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Charidemou E, Noberini R, Ghirardi C, Georgiou P, Marcou P, Theophanous A, Strati K, Keun H, Behrends V, Bonaldi T, Kirmizis A. Hyperacetylated histone H4 is a source of carbon contributing to lipid synthesis. EMBO J 2024; 43:1187-1213. [PMID: 38383863 PMCID: PMC10987603 DOI: 10.1038/s44318-024-00053-0] [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: 06/26/2023] [Revised: 01/12/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Histone modifications commonly integrate environmental cues with cellular metabolic outputs by affecting gene expression. However, chromatin modifications such as acetylation do not always correlate with transcription, pointing towards an alternative role of histone modifications in cellular metabolism. Using an approach that integrates mass spectrometry-based histone modification mapping and metabolomics with stable isotope tracers, we demonstrate that elevated lipids in acetyltransferase-depleted hepatocytes result from carbon atoms derived from deacetylation of hyperacetylated histone H4 flowing towards fatty acids. Consistently, enhanced lipid synthesis in acetyltransferase-depleted hepatocytes is dependent on histone deacetylases and acetyl-CoA synthetase ACSS2, but not on the substrate specificity of the acetyltransferases. Furthermore, we show that during diet-induced lipid synthesis the levels of hyperacetylated histone H4 decrease in hepatocytes and in mouse liver. In addition, overexpression of acetyltransferases can reverse diet-induced lipogenesis by blocking lipid droplet accumulation and maintaining the levels of hyperacetylated histone H4. Overall, these findings highlight hyperacetylated histones as a metabolite reservoir that can directly contribute carbon to lipid synthesis, constituting a novel function of chromatin in cellular metabolism.
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Affiliation(s)
- Evelina Charidemou
- Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milano, Via Festa del Perdono 7, 20122, Milano, Italy
| | - Chiara Ghirardi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milano, Via Festa del Perdono 7, 20122, Milano, Italy
| | - Polymnia Georgiou
- Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - Panayiota Marcou
- Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - Andria Theophanous
- Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - Katerina Strati
- Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - Hector Keun
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Volker Behrends
- School of Life and Health Sciences, Whitelands College, University of Roehampton, London, UK
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milano, Via Festa del Perdono 7, 20122, Milano, Italy
| | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus.
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52
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Konuma T, Zhou MM. Distinct Histone H3 Lysine 27 Modifications Dictate Different Outcomes of Gene Transcription. J Mol Biol 2024; 436:168376. [PMID: 38056822 DOI: 10.1016/j.jmb.2023.168376] [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: 09/29/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023]
Abstract
Site-specific histone modifications have long been recognized to play an important role in directing gene transcription in chromatin in biology of health and disease. However, concrete illustration of how different histone modifications in a site-specific manner dictate gene transcription outcomes, as postulated in the influential "Histone code hypothesis", introduced by Allis and colleagues in 2000, has been lacking. In this review, we summarize our latest understanding of the dynamic regulation of gene transcriptional activation, silence, and repression in chromatin that is directed distinctively by histone H3 lysine 27 acetylation, methylation, and crotonylation, respectively. This represents a special example of a long-anticipated verification of the "Histone code hypothesis."
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Affiliation(s)
- Tsuyoshi Konuma
- Graduate School of Medical Life Science, Yokohama 230-0045, Japan; School of Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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53
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Gates LA, Reis BS, Lund PJ, Paul MR, Leboeuf M, Djomo AM, Nadeem Z, Lopes M, Vitorino FN, Unlu G, Carroll TS, Birsoy K, Garcia BA, Mucida D, Allis CD. Histone butyrylation in the mouse intestine is mediated by the microbiota and associated with regulation of gene expression. Nat Metab 2024; 6:697-707. [PMID: 38413806 DOI: 10.1038/s42255-024-00992-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024]
Abstract
Post-translational modifications (PTMs) on histones are a key source of regulation on chromatin through impacting cellular processes, including gene expression1. These PTMs often arise from metabolites and are thus impacted by metabolism and environmental cues2-7. One class of metabolically regulated PTMs are histone acylations, which include histone acetylation, butyrylation, crotonylation and propionylation3,8. As these PTMs can be derived from short-chain fatty acids, which are generated by the commensal microbiota in the intestinal lumen9-11, we aimed to define how microbes impact the host intestinal chromatin landscape, mainly in female mice. Here we show that in addition to acetylation, intestinal epithelial cells from the caecum and distal mouse intestine also harbour high levels of butyrylation and propionylation on lysines 9 and 27 of histone H3. We demonstrate that these acylations are regulated by the microbiota and that histone butyrylation is additionally regulated by the metabolite tributyrin. Tributyrin-regulated gene programmes are correlated with histone butyrylation, which is associated with active gene-regulatory elements and levels of gene expression. Together, our study uncovers a regulatory layer of how the microbiota and metabolites influence the intestinal epithelium through chromatin, demonstrating a physiological setting in which histone acylations are dynamically regulated and associated with gene regulation.
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Affiliation(s)
- Leah A Gates
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, USA.
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
| | | | - Peder J Lund
- Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Matthew R Paul
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Marylene Leboeuf
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, USA
| | - Annaelle M Djomo
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, USA
| | - Zara Nadeem
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, USA
- Hunter College of the City University of New York, Yalow Honors Scholar Program, New York, NY, USA
| | - Mariana Lopes
- Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Francisca N Vitorino
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Gokhan Unlu
- Laboratory of Metabolic Regulation & Genetics, The Rockefeller University, New York, NY, USA
| | - Thomas S Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Kivanç Birsoy
- Laboratory of Metabolic Regulation & Genetics, The Rockefeller University, New York, NY, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - C David Allis
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY, USA
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54
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Gao J, Zhao Y, Chen C, Ning Q. MVNN-HNHC:A multi-view neural network for identification of human non-histone crotonylation sites. Anal Biochem 2024; 687:115426. [PMID: 38141798 DOI: 10.1016/j.ab.2023.115426] [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: 08/28/2023] [Revised: 11/21/2023] [Accepted: 12/06/2023] [Indexed: 12/25/2023]
Abstract
Crotonylation on lysine sites in human non-histone proteins plays a crucial role in biology activities. However, because traditional experimental methods for crotonylation site identification are time-consuming and labor-intensive, computational prediction methods have become increasingly popular in recent years. Despite its significance, crotonylation site prediction has received less attention in non-histone proteins than in histones. In this study, we proposed a Multi-View Neural Network for identification of Human Non-Histone Crotonylation sites, named MVNN-HNHC. MVNN-HNHC integrated multi-view encoding features and adaptive encoding features through multi-channel neural network to deeply learn about attribute differences between crotonylation sites and non-crotonylation sites from various aspects. In MVNN-HNHC, convolutional neural networks can obtain local information from these features, and bidirectional long short term memory networks were utilized to extract sequence information. Then, we employ the attention mechanism to fuse the outputs of various feature extraction modules. Finally, the fully connection network acted as the classifier to predict whether a lysine site was crotonylation site or non-crotonylation site. Performance metrics on independent test set, including sensitivity, specificity, accuracy, Matthews correlation coefficient, and area under the curve (AUC) values reach 80.06 %, 75.77 %, 77.06 %, 0.5203, and 0.7792, respectively. To verify the effectiveness of this method, we carry out a series of experiments and the results show that MVNN-HNHC is an effective tool for predicting crotonylation sites in non-histone proteins. The data and code are available on https://github.com/xbbxhbc/junjun0612.git.
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Affiliation(s)
- Jun Gao
- Department of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Yaomiao Zhao
- Department of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Chen Chen
- Naval Architecture and Ocean Engineering College, Dalian Maritime University, Dalian, 116026, China.
| | - Qiao Ning
- Department of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China.
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55
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Sun Y, Locasale JW. Histone butyrylation is a dietary link to epigenetics. Nat Metab 2024; 6:606-607. [PMID: 38413805 DOI: 10.1038/s42255-024-01013-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Affiliation(s)
- Yudong Sun
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
- Department of Structural and Molecular Biochemistry, North Carolina State University, Raleigh, NC, USA.
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56
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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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57
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Li J, Zeng G, Zhang Z, Wang Y, Shao M, Li C, Lu Z, Zhao Y, Zhang F, Ding W. Urban airborne PM 2.5 induces pulmonary fibrosis through triggering glycolysis and subsequent modification of histone lactylation in macrophages. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 273:116162. [PMID: 38458067 DOI: 10.1016/j.ecoenv.2024.116162] [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: 04/10/2023] [Revised: 02/05/2024] [Accepted: 02/26/2024] [Indexed: 03/10/2024]
Abstract
Airborne fine particulate matter (PM2.5) can cause pulmonary inflammation and even fibrosis, however, the underlying molecular mechanisms of the pathogenesis of PM2.5 exposure have not been fully appreciated. In the present study, we explored the dynamics of glycolysis and modification of histone lactylation in macrophages induced by PM2.5-exposure in both in vivo and in vitro models. Male C57BL/6 J mice were anesthetized and administrated with PM2.5 by intratracheal instillation once every other day for 4 weeks. Mouse RAW264.7 macrophages and alveolar epithelial MLE-12 cells were treated with PM2.5 for 24 h. We found that PM2.5 significantly increased lactate dehydrogenase (LDH) activities and lactate contents, and up-regulated the mRNA expression of key glycolytic enzymes in the lungs and bronchoalveolar lavage fluids of mice. Moreover, PM2.5 increased the levels of histone lactylation in both PM2.5-exposed lungs and RAW264.7 cells. The pro-fibrotic cytokines secreted from PM2.5-treated RAW264.7 cells triggered epithelial-mesenchymal transition (EMT) in MLE-12 cells through activating transforming growth factor-β (TGF-β)/Smad2/3 and VEGFA/ERK pathways. In contrast, LDHA inhibitor (GNE-140) pretreatment effectively alleviated PM2.5-induced pulmonary inflammation and fibrosis via inhibiting glycolysis and subsequent modification of histone lactylation in mice. Thus, our findings suggest that PM2.5-induced glycolysis and subsequent modification of histone lactylation play critical role in the PM2.5-associated pulmonary fibrosis.
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Affiliation(s)
- Jingyi Li
- Laboratory of Environment and Health, College of Life Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Guodong Zeng
- Laboratory of Environment and Health, College of Life Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Zezhong Zhang
- Laboratory of Environment and Health, College of Life Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yuanli Wang
- Laboratory of Environment and Health, College of Life Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Mengyao Shao
- Laboratory of Environment and Health, College of Life Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Chunjiang Li
- Laboratory of Environment and Health, College of Life Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Zhongbing Lu
- Laboratory of Environment and Health, College of Life Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yong Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing 100101, China.
| | - Fang Zhang
- Laboratory of Environment and Health, College of Life Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.
| | - Wenjun Ding
- Laboratory of Environment and Health, College of Life Sciences, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.
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58
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Liu T, Zhang M, Fan Y, Zhao L, Huang D, Zhao L, Tan M, Ye BC, Xu JY. Characterization of diverse lysine acylations in Bacillus thuringiensis: Substrate profiling and functional exploration. Proteomics 2024:e2300350. [PMID: 38491406 DOI: 10.1002/pmic.202300350] [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: 09/12/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/18/2024]
Abstract
Lysine acylation has been extensively investigated due to its regulatory role in a diverse range of biological functions across prokaryotic and eukaryotic species. In-depth acylomic profiles have the potential to enhance comprehension of the biological implications of organisms. However, the extent of research on global acylation profiles in microorganisms is limited. Here, four lysine acylomes were conducted in Bacillus thuringiensis by using the LC-MS/MS based proteomics combined with antibody-enrichment strategies, and a total of 3438 acetylated sites, 5797 propionylated sites, 1705 succinylated sites, and 925 malonylated sites were identified. The motif analysis of these modified proteins revealed a high conservation of glutamate in acetylation and propionylation, whereas such conservation was not observed in succinylation and malonylation modifications. Besides, conservation analysis showed that homologous acylated proteins in Bacillus subtilis and Escherichia coli were connected with ribosome and aminoacyl-tRNA biosynthesis. Further biological experiments showed that lysine acylation lowered the RNA binding ability of CodY and impaired the in vivo protein activity of MetK. In conclusion, our study expanded the current understanding of the global acylation in Bacillus, and the comparative analysis demonstrated that shared acylation proteins could play important roles in regulating both metabolism and RNA transcription progression.
