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Sanjuan-Badillo A, P. Martínez-Castilla L, García-Sandoval R, Ballester P, Ferrándiz C, Sanchez MDLP, García-Ponce B, Garay-Arroyo A, R. Álvarez-Buylla E. HDACs MADS-domain protein interaction: a case study of HDA15 and XAL1 in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2024; 19:2353536. [PMID: 38771929 PMCID: PMC11110687 DOI: 10.1080/15592324.2024.2353536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/01/2024] [Indexed: 05/23/2024]
Abstract
Cellular behavior, cell differentiation and ontogenetic development in eukaryotes result from complex interactions between epigenetic and classic molecular genetic mechanisms, with many of these interactions still to be elucidated. Histone deacetylase enzymes (HDACs) promote the interaction of histones with DNA by compacting the nucleosome, thus causing transcriptional repression. MADS-domain transcription factors are highly conserved in eukaryotes and participate in controlling diverse developmental processes in animals and plants, as well as regulating stress responses in plants. In this work, we focused on finding out putative interactions of Arabidopsis thaliana HDACs and MADS-domain proteins using an evolutionary perspective combined with bioinformatics analyses and testing the more promising predicted interactions through classic molecular biology tools. Through bioinformatic analyses, we found similarities between HDACs proteins from different organisms, which allowed us to predict a putative protein-protein interaction between the Arabidopsis thaliana deacetylase HDA15 and the MADS-domain protein XAANTAL1 (XAL1). The results of two-hybrid and Bimolecular Fluorescence Complementation analysis demonstrated in vitro and in vivo HDA15-XAL1 interaction in the nucleus. Likely, this interaction might regulate developmental processes in plants as is the case for this type of interaction in animals.
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Affiliation(s)
- Andrea Sanjuan-Badillo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Programa de Doctorado en Ciencias Biomédicas, de la Universidad Nacional Autónoma de México, Ciudad de México, México
| | - León P. Martínez-Castilla
- Investigadoras e Investigadores por México, Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes, Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | | | - Patricia Ballester
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, Valencia, España
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, Valencia, España
| | - Maria de la Paz Sanchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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Krushkal J, Zhao Y, Roney K, Zhu W, Brooks A, Wilsker D, Parchment RE, McShane LM, Doroshow JH. Association of changes in expression of HDAC and SIRT genes after drug treatment with cancer cell line sensitivity to kinase inhibitors. Epigenetics 2024; 19:2309824. [PMID: 38369747 PMCID: PMC10878021 DOI: 10.1080/15592294.2024.2309824] [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: 07/24/2023] [Accepted: 01/14/2024] [Indexed: 02/20/2024] Open
Abstract
Histone deacetylases (HDACs) and sirtuins (SIRTs) are important epigenetic regulators of cancer pathways. There is a limited understanding of how transcriptional regulation of their genes is affected by chemotherapeutic agents, and how such transcriptional changes affect tumour sensitivity to drug treatment. We investigated the concerted transcriptional response of HDAC and SIRT genes to 15 approved antitumor agents in the NCI-60 cancer cell line panel. Antitumor agents with diverse mechanisms of action induced upregulation or downregulation of multiple HDAC and SIRT genes. HDAC5 was upregulated by dasatinib and erlotinib in the majority of the cell lines. Tumour cell line sensitivity to kinase inhibitors was associated with upregulation of HDAC5, HDAC1, and several SIRT genes. We confirmed changes in HDAC and SIRT expression in independent datasets. We also experimentally validated the upregulation of HDAC5 mRNA and protein expression by dasatinib in the highly sensitive IGROV1 cell line. HDAC5 was not upregulated in the UACC-257 cell line resistant to dasatinib. The effects of cancer drug treatment on expression of HDAC and SIRT genes may influence chemosensitivity and may need to be considered during chemotherapy.
