jiao Luo
- School of Public Health, Qingdao University, Qingdao, China
| | - Tao Zhou
- School of Public Health, Qingdao University, Qingdao, China
| | - Yingqing Shou
- School of Public Health, Qingdao University, Qingdao, China
| | - Chenlong Du
- School of Public Health, Qingdao University, Qingdao, China
| | - Ge Song
- School of Public Health, Qingdao University, Qingdao, China
| | - Lin Xu
- School of Public Health, Qingdao University, Qingdao, China
| | - Kunming Zhao
- School of Public Health, Qingdao University, Qingdao, China
| | - Yuan Jin
- School of Public Health, Qingdao University, Qingdao, China
| | - Chuanhai Li
- School of Public Health, Qingdao University, Qingdao, China
| | - Dianke Yu
- School of Public Health, Qingdao University, Qingdao, China.
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Li Z, Li J, Li F, Han L, Sui C, Zhou L, Zhang D, Fu Y, Du R, Kou J, Dionigi G, Sun H, Liang N. Potential functions and mechanisms of lysine crotonylation modification (Kcr) in tumorigenesis and lymphatic metastasis of papillary thyroid cancer (PTC). J Transl Med 2024; 22:874. [PMID: 39342359 PMCID: PMC11439252 DOI: 10.1186/s12967-024-05651-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 09/16/2024] [Indexed: 10/01/2024] Open
Abstract
OBJECTIVES To examine the putative functions and mechanisms of lysine crotonylation (Kcr) during the development and progression of papillary thyroid cancer (PTC). METHODS Samples of thyroid cancer tissues were collected and subjected to liquid chromatography-tandem mass spectrometry. Crotonylated differentially expressed proteins (DEPs) and differentially expressed Kcr sites (DEKSs) were analyzed by Motif, dynamic expression model analysis (Mfuzz), subcellular localization, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation, Go Ontology (GO) annotation, and protein-protein interaction analysis (PPI). Validation was performed by immunohistochemistry (IHC). RESULTS A total of 262 crotonylated DEPs and 702 DEKSs were quantitated. First, for the tumor/normal comparison, a dynamic expression model analysis (Mfuzz) of the DEKSs revealed that clusters 1, 3, and 4 increased with the progression of thyroid cancer; however, cluster 6 showed a dramatic increase during the transition from N0-tumor to N1-tumor. Furthermore, based on GO annotation, KEGG, and PPI, the crotonylated DEPs were primarily enriched in the PI3K-Akt signaling pathway, Cell cycle, and Hippo signaling pathway. Of note, crosstalk between the proteome and Kcr proteome suggested a differential changing trend, which was enriched in Thyroid hormone synthesis, Pyruvate metabolism, TCA cycle, Cell cycle, and Apoptosis pathways. Similarly, for the LNM comparison group, the DEKSs and related DEPs were primarily enriched in Hydrogen peroxide catabolic process and Tight junction pathway. Finally, according to The Cancer Genome Atlas Program (TCGA) database, the differential expression of Kcr DEPs were associated with the prognosis of thyroid cancer, indicating the prognostic significance of these proteins. Moreover, based on the clinical validation of 47 additional samples, Kcr was highly expressed in thyroid tumor tissues compared with normal tissue (t = 9.792, P < 0.001). In addition, a positive correlation was observed between Kcr and N-cadherin (r = 0.5710, P = 0.0015). Moreover, N-cadherin expression was higher in the relatively high Kcr expression group (χ2 = 18.966, P < 0.001). CONCLUSIONS Higher Kcr expression was correlated with thyroid tumorigenesis and lymphatic metastasis, which may regulate thyroid cancer progression by Pyruvate metabolism, TCA cycle, Cell cycle, and other pathways.
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Affiliation(s)
- Zhaokun Li
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine On Differentiated Thyroid Carcinoma, The China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - Jingting Li
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine On Differentiated Thyroid Carcinoma, The China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - Fang Li
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine On Differentiated Thyroid Carcinoma, The China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - Liang Han
- Division of Pathology, The China-Japan Union Hospital of Jilin University, Changchun City, , Jilin Province, China
| | - Chengqiu Sui
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine On Differentiated Thyroid Carcinoma, The China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - Le Zhou
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine On Differentiated Thyroid Carcinoma, The China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - Daqi Zhang
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine On Differentiated Thyroid Carcinoma, The China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - Yantao Fu
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine On Differentiated Thyroid Carcinoma, The China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - Rui Du
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine On Differentiated Thyroid Carcinoma, The China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - Jiedong Kou
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine On Differentiated Thyroid Carcinoma, The China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - Gianlorenzo Dionigi
- Division of General and Endocrine Surgery, Istituto Auxologico Italiano IRCCS, Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Hui Sun
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine On Differentiated Thyroid Carcinoma, The China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China.
| | - Nan Liang
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine On Differentiated Thyroid Carcinoma, The China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China.
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Xie J, Yu Z, Zhu Y, Zheng M, Zhu Y. Functions of Coenzyme A and Acyl-CoA in Post-Translational Modification and Human Disease. FRONT BIOSCI-LANDMRK 2024; 29:331. [PMID: 39344325 DOI: 10.31083/j.fbl2909331] [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: 12/02/2023] [Revised: 05/24/2024] [Accepted: 07/17/2024] [Indexed: 10/01/2024]
Abstract
Coenzyme A (CoA) is synthesized from pantothenate, L-cysteine and adenosine triphosphate (ATP), and plays a vital role in diverse physiological processes. Protein acylation is a common post-translational modification (PTM) that modifies protein structure, function and interactions. It occurs via the transfer of acyl groups from acyl-CoAs to various amino acids by acyltransferase. The characteristics and effects of acylation vary according to the origin, structure, and location of the acyl group. Acetyl-CoA, formyl-CoA, lactoyl-CoA, and malonyl-CoA are typical acyl group donors. The major acyl donor, acyl-CoA, enables modifications that impart distinct biological functions to both histone and non-histone proteins. These modifications are crucial for regulating gene expression, organizing chromatin, managing metabolism, and modulating the immune response. Moreover, CoA and acyl-CoA play significant roles in the development and progression of neurodegenerative diseases, cancer, cardiovascular diseases, and other health conditions. The goal of this review was to systematically describe the types of commonly utilized acyl-CoAs, their functions in protein PTM, and their roles in the progression of human diseases.
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Affiliation(s)
- Jumin Xie
- Hubei Key Laboratory of Renal Disease Occurrence and Intervention, Medical School, Hubei Polytechnic University, 435003 Huangshi, Hubei, China
| | - Zhang Yu
- Hubei Key Laboratory of Renal Disease Occurrence and Intervention, Medical School, Hubei Polytechnic University, 435003 Huangshi, Hubei, China
| | - Ying Zhu
- Hubei Key Laboratory of Renal Disease Occurrence and Intervention, Medical School, Hubei Polytechnic University, 435003 Huangshi, Hubei, China
| | - Mei Zheng
- Hubei Key Laboratory of Renal Disease Occurrence and Intervention, Medical School, Hubei Polytechnic University, 435003 Huangshi, Hubei, China
| | - Yanfang Zhu
- Department of Critical Care Medicine, Huangshi Hospital of TCM (Infectious Disease Hospital), 435003 Huangshi, Hubei, China
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Qin Z, Ren H, Zhao P, Wang K, Liu H, Miao C, Du Y, Li J, Wu L, Chen Z. Current computational tools for protein lysine acylation site prediction. Brief Bioinform 2024; 25:bbae469. [PMID: 39316944 PMCID: PMC11421846 DOI: 10.1093/bib/bbae469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/20/2024] [Accepted: 09/07/2024] [Indexed: 09/26/2024] Open
Abstract
As a main subtype of post-translational modification (PTM), protein lysine acylations (PLAs) play crucial roles in regulating diverse functions of proteins. With recent advancements in proteomics technology, the identification of PTM is becoming a data-rich field. A large amount of experimentally verified data is urgently required to be translated into valuable biological insights. With computational approaches, PLA can be accurately detected across the whole proteome, even for organisms with small-scale datasets. Herein, a comprehensive summary of 166 in silico PLA prediction methods is presented, including a single type of PLA site and multiple types of PLA sites. This recapitulation covers important aspects that are critical for the development of a robust predictor, including data collection and preparation, sample selection, feature representation, classification algorithm design, model evaluation, and method availability. Notably, we discuss the application of protein language models and transfer learning to solve the small-sample learning issue. We also highlight the prediction methods developed for functionally relevant PLA sites and species/substrate/cell-type-specific PLA sites. In conclusion, this systematic review could potentially facilitate the development of novel PLA predictors and offer useful insights to researchers from various disciplines.
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Affiliation(s)
- Zhaohui Qin
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Haoran Ren
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Pei Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China
| | - Kaiyuan Wang
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Huixia Liu
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Chunbo Miao
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Yanxiu Du
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Junzhou Li
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Liuji Wu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhen Chen
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
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Chen C, Chen C, Wang A, Jiang Z, Zhao F, Li Y, Han Y, Niu Z, Tian S, Bai X, Zhang K, Zhai G. ENL reads histone β-hydroxybutyrylation to modulate gene transcription. Nucleic Acids Res 2024; 52:10029-10039. [PMID: 38880495 PMCID: PMC11417371 DOI: 10.1093/nar/gkae504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/03/2024] [Accepted: 05/30/2024] [Indexed: 06/18/2024] Open
Abstract
Histone modifications are typically recognized by chromatin-binding protein modules (referred to as 'readers') to mediate fundamental processes such as transcription. Lysine β-hydroxybutyrylation (Kbhb) is a new type of histone mark that couples metabolism to gene expression. However, the readers that prefer histone Kbhb remain elusive. This knowledge gap should be filled in order to reveal the molecular mechanism of this epigenetic regulation. Herein, we developed a chemical proteomic approach, relying upon multivalent photoaffinity probes to capture binders of the mark, and identified ENL as a novel target of H3K9bhb. Biochemical studies and CUT&Tag analysis further suggested that ENL favorably binds to H3K9bhb, and co-localizes with it on promoter regions to modulate gene expression. Notably, disrupting the interaction between H3K9bhb and ENL via structure-based mutation led to the suppressed expression of genes such MYC that drive cell proliferation. Together, our work offered a chemoproteomics approach and identified ENL as a novel histone β-hydroxybutyrylation effector that regulates gene transcription, providing new insight into the regulation mechanism and function of histone Kbhb.
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Affiliation(s)
- Chen Chen
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Cong Chen
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Aiyuan Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Zixin Jiang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Fei Zhao
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Yanan Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Yue Han
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Ziping Niu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Shanshan Tian
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Xue Bai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Kai Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
- Tianjin Key Laboratory of Digestive Diseases, Department of Gastroenterology and Hepatology, Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Guijin Zhai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
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8
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Torres JA, Holznecht N, Asplund DA, Kroes BC, Amarlkhagva T, Haeffner MM, Sharpe EH, Koestner S, Strubl S, Schimmel MF, Kruger S, Agrawal S, Aceves BA, Thangaraju M, Weimbs T. β-hydroxybutyrate recapitulates the beneficial effects of ketogenic metabolic therapy in polycystic kidney disease. iScience 2024; 27:110773. [PMID: 39314240 PMCID: PMC11418134 DOI: 10.1016/j.isci.2024.110773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/30/2024] [Accepted: 08/15/2024] [Indexed: 09/25/2024] Open
Abstract
Autosomal-dominant polycystic kidney disease (ADPKD) is a common monogenic disease characterized by the formation of fluid-filled renal cysts, loss of mitochondrial function, decreased fatty acid oxidation, increased glycolysis, and likely renal failure. We previously demonstrated that inducing a state of ketosis ameliorates or reverses PKD progression in multiple animal models. In this study, we compare time-restricted feeding and 48-h periodic fasting regimens in both juvenile and adult Cy/+ rats. Both fasting regimens potently prevent juvenile disease progression and partially reverse PKD in adults. To explore the mechanism of fasting, we administered β-hydroxybutyrate (BHB) to Cy/+ rats and orthologous mouse models of PKD (Pkd1 RC/RC , Pkd1-Ksp:Cre). BHB recapitulated the effects of fasting in these models independent of stereoisomer, suggesting the effects of BHB are largely due to its signaling functions. These findings implicate the use of ketogenic metabolic therapy and BHB supplementation as potential disease modifiers of PKD and point toward underlying mechanisms.