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Affiliation(s)
- Tianxian Liu
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Mingya Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yameng Fan
- School of Pharmacy, Henan University, Kaifeng, China
| | - Lei Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
| | - Dan Huang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Liuchang Zhao
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, Henan University, Kaifeng, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jun-Yu Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China
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Wei S, Zhang J, Zhao R, Shi R, An L, Yu Z, Zhang Q, Zhang J, Yao Y, Li H, Wang H. Histone lactylation promotes malignant progression by facilitating USP39 expression to target PI3K/AKT/HIF-1α signal pathway in endometrial carcinoma. Cell Death Discov 2024; 10:121. [PMID: 38459014 PMCID: PMC10923933 DOI: 10.1038/s41420-024-01898-4] [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: 11/24/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/10/2024] Open
Abstract
Histone lactylation has been reported to involve in tumorigenesis and development. However, its biological regulatory mechanism in endometrial carcinoma (EC) is yet to be reported in detail. In the present study, we evaluated the modification levels of global lactylation in EC tissues by immunohistochemistry and western blot, and it was elevated. The non-metabolizable glucose analog 2-deoxy-d-glucose (2-DG) and oxamate treatment could decrease the level of lactylation so as to inhibit the proliferation and migration ability, induce apoptosis significantly, and arrest the cell cycle of EC cells. Mechanically, histone lactylation stimulated USP39 expression to promote tumor progression. Moreover, USP39 activated PI3K/AKT/HIF-1α signaling pathway via interacting with and stabilizing PGK1 to stimulate glycolysis. The results of present study suggest that histone lactylation plays an important role in the progression of EC by promoting the malignant biological behavior of EC cells, thus providing insights into potential therapeutic strategies for endometrial cancer.
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Affiliation(s)
- Sitian Wei
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Jun Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Rong Zhao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Rui Shi
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Lanfen An
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Zhicheng Yu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Qi Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Jiarui Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Yuwei Yao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Haojia Li
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China
| | - Hongbo Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, PR China.
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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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61
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Fang Y, Li X. Protein lysine four-carbon acylations in health and disease. J Cell Physiol 2024; 239:e30981. [PMID: 36815448 PMCID: PMC10704440 DOI: 10.1002/jcp.30981] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/24/2023]
Abstract
Lysine acylation, a type of posttranslational protein modification sensitive to cellular metabolic states, influences the functions of target proteins involved in diverse cellular processes. Particularly, lysine butyrylation, crotonylation, β-hydroxybutyrylation, and 2-hydroxyisobutyrylation, four types of four-carbon acylations, are modulated by intracellular concentrations of their respective acyl-CoAs and sensitive to alterations of nutrient metabolism induced by cellular and/or environmental signals. In this review, we discussed the metabolic pathways producing these four-carbon acyl-CoAs, the regulation of lysine acylation and deacylation, and the functions of individual lysine acylation.
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Affiliation(s)
- Yi Fang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
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Wang C, Cui W, Yu B, Zhou H, Cui Z, Guo P, Yu T, Feng Y. Role of succinylation modification in central nervous system diseases. Ageing Res Rev 2024; 95:102242. [PMID: 38387517 DOI: 10.1016/j.arr.2024.102242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Diseases of the central nervous system (CNS), including stroke, brain tumors, and neurodegenerative diseases, have a serious impact on human health worldwide, especially in elderly patients. The brain, which is one of the body's most metabolically dynamic organs, lacks fuel stores and therefore requires a continuous supply of energy substrates. Metabolic abnormalities are closely associated with the pathogenesis of CNS disorders. Post-translational modifications (PTMs) are essential regulatory mechanisms that affect the functions of almost all proteins. Succinylation, a broad-spectrum dynamic PTM, primarily occurs in mitochondria and plays a crucial regulatory role in various diseases. In addition to directly affecting various metabolic cycle pathways, succinylation serves as an efficient and rapid biological regulatory mechanism that establishes a connection between metabolism and proteins, thereby influencing cellular functions in CNS diseases. This review offers a comprehensive analysis of succinylation and its implications in the pathological mechanisms of CNS diseases. The objective is to outline novel strategies and targets for the prevention and treatment of CNS conditions.
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Affiliation(s)
- Chao Wang
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao 266000, People's Republic of China
| | - Weigang Cui
- Department of Cardiology, People's Hospital of Rizhao, Rizhao 276800, People's Republic of China
| | - Bing Yu
- Qingdao University, Qingdao 266000, People's Republic of China
| | - Han Zhou
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao 266000, People's Republic of China
| | - Zhenwen Cui
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao 266000, People's Republic of China
| | - Pin Guo
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao 266000, People's Republic of China
| | - Tao Yu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao 266000, People's Republic of China.
| | - Yugong Feng
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao 266000, People's Republic of China.
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Moreno-Yruela C, Fierz B. Revealing chromatin-specific functions of histone deacylases. Biochem Soc Trans 2024; 52:353-365. [PMID: 38189424 DOI: 10.1042/bst20230693] [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: 11/09/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/09/2024]
Abstract
Histone deacylases are erasers of Nε-acyl-lysine post-translational modifications and have been targeted for decades for the treatment of cancer, neurodegeneration and other disorders. Due to their relatively promiscuous activity on peptide substrates in vitro, it has been challenging to determine the individual targets and substrate identification mechanisms of each isozyme, and they have been considered redundant regulators. In recent years, biochemical and biophysical studies have incorporated the use of reconstituted nucleosomes, which has revealed a diverse and complex arsenal of recognition mechanisms by which histone deacylases may differentiate themselves in vivo. In this review, we first present the peptide-based tools that have helped characterize histone deacylases in vitro to date, and we discuss the new insights that nucleosome tools are providing into their recognition of histone substrates within chromatin. Then, we summarize the powerful semi-synthetic approaches that are moving forward the study of chromatin-associated factors, both in vitro by detailed single-molecule mechanistic studies, and in cells by live chromatin modification. We finally offer our perspective on how these new techniques would advance the study of histone deacylases. We envision that such studies will help elucidate the role of individual isozymes in disease and provide a platform for the development of the next generation of therapeutics.
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Affiliation(s)
- Carlos Moreno-Yruela
- Laboratory of Biophysical Chemistry of Macromolecules (LCBM), Institute of Chemical Sciences and Engineering (ISIC), School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department of Drug Design and Pharmacology (ILF), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules (LCBM), Institute of Chemical Sciences and Engineering (ISIC), School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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Shi L, Luo J, Wei X, Xu X, Tu L. The protective role of ginsenoside Rg3 in heart diseases and mental disorders. Front Pharmacol 2024; 15:1327033. [PMID: 38469409 PMCID: PMC10926849 DOI: 10.3389/fphar.2024.1327033] [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: 10/24/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024] Open
Abstract
Ginsenoside Rg3, a compound derived from Panax ginseng C. A. Mey., is increasingly recognized for its wide range of pharmacological effects. Under the worldwide healthcare challenges posed by heart diseases, Rg3 stands out as a key subject in modern research on Chinese herbal medicine, offering a novel approach to therapy. Mental illnesses are significant contributors to global disease mortality, and there is a well-established correlation between cardiac and psychiatric conditions. This connection is primarily due to dysfunctions in the sympathetic-adrenomedullary system (SAM), the hypothalamic-pituitary-adrenal axis, inflammation, oxidative stress, and brain-derived neurotrophic factor impairment. This review provides an in-depth analysis of Rg3's therapeutic benefits and its pharmacological actions in treating cardiac and mental health disorders respectively. Highlighting its potential for the management of these conditions, Rg3 emerges as a promising, multifunctional therapeutic agent.
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Affiliation(s)
- Lili Shi
- Department of Geriatric Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
| | - Jinlan Luo
- Department of Geriatric Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
| | - Xiupan Wei
- Department of Rehabilitation Medicine, Zhongda Hospital, Southeast University, Nanjing, China
| | - Xizhen Xu
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
- Division of Cardiology and Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ling Tu
- Department of Geriatric Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
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Shi J, Lv Q, Miao D, Xiong Z, Wei Z, Wu S, Tan D, Wang K, Zhang X. HIF2α Promotes Cancer Metastasis through TCF7L2-Dependent Fatty Acid Synthesis in ccRCC. RESEARCH (WASHINGTON, D.C.) 2024; 7:0322. [PMID: 38390305 PMCID: PMC10882601 DOI: 10.34133/research.0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/27/2024] [Indexed: 02/24/2024]
Abstract
Recent studies have highlighted the notable involvement of the crosstalk between hypoxia-inducible factor 2 alpha (HIF2α) and Wnt signaling components in tumorigenesis. However, the cellular function and precise regulatory mechanisms of HIF2α and Wnt signaling interactions in clear cell renal cell carcinoma (ccRCC) remain elusive. To analyze the correlation between HIF2α and Wnt signaling, we utilized the Cancer Genome Atlas - Kidney Renal Clear Cell Carcinoma (TCGA-KIRC) public database, HIF2α RNA sequencing data, and conducted luciferase reporter assays. A Wnt-related gene set was employed to identify key regulators of Wnt signaling controlled by HIF2α in ccRCC. Furthermore, we assessed the biological effects of TCF7L2 on ccRCC metastasis and lipid metabolism in both in vivo and in vitro settings. Our outcomes confirm TCF7L2 as a key gene involved in HIF2α-mediated regulation of the canonical Wnt pathway. Functional studies demonstrate that TCF7L2 promotes metastasis in ccRCC. Mechanistic investigations reveal that HIF2α stabilizes TCF7L2 mRNA in a method based on m6A by transcriptionally regulating METTL3. Up-regulation of TCF7L2 enhances cellular fatty acid oxidation, which promotes histone acetylation. This facilitates the transcription of genes connected to epithelial-mesenchymal transition and ultimately enhances metastasis of ccRCC. These outcomes offer a novel understanding into the involvement of lipid metabolism in the signaling pathway regulation, offering valuable implications for targeted treatment in ccRCC.
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Affiliation(s)
- Jian Shi
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
| | - Qingyang Lv
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
| | - Daojia Miao
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
| | - Zhiyong Xiong
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
| | - Zhihao Wei
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
| | - Songming Wu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
| | - Diaoyi Tan
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
| | - Keshan Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
| | - Xiaoping Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
- Institute of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, P. R. China
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Hu H, Hu W, Guo AD, Zhai L, Ma S, Nie HJ, Zhou BS, Liu T, Jia X, Liu X, Yao X, Tan M, Chen XH. Spatiotemporal and direct capturing global substrates of lysine-modifying enzymes in living cells. Nat Commun 2024; 15:1465. [PMID: 38368419 PMCID: PMC10874396 DOI: 10.1038/s41467-024-45765-3] [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: 12/13/2023] [Accepted: 02/04/2024] [Indexed: 02/19/2024] Open
Abstract
Protein-modifying enzymes regulate the dynamics of myriad post-translational modification (PTM) substrates. Precise characterization of enzyme-substrate associations is essential for the molecular basis of cellular function and phenotype. Methods for direct capturing global substrates of protein-modifying enzymes in living cells are with many challenges, and yet largely unexplored. Here, we report a strategy to directly capture substrates of lysine-modifying enzymes via PTM-acceptor residue crosslinking in living cells, enabling global profiling of substrates of PTM-enzymes and validation of PTM-sites in a straightforward manner. By integrating enzymatic PTM-mechanisms, and genetically encoding residue-selective photo-crosslinker into PTM-enzymes, our strategy expands the substrate profiles of both bacterial and mammalian lysine acylation enzymes, including bacterial lysine acylases PatZ, YiaC, LplA, TmcA, and YjaB, as well as mammalian acyltransferases GCN5 and Tip60, leading to discovery of distinct yet functionally important substrates and acylation sites. The concept of direct capturing substrates of PTM-enzymes via residue crosslinking may extend to the other types of amino acid residues beyond lysine, which has the potential to facilitate the investigation of diverse types of PTMs and substrate-enzyme interactive proteomics.