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Affiliation(s)
- Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Kyle Roney
- Department of Biostatistics and Bioinformatics, George Washington University, Washington, DC, USA
| | - Weimin Zhu
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Alan Brooks
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Deborah Wilsker
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ralph E. Parchment
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lisa M. McShane
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - James H. Doroshow
- Division of Cancer Treatment and Diagnosis and Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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Liu W, Luo G. NEDD9 is transcriptionally regulated by HDAC4 and promotes breast cancer metastasis and macrophage M2 polarization via the FAK/NF-κB signaling pathway. Neoplasia 2024; 57:101059. [PMID: 39326322 PMCID: PMC11470473 DOI: 10.1016/j.neo.2024.101059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 09/11/2024] [Accepted: 09/12/2024] [Indexed: 09/28/2024]
Abstract
BACKGROUND Breast cancer is a malignancy with a generally poor prognosis. With the advancement of molecular research, we have gained deeper insights into the cellular processes that drive breast cancer development. However, the precise mechanisms remain elusive. RESULTS Based on the CPTAC database, we found that NEDD9 expression is up-regulated in breast cancer tissues and is associated with poor prognosis in breast cancer patients. Functional experiments showed that NEDD9 promotes tumor growth and metastasis both in vitro and in vivo. Overexpression of NEDD9 disrupts mammary epithelial acinus formation and triggers epithelial-mesenchymal transition in breast cancer cells, effects that are reversed upon NEDD9 gene silencing. Mechanistically, NEDD9 upregulates its expression by inhibiting HDAC4 activity, leading to enhanced H3K9 acetylation of the NEDD9 gene promoter and activation of the FAK/NF-κB signaling pathway. Furthermore, NEDD9 overexpression promotes IL-6 secretion, which further drives breast cancer progression. Notably, NEDD9 activation fosters the pro-tumoral M2 macrophage polarization in the tumor microenvironment. NEDD9 stimulates IL-6 secretion, polarizes monocytes towards an M2-like phenotype, and enhances BC cell invasiveness. CONCLUSIONS These findings suggest that NEDD9 upregulation plays a pivotal role in breast cancer metastasis and macrophage M2 polarization via the FAK/NF-κB signaling axis. Targeting NEDD9 may offer a promising therapeutic approach for breast cancer treatment.
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Affiliation(s)
- Wenhong Liu
- Department of Radiology, The First Affiliated Hospital of University of South China, Hengyang City, 421001, Hunan Province, China
| | - Guanghua Luo
- Department of Radiology, The First Affiliated Hospital of University of South China, Hengyang City, 421001, Hunan Province, China.
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4
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Li S, Cai Q, Liu Q, Gong Y, Zhao D, Wan J, Wang D, Shao Y. Effective enhancement of the ability of Monascus pilosus to produce lipid-lowering compound Monacolin K via perturbation of metabolic flux and histone acetylation modification. Food Res Int 2024; 195:114961. [PMID: 39277234 DOI: 10.1016/j.foodres.2024.114961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 08/17/2024] [Accepted: 08/20/2024] [Indexed: 09/17/2024]
Abstract
Monacolin K (MK), also known as lovastatin, is a polyketide compound with the ability to reduce plasma cholesterol levels and many other bio-activities. Red yeast rice (also named Hongqu) rich in MK derived from Monascus fermentation has attracted widespread attention due to its excellent performance in reducing blood lipids. However, industrial Monascus fermentation suffers from the limitations such as low yield of MK, long fermentation period, and susceptibility to contamination. In this study, we firstly blocked the competitive pathway of MK biosynthesis to create polyketide synthase gene pigA (the key gene responsible for the biosynthesis of Monascus azaphilone pigments) deficient strain A1. Then, based on the strategies to increase precursor supply for MK biosynthesis, acetyl-CoA carboxylase gene acc overexpression strains C1 and C2 were constructed with WT and A1 as the parent, respectively. Finally, histone deacetylase gene hos2 overexpression strain H1 was constructed by perturbation of histone acetylation modification. HPLC detection revealed all these four strains significantly increased their abilities to produce MK. After 14 days of solid-state fermentation, the MK yields of strains A1, C1, C2, and H1 reached 2.03 g/100 g, 1.81 g/100 g, 2.45 g/100 g and 2.52 g/100 g, which increased by 28.5 %, 14.7 %, 43.9 % and 36.1 % compared to WT, respectively. RT-qPCR results showed that overexpression of hos2 significantly increased the expression level of almost all genes responsible for MK biosynthesis after 5-day growth. Overall, the abilities of these strains to produce MK has been greatly improved, and MK production period has been shortened to 14 days from 20 days, providing new approaches for efficient production of Hongqu rich in MK.