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Affiliation(s)
- Jacob A. Torres
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Nickolas Holznecht
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - David A. Asplund
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Bradley C. Kroes
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Tselmeg Amarlkhagva
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Matthias M. Haeffner
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Elizabeth H. Sharpe
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Stella Koestner
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Sebastian Strubl
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Margaret F. Schimmel
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Samantha Kruger
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Shagun Agrawal
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Brina A. Aceves
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Muthusamy Thangaraju
- Department of Biochemistry and Molecular Biology, University of Augusta, Augusta, GA, USA
| | - Thomas Weimbs
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
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9
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Qin Z, Liu H, Zhao P, Wang K, Ren H, Miao C, Li J, Chen YZ, Chen Z. SLAM: Structure-aware lysine β-hydroxybutyrylation prediction with protein language model. Int J Biol Macromol 2024; 280:135741. [PMID: 39293623 DOI: 10.1016/j.ijbiomac.2024.135741] [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: 07/04/2024] [Revised: 09/13/2024] [Accepted: 09/15/2024] [Indexed: 09/20/2024]
Abstract
Post-translational modifications (PTMs) diversify protein functions by adding/removing chemical groups to certain amino acid. As a newly-reported PTM, lysine β-hydroxybutyrylation (Kbhb) presents a new avenue to functional proteomics. Therefore, accurate and efficient prediction of Kbhb sites is imperative. However, the current experimental methods for identifying PTM sites are often expensive and time-consuming. Up to now, there is no computational method proposed for Kbhb sites detection. To this end, we present the first deep learning-based method, termed SLAM, to in silico identify lysine β-hydroxybutyrylation sites. The performance of SLAM is evaluated on both 5-fold cross-validation and independent test, achieving 0.890, 0.899, 0.907 and 0.923 in terms of AUROC values, on the general and species-specific independent test sets, respectively. As one example, we predicted the potential Kbhb sites in human S-adenosyl-L-homocysteine hydrolase, which is in agreement with experimentally-verified Kbhb sites. In summary, our method could enable accurate and efficient characterization of novel Kbhb sites that are crucial for the function and stability of proteins and could be applied in the structure-guided identification of other important PTM sites. The SLAM online service and source code is available at https://ai4bio.online/SLAM and https://github.com/Gabriel-QIN/SLAM, respectively.
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Affiliation(s)
- Zhaohui Qin
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Huixia Liu
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Pei Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China
| | - Kaiyuan Wang
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Haoran Ren
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Chunbo Miao
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Junzhou Li
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China.
| | - Yong-Zi Chen
- Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China; Laboratory of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China.
| | - Zhen Chen
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Molecular Breeding and High Efficiency Production, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China.
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10
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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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11
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Cao D, Sun W, Li X, Jian L, Zhou X, Bode AM, Luo X. The role of novel protein acylations in cancer. Eur J Pharmacol 2024; 979:176841. [PMID: 39033839 DOI: 10.1016/j.ejphar.2024.176841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/23/2024]
Abstract
Novel protein acylations are a class of protein post-translational modifications, such as lactylation, succinylation, crotonylation, palmitoylation, and β-hydroxybutyrylation. These acylation modifications are common in prokaryotes and eukaryotes and play pivotal roles in various key cellular processes by regulating gene transcription, protein subcellular localization, stability and activity, protein-protein interactions, and protein-DNA interactions. The diversified acylations are closely associated with various human diseases, especially cancer. In this review, we provide an overview of the distinctive characteristics, effects, and regulatory factors of novel protein acylations. We also explore the various mechanisms through which novel protein acylations are involved in the occurrence and progression of cancer. Furthermore, we discuss the development of anti-cancer drugs targeting novel acylations, offering promising avenues for cancer treatment.
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Affiliation(s)
- Dan Cao
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Wenxuan Sun
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Xinyi Li
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Lian Jian
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Xinran Zhou
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
| | - Xiangjian Luo
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China; Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, China; Molecular Imaging Research Center of Central South University, Changsha, Hunan, 410078, China; Key Laboratory of Biological Nanotechnology of National Health Commission, Central South University, Changsha, Hunan, 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410078, China.
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12
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Moya-Garzon MD, Wang M, Li VL, Lyu X, Wei W, Tung ASH, Raun SH, Zhao M, Coassolo L, Islam H, Oliveira B, Dai Y, Spaas J, Delgado-Gonzalez A, Donoso K, Alvarez-Buylla A, Franco-Montalban F, Letian A, Ward C, Liu L, Svensson KJ, Goldberg EL, Gardner CD, Little JP, Banik SM, Xu Y, Long JZ. A secondary β-hydroxybutyrate metabolic pathway linked to energy balance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.612087. [PMID: 39314488 PMCID: PMC11418978 DOI: 10.1101/2024.09.09.612087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
β-hydroxybutyrate (BHB) is an abundant ketone body. To date, all known pathways of BHB metabolism involve interconversion of BHB and primary energy intermediates. Here we show that CNDP2 controls a previously undescribed secondary BHB metabolic pathway via enzymatic conjugation of BHB and free amino acids. This BHB-ylation reaction produces a family of endogenous ketone metabolites, the BHB-amino acids. Genetic ablation of CNDP2 in mice eliminates tissue amino acid BHB-ylation activity and reduces BHB-amino acid levels. Administration of BHB-Phe, the most abundant BHB-amino acid, to obese mice activates neural populations in the hypothalamus and brainstem and suppresses feeding and body weight. Conversely, CNDP2-KO mice exhibit increased food intake and body weight upon ketosis stimuli. CNDP2-dependent amino acid BHB-ylation and BHB-amino acid metabolites are also conserved in humans. Therefore, the metabolic pathways of BHB extend beyond primary metabolism and include secondary ketone metabolites linked to energy balance.
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Affiliation(s)
- Maria Dolores Moya-Garzon
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Mengjie Wang
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Veronica L Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Xuchao Lyu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
| | - Wei Wei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Alan Sheng-Hwa Tung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Steffen H Raun
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Meng Zhao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Laetitia Coassolo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hashim Islam
- School of Health and Exercise Sciences, University of British Columbia, Kelowna, British Columbia, Canada
| | - Barbara Oliveira
- School of Health and Exercise Sciences, University of British Columbia, Kelowna, British Columbia, Canada
| | - Yuqin Dai
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Jan Spaas
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | | | - Kenyi Donoso
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Francisco Franco-Montalban
- Departamento de Química Farmacéutica y Orgánica, Universidad de Granada, Campus de Cartuja sn, 18011, Granada, Spain
| | - Anudari Letian
- Department of Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Catherine Ward
- Stanford Prevention Research Center, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Lichao Liu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Katrin J Svensson
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Emily L Goldberg
- Department of Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher D Gardner
- Stanford Prevention Research Center, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan P Little
- School of Health and Exercise Sciences, University of British Columbia, Kelowna, British Columbia, Canada
| | - Steven M Banik
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Yong Xu
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jonathan Z Long
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA, USA
- The Phil & Penny Knight Initiative for Brain Resilience at the Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
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13
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Thapak P, Gomez-Pinilla F. The bioenergetics of traumatic brain injury and its long-term impact for brain plasticity and function. Pharmacol Res 2024; 208:107389. [PMID: 39243913 DOI: 10.1016/j.phrs.2024.107389] [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: 06/05/2024] [Revised: 08/19/2024] [Accepted: 08/28/2024] [Indexed: 09/09/2024]
Abstract
Mitochondria provide the energy to keep cells alive and functioning and they have the capacity to influence highly complex molecular events. Mitochondria are essential to maintain cellular energy homeostasis that determines the course of neurological disorders, including traumatic brain injury (TBI). Various aspects of mitochondria metabolism such as autophagy can have long-term consequences for brain function and plasticity. In turn, mitochondria bioenergetics can impinge on molecular events associated with epigenetic modifications of DNA, which can extend cellular memory for a long time. Mitochondrial dysfunction leads to pathological manifestations such as oxidative stress, inflammation, and calcium imbalance that threaten brain plasticity and function. Hence, targeting mitochondrial function may have great potential to lessen the outcomes of TBI.
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Affiliation(s)
- Pavan Thapak
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90095, USA
| | - Fernando Gomez-Pinilla
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90095, USA; Department of Neurosurgery, UCLA Brain Injury Research Center, University of California, Los Angeles, CA 90095, USA.
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14
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Adam SY, Muniyappan M, Huang H, Ennab W, Liu HY, Ahmed AA, Sun MA, Dessie T, Kim IH, Hu Y, Luo X, Cai D. Dietary Organic Zinc Supplementation Modifies the Oxidative Genes via RORγ and Epigenetic Regulations in the Ileum of Broiler Chickens Exposed to High-Temperature Stress. Antioxidants (Basel) 2024; 13:1079. [PMID: 39334738 PMCID: PMC11429418 DOI: 10.3390/antiox13091079] [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: 08/05/2024] [Revised: 08/28/2024] [Accepted: 08/29/2024] [Indexed: 09/30/2024] Open
Abstract
Heat stress (HS) is a significant concern in broiler chickens, which is vital for global meat supply in the dynamic field of poultry farming. The impact of heat stress on the ileum and its influence on the redox homeostatic genes in chickens remains unclear. We hypothesized that adding zinc to the feed of heat-stressed broilers would improve their resilience to heat stress. However, this study aimed to explore the effects of organic zinc supplementation under HS conditions on broiler chickens' intestinal histology and regulation of HS index genes. In this study, 512 Xueshan chickens were divided into four groups: vehicle, HS, 60 mg/kg zinc, and HS + 60 mg/kg zinc groups. Findings revealed that zinc supply positively increased the VH and VH: CD in the ileum of the broilers compared to the HS group, while CD and VW decreased in Zn and HS+Zn supplemented broilers. Zn administration significantly increased superoxide dismutase (SOD), catalase (CAT), glutathione (GSH), and decreased the enzymatic activities of reactive oxygen species (ROS) and malondialdehyde (MDA) compared to the HS group. In addition, Zn administration significantly increased relative ATP, complex I, III, and V enzyme activity compared to the HS group. Furthermore, the expression of acyl-CoA synthetase long-chain family member 4 (ACSL4), lactate transporter 3 (LPCAT3), peroxiredoxin (PRX), and transferrin receptor (TFRC) in the protein levels was extremely downregulated in HS+Zn compared to the HS group. Zn supply significantly decreased the enrichment of RORγ, P300, and SRC1 at target loci of ACSL4, LPCAT3, and PRX compared to the HS group. The occupancies of histone active marks H3K9ac, H3K18ac, H3K27ac, H3K4me1, and H3K18bhb at the locus of ACSL4 and LPCAT3 were significantly decreased in HS+Zn compared to the HS group. Moreover, H3K9la and H3K18la at the locus of ACSL4 and LPCAT3 were significantly decreased in HS+Zn compared to the HS group. This study emphasizes that organic Zn is a potential strategy for modulating the oxidative genes ACSL4, LPCAT3, PRX, and TFRC in the ileum of chickens via nuclear receptor RORγ regulation and histone modifications.
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Affiliation(s)
- Saber Y. Adam
- Laboratory of Animal Physiology and Molecular Nutrition, Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.Y.A.); (M.M.); (H.H.); (W.E.); (H.-Y.L.); (Y.H.)
| | - Madesh Muniyappan
- Laboratory of Animal Physiology and Molecular Nutrition, Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.Y.A.); (M.M.); (H.H.); (W.E.); (H.-Y.L.); (Y.H.)
| | - Hao Huang
- Laboratory of Animal Physiology and Molecular Nutrition, Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.Y.A.); (M.M.); (H.H.); (W.E.); (H.-Y.L.); (Y.H.)
| | - Wael Ennab
- Laboratory of Animal Physiology and Molecular Nutrition, Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.Y.A.); (M.M.); (H.H.); (W.E.); (H.-Y.L.); (Y.H.)
| | - Hao-Yu Liu
- Laboratory of Animal Physiology and Molecular Nutrition, Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.Y.A.); (M.M.); (H.H.); (W.E.); (H.-Y.L.); (Y.H.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
| | - Abdelkareem A. Ahmed
- Department of Veterinary Biomedical Sciences, Botswana University of Agriculture and Agriculture and Natural Resources, Gaborone P.O. Box 100, Botswana;
- Biomeidcal Research Institute, Darfur University College, Nyala P.O. Box 160, South Darfur State, Sudan
- Department of Physiology and Biochemistry, Faculty of Veterinary Science, University of Nyala, Nyala P.O. Box 155, South Darfur State, Sudan
| | - Ming-an Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
| | - Tadelle Dessie
- International Livestock Research Institute, Addis Ababa 5689, Ethiopia;
| | - In Ho Kim
- Department of Animal Resource and Science, Dankook University, Cheonan-si 31116, Choongnam, Republic of Korea;
| | - Yun Hu
- Laboratory of Animal Physiology and Molecular Nutrition, Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.Y.A.); (M.M.); (H.H.); (W.E.); (H.-Y.L.); (Y.H.)
| | - Xugang Luo
- Laboratory of Animal Physiology and Molecular Nutrition, Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.Y.A.); (M.M.); (H.H.); (W.E.); (H.-Y.L.); (Y.H.)
| | - Demin Cai
- Laboratory of Animal Physiology and Molecular Nutrition, Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.Y.A.); (M.M.); (H.H.); (W.E.); (H.-Y.L.); (Y.H.)