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Affiliation(s)
- Hao Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Wei Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - An-Di Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
| | - Song Ma
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hui-Jun Nie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Bin-Shan Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Tianxian Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xinglong Jia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xing Liu
- MOE Key Laboratory for Cellular Dynamics and Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Xuebiao Yao
- MOE Key Laboratory for Cellular Dynamics and Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, 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, Guangdong, 528400, China.
| | - Xiao-Hua 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.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
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Nshanian M, Geller BS, Gruber JJ, Chleilat F, Camarillo JM, Kelleher NL, Zhao Y, Snyder MP. Short-chain fatty acids propionate and butyrate control growth and differentiation linked to cellular metabolism. RESEARCH SQUARE 2024:rs.3.rs-3935562. [PMID: 38410440 PMCID: PMC10896393 DOI: 10.21203/rs.3.rs-3935562/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
The short-chain fatty acids (SCFA) propionate and butyrate are produced in large amounts by microbial metabolism and have been identified as unique acyl lysine histone marks. In order to better understand the function of these modifications we used ChIP-seq to map the genome-wide location of four short-chain acyl histone marks H3K18pr/bu and H4K12pr/bu in treated and untreated colorectal cancer (CRC) and normal cells, as well as in mouse intestines in vivo. We correlate these marks with open chromatin regions along with gene expression to access the function of the target regions. Our data demonstrate that propionate and butyrate act as promoters of growth, differentiation as well as ion transport. We propose a mechanism involving direct modification of specific genomic regions, resulting in increased chromatin accessibility, and in case of butyrate, opposing effects on the proliferation of normal versus CRC cells.
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Affiliation(s)
- Michael Nshanian
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA
| | - Benjamin S Geller
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA
| | - Joshua J Gruber
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA
| | - Faye Chleilat
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA
| | - Jeannie Marie Camarillo
- Department of Chemistry, Molecular Biosciences and Proteomics Center of Excellence, Northwestern University, Evanston, IL
| | - Neil L Kelleher
- Department of Chemistry, Molecular Biosciences and Proteomics Center of Excellence, Northwestern University, Evanston, IL
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Evanston, IL
| | - Yingming Zhao
- Ben May Department of Cancer Research Committee on Cancer Biology, University of Chicago; Chicago, IL
| | - Michael P Snyder
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA
- Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA
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Xia Y, Pei T, Zhao J, Wang Z, Shen Y, Yang Y, Liang J. Long noncoding RNA H19: functions and mechanisms in regulating programmed cell death in cancer. Cell Death Discov 2024; 10:76. [PMID: 38355574 PMCID: PMC10866971 DOI: 10.1038/s41420-024-01832-8] [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: 09/11/2023] [Revised: 01/16/2024] [Accepted: 01/25/2024] [Indexed: 02/16/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) are a group of noncoding RNAs with transcript lengths of >200 nucleotides. Mounting evidence suggests that lncRNAs are closely associated with tumorigenesis. LncRNA H19 (H19) was the first lncRNA to function as an oncogene in many malignant tumors. Apart from the established role of H19 in promoting cell growth, proliferation, invasion, migration, epithelial-mesenchymal transition (EMT), and metastasis, it has been recently discovered that H19 also inhibits programmed cell death (PCD) of cancer cells. In this review, we summarize the mechanisms by which H19 regulates PCD in cancer cells through various signaling pathways, molecular mechanisms, and epigenetic modifications. H19 regulates PCD through the Wnt/β-catenin pathway and the PI3K-Akt-mTOR pathway. It also acts as a competitive endogenous RNA (ceRNA) in PCD regulation. The interaction between H19 and RNA-binding proteins (RBP) regulates apoptosis in cancer. Moreover, epigenetic modifications, including DNA and RNA methylation and histone modifications, are also involved in H19-associated PCD regulation. In conclusion, we summarize the role of H19 signaling via PCD in cancer chemoresistance, highlighting the promising research significance of H19 as a therapeutic target. We hope that our study will contribute to a broader understanding of H19 in cancer development and treatment.
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Affiliation(s)
- Yuyang Xia
- Department of Urology, Institute of Urology, West China Hospital, West China School of Medicine, Sichuan University, 610041, Chengdu, China
| | - Tianjiao Pei
- Department of Reproductive Medicine, West China Second University Hospital of Sichuan University, Chengdu, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, China.
| | - Junjie Zhao
- Department of Urology, Institute of Urology, West China Hospital, West China School of Medicine, Sichuan University, 610041, Chengdu, China
| | - Zilin Wang
- Department of Urology, Institute of Urology, West China Hospital, West China School of Medicine, Sichuan University, 610041, Chengdu, China
| | - Yu Shen
- Department of Urology, Institute of Urology, West China Hospital, West China School of Medicine, Sichuan University, 610041, Chengdu, China
| | - Yang Yang
- Department of Urology, Institute of Urology, West China Hospital, West China School of Medicine, Sichuan University, 610041, Chengdu, China
| | - Jiayu Liang
- Department of Urology, Institute of Urology, West China Hospital, West China School of Medicine, Sichuan University, 610041, Chengdu, China.
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69
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Xie JY, Ju J, Zhou P, Chen H, Wang SC, Wang K, Wang T, Chen XZ, Chen YC, Wang K. The mechanisms, regulations, and functions of histone lysine crotonylation. Cell Death Discov 2024; 10:66. [PMID: 38331935 PMCID: PMC10853258 DOI: 10.1038/s41420-024-01830-w] [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: 10/23/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
Histone lysine crotonylation (Kcr) is a new acylation modification first discovered in 2011, which has important biological significance for gene expression, cell development, and disease treatment. In the past over ten years, numerous signs of progress have been made in the research on the biochemistry of Kcr modification, especially a series of Kcr modification-related "reader", "eraser", and "writer" enzyme systems are identified. The physiological function of crotonylation and its correlation with development, heredity, and spermatogenesis have been paid more and more attention. However, the development of disease is usually associated with abnormal Kcr modification. In this review, we summarized the identification of crotonylation modification, Kcr-related enzyme system, biological functions, and diseases caused by abnormal Kcr. This knowledge supplies a theoretical basis for further exploring the function of crotonylation in the future.
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Affiliation(s)
- Jing-Yi Xie
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China
| | - Jie Ju
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China.
- Department of Physiology, School of Basic Medical Sciences, Shandong Second Medical University, Weifang, 261053, China.
| | - Ping Zhou
- State Key Laboratory of Cardiovascular Disease, Heart Failure center, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100037, China
| | - Hao Chen
- Department of Physiology, School of Basic Medical Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Shao-Cong Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China
| | - Kai Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China
| | - Tao Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China
| | - Xin-Zhe Chen
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China
| | - Yan-Chun Chen
- Neurologic Disorders and Regenerative Repair Laboratory, Shandong Second Medical University, Weifang, 261053, China.
| | - Kun Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China.
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Shi H, Cui W, Qin Y, Chen L, Yu T, Lv J. A glimpse into novel acylations and their emerging role in regulating cancer metastasis. Cell Mol Life Sci 2024; 81:76. [PMID: 38315203 PMCID: PMC10844364 DOI: 10.1007/s00018-023-05104-z] [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: 08/30/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
Metastatic cancer is a major cause of cancer-related mortality; however, the complex regulation process remains to be further elucidated. A large amount of preliminary investigations focus on the role of epigenetic mechanisms in cancer metastasis. Notably, the posttranslational modifications were found to be critically involved in malignancy, thus attracting considerable attention. Beyond acetylation, novel forms of acylation have been recently identified following advances in mass spectrometry, proteomics technologies, and bioinformatics, such as propionylation, butyrylation, malonylation, succinylation, crotonylation, 2-hydroxyisobutyrylation, lactylation, among others. These novel acylations play pivotal roles in regulating different aspects of energy mechanism and mediating signal transduction by covalently modifying histone or nonhistone proteins. Furthermore, these acylations and their modifying enzymes show promise regarding the diagnosis and treatment of tumors, especially tumor metastasis. Here, we comprehensively review the identification and characterization of 11 novel acylations, and the corresponding modifying enzymes, highlighting their significance for tumor metastasis. We also focus on their potential application as clinical therapeutic targets and diagnostic predictors, discussing the current obstacles and future research prospects.
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Affiliation(s)
- Huifang Shi
- Clinical Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China
| | - Weigang Cui
- Central Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China
| | - Yan Qin
- Clinical Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China
| | - Lei Chen
- Clinical Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China
| | - Tao Yu
- Center for Regenerative Medicine, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Qingdao, 266000, China.
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Qingdao, 266000, China.
| | - Jie Lv
- Clinical Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China.
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Du J, Liu N, Ma L, Liu R, Zuo D, Lan X, Yang J, Wei W, Peng X, Yu J. Antidepressant effect of the novel histone deacetylase-5 inhibitor T2943 in a chronic restraint stress mouse model. Biomed Pharmacother 2024; 171:116176. [PMID: 38242038 DOI: 10.1016/j.biopha.2024.116176] [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: 11/15/2023] [Revised: 01/12/2024] [Accepted: 01/13/2024] [Indexed: 01/21/2024] Open
Abstract
Depression is a prevalent and debilitating psychiatric illness. However, the antidepressant drugs currently prescribed are only effective in a limited group of patients. Histone modifications mediated by histone acetylation are considered to play an important role in the pathogenesis and treatment of depression. Recent studies have revealed that histone deacetylase inhibitors may be involved in the pathogenesis of depression and the underlying mechanism of the antidepressant therapeutic action. Here, we first conducted virtual screening of histone deacetylase-5 (HDAC5) inhibitors against HDAC5, a target closely related to depression, and identified compound T2943, further verifying its inhibitory effect on enzyme activities in vitro. After stereotaxic injection of T2943 into the hippocampus of mice, the antidepressant effect of T2943 was evaluated using behavioral experiments. We also used different proteomic and molecular biology analyses to determine and confirm that T2943 promoted histone 3 lysine 14 acetylation (H3K14ac) by inhibiting HDAC5 activity. Following the overexpression of adenoviral HDAC5 in the hippocampus of mice and subsequent behavioral analyses, we confirmed that T2943 exerts antidepressant effects by inhibiting HDAC5 activity. Our findings highlight the efficacy of targeting HDAC5 to treat depression and demonstrate the potential of using T2943 as an antidepressant.
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Affiliation(s)
- Juan Du
- College of Basic Medicine, Ningxia Medical University, Yin Chuan, China; Department of Pharmacology, College of Pharmacy, Ningxia Medical University, Yin Chuan, China; Ningxia Key Laboratory of Craniocerebral Diseases, Ningxia Medical University, Yin Chuan, China
| | - Ning Liu
- Department of Pharmacology, College of Pharmacy, Ningxia Medical University, Yin Chuan, China
| | - Lin Ma
- Department of Pharmacology, College of Pharmacy, Ningxia Medical University, Yin Chuan, China
| | - Ruyun Liu
- Department of Pharmacology, College of Pharmacy, Ningxia Medical University, Yin Chuan, China
| | - Di Zuo
- Ningxia Key Laboratory of Craniocerebral Diseases, Ningxia Medical University, Yin Chuan, China
| | - Xiaobing Lan
- Department of Pharmacology, College of Pharmacy, Ningxia Medical University, Yin Chuan, China
| | - Jiamei Yang
- Department of Pharmacology, College of Pharmacy, Ningxia Medical University, Yin Chuan, China
| | - Wei Wei
- Department of Pharmacology, College of Pharmacy, Ningxia Medical University, Yin Chuan, China
| | - Xiaodong Peng
- Department of Pharmacology, College of Pharmacy, Ningxia Medical University, Yin Chuan, China.
| | - Jianqiang Yu
- Department of Pharmacology, College of Pharmacy, Ningxia Medical University, Yin Chuan, China.
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72
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Li Y, Liu A, Chen K, Li L, Zhang X, Zou F, Zhang X, Meng X. Sodium butyrate alleviates lead-induced neuroinflammation and improves cognitive and memory impairment through the ACSS2/H3K9ac/BDNF pathway. ENVIRONMENT INTERNATIONAL 2024; 184:108479. [PMID: 38340407 DOI: 10.1016/j.envint.2024.108479] [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: 09/29/2023] [Revised: 12/09/2023] [Accepted: 02/02/2024] [Indexed: 02/12/2024]
Abstract
Lead is an environmentally widespread neurotoxic pollutant. Although the neurotoxicity of lead has been found to be closely associated with metabolic disorders, the effects of short-chain fatty acids on the neurotoxicity of lead and its mechanisms have not yet been explored. In this study, the results of open field tests and Morris water maze tests demonstrated that chronic lead exposure caused learning and memory deficits and anxiety-like symptoms in mice. The serum butyric acid content of lead-treated mice decreased in a dose-dependent manner, and oral administration of butyrate significantly improved cognitive memory impairment and anxiety symptoms in lead-exposed mice. Moreover, butyrate alleviated neuroinflammation caused by lead exposure by inhibiting the STAT3 signaling in microglia. Butyrate also promoted the expression of acetyl-CoA synthetase ACSS2 in hippocampal neurons, thereby increasing the content of acetyl-CoA and restoring the expression of both histone H3K9ac and the downstream BDNF. We also found that the median butyric acid concentration in high-lead exposure humans was remarkably lower than that in the low-lead exposure humans (45.16 μg/L vs. 60.92 μg/L, P < 0.01), and that butyric acid significantly mediated the relationship of lead exposure with the Montreal cognitive assessment scores, with a contribution rate of 27.57 %. In conclusion, our results suggest that butyrate supplementation is a possible therapeutic strategy for lead-induced neurotoxicity.
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Affiliation(s)
- Yunting Li
- Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Anfei Liu
- Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Kaiju Chen
- Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Lifan Li
- Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Xiaoshun Zhang
- Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Fei Zou
- Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Xingmei Zhang
- Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiaojing Meng
- Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China.
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73
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Schnee P, Pleiss J, Jeltsch A. Approaching the catalytic mechanism of protein lysine methyltransferases by biochemical and simulation techniques. Crit Rev Biochem Mol Biol 2024; 59:20-68. [PMID: 38449437 DOI: 10.1080/10409238.2024.2318547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/10/2024] [Indexed: 03/08/2024]
Abstract
Protein lysine methyltransferases (PKMTs) transfer up to three methyl groups to the side chains of lysine residues in proteins and fulfill important regulatory functions by controlling protein stability, localization and protein/protein interactions. The methylation reactions are highly regulated, and aberrant methylation of proteins is associated with several types of diseases including neurologic disorders, cardiovascular diseases, and various types of cancer. This review describes novel insights into the catalytic machinery of various PKMTs achieved by the combined application of biochemical experiments and simulation approaches during the last years, focusing on clinically relevant and well-studied enzymes of this group like DOT1L, SMYD1-3, SET7/9, G9a/GLP, SETD2, SUV420H2, NSD1/2, different MLLs and EZH2. Biochemical experiments have unraveled many mechanistic features of PKMTs concerning their substrate and product specificity, processivity and the effects of somatic mutations observed in PKMTs in cancer cells. Structural data additionally provided information about the substrate recognition, enzyme-substrate complex formation, and allowed for simulations of the substrate peptide interaction and mechanism of PKMTs with atomistic resolution by molecular dynamics and hybrid quantum mechanics/molecular mechanics methods. These simulation technologies uncovered important mechanistic details of the PKMT reaction mechanism including the processes responsible for the deprotonation of the target lysine residue, essential conformational changes of the PKMT upon substrate binding, but also rationalized regulatory principles like PKMT autoinhibition. Further developments are discussed that could bring us closer to a mechanistic understanding of catalysis of this important class of enzymes in the near future. The results described here illustrate the power of the investigation of enzyme mechanisms by the combined application of biochemical experiments and simulation technologies.
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Affiliation(s)
- Philipp Schnee
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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74
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Jackson BT, Finley LWS. Metabolic regulation of the hallmarks of stem cell biology. Cell Stem Cell 2024; 31:161-180. [PMID: 38306993 PMCID: PMC10842269 DOI: 10.1016/j.stem.2024.01.003] [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: 12/03/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Stem cells perform many different functions, each of which requires specific metabolic adaptations. Over the past decades, studies of pluripotent and tissue stem cells have uncovered a range of metabolic preferences and strategies that correlate with or exert control over specific cell states. This review aims to describe the common themes that emerge from the study of stem cell metabolism: (1) metabolic pathways supporting stem cell proliferation, (2) metabolic pathways maintaining stem cell quiescence, (3) metabolic control of cellular stress responses and cell death, (4) metabolic regulation of stem cell identity, and (5) metabolic requirements of the stem cell niche.
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Affiliation(s)
- Benjamin T Jackson
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY, USA
| | - Lydia W S Finley
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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75
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Neja S, Dashwood WM, Dashwood RH, Rajendran P. Histone Acyl Code in Precision Oncology: Mechanistic Insights from Dietary and Metabolic Factors. Nutrients 2024; 16:396. [PMID: 38337680 PMCID: PMC10857208 DOI: 10.3390/nu16030396] [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: 12/30/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
Cancer etiology involves complex interactions between genetic and non-genetic factors, with epigenetic mechanisms serving as key regulators at multiple stages of pathogenesis. Poor dietary habits contribute to cancer predisposition by impacting DNA methylation patterns, non-coding RNA expression, and histone epigenetic landscapes. Histone post-translational modifications (PTMs), including acyl marks, act as a molecular code and play a crucial role in translating changes in cellular metabolism into enduring patterns of gene expression. As cancer cells undergo metabolic reprogramming to support rapid growth and proliferation, nuanced roles have emerged for dietary- and metabolism-derived histone acylation changes in cancer progression. Specific types and mechanisms of histone acylation, beyond the standard acetylation marks, shed light on how dietary metabolites reshape the gut microbiome, influencing the dynamics of histone acyl repertoires. Given the reversible nature of histone PTMs, the corresponding acyl readers, writers, and erasers are discussed in this review in the context of cancer prevention and treatment. The evolving 'acyl code' provides for improved biomarker assessment and clinical validation in cancer diagnosis and prognosis.
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Affiliation(s)
- Sultan Neja
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX 77030, USA; (S.N.); (W.M.D.)
| | - Wan Mohaiza Dashwood
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX 77030, USA; (S.N.); (W.M.D.)
| | - Roderick H. Dashwood
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX 77030, USA; (S.N.); (W.M.D.)
- Department of Translational Medical Sciences, Texas A&M College of Medicine, Houston, TX 77030, USA
| | - Praveen Rajendran
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX 77030, USA; (S.N.); (W.M.D.)
- Department of Translational Medical Sciences, Texas A&M College of Medicine, Houston, TX 77030, USA
- Antibody & Biopharmaceuticals Core, Texas A&M Health, Houston, TX 77030, USA
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Nshanian M, Geller BS, Gruber JJ, Chleilat F, Camarillo JM, Kelleher NL, Zhao Y, Snyder MP. Short-chain fatty acids propionate and butyrate control growth and differentiation linked to cellular metabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575111. [PMID: 38293216 PMCID: PMC10827076 DOI: 10.1101/2024.01.11.575111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The short-chain fatty acids (SCFA) propionate and butyrate are produced in large amounts by microbial metabolism and have been identified as unique acyl lysine histone marks. In order to better understand the function of these modifications we used ChIP-seq to map the genome-wide location of four short-chain acyl histone marks H3K18pr/bu and H4K12pr/bu in treated and untreated colorectal cancer (CRC) and normal cells, as well as in mouse intestines in vivo . We correlate these marks with open chromatin regions along with gene expression to access the function of the target regions. Our data demonstrate that propionate and butyrate act as promoters of growth, differentiation as well as ion transport. We propose a mechanism involving direct modification of specific genomic regions, resulting in increased chromatin accessibility, and in case of butyrate, opposing effects on the proliferation of normal versus CRC cells.
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77
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Adejor J, Tumukunde E, Li G, Lin H, Xie R, Wang S. Impact of Lysine Succinylation on the Biology of Fungi. Curr Issues Mol Biol 2024; 46:1020-1046. [PMID: 38392183 PMCID: PMC10888112 DOI: 10.3390/cimb46020065] [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: 12/09/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 02/24/2024] Open
Abstract
Post-translational modifications (PTMs) play a crucial role in protein functionality and the control of various cellular processes and secondary metabolites (SMs) in fungi. Lysine succinylation (Ksuc) is an emerging protein PTM characterized by the addition of a succinyl group to a lysine residue, which induces substantial alteration in the chemical and structural properties of the affected protein. This chemical alteration is reversible, dynamic in nature, and evolutionarily conserved. Recent investigations of numerous proteins that undergo significant succinylation have underscored the potential significance of Ksuc in various biological processes, encompassing normal physiological functions and the development of certain pathological processes and metabolites. This review aims to elucidate the molecular mechanisms underlying Ksuc and its diverse functions in fungi. Both conventional investigation techniques and predictive tools for identifying Ksuc sites were also considered. A more profound comprehension of Ksuc and its impact on the biology of fungi have the potential to unveil new insights into post-translational modification and may pave the way for innovative approaches that can be applied across various clinical contexts in the management of mycotoxins.
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Affiliation(s)
- John Adejor
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Elisabeth Tumukunde
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guoqi Li
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hong Lin
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Rui Xie
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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78
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Wang Q, Su Y, Sun R, Xiong X, Guo K, Wei M, Yang G, Ru Y, Zhang Z, Li J, Zhang J, Qiao Q, Li X. MIIP downregulation drives colorectal cancer progression through inducing peri-cancerous adipose tissue browning. Cell Biosci 2024; 14:12. [PMID: 38245780 PMCID: PMC10800076 DOI: 10.1186/s13578-023-01179-0] [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: 05/05/2023] [Accepted: 12/05/2023] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND The enrichment of peri-cancerous adipose tissue is a distinctive feature of colorectal cancer (CRC), accelerating disease progression and worsening prognosis. The communication between tumor cells and adjacent adipocytes plays a crucial role in CRC advancement. However, the precise regulatory mechanisms are largely unknown. This study aims to explore the mechanism of migration and invasion inhibitory protein (MIIP) downregulation in the remodeling of tumor cell-adipocyte communication and its role in promoting CRC. RESULTS MIIP expression was found to be decreased in CRC tissues and closely associated with adjacent adipocyte browning. In an in vitro co-culture model, adipocytes treated with MIIP-downregulated tumor supernatant exhibited aggravated browning and lipolysis. This finding was further confirmed in subcutaneously allografted mice co-injected with adipocytes and MIIP-downregulated murine CRC cells. Mechanistically, MIIP interacted with the critical lipid mobilization factor AZGP1 and regulated AZGP1's glycosylation status by interfering with its association with STT3A. MIIP downregulation promoted N-glycosylation and over-secretion of AZGP1 in tumor cells. Subsequently, AZGP1 induced adipocyte browning and lipolysis through the cAMP-PKA pathway, releasing free fatty acids (FFAs) into the microenvironment. These FFAs served as the primary energy source, promoting CRC cell proliferation, invasion, and apoptosis resistance, accompanied by metabolic reprogramming. In a tumor-bearing mouse model, inhibition of β-adrenergic receptor or FFA uptake, combined with oxaliplatin, significantly improved therapeutic efficacy in CRC with abnormal MIIP expression. CONCLUSIONS Our data demonstrate that MIIP plays a regulatory role in the communication between CRC and neighboring adipose tissue by regulating AZGP1 N-glycosylation and secretion. MIIP reduction leads to AZGP1 oversecretion, resulting in adipose browning-induced CRC rapid progression and poor prognosis. Inhibition of β-adrenergic receptor or FFA uptake, combined with oxaliplatin, may represent a promising therapeutic strategy for CRC with aberrant MIIP expression.
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Affiliation(s)
- Qinhao Wang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China.
| | - Yuanyuan Su
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China
- Department of Pharmacology, Medical College, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Ruiqi Sun
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Xin Xiong
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China
| | - Kai Guo
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China
| | - Mengying Wei
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China
| | - Guodong Yang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China
| | - Yi Ru
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China
| | - Zhengxiang Zhang
- Department of Pharmacology, Medical College, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Jing Li
- Department of Orthopedics, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China
| | - Jing Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. School of Medicine, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Qing Qiao
- Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, No. 569 Xinsi Road, Xi'an, 710038, Shaanxi, China.
| | - Xia Li
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China.
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79
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Cheng Z, Huang H, Li M, Chen Y. Proteomic analysis identifies PFKP lactylation in SW480 colon cancer cells. iScience 2024; 27:108645. [PMID: 38155775 PMCID: PMC10753066 DOI: 10.1016/j.isci.2023.108645] [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: 02/18/2023] [Revised: 06/23/2023] [Accepted: 12/01/2023] [Indexed: 12/30/2023] Open
Abstract
Aerobic glycolysis is a pivotal hallmark of cancers, including colorectal cancer. Evidence shows glycolytic enzymes are regulated by post-translational modifications (PTMs), thereby affecting the Warburg effect and reprograming cancer metabolism. Lysine lactylation is a PTM reported in 2019 in histones. In this study, we identified protein lactylation in FHC cells and SW480 colon cancer cells through mass spectrometry. Totally, 637 lysine lactylation sites in 444 proteins were identified in FHC and SW480 cells. Lactylated proteins were enriched in the glycolysis pathway, and we identified lactylation sites in phosphofructokinase, platelet (PFKP) lysine 688 and aldolase A (ALDOA) lysine 147. We also showed that PFKP lactylation directly attenuated enzyme activity. Collectively, our study presented a resource to investigate proteome-wide lactylation in SW480 cells and found PFKP lactylation led to activity inhibition, indicating that lactic acid and lactylated PFKP may form a negative feedback pathway in glycolysis and lactic acid production.
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Affiliation(s)
- Zhe Cheng
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Huichao Huang
- Department of Infectious Disease, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Maoyu Li
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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80
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Ma Q, Zeng Q, Wang K, Qian M, Li J, Wang H, Zhang H, Jiang J, Chen Z, Huang W. Acetyltransferase P300 Regulates Glucose Metabolic Reprogramming through Catalyzing Succinylation in Lung Cancer. Int J Mol Sci 2024; 25:1057. [PMID: 38256128 PMCID: PMC10816063 DOI: 10.3390/ijms25021057] [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: 10/17/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Aberrant protein post-translational modification is a hallmark of malignant tumors. Lysine succinylation (Ksucc) plays a vital role in cell energy metabolism in various cancers. However, whether succinylation can be catalyzed by acetyltransferase p300 remains unclear. In this study, we unveiled that p300 is a "writer" for succinylation, and p300-mediated Ksucc promotes cell glycometabolism in lung adenocarcinoma (LUAD). Specifically, our succinylome data revealed that EP300 deficiency leads to the systemic reduction of Ksucc, and 79.55% of the p300-succinylated proteins were found in the cytoplasm, which were primarily enriched in the carbohydrate metabolism process. Interestingly, deleting EP300 led to a notable decrease in Ksucc levels on several glycolytic enzymes, especially Phosphoglycerate Kinase 1 (PGK1). Mutation of the succinylated site of PGK1 notably hindered cell glycolysis and lactic acid excretion. Metabolomics in vivo indicated that p300-caused metabolic reprogramming was mainly attributed to the altered carbohydrate metabolism. In addition, 89.35% of LUAD patients exhibited cytoplasmic localization of p300, with higher levels in tumor tissues than adjacent normal tissues. High levels of p300 correlated with advanced tumor stages and poor prognosis of LUAD patients. Briefly, we disclose the activity of p300 to catalyze succinylation, which contributes to cell glucose metabolic reprogramming and malignant progression of lung cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zhinan Chen
- Department of Cell Biology, National Translational Science Center for Molecular Medicine, Fourth Military Medical University, Xi’an 710032, China
| | - Wan Huang
- Department of Cell Biology, National Translational Science Center for Molecular Medicine, Fourth Military Medical University, Xi’an 710032, China
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81
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Tao Z, Wang Y. The health benefits of dietary short-chain fatty acids in metabolic diseases. Crit Rev Food Sci Nutr 2024:1-14. [PMID: 38189336 DOI: 10.1080/10408398.2023.2297811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Short-chain fatty acids (SCFAs) are a subset of fatty acids that play crucial roles in maintaining normal physiology and developing metabolic diseases, such as obesity, diabetes, cardiovascular disease, and liver disease. Even though dairy products and vegetable oils are the direct dietary sources of SCFAs, their quantities are highly restricted. SCFAs are produced indirectly through microbial fermentation of fibers. The biological roles of SCFAs in human health and metabolic diseases are mainly due to their receptors, GPR41 and GPR43, FFAR2 and FFAR3. Additionally, it has been demonstrated that SCFAs modulate DNMTs and HDAC activities, inhibit NF-κB-STAT signaling, and regulate G(i/o)βγ-PLC-PKC-PTEN signaling and PPARγ-UCP2-AMPK autophagic signaling, thus mitigating metabolic diseases. Recent studies have uncovered that SCFAs play crucial roles in epigenetic modifications of DNAs, RNAs, and post-translational modifications of proteins, which are critical regulators of metabolic health and diseases. At the same time, dietary recommendations for the purpose of SCFAs have been proposed. The objective of the review is to summarize the most recent research on the role of dietary SCFAs in metabolic diseases, especially the signal transduction of SCFAs in metabolic diseases and their functional efficacy in different backgrounds and models of metabolic diseases, at the same time, to provide dietary and nutritional recommendations for using SCFAs as food ingredients to prevent metabolic diseases.
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Affiliation(s)
- Zhipeng Tao
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts, USA
- Department of Nutrition Sciences, Texas Woman's University, Denton, Texas, USA
| | - Yao Wang
- Diabetes Center, University of California San Francisco, San Francisco, California, USA
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82
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Theys C, Vanderhaeghen T, Van Dijck E, Peleman C, Scheepers A, Ibrahim J, Mateiu L, Timmermans S, Vanden Berghe T, Francque SM, Van Hul W, Libert C, Vanden Berghe W. Loss of PPARα function promotes epigenetic dysregulation of lipid homeostasis driving ferroptosis and pyroptosis lipotoxicity in metabolic dysfunction associated Steatotic liver disease (MASLD). FRONTIERS IN MOLECULAR MEDICINE 2024; 3:1283170. [PMID: 39086681 PMCID: PMC11285560 DOI: 10.3389/fmmed.2023.1283170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/14/2023] [Indexed: 08/02/2024]
Abstract
Metabolic Dysfunction Associated Steatotic Liver Disease (MASLD) is a growing epidemic with an estimated prevalence of 20%-30% in Europe and the most common cause of chronic liver disease worldwide. The onset and progression of MASLD are orchestrated by an interplay of the metabolic environment with genetic and epigenetic factors. Emerging evidence suggests altered DNA methylation pattern as a major determinant of MASLD pathogenesis coinciding with progressive DNA hypermethylation and gene silencing of the liver-specific nuclear receptor PPARα, a key regulator of lipid metabolism. To investigate how PPARα loss of function contributes to epigenetic dysregulation in MASLD pathology, we studied DNA methylation changes in liver biopsies of WT and hepatocyte-specific PPARα KO mice, following a 6-week CDAHFD (choline-deficient, L-amino acid-defined, high-fat diet) or chow diet. Interestingly, genetic loss of PPARα function in hepatocyte-specific KO mice could be phenocopied by a 6-week CDAHFD diet in WT mice which promotes epigenetic silencing of PPARα function via DNA hypermethylation, similar to MASLD pathology. Remarkably, genetic and lipid diet-induced loss of PPARα function triggers compensatory activation of multiple lipid sensing transcription factors and epigenetic writer-eraser-reader proteins, which promotes the epigenetic transition from lipid metabolic stress towards ferroptosis and pyroptosis lipid hepatoxicity pathways associated with advanced MASLD. In conclusion, we show that PPARα function is essential to support lipid homeostasis and to suppress the epigenetic progression of ferroptosis-pyroptosis lipid damage associated pathways towards MASLD fibrosis.
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Affiliation(s)
- Claudia Theys
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Tineke Vanderhaeghen
- Center for Inflammation Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | | | - Cedric Peleman
- Laboratory of Experimental Medicine and Pediatrics, Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
- Pathophysiology Lab, Infla-Med Centre of Excellence, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Anne Scheepers
- Center of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Joe Ibrahim
- Center of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Ligia Mateiu
- Center of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Steven Timmermans
- Center for Inflammation Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Tom Vanden Berghe
- Center for Inflammation Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Pathophysiology Lab, Infla-Med Centre of Excellence, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sven M. Francque
- Laboratory of Experimental Medicine and Pediatrics, Infla-Med Centre of Excellence, University of Antwerp, Antwerp, Belgium
- Department of Gastroenterology and Hepatology, Antwerp University Hospital, Edegem, Belgium
| | - Wim Van Hul
- Center of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Claude Libert
- Center for Inflammation Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Wim Vanden Berghe
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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83
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Bacigalupa ZA, Landis MD, Rathmell JC. Nutrient inputs and social metabolic control of T cell fate. Cell Metab 2024; 36:10-20. [PMID: 38118440 PMCID: PMC10872404 DOI: 10.1016/j.cmet.2023.12.009] [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: 07/12/2023] [Revised: 10/25/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023]
Abstract
Cells in multicellular organisms experience diverse neighbors, signals, and evolving physical environments that drive functional and metabolic demands. To maintain proper development and homeostasis while avoiding inappropriate cell proliferation or death, individual cells interact with their neighbors via "social" cues to share and partition available nutrients. Metabolic signals also contribute to cell fate by providing biochemical links between cell-extrinsic signals and available resources. In addition to metabolic checkpoints that sense nutrients and directly supply molecular intermediates for biosynthetic pathways, many metabolites directly signal or provide the basis for post-translational modifications of target proteins and chromatin. In this review, we survey the landscape of T cell nutrient sensing and metabolic signaling that supports proper immunity while avoiding immunodeficiency or autoimmunity. The integration of cell-extrinsic microenvironmental cues with cell-intrinsic metabolic signaling provides a social metabolic control model to integrate cell signaling, metabolism, and fate.
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Affiliation(s)
- Zachary A Bacigalupa
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Madelyn D Landis
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jeffrey C Rathmell
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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84
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Jun JH, Kim JS, Palomera LF, Jo DG. Dysregulation of histone deacetylases in ocular diseases. Arch Pharm Res 2024; 47:20-39. [PMID: 38151648 DOI: 10.1007/s12272-023-01482-x] [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: 06/15/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
Ocular diseases are a growing global concern and have a significant impact on the quality of life. Cataracts, glaucoma, age-related macular degeneration, and diabetic retinopathy are the most prevalent ocular diseases. Their prevalence and the global market size are also increasing. However, the available pharmacotherapy is currently limited. These diseases share common pathophysiological features, including neovascularization, inflammation, and/or neurodegeneration. Histone deacetylases (HDACs) are a class of enzymes that catalyze the removal of acetyl groups from lysine residues of histone and nonhistone proteins. HDACs are crucial for regulating various cellular processes, such as gene expression, protein stability, localization, and function. They have also been studied in various research fields, including cancer, inflammatory diseases, neurological disorders, and vascular diseases. Our study aimed to investigate the relationship between HDACs and ocular diseases, to identify a new strategy for pharmacotherapy. This review article explores the role of HDACs in ocular diseases, specifically focusing on diabetic retinopathy, age-related macular degeneration, and retinopathy of prematurity, as well as optic nerve disorders, such as glaucoma and optic neuropathy. Additionally, we explore the interplay between HDACs and key regulators of fibrosis and angiogenesis, such as TGF-β and VEGF, highlighting the potential of targeting HDAC as novel therapeutic strategies for ocular diseases.
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Affiliation(s)
- Jae Hyun Jun
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Korea
- Department of Pharmacology, CKD Research Institute, Chong Kun Dang Pharmaceutical Co., Yongin, 16995, Korea
| | - Jun-Sik Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Korea
| | - Leon F Palomera
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Korea
| | - Dong-Gyu Jo
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Korea.
- Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, 06351, Korea.
- Biomedical Institute for Convergence, Sungkyunkwan University, Suwon, 16419, Korea.
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85
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Verdikt R, Thienpont B. Epigenetic remodelling under hypoxia. Semin Cancer Biol 2024; 98:1-10. [PMID: 38029868 DOI: 10.1016/j.semcancer.2023.10.005] [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: 08/21/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
Hypoxia is intrinsic to tumours and contributes to malignancy and metastasis while hindering the efficiency of existing treatments. Epigenetic mechanisms play a crucial role in the regulation of hypoxic cancer cell programs, both in the initial phases of sensing the decrease in oxygen levels and during adaptation to chronic lack of oxygen. During the latter, the epigenetic regulation of tumour biology intersects with hypoxia-sensitive transcription factors in a complex network of gene regulation that also involves metabolic reprogramming. Here, we review the current literature on the epigenetic control of gene programs in hypoxic cancer cells. We highlight common themes and features of such epigenetic remodelling and discuss their relevance for the development of therapeutic strategies.
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Affiliation(s)
- Roxane Verdikt
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium
| | - Bernard Thienpont
- Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium; KU Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium.
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86
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Yang Y, Mei G, Yang L, Luo T, Wu R, Peng S, Peng Z, Cui J, Cheng Y. PCB126 impairs human sperm functions by affecting post-translational modifications and mitochondrial functions. CHEMOSPHERE 2024; 346:140532. [PMID: 37918541 DOI: 10.1016/j.chemosphere.2023.140532] [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: 04/22/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023]
Abstract
Over the past few decades, there has been a consistent decline in semen quality across the globe, with environmental pollution being identified as the primary cause. Among the various contaminants present in the environment, persistent organic pollutants (POPs) have garnered significant attention due to their high toxicity, slow degradation, bio-accumulation, and long-range migration. PCBs, which include 210 congeners, are a crucial type of POPs that are known to have harmful effects on the environment and human health. Among the various PCB congeners, 3,3',4,4',5-pentachlorobiphenyl (PCB126) is a typical environmental endocrine-disrupting chemical that is widely distributed and has been associated with several health hazards. However, the impact and mechanism of PCB126 on human sperm function has not been fully elucidated. We aimed to investigate the effects of different concentrations of PCB126 (0.01, 0.1, 1, 10 μg/mL) on sperm motility, viability, hyperactivation, and acrosome reaction after incubation for different periods (1 and 2 h), delving deeper into the molecular mechanism of human sperm dysfunction caused by PCB126. First, we investigated the link between PCB126 treatment and the occurrence of protein modifications that are critical to sperm function regulation, such as tyrosine phosphorylation and lysine glutarylation. Second, we examined the potential impact of PCB126 on different parameters related to mitochondrial function, including reactive oxygen species, malondialdehyde levels, mitochondrial membrane potential, mitochondria respiration and adenosine triphosphate generation. Our findings indicate that exposure to environmental pollutants such as PCB126 in vitro may have a negative impact on human sperm functions by interfering with post-translational modifications and mitochondrial functions.
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Affiliation(s)
- Yebin Yang
- College of Chemistry and Biological Engineering, Yichun University, Yichun, China
| | - Guangquan Mei
- Jiangxi Provincial Key Laboratory of Natural Active Pharmaceutical Constituents, Department of Chemistry and Bioengineering, Yichun University, Yichun, China; Key Laboratory of Jiangxi University for Applied Chemistry and Chemical Biology, Yichun University, Yichun, China
| | - Liu Yang
- College of Chemistry and Biological Engineering, Yichun University, Yichun, China
| | - Tao Luo
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Runwen Wu
- Center for Translational Medicine, Department of Medicine, Yichun University, Yichun, China
| | - Shenglin Peng
- Yichun People's Hospital, Jiangxi Province, Yichun, China
| | - Zhen Peng
- Yichun People's Hospital, Jiangxi Province, Yichun, China
| | - Jiajun Cui
- Center for Translational Medicine, Department of Medicine, Yichun University, Yichun, China
| | - Yimin Cheng
- Jiangxi Provincial Key Laboratory of Natural Active Pharmaceutical Constituents, Department of Chemistry and Bioengineering, Yichun University, Yichun, China; Center for Translational Medicine, Department of Medicine, Yichun University, Yichun, China.
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87
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Gan Z, Zhao M, Xia Y, Yan Y, Ren W. Carbon metabolism in the regulation of macrophage functions. Trends Endocrinol Metab 2024; 35:62-73. [PMID: 37778898 DOI: 10.1016/j.tem.2023.09.003] [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: 07/29/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 10/03/2023]
Abstract
Carbon metabolism, including one-carbon (1C) metabolism and central carbon metabolism (CCM), provides energy for the cell and generates metabolites with signaling activities. The regulation of macrophage polarization involves complex signals and includes an epigenetic level. Epigenetic modifications through changes in carbon metabolism allow macrophages to respond in a timely manner to their environment and adapt to metabolic demands during macrophage polarization. Here we summarize the current understanding of the crosstalk between carbon metabolism and epigenetic modifications in macrophages under physiological conditions and in the tumor microenvironment (TME) and provide targets and further directions for macrophage-associated diseases.
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Affiliation(s)
- Zhending Gan
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou 510000, Guangdong, China
| | - Muyang Zhao
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou 510000, Guangdong, China
| | - Yaoyao Xia
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Yuqi Yan
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Wenkai Ren
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou 510000, Guangdong, China.
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88
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Kubatzky KF, Gao Y, Yu D. Post-translational modulation of cell signalling through protein succinylation. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:1260-1285. [PMID: 38213532 PMCID: PMC10776603 DOI: 10.37349/etat.2023.00196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/22/2023] [Indexed: 01/13/2024] Open
Abstract
Cells need to adapt their activities to extra- and intracellular signalling cues. To translate a received extracellular signal, cells have specific receptors that transmit the signal to downstream proteins so that it can reach the nucleus to initiate or repress gene transcription. Post-translational modifications (PTMs) of proteins are reversible or irreversible chemical modifications that help to further modulate protein activity. The most commonly observed PTMs are the phosphorylation of serine, threonine, and tyrosine residues, followed by acetylation, glycosylation, and amidation. In addition to PTMs that involve the modification of a certain amino acid (phosphorylation, hydrophobic groups for membrane localisation, or chemical groups like acylation), or the conjugation of peptides (SUMOylation, NEDDylation), structural changes such as the formation of disulphide bridge, protein cleavage or splicing can also be classified as PTMs. Recently, it was discovered that metabolites from the tricarboxylic acid (TCA) cycle are not only intermediates that support cellular metabolism but can also modify lysine residues. This has been shown for acetate, succinate, and lactate, among others. Due to the importance of mitochondria for the overall fitness of organisms, the regulatory function of such PTMs is critical for protection from aging, neurodegeneration, or cardiovascular disease. Cancer cells and activated immune cells display a phenotype of accelerated metabolic activity known as the Warburg effect. This metabolic state is characterised by enhanced glycolysis, the use of the pentose phosphate pathway as well as a disruption of the TCA cycle, ultimately causing the accumulation of metabolites like citrate, succinate, and malate. Succinate can then serve as a signalling molecule by directly interacting with proteins, by binding to its G protein-coupled receptor 91 (GPR91) and by post-translationally modifying proteins through succinylation of lysine residues, respectively. This review is focus on the process of protein succinylation and its importance in health and disease.
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Affiliation(s)
- Katharina F. Kubatzky
- Department of Infectious Diseases, Medical Faculty Heidelberg, Medical Microbiology and Hygiene, Heidelberg University, 69120 Heidelberg, Germany
- Department of Infectious Diseases, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Yue Gao
- Department of Infectious Diseases, Medical Faculty Heidelberg, Medical Microbiology and Hygiene, Heidelberg University, 69120 Heidelberg, Germany
- Department of Infectious Diseases, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Dayoung Yu
- Department of Infectious Diseases, Medical Faculty Heidelberg, Medical Microbiology and Hygiene, Heidelberg University, 69120 Heidelberg, Germany
- Department of Infectious Diseases, University Hospital Heidelberg, 69120 Heidelberg, Germany
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89
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Li H, Seessle J, Staffer S, Tuma-Kellner S, Poschet G, Herrmann T, Chamulitrat W. FATP4 deletion in liver cells induces elevation of extracellular lipids via metabolic channeling towards triglycerides and lipolysis. Biochem Biophys Res Commun 2023; 687:149161. [PMID: 37931418 DOI: 10.1016/j.bbrc.2023.149161] [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: 08/14/2023] [Revised: 10/13/2023] [Accepted: 10/26/2023] [Indexed: 11/08/2023]
Abstract
Evidence from mice with global deletion of fatty-acid transport protein4 (FATP4) indicates its role on β-oxidation and triglycerides (TG) metabolism. We reported that plasma glycerol and free fatty acids (FA) were increased in liver-specific Fatp4 deficient (L-FATP4-/-) mice under dietary stress. We hypothesized that FATP4 may mediate hepatocellular TG lipolysis. Here, we demonstrated that L-FATP4-/- mice showed an increase in these blood lipids, liver TG, and subcutaneous fat weights. We therefore studied TG metabolism in response to oleate treatment in two experimental models using FATP4-knockout HepG2 (HepKO) cells and L-FATP4-/- hepatocytes. Both FATP4-deificient liver cells showed a significant decrease in β-oxidation products by ∼30-35% concomitant with marked upregulation of CD36, FATP2, and FATP5 as well as lipoprotein microsomal-triglyceride-transfer protein genes. By using 13C3D5-glycerol, HepKO cells displayed an increase in metabolically labelled TG species which were further increased with oleate treatment. This increase was concomitant with a step-wise elevation of TG in cells and supernatants as well as the secretion of cholesterol very low-density and high-density lipoproteins. Upon analyzing TG lipolytic enzymes, both mutant liver cells showed marked upregulated expression of hepatic lipase, while that of hormone-sensitive lipase and adipose-triglyceride lipase was downregulated. Lipolysis measured by extracellular glycerol and free FA was indeed increased in mutant cells, and this event was exacerbated by oleate treatment. Taken together, FATP4 deficiency in liver cells led to a metabolic shift from β-oxidation towards lipolysis-directed TG and lipoprotein secretion, which is in line with an association of FATP4 polymorphisms with blood lipids.
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Affiliation(s)
- Huili Li
- Department of Internal Medicine IV, University Hospital Heidelberg, 69120, Heidelberg, Germany; Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, Hubei, China
| | - Jessica Seessle
- Department of Internal Medicine IV, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Simone Staffer
- Department of Internal Medicine IV, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Sabine Tuma-Kellner
- Department of Internal Medicine IV, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Gernot Poschet
- Metabolomics Core Technology Platform, Centre for Organismal Studies, University of Heidelberg, 69120, Heidelberg, Germany
| | - Thomas Herrmann
- Westkuesten Hospital, Esmarchstraße 50, 25746, Heide, Germany
| | - Walee Chamulitrat
- Department of Internal Medicine IV, University Hospital Heidelberg, 69120, Heidelberg, Germany.
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90
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McCrory C, Verma J, Tucey TM, Turner R, Weerasinghe H, Beilharz TH, Traven A. The short-chain fatty acid crotonate reduces invasive growth and immune escape of Candida albicans by regulating hyphal gene expression. mBio 2023; 14:e0260523. [PMID: 37929941 PMCID: PMC10746253 DOI: 10.1128/mbio.02605-23] [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: 09/26/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023] Open
Abstract
IMPORTANCE Macrophages curtail the proliferation of the pathogen Candida albicans within human body niches. Within macrophages, C. albicans adapts its metabolism and switches to invasive hyphal morphology. These adaptations enable fungal growth and immune escape by triggering macrophage lysis. Transcriptional programs regulate these metabolic and morphogenetic adaptations. Here we studied the roles of chromatin in these processes and implicate lysine crotonylation, a histone mark regulated by metabolism, in hyphal morphogenesis and macrophage interactions by C. albicans. We show that the short-chain fatty acid crotonate increases histone crotonylation, reduces hyphal formation within macrophages, and slows macrophage lysis and immune escape of C. albicans. Crotonate represses hyphal gene expression, and we propose that C. albicans uses diverse acylation marks to regulate its cell morphology in host environments. Hyphal formation is a virulence property of C. albicans. Therefore, a further importance of our study stems from identifying crotonate as a hyphal inhibitor.
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Affiliation(s)
- Christopher McCrory
- Department of Biochemistry and Molecular Biology and Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Jiyoti Verma
- Department of Biochemistry and Molecular Biology and Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Timothy M. Tucey
- Department of Biochemistry and Molecular Biology and Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Rachael Turner
- Department of Biochemistry and Molecular Biology and Stem Cells and Development Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Harshini Weerasinghe
- Department of Biochemistry and Molecular Biology and Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Traude H. Beilharz
- Department of Biochemistry and Molecular Biology and Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
- Department of Biochemistry and Molecular Biology and Stem Cells and Development Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Ana Traven
- Department of Biochemistry and Molecular Biology and Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
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91
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Holcombe J, Weavers H. Functional-metabolic coupling in distinct renal cell types coordinates organ-wide physiology and delays premature ageing. Nat Commun 2023; 14:8405. [PMID: 38110414 PMCID: PMC10728150 DOI: 10.1038/s41467-023-44098-x] [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: 05/26/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023] Open
Abstract
Precise coupling between cellular physiology and metabolism is emerging as a vital relationship underpinning tissue health and longevity. Nevertheless, functional-metabolic coupling within heterogenous microenvironments in vivo remains poorly understood due to tissue complexity and metabolic plasticity. Here, we establish the Drosophila renal system as a paradigm for linking mechanistic analysis of metabolism, at single-cell resolution, to organ-wide physiology. Kidneys are amongst the most energetically-demanding organs, yet exactly how individual cell types fine-tune metabolism to meet their diverse, unique physiologies over the life-course remains unclear. Integrating live-imaging of metabolite and organelle dynamics with spatio-temporal genetic perturbation within intact functional tissue, we uncover distinct cellular metabolic signatures essential to support renal physiology and healthy ageing. Cell type-specific programming of glucose handling, PPP-mediated glutathione regeneration and FA β-oxidation via dynamic lipid-peroxisomal networks, downstream of differential ERR receptor activity, precisely match cellular energetic demands whilst limiting damage and premature senescence; however, their dramatic dysregulation may underlie age-related renal dysfunction.
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Affiliation(s)
- Jack Holcombe
- School of Biochemistry, Biomedical Sciences, University of Bristol, Bristol, BS8 1TD, UK
| | - Helen Weavers
- School of Biochemistry, Biomedical Sciences, University of Bristol, Bristol, BS8 1TD, UK.
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92
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Ahamed A, Hosea R, Wu S, Kasim V. The Emerging Roles of the Metabolic Regulator G6PD in Human Cancers. Int J Mol Sci 2023; 24:17238. [PMID: 38139067 PMCID: PMC10743588 DOI: 10.3390/ijms242417238] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Metabolic reprogramming, especially reprogrammed glucose metabolism, is a well-known cancer hallmark related to various characteristics of tumor cells, including proliferation, survival, metastasis, and drug resistance. Glucose-6-phosphate dehydrogenase (G6PD) is the first and rate-limiting enzyme of the pentose phosphate pathway (PPP), a branch of glycolysis, that converts glucose-6-phosphate (G6P) into 6-phosphogluconolactone (6PGL). Furthermore, PPP produces ribose-5-phosphate (R5P), which provides sugar-phosphate backbones for nucleotide synthesis as well as nicotinamide adenine dinucleotide phosphate (NADPH), an important cellular reductant. Several studies have shown enhanced G6PD expression and PPP flux in various tumor cells, as well as their correlation with tumor progression through cancer hallmark regulation, especially reprogramming cellular metabolism, sustaining proliferative signaling, resisting cell death, and activating invasion and metastasis. Inhibiting G6PD could suppress tumor cell proliferation, promote cell death, reverse chemoresistance, and inhibit metastasis, suggesting the potential of G6PD as a target for anti-tumor therapeutic strategies. Indeed, while challenges-including side effects-still remain, small-molecule G6PD inhibitors showing potential anti-tumor effect either when used alone or in combination with other anti-tumor drugs have been developed. This review provides an overview of the structural significance of G6PD, its role in and regulation of tumor development and progression, and the strategies explored in relation to G6PD-targeted therapy.
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Affiliation(s)
- Alfar Ahamed
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Rendy Hosea
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Shourong Wu
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing 400044, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing 400030, China
| | - Vivi Kasim
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing 400044, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing 400030, China
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93
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Park KC, Crump NT, Louwman N, Krywawych S, Cheong YJ, Vendrell I, Gill EK, Gunadasa-Rohling M, Ford KL, Hauton D, Fournier M, Pires E, Watson L, Roseman G, Holder J, Koschinski A, Carnicer R, Curtis MK, Zaccolo M, Hulikova A, Fischer R, Kramer HB, McCullagh JSO, Trefely S, Milne TA, Swietach P. Disrupted propionate metabolism evokes transcriptional changes in the heart by increasing histone acetylation and propionylation. NATURE CARDIOVASCULAR RESEARCH 2023; 2:1221-1245. [PMID: 38500966 PMCID: PMC7615744 DOI: 10.1038/s44161-023-00365-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/15/2023] [Indexed: 03/20/2024]
Abstract
Propiogenic substrates and gut bacteria produce propionate, a post-translational protein modifier. In this study, we used a mouse model of propionic acidaemia (PA) to study how disturbances to propionate metabolism result in histone modifications and changes to gene expression that affect cardiac function. Plasma propionate surrogates were raised in PA mice, but female hearts manifested more profound changes in acyl-CoAs, histone propionylation and acetylation, and transcription. These resulted in moderate diastolic dysfunction with raised diastolic Ca2+, expanded end-systolic ventricular volume and reduced stroke volume. Propionate was traced to histone H3 propionylation and caused increased acetylation genome-wide, including at promoters of Pde9a and Mme, genes related to contractile dysfunction through downscaled cGMP signaling. The less severe phenotype in male hearts correlated with β-alanine buildup. Raising β-alanine in cultured myocytes treated with propionate reduced propionyl-CoA levels, indicating a mechanistic relationship. Thus, we linked perturbed propionate metabolism to epigenetic changes that impact cardiac function.
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Affiliation(s)
- Kyung Chan Park
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Nicholas T. Crump
- MRC Molecular Haematology Unit, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Present Address: Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Niamh Louwman
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Steve Krywawych
- Department of Chemical Pathology, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Yuen Jian Cheong
- Epigenetics & Signalling Programmes, Babraham Institute, Cambridge, UK
| | - Iolanda Vendrell
- Nuffield Department of Medicine, Target Discovery Institute, Oxford, UK
- Nuffield Department of Medicine, Chinese Academy for Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Eleanor K. Gill
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | | | - Kerrie L. Ford
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - David Hauton
- Department of Chemistry, University of Oxford, Oxford, UK
| | | | | | - Lydia Watson
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Gerald Roseman
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - James Holder
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Andreas Koschinski
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Ricardo Carnicer
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - M. Kate Curtis
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Manuela Zaccolo
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Alzbeta Hulikova
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, Oxford, UK
- Nuffield Department of Medicine, Chinese Academy for Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Holger B. Kramer
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Sophie Trefely
- Epigenetics & Signalling Programmes, Babraham Institute, Cambridge, UK
| | - Thomas A. Milne
- MRC Molecular Haematology Unit, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Pawel Swietach
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
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94
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Liu M, Yang Q, Zuo H, Zhang X, Mishina Y, Chen Z, Yang J. Dynamic patterns of histone lactylation during early tooth development in mice. J Mol Histol 2023; 54:665-673. [PMID: 37787911 DOI: 10.1007/s10735-023-10154-5] [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: 02/26/2023] [Accepted: 09/12/2023] [Indexed: 10/04/2023]
Abstract
Histone lactylation on its lysine (K) residues has been reported to have indispensable roles in lung fibrosis, embryogenesis, neural development, inflammation, and tumors. However, little is known about the lactylation activity towards histone lysine residue during tooth development. We investigated the dynamic patterns of lactate-derived histone lysine lactylation (Kla) using a pan-Kla antibody during murine tooth development, including lower first molar and lower incisor. The results showed that pan-Kla exhibited temporo-spatial patterns in both dental epithelium and mesenchyme cells during development. Notably, pan-Kla was identified in primary enamel knot (PEK), stratum intermedium (SI), stellate reticulum (SR), dental follicle cells, odontoblasts, ameloblasts, proliferating cells in dental mesenchyme, as well as osteoblasts around the tooth germ. More importantly, pan-Kla was also identified to be co-localized with neurofilament during tooth development, suggesting histone lysine lactylation may be involved in neural invasion during tooth development. These findings suggest that histone lysine lactylation may play important roles in regulating tooth development.
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Affiliation(s)
- Ming Liu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, 430079, Wuhan, China
| | - Qian Yang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, 430079, Wuhan, China
| | - Huanyan Zuo
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, 430079, Wuhan, China
| | - Xinye Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, 430079, Wuhan, China
| | - Yuji Mishina
- Department of Biologic & Materials Sciences, School of Dentistry, University Michigan, Ann Arbor, MI, 48109, USA
| | - Zhi Chen
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, 430079, Wuhan, China
| | - Jingwen Yang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, 430079, Wuhan, China.
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95
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Huang J, Liang L, Jiang S, Liu Y, He H, Sun X, Li Y, Xie L, Tao Y, Cong L, Jiang Y. BDH1-mediated LRRC31 regulation dependent on histone lysine β-hydroxybutyrylation to promote lung adenocarcinoma progression. MedComm (Beijing) 2023; 4:e449. [PMID: 38098610 PMCID: PMC10719427 DOI: 10.1002/mco2.449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common form of lung cancer, with a consistently low 5-year survival rate. Therefore, we aim to identify key genes involved in LUAD progression to pave the way for targeted therapies in the future. BDH1 plays a critical role in the conversion between acetoacetate and β-hydroxybutyrate. The presence of β-hydroxybutyrate is essential for initiating lysine β-hydroxybutyrylation (Kbhb) modifications. Histone Kbhb at the H3K9 site is attributed to transcriptional activation. We unveiled that β-hydroxybutyrate dehydrogenase 1 (BDH1) is not only conspicuously overexpressed in LUAD, but it also modulates the overall intracellular Kbhb modification levels. The RNA sequencing analysis revealed leucine-rich repeat-containing protein 31 (LRRC31) as a downstream target gene regulated by BDH1. Ecologically expressed BDH1 hinders the accumulation of H3K9bhb in the transcription start site of LRRC31, consequently repressing the transcriptional expression of LRRC31. Furthermore, we identified potential BDH1 inhibitors, namely pimozide and crizotinib, which exhibit a synergistic inhibitory effect on the proliferation of LUAD cells exhibiting high expression of BDH1. In summary, this study elucidates the molecular mechanism by which BDH1 mediates LUAD progression through the H3K9bhb/LRRC31 axis and proposes a therapeutic strategy targeting BDH1-high-expressing LUAD, providing a fresh perspective for LUAD treatment.
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Affiliation(s)
- Jingjing Huang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal UniversityChangshaHunanChina
- Department of Basic Medicine, School of Medicine, Hunan Normal UniversityChangshaHunanChina
| | - Lu Liang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal UniversityChangshaHunanChina
- Department of Basic Medicine, School of Medicine, Hunan Normal UniversityChangshaHunanChina
| | - Shiyao Jiang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal UniversityChangshaHunanChina
- Department of Basic Medicine, School of Medicine, Hunan Normal UniversityChangshaHunanChina
| | - Yueying Liu
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal UniversityChangshaHunanChina
- Department of Basic Medicine, School of Medicine, Hunan Normal UniversityChangshaHunanChina
| | - Hua He
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal UniversityChangshaHunanChina
- Department of Basic Medicine, School of Medicine, Hunan Normal UniversityChangshaHunanChina
| | - Xiaoyan Sun
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal UniversityChangshaHunanChina
- Department of Basic Medicine, School of Medicine, Hunan Normal UniversityChangshaHunanChina
| | - Yi Li
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal UniversityChangshaHunanChina
- Department of Basic Medicine, School of Medicine, Hunan Normal UniversityChangshaHunanChina
| | - Li Xie
- Department of Head and Neck SurgeryHunan Cancer Hospital, Xiangya School of Medicine, Central South UniversityChangshaHunanChina
| | - Yongguang Tao
- Department of PathologyKey Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, School of Basic Medicine, Central South UniversityChangshaHunanChina
| | - Li Cong
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal UniversityChangshaHunanChina
- Department of Basic Medicine, School of Medicine, Hunan Normal UniversityChangshaHunanChina
| | - Yiqun Jiang
- The Key Laboratory of Model Animal and Stem Cell Biology in Hunan Province, Hunan Normal UniversityChangshaHunanChina
- Department of Basic Medicine, School of Medicine, Hunan Normal UniversityChangshaHunanChina
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96
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Zeng H, Li D, Dong J, Zhou X, Ou M, Xue W, Zhang R, Zou Y, Tang D, Yin L, Dai Y. Qualitative Proteome-wide Lysine Crotonylation Profiling Reveals Protein Modification Alteration in the Leukocyte Extravasation Pathway in Systemic Lupus Erythematosus. ACS OMEGA 2023; 8:44905-44919. [PMID: 38046296 PMCID: PMC10688171 DOI: 10.1021/acsomega.3c06293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/29/2023] [Accepted: 10/10/2023] [Indexed: 12/05/2023]
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is a severe systemic autoimmune disease with multiple manifestations. Lysine crotonylation (Kcr) is a newly discovered posttranslational modification epigenetic pattern that may affect gene expression and is linked to diseases causally. METHODS We collected blood samples from 11 SLE individuals and 36 healthy subjects. Then, we used highly sensitive liquid chromatography-mass spectrometry technology to carry out proteomics and quantitative crotonylome analysis of SLE peripheral blood mononuclear cells in this investigation, which indicated the unique etiology of SLE. Finally, we verified the expression of critical protein in the leukocyte extravasation pathway by online database analysis and Western blot. RESULTS There were 618 differentially expressed proteins (DEPs), and 612 crotonylated lysine sites for 272 differentially modified proteins (DMPs) found. These DEPs and DMPs are primarily enriched in the leukocyte extravasation signaling pathway, such as MMP8, MMP9, and ITGAM. CONCLUSIONS This is the first study of crotonylated modification proteomics in SLE. The leukocyte extravasation signaling pathway had a considerable concentration of DEPs and DMPs, indicating that this pathway may be involved in the pathogenic development of SLE.
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Affiliation(s)
- Huiyi Zeng
- Institute
of Nephrology and Blood Purification, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510632, China
- The First
Affiliated Hospital, School of Medicine, Anhui University of Science and Technology, Huainan, Anhui 232001, China
| | - Dandan Li
- Department
of Clinical Medical Research Center, The
Second Clinical Medical College of Jinan University, Shenzhen People’s
Hospital, Shenzhen, Guangdong 518020, China
- Experimental
Center, Shenzhen Pingle Orthopedic Hospital
(Shenzhen Pingshan Traditional Chinese Medicine Hospital), Shenzhen, Guangdong 518118, China
- The First
Affiliated Hospital, School of Medicine, Anhui University of Science and Technology, Huainan, Anhui 232001, China
| | - Jingjing Dong
- Institute
of Nephrology and Blood Purification, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510632, China
- Department
of Clinical Medical Research Center, The
Second Clinical Medical College of Jinan University, Shenzhen People’s
Hospital, Shenzhen, Guangdong 518020, China
| | - Xianqing Zhou
- Guangxi
Key Laboratory of Metabolic Diseases Research, No. 924 Hospital of PLA Joint Logistic Support
Force, Guilin, Guangxi 541002, China
| | - Minglin Ou
- Guangxi
Key Laboratory of Metabolic Diseases Research, No. 924 Hospital of PLA Joint Logistic Support
Force, Guilin, Guangxi 541002, China
| | - Wen Xue
- Guangxi
Key Laboratory of Metabolic Diseases Research, No. 924 Hospital of PLA Joint Logistic Support
Force, Guilin, Guangxi 541002, China
| | - Ruohan Zhang
- Guangxi
Key Laboratory of Metabolic Diseases Research, No. 924 Hospital of PLA Joint Logistic Support
Force, Guilin, Guangxi 541002, China
| | - Yaoshuang Zou
- Guangxi
Key Laboratory of Metabolic Diseases Research, No. 924 Hospital of PLA Joint Logistic Support
Force, Guilin, Guangxi 541002, China
| | - Donge Tang
- Department
of Clinical Medical Research Center, The
Second Clinical Medical College of Jinan University, Shenzhen People’s
Hospital, Shenzhen, Guangdong 518020, China
| | - Lianghong Yin
- Institute
of Nephrology and Blood Purification, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510632, China
- Huangpu
Institute of Materials, Guangzhou, Guangdong 510663, China
| | - Yong Dai
- Department
of Clinical Medical Research Center, The
Second Clinical Medical College of Jinan University, Shenzhen People’s
Hospital, Shenzhen, Guangdong 518020, China
- Guangxi
Key Laboratory of Metabolic Diseases Research, No. 924 Hospital of PLA Joint Logistic Support
Force, Guilin, Guangxi 541002, China
- The First
Affiliated Hospital, School of Medicine, Anhui University of Science and Technology, Huainan, Anhui 232001, China
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97
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Guo J, Zhang H, Lin W, Lu L, Su J, Chen X. Signaling pathways and targeted therapies for psoriasis. Signal Transduct Target Ther 2023; 8:437. [PMID: 38008779 PMCID: PMC10679229 DOI: 10.1038/s41392-023-01655-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/10/2023] [Accepted: 09/14/2023] [Indexed: 11/28/2023] Open
Abstract
Psoriasis is a common, chronic, and inflammatory skin disease with a high burden on individuals, health systems, and society worldwide. With the immunological pathologies and pathogenesis of psoriasis becoming gradually revealed, the therapeutic approaches for this disease have gained revolutionary progress. Nevertheless, the mechanisms of less common forms of psoriasis remain elusive. Furthermore, severe adverse effects and the recurrence of disease upon treatment cessation should be noted and addressed during the treatment, which, however, has been rarely explored with the integration of preliminary findings. Therefore, it is crucial to have a comprehensive understanding of the mechanisms behind psoriasis pathogenesis, which might offer new insights for research and lead to more substantive progress in therapeutic approaches and expand clinical options for psoriasis treatment. In this review, we looked to briefly introduce the epidemiology, clinical subtypes, pathophysiology, and comorbidities of psoriasis and systematically discuss the signaling pathways involving extracellular cytokines and intracellular transmission, as well as the cross-talk between them. In the discussion, we also paid more attention to the potential metabolic and epigenetic mechanisms of psoriasis and the molecular mechanistic cascades related to its comorbidities. This review also outlined current treatment for psoriasis, especially targeted therapies and novel therapeutic strategies, as well as the potential mechanism of disease recurrence.
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Affiliation(s)
- Jia Guo
- Department of Dermatology, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, Hunan, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, Hunan, China
| | - Hanyi Zhang
- Department of Dermatology, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, Hunan, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, Hunan, China
| | - Wenrui Lin
- Department of Dermatology, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, Hunan, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, Hunan, China
| | - Lixia Lu
- Department of Dermatology, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, Hunan, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, Hunan, China
| | - Juan Su
- Department of Dermatology, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, Hunan, China.
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, 410008, Hunan, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, Hunan, China.
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, Hunan, China.
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, Hunan, China.
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, 410008, Hunan, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, Hunan, China.
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, Hunan, China.
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98
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Zhang Z, Wang Y, Liang Z, Meng Z, Zhang X, Ma G, Chen Y, Zhang M, Su Y, Li Z, Liang Y, Niu H. Modification of lysine-260 2-hydroxyisobutyrylation destabilizes ALDH1A1 expression to regulate bladder cancer progression. iScience 2023; 26:108142. [PMID: 37867947 PMCID: PMC10585400 DOI: 10.1016/j.isci.2023.108142] [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: 05/02/2023] [Revised: 08/11/2023] [Accepted: 10/02/2023] [Indexed: 10/24/2023] Open
Abstract
ALDH1A1 is one of the classical stem cell markers for bladder cancer. Lysine 2-hydroxyisobutyrylation (Khib) is a newfound modification to modulate the protein expression, and the underlying mechanisms of how ALDH1A1 was regulated by Khib modification in bladder cancer remains unknown. Here, ALDH1A1 showed a decreased K260hib modification, as identified by protein modification omics in bladder cancer. Decreasing ALDH1A1 expression significantly suppressed the proliferation, migration and invasion of bladder cancer cells. Moreover, K260hib modification is responsible for the activity of ALDH1A1 in bladder cancer, which is regulated by HDAC2/3. Higher K260hib modification on ALDH1A1 promotes protein degradation through chaperone-mediated autophagy (CMA), and ALDH1A1 K260hib could sensitize bladder cancer cells to chemotherapeutic drugs. Higher ALDH1A1 expression with a lower K260hib modification indicates a poor prognosis in patients with bladder cancer. Overall, we demonstrated that K260hib of ALDH1A1 can be used as a potential therapeutic target for bladder cancer treatment.
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Affiliation(s)
- Zhilei Zhang
- Department of Urology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao 266003, China
- Key Laboratory, Department of Urology and Andrology, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Yonghua Wang
- Department of Urology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao 266003, China
| | - Zhijuan Liang
- Key Laboratory, Department of Urology and Andrology, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Zhaoyuan Meng
- School of Basic Medicine, Qingdao University, No.308 Ningxia Road, Qingdao 266071, China
| | - Xiangyan Zhang
- Department of Pathology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao 266003, China
| | - Guofeng Ma
- Department of Urology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao 266003, China
- Key Laboratory, Department of Urology and Andrology, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Yuanbin Chen
- Key Laboratory, Department of Urology and Andrology, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Mingxin Zhang
- Department of Urology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao 266003, China
| | - Yinjie Su
- Department of Urology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao 266003, China
- Key Laboratory, Department of Urology and Andrology, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Zhiqiang Li
- The Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao 266071, China
| | - Ye Liang
- Key Laboratory, Department of Urology and Andrology, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - Haitao Niu
- Department of Urology, The Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao 266003, China
- Key Laboratory, Department of Urology and Andrology, The Affiliated Hospital of Qingdao University, Qingdao 266003, China
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99
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Bilgin N, Türkmen VA, Hammami N, Christensen NR, Hintzen JCJ, Mecinović J. Reading and erasing of histone crotonyllysine mimics by the AF9 YEATS domain and SIRT2 deacylase. Bioorg Med Chem 2023; 95:117500. [PMID: 37839329 DOI: 10.1016/j.bmc.2023.117500] [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: 09/12/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023]
Abstract
Lysine acylations on histones and their recognition by chromatin-binding reader domains and removal by histone deacylases function as an important mechanism for eukaryotic gene regulation. Histone lysine crotonylation (Kcr) is an epigenetic mark associated with active transcription, and its installation and removal are dynamically regulated by cellular epigenetic enzymes. Here, we report binding studies and enzyme assays with histone H3K9 peptides bearing simplest Kcr analogs with varying hydrocarbon chain length, bulkiness, rigidity and polarity. We demonstrate that the AF9 YEATS domain displays selectivity for binding of different acylation modifications on histone H3K9 peptides and exhibits preference for bulkier cinnamoylated lysine over crotonylated lysine and its mimics. SIRT2 shows deacylase activity against most of acylated H3K9 peptides bearing different crotonyllysine mimics, however, it displays a poor ability for the removal of cinnamoyl and trifluorocrotonyl groups. These results demonstrate different substrate selectivities of epigenetic proteins acting on crotonyllysine and pave the way for rational design and development of AF9 YEATS and SIRT2 inhibitors for treatment of human diseases, including cancer.
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Affiliation(s)
- Nurgül Bilgin
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Vildan A Türkmen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Nesrin Hammami
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Nadja R Christensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Jordi C J Hintzen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
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100
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Guo X, Wang Y, An Y, Liu Z, Liu J, Chen J, Zhan MM, Liang M, Hou Z, Wan C, Yin F, Wang R, Li Z. Development of Lysine Crotonyl-Mimic Probe to Covalently Identify H3K27Cr Interacting Proteins. Chemistry 2023; 29:e202301624. [PMID: 37587551 DOI: 10.1002/chem.202301624] [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: 05/22/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023]
Abstract
Histone lysine crotonylation (Kcr) is one newly discovered acylation modification and regulates numerous pathophysiological processes. The binding affinity between Kcr and its interacting proteins is generally weak, which makes it difficult to effectively identify Kcr-interacting partners. Changing the amide of crotonyl to an ester increased reactivity with proximal cysteines and retained specificity for Kcr antibody. The probe "H3g27Cr" was designed by incorporating the ester functionality into a H3K27 peptide. Using this probe, multiple Kcr-interacting partners including STAT3 were successfully identified, and this has not been reported previously. Further experiments suggested that STAT3 possibly could form complexes with Histone deacetylase HDACs to downregulate the acetylation and crotonylation of Histone H3K27. Our unique design provided intriguing tools to further explore Kcr-interacting proteins and elucidate their working mechanisms.
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Affiliation(s)
- Xiaochun Guo
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Yuena Wang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Yuhao An
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Zhihong Liu
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Jianbo Liu
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Jiaxin Chen
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Mei-Miao Zhan
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Mingcha Liang
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Zhanfeng Hou
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Chuan Wan
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Feng Yin
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Rui Wang
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
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