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Affiliation(s)
- Shengfa Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qinhua Cai
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qianrui Liu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yunxia Gong
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Deqing Zhao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jun Wan
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Danjuan Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanchun Shao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan 430070, China.
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5
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Baba AM, Shah AA, Bayil I, Nayak S, Shyanti RK, Nissa N, Muzaffar M, Hajam MA, Akhtar R, Malla BA, Akhtar S, Singh RP, Dar NA. Polydatin inhibits histone deacetylase 1 and shows an anti-angiogenic action in head and neck squamous cell carcinoma. Med Oncol 2024; 41:278. [PMID: 39400755 DOI: 10.1007/s12032-024-02490-7] [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: 07/28/2024] [Accepted: 08/27/2024] [Indexed: 10/15/2024]
Abstract
Polydatin, a natural derivative of resveratrol, has shown many anticancer properties. However, the underlying mechanisms of its anticancer properties including its effect on the epigenetic landscape are not well understood. Here, we explored the effect of polydatin on histone deacetylase 1 (HDAC1) activity. We used in silico approaches to assess the possible binding of polydatin to the active site pockets of HDAC1 and in vitro approaches to test the potential effects of the interaction on its enzymatic activity. As compared to SAHA, an approved drug, the polydatin showed stronger and stable binding to the HDAC1. The binding energy, conformational changes, formation of extra hydrogen bonding, and other interactions within and outside the active site all favour largely stable and strong polydatin binding to the enzyme. Further, the ADME and toxicity prediction values are encouraging for the evaluation of polydatin as a drug. The laboratory leg of the study substantiated that the polydatin binding was strong and stable enough to inhibit HDAC1 activity in UMS-CC-22B cells as demonstrated by an increase in H3K9 acetylation. In addition, polydatin treated cells showed attenuated proliferation. The in vitro tube formation and migration by HUVEC and UM-SCC-22B cells were inhibited by polydatin. The decreased tube formation due to HDAC1 inhibition is possibly due to up-regulation of the anti-angiogenic gene - TSP1 in UM-SCC-22B cells. As compared to SAHA, more promising results were shown both in its computational calculations and on the cell physiology features. Stronger and stable binding, more anti-proliferative and anti-angiogenic potential were observed with respect to polydatin. Further, the cell death was more pronounced with SAHA treatment. Therefore, polydatin might be a better anticancer drug and can have a potential to replace SAHA in combinational therapeutic regimen.
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Affiliation(s)
| | - Altaf Ahmad Shah
- Department of Bioengineering, Integral University, Lucknow, Uttar Pradesh, 226026, India
| | - Imren Bayil
- Department of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, Turkey
| | - Satyabrata Nayak
- School of Life Science, Jawaharlal Nehru University, New Delhi, India
| | - Ritis Kumar Shyanti
- School of Life Science, Jawaharlal Nehru University, New Delhi, India
- Department of Biological Sciences, Alabama State University, Montgomery, USA
| | - Najma Nissa
- Department of Biochemistry, University of Kashmir, Srinagar, India
| | - Mansha Muzaffar
- Department of Biochemistry, University of Kashmir, Srinagar, India
| | | | - Rezwan Akhtar
- Department of Biochemistry, University of Kashmir, Srinagar, India
| | | | - Salman Akhtar
- Department of Bioengineering, Integral University, Lucknow, Uttar Pradesh, 226026, India
- Novel Global Community Educational Foundation, Hebersham, NSW, 2770, Australia
| | - Rana P Singh
- School of Life Science, Jawaharlal Nehru University, New Delhi, India.
| | - Nazir Ahmad Dar
- Department of Biochemistry, University of Kashmir, Srinagar, India.
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6
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Chou PY, Lai MJ, Tsai KK, Cheng LH, Wu YW, Chen MC, Pan SL, Ho HO, Nepali K, Liou JP. Syntheses of LSD1/HDAC Inhibitors with Demonstrated Efficacy against Colorectal Cancer: In Vitro and In Vivo Studies Including Patient-Derived Organoids. J Med Chem 2024; 67:17207-17225. [PMID: 39320444 PMCID: PMC11472331 DOI: 10.1021/acs.jmedchem.4c01098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 08/07/2024] [Accepted: 09/05/2024] [Indexed: 09/26/2024]
Abstract
Precedential evidence ascertaining the overexpression of LSD1 and HDACs in colorectal cancer spurred us to design a series of dual LSD1-HDAC inhibitors. Capitalizing on the modular nature of the three-component HDAC inhibitory model, tranylcypromine as a surface recognition motif was appended to zinc-binding motifs via diverse linkers. A compendium of hydroxamic acids was generated and evaluated for in vitro cytotoxicity against HCT-116 cells (human colorectal cancer cell lines). The most potent cell growth inhibitor 2 (GI50 = 0.495 μMm HCT-116 cells) shows promising anticancer effects by reducing colony formation and inducing cell cycle arrest in HCT-116 cells. It exhibits preferential inhibition of HDAC6, along with potent inhibition of LSD1 compared to standard inhibitors. Moreover, Compound 2 upregulates acetyl-tubulin, acetyl-histone H3, and H3K4me2, indicative of LSD1 and HDAC inhibition. In vivo, it demonstrates significant antitumor activity against colorectal cancer, better than irinotecan, and effectively inhibits growth in patient-derived CRC organoids.
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Affiliation(s)
- Po-Yu Chou
- School
of Pharmacy, College of Pharmacy, Taipei
Medical University, Taipei 110, Taiwan
| | - Mei-Jung Lai
- TMU
Research Center for Drug Discovery, Taipei
Medical University, Taipei 110, Taiwan
| | - Kelvin K. Tsai
- Laboratory
of Advanced Molecular Therapeutics, Graduate Institute of Clinical
Medicine, College of Medicine, Taipei Medical
University, Taipei 110, Taiwan
- Organoids
Technology Core, Taipei Medical University, Taipei 110, Taiwan
| | - Li-Hsin Cheng
- Organoids
Technology Core, Taipei Medical University, Taipei 110, Taiwan
| | - Yi-Wen Wu
- Graduate
Institute of Cancer Biology and Drug Discovery, College of Medical
Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Mei-Chuan Chen
- School
of Pharmacy, College of Pharmacy, Taipei
Medical University, Taipei 110, Taiwan
- TMU
Research Center for Drug Discovery, Taipei
Medical University, Taipei 110, Taiwan
- Ph.D.
Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan
- Clinical
Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan
- Traditional
Herbal Medicine Research Center of Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Shiow-Lin Pan
- TMU
Research Center for Drug Discovery, Taipei
Medical University, Taipei 110, Taiwan
- Graduate
Institute of Cancer Biology and Drug Discovery, College of Medical
Science and Technology, Taipei Medical University, Taipei 110, Taiwan
- TMU Research
Center of Cancer Translational Medicine, Taipei 110, Taiwan
- Ph.D.
Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan
- Ph.D.
Program for Cancer Molecular Biology and Drug Discovery, College of
Medical Science and Technology, Taipei Medical
University, Taipei 110, Taiwan
| | - Hsiu-O Ho
- School
of Pharmacy, College of Pharmacy, Taipei
Medical University, Taipei 110, Taiwan
| | - Kunal Nepali
- School
of Pharmacy, College of Pharmacy, Taipei
Medical University, Taipei 110, Taiwan
- TMU
Research Center for Drug Discovery, Taipei
Medical University, Taipei 110, Taiwan
- Ph.D.
Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan
| | - Jing-Ping Liou
- School
of Pharmacy, College of Pharmacy, Taipei
Medical University, Taipei 110, Taiwan
- TMU
Research Center for Drug Discovery, Taipei
Medical University, Taipei 110, Taiwan
- TMU Research
Center of Cancer Translational Medicine, Taipei 110, Taiwan
- Ph.D.
Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan
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7
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Ma Q, Li J, Yu S, Zhou J, Liu Y, Wang X, Ye D, Wu Y, Gong T, Zhang Q, Wang L, Zou J, Li Y. YkuR functions as a protein deacetylase in Streptococcus mutans. Proc Natl Acad Sci U S A 2024; 121:e2407820121. [PMID: 39356671 DOI: 10.1073/pnas.2407820121] [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: 04/18/2024] [Accepted: 08/13/2024] [Indexed: 10/04/2024] Open
Abstract
Protein acetylation is a common and reversible posttranslational modification tightly governed by protein acetyltransferases and deacetylases crucial for various biological processes in both eukaryotes and prokaryotes. Although recent studies have characterized many acetyltransferases in diverse bacterial species, only a few protein deacetylases have been identified in prokaryotes, perhaps in part due to their limited sequence homology. In this study, we identified YkuR, encoded by smu_318, as a unique protein deacetylase in Streptococcus mutans. Through protein acetylome analysis, we demonstrated that the deletion of ykuR significantly upregulated protein acetylation levels, affecting key enzymes in translation processes and metabolic pathways, including starch and sucrose metabolism, glycolysis/gluconeogenesis, and biofilm formation. In particular, YkuR modulated extracellular polysaccharide synthesis and biofilm formation through the direct deacetylation of glucosyltransferases (Gtfs) in the presence of NAD+. Intriguingly, YkuR can be acetylated in a nonenzymatic manner, which then negatively regulated its deacetylase activity, suggesting the presence of a self-regulatory mechanism. Moreover, in vivo studies further demonstrated that the deletion of ykuR attenuated the cariogenicity of S. mutans in the rat caries model, substantiating its involvement in the pathogenesis of dental caries. Therefore, our study revealed a unique regulatory mechanism mediated by YkuR through protein deacetylation that regulates the physiology and pathogenicity of S. mutans.
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Affiliation(s)
- Qizhao Ma
- Laboratory of Oral Microbiology, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Jing Li
- Laboratory of Oral Microbiology, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Shuxing Yu
- Laboratory of Oral Microbiology, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Jing Zhou
- Laboratory of Oral Microbiology, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yaqi Liu
- Laboratory of Oral Microbiology, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Xinyue Wang
- Laboratory of Oral Microbiology, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Dingwei Ye
- Laboratory of Oral Microbiology, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yumeng Wu
- Laboratory of Oral Microbiology, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Tao Gong
- Laboratory of Oral Microbiology, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Qiong Zhang
- Laboratory of Oral Microbiology, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Lingyun Wang
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510
| | - Jing Zou
- Laboratory of Oral Microbiology, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yuqing Li
- Laboratory of Oral Microbiology, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- Laboratory of Archaeological Repository, Center for Archaeological Science, Sichuan University, Chengdu 610041, China
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8
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Scheuerer S, Motlova L, Schäker-Hübner L, Sellmer A, Feller F, Ertl FJ, Koch P, Hansen FK, Barinka C, Mahboobi S. Biological and structural investigation of tetrahydro-β-carboline-based selective HDAC6 inhibitors with improved stability. Eur J Med Chem 2024; 276:116676. [PMID: 39067437 DOI: 10.1016/j.ejmech.2024.116676] [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: 04/03/2024] [Revised: 06/30/2024] [Accepted: 07/10/2024] [Indexed: 07/30/2024]
Abstract
Our previously reported HDAC6 inhibitor (HDAC6i) Marbostat-100 (4) has provided many arguments for further clinical evaluation. By the substitution of the acidic hydrogen of 4 for different carbon residues, we were able to generate an all-carbon stereocenter, which significantly improves the hydrolytic stability of the inhibitor. Further asymmetric synthesis has shown that the (S)-configured inhibitors preferentially bind to HDAC6. This led to the highly selective and potent methyl-substituted derivative S-29b, which elicited a long-lasting tubulin hyperacetylation in MV4-11 cells. Finally, a crystal structure of the HDAC6/S-29b complex provided mechanistic explanation for the high potency and stereoselectivity of synthesized compound series.
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Affiliation(s)
- Simon Scheuerer
- Institute of Pharmacy, Department of Pharmaceutical/Medicinal Chemistry I, University of Regensburg, 93040, Regensburg, Germany
| | - Lucia Motlova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Linda Schäker-Hübner
- Pharmaceutical Institute, Department of Pharmaceutical and Cell Biological Chemistry, University of Bonn, 53121, Bonn, Germany
| | - Andreas Sellmer
- Institute of Pharmacy, Department of Pharmaceutical/Medicinal Chemistry I, University of Regensburg, 93040, Regensburg, Germany
| | - Felix Feller
- Pharmaceutical Institute, Department of Pharmaceutical and Cell Biological Chemistry, University of Bonn, 53121, Bonn, Germany
| | - Fabian J Ertl
- Institute of Pharmacy, Department of Pharmaceutical/Medicinal Chemistry II, University of Regensburg, 93040, Regensburg, Germany
| | - Pierre Koch
- Institute of Pharmacy, Department of Pharmaceutical/Medicinal Chemistry II, University of Regensburg, 93040, Regensburg, Germany
| | - Finn K Hansen
- Pharmaceutical Institute, Department of Pharmaceutical and Cell Biological Chemistry, University of Bonn, 53121, Bonn, Germany
| | - Cyril Barinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Siavosh Mahboobi
- Institute of Pharmacy, Department of Pharmaceutical/Medicinal Chemistry I, University of Regensburg, 93040, Regensburg, Germany.
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9
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Yasuda T, Nakajima N, Ogi T, Yanaka T, Tanaka I, Gotoh T, Kagawa W, Sugasawa K, Tajima K. Heavy water inhibits DNA double-strand break repairs and disturbs cellular transcription, presumably via quantum-level mechanisms of kinetic isotope effects on hydrolytic enzyme reactions. PLoS One 2024; 19:e0309689. [PMID: 39361575 PMCID: PMC11449287 DOI: 10.1371/journal.pone.0309689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 08/16/2024] [Indexed: 10/05/2024] Open
Abstract
Heavy water, containing the heavy hydrogen isotope, is toxic to cells, although the underlying mechanism remains incompletely understood. In addition, certain enzymatic proton transfer reactions exhibit kinetic isotope effects attributed to hydrogen isotopes and their temperature dependencies, indicative of quantum tunneling phenomena. However, the correlation between the biological effects of heavy water and the kinetic isotope effects mediated by hydrogen isotopes remains elusive. In this study, we elucidated the kinetic isotope effects arising from hydrogen isotopes of water and their temperature dependencies in vitro, focusing on deacetylation, DNA cleavage, and protein cleavage, which are crucial enzymatic reactions mediated by hydrolysis. Intriguingly, the intracellular isotope effects of heavy water, related to the in vitro kinetic isotope effects, significantly impeded multiple DNA double-strand break repair mechanisms crucial for cell survival. Additionally, heavy water exposure enhanced histone acetylation and associated transcriptional activation in cells, consistent with the in vitro kinetic isotope effects observed in histone deacetylation reactions. Moreover, as observed for the in vitro kinetic isotope effects, the cytotoxic effect on cell proliferation induced by heavy water exhibited temperature-dependency. These findings reveal the substantial impact of heavy water-induced isotope effects on cellular functions governed by hydrolytic enzymatic reactions, potentially mediated by quantum-level mechanisms underlying kinetic isotope effects.
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Affiliation(s)
- Takeshi Yasuda
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Nakako Nakajima
- QST Hospital, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Tomoko Yanaka
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Izumi Tanaka
- Institute for Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Takaya Gotoh
- Department of Health Science, Daito Bunka University, Saitama, Japan
| | - Wataru Kagawa
- Department of Interdisciplinary Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, Tokyo, Japan
| | - Kaoru Sugasawa
- Biosignal Research Center, and Graduate School of Science, Kobe University, Kobe, Japan
| | - Katsushi Tajima
- Department of Hematology, Yamagata Prefectural Central Hospital, Yamagata, Japan
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10
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Gunn JC, Christensen BM, Bueno EM, Cohen ZP, Kissonergis AS, Chen YH. Agricultural insect pests as models for studying stress-induced evolutionary processes. INSECT MOLECULAR BIOLOGY 2024; 33:432-443. [PMID: 38655882 DOI: 10.1111/imb.12915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/14/2024] [Indexed: 04/26/2024]
Abstract
Agricultural insect pests (AIPs) are widely successful in adapting to natural and anthropogenic stressors, repeatedly overcoming population bottlenecks and acquiring resistance to intensive management practices. Although they have been largely overlooked in evolutionary studies, AIPs are ideal systems for understanding rapid adaptation under novel environmental conditions. Researchers have identified several genomic mechanisms that likely contribute to adaptive stress responses, including positive selection on de novo mutations, polygenic selection on standing allelic variation and phenotypic plasticity (e.g., hormesis). However, new theory suggests that stress itself may induce epigenetic modifications, which may confer heritable physiological changes (i.e., stress-resistant phenotypes). In this perspective, we discuss how environmental stress from agricultural management generates the epigenetic and genetic modifications that are associated with rapid adaptation in AIPs. We summarise existing evidence for stress-induced evolutionary processes in the context of insecticide resistance. Ultimately, we propose that studying AIPs offers new opportunities and resources for advancing our knowledge of stress-induced evolution.
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Affiliation(s)
- Joe C Gunn
- Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, USA
| | - Blair M Christensen
- Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, USA
| | - Erika M Bueno
- Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, USA
| | - Zachary P Cohen
- Insect Control and Cotton Disease Research, USDA ARS, College Station, Texas, USA
| | | | - Yolanda H Chen
- Department of Plant and Soil Science, University of Vermont, Burlington, Vermont, USA
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11
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Kodila ZN, Shultz SR, Yamakawa GR, Mychasiuk R. Critical Windows: Exploring the Association Between Perinatal Trauma, Epigenetics, and Chronic Pain. Neuroscientist 2024; 30:574-596. [PMID: 37212380 PMCID: PMC11439237 DOI: 10.1177/10738584231176233] [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] [Indexed: 05/23/2023]
Abstract
Chronic pain is highly prevalent and burdensome, affecting millions of people worldwide. Although it emerges at any point in life, it often manifests in adolescence. Given that adolescence is a unique developmental period, additional strains associated with persistent and often idiopathic pain lead to significant long-term consequences. While there is no singular cause for the chronification of pain, epigenetic modifications that lead to neural reorganization may underpin central sensitization and subsequent manifestation of pain hypersensitivity. Epigenetic processes are particularly active during the prenatal and early postnatal years. We demonstrate how exposure to various traumas, such as intimate partner violence while in utero or adverse childhood experiences, can significantly influence epigenetic regulation within the brain and in turn modify pain-related processes. We provide compelling evidence that the burden of chronic pain is likely initiated early in life, often being transmitted from mother to offspring. We also highlight two promising prophylactic strategies, oxytocin administration and probiotic use, that have the potential to attenuate the epigenetic consequences of early adversity. Overall, we advance understanding of the causal relationship between trauma and adolescent chronic pain by highlighting epigenetic mechanisms that underlie this transmission of risk, ultimately informing how to prevent this rising epidemic.
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Affiliation(s)
- Zoe N. Kodila
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Sandy R. Shultz
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Health Sciences, Vancouver Island University, Nanaimo, Canada
| | - Glenn R. Yamakawa
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Richelle Mychasiuk
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
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12
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Wu J, Wang X, Yao Y, Du N, Duan L, Gong P. Design, synthesis and antitumor activities of phthalazinone derivatives as PARP-1 inhibitors and PARP-1/HDAC-1 inhibitors. Bioorg Chem 2024; 151:107556. [PMID: 39068717 DOI: 10.1016/j.bioorg.2024.107556] [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: 04/11/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 07/30/2024]
Abstract
In recent years, poly(ADP-ribose)polymerase-1 (PARP-1) and histone deacetylase (HDAC) have emerged as significant targets in tumor therapy, garnering widespread attention. In this study, we designed and synthesized two novel phthalazinone PARP-1 inhibitors and dual PARP-1/HDAC-1 inhibitors, named DLC-1-46 containing dithiocarboxylate fragments and DLC-47-63 containing hydroxamic acid fragments, and evaluated their inhibitory activities on enzymes and cells. Among the PARP-1 inhibitors, most compounds exhibited high inhibitory activity against the PARP-1 enzyme, with DLC-1-6 being particularly notable, showing IC50 values <0.2 nM. Notably, DLC-1 demonstrated significant anti-proliferative activity, with IC50 values for inhibiting the proliferation of MDA-MB-436, MDA-MB-231, and MCF-7 cells reaching 0.08, 26.39, and 1.01 μM, respectively. Further investigation revealed that DLC-1 arrested MDA-MB-231 cells in the G1 phase and induced apoptosis in a dose-dependent manner. Among the designed dual PARP-1/HDAC-1 inhibitors, several compounds exhibited potent dual-target inhibitory activity, with DLC-49 displaying IC50 values of 0.53 nM and 17 nM for PARP-1 and HDAC-1, respectively. DLC-50 demonstrated the most potent anti-proliferative activity, with IC50 values for inhibiting the proliferation of MDA-MB-436, MDA-MB-231, and MCF-7 cells at 0.30, 2.70, and 2.41 μM, respectively. Cell cycle arrest and apoptosis assays indicated that DