1
|
Yan W, Zhang Y, Dai Y, Ge J. Application of crotonylation modification in pan-vascular diseases. J Drug Target 2024; 32:996-1004. [PMID: 38922829 DOI: 10.1080/1061186x.2024.2372316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Pan-vascular diseases, based on systems biology theory, explore the commonalities and individualities of important target organs such as cardiovascular, cerebrovascular and peripheral blood vessels, starting from the systemic and holistic aspects of vascular diseases. The purpose is to understand the interrelationships and results between them, achieve vascular health or sub-health, and comprehensively improve the physical and mental health of the entire population. Post-translational modification (PTM) is an important part of epigenetics, including phosphorylation, acetylation, ubiquitination, methylation, etc., playing a crucial role in the pan-vascular system. Crotonylation is a novel type of PTM that has made significant progress in the research of pan-vascular related diseases in recent years. Based on the review of previous studies, this article summarises the various regulatory factors of crotonylation, physiological functions and the mechanisms of histone and non-histone crotonylation in regulating pan-vascular related diseases to explore the possibility of precise regulation of crotonylation sites as potential targets for disease treatment and the value of clinical translation.
Collapse
Affiliation(s)
- Wendi Yan
- Oriental Pan-vascular Devices Innovation College, University of Shanghai for Science and Technology, Shanghai, China
| | - Yang Zhang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
| | - Yuxiang Dai
- Oriental Pan-vascular Devices Innovation College, University of Shanghai for Science and Technology, Shanghai, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Junbo Ge
- Oriental Pan-vascular Devices Innovation College, University of Shanghai for Science and Technology, Shanghai, China
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| |
Collapse
|
2
|
Liao M, Zheng W, Wang Y, Li M, Sun X, Liu N, Yao J, Dong F, Wang Q, Ma Y, Mou J. LINC00887 promotes GCN5-dependent H3K27cr level and CRC metastasis via recruitment of YEATS2 and enhancing ETS1 expression. Cell Death Dis 2024; 15:711. [PMID: 39349460 PMCID: PMC11443008 DOI: 10.1038/s41419-024-07091-w] [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: 04/02/2024] [Revised: 09/15/2024] [Accepted: 09/18/2024] [Indexed: 10/02/2024]
Abstract
Recent observations have revealed upregulation of H3K27cr in colorectal cancer (CRC) tissues; however, the underlying cause remains elusive. This study aimed to investigate the mechanism of H3K27cr upregulation and its roles in CRC metastasis. Clinically, our findings showed that H3K27cr served as a highly accurate diagnostic marker to distinguish CRC tissues from healthy controls. Elevated levels of LINC00887 and H3K27cr were associated with a poorer prognosis in CRC patients. Functionally, LINC00887 and H3K27cr facilitated the migration and invasion of CRC cells. Mechanistically, LINC00887 interacted with SIRT3 protein. Overexpressed of LINC00887 obstructed the enrichment of SIRT3 within GCN5 promoter, thereby elevating H3K27ac but not H3K27cr level within this region, subsequently activating GCN5 expression. This activation increased the global level of H3K27cr, promoting the enrichment of GCN5, H3K27cr, and YEATS2 within ETS1 promoter, activating ETS1 transcription and ultimately promoting the metastasis of CRC. The in vivo study demonstrated that inhibition of LINC00887 suppressed CRC metastasis, but this inhibitory effect was nullified when mice were treated with NaCr. In conclusion, our results confirmed the diagnostic biomarker potential of H3K27cr in individuals with CRC, and proposed a functional model to elucidate the involvement of LINC00887 in promoting CRC metastasis by elevating H3K27cr level.
Collapse
Affiliation(s)
- Meijian Liao
- Department of Pathology, Xuzhou Medical University, Xuzhou, 221004, PR China
| | - Wendan Zheng
- Department of Pathology, Xuzhou Medical University, Xuzhou, 221004, PR China
| | - Yifan Wang
- Department of Pathology, Xuzhou Medical University, Xuzhou, 221004, PR China
| | - Mengting Li
- Department of Pathology, Xuzhou Medical University, Xuzhou, 221004, PR China
| | - Xiaolin Sun
- Department of Pathology, Xuzhou Medical University, Xuzhou, 221004, PR China
| | - Nan Liu
- Department of Infectious Diseases and Center of Infectious Diseases and Pathogen Biology, the First Hospital of Jilin University, Changchun, 130061, PR China
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, the First Hospital of Jilin University, Changchun, 130061, PR China
| | - Jia Yao
- Department of Pathology, Xuzhou Medical University, Xuzhou, 221004, PR China
| | - Fuxing Dong
- Public Experimental Research Center, Xuzhou Medical University, Xuzhou, 221004, PR China
| | - Qingling Wang
- Department of Pathology, Xuzhou Medical University, Xuzhou, 221004, PR China
| | - Yu Ma
- Department of Pathology, Xuzhou Medical University, Xuzhou, 221004, PR China.
| | - Jie Mou
- School of Pharmacy, Xuzhou Medical University, Xuzhou, 221004, PR China.
| |
Collapse
|
3
|
Cao D, Sun W, Li X, Jian L, Zhou X, Bode AM, Luo X. The role of novel protein acylations in cancer. Eur J Pharmacol 2024; 979:176841. [PMID: 39033839 DOI: 10.1016/j.ejphar.2024.176841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/23/2024]
Abstract
Novel protein acylations are a class of protein post-translational modifications, such as lactylation, succinylation, crotonylation, palmitoylation, and β-hydroxybutyrylation. These acylation modifications are common in prokaryotes and eukaryotes and play pivotal roles in various key cellular processes by regulating gene transcription, protein subcellular localization, stability and activity, protein-protein interactions, and protein-DNA interactions. The diversified acylations are closely associated with various human diseases, especially cancer. In this review, we provide an overview of the distinctive characteristics, effects, and regulatory factors of novel protein acylations. We also explore the various mechanisms through which novel protein acylations are involved in the occurrence and progression of cancer. Furthermore, we discuss the development of anti-cancer drugs targeting novel acylations, offering promising avenues for cancer treatment.
Collapse
Affiliation(s)
- Dan Cao
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Wenxuan Sun
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Xinyi Li
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Lian Jian
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Xinran Zhou
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
| | - Xiangjian Luo
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, China; Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, China; Molecular Imaging Research Center of Central South University, Changsha, Hunan, 410078, China; Key Laboratory of Biological Nanotechnology of National Health Commission, Central South University, Changsha, Hunan, 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410078, China.
| |
Collapse
|
4
|
Zhao H, Han Y, Zhou P, Guan H, Gao S. Protein lysine crotonylation in cellular processions and disease associations. Genes Dis 2024; 11:101060. [PMID: 38957707 PMCID: PMC11217610 DOI: 10.1016/j.gendis.2023.06.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 05/05/2023] [Accepted: 06/27/2023] [Indexed: 07/04/2024] Open
Abstract
Protein lysine crotonylation (Kcr) is one conserved form of posttranslational modifications of proteins, which plays an important role in a series of cellular physiological and pathological processes. Lysine ε-amino groups are the primary sites of such modification, resulting in four-carbon planar lysine crotonylation that is structurally and functionally distinct from the acetylation of these residues. High levels of Kcr modifications have been identified on both histone and non-histone proteins. The present review offers an update on the research progression regarding protein Kcr modifications in biomedical contexts and provides a discussion of the mechanisms whereby Kcr modification governs a range of biological processes. In addition, given the importance of protein Kcr modification in disease onset and progression, the potential viability of Kcr regulators as therapeutic targets is elucidated.
Collapse
Affiliation(s)
- Hongling Zhao
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yang Han
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Pingkun Zhou
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hua Guan
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Shanshan Gao
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| |
Collapse
|
5
|
Li D, Lin L, Xu F, Feng T, Tao Y, Miao H, Yang F. Protein crotonylation: Basic research and clinical diseases. Biochem Biophys Rep 2024; 38:101694. [PMID: 38586826 PMCID: PMC10997999 DOI: 10.1016/j.bbrep.2024.101694] [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: 12/07/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/09/2024] Open
Abstract
Crotonylation is an importantly conserved post-translational modification, which is completely different from acetylation. In recent years, it has been confirmed that crotonylation occurs on histone and non-histone. Crotonylated Histone primarily affects gene expression through transcriptional regulation, while non-histone Crotonylation mainly regulates protein functions including protein activity, localization, and stability, as well as protein-protein interactions. The change in protein expression and function will affect the physiological process of cells and even cause disease. Reviewing previous studies, this article summarizes the mechanisms of histone and non-histone crotonylation in regulating diseases and cellular physiological processes to explore the possibility of precise regulation of crotonylation sites as potential targets for disease treatment.
Collapse
Affiliation(s)
- Dongling Li
- School of Medicine, Chongqing University, Chongqing, 400044, China
- Central Laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Ling Lin
- Central Laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Fan Xu
- School of Medicine, Chongqing University, Chongqing, 400044, China
- Central Laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Tianlin Feng
- Central Laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Yang Tao
- Central Laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
- Department of Critical Care Medicine, Chongqing University Central Hospital, Chongqing, 400000, China
| | - Hongming Miao
- Department of Pathophysiology, College of High Altitude Military Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Fan Yang
- Central Laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
- Department of Biochemistry and Molecular Biology, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| |
Collapse
|
6
|
Lao Y, Cui X, Xu Z, Yan H, Zhang Z, Zhang Z, Geng L, Li B, Lu Y, Guan Q, Pu X, Zhao S, Zhu J, Qin X, Sun B. Glutaryl-CoA dehydrogenase suppresses tumor progression and shapes an anti-tumor microenvironment in hepatocellular carcinoma. J Hepatol 2024:S0168-8278(24)00369-6. [PMID: 38825017 DOI: 10.1016/j.jhep.2024.05.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 05/12/2024] [Accepted: 05/23/2024] [Indexed: 06/04/2024]
Abstract
BACKGROUND & AIMS Crotonylation, a crotonyl-CoA-based non-enzymatic protein translational modification, affects diverse biological processes, such as spermatogenesis, tissue injury, inflammation, and neuropsychiatric diseases. Crotonylation is decreased in hepatocellular carcinomas (HCCs), but the mechanism remains unknown. In this study, we aim to describe the role of glutaryl-CoA dehydrogenase (GCDH) in tumor suppression. METHODS Three cohorts containing 40, 248 and 17 pairs of samples were used to evaluate the link between GCDH expression levels and clinical characteristics of HCC, as well as responses to anti-programmed cell death protein 1 (PD-1) treatment. Subcutaneous xenograft, orthotopic xenograft, Trp53Δhep/Δhep; MYC- and Ctnnboe;METoe-driven mouse models were adopted to validate the effects of GCDH on HCC suppression. RESULTS GCDH depletion promoted HCC growth and metastasis, whereas its overexpression reversed these processes. As GCDH converts glutaryl-CoA to crotonyl-CoA to increase crotonylation levels, we performed lysine crotonylome analysis and identified the pentose phosphate pathway (PPP) and glycolysis-related proteins PGD, TKT, and ALDOC as GCDH-induced crotonylation targets. Crotonyl-bound targets showed allosteric effects that controlled their enzymatic activities, leading to decreases in ribose 5-phosphate and lactate production, further limiting the Warburg effect. PPP blockade also stimulated peroxidation, synergizing with senescent modulators to induce senescence in GCDHhigh cells. These cells induced the infiltration of immune cells by the SASP (senescence-associated secretory cell phenotype) to shape an anti-tumor immune microenvironment. Meanwhile, the GCDHlow population was sensitized to anti-PD-1 therapy. CONCLUSION GCDH inhibits HCC progression via crotonylation-induced suppression of the PPP and glycolysis, resulting in HCC cell senescence. The senescent cell further shapes an anti-tumor microenvironment via the SASP. The GCDHlow population is responsive to anti-PD-1 therapy because of the increased presence of PD-1+CD8+ T cells. IMPACT AND IMPLICATIONS Glutaryl-CoA dehydrogenase (GCDH) is a favorable prognostic indicator in liver, lung, and renal cancers. In addition, most GCDH depletion-induced toxic metabolites originate from the liver, accumulate locally, and cannot cross the blood-brain barrier. Herein, we show that GCDH inhibits hepatocellular carcinoma (HCC) progression via crotonylation-induced suppression of the pentose phosphate pathway and glycolysis, resulting in HCC cell senescence. We also found that more PD-1+CD8+ T cells are present in the GCDHlow population, who are thus more responsive to anti-PD-1 therapy. Given that the GCDHlow and GCDHhigh HCC population can be distinguished based on serum glucose and ammonia levels, it will be worthwhile to evaluate the curative effects of pro-senescent and immune-therapeutic strategies based on the expression levels of GCDH.
Collapse
Affiliation(s)
- Yuanxiang Lao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University & Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China; Innovative Institute of Tumor Immunity and Medicine (ITIM); Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, Hefei, Anhui, China
| | - Xiaohan Cui
- Department of Gastrointestinal Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Zhu Xu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University & Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China; Innovative Institute of Tumor Immunity and Medicine (ITIM); Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, Hefei, Anhui, China
| | - Hongyao Yan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University & Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China; Innovative Institute of Tumor Immunity and Medicine (ITIM); Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, Hefei, Anhui, China
| | - Zechuan Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University & Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China; Innovative Institute of Tumor Immunity and Medicine (ITIM); Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, Hefei, Anhui, China
| | - Zhenwei Zhang
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Longpo Geng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University & Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China; Innovative Institute of Tumor Immunity and Medicine (ITIM); Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, Hefei, Anhui, China
| | - Binghua Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University & Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China; Innovative Institute of Tumor Immunity and Medicine (ITIM); Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, Hefei, Anhui, China
| | - Yijun Lu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University & Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China; Innovative Institute of Tumor Immunity and Medicine (ITIM); Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, Hefei, Anhui, China
| | - Qifei Guan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University & Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China; Innovative Institute of Tumor Immunity and Medicine (ITIM); Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, Hefei, Anhui, China
| | - Xiaohong Pu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University & Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China; Department of Pathology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing Jiangsu, China
| | - Suwen Zhao
- The iHuman Institute, Shanghai Tech University, Shanghai, China
| | - Jiapeng Zhu
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing Jiangsu, China
| | - Xihu Qin
- Department of Hepato-Biliary-Pancreatic Surgery, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou Jiangsu, China
| | - Beicheng Sun
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University & Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, China; Innovative Institute of Tumor Immunity and Medicine (ITIM); Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, Hefei, Anhui, China.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Zheng J, Liu Y, Wei K, Shi J, Li L, Jiang X, Tao L. Identification of Crotonylation Metabolism Signature Predicting Overall Survival for Clear Cell Renal Cell Carcinoma. Int J Clin Pract 2023; 2023:5558034. [PMID: 38058677 PMCID: PMC10697778 DOI: 10.1155/2023/5558034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/24/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023] Open
Abstract
Background Immunotherapy shows promise in treating cancer by leveraging the immune system to combat cancer cells. However, the influence of crotonylation metabolism on the prognosis and tumor environment in ccRCC patients is not fully understood. Methods We conducted various systematic analyses, including prognosis and cluster analyses, to investigate the role of KAT2A in immunotherapy. We used qRT-PCR to compare KAT2A expression in cancer and adjacent tissues and among different cell lines. Additionally, we employed Cell Counting Kit-8, wound healing, and Transwell chamber assays to assess changes in the proliferative and metastatic ability of A498 and 786-O cells. Results We identified three clusters related to crotonylation metabolism, each with distinct prognosis and immune characteristics in ccRCC. We categorized CT1 as immune-inflamed, CT2 as immune-excluded, and CR3 as immune-desert. A new system, CRS, emerged as an effective predictor of patient outcomes with differing immune characteristics. Moreover, qRT-PCR revealed elevated KAT2A levels in ccRCC tissues and cell lines. KAT2A was found to promote ccRCC and correlate significantly with immunosuppressive elements and checkpoints. Reducing KAT2A expression hindered ccRCC cell growth and metastasis. Conclusion Our study highlights the critical role of crotonylation metabolism in cancer development and progression, particularly its link to poor prognosis. CRS proves to be an accurate predictor of patient outcomes and immune features in ccRCC. KAT2A shows strong associations with clinical factors and the immunosuppressive environment, suggesting potential for innovative immunotherapies in ccRCC treatment.
Collapse
Affiliation(s)
- Jie Zheng
- Department of Urology, Wuhu Hospital Affiliated to East China Normal University, Wuhu 241000, Anhui, China
| | - Yingqing Liu
- Department of Urology, Wuhu Hospital Affiliated to East China Normal University, Wuhu 241000, Anhui, China
| | - Kai Wei
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Jiewu Shi
- Department of Urology, Wuhu Hospital Affiliated to East China Normal University, Wuhu 241000, Anhui, China
| | - Lin Li
- Department of Urology, Wuhu Hospital Affiliated to East China Normal University, Wuhu 241000, Anhui, China
| | - Xuefeng Jiang
- Department of Urology, Wuhu Hospital Affiliated to East China Normal University, Wuhu 241000, Anhui, China
| | - Lingsong Tao
- Department of Urology, Wuhu Hospital Affiliated to East China Normal University, Wuhu 241000, Anhui, China
| |
Collapse
|
11
|
Shen R, Ruan H, Lin S, Liu B, Song H, Li L, Ma T. Lysine succinylation, the metabolic bridge between cancer and immunity. Genes Dis 2023; 10:2470-2478. [PMID: 37554179 PMCID: PMC10404875 DOI: 10.1016/j.gendis.2022.10.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/17/2022] [Accepted: 10/25/2022] [Indexed: 12/04/2022] Open
Abstract
Lysine succinylation is a naturally occurring post-translational modification (PTM) that regulates the stability and function of proteins. It can be regulated by enzymes such as SIRT5 and SIRT7. Recently, the effect and significance of lysine succinylation in cancer and its implication in immunity have been extensively explored. Lysine succinylation is involved in the malignant phenotype of cancer cells. Abnormal regulation of lysine succinylation occurs in different cancers, and inhibitors targeting lysine succinylation regulatory enzymes can be used as potential anti-cancer strategies. Therefore, this review focused on the target protein lysine succinylation and its functions in cancer and immunity, in order to provide a reference for finding more potential clinical cancer targets in the future.
Collapse
Affiliation(s)
- Rui Shen
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui 230012, China
| | - Hongyun Ruan
- Cancer Research Centre, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Shuye Lin
- Cancer Research Centre, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Bin Liu
- Cancer Research Centre, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Hang Song
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui 230012, China
- Department of Biochemistry and Molecular Biology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui 230012, China
| | - Lu Li
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui 230012, China
- Department of Biochemistry and Molecular Biology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui 230012, China
| | - Teng Ma
- Cancer Research Centre, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| |
Collapse
|
12
|
Ji K, Li L, Liu H, Shen Y, Jiang J, Zhang M, Teng H, Yan X, Zhang Y, Cai Y, Zhou H. Unveiling the role of GAS41 in cancer progression. Cancer Cell Int 2023; 23:245. [PMID: 37853482 PMCID: PMC10583379 DOI: 10.1186/s12935-023-03098-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023] Open
Abstract
GAS41, a member of the human YEATS domain family, plays a pivotal role in human cancer development. It serves as a highly promising epigenetic reader, facilitating precise regulation of cell growth and development by recognizing essential histone modifications, including histone acetylation, benzoylation, succinylation, and crotonylation. Functional readouts of these histone modifications often coincide with cancer progression. In addition, GAS41 functions as a novel oncogene, participating in numerous signaling pathways. Here, we summarize the epigenetic functions of GAS41 and its role in the carcinoma progression. Moving forward, elucidating the downstream target oncogenes regulated by GAS41 and the developing small molecule inhibitors based on the distinctive YEATS recognition properties will be pivotal in advancing this research field.
Collapse
Affiliation(s)
- Kangkang Ji
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Li Li
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Hui Liu
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Yucheng Shen
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Jian Jiang
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Minglei Zhang
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Hongwei Teng
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Xun Yan
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Yanhua Zhang
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Yong Cai
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China
| | - Hai Zhou
- Department of Central Laboratory, Binhai County People's Hospital, Yancheng, 224000, China.
| |
Collapse
|
13
|
Yin X, Zhang H, Wei Z, Wang Y, Han S, Zhou M, Xu W, Han W. Large-Scale Identification of Lysine Crotonylation Reveals Its Potential Role in Oral Squamous Cell Carcinoma. Cancer Manag Res 2023; 15:1165-1179. [PMID: 37868687 PMCID: PMC10590141 DOI: 10.2147/cmar.s424422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/11/2023] [Indexed: 10/24/2023] Open
Abstract
Purpose Lysine crotonylation, an emerging posttranslational modification, has been implicated in the regulation of diverse biological processes. However, its involvement in oral squamous cell carcinoma (OSCC) remains elusive. This study aims to reveal the global crotonylome in OSCC under hypoxic conditions and explore the potential regulatory mechanism of crotonylation in OSCC. Methods Liquid-chromatography fractionation, affinity enrichment of crotonylated peptides, and high-resolution mass spectrometry were employed to detect differential crotonylation in CAL27 cells cultured under hypoxia. The obtained data were further subjected to bioinformatics analysis to uncover the involved biological processes and pathways of the dysregulated crotonylated proteins. A site-mutated plasmid was utilized to investigate the effect of crotonylation on Heat Shock Protein 90 Alpha Family Class B Member 1 (HAP90AB1) function. Results A large-scale crotonylome analysis revealed 1563 crotonylated modification sites on 605 proteins in CAL27 cells under hypoxia. Bioinformatics analysis revealed a significant decrease in histone crotonylation levels, while up-regulated crotonylated proteins were mainly concentrated in non-histone proteins. Notably, glycolysis-related proteins exhibited prominent up-regulation among the identified crotonylated proteins, with HSP90AB1 displaying the most significant changes. Subsequent experimental findings confirmed that mutating lysine 265 of HSP90AB1 into a silent arginine impaired its function in promoting glycolysis. Conclusion Our study provides insights into the crotonylation modification of proteins in OSCC under hypoxic conditions and elucidates the associated biological processes and pathways. Crotonylation of HSP90AB1 in hypoxic conditions may enhance the glycolysis regulation ability in OSCC, offering novel perspectives on the regulatory mechanism of crotonylation in hypoxic OSCC and potential therapeutic targets for OSCC treatment.
Collapse
Affiliation(s)
- Xiteng Yin
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
| | - Hongbo Zhang
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
| | - Zheng Wei
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
- Pediatric Dentistry, Nanjing Stomatology Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
| | - Yufeng Wang
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
| | - Shengwei Han
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
| | - Meng Zhou
- Department of Oral and Maxillofacial Surgery, the Affiliated Stomatological Hospital of Xuzhou Medical University, Xuzhou, People’s Republic of China
| | - Wenguang Xu
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
| | - Wei Han
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People’s Republic of China
| |
Collapse
|
14
|
Ji P, Zhang G, Guo Y, Song H, Yuan X, Hu X, Guo Z, Xia P, Shen R, Wang D. Protein crotonylation: An emerging regulator in DNA damage response. Life Sci 2023; 331:122059. [PMID: 37652154 DOI: 10.1016/j.lfs.2023.122059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/16/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
DNA damage caused by internal or external factors lead to increased genomic instability and various diseases. The DNA damage response (DDR) is a crucial mechanism that maintaining genomic stability through detecting and repairing DNA damage timely. Post-translational modifications (PTMs) play significant roles in regulation of DDR. Among the present PTMs, crotonylation has emerged as a novel identified modification that is involved in a wide range of biological processes including gene expression, spermatogenesis, cell cycle, and the development of diverse diseases. In the past decade, numerous crotonylation sites have been identified in histone and non-histone proteins, leading to a more comprehensive and deep understanding of the function and mechanisms in protein crotonylation. This review provides a comprehensive overview of the regulatory mechanisms of protein crotonylation and the effect of crotonylation in DDR. Furthermore, the effect of protein crotonylation in tumor development and progression is presented, to inspire and explore the novel strategies for tumor therapy.
Collapse
Affiliation(s)
- Pengfei Ji
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Guokun Zhang
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Yanan Guo
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Haoyun Song
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Xinyi Yuan
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Xiaohui Hu
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Zhao Guo
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Peng Xia
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Rong Shen
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China.
| | - Degui Wang
- School of basic medical sciences, Lanzhou University, Lanzhou, Gansu Province 73000, China; NHC Key Laboratory of diagnosis and therapy of Gastrointestinal Tumor, Lanzhou, Gansu Province 730000, China.
| |
Collapse
|
15
|
Liao M, Sun X, Zheng W, Wu M, Wang Y, Yao J, Ma Y, Gao S, Pei D. LINC00922 decoys SIRT3 to facilitate the metastasis of colorectal cancer through up-regulation the H3K27 crotonylation of ETS1 promoter. Mol Cancer 2023; 22:163. [PMID: 37789393 PMCID: PMC10548613 DOI: 10.1186/s12943-023-01859-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 09/10/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND Lysine crotonylation (Kcr) is up-regulation in colorectal cancer (CRC) tissues, while its specific contribution remains uncertain. This study aimed to elucidate the role and mechanism of crotonylation on Lys27 of histone H3 (H3K27cr) in facilitating CRC metastasis. METHODS Immunohistochemistry was employed to investigate the correlation between H3K27cr and CRC metastasis. Both in vitro and in vivo assays employing loss function or gain function approaches were conducted to elucidate the role of LINC00922 in promoting CRC metastasis. ScRNA-seq analysis and immunoprecipitation analyses were employed to explore the underlying mechanism by which LINC00922 facilitates CRC metastasis through H3K27cr. RESULTS Clinically, H3K27cr was upregulated in metastatic CRC tissues and positively correlated with advanced clinical stages. Functionally, knockdown of LINC00922 inhibited migration of CRC cells both in vitro and in vivo. Furthermore, the supplementation of NaCr restored the migration and invasion levels of LINC00922 stable knockdown cells by restoring the H3K27cr level. Mechanistically, LINC00922 promoted invasion and migration through H3K27cr mediated cell adhesion molecules (CAMs) in epithelial cells. Notably, LINC00922 interacted with the protein sirtuin 3 (SIRT3) and obstructed its binding to the promoter region of ETS1, leading to an elevation in the level of H3K27cr in this promoter region and the subsequent activation of ETS1 transcription. CONCLUSIONS Our findings uncovered a novel regulatory function of H3K27cr, regulated by LINC00922, in facilitating CRC metastasis. This discovery contributed to a deeper comprehension of the involvement of histone crotonylation in the metastatic process of CRC.
Collapse
Affiliation(s)
- Meijian Liao
- Department of Pathology, Xuzhou Medical University, Xuzhou, 221004, P.R. China
| | - Xiaolin Sun
- Department of Pathology, Xuzhou Medical University, Xuzhou, 221004, P.R. China
| | - Wendan Zheng
- Department of Pathology, Xuzhou Medical University, Xuzhou, 221004, P.R. China
| | - Mengdi Wu
- Department of Pathology, Xuzhou Medical University, Xuzhou, 221004, P.R. China
| | - Yifan Wang
- Department of Pathology, Xuzhou Medical University, Xuzhou, 221004, P.R. China
| | - Jia Yao
- Department of Pathology, Xuzhou Medical University, Xuzhou, 221004, P.R. China
| | - Yu Ma
- Department of Pathology, Xuzhou Medical University, Xuzhou, 221004, P.R. China
| | - Shoucui Gao
- Department of Pathology, Xuzhou Medical University, Xuzhou, 221004, P.R. China.
| | - Dongsheng Pei
- Department of Pathology, Xuzhou Medical University, Xuzhou, 221004, P.R. China.
| |
Collapse
|
16
|
Xie Y, Chen S, Guo Z, Tian Y, Hong X, Feng P, Xie Q, Yu Q. Down-regulation of Lon protease 1 lysine crotonylation aggravates mitochondrial dysfunction in polycystic ovary syndrome. MedComm (Beijing) 2023; 4:e396. [PMID: 37817894 PMCID: PMC10560969 DOI: 10.1002/mco2.396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 10/12/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) is a prevalent reproductive endocrine disorder, with metabolic abnormalities and ovulation disorders. The post-translational modifications (PTMs) are functionally relevant and strengthen the link between metabolism and cellular functions. Lysine crotonylation is a newly identified PTM, the function of which in PCOS has not yet been reported. To explore the molecular mechanisms of crotonylation involved in the abnormalities of metabolic homeostasis and oocyte maturation in PCOS, by using liquid chromatography-tandem mass spectrometry analysis, we constructed a comprehensive map of crotonylation modifications in ovarian tissue of PCOS-like mouse model established by dehydroepiandrosterone induction. The crotonylation levels of proteins involved in metabolic processes were significantly decreased in PCOS ovaries compared to control samples. Further investigation showed that decrotonylation of Lon protease 1 (LONP1) at lysine 390 was associated with mitochondrial dysfunction in PCOS. Moreover, LONP1 crotonylation levels in PCOS were correlated with ovarian tissue oxidative stress levels, androgen levels, and oocyte development. Consistently, down-regulation of LONP1 and LONP1 crotonylation levels were also observed in the blood samples of PCOS patients. Collectively, our study revealed a mechanism by which the decrotonylation of LONP1 may attenuate its activity and alter follicular microenvironment to affect oocyte maturation in PCOS.
Collapse
Affiliation(s)
- Yuan Xie
- Department of Obstetrics and GynecologyNational Clinical Research Center for Obstetric & Gynecologic DiseasesState Key Laboratory for Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegePeking Union Medical College Hospital (Dongdan Campus)BeijingChina
| | - Shuwen Chen
- Department of Obstetrics and GynecologyNational Clinical Research Center for Obstetric & Gynecologic DiseasesState Key Laboratory for Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegePeking Union Medical College Hospital (Dongdan Campus)BeijingChina
| | - Zaixin Guo
- Department of Obstetrics and GynecologyNational Clinical Research Center for Obstetric & Gynecologic DiseasesState Key Laboratory for Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegePeking Union Medical College Hospital (Dongdan Campus)BeijingChina
| | - Ying Tian
- Department of Obstetrics and GynecologyNational Clinical Research Center for Obstetric & Gynecologic DiseasesState Key Laboratory for Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegePeking Union Medical College Hospital (Dongdan Campus)BeijingChina
| | - Xinyu Hong
- Department of Obstetrics and GynecologyNational Clinical Research Center for Obstetric & Gynecologic DiseasesState Key Laboratory for Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegePeking Union Medical College Hospital (Dongdan Campus)BeijingChina
| | - Penghui Feng
- Department of Obstetrics and GynecologyNational Clinical Research Center for Obstetric & Gynecologic DiseasesState Key Laboratory for Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegePeking Union Medical College Hospital (Dongdan Campus)BeijingChina
| | - Qiu Xie
- Department of Medical Research CenterState Key Laboratory for Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Science and Peking Union Medical CollegeBeijingChina
| | - Qi Yu
- Department of Obstetrics and GynecologyNational Clinical Research Center for Obstetric & Gynecologic DiseasesState Key Laboratory for Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegePeking Union Medical College Hospital (Dongdan Campus)BeijingChina
| |
Collapse
|
17
|
Hou JY, Li N, Wang J, Gao LJ, Chang JS, Cao JM. Histone crotonylation of peripheral blood mononuclear cells is a potential biomarker for diagnosis of colorectal cancer. Epigenetics Chromatin 2023; 16:35. [PMID: 37749610 PMCID: PMC10521402 DOI: 10.1186/s13072-023-00509-3] [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: 06/28/2023] [Accepted: 09/17/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Blood-based tests have public appeal in screening cancers due to their minimally invasive nature, ability to integrate with other routine blood tests, and high compliance. This study aimed to investigate whether certain epigenetic modulation of peripheral blood mononuclear cells (PBMCs) could be a biomarker of colorectal cancer (CRC). RESULTS Western blotting of histones in the PBMCs from 40 colorectal cancer patients and 40 healthy controls was performed to identify the crotonylation sites of proteins. The correlation of crotonylation with tumor staging and diagnostic efficacy were analyzed. Crotonylation of H2BK12 (H2BK12cr) was identified significantly upregulated in the PBMCs of CRC patients compared to healthy controls, and were closely related to distant metastasis (P = 0.0478) and late TNM stage (P = 0.0201). Receiver operator characteristic curve (ROC) analysis demonstrated that the area under curve (AUC) of H2BK12cr was 0.8488, the sensitivity was 70%, and the specificity was 92.5%. The H2BK12cr parameter significantly increased the diagnostic effectiveness of CRC compared with the commercial carcinoembryonic antigen assays. CONCLUSIONS The H2BK12cr level in PBMCs of CRC patients has a potential to be a biomarker for distinguishing CRC patients from healthy controls with the advantages of easy operation and high diagnostic efficacy.
Collapse
Affiliation(s)
- Jia-Yi Hou
- Department of Clinical Laboratory, Shanxi Provincial Academy of Traditional Chinese Medicine, Taiyuan, China
| | - Ning Li
- Department of Gastrointestinal and Pancreatic Surgery and Hernia and Abdominal Surgery, Shanxi Provincial People's Hospital, Taiyuan, China
| | - Jie Wang
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Li-Juan Gao
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Jia-Song Chang
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Ji-Min Cao
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China.
| |
Collapse
|
18
|
Scumaci D, Zheng Q. Epigenetic meets metabolism: novel vulnerabilities to fight cancer. Cell Commun Signal 2023; 21:249. [PMID: 37735413 PMCID: PMC10512595 DOI: 10.1186/s12964-023-01253-7] [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: 06/24/2023] [Accepted: 08/01/2023] [Indexed: 09/23/2023] Open
Abstract
Histones undergo a plethora of post-translational modifications (PTMs) that regulate nucleosome and chromatin dynamics and thus dictate cell fate. Several evidences suggest that the accumulation of epigenetic alterations is one of the key driving forces triggering aberrant cellular proliferation, invasion, metastasis and chemoresistance pathways. Recently a novel class of histone "non-enzymatic covalent modifications" (NECMs), correlating epigenome landscape and metabolic rewiring, have been described. These modifications are tightly related to cell metabolic fitness and are able to impair chromatin architecture. During metabolic reprogramming, the high metabolic flux induces the accumulation of metabolic intermediate and/or by-products able to react with histone tails altering epigenome homeostasis. The accumulation of histone NECMs is a damaging condition that cancer cells counteracts by overexpressing peculiar "eraser" enzymes capable of removing these modifications preserving histones architecture. In this review we explored the well-established NECMs, emphasizing the role of their corresponding eraser enzymes. Additionally, we provide a parterre of drugs aiming to target those eraser enzymes with the intent to propose novel routes of personalized medicine based on the identification of epi-biomarkers which might be selectively targeted for therapy. Video Abstract.
Collapse
Affiliation(s)
- Domenica Scumaci
- Research Center On Advanced Biochemistry and Molecular Biology, Magna Græcia University of Catanzaro, 88100, Catanzaro, Italy.
- Department of Experimental and Clinical Medicine, Magna Græcia University of Catanzaro, 88100, Catanzaro, Italy.
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
19
|
Dutta H, Jain N. Post-translational modifications and their implications in cancer. Front Oncol 2023; 13:1240115. [PMID: 37795435 PMCID: PMC10546021 DOI: 10.3389/fonc.2023.1240115] [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: 06/14/2023] [Accepted: 08/21/2023] [Indexed: 10/06/2023] Open
Abstract
Post-translational modifications (PTMs) are crucial regulatory mechanisms that alter the properties of a protein by covalently attaching a modified chemical group to some of its amino acid residues. PTMs modulate essential physiological processes such as signal transduction, metabolism, protein localization, and turnover and have clinical relevance in cancer and age-related pathologies. Majority of proteins undergo post-translational modifications, irrespective of their occurrence in or after protein biosynthesis. Post-translational modifications link to amino acid termini or side chains, causing the protein backbone to get cleaved, spliced, or cyclized, to name a few. These chemical modifications expand the diversity of the proteome and regulate protein activity, structure, locations, functions, and protein-protein interactions (PPIs). This ability to modify the physical and chemical properties and functions of proteins render PTMs vital. To date, over 200 different protein modifications have been reported, owing to advanced detection technologies. Some of these modifications include phosphorylation, glycosylation, methylation, acetylation, and ubiquitination. Here, we discuss about the existing as well as some novel post-translational protein modifications, with their implications in aberrant states, which will help us better understand the modified sites in different proteins and the effect of PTMs on protein functions in core biological processes and progression in cancer.
Collapse
Affiliation(s)
- Hashnu Dutta
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Nishant Jain
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
20
|
Yang P, Qin Y, Zeng L, He Y, Xie Y, Cheng X, Huang W, Cao L. Crotonylation and disease: Current progress and future perspectives. Biomed Pharmacother 2023; 165:115108. [PMID: 37392654 DOI: 10.1016/j.biopha.2023.115108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/18/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023] Open
Abstract
Histone lysine crotonylation was first identified as a new type of post-translational modification in 2011. In recent years, prominent progress has been made in the study of histone and nonhistone crotonylation in reproduction, development, and disease. Although the regulatory enzyme systems and targets of crotonylation partially overlap with those of acetylation, the peculiar CC bond structure of crotonylation suggests that crotonylation may have specific biological functions. In this review, we summarize the latest research progress regarding crotonylation, especially its regulatory factors and relationship with diseases, which suggest further research directions for crotonylation and provide new ideas for developing disease intervention and treatment regimens.
Collapse
Affiliation(s)
- Ping Yang
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000 Sichuan, China
| | - Yuanyuan Qin
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000 Sichuan, China
| | - Lisha Zeng
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China
| | - Yanqiu He
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000 Sichuan, China
| | - Yumei Xie
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000 Sichuan, China
| | - Xi Cheng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000 Sichuan, China
| | - Wei Huang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Metabolic Vascular Disease Key Laboratory of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China; Sichuan Clinical Research Center for Nephropathy, Luzhou 646000 Sichuan, China.
| | - Ling Cao
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000 Sichuan, China.
| |
Collapse
|
21
|
Stein RA, Riber L. Epigenetic effects of short-chain fatty acids from the large intestine on host cells. MICROLIFE 2023; 4:uqad032. [PMID: 37441522 PMCID: PMC10335734 DOI: 10.1093/femsml/uqad032] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/04/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023]
Abstract
Adult humans harbor at least as many microbial cells as eukaryotic ones. The largest compartment of this diverse microbial population, the gut microbiota, encompasses the collection of bacteria, archaea, viruses, and eukaryotic organisms that populate the gastrointestinal tract, and represents a complex and dynamic ecosystem that has been increasingly implicated in health and disease. The gut microbiota carries ∼100-to-150-times more genes than the human genome and is intimately involved in development, homeostasis, and disease. Of the several microbial metabolites that have been studied, short-chain fatty acids emerge as a group of molecules that shape gene expression in several types of eukaryotic cells by multiple mechanisms, which include DNA methylation changes, histone post-translational modifications, and microRNA-mediated gene silencing. Butyric acid, one of the most extensively studied short-chain fatty acids, reaches higher concentrations in the colonic lumen, where it provides a source of energy for healthy colonocytes, and its concentrations decrease towards the bottom of the colonic crypts, where stem cells reside. The lower butyric acid concentration in the colonic crypts allows undifferentiated cells, such as stem cells, to progress through the cell cycle, pointing towards the importance of the crypts in providing them with a protective niche. In cancerous colonocytes, which metabolize relatively little butyric acid and mostly rely on glycolysis, butyric acid preferentially acts as a histone deacetylase inhibitor, leading to decreased cell proliferation and increased apoptosis. A better understanding of the interface between the gut microbiota metabolites and epigenetic changes in eukaryotic cells promises to unravel in more detail processes that occur physiologically and as part of disease, help develop novel biomarkers, and identify new therapeutic modalities.
Collapse
Affiliation(s)
- Richard A Stein
- Corresponding author. Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA. Tel: +1-917-684-9438; E-mail: ;
| | - Leise Riber
- Department of Plant & Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| |
Collapse
|
22
|
Liu R, Wu J, Guo H, Yao W, Li S, Lu Y, Jia Y, Liang X, Tang J, Zhang H. Post-translational modifications of histones: Mechanisms, biological functions, and therapeutic targets. MedComm (Beijing) 2023; 4:e292. [PMID: 37220590 PMCID: PMC10200003 DOI: 10.1002/mco2.292] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023] Open
Abstract
Histones are DNA-binding basic proteins found in chromosomes. After the histone translation, its amino tail undergoes various modifications, such as methylation, acetylation, phosphorylation, ubiquitination, malonylation, propionylation, butyrylation, crotonylation, and lactylation, which together constitute the "histone code." The relationship between their combination and biological function can be used as an important epigenetic marker. Methylation and demethylation of the same histone residue, acetylation and deacetylation, phosphorylation and dephosphorylation, and even methylation and acetylation between different histone residues cooperate or antagonize with each other, forming a complex network. Histone-modifying enzymes, which cause numerous histone codes, have become a hot topic in the research on cancer therapeutic targets. Therefore, a thorough understanding of the role of histone post-translational modifications (PTMs) in cell life activities is very important for preventing and treating human diseases. In this review, several most thoroughly studied and newly discovered histone PTMs are introduced. Furthermore, we focus on the histone-modifying enzymes with carcinogenic potential, their abnormal modification sites in various tumors, and multiple essential molecular regulation mechanism. Finally, we summarize the missing areas of the current research and point out the direction of future research. We hope to provide a comprehensive understanding and promote further research in this field.
Collapse
Affiliation(s)
- Ruiqi Liu
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Jiajun Wu
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
- Otolaryngology & Head and Neck CenterCancer CenterDepartment of Head and Neck SurgeryZhejiang Provincial People's HospitalAffiliated People's Hospital, Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Haiwei Guo
- Otolaryngology & Head and Neck CenterCancer CenterDepartment of Head and Neck SurgeryZhejiang Provincial People's HospitalAffiliated People's Hospital, Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Weiping Yao
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Shuang Li
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentJinzhou Medical UniversityJinzhouLiaoningChina
| | - Yanwei Lu
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
| | - Yongshi Jia
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
| | - Xiaodong Liang
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Jianming Tang
- Department of Radiation OncologyThe First Hospital of Lanzhou UniversityLanzhou UniversityLanzhouGansuChina
| | - Haibo Zhang
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
| |
Collapse
|
23
|
Zhong Q, Xiao X, Qiu Y, Xu Z, Chen C, Chong B, Zhao X, Hai S, Li S, An Z, Dai L. Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications. MedComm (Beijing) 2023; 4:e261. [PMID: 37143582 PMCID: PMC10152985 DOI: 10.1002/mco2.261] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
Protein posttranslational modifications (PTMs) refer to the breaking or generation of covalent bonds on the backbones or amino acid side chains of proteins and expand the diversity of proteins, which provides the basis for the emergence of organismal complexity. To date, more than 650 types of protein modifications, such as the most well-known phosphorylation, ubiquitination, glycosylation, methylation, SUMOylation, short-chain and long-chain acylation modifications, redox modifications, and irreversible modifications, have been described, and the inventory is still increasing. By changing the protein conformation, localization, activity, stability, charges, and interactions with other biomolecules, PTMs ultimately alter the phenotypes and biological processes of cells. The homeostasis of protein modifications is important to human health. Abnormal PTMs may cause changes in protein properties and loss of protein functions, which are closely related to the occurrence and development of various diseases. In this review, we systematically introduce the characteristics, regulatory mechanisms, and functions of various PTMs in health and diseases. In addition, the therapeutic prospects in various diseases by targeting PTMs and associated regulatory enzymes are also summarized. This work will deepen the understanding of protein modifications in health and diseases and promote the discovery of diagnostic and prognostic markers and drug targets for diseases.
Collapse
Affiliation(s)
- Qian Zhong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xina Xiao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Yijie Qiu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhiqiang Xu
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Chunyu Chen
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Baochen Chong
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Xinjun Zhao
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shan Hai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Shuangqing Li
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Zhenmei An
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| | - Lunzhi Dai
- Department of Endocrinology and MetabolismGeneral Practice Ward/International Medical Center WardGeneral Practice Medical Center and National Clinical Research Center for GeriatricsState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduChina
| |
Collapse
|
24
|
Zhang XY, Liu ZX, Zhang YF, Xu LX, Chen MK, Zhou YF, Yu J, Li XX, Zhang N. SEPT2 crotonylation promotes metastasis and recurrence in hepatocellular carcinoma and is associated with poor survival. Cell Biosci 2023; 13:63. [PMID: 36949517 PMCID: PMC10032003 DOI: 10.1186/s13578-023-00996-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/22/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) metastasis and recurrence lead to therapy failure, which are closely associated with the proteome. However, the role of post-translational modification (PTM) in HCC, especially for the recently discovered lysine crotonylation (Kcr), is elusive. RESULTS We investigated the correlation between crotonylation and HCC in 100 tumor tissues and performed stable isotope labeling by amino acids and liquid chromatography tandem mass spectrometry in HCC cells, and we found that crotonylation was positively correlated with HCC metastasis, and higher crotonylation in HCC cells facilitated cell invasiveness. Through bioinformatic analysis, we found that the crotonylated protein SEPT2 was significantly hypercrotonylated in highly invasive cells, while the decrotonylated mutation of SEPT2-K74 impaired SEPT2 GTPase activity and inhibited HCC metastasis in vitro and in vivo. Mechanistically, SIRT2 decrotonylated SEPT2, and P85α was found to be the downstream effector of SEPT2. Moreover, we identified that SEPT2-K74cr was correlated with poor prognosis and recurrence in HCC patients, thus indicating its clinical potential as an independent prognostic factor. CONCLUSIONS We revealed the role of nonhistone protein crotonylation in regulating HCC metastasis and invasion. Crotonylation facilitated cell invasion through the crotonylated SEPT2-K74-P85α-AKT pathway. High SEPT2-K74 crotonylation predicted poor prognosis and a high recurrence rate in HCC patients. Our study revealed a novel role of crotonylation in promoting HCC metastasis.
Collapse
Affiliation(s)
- Xin-Yue Zhang
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Ze-Xian Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Yi-Fan Zhang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
- Department of Liver Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Li-Xia Xu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
- Department of Oncology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Meng-Ke Chen
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Yu-Feng Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Jun Yu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
- Department of Medicine and Therapeutics, Institute of Digestive Disease, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiao-Xing Li
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.
- Department of Oncology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Ning Zhang
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.
| |
Collapse
|
25
|
Development and Validation of a Prognostic Signature Based on the Lysine Crotonylation Regulators in Head and Neck Squamous Cell Carcinoma. BIOMED RESEARCH INTERNATIONAL 2023; 2023:4444869. [PMID: 36814797 PMCID: PMC9940974 DOI: 10.1155/2023/4444869] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 02/16/2023]
Abstract
Background Lysine crotonylation (Kcr) is a newly identified posttranslational modification type regulated by various enzymes and coenzymes, including lysine crotonyltransferase, lysine decrotonylase, and binding proteins. However, the role of Kcr regulators in head and neck squamous cell carcinoma (HNSCC) remains unknown. The aim of this study was to establish and validate a Kcr-related prognostic signature of HNSCC and to assess the clinical predictive value of this signature. Methods The mRNA expression profiles and clinicopathological data from The Cancer Genome Atlas (TCGA) database were downloaded to explore the clinical significance and prognostic value of these regulators in HNSCC. The least absolute shrinkage and selection operator (LASSO) Cox regression model was used to generate the Kcr-related prognostic signature for HNSCC. Subsequently, the GSE65858 dataset from the Gene Expression Omnibus (GEO) database was used to validate the signature. The prognostic value of the signature was evaluated using the Kaplan-Meier survival, receiver operating characteristic (ROC) curve, and univariate and multivariate Cox regression analyses. Results We established a nine-gene risk signature associated with the prognosis of HNSCC based on Kcr regulators. High-risk patients demonstrated significantly poorer overall survival (OS) than low-risk patients in the training (TCGA) and validation (GEO) datasets. Then, the time-dependent receiver operating characteristic (ROC) curve analysis showed that the nine-gene risk signature was more accurate for predicting the 5-year OS than other clinical parameters, including age, gender, T stage, N stage, and histologic grade in the TCGA and GEO datasets. Moreover, the Cox regression analysis showed that the constructed risk signature was an independent risk factor for HNSCC. Conclusion Our study identified and validated a nine-gene signature for HNSCC based on Kcr regulators. These results might contribute to prognosis stratification and treatment escalation for HNSCC patients.
Collapse
|
26
|
Shang S, Liu J, Hua F. Protein acylation: mechanisms, biological functions and therapeutic targets. Signal Transduct Target Ther 2022; 7:396. [PMID: 36577755 PMCID: PMC9797573 DOI: 10.1038/s41392-022-01245-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/27/2022] [Accepted: 11/06/2022] [Indexed: 12/30/2022] Open
Abstract
Metabolic reprogramming is involved in the pathogenesis of not only cancers but also neurodegenerative diseases, cardiovascular diseases, and infectious diseases. With the progress of metabonomics and proteomics, metabolites have been found to affect protein acylations through providing acyl groups or changing the activities of acyltransferases or deacylases. Reciprocally, protein acylation is involved in key cellular processes relevant to physiology and diseases, such as protein stability, protein subcellular localization, enzyme activity, transcriptional activity, protein-protein interactions and protein-DNA interactions. Herein, we summarize the functional diversity and mechanisms of eight kinds of nonhistone protein acylations in the physiological processes and progression of several diseases. We also highlight the recent progress in the development of inhibitors for acyltransferase, deacylase, and acylation reader proteins for their potential applications in drug discovery.
Collapse
Affiliation(s)
- Shuang Shang
- grid.506261.60000 0001 0706 7839CAMS Key Laboratory of Molecular Mechanism and Target Discovery of Metabolic Disorder and Tumorigenesis, State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 100050 Beijing, P.R. China
| | - Jing Liu
- grid.506261.60000 0001 0706 7839CAMS Key Laboratory of Molecular Mechanism and Target Discovery of Metabolic Disorder and Tumorigenesis, State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 100050 Beijing, P.R. China
| | - Fang Hua
- grid.506261.60000 0001 0706 7839CAMS Key Laboratory of Molecular Mechanism and Target Discovery of Metabolic Disorder and Tumorigenesis, State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 100050 Beijing, P.R. China
| |
Collapse
|
27
|
Khanal J, Kandel J, Tayara H, Chong KT. CapsNh-Kcr: Capsule network-based prediction of lysine crotonylation sites in human non-histone proteins. Comput Struct Biotechnol J 2022; 21:120-127. [PMID: 36544479 PMCID: PMC9735261 DOI: 10.1016/j.csbj.2022.11.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/10/2022] [Accepted: 11/26/2022] [Indexed: 12/04/2022] Open
Abstract
Lysine crotonylation (Kcr) is one of the most important post-translational modifications (PTMs) that is widely detected in both histone and non-histone proteins. In fact, Kcr is reported to be involved in various biological processes, such as metabolism and cell differentiation. However, the available experimental methods for Kcr site identification are laborious and costly. To effectively replace existing experimental approaches, some computational methods have been developed in the last few years. The available computational methods still lack some important aspects, as they can only identify Kcr sites on either histone-only or combined histone and nonhistone proteins. Although a tool was developed to identify Kcr sites on non-histone proteins only, its performance is inadequate and the exploration of hidden Kcr patterns (motifs) has been completely ignored, which might be significant for detailed Kcr studies. Therefore, algorithms that can more effectively predict Kcr sites on non-histone proteins with their biological meaning need to be designed. Accordingly, we developed a novel deep learning (capsule network)-based model, named CapsNh-Kcr, for Kcr site prediction, particularly focusing on non-histone proteins. Based on the independent results, the proposed model achieves an AUC of 0.9120, which is approximately 6% higher than that of previous nhKcr model in the prediction of Kcr sites on non-histone proteins. Further, we revealed, for the first time, that the proposed model can represent obvious motif distribution across Kcr sites in non-histone proteins. The source code (in Python) is publicly available at https://github.com/Jhabindra-bioinfo/CapsNh-Kcr.
Collapse
Affiliation(s)
- Jhabindra Khanal
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
| | - Jeevan Kandel
- Graduate School of Integrated Energy-AI, Jeonbuk National University, Jeonju 54896, South Korea
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea,Corresponding authors at: School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea (H. Tayara); Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea (K.T. Chong).
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea,Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, South Korea,Corresponding authors at: School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea (H. Tayara); Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea (K.T. Chong).
| |
Collapse
|
28
|
Fu Y, Yu J, Li F, Ge S. Oncometabolites drive tumorigenesis by enhancing protein acylation: from chromosomal remodelling to nonhistone modification. J Exp Clin Cancer Res 2022; 41:144. [PMID: 35428309 PMCID: PMC9013066 DOI: 10.1186/s13046-022-02338-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/21/2022] [Indexed: 02/02/2023] Open
Abstract
AbstractMetabolites are intermediate products of cellular metabolism catalysed by various enzymes. Metabolic remodelling, as a biochemical fingerprint of cancer cells, causes abnormal metabolite accumulation. These metabolites mainly generate energy or serve as signal transduction mediators via noncovalent interactions. After the development of highly sensitive mass spectrometry technology, various metabolites were shown to covalently modify proteins via forms of lysine acylation, including lysine acetylation, crotonylation, lactylation, succinylation, propionylation, butyrylation, malonylation, glutarylation, 2-hydroxyisobutyrylation and β-hydroxybutyrylation. These modifications can regulate gene expression and intracellular signalling pathways, highlighting the extensive roles of metabolites. Lysine acetylation is not discussed in detail in this review since it has been broadly investigated. We focus on the nine aforementioned novel lysine acylations beyond acetylation, which can be classified into two categories: histone acylations and nonhistone acylations. We summarize the characteristics and common functions of these acylation types and, most importantly, provide a glimpse into their fine-tuned control of tumorigenesis and potential value in tumour diagnosis, monitoring and therapy.
Collapse
|
29
|
Post-Translational Modifications by Lipid Metabolites during the DNA Damage Response and Their Role in Cancer. Biomolecules 2022; 12:biom12111655. [DOI: 10.3390/biom12111655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Genomic DNA damage occurs as an inevitable consequence of exposure to harmful exogenous and endogenous agents. Therefore, the effective sensing and repair of DNA damage are essential for maintaining genomic stability and cellular homeostasis. Inappropriate responses to DNA damage can lead to genomic instability and, ultimately, cancer. Protein post-translational modifications (PTMs) are a key regulator of the DNA damage response (DDR), and recent progress in mass spectrometry analysis methods has revealed that a wide range of metabolites can serve as donors for PTMs. In this review, we will summarize how the DDR is regulated by lipid metabolite-associated PTMs, including acetylation, S-succinylation, N-myristoylation, palmitoylation, and crotonylation, and the implications for tumorigenesis. We will also discuss potential novel targets for anti-cancer drug development.
Collapse
|
30
|
Philips O, Sultonova M, Blackmore B, Murphy JP. Understanding emerging bioactive metabolites with putative roles in cancer biology. Front Oncol 2022; 12:1014748. [PMID: 36249070 PMCID: PMC9557195 DOI: 10.3389/fonc.2022.1014748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Dysregulated metabolism in cancers is, by now, well established. Although metabolic adaptations provide cancers with the ability to synthesize the precursors required for rapid biosynthesis, some metabolites have direct functional, or bioactive, effects in human cells. Here we summarize recently identified metabolites that have bioactive roles either as post-translational modifications (PTMs) on proteins or in, yet unknown ways. We propose that these metabolites could play a bioactive role in promoting or inhibiting cancer cell phenotypes in a manner that is mostly unexplored. To study these potentially important bioactive roles, we discuss several novel metabolomic and proteomic approaches aimed at defining novel PTMs and metabolite-protein interactions. Understanding metabolite PTMs and protein interactors of bioactive metabolites may provide entirely new therapeutic targets for cancer.
Collapse
Affiliation(s)
| | | | | | - J. Patrick Murphy
- Department of Biology, University of Prince Edward Island, Charlottetown, PE, Canada
| |
Collapse
|
31
|
Bhattacharya A, Chatterjee S, Bhaduri U, Singh AK, Vasudevan M, Sashidhara KV, Guha R, Nazir A, Rath SK, Natesh N, Kundu TK. Butyrylation Meets Adipogenesis-Probed by a p300-Catalyzed Acylation-Specific Small Molecule Inhibitor: Implication in Anti-obesity Therapy. J Med Chem 2022; 65:12273-12291. [PMID: 36074919 DOI: 10.1021/acs.jmedchem.2c00943] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The enzyme p300, besides having acetyltransferase activity, can also catalyze other acylation modifications, whose physiological implications are still being investigated. Here, we report that the level of histone butyrylation increases globally as well as locally in the promoters of pro-adipogenic genes during adipogenesis. To delineate the role of p300-catalyzed butyrylation from acetylation in adipogenesis, we identified a semisynthetic derivative (LTK-14A) of garcinol, which specifically inhibited histone butyrylation without affecting acetylation. Treatment of 3T3L1 cells with LTK-14A abolished adipogenesis with downregulation of pro-adipogenic genes along with inhibition of H4K5 butyrylation. Administering LTK-14A to high-fat diet-fed and genetically obese db/db mice led to attenuation/decrease in their weight gain. The reduced obesity could be partially attributed to the inhibition of H4K5 butyrylation in adipocytes and liver. This report therefore not only, for the first time, causally links histone butyrylation with adipogenesis but also presents a probable candidate for anti-obesity therapeutics.
Collapse
Affiliation(s)
- Aditya Bhattacharya
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Sourav Chatterjee
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Utsa Bhaduri
- Chromatin Biology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Akash Kumar Singh
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | | | - Koneni V Sashidhara
- Division of Medicinal and Process Chemistry, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Rajdeep Guha
- Division of Laboratory Animal Facility, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Aamir Nazir
- Division of Toxicology and Experimental Medicine, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Srikanta Kumar Rath
- Division of Toxicology and Experimental Medicine, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Nagashayana Natesh
- Central Government Health Scheme Wellness Centre Number 8, Domlur, Bangalore 560071, India
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.,Division of Neuroscience and Aging Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| |
Collapse
|
32
|
Zhang D, Tang J, Xu Y, Huang X, Wang Y, Jin X, Wu G, Liu P. Global crotonylome reveals hypoxia-mediated lamin A crotonylation regulated by HDAC6 in liver cancer. Cell Death Dis 2022; 13:717. [PMID: 35977926 PMCID: PMC9385620 DOI: 10.1038/s41419-022-05165-1] [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: 03/21/2022] [Revised: 08/02/2022] [Accepted: 08/04/2022] [Indexed: 01/21/2023]
Abstract
Lysine crotonylation is a recently discovered post-translation modification involved in transcription regulation, cell signal transduction, and other processes. Scientists have identified several crotonylases and decrotonylases of histones, including P300/CBP, HDACs, and SIRTs. However, the regulation of non-histone protein crotonylation remains unclear. In the current study, we verified that crotonylation was upregulated in hypoxia and promoted liver cancer cell growth. We performed TMT-labeled quantitative lysine crotonylome analysis in 12 pairs of hepatocellular carcinoma and adjacent liver tissue and identified 3,793 lysine crotonylation sites in 1,428 proteins. We showed that crotonylation of lamin A at the site of K265/270 maintains its subcellular position, promotes liver cancer cell proliferation, and prevents cellular senescence. Our data indicate that HDAC6 is the decrotonylase of lamin A and downregulated in response to hypoxia, resulting in lamin A K265/270cr. Taken together, our study reveals the lamin A crotonylation in liver cancer progression and fills the research gap in non-histone protein crotonylation function.
Collapse
Affiliation(s)
- Dan Zhang
- grid.33199.310000 0004 0368 7223Cancer center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China ,grid.33199.310000 0004 0368 7223Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Jing Tang
- grid.33199.310000 0004 0368 7223Cancer center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China ,grid.33199.310000 0004 0368 7223Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Yunhong Xu
- grid.33199.310000 0004 0368 7223Cancer center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China ,grid.33199.310000 0004 0368 7223Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Xiaoju Huang
- grid.33199.310000 0004 0368 7223Cancer center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China ,grid.33199.310000 0004 0368 7223Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Yilin Wang
- grid.33199.310000 0004 0368 7223Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Xin Jin
- grid.216417.70000 0001 0379 7164Department of Urology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011 China ,grid.216417.70000 0001 0379 7164Uro-Oncology Institute of Central South University, Changsha, Hunan 410011 China
| | - Gang Wu
- grid.33199.310000 0004 0368 7223Cancer center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China ,grid.33199.310000 0004 0368 7223Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Pian Liu
- grid.33199.310000 0004 0368 7223Cancer center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China ,grid.33199.310000 0004 0368 7223Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| |
Collapse
|
33
|
The Potential Mechanism of HDAC1-Catalyzed Histone Crotonylation of Caspase-1 in Nonsmall Cell Lung Cancer. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:5049116. [PMID: 35958929 PMCID: PMC9363190 DOI: 10.1155/2022/5049116] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/18/2022]
Abstract
Nonsmall cell lung cancer (NSCLC) is a predominant subtype of lung cancer and accounts for over 80% of all lung cancer cases. The resistance to pemetrexed (PEM) is frequently occurred and severely affects the NSCLC therapy. Proteomic analysis of histones indicated that the histone deacetylase 1 (HDAC1) complex could hydrolyze lysine crotonylation on histone3 (H3K18cr), affecting epigenetic regulation in cancers. However, the effect of HDAC1-mediated H3K18cr on the PEM resistance of NSCLC is still unclear. Here, we aimed to explore the function of HDAC1-mediated H3K18cr in NSCLC PEM resistance. The expression of HDAC1 was upregulated in clinical NSCLC tissues and cell lines and correlated with the poor prognosis of NSCLC samples. We constructed the PEM-resistant NSCLC cell lines, and the depletion of HDAC1 remarkably reduced the viability of the cells. The proliferation of PEM-resistant NSCLC cells was decreased by HDAC1 knockdown, and the IC50 of PEM was repressed by the silencing of HDAC1 in the cells. Mechanically, we identified the enrichment of HDAC1 on the promoter of caspase-1 in PEM-resistant NSCLC cells. The depletion of HDAC1 inhibited the enrichment of histone H3K18cr and RNA polymerase II (RNA pol II) on the caspase-1 promoter in the cells. The expression of caspase-1 was suppressed by HDAC1 knockdown. The knockdown of HDAC1 reduced proliferation of PEM-resistant NSCLC cells, in which caspase-1 or GSDMD depletion reversed the effect. Clinically, the HDAC1 expression was negatively associated with caspase-1 and GSDMD in clinical NSCLC tissues, while caspase-1 and GSDMD expression was positively correlated in the samples. Therefore, we concluded that HDAC1-catalyzed histone crotonylation of caspase-1 modulates PEM sensitivity of NSCLC by targeting GSDMD.
Collapse
|
34
|
Liao M, Chu W, Sun X, Zheng W, Gao S, Li D, Pei D. Reduction of H3K27cr Modification During DNA Damage in Colon Cancer. Front Oncol 2022; 12:924061. [PMID: 35936700 PMCID: PMC9353715 DOI: 10.3389/fonc.2022.924061] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/08/2022] [Indexed: 11/24/2022] Open
Abstract
DNA damage plays an essential role in the initiation and development of colon cancer. Histone crotonylation is a newly discovered post-translational modification that is thought to promote gene expression. Whether histone crotonylation plays a role in DNA damage of cancer remains unknown, as does the putative underlying molecular mechanism. This study aimed to investigate the relationship between histone crotonylation and DNA damage of colon cancer using multiple bioinformatics analysis and western blotting. We discovered that genes with promoter occupied by histone crotonylation were associated with the activity of DNA damage in colon cancer patients. Additionally, we uncovered that the level of crotonylation on Lys27 of histone H3 (H3K27cr) decreased during camptothecin and etoposide treatment. Interestingly, sirtuin 6 was found to regulate the cellular level of H3K27cr. Taking these data together, our study provided a new perspective about histone crotonylation and DNA damage in colon cancer.
Collapse
Affiliation(s)
- Meijian Liao
- Department of Pathology, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Meijian Liao, ; Dongsheng Pei,
| | - Weiwei Chu
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Xiaolin Sun
- Department of Pathology, Xuzhou Medical University, Xuzhou, China
| | - Wendan Zheng
- Department of Pathology, Xuzhou Medical University, Xuzhou, China
| | - Shoucui Gao
- Department of Pathology, Xuzhou Medical University, Xuzhou, China
| | - Danhua Li
- Department of Pathology, Xuzhou Medical University, Xuzhou, China
| | - Dongsheng Pei
- Department of Pathology, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Meijian Liao, ; Dongsheng Pei,
| |
Collapse
|
35
|
Chen XF, Ji S. Sorafenib Attenuates Fibrotic Hepatic Injury Through Mediating Lysine Crotonylation. Drug Des Devel Ther 2022; 16:2133-2144. [PMID: 35812135 PMCID: PMC9262635 DOI: 10.2147/dddt.s368306] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/28/2022] [Indexed: 01/13/2023] Open
Abstract
Background Liver fibrosis is an independent contributor of chronic liver diseases, and regressing liver fibrosis is considered a potential therapeutic target for chronic liver diseases. We aimed to explore the effects and mechanism of sorafenib in liver fibrosis. Methods Male Sprague Dawley (SD) rats were subjected to subcutaneous injection of carbon tetrachloride (CCl4) for 8 weeks to induce liver fibrosis and then treated with sorafenib. The degree of liver fibrosis was analyzed by hematoxylin–eosin (H&E) staining, Masson staining, and Picrosirius red (PSR) staining. Serum biochemical indexes were detected by fully automatic biochemical analyzer or enzyme-linked immunosorbent assay (ELISA). Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to detect the expression of pro-fibrotic genes. Immunohistochemical staining and Western blotting were carried out to evaluate the levels of lysine crotonylation. Results Liver index was reduced with oral sorafenib in CCl4-induced rats. Serum liver function (alanine aminotransferase (ALT), aspartate aminotransferase (AST), and total bilirubin (TBIL)) and fibrosis indicators (type III procollagen (PC-III), hyaluronic acid (HA), and laminin (LN)) were attenuated with sorafenib treatment. Sorafenib improved the hepatic structure and fibrotic progression. The expression of fibrosis-related genes was remarkely reduced with sorafenib treatment. Meanwhile, sorafenib inhibited α-SMA and collagen I cumulation induced by CCl4 injection. Besides, protein lysine crotonylation especially the crotonylated H2BK12 (H2BK12cr) and crotonylated H3K18 (H3K18cr) were reversed by sorafenib, which were decreased in response to CCl4 treatment. Spearman correlation analysis shown lysine crotonylation expression was negatively correlated with serum fibrotic indicators. Conversely, crotonylation-regulated enzymes, which negatively regulate protein crotonylation, were increased in response to CCl4 treatment, while sorafenib reduced their expression. Conclusion Sorafenib exerts significant anti-fibrotic effects through mediating crotonylation-regulated enzymes and protein crotonylation in fibrotic rats.
Collapse
Affiliation(s)
- Xiao-Feng Chen
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
- Correspondence: Xiao-Feng Chen, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, No. 1166, Liutai Avenue, Wenjiang District, Chengdu, People’s Republic of China, Tel +86-28-61800219, Email
| | - Shaoxiu Ji
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| |
Collapse
|
36
|
Braghini MR, Lo Re O, Romito I, Fernandez-Barrena MG, Barbaro B, Pomella S, Rota R, Vinciguerra M, Avila MA, Alisi A. Epigenetic remodelling in human hepatocellular carcinoma. J Exp Clin Cancer Res 2022; 41:107. [PMID: 35331312 PMCID: PMC8943959 DOI: 10.1186/s13046-022-02297-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/19/2022] [Indexed: 04/13/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most frequent primary liver cancer, being the sixth most commonly diagnosed cancer and the fourth leading cause of cancer-related death. As other heterogeneous solid tumours, HCC results from a unique synergistic combination of genetic alterations mixed with epigenetic modifications.In HCC the patterns and frequencies of somatic variations change depending on the nearby chromatin. On the other hand, epigenetic alterations often induce genomic instability prone to mutations. Epigenetics refers to heritable states of gene expression without alteration to the DNA sequence itself and, unlike genetic changes, the epigenetic modifications are reversible and affect gene expression more extensively than genetic changes. Thus, studies of epigenetic regulation and the involved molecular machinery are greatly contributing to the understanding of the mechanisms that underline HCC onset and heterogeneity. Moreover, this knowledge may help to identify biomarkers for HCC diagnosis and prognosis, as well as future new targets for more efficacious therapeutic approaches.In this comprehensive review we will discuss the state-of-the-art knowledge about the epigenetic landscape in hepatocarcinogenesis, including evidence on the diagnostic and prognostic role of non-coding RNAs, modifications occurring at the chromatin level, and their role in the era of precision medicine.Apart from other better-known risk factors that predispose to the development of HCC, characterization of the epigenetic remodelling that occurs during hepatocarcinogenesis could open the way to the identification of personalized biomarkers. It may also enable a more accurate diagnosis and stratification of patients, and the discovery of new targets for more efficient therapeutic approaches.
Collapse
Affiliation(s)
- Maria Rita Braghini
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy
| | - Oriana Lo Re
- Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna, Varna, Bulgaria
| | - Ilaria Romito
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy
| | - Maite G Fernandez-Barrena
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Barbara Barbaro
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy
| | - Silvia Pomella
- Department of Paediatric Haematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rossella Rota
- Department of Paediatric Haematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Manlio Vinciguerra
- Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna, Varna, Bulgaria
| | - Matias A Avila
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Anna Alisi
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy.
| |
Collapse
|
37
|
Xu X, Hu X, Dong J, Xue Y, Liu T, Jin Q. Proteome-Wide Identification and Functional Analysis of Lysine Crotonylation in Trichophyton rubrum Conidial and Mycelial Stages. Front Genet 2022; 13:832668. [PMID: 35356433 PMCID: PMC8960058 DOI: 10.3389/fgene.2022.832668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
Lysine crotonylation is a newly discovered post-translational modification (PTM) with key roles in various important regulatory pathways. Despite its functional significance, there is limited knowledge about crotonylation in fungi. Trichophyton rubrum is the most common fungal pathogen in human infection and is considered a model organism of dermatophytes and human pathogenic filamentous fungi. In this study, we obtained a proteome-wide crotonylation profile of T. rubrum, leading to the identification of 14,019 crotonylated sites on 3144 proteins. The crotonylated proteins were significantly involved in translation and in various metabolic and biosynthetic processes. Some proteins related to fungal pathogenicity were also found to be targets of crotonylation. In addition, extensive crotonylation was found on histones, suggesting a role in epigenetic regulation. Furthermore, about half of the crotonylated proteins were specific to either the conidial or the mycelial stage, and functional enrichment analysis showed some differences between the two stages. The results suggest that the difference in crotonylation between the two stages is not due to differences in protein abundance. Crosstalk of crotonylation with acetylation, propionylation, and succinylation suggests distinct regulatory roles. This study is the first crotonylation analysis in dermatophytes and human pathogenic filamentous fungi. These results represent a solid foundation for further research on PTM regulatory mechanisms in fungi and should facilitate improved antifungal strategies against these medical important species.
Collapse
Affiliation(s)
| | | | | | | | - Tao Liu
- *Correspondence: Tao Liu, ; Qi Jin,
| | - Qi Jin
- *Correspondence: Tao Liu, ; Qi Jin,
| |
Collapse
|
38
|
Morrison AJ. Cancer cell metabolism connects epigenetic modifications to transcriptional regulation. FEBS J 2022; 289:1302-1314. [PMID: 34036737 PMCID: PMC8613311 DOI: 10.1111/febs.16032] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 04/12/2021] [Accepted: 05/21/2021] [Indexed: 12/12/2022]
Abstract
Adaptation of cellular function with the nutrient environment is essential for survival. Failure to adapt can lead to cell death and/or disease. Indeed, energy metabolism alterations are a major contributing factor for many pathologies, including cancer, cardiovascular disease, and diabetes. In particular, a primary characteristic of cancer cells is altered metabolism that promotes survival and proliferation even in the presence of limited nutrients. Interestingly, recent studies demonstrate that metabolic pathways produce intermediary metabolites that directly influence epigenetic modifications in the genome. Emerging evidence demonstrates that metabolic processes in cancer cells fuel malignant growth, in part, through epigenetic regulation of gene expression programs important for proliferation and adaptive survival. In this review, recent progress toward understanding the relationship of cancer cell metabolism, epigenetic modification, and transcriptional regulation will be discussed. Specifically, the need for adaptive cell metabolism and its modulation in cancer cells will be introduced. Current knowledge on the emerging field of metabolite production and epigenetic modification will also be reviewed. Alterations of DNA (de)methylation, histone modifications, such as (de)methylation and (de)acylation, as well as chromatin remodeling, will be discussed in the context of cancer cell metabolism. Finally, how these epigenetic alterations contribute to cancer cell phenotypes will be summarized. Collectively, these studies reveal that both metabolic and epigenetic pathways in cancer cells are closely linked, representing multiple opportunities to therapeutically target the unique features of malignant growth.
Collapse
|
39
|
Tang SY, Zhou PJ, Meng Y, Zeng FR, Deng GT. Gastric cancer: An epigenetic view. World J Gastrointest Oncol 2022; 14:90-109. [PMID: 35116105 PMCID: PMC8790429 DOI: 10.4251/wjgo.v14.i1.90] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/17/2021] [Accepted: 12/23/2021] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer (GC) poses a serious threat worldwide with unfavorable prognosis mainly due to late diagnosis and limited therapies. Therefore, precise molecular classification and search for potential targets are required for diagnosis and treatment, as GC is complicated and heterogeneous in nature. Accumulating evidence indicates that epigenetics plays a vital role in gastric carcinogenesis and progression, including histone modifications, DNA methylation and non-coding RNAs. Epigenetic biomarkers and drugs are currently under intensive evaluations to ensure efficient clinical utility in GC. In this review, key epigenetic alterations and related functions and mechanisms are summarized in GC. We focus on integration of existing epigenetic findings in GC for the bench-to-bedside translation of some pivotal epigenetic alterations into clinical practice and also describe the vacant field waiting for investigation.
Collapse
Affiliation(s)
- Si-Yuan Tang
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Pei-Jun Zhou
- Cancer Research Institute, School of Basic Medicine Science, Central South University, School of Basic Medicine Science, Central South University 410008, Hunan Province, China
| | - Yu Meng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Fu-Rong Zeng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Guang-Tong Deng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| |
Collapse
|
40
|
Li W, Li F, Zhang X, Lin HK, Xu C. Insights into the post-translational modification and its emerging role in shaping the tumor microenvironment. Signal Transduct Target Ther 2021; 6:422. [PMID: 34924561 PMCID: PMC8685280 DOI: 10.1038/s41392-021-00825-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 12/11/2022] Open
Abstract
More and more in-depth studies have revealed that the occurrence and development of tumors depend on gene mutation and tumor heterogeneity. The most important manifestation of tumor heterogeneity is the dynamic change of tumor microenvironment (TME) heterogeneity. This depends not only on the tumor cells themselves in the microenvironment where the infiltrating immune cells and matrix together forming an antitumor and/or pro-tumor network. TME has resulted in novel therapeutic interventions as a place beyond tumor beds. The malignant cancer cells, tumor infiltrate immune cells, angiogenic vascular cells, lymphatic endothelial cells, cancer-associated fibroblastic cells, and the released factors including intracellular metabolites, hormonal signals and inflammatory mediators all contribute actively to cancer progression. Protein post-translational modification (PTM) is often regarded as a degradative mechanism in protein destruction or turnover to maintain physiological homeostasis. Advances in quantitative transcriptomics, proteomics, and nuclease-based gene editing are now paving the global ways for exploring PTMs. In this review, we focus on recent developments in the PTM area and speculate on their importance as a critical functional readout for the regulation of TME. A wealth of information has been emerging to prove useful in the search for conventional therapies and the development of global therapeutic strategies.
Collapse
Affiliation(s)
- Wen Li
- Integrative Cancer Center & Cancer Clinical Research Center, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, 610042, Chengdu, P. R. China
| | - Feifei Li
- Integrative Cancer Center & Cancer Clinical Research Center, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, 610042, Chengdu, P. R. China
- Guangxi Collaborative Innovation Center for Biomedicine (Guangxi-ASEAN Collaborative Innovation Center for Major Disease Prevention and Treatment), Guangxi Medical University, 530021, Nanning, Guangxi, China
| | - Xia Zhang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Hui-Kuan Lin
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Wake Forest University, Winston Salem, NC, 27101, USA
| | - Chuan Xu
- Integrative Cancer Center & Cancer Clinical Research Center, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, 610042, Chengdu, P. R. China.
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Wake Forest University, Winston Salem, NC, 27101, USA.
| |
Collapse
|
41
|
Tng SS, Le NQK, Yeh HY, Chua MCH. Improved Prediction Model of Protein Lysine Crotonylation Sites Using Bidirectional Recurrent Neural Networks. J Proteome Res 2021; 21:265-273. [PMID: 34812044 DOI: 10.1021/acs.jproteome.1c00848] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Histone lysine crotonylation (Kcr) is a post-translational modification of histone proteins that is involved in the regulation of gene transcription, acute and chronic kidney injury, spermatogenesis, depression, cancer, and so forth. The identification of Kcr sites in proteins is important for characterizing and regulating primary biological mechanisms. The use of computational approaches such as machine learning and deep learning algorithms have emerged in recent years as the traditional wet-lab experiments are time-consuming and costly. We propose as part of this study a deep learning model based on a recurrent neural network (RNN) termed as Sohoko-Kcr for the prediction of Kcr sites. Through the embedded encoding of the peptide sequences, we investigate the efficiency of RNN-based models such as long short-term memory (LSTM), bidirectional LSTM (BiLSTM), and bidirectional gated recurrent unit (BiGRU) networks using cross-validation and independent tests. We also established the comparison between Sohoko-Kcr and other published tools to verify the efficiency of our model based on 3-fold, 5-fold, and 10-fold cross-validations using independent set tests. The results then show that the BiGRU model has consistently displayed outstanding performance and computational efficiency. Based on the proposed model, a webserver called Sohoko-Kcr was deployed for free use and is accessible at https://sohoko-research-9uu23.ondigitalocean.app.
Collapse
Affiliation(s)
- Sian Soo Tng
- Institute of Systems Science, National University of Singapore, 29 Heng Mui Keng Terrace, Singapore 119620, Singapore
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei 106, Taiwan.,Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei 106, Taiwan.,Translational Imaging Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Hui-Yuan Yeh
- Medical Humanities Research Cluster, School of Humanities, Nanyang Technological University, 48 Nanyang Avenue, Singapore 639818, Singapore
| | - Matthew Chin Heng Chua
- Institute of Systems Science, National University of Singapore, 29 Heng Mui Keng Terrace, Singapore 119620, Singapore
| |
Collapse
|
42
|
Upregulation of α enolase (ENO1) crotonylation in colorectal cancer and its promoting effect on cancer cell metastasis. Biochem Biophys Res Commun 2021; 578:77-83. [PMID: 34547627 DOI: 10.1016/j.bbrc.2021.09.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 09/14/2021] [Indexed: 12/17/2022]
Abstract
Lysine crotonylation (Kcr) is a newly identified protein translational modification and is involved in major biological processes including glycolysis, but its role in colorectal cancer (CRC) is unknown. Here, we found that the Kcr of α enolase (ENO1) was significantly elevated in human CRC tissues compared with the paratumoral tissues. CREB-binding protein (CBP) functioned as a crotonyltranferase of ENO1, and SIRT2 was involved in the decrotonylation of ENO1. Using quantitative mass spectrometry for crotonylomics analysis, we further found that K420 was the main Kcr site of ENO1 and ENO1 K420 Kcr promoted the growth, migration, and invasion of CRC cells in vitro by enhancing the activity of ENO1 and regulating the expression of tumor-associated genes. Our study reveals an important mechanism by which ENO1 regulates CRC through crotonylation.
Collapse
|
43
|
Zheng C, Sun L. Qualitative lysine crotonylome analysis in the ovarian tissue of Harmonia axyridis (Pallas). PLoS One 2021; 16:e0258371. [PMID: 34662345 PMCID: PMC8523065 DOI: 10.1371/journal.pone.0258371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/24/2021] [Indexed: 11/19/2022] Open
Abstract
Lysine crotonylation (Kcr) is a newly discovered posttranslational modification (PTM), which has been studied at the proteomics level in a few species, with the study of Kcr in female fertility and in insect species is still lacking. Harmonia axyridis (Pallas) is a well-known beneficial insect used as a natural biological control agent against aphids in agriculture. Here, global Kcr identification in ovarian tissue of H. axyridis at diapause stage was performed to reveal potential roles for Kcr in H. axyridis ovarian cellular processes, female fertility and diapause regulation. In total, 3084 Kcr sites in 920 proteins were identified. Bioinformatic analyses revealed the distribution of these proteins in multiple subcellular localization categories and their involvement in diverse biological processes and metabolism pathways. Carbohydrate and energy metabolism related cellular processes including citric acid cycle, glycolysis and oxidative phosphorylation appeared be affected by Kcr modification. In addition, regulation of translation and protein biosynthesis may reflect Kcr involvement in diapause in H. axyridis, with Kcr affecting ribosome activities and amino acid metabolism. Moreover, Kcr modulation H. axyridis ovary development regulation may share some common mechanism with Kcr participation in some disease progression. These processes and pathways were uncovered under diapause stage, but possibly not enriched/specific for diapause stage due to limitations of qualitative proteomics experimental design. Our results informs on the potential for Kcr modifications to regulate female fertility and insect physiology.
Collapse
Affiliation(s)
- Changying Zheng
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao City, Shandong Province, P. R. China
| | - Lijuan Sun
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao City, Shandong Province, P. R. China
| |
Collapse
|
44
|
Liu H, Wan J, Feng Q, Li J, Liu J, Cui S. Long non-coding RNA SOS1-IT1 promotes endometrial cancer progression by regulating hypoxia signaling pathway. J Cell Commun Signal 2021; 16:253-270. [PMID: 34637090 DOI: 10.1007/s12079-021-00651-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/03/2021] [Indexed: 12/18/2022] Open
Abstract
Endometrial cancer (EC) is one of the most common types of gynecological cancer. Hypoxia is an important clinical feature and regulates various tumor processes. However, the prognostic value of hypoxia-related lncRNA in EC remains to be further elucidated. Here, we aimed to characterize the molecular features of EC by the development of a classification system based on the expression profile of hypoxia-related lncRNA. Based on univariate Cox regression analysis, we identified 17 hypoxia-related lncRNAs significantly associated with overall survival. Next, the least absolute shrinkage and selection operator Cox regression model was utilized to construct a multigene signature in the TCGA EC cohort. The risk score was confirmed as an independent predictor for overall survival in multivariate Cox regression analysis and receiver operating characteristic (ROC) curve analysis. Besides, the survival time of EC patients in different risk group was significantly correlated to clinicopathologic factors, such as age, stage and grade. Furthermore, hypoxia-related lncRNA associated with the high-risk group were involved in various aspects of the malignant progression of EC via Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway, and Gene Set Enrichment Analysis. Moreover, the risk score was closely correlated to immunotherapy response, microsatellite instability and tumor mutation burden. Finally, we select one hypoxia-related lncRNA SOS1-IT1 to validate its role in hypoxia and EC progression. Interestingly, we found SOS1-IT1 was overexpressed in tumor tissues, and closely correlated with clinicopathological parameters of EC. The expression level of SOS1-IT1 was significantly increased under hypoxia condition. Additionally, the important hypoxia regulatory factor HIF-1α can directly bind SOS1-IT1 promoter region, and affect its expression level. In summary, this study established a new EC classification based on the hypoxia-related lncRNA signature, thereby provide a novel sight to understand the potential mechanism of human EC development.
Collapse
Affiliation(s)
- Hongyang Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Junhu Wan
- Department of Clinical Laboratory, Key Clinical Laboratory of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Quanling Feng
- Department of Clinical Laboratory, Key Clinical Laboratory of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jingyu Li
- Department of Neurology, Yuzhou People's Hospital, Yuzhou, 461670, Henan, China
| | - Jun Liu
- Department of General Surgery, Shangqiu Medical College, Zhecheng People's Hospital, Shangqiu, 476000, Henan, China
| | - Shihong Cui
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
| |
Collapse
|
45
|
Subba P, Prasad TSK. Protein Crotonylation Expert Review: A New Lens to Take Post-Translational Modifications and Cell Biology to New Heights. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:617-625. [PMID: 34582706 DOI: 10.1089/omi.2021.0132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Genome regulation, temporal and spatial variations in cell function, continues to puzzle and interest life scientists who aim to unravel the molecular basis of human health and disease, not to mention plant biology and ecosystem diversity. Despite important advances in epigenomics and protein post-translational modifications over the past decade, there is a need for new conceptual lenses to understand biological mechanisms that can help unravel the fundamental regulatory questions in genomes and the cell. To these ends, lys crotonylation (Kcr) is a reversible protein modification catalyzed by protein crotonyl transferases and decrotonylases. First identified on histones, Kcr regulates cellular processes at the chromatin level. Research thus far has revealed that Kcr marks promoter sites of active genes and potential enhancers. Eventually, Kcr on a number of nonhistone proteins was reported. The abundance of Kcr on ribosomal and myofilament proteins indicates its functional roles in protein synthesis and muscle contraction. Kcr has also been associated with pluripotency, spermiogenesis, and DNA repair. In plants, large-scale mass spectrometry-based experiments validated the roles of Kcr in photosynthesis. In this expert review, we present the latest thinking and findings on lys crotonylation with an eye to regulation of cell biology. We discuss the enrichment techniques, putative biological functions, and challenges associated with studying this protein modification with vast biological implications. Finally, we reflect on the future outlook about the broader relevance of Kcr in animals, microbes, and plant species.
Collapse
Affiliation(s)
- Pratigya Subba
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | | |
Collapse
|
46
|
Wang S, Mu G, Qiu B, Wang M, Yu Z, Wang W, Wang J, Yang Y. The Function and related Diseases of Protein Crotonylation. Int J Biol Sci 2021; 17:3441-3455. [PMID: 34512158 PMCID: PMC8416722 DOI: 10.7150/ijbs.58872] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 07/14/2021] [Indexed: 02/07/2023] Open
Abstract
Crotonylation is a kind of newly discovered acylation modification. Thousands of crotonylation sites have been identified in histone and non-histone proteins over the past decade. As a modification closely related to acetylation, crotonylation was reported to share many universal enzymes with acetylation. Crotonylated proteins have important roles in the regulation of various biological processes, such as gene expression, process of spermatogenesis, cell cycle, and also in the pathogenesis of different diseases, which range from depression to cancer. In this review, we summarize the research processes of crotonylation and discuss the advances of regulation mechanism of both histone and non-histone proteins crotonylation in difference physiological processes. Also, we focus on the alteration of the crotonylation under certain pathological conditions and its role in the pathogenesis of each disease.
Collapse
Affiliation(s)
- Shuo Wang
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Guanqun Mu
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Bingquan Qiu
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Meng Wang
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zunbo Yu
- China Institute of Veterinary Drugs Control, Beijing 100181, China
| | - Weibin Wang
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jiadong Wang
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yang Yang
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| |
Collapse
|
47
|
Jiang G, Li C, Lu M, Lu K, Li H. Protein lysine crotonylation: past, present, perspective. Cell Death Dis 2021; 12:703. [PMID: 34262024 PMCID: PMC8280118 DOI: 10.1038/s41419-021-03987-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 02/08/2023]
Abstract
Lysine crotonylation has been discovered in histone and non-histone proteins and found to be involved in diverse diseases and biological processes, such as neuropsychiatric disease, carcinogenesis, spermatogenesis, tissue injury, and inflammation. The unique carbon–carbon π-bond structure indicates that lysine crotonylation may use distinct regulatory mechanisms from the widely studied other types of lysine acylation. In this review, we discussed the regulation of lysine crotonylation by enzymatic and non-enzymatic mechanisms, the recognition of substrate proteins, the physiological functions of lysine crotonylation and its cross-talk with other types of modification. The tools and methods for prediction and detection of lysine crotonylation were also described.
Collapse
Affiliation(s)
- Gaoyue Jiang
- West China Second University Hospital, State Key Laboratory of Biotherapy, and Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, 610041, Chengdu, China
| | - Chunxia Li
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and The Research Units of West China, Chinese Academy of Medical Sciences, Chengdu, China
| | - Meng Lu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and The Research Units of West China, Chinese Academy of Medical Sciences, Chengdu, China
| | - Kefeng Lu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and The Research Units of West China, Chinese Academy of Medical Sciences, Chengdu, China.
| | - Huihui Li
- West China Second University Hospital, State Key Laboratory of Biotherapy, and Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, 610041, Chengdu, China.
| |
Collapse
|
48
|
Hou JY, Zhou L, Li JL, Wang DP, Cao JM. Emerging roles of non-histone protein crotonylation in biomedicine. Cell Biosci 2021; 11:101. [PMID: 34059135 PMCID: PMC8166067 DOI: 10.1186/s13578-021-00616-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 05/22/2021] [Indexed: 12/25/2022] Open
Abstract
Crotonylation of proteins is a newly found type of post-translational modifications (PTMs) which occurs leadingly on the lysine residue, namely, lysine crotonylation (Kcr). Kcr is conserved and is regulated by a series of enzymes and co-enzymes including lysine crotonyltransferase (writer), lysine decrotonylase (eraser), certain YEATS proteins (reader), and crotonyl-coenzyme A (donor). Histone Kcr has been substantially studied since 2011, but the Kcr of non-histone proteins is just an emerging field since its finding in 2017. Recent advances in the identification and quantification of non-histone protein Kcr by mass spectrometry have increased our understanding of Kcr. In this review, we summarized the main proteomic characteristics of non-histone protein Kcr and discussed its biological functions, including gene transcription, DNA damage response, enzymes regulation, metabolic pathways, cell cycle, and localization of heterochromatin in cells. We further proposed the performance of non-histone protein Kcr in diseases and the prospect of Kcr manipulators as potential therapeutic candidates in the diseases.
Collapse
Affiliation(s)
- Jia-Yi Hou
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China.,Department of Clinical Laboratory, Shanxi Provincial Academy of Traditional Chinese Medicine, Taiyuan, China
| | - Lan Zhou
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Jia-Lei Li
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - De-Ping Wang
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Ji-Min Cao
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China.
| |
Collapse
|
49
|
Nalbantoglu S, Karadag A. Metabolomics bridging proteomics along metabolites/oncometabolites and protein modifications: Paving the way toward integrative multiomics. J Pharm Biomed Anal 2021; 199:114031. [PMID: 33857836 DOI: 10.1016/j.jpba.2021.114031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 03/02/2021] [Accepted: 03/16/2021] [Indexed: 02/08/2023]
Abstract
Systems biology adopted functional and integrative multiomics approaches enable to discover the whole set of interacting regulatory components such as genes, transcripts, proteins, metabolites, and metabolite dependent protein modifications. This interactome build up the midpoint of protein-protein/PTM, protein-DNA/RNA, and protein-metabolite network in a cell. As the key drivers in cellular metabolism, metabolites are precursors and regulators of protein post-translational modifications [PTMs] that affect protein diversity and functionality. The precisely orchestrated core pattern of metabolic networks refer to paradigm 'metabolites regulate PTMs, PTMs regulate enzymes, and enzymes modulate metabolites' through a multitude of feedback and feed-forward pathway loops. The concept represents a flawless PTM-metabolite-enzyme(protein) regulomics underlined in reprogramming cancer metabolism. Immense interconnectivity of those biomolecules in their spectacular network of intertwined metabolic pathways makes integrated proteomics and metabolomics an excellent opportunity, and the central component of integrative multiomics framework. It will therefore be of significant interest to integrate global proteome and PTM-based proteomics with metabolomics to achieve disease related altered levels of those molecules. Thereby, present update aims to highlight role and analysis of interacting metabolites/oncometabolites, and metabolite-regulated PTMs loop which may function as translational monitoring biomarkers along the reprogramming continuum of oncometabolism.
Collapse
Affiliation(s)
- Sinem Nalbantoglu
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey.
| | - Abdullah Karadag
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey
| |
Collapse
|
50
|
Function and Mechanism of Novel Histone Posttranslational Modifications in Health and Disease. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6635225. [PMID: 33763479 PMCID: PMC7952163 DOI: 10.1155/2021/6635225] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/15/2021] [Accepted: 02/23/2021] [Indexed: 02/06/2023]
Abstract
Histone posttranslational modifications (HPTMs) are crucial epigenetic mechanisms regulating various biological events. Different types of HPTMs characterize and shape functional chromatin states alone or in combination, and dedicated effector proteins selectively recognize these modifications for gene expression. The dysregulation of HPTM recognition events takes part in human diseases. With the application of mass spectrometry- (MS-) based proteomics, novel histone lysine acylation has been successively discovered, e.g., propionylation, butyrylation, 2-hydroxyisobutyrylation, β-hydroxybutyrylation, malonylation, succinylation, crotonylation, glutarylation, and lactylation. These nine types of modifications expand the repertoire of HPTMs and regulate chromatin remodeling, gene expression, cell cycle, and cellular metabolism. Recent researches show that HPTMs have a close connection with the pathogenesis of cancer, metabolic diseases, neuropsychiatric disorders, infertility, kidney diseases, and acquired immunodeficiency syndrome (AIDS). This review focuses on the chemical structure, sites, functions of these novel HPTMs, and underlying mechanism in gene expression, providing a glimpse into their complex regulation in health and disease.
Collapse
|