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
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15
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Li X, Yu T, Li X, He X, Zhang B, Yang Y. Role of novel protein acylation modifications in immunity and its related diseases. Immunology 2024; 173:53-75. [PMID: 38866391 DOI: 10.1111/imm.13822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/21/2024] [Indexed: 06/14/2024] Open
Abstract
The cross-regulation of immunity and metabolism is currently a research hotspot in life sciences and immunology. Metabolic immunology plays an important role in cutting-edge fields such as metabolic regulatory mechanisms in immune cell development and function, and metabolic targets and immune-related disease pathways. Protein post-translational modification (PTM) is a key epigenetic mechanism that regulates various biological processes and highlights metabolite functions. Currently, more than 400 PTM types have been identified to affect the functions of several proteins. Among these, metabolic PTMs, particularly various newly identified histone or non-histone acylation modifications, can effectively regulate various functions, processes and diseases of the immune system, as well as immune-related diseases. Thus, drugs aimed at targeted acylation modification can have substantial therapeutic potential in regulating immunity, indicating a new direction for further clinical translational research. This review summarises the characteristics and functions of seven novel lysine acylation modifications, including succinylation, S-palmitoylation, lactylation, crotonylation, 2-hydroxyisobutyrylation, β-hydroxybutyrylation and malonylation, and their association with immunity, thereby providing valuable references for the diagnosis and treatment of immune disorders associated with new acylation modifications.
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Affiliation(s)
- Xiaoqian Li
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, People's Republic of China
| | - Tao Yu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Xiaolu Li
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Xiangqin He
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Bei Zhang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, People's Republic of China
| | - Yanyan Yang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, People's Republic of China
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16
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Zhao H, Han Y, Zhou P, Guan H, Gao S. Protein lysine crotonylation in cellular processions and disease associations. Genes Dis 2024; 11:101060. [PMID: 38957707 PMCID: PMC11217610 DOI: 10.1016/j.gendis.2023.06.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 05/05/2023] [Accepted: 06/27/2023] [Indexed: 07/04/2024] Open
Abstract
Protein lysine crotonylation (Kcr) is one conserved form of posttranslational modifications of proteins, which plays an important role in a series of cellular physiological and pathological processes. Lysine ε-amino groups are the primary sites of such modification, resulting in four-carbon planar lysine crotonylation that is structurally and functionally distinct from the acetylation of these residues. High levels of Kcr modifications have been identified on both histone and non-histone proteins. The present review offers an update on the research progression regarding protein Kcr modifications in biomedical contexts and provides a discussion of the mechanisms whereby Kcr modification governs a range of biological processes. In addition, given the importance of protein Kcr modification in disease onset and progression, the potential viability of Kcr regulators as therapeutic targets is elucidated.
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Affiliation(s)
- Hongling Zhao
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yang Han
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Pingkun Zhou
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hua Guan
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Shanshan Gao
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
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17
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Shang S, Wang L, Lu X. β-Hydroxybutyrate enhances astrocyte glutamate uptake through EAAT1 expression regulation. Mol Cell Neurosci 2024; 131:103959. [PMID: 39179164 DOI: 10.1016/j.mcn.2024.103959] [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: 04/07/2024] [Revised: 07/28/2024] [Accepted: 08/18/2024] [Indexed: 08/26/2024] Open
Abstract
β-Hydroxybutyrate (BHB) has been reported to exert neuroprotective functions and is considered a promising treatment for neurodegenerative diseases such as Parkinson's and Alzheimer's. Numerous studies have revealed BHB's multifaceted roles, including anti-senescence, anti-oxidative, and anti-inflammatory activities. However, the underlying mechanisms warrant further investigation. Astrocytes, the most abundant glial cells in the central nervous system, play a pivotal role in the development and progression of neurodegenerative diseases. While BHB is known to alter neuronal metabolism and function, its effects on astrocytes remain poorly understood. In this study, we conducted transcriptome sequencing analysis to identify differentially expressed genes induced by BHB in astrocytes and found that the gene Solute carrier family 1 member 3 (Slc1a3), encoding the glutamate transporter EAAT1, was significantly upregulated by BHB treatment. Cellular and animal-based experiments confirmed an increase in EAAT1 protein expression in primary astrocytes and the hippocampus of mice treated with BHB. This upregulation may be due to the activation of the Ca2+/CAMKII pathway by BHB. Furthermore, BHB improved astrocytes' glutamate uptake and partially restored neuronal viability impaired by glutamate-induced excitotoxicity when astrocytes were functionalized. Our results suggest that BHB may alleviate neuronal damage caused by excessive glutamate by enhancing the glutamate absorption and uptake capacity of astrocytes. This study proposes a novel mechanism for the neuroprotective effects of BHB and reinforces its beneficial impact on the central nervous system (CNS).
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Affiliation(s)
- Sen Shang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, PR China
| | - Leilei Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, PR China
| | - Xiaoyun Lu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi, PR China.
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18
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Feola K, Venable AH, Broomfield T, Villegas M, Fu X, Burgess S, Huen SC. Hepatic ketogenesis is not required for starvation adaptation in mice. Mol Metab 2024; 86:101967. [PMID: 38876267 PMCID: PMC11246062 DOI: 10.1016/j.molmet.2024.101967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
OBJECTIVE In response to bacterial inflammation, anorexia of acute illness is protective and is associated with the induction of fasting metabolic programs such as ketogenesis. Forced feeding during the anorectic period induced by bacterial inflammation is associated with suppressed ketogenesis and increased mortality. As ketogenesis is considered essential in fasting adaptation, we sought to determine the role of ketogenesis in illness-induced anorexia. METHODS A mouse model of inducible hepatic specific deletion of the rate limiting enzyme for ketogenesis (HMG-CoA synthase 2, Hmgcs2) was used to investigate the role of ketogenesis in endotoxemia, a model of bacterial inflammation, and in prolonged starvation. RESULTS Mice deficient of hepatic Hmgcs2 failed to develop ketosis during endotoxemia and during prolonged fasting. Surprisingly, hepatic HMGCS2 deficiency and the lack of ketosis did not affect survival, glycemia, or body temperature in response to endotoxemia. Mice with hepatic ketogenic deficiency also did not exhibit any defects in starvation adaptation and were able to maintain blood glucose, body temperature, and lean mass compared to littermate wild-type controls. Mice with hepatic HMGCS2 deficiency exhibited higher levels of plasma acetate levels in response to fasting. CONCLUSIONS Circulating hepatic-derived ketones do not provide protection against endotoxemia, suggesting that alternative mechanisms drive the increased mortality from forced feeding during illness-induced anorexia. Hepatic ketones are also dispensable for surviving prolonged starvation in the absence of inflammation. Our study challenges the notion that hepatic ketogenesis is required to maintain blood glucose and preserve lean mass during starvation, raising the possibility of extrahepatic ketogenesis and use of alternative fuels as potential means of metabolic compensation.
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Affiliation(s)
- Kyle Feola
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Andrea H Venable
- Department of Internal Medicine (Nephrology), University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tatyana Broomfield
- Department of Internal Medicine (Nephrology), University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Morgan Villegas
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaorong Fu
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shawn Burgess
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sarah C Huen
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine (Nephrology), University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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19
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Qin J, Huang X, Gou S, Zhang S, Gou Y, Zhang Q, Chen H, Sun L, Chen M, Liu D, Han C, Tang M, Feng Z, Niu S, Zhao L, Tu Y, Liu Z, Xuan W, Dai L, Jia D, Xue Y. Ketogenic diet reshapes cancer metabolism through lysine β-hydroxybutyrylation. Nat Metab 2024; 6:1505-1528. [PMID: 39134903 DOI: 10.1038/s42255-024-01093-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 07/02/2024] [Indexed: 08/29/2024]
Abstract
Lysine β-hydroxybutyrylation (Kbhb) is a post-translational modification induced by the ketogenic diet (KD), a diet showing therapeutic effects on multiple human diseases. Little is known how cellular processes are regulated by Kbhb. Here we show that protein Kbhb is strongly affected by the KD through a multi-omics analysis of mouse livers. Using a small training dataset with known functions, we developed a bioinformatics method for the prediction of functionally important lysine modification sites (pFunK), which revealed functionally relevant Kbhb sites on various proteins, including aldolase B (ALDOB) Lys108. KD consumption or β-hydroxybutyrate supplementation in hepatocellular carcinoma cells increases ALDOB Lys108bhb and inhibits the enzymatic activity of ALDOB. A Kbhb-mimicking mutation (p.Lys108Gln) attenuates ALDOB activity and its binding to substrate fructose-1,6-bisphosphate, inhibits mammalian target of rapamycin signalling and glycolysis, and markedly suppresses cancer cell proliferation. Our study reveals a critical role of Kbhb in regulating cancer cell metabolism and provides a generally applicable algorithm for predicting functionally important lysine modification sites.
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Affiliation(s)
- Junhong Qin
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Xinhe Huang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Shengsong Gou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Sitao Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Yujie Gou
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Hongyu Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Lin Sun
- Frontiers Science Center for Synthetic Biology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Miaomiao Chen
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Dan Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Cheng Han
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Min Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Zihao Feng
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Shenghui Niu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Lin Zhao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Yingfeng Tu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Zexian Liu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
| | - Weimin Xuan
- Frontiers Science Center for Synthetic Biology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China.
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
- Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing, China.
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20
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Wang Q, Lan X, Ke H, Xu S, Huang C, Wang J, Wang X, Huang T, Wu X, Chen M, Guo Y, Zeng L, Tian XL, Xiang Y. Histone β-hydroxybutyrylation is critical in reversal of sarcopenia. Aging Cell 2024:e14284. [PMID: 39076122 DOI: 10.1111/acel.14284] [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: 03/25/2024] [Revised: 06/30/2024] [Accepted: 07/03/2024] [Indexed: 07/31/2024] Open
Abstract
Sarcopenia, a leading cause for global disability and mortality, is an age-related muscular disorder, characterized by accelerated muscle mass loss and functional decline. It is known that caloric restriction (CR), ketogenic diet or endurance exercise lessen sarcopenia and elevate circulating β-hydroxybutyrate (β-HB) levels. Whether the elevated β-HB is essential to the reversal of sarcopenia, however, remains unclear. Here we show in both Caenorhabditis elegans and mouse models that an increase of β-HB reverse myofiber atrophy and improves motor functions at advanced ages. β-HB-induced histone lysine β-hydroxybutyrylation (Kbhb) is indispensable for the reversal of sarcopenia. Histone Kbhb enhances transcription of genes associated with mitochondrial pathways, including oxidative phosphorylation, ATP metabolic process and aerobic respiration. This ultimately leads to improve mitochondrial integrity and enhance mitochondrial respiration. The histone Kbhb are validated in mouse model with CR. Thus, we demonstrate that β-HB induces histone Kbhb, increases mitochondrial function, and reverses sarcopenia.
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Affiliation(s)
- Qiquan Wang
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Xinqiang Lan
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Hao Ke
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Siman Xu
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Chunping Huang
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Jiali Wang
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Xiang Wang
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Tiane Huang
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Xia Wu
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Mengxin Chen
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Yingqi Guo
- Institutional Center for Shared Technologies and Facilities of the Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Lin Zeng
- Institutional Center for Shared Technologies and Facilities of the Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiao-Li Tian
- Aging and Vascular Diseases, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Yang Xiang
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
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21
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Feng G, Wu Z, Yang L, Wang K, Wang H. β-hydroxybutyrate and ischemic stroke: roles and mechanisms. Mol Brain 2024; 17:48. [PMID: 39075604 PMCID: PMC11287974 DOI: 10.1186/s13041-024-01119-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 07/14/2024] [Indexed: 07/31/2024] Open
Abstract
Stroke is a significant global burden, causing extensive morbidity and mortality. In metabolic states where glucose is limited, ketone bodies, predominantly β-hydroxybutyrate (BHB), act as alternative fuel sources. Elevated levels of BHB have been found in the ischemic hemispheres of animal models of stroke, supporting its role in the pathophysiology of cerebral ischemia. Clinically, higher serum and urinary BHB concentrations have been associated with adverse outcomes in ischemic stroke, highlighting its potential utility as a prognostic biomarker. In both animal and cellular models, exogenous BHB administration has exhibited neuroprotective effects, reduction of infarct size, and improvement of neurological outcomes. In this review, we focus on the role of BHB before and after ischemic stroke, with an emphasis on the therapeutic potential and mechanisms of ketone administration after ischemic stroke.
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Affiliation(s)
- Ge Feng
- Graduate School of Hebei Medical University, Shijiazhuang, Hebei, China
- Department of Neurology, Hebei General Hospital, No. 348 21 Heping West Road, Shijiazhuang, 050051, Hebei, China
| | - Zongkai Wu
- Department of Neurology, Hebei General Hospital, No. 348 21 Heping West Road, Shijiazhuang, 050051, Hebei, China
| | - Leyi Yang
- Graduate School of Hebei Medical University, Shijiazhuang, Hebei, China
- Department of Neurology, Hebei General Hospital, No. 348 21 Heping West Road, Shijiazhuang, 050051, Hebei, China
| | - Kaimeng Wang
- Graduate School of Hebei Medical University, Shijiazhuang, Hebei, China
- Department of Neurology, Hebei General Hospital, No. 348 21 Heping West Road, Shijiazhuang, 050051, Hebei, China
| | - Hebo Wang
- Department of Neurology, Hebei General Hospital, No. 348 21 Heping West Road, Shijiazhuang, 050051, Hebei, China.
- Hebei Provincial Key Laboratory of Cerebral Networks and Cognitive Disorders, Shijiazhuang, Hebei, China.
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22
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Zhang D, Gao J, Zhu Z, Mao Q, Xu Z, Singh PK, Rimayi CC, Moreno-Yruela C, Xu S, Li G, Sin YC, Chen Y, Olsen CA, Snyder NW, Dai L, Li L, Zhao Y. Lysine L-lactylation is the dominant lactylation isomer induced by glycolysis. Nat Chem Biol 2024:10.1038/s41589-024-01680-8. [PMID: 39030363 DOI: 10.1038/s41589-024-01680-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 06/13/2024] [Indexed: 07/21/2024]
Abstract
Lysine L-lactylation (Kl-la) is a novel protein posttranslational modification (PTM) driven by L-lactate. This PTM has three isomers: Kl-la, N-ε-(carboxyethyl)-lysine (Kce) and D-lactyl-lysine (Kd-la), which are often confused in the context of the Warburg effect and nuclear presence. Here we introduce two methods to differentiate these isomers: a chemical derivatization and high-performance liquid chromatography analysis for efficient separation, and isomer-specific antibodies for high-selectivity identification. We demonstrated that Kl-la is the primary lactylation isomer on histones and dynamically regulated by glycolysis, not Kd-la or Kce, which are observed when the glyoxalase system was incomplete. The study also reveals that lactyl-coenzyme A, a precursor in L-lactylation, correlates positively with Kl-la levels. This work not only provides a methodology for distinguishing other PTM isomers, but also highlights Kl-la as the primary responder to glycolysis and the Warburg effect.
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Affiliation(s)
- Di Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
| | - Jinjun Gao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Zhijun Zhu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Qianying Mao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Zhiqiang Xu
- National Clinical Research Center for Geriatrics and General Practice Ward/International Medical Center Ward, General Practice Medical Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Pankaj K Singh
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Center for Metabolic Disease Research, Philadelphia, PA, USA
| | - Cornelius C Rimayi
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Center for Metabolic Disease Research, Philadelphia, PA, USA
| | - Carlos Moreno-Yruela
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Shuling Xu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Gongyu Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
- Research Center for Analytical Science and Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, China
| | - Yi-Cheng Sin
- Department of Biochemistry, Molecular Biology and Biophysics, The University of Minnesota at Twin Cities, Minneapolis, MN, USA
| | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics, The University of Minnesota at Twin Cities, Minneapolis, MN, USA
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nathaniel W Snyder
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Center for Metabolic Disease Research, Philadelphia, PA, USA
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and General Practice Ward/International Medical Center Ward, General Practice Medical Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA.
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23
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Stacpoole PW, Dirain CO. The pyruvate dehydrogenase complex at the epigenetic crossroads of acetylation and lactylation. Mol Genet Metab 2024; 143:108540. [PMID: 39067348 DOI: 10.1016/j.ymgme.2024.108540] [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: 02/22/2024] [Revised: 06/25/2024] [Accepted: 07/15/2024] [Indexed: 07/30/2024]
Abstract
The pyruvate dehydrogenase complex (PDC) is remarkable for its size and structure as well as for its physiological and pathological importance. Its canonical location is in the mitochondrial matrix, where it primes the tricarboxylic acid (TCA) cycle by decarboxylating glycolytically-derived pyruvate to acetyl-CoA. Less well appreciated is its role in helping to shape the epigenetic landscape, from early development throughout mammalian life by its ability to "moonlight" in the nucleus, with major repercussions for human healthspan and lifespan. The PDC's influence on two crucial modifiers of the epigenome, acetylation and lactylation, is the focus of this brief review.
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Affiliation(s)
- Peter W Stacpoole
- University of Florida, College of Medicine Department of Medicine, Department of Biochemistry & Molecular Biology, Gainesville, FL, United States.
| | - Carolyn O Dirain
- University of Florida, College of Medicine Department of Medicine, Gainesville, FL, United States
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24
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Jamerson LE, Bradshaw PC. The Roles of White Adipose Tissue and Liver NADPH in Dietary Restriction-Induced Longevity. Antioxidants (Basel) 2024; 13:820. [PMID: 39061889 PMCID: PMC11273496 DOI: 10.3390/antiox13070820] [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: 05/29/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
Dietary restriction (DR) protocols frequently employ intermittent fasting. Following a period of fasting, meal consumption increases lipogenic gene expression, including that of NADPH-generating enzymes that fuel lipogenesis in white adipose tissue (WAT) through the induction of transcriptional regulators SREBP-1c and CHREBP. SREBP-1c knockout mice, unlike controls, did not show an extended lifespan on the DR diet. WAT cytoplasmic NADPH is generated by both malic enzyme 1 (ME1) and the pentose phosphate pathway (PPP), while liver cytoplasmic NADPH is primarily synthesized by folate cycle enzymes provided one-carbon units through serine catabolism. During the daily fasting period of the DR diet, fatty acids are released from WAT and are transported to peripheral tissues, where they are used for beta-oxidation and for phospholipid and lipid droplet synthesis, where monounsaturated fatty acids (MUFAs) may activate Nrf1 and inhibit ferroptosis to promote longevity. Decreased WAT NADPH from PPP gene knockout stimulated the browning of WAT and protected from a high-fat diet, while high levels of NADPH-generating enzymes in WAT and macrophages are linked to obesity. But oscillations in WAT [NADPH]/[NADP+] from feeding and fasting cycles may play an important role in maintaining metabolic plasticity to drive longevity. Studies measuring the WAT malate/pyruvate as a proxy for the cytoplasmic [NADPH]/[NADP+], as well as studies using fluorescent biosensors expressed in the WAT of animal models to monitor the changes in cytoplasmic [NADPH]/[NADP+], are needed during ad libitum and DR diets to determine the changes that are associated with longevity.
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Affiliation(s)
| | - Patrick C. Bradshaw
- Department of Biomedical Sciences, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
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25
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Ma W, Ding X, Xu J, Poon TCW. CHHM: a Manually Curated Catalogue of Human Histone Modifications Revealing Hotspot Regions and Unique Distribution Patterns. Int J Biol Sci 2024; 20:3760-3772. [PMID: 39113691 PMCID: PMC11302869 DOI: 10.7150/ijbs.95954] [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: 03/05/2024] [Accepted: 06/13/2024] [Indexed: 08/10/2024] Open
Abstract
Histone modification is one of the key elements in epigenetic control and plays important roles in regulation of biological processes and disease development. Currently, records of human histone modifications with various levels of confidence in evidence are scattered in various knowledgebases and databases. In the present study, a curated catalogue of human histone modifications, CHHM, was obtained by manual retrieval, evidence assessment, and integration of modification records from 10 knowledgebases/databases and 3 complementary articles. CHHM contains 6612 nonredundant modification entries covering 31 types of modifications (including 9 types of emerging modifications) and 2 types of histone-DNA crosslinks, that were identified in 11 H1 variants, 21 H2A variants, 21 H2B variants, 9 H3 variants, and 2 H4 variants. For ease of visualization and accessibility, modification entries are presented with aligned protein sequences in an Excel file. Confidence level in evidence is provided for each entry. Acylation modifications contribute to the highest number of modification entries in CHHM. This supports that cellular metabolic status plays a very important role in epigenetic control. CHHM reveals modification hotspot regions and uneven distribution of the modification entries across the histone families. Such uneven distribution may suggest that a particular histone family is more susceptible to certain types of modifications. CHHM not only serves as an important and user-friendly resource for biomedical and clinical researches involving histone modifications and transcriptional regulation, but also provides new insights for basic researches in the mechanism of human histone modifications and epigenetic control.
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Affiliation(s)
| | | | | | - Terence Chuen Wai Poon
- Institute of Translational Medicine, Centre for Precision Medicine Research and Training, MoE Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau, 999078, China
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26
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Chen L, Liu L, Su H, Xu Y. KbhbXG: A Machine learning architecture based on XGBoost for prediction of lysine β-Hydroxybutyrylation (Kbhb) modification sites. Methods 2024; 227:27-34. [PMID: 38679187 DOI: 10.1016/j.ymeth.2024.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/16/2024] [Accepted: 04/20/2024] [Indexed: 05/01/2024] Open
Abstract
Lysine β-hydroxybutyrylation is an important post-translational modification (PTM) involved in various physiological and biological processes. In this research, we introduce a novel predictor KbhbXG, which utilizes XGBoost to identify β-hydroxybutyrylation modification sites based on protein sequence information. The traditional experimental methods employed for the identification of β-hydroxybutyrylated sites using proteomic techniques are both costly and time-consuming. Thus, the development of computational methods and predictors can play a crucial role in facilitating the rapid identification of β-hydroxybutyrylation sites. Our proposed KbhbXG model first utilizes machine learning algorithm XGBoost to predict β-hydroxybutyrylation modification sites. On the independent test set, KbhbXG achieves an accuracy of 0.7457, specificity of 0.7771, and an impressive area under the curve (AUC) score of 0.8172. The high AUC score achieved by our method demonstrates its potential for effectively identifying novel β-hydroxybutyrylation sites, thereby facilitating further research and exploration of the β-hydroxybutyrylation process. Also, functional analyses have revealed that different organisms preferentially engage in distinct biological processes and pathways, which can provide valuable insights for understanding the mechanism of β-hydroxybutyrylation and guide experimental verification. To promote transparency and reproducibility, we have made both the codes and dataset of KbhbXG publicly available. Researchers interested in utilizing our proposed model can access these resources at https://github.com/Lab-Xu/KbhbXG.
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Affiliation(s)
- Leqi Chen
- Department of Statistics, University of Science and Technology Beijing, Beijing 100083, China
| | - Liwen Liu
- The Open University of China, Beijing 100039, China
| | - Haiyan Su
- School of Computing, Montclair State University, NJ 07043, USA
| | - Yan Xu
- Department of Statistics, University of Science and Technology Beijing, Beijing 100083, China.
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Xu K, Zhang K, Wang Y, Gu Y. Comprehensive review of histone lactylation: Structure, function, and therapeutic targets. Biochem Pharmacol 2024; 225:116331. [PMID: 38821374 DOI: 10.1016/j.bcp.2024.116331] [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: 04/02/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Histone lysine lactylation (Kla) has emerged as a distinct epigenetic modification that differs markedly from established acylation modifications through the unique addition of a lactyl group to a lysine residue. Such modifications not only alter nucleosome structure but also significantly impact chromatin dynamics and gene expression, thus playing a crucial role in cellular metabolism, inflammatory responses, and embryonic development. The association of histone Kla with various metabolic processes, particularly glycolysis and glutamine metabolism, underscores its pivotal role in metabolic reprogramming, including in cancerous tissues, where it contributes to tumorigenesis, immune evasion, and angiogenesis. In addition, histone Kla is involved in the pathogenesis of various diseases, particularly several cancers and neurodegenerative diseases. The identification of histone Kla opens new avenues for therapeutic interventions targeting specific Kla sites. In this review, we summarize the differences between histone Kla modifications and other acylation modifications, discuss the mechanisms and roles of histone Kla in disease, and conclude by describing existing drugs and potential targets. This study provides new insights into the mechanisms linking histone Kla to diseases and into the discovery of new drugs and targets.
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Affiliation(s)
- Kaiwen Xu
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, China
| | - Keyi Zhang
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, China
| | - Yanshuang Wang
- NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou 571199, China
| | - Yue Gu
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, China.
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Li R, Liu Y, Wu J, Chen X, Lu Q, Xia K, Liu C, Sui X, Liu Y, Wang Y, Qiu Y, Chen J, Wang Y, Li R, Ba Y, Fang J, Huang W, Lu Z, Li Y, Liao X, Xiang AP, Huang Y. Adaptive Metabolic Responses Facilitate Blood-Brain Barrier Repair in Ischemic Stroke via BHB-Mediated Epigenetic Modification of ZO-1 Expression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400426. [PMID: 38666466 PMCID: PMC11220715 DOI: 10.1002/advs.202400426] [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: 01/11/2024] [Revised: 04/11/2024] [Indexed: 07/04/2024]
Abstract
Adaptive metabolic responses and innate metabolites hold promising therapeutic potential for stroke, while targeted interventions require a thorough understanding of underlying mechanisms. Adiposity is a noted modifiable metabolic risk factor for stroke, and recent research suggests that it benefits neurological rehabilitation. During the early phase of experimental stroke, the lipidomic results showed that fat depots underwent pronounced lipolysis and released fatty acids (FAs) that feed into consequent hepatic FA oxidation and ketogenesis. Systemic supplementation with the predominant ketone beta-hydroxybutyrate (BHB) is found to exert discernible effects on preserving blood-brain barrier (BBB) integrity and facilitating neuroinflammation resolution. Meanwhile, blocking FAO-ketogenesis processes by administration of CPT1α antagonist or shRNA targeting HMGCS2 exacerbated endothelial damage and aggravated stroke severity, whereas BHB supplementation blunted these injuries. Mechanistically, it is unveiled that BHB infusion is taken up by monocarboxylic acid transporter 1 (MCT1) specifically expressed in cerebral endothelium and upregulated the expression of tight junction protein ZO-1 by enhancing local β-hydroxybutyrylation of H3K9 at the promoter of TJP1 gene. Conclusively, an adaptive metabolic mechanism is elucidated by which acute lipolysis stimulates FAO-ketogenesis processes to restore BBB integrity after stroke. Ketogenesis functions as an early metabolic responder to restrain stroke progression, providing novel prospectives for clinical translation.
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Li Q, Fu C, Hu B, Yang B, Yu H, He H, Xu Q, Chen X, Dai X, Fang R, Xiong X, Zhou K, Yang S, Zou X, Liu Z, Ou L. Lysine 2-hydroxyisobutyrylation proteomics analyses reveal the regulatory mechanism of CaMYB61-CaAFR1 module in regulating stem development in Capsicum annuum L. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1039-1058. [PMID: 38804740 DOI: 10.1111/tpj.16815] [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: 11/08/2023] [Revised: 04/07/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024]
Abstract
Plant stems constitute the most abundant renewable resource on earth. The function of lysine (K)-2-hydroxyisobutyrylation (Khib), a novel post-translational modification (PTM), has not yet been elucidated in plant stem development. Here, by assessing typical pepper genotypes with straight stem (SS) and prostrate stem (PS), we report the first large-scale proteomics analysis for protein Khib to date. Khib-modifications influenced central metabolic processes involved in stem development, such as glycolysis/gluconeogenesis and protein translation. The high Khib level regulated gene expression and protein accumulation associated with cell wall formation in the pepper stem. Specially, we found that CaMYB61 knockdown lines that exhibited prostrate stem phenotypes had high Khib levels. Most histone deacetylases (HDACs, e.g., switch-independent 3 associated polypeptide function related 1, AFR1) potentially function as the "erasing enzymes" involved in reversing Khib level. CaMYB61 positively regulated CaAFR1 expression to erase Khib and promote cellulose and hemicellulose accumulation in the stem. Therefore, we propose a bidirectional regulation hypothesis of "Khib modifications" and "Khib erasing" in stem development, and reveal a novel epigenetic regulatory network in which the CaMYB61-CaAFR1 molecular module participating in the regulation of Khib levels and biosynthesis of cellulose and hemicellulose for the first time.
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Affiliation(s)
- Qing Li
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410125, China
- Yuelushan Lab, Changsha, 410128, China
| | - Canfang Fu
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410125, China
- Yuelushan Lab, Changsha, 410128, China
| | - Bowen Hu
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410125, China
- Yuelushan Lab, Changsha, 410128, China
| | - Bozhi Yang
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410125, China
- Yuelushan Lab, Changsha, 410128, China
| | - Huiyang Yu
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410125, China
- Yuelushan Lab, Changsha, 410128, China
| | - Huan He
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410125, China
- Yuelushan Lab, Changsha, 410128, China
| | - Qing Xu
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410125, China
- Yuelushan Lab, Changsha, 410128, China
| | - Xuejun Chen
- Vegetable and Flower Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Xiongze Dai
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410125, China
- Yuelushan Lab, Changsha, 410128, China
| | - Rong Fang
- Vegetable and Flower Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Xingyao Xiong
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Kunhua Zhou
- Vegetable and Flower Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Sha Yang
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410125, China
- Yuelushan Lab, Changsha, 410128, China
| | - Xuexiao Zou
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410125, China
- Yuelushan Lab, Changsha, 410128, China
| | - Zhoubin Liu
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410125, China
- Yuelushan Lab, Changsha, 410128, China
| | - Lijun Ou
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, 410125, China
- Yuelushan Lab, Changsha, 410128, China
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Deng M, Yan P, Gong H, Li G, Wang J. β-hydroxybutyrate resensitizes colorectal cancer cells to oxaliplatin by suppressing H3K79 methylation in vitro and in vivo. Mol Med 2024; 30:95. [PMID: 38910244 PMCID: PMC11194918 DOI: 10.1186/s10020-024-00864-1] [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: 12/03/2023] [Accepted: 06/12/2024] [Indexed: 06/25/2024] Open
Abstract
BACKGROUND Ketone β-hydroxybutyrate (BHB) has been reported to prevent tumor cell proliferation and improve drug resistance. However, the effectiveness of BHB in oxaliplatin (Oxa)-resistant colorectal cancer (CRC) and the underlying mechanism still require further proof. METHODS CRC-Oxa-resistant strains were established by increasing concentrations of CRC cells to Oxa. CRC-Oxa cell proliferation, apoptosis, invasion, migration, and epithelial-mesenchymal transition (EMT) were checked following BHB intervention in vitro. The subcutaneous and metastasis models were established to assess the effects of BHB on the growth and metastasis of CRC-Oxa in vivo. Eight Oxa responders and seven nonresponders with CRC were enrolled in the study. Then, the serum BHB level and H3K79me, H3K27ac, H3K14ac, and H3K9me levels in tissues were detected. DOT1L (H3K79me methyltransferase) gene knockdown or GNE-049 (H3K27ac inhibitor) use was applied to analyze further whether BHB reversed CRC-Oxa resistance via H3K79 demethylation and/or H3K27 deacetylation in vivo and in vitro. RESULTS Following BHB intervention based on Oxa, the proliferation, migration, invasion, and EMT of CRC-Oxa cells and the growth and metastasis of transplanted tumors in mice were suppressed. Clinical analysis revealed that the differential change in BHB level was associated with drug resistance and was decreased in drug-resistant patient serum. The H3K79me, H3K27ac, and H3K14ac expressions in CRC were negatively correlated with BHB. Furthermore, results indicated that H3K79me inhibition may lead to BHB target deletion, resulting in its inability to function. CONCLUSIONS β-hydroxybutyrate resensitized CRC cells to Oxa by suppressing H3K79 methylation in vitro and in vivo.
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Affiliation(s)
- Meng Deng
- School of Basic Medicine, Jiamusi University, No. 258 Xuefu Street, Jiamusi, 154007, Heilongjiang Province, China
| | - Peijie Yan
- The Heilongjiang Hospital of Beijing Children's Hospital, Capital Medical University, Harbin, 150000, China
| | - Hui Gong
- Clinical Laboratory, Huazhong University of Science and Technology Union Shenzhen Hospital and the Affiliated Shenzhen Sixth Hospital of Shenzhen University, No. 89 Taoyuan road, Nanshan district, Shenzhen, 518052, China
| | - Guiqiu Li
- Clinical Laboratory, Huazhong University of Science and Technology Union Shenzhen Hospital and the Affiliated Shenzhen Sixth Hospital of Shenzhen University, No. 89 Taoyuan road, Nanshan district, Shenzhen, 518052, China.
| | - Jianjie Wang
- School of Basic Medicine, Jiamusi University, No. 258 Xuefu Street, Jiamusi, 154007, Heilongjiang Province, China.
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Ito M, Nishida Y, Iwamoto T, Kanai A, Aoyama S, Ueki K, Uzawa H, Iida H, Watada H. Protein acylations induced by a ketogenic diet demonstrate diverse patterns depending on organs and differ between histones and global proteins. Biochem Biophys Res Commun 2024; 712-713:149960. [PMID: 38640734 DOI: 10.1016/j.bbrc.2024.149960] [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: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 04/21/2024]
Abstract
An essential ketone body, β-hydroxybutyrate (BOHB), plays various roles in physiological regulations via protein acylations such as lysine acetylation and β-hydroxybutyrylation. Here, to understand how BOHB systemically regulates acylations from an overarching perspective, we administered a ketogenic diet to mice to increase BOHB concentration and examined acylations. We found that global acetylation and β-hydroxybutyrylation dramatically increase in various organs except for the brains, where the increase was much smaller than in the other organs. Interestingly, we observe no increase in histone acetylation in the organs where significant global protein acetylation occurs despite a substantial rise in histone β-hydroxybutyrylation. Finally, we compared the transcriptome data of the mice's liver after the ketogenic diet to the public databases, showing that upregulated genes are enriched in those related to histone β-hydroxybutyrylation in starvation. Our data indicate that a ketogenic diet induces diverse patterns of acylations depending on organs and protein localizations, suggesting that different mechanisms regulate acylations and that the ketogenic diet is associated with starvation in terms of protein modifications.
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Affiliation(s)
- Minami Ito
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yuya Nishida
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
| | - Tatsuya Iwamoto
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Akiko Kanai
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Shuhei Aoyama
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Kyosei Ueki
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Hirotsugu Uzawa
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Hitoshi Iida
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Hirotaka Watada
- Department of Endocrinology & Metabolism, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
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Shin JM, Son S, Jung KE, Kim CD, Lee Y. Possible role of β-hydroxybutyrate in inducing inflammation in alopecia areata. Exp Dermatol 2024; 33:e15117. [PMID: 38884504 DOI: 10.1111/exd.15117] [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: 01/22/2024] [Revised: 05/03/2024] [Accepted: 05/26/2024] [Indexed: 06/18/2024]
Abstract
Alopecia areata (AA) is an autoimmune inflammatory disease characterized by non-scarring hair loss due to an immune response that targets hair follicles. The current treatment approach for AA involves the use of immunosuppressants and immunomodulators to reduce cytokine levels around affected hair follicles. Sodium-glucose cotransporter 2 (SGLT2) inhibitors have emerged as potential anti-inflammatory agents with diverse beneficial effects in various medical conditions. This study investigates the role of beta-hydroxybutyrate (BHB), a ketone body produced during SGLT2 inhibition, in the pathogenesis of AA. Serum BHB levels were found to be significantly elevated in patients with AA compared with healthy controls, with higher levels correlating with severity of hair loss. BHB treatment increased inflammatory cytokine production in outer root sheath (ORS) cells, mimicking the inflammatory conditions seen in AA. The results suggest that elevated BHB levels may exacerbate the inflammatory immune response in AA patients and may be associated with chronic hair loss and resistance to treatment. Serum BHB levels may serve as a potential marker of poor prognosis in patients with severe AA. Further research is needed to elucidate the precise role of BHB in the pathogenesis of AA and its implications for disease management.
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Affiliation(s)
- Jung-Min Shin
- Department of Dermatology, School of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Seungjin Son
- Department of Dermatology, School of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Kyung Eun Jung
- Department of Dermatology, School of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Chang Deok Kim
- Department of Dermatology, School of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Young Lee
- Department of Dermatology, School of Medicine, Chungnam National University, Daejeon, Republic of Korea
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Khouri H, Roberge M, Ussher JR, Aguer C. Acetoacetate and d- and l-β-hydroxybutyrate have distinct effects on basal and insulin-stimulated glucose uptake in L6 skeletal muscle cells. Am J Physiol Cell Physiol 2024; 326:C1710-C1720. [PMID: 38708524 DOI: 10.1152/ajpcell.00718.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 05/07/2024]
Abstract
Ketone bodies (acetoacetate and β-hydroxybutyrate) are oxidized in skeletal muscle mainly during fasting as an alternative source of energy to glucose. Previous studies suggest that there is a negative relationship between increased muscle ketolysis and muscle glucose metabolism in mice with obesity and/or type 2 diabetes. Therefore, we investigated the connection between increased ketone body exposure and muscle glucose metabolism by measuring the effect of a 3-h exposure to ketone bodies on glucose uptake in differentiated L6 myotubes. We showed that exposure to acetoacetate at a typical concentration (0.2 mM) resulted in increased basal glucose uptake in L6 myotubes, which was dependent on increased membrane glucose transporter type 4 (GLUT4) translocation. Basal and insulin-stimulated glucose uptake was also increased with a concentration of acetoacetate reflective of diabetic ketoacidosis or a ketogenic diet (1 mM). We found that β-hydroxybutyrate had a variable effect on basal glucose uptake: a racemic mixture of the two β-hydroxybutyrate enantiomers (d and l) appeared to decrease basal glucose uptake, while 3 mM d-β-hydroxybutyrate alone increased basal glucose uptake. However, the effects of the ketone bodies individually were not observed when acetoacetate was present in combination with β-hydroxybutyrate. These results provide insight that will help elucidate the effect of ketone bodies in the context of specific metabolic diseases and nutritional states (e.g., type 2 diabetes and ketogenic diets).NEW & NOTEWORTHY A limited number of studies investigate the effect of ketone bodies at concentrations reflective of both typical fasting and ketoacidosis. We tested a mix of physiologically relevant concentrations of ketone bodies, which allowed us to highlight the differential effects of d- and l-β-hydroxybutyrate and acetoacetate on skeletal muscle cell glucose uptake. Our findings will assist in better understanding the mechanisms that contribute to muscle insulin resistance and provide guidance on recommendations regarding ketogenic diets.
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Affiliation(s)
- Hannah Khouri
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Institut du Savoir Montfort - recherche, Ottawa, Ontario, Canada
| | - Mathilde Roberge
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Institut du Savoir Montfort - recherche, Ottawa, Ontario, Canada
| | - John R Ussher
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Céline Aguer
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Institut du Savoir Montfort - recherche, Ottawa, Ontario, Canada
- Department of Physiology, Faculty of Medicine and Health Sciences, McGill University - Campus Outaouais, Gatineau, Quebec, Canada
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Hatano R, Lee E, Sato H, Kiuchi M, Hirahara K, Nakagawa Y, Shimano H, Nakayama T, Tanaka T, Miki T. Hepatic ketone body regulation of renal gluconeogenesis. Mol Metab 2024; 84:101934. [PMID: 38604598 PMCID: PMC11039402 DOI: 10.1016/j.molmet.2024.101934] [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: 01/08/2024] [Revised: 02/20/2024] [Accepted: 04/02/2024] [Indexed: 04/13/2024] Open
Abstract
OBJECTIVES During fasting, liver pivotally regulates blood glucose levels through glycogenolysis and gluconeogenesis. Kidney also produces glucose through gluconeogenesis. Gluconeogenic genes are transactivated by fasting, but their expression patterns are chronologically different between the two organs. We find that renal gluconeogenic gene expressions are positively correlated with the blood β-hydroxybutyrate concentration. Thus, we herein aim to investigate the regulatory mechanism and its physiological implications. METHODS Gluconeogenic gene expressions in liver and kidney were examined in hyperketogenic mice such as high-fat diet (HFD)-fed and ketogenic diet-fed mice, and in hypoketogenic PPARα knockout (PPARα-/-) mice. Renal gluconeogenesis was evaluated by rise in glycemia after glutamine loading in vivo. Functional roles of β-hydroxybutyrate in the regulation of renal gluconeogenesis were investigated by metabolome analysis and RNA-seq analysis of proximal tubule cells. RESULTS Renal gluconeogenic genes were transactivated concurrently with blood β-hydroxybutyrate uprise under ketogenic states, but the increase was blunted in hypoketogenic PPARα-/- mice. Administration of 1,3-butandiol, a ketone diester, transactivated renal gluconeogenic gene expression in fasted PPARα-/- mice. In addition, HFD-fed mice showed fasting hyperglycemia along with upregulated renal gluconeogenic gene expression, which was blunted in HFD-fed PPARα-/- mice. In vitro experiments and metabolome analysis in renal tubular cells showed that β-hydroxybutyrate directly promotes glucose and NH3 production through transactivating gluconeogenic genes. In addition, RNA-seq analysis revealed that β-hydroxybutyrate-induced transactivation of Pck1 was mediated by C/EBPβ. CONCLUSIONS Our findings demonstrate that β-hydroxybutyrate mediates hepato-renal interaction to maintain homeostatic regulation of blood glucose and systemic acid-base balance through renal gluconeogenesis regulation.
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Affiliation(s)
- Ryo Hatano
- Department of Medical Physiology, Chiba University, Graduate School of Medicine, Chiba 260-8670, Japan
| | - Eunyoung Lee
- Department of Medical Physiology, Chiba University, Graduate School of Medicine, Chiba 260-8670, Japan; Research Institute of Disaster Medicine (RIDM), Chiba University, Graduate School of Medicine, Chiba 260-8670, Japan
| | - Hiromi Sato
- Laboratory of Clinical Pharmacology and Pharmacometrics, Chiba University, Graduate School of Pharmaceutical Sciences, Chiba 260-8670, Japan
| | - Masahiro Kiuchi
- Department of Immunology, Chiba University, Graduate School of Medicine, Chiba 260-8670, Japan
| | - Kiyoshi Hirahara
- Research Institute of Disaster Medicine (RIDM), Chiba University, Graduate School of Medicine, Chiba 260-8670, Japan; Department of Immunology, Chiba University, Graduate School of Medicine, Chiba 260-8670, Japan
| | - Yoshimi Nakagawa
- Division of Complex Biosystem Research, Department of Research and Development, Institute of Natural Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Hitoshi Shimano
- Department of Endocrinology and Metabolism, Institute of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Toshinori Nakayama
- Department of Immunology, Chiba University, Graduate School of Medicine, Chiba 260-8670, Japan
| | - Tomoaki Tanaka
- Research Institute of Disaster Medicine (RIDM), Chiba University, Graduate School of Medicine, Chiba 260-8670, Japan; Department of Molecular Diagnosis, Chiba University, Graduate School of Medicine, Chiba 260-8670, Japan
| | - Takashi Miki
- Department of Medical Physiology, Chiba University, Graduate School of Medicine, Chiba 260-8670, Japan; Research Institute of Disaster Medicine (RIDM), Chiba University, Graduate School of Medicine, Chiba 260-8670, Japan.
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Bhattacharya S, Tu BP. Histone acylation at a glance. J Cell Sci 2024; 137:jcs261250. [PMID: 38842578 PMCID: PMC11213524 DOI: 10.1242/jcs.261250] [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] [Indexed: 06/07/2024] Open
Abstract
An important mechanism of gene expression regulation is the epigenetic modification of histones. The cofactors and substrates for these modifications are often intermediary metabolites, and it is becoming increasingly clear that the metabolic and nutritional state of cells can influence these marks. These connections between the balance of metabolites, histone modifications and downstream transcriptional changes comprise a metabolic signaling program that can enable cells to adapt to changes in nutrient availability. Beyond acetylation, there is evidence now that histones can be modified by other acyl groups. In this Cell Science at a Glance article and the accompanying poster, we focus on these histone acylation modifications and provide an overview of the players that govern these acylations and their connections with metabolism.
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Affiliation(s)
- Saikat Bhattacharya
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390-9038, USA
| | - Benjamin P. Tu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390-9038, USA
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36
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Hao B, Chen K, Zhai L, Liu M, Liu B, Tan M. Substrate and Functional Diversity of Protein Lysine Post-translational Modifications. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae019. [PMID: 38862432 DOI: 10.1093/gpbjnl/qzae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 11/11/2023] [Accepted: 01/08/2024] [Indexed: 06/13/2024]
Abstract
Lysine post-translational modifications (PTMs) are widespread and versatile protein PTMs that are involved in diverse biological processes by regulating the fundamental functions of histone and non-histone proteins. Dysregulation of lysine PTMs is implicated in many diseases, and targeting lysine PTM regulatory factors, including writers, erasers, and readers, has become an effective strategy for disease therapy. The continuing development of mass spectrometry (MS) technologies coupled with antibody-based affinity enrichment technologies greatly promotes the discovery and decoding of PTMs. The global characterization of lysine PTMs is crucial for deciphering the regulatory networks, molecular functions, and mechanisms of action of lysine PTMs. In this review, we focus on lysine PTMs, and provide a summary of the regulatory enzymes of diverse lysine PTMs and the proteomics advances in lysine PTMs by MS technologies. We also discuss the types and biological functions of lysine PTM crosstalks on histone and non-histone proteins and current druggable targets of lysine PTM regulatory factors for disease therapy.
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Affiliation(s)
- Bingbing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Institute of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Kaifeng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Muyin Liu
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Bin Liu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
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Tsuruta H, Yamahara K, Yasuda-Yamahara M, Kume S. Emerging Pathophysiological Roles of Ketone Bodies. Physiology (Bethesda) 2024; 39:0. [PMID: 38260943 DOI: 10.1152/physiol.00031.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/24/2024] Open
Abstract
The discovery of insulin approximately a century ago greatly improved the management of diabetes, including many of its life-threatening acute complications like ketoacidosis. This breakthrough saved many lives and extended the healthy lifespan of many patients with diabetes. However, there is still a negative perception of ketone bodies stemming from ketoacidosis. Originally, ketone bodies were thought of as a vital source of energy during fasting and exercise. Furthermore, in recent years, research on calorie restriction and its potential impact on extending healthy lifespans, as well as studies on ketone bodies, have gradually led to a reevaluation of the significance of ketone bodies in promoting longevity. Thus, in this review, we discuss the emerging and hidden roles of ketone bodies in various organs, including the heart, kidneys, skeletal muscles, and brain, as well as their potential impact on malignancies and lifespan.
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Affiliation(s)
- Hiroaki Tsuruta
- Department of Medicine, Shiga University of Medical Science, Seta, Otsu, Shiga, Japan
| | - Kosuke Yamahara
- Department of Medicine, Shiga University of Medical Science, Seta, Otsu, Shiga, Japan
| | - Mako Yasuda-Yamahara
- Department of Medicine, Shiga University of Medical Science, Seta, Otsu, Shiga, Japan
| | - Shinji Kume
- Department of Medicine, Shiga University of Medical Science, Seta, Otsu, Shiga, Japan
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Wang X, Liu Q, Yu HT, Xie JZ, Zhao JN, Fang ZT, Qu M, Zhang Y, Yang Y, Wang JZ. A positive feedback inhibition of isocitrate dehydrogenase 3β on paired-box gene 6 promotes Alzheimer-like pathology. Signal Transduct Target Ther 2024; 9:105. [PMID: 38679634 PMCID: PMC11056379 DOI: 10.1038/s41392-024-01812-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 02/28/2024] [Accepted: 03/20/2024] [Indexed: 05/01/2024] Open
Abstract
Impaired brain glucose metabolism is an early indicator of Alzheimer's disease (AD); however, the fundamental mechanism is unknown. In this study, we found a substantial decline in isocitrate dehydrogenase 3β (IDH3β) levels, a critical tricarboxylic acid cycle enzyme, in AD patients and AD-transgenic mice's brains. Further investigations demonstrated that the knockdown of IDH3β induced oxidation-phosphorylation uncoupling, leading to reduced energy metabolism and lactate accumulation. The resulting increased lactate, a source of lactyl, was found to promote histone lactylation, thereby enhancing the expression of paired-box gene 6 (PAX6). As an inhibitory transcription factor of IDH3β, the elevated PAX6 in turn inhibited the expression of IDH3β, leading to tau hyperphosphorylation, synapse impairment, and learning and memory deficits resembling those seen in AD. In AD-transgenic mice, upregulating IDH3β and downregulating PAX6 were found to improve cognitive functioning and reverse AD-like pathologies. Collectively, our data suggest that impaired oxidative phosphorylation accelerates AD progression via a positive feedback inhibition loop of IDH3β-lactate-PAX6-IDH3β. Breaking this loop by upregulating IDH3β or downregulating PAX6 attenuates AD neurodegeneration and cognitive impairments.
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Affiliation(s)
- Xin Wang
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Liu
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hai-Tao Yu
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Fundamental Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Jia-Zhao Xie
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jun-Ning Zhao
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhi-Ting Fang
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Qu
- Hubei Provincial Key Laboratory for Applied Toxicology, Hubei Provincial Center for Disease Control and Prevention, Hubei Provincial Academy of Preventive Medicine, Wuhan, 430000, China
| | - Yao Zhang
- Endocrine Department of Liyuan Hospital; Key Laboratory of Ministry of Education of China for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430077, China.
| | - Ying Yang
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Jian-Zhi Wang
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226000, China.
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Stephens EB, Senadheera C, Roa-Diaz S, Peralta S, Alexander L, Silverman-Martin W, Yukawa M, Morris J, Johnson JB, Newman JC, Stubbs BJ. A randomized open-label, observational study of the novel ketone ester, bis octanoyl (R)-1,3-butanediol, and its acute effect on ß-hydroxybutyrate and glucose concentrations in healthy older adults. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.16.24305925. [PMID: 38699344 PMCID: PMC11065008 DOI: 10.1101/2024.04.16.24305925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Bis-octanoyl (R)-1,3-butanediol (BO-BD) is a novel ketone ester (KE) ingredient which increases blood beta-hydroxybutyrate (BHB) concentrations rapidly after ingestion. KE is hypothesized to have beneficial metabolic effects on health and performance, especially in older adults. Whilst many studies have investigated the ketogenic effect of KE in young adults, they have not been studied in an exclusively older adult population, for whom age-related differences in body composition and metabolism may alter the effects. This randomized, observational, open-label study in healthy older adults (n = 30, 50% male, age = 76.5 years, BMI = 25.2 kg/m2) aimed to elucidate acute tolerance, blood BHB and blood glucose concentrations for 4 hours following consumption of either 12.5 or 25 g of BO-BD formulated firstly as a ready-to-drink beverage (n = 30), then as a re-constituted powder (n = 21), taken with a standard meal. Both serving sizes and formulations of BO-BD were well tolerated, and increased blood BHB, inducing nutritional ketosis (≥ 0.5mM) that lasted until the end of the study. Ketosis was dose responsive; peak BHB concentration (Cmax) and incremental area under the curve (iAUC) were significantly greater with 25 g compared to 12.5 g of BO-BD in both formulations. There were no significant differences in Cmax or iAUC between formulations. Blood glucose increased in all conditions following the meal; there were no consistent significant differences in glucose response between conditions. These results demonstrate that both powder and beverage formulations of the novel KE, BO-BD, induce ketosis in healthy older adults, facilitating future research on functional effects of this ingredient in aging.
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Affiliation(s)
| | | | | | | | | | | | - Michi Yukawa
- Veteran’s Affairs Medical Center, San Francisco, CA, USA
| | | | | | - John C. Newman
- Buck Institute for Research on Aging, Novato, CA, USA
- Division of Geriatrics, University of California, San Francisco, CA, USA
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Chen HS, Wang F, Chen JG. Epigenetic mechanisms in depression: Implications for pathogenesis and treatment. Curr Opin Neurobiol 2024; 85:102854. [PMID: 38401316 DOI: 10.1016/j.conb.2024.102854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/26/2024]
Abstract
The risk of depression is influenced by both genetic and environmental factors. It has been suggested that epigenetic mechanisms may mediate the risk of depression following exposure to adverse life events. Epigenetics encompasses stable alterations in gene expression that are controlled through transcriptional, post-transcriptional, translational, or post-translational processes, including DNA modifications, chromatin remodeling, histone modifications, RNA modifications, and non-coding RNA (ncRNA) regulation, without any changes in the DNA sequence. In this review, we explore recent research advancements in the realm of epigenetics concerning depression. Furthermore, we evaluate the potential of epigenetic changes as diagnostic and therapeutic biomarkers for depression.
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Affiliation(s)
- Hong-Sheng Chen
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan 430030, China; The Research Center for Depression, Tongji Medical College, Huazhong University of Science, Wuhan 430030, China
| | - Fang Wang
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan 430030, China; The Research Center for Depression, Tongji Medical College, Huazhong University of Science, Wuhan 430030, China; The Key Laboratory of Neurological Diseases (HUST), Ministry of Education of China, Wuhan 430030, China
| | - Jian-Guo Chen
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan 430030, China; The Research Center for Depression, Tongji Medical College, Huazhong University of Science, Wuhan 430030, China; The Key Laboratory of Neurological Diseases (HUST), Ministry of Education of China, Wuhan 430030, China.
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41
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Moore MP, Shryack G, Alessi I, Wieschhaus N, Meers GM, Johnson SA, Wheeler AA, Ibdah JA, Parks EJ, Rector RS. Relationship between serum β-hydroxybutyrate and hepatic fatty acid oxidation in individuals with obesity and NAFLD. Am J Physiol Endocrinol Metab 2024; 326:E493-E502. [PMID: 38381399 PMCID: PMC11194052 DOI: 10.1152/ajpendo.00336.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/22/2024]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is characterized by excess lipid accumulation that can progress to inflammation (nonalcoholic steatohepatitis, NASH), and fibrosis. Serum β-hydroxybutyrate (β-HB), a product of the ketogenic pathway, is commonly used as a surrogate marker for hepatic fatty acid oxidation (FAO). However, it remains uncertain whether this relationship holds true in the context of NAFLD in humans. We compared fasting serum β-HB levels with direct measurement of liver mitochondrial palmitate oxidation in humans stratified based on NAFLD severity (n = 142). Patients were stratified based on NAFLD activity score (NAS): NAS = 0 (no disease), NAS = 1-2 (mild), NAS = 3-4 (moderate), and NAS ≥ 5 (advanced). Moderate and advanced NAFLD is associated with reductions in liver 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2), serum β-HB, but not 3-hydroxy-3-methylglutaryl-CoA lyase (HMGCL) mRNA, relative to no disease. Worsening liver mitochondrial complete palmitate oxidation corresponded with lower HMGCS2 mRNA but not total (complete + incomplete) palmitate oxidation. Interestingly, we found that liver HMGCS2 mRNA and serum β-HB correlated with liver mitochondrial β-hydroxyacyl-CoA dehydrogenase (β-HAD) activity and CPT1A mRNA. Also, lower mitochondrial mass and markers of mitochondrial turnover positively correlated with lower HMGCS2 in the liver. These data suggest that liver ketogenesis and FAO occur at comparable rates in individuals with NAFLD. Our findings support the utility of serum β-HB to serve as a marker of liver injury and hepatic FAO in the context of NAFLD.NEW & NOTEWORTHY Serum β-hydroxybutyrate (β-HB) is frequently utilized as a surrogate marker for hepatic fatty acid oxidation; however, few studies have investigated this relationship during states of liver disease. We found that the progression of nonalcoholic fatty liver disease (NAFLD) is associated with reductions in circulating β-HB and liver 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2). As well, decreased rates of hepatic fatty acid oxidation correlated with liver HMGCS2 mRNA and serum β-HB. Our work supports serum β-HB as a potential marker for hepatic fatty acid oxidation and liver injury during NAFLD.
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Affiliation(s)
- Mary P Moore
- Research Service, Harry S Truman Memorial Veterans Medical Center, Columbia, Missouri, United States
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri, United States
| | - Grace Shryack
- Research Service, Harry S Truman Memorial Veterans Medical Center, Columbia, Missouri, United States
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri, United States
- NextGen Precision Health, Columbia, Missouri, United States
| | - Isabella Alessi
- Research Service, Harry S Truman Memorial Veterans Medical Center, Columbia, Missouri, United States
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri, United States
- NextGen Precision Health, Columbia, Missouri, United States
| | - Nicole Wieschhaus
- Research Service, Harry S Truman Memorial Veterans Medical Center, Columbia, Missouri, United States
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri, United States
- NextGen Precision Health, Columbia, Missouri, United States
| | - Grace M Meers
- Research Service, Harry S Truman Memorial Veterans Medical Center, Columbia, Missouri, United States
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri, United States
- NextGen Precision Health, Columbia, Missouri, United States
| | - Sarah A Johnson
- Research Service, Harry S Truman Memorial Veterans Medical Center, Columbia, Missouri, United States
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Missouri, Columbia, Missouri, United States
| | - Andrew A Wheeler
- Department of Surgery, University of Missouri, Columbia, Missouri, United States
| | - Jamal A Ibdah
- Research Service, Harry S Truman Memorial Veterans Medical Center, Columbia, Missouri, United States
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri, United States
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Missouri, Columbia, Missouri, United States
| | - Elizabeth J Parks
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri, United States
- NextGen Precision Health, Columbia, Missouri, United States
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Missouri, Columbia, Missouri, United States
| | - R Scott Rector
- Research Service, Harry S Truman Memorial Veterans Medical Center, Columbia, Missouri, United States
- Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, Missouri, United States
- NextGen Precision Health, Columbia, Missouri, United States
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Missouri, Columbia, Missouri, United States
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42
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Zhang Y, Li Y. β-hydroxybutyrate inhibits malignant phenotypes of prostate cancer cells through β-hydroxybutyrylation of indoleacetamide-N-methyltransferase. Cancer Cell Int 2024; 24:121. [PMID: 38555451 PMCID: PMC10981303 DOI: 10.1186/s12935-024-03277-6] [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: 10/09/2023] [Accepted: 02/19/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Prostate cancer (PCa) is one of the most prevalent cancers in men and is associated with high mortality and disability rates. β-hydroxybutyrate (BHB), a ketone body, has received increasing attention for its role in cancer. However, its role in PCa remains unclear. This study aimed to explore the mechanism and feasibility of BHB as a treatment alternative for PCa. METHODS Colony formation assay, flow cytometry, western blot assay, and transwell assays were performed to determine the effect of BHB on the proliferation and metastasis of PCa cells. Tumor sphere formation and aldehyde dehydrogenase assays were used to identify the impact of BHB or indoleacetamide-N-methyltransferase (INMT) on the stemness of PCa cells. N6-methyladenosine (m6A)-meRIP real-time reverse transcription polymerase chain reaction and dual luciferase assays were conducted to confirm INMT upregulation via the METTL3-m6A pathway. Co-IP assay was used to detect the epigenetic modification of INMT by BHB-mediated β-hydroxybutyrylation (kbhb) and screen enzymes that regulate INMT kbhb. Mouse xenograft experiments demonstrated the antitumor effects of BHB in vivo. RESULTS BHB can inhibit the proliferation, migration, and invasion of PCa cells by suppressing their stemness. Mechanistically, INMT, whose expression is upregulated by the METTL3-m6A pathway, was demonstrated to be an oncogenic gene that promotes the stem-like characteristics of PCa cells. BHB can suppress the malignant phenotypes of PCa by kbhb of INMT, which in turn inhibits INMT expression. CONCLUSIONS Our findings indicate a role of BHB in PCa metabolic therapy, thereby suggesting an epigenetic therapeutic strategy to target INMT in aggressive PCa. TRIAL REGISTRATION Not applicable.
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Affiliation(s)
- Yifan Zhang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, Henan, Henan, 450000, China.
| | - Yunlong Li
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Erqi District, Zhengzhou, Henan, Henan, 450000, China
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Gupta A, Das D, Taneja R. Targeting Dysregulated Lipid Metabolism in Cancer with Pharmacological Inhibitors. Cancers (Basel) 2024; 16:1313. [PMID: 38610991 PMCID: PMC11010992 DOI: 10.3390/cancers16071313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/19/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024] Open
Abstract
Metabolic plasticity is recognised as a hallmark of cancer cells, enabling adaptation to microenvironmental changes throughout tumour progression. A dysregulated lipid metabolism plays a pivotal role in promoting oncogenesis. Oncogenic signalling pathways, such as PI3K/AKT/mTOR, JAK/STAT, Hippo, and NF-kB, intersect with the lipid metabolism to drive tumour progression. Furthermore, altered lipid signalling in the tumour microenvironment contributes to immune dysfunction, exacerbating oncogenesis. This review examines the role of lipid metabolism in tumour initiation, invasion, metastasis, and cancer stem cell maintenance. We highlight cybernetic networks in lipid metabolism to uncover avenues for cancer diagnostics, prognostics, and therapeutics.
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Affiliation(s)
| | | | - Reshma Taneja
- Department of Physiology, Healthy Longevity and NUS Centre for Cancer Research Translation Research Program, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 2 Medical Drive, MD9, Singapore 117593, Singapore
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Kopczyńska J, Kowalczyk M. The potential of short-chain fatty acid epigenetic regulation in chronic low-grade inflammation and obesity. Front Immunol 2024; 15:1380476. [PMID: 38605957 PMCID: PMC11008232 DOI: 10.3389/fimmu.2024.1380476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Obesity and chronic low-grade inflammation, often occurring together, significantly contribute to severe metabolic and inflammatory conditions like type 2 diabetes (T2D), cardiovascular disease (CVD), and cancer. A key player is elevated levels of gut dysbiosis-associated lipopolysaccharide (LPS), which disrupts metabolic and immune signaling leading to metabolic endotoxemia, while short-chain fatty acids (SCFAs) beneficially regulate these processes during homeostasis. SCFAs not only safeguard the gut barrier but also exert metabolic and immunomodulatory effects via G protein-coupled receptor binding and epigenetic regulation. SCFAs are emerging as potential agents to counteract dysbiosis-induced epigenetic changes, specifically targeting metabolic and inflammatory genes through DNA methylation, histone acetylation, microRNAs (miRNAs), and long non-coding RNAs (lncRNAs). To assess whether SCFAs can effectively interrupt the detrimental cascade of obesity and inflammation, this review aims to provide a comprehensive overview of the current evidence for their clinical application. The review emphasizes factors influencing SCFA production, the intricate connections between metabolism, the immune system, and the gut microbiome, and the epigenetic mechanisms regulated by SCFAs that impact metabolism and the immune system.
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Affiliation(s)
- Julia Kopczyńska
- Laboratory of Lactic Acid Bacteria Biotechnology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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45
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Fan S, Kong C, Zhou R, Zheng X, Ren D, Yin Z. Protein Post-Translational Modifications Based on Proteomics: A Potential Regulatory Role in Animal Science. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6077-6088. [PMID: 38501450 DOI: 10.1021/acs.jafc.3c08332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Genomic studies in animal breeding have provided a wide range of references; however, it is important to note that genes and mRNA alone do not fully capture the complexity of living organisms. Protein post-translational modification, which involves covalent modifications regulated by genetic and environmental factors, serves as a fundamental epigenetic mechanism that modulates protein structure, activity, and function. In this review, we comprehensively summarize various phosphorylation and acylation modifications on metabolic enzymes relevant to energy metabolism in animals, including acetylation, succinylation, crotonylation, β-hydroxybutylation, acetoacetylation, and lactylation. It is worth noting that research on animal energy metabolism and modification regulation lags behind the demands for growth and development in animal breeding compared to human studies. Therefore, this review provides a novel research perspective by exploring unreported types of modifications in livestock based on relevant findings from human or animal models.
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Affiliation(s)
- Shuhao Fan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Chengcheng Kong
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230013, China
| | - Ren Zhou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xianrui Zheng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Dalong Ren
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
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46
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Gan Q, Fan C. Orthogonal Translation for Site-Specific Installation of Post-translational Modifications. Chem Rev 2024; 124:2805-2838. [PMID: 38373737 PMCID: PMC11230630 DOI: 10.1021/acs.chemrev.3c00850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Post-translational modifications (PTMs) endow proteins with new properties to respond to environmental changes or growth needs. With the development of advanced proteomics techniques, hundreds of distinct types of PTMs have been observed in a wide range of proteins from bacteria, archaea, and eukarya. To identify the roles of these PTMs, scientists have applied various approaches. However, high dynamics, low stoichiometry, and crosstalk between PTMs make it almost impossible to obtain homogeneously modified proteins for characterization of the site-specific effect of individual PTM on target proteins. To solve this problem, the genetic code expansion (GCE) strategy has been introduced into the field of PTM studies. Instead of modifying proteins after translation, GCE incorporates modified amino acids into proteins during translation, thus generating site-specifically modified proteins at target positions. In this review, we summarize the development of GCE systems for orthogonal translation for site-specific installation of PTMs.
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Affiliation(s)
- Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas 72701, United States
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Qin Y, Yang P, He W, Li D, Zeng L, Li J, Zhou T, Peng J, Cao L, Huang W. Novel histone post-translational modifications in Alzheimer's disease: current advances and implications. Clin Epigenetics 2024; 16:39. [PMID: 38461320 PMCID: PMC10924326 DOI: 10.1186/s13148-024-01650-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 02/21/2024] [Indexed: 03/11/2024] Open
Abstract
Alzheimer's disease (AD) has a complex pathogenesis, and multiple studies have indicated that histone post-translational modifications, especially acetylation, play a significant role in it. With the development of mass spectrometry and proteomics, an increasing number of novel HPTMs, including lactoylation, crotonylation, β-hydroxybutyrylation, 2-hydroxyisobutyrylation, succinylation, and malonylation, have been identified. These novel HPTMs closely link substance metabolism to gene regulation, and an increasing number of relevant studies on the relationship between novel HPTMs and AD have become available. This review summarizes the current advances and implications of novel HPTMs in AD, providing insight into the deeper pathogenesis of AD and the development of novel drugs.
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Affiliation(s)
- Yuanyuan Qin
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, 25 Taiping Rd, Jiangyang District, Luzhou, 646000, Sichuan, People's Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, 646000, Sichuan, China
| | - Ping Yang
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, 25 Taiping Rd, Jiangyang District, Luzhou, 646000, Sichuan, People's Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, 646000, Sichuan, China
| | - Wanhong He
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, 25 Taiping Rd, Jiangyang District, Luzhou, 646000, Sichuan, People's Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, 646000, Sichuan, China
| | - Dongze Li
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, 25 Taiping Rd, Jiangyang District, Luzhou, 646000, Sichuan, People's Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, 646000, Sichuan, China
| | - Lisha Zeng
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, 25 Taiping Rd, Jiangyang District, Luzhou, 646000, Sichuan, People's Republic of China
| | - Junle Li
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, 25 Taiping Rd, Jiangyang District, Luzhou, 646000, Sichuan, People's Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, 646000, Sichuan, China
| | - Tingting Zhou
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, 25 Taiping Rd, Jiangyang District, Luzhou, 646000, Sichuan, People's Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, 646000, Sichuan, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, 646000, Sichuan, China
| | - Juan Peng
- Department of Rehabilitation, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Ling Cao
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, 25 Taiping Rd, Jiangyang District, Luzhou, 646000, Sichuan, People's Republic of China.
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, 646000, Sichuan, China.
| | - Wei Huang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, 25 Taiping Rd, Jiangyang District, Luzhou, 646000, Sichuan, People's Republic of China.
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Sichuan Clinical Research Center for Diabetes and Metabolic Diseases, Luzhou, 646000, Sichuan, China.
- Sichuan Clinical Research Center for Nephropathy, Luzhou, 646000, Sichuan, China.
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Mohammadipoor N, Naiebi R, Mazhari SA, Amooei F, Owrang M, Dastghaib S, Shams M, Maleki MH, Dastghaib S. Improved therapy for clear cell renal cell carcinoma: beta-hydroxybutyrate and quercetin target hypoxia-induced angiogenesis and multidrug resistance. Mol Biol Rep 2024; 51:379. [PMID: 38429605 DOI: 10.1007/s11033-024-09355-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 02/14/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is a form of kidney cancer characterized by dysregulated angiogenesis and multidrug resistance. Hypoxia-induced tumor progression plays a crucial role in ccRCC pathogenesis. Beta-hydroxybutyrate (BHB) and quercetin (QCT) have shown potential in targeting angiogenesis and drug resistance in various cancer types. This study investigates the combined effects of BHB and QCT in hypoxia-induced Caki-1 cells. METHODS Caki-1 cells were subjected to normoxic and hypoxic conditions and treated with BHB, QCT, or a combination of both. Cell-viability was assessed using the MTT assay, and mRNA expression levels of key angiogenesis-related genes (HIF-1α/2α, VEGF, Ang-1, Ang-2, and MDR4) were quantified through real-time PCR during 24 and 48 h. RESULTS BHB and QCT treatments, either alone or in combination, significantly reduced cell-viability in Caki-1 cells (p < 0.05). Moreover, the combined therapy demonstrated a potential effect in downregulating the expression of angiogenesis-related genes and MDR4 in hypoxia-induced cells, with a marked reduction in HIF-1α/2α, VEGF, Ang-1, and MDR4 expression (p < 0.05). The expression of Ang-2 increases significantly in presence of BHB combined QCT treatment. CONCLUSION This study highlights the promising potential of a combination therapy involving BHB and QCT in mitigating angiogenesis and MDR4 expression in hypoxia-induced ccRCC cells. These findings support further investigation into the underlying mechanisms and warrant clinical studies to evaluate the therapeutic value of this combined treatment for ccRCC patients. This research provides new insights into addressing the challenges posed by angiogenesis and drug resistance in ccRCC.
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Affiliation(s)
- Nima Mohammadipoor
- Department of Nutrition, School of Public Health, Iran University of Medical Science, Tehran, Iran
| | - Raika Naiebi
- Department of Hematology and Blood Banking, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Fateme Amooei
- Department of Anatomical Sciences, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Reproductive Biology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Marzieh Owrang
- Department of Anatomical Sciences, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Histomorphometry and Stereology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sahar Dastghaib
- School of Neurobiology Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Mesbah Shams
- Endocrinology and Metabolism Research Center, Shiraz University of Medical Science, P.O. Box: 71345-1744, Shiraz, Iran
| | - Mohammad Hassan Maleki
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, P.O. Box: 71348-45794, Shiraz, Iran.
| | - Sanaz Dastghaib
- Endocrinology and Metabolism Research Center, Shiraz University of Medical Science, P.O. Box: 71345-1744, Shiraz, Iran.
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Giuliani G, Longo VD. Ketone bodies in cell physiology and cancer. Am J Physiol Cell Physiol 2024; 326:C948-C963. [PMID: 38189128 DOI: 10.1152/ajpcell.00441.2023] [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: 09/12/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
Ketogenic diets (KDs), fasting, or prolonged physical activity elevate serum ketone bodies (KBs) levels, providing an alternative fuel source for the brain and other organs. However, KBs play pleiotropic roles that go beyond their role in energy production. KBs can act as signaling metabolites, influence gene expression, proteins' posttranslational modifications (PTMs), inflammation, and oxidative stress. Here, we explore the impact of KBs on mammalian cell physiology, including aging and tissue regeneration. We also concentrate on KBs and cancer, given the extensive evidence that dietary approaches inducing ketosis, including fasting-mimicking diets (FMDs) and KDs, can prevent cancer and affect tumor progression.
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Affiliation(s)
- Giacomo Giuliani
- Longevity Institute and Davis School of Gerontology, University of Southern California, Los Angeles, California, United States
| | - Valter D Longo
- Longevity Institute and Davis School of Gerontology, University of Southern California, Los Angeles, California, United States
- IFOM, FIRC Institute of Molecular Oncology, Milan, Italy
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Zeaiter N, Belot L, Cunin V, Nahed RA, Tokarska-Schlattner M, Le Gouellec A, Petosa C, Khochbin S, Schlattner U. Acetyl-CoA synthetase (ACSS2) does not generate butyryl- and crotonyl-CoA. Mol Metab 2024; 81:101903. [PMID: 38369012 PMCID: PMC10906504 DOI: 10.1016/j.molmet.2024.101903] [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: 12/30/2023] [Revised: 02/05/2024] [Accepted: 02/15/2024] [Indexed: 02/20/2024] Open
Abstract
Acetyl and other acyl groups from different short-chain fatty acids (SCFA) competitively modify histones at various lysine sites. To fully understand the functional significance of such histone acylation, a key epigenetic mechanism, it is crucial to characterize the cellular sources of the corresponding acyl-CoA molecules required for the lysine modification. Like acetate, SCFAs such as propionate, butyrate and crotonate are thought to be the substrates used to generate the corresponding acyl-CoAs by enzymes known as acyl-CoA synthetases. The acetyl-CoA synthetase, ACSS2, which produces acetyl-CoA from acetate in the nucleocytoplasmic compartment, has been proposed to also mediate the synthesis of acyl-CoAs such as butyryl- and crotonyl-CoA from the corresponding SCFAs. This idea is now widely accepted and is sparking new research projects. However, based on our direct in vitro experiments with purified or recombinant enzymes and structural considerations, we demonstrate that ACSS2 is unable to mediate the generation of non-acetyl acyl-CoAs like butyryl- and crotonyl-CoA. It is therefore essential to re-examine published data and corresponding discussions in the light of this new finding.
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Affiliation(s)
- Nour Zeaiter
- Univ. Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France
| | - Laura Belot
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Valérie Cunin
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, CHU Grenoble Alpes, TIMC, 38000 Grenoble, France
| | - Roland Abi Nahed
- Univ. Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France
| | | | - Audrey Le Gouellec
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, CHU Grenoble Alpes, TIMC, 38000 Grenoble, France
| | - Carlo Petosa
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Saadi Khochbin
- Univ. Grenoble Alpes, Inserm U1209 and CNRS UMR5309, Institute for Advanced Biosciences (IAB), 38058 Grenoble, France.
| | - Uwe Schlattner
- Univ. Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; Institut Universitaire de France, Paris, France.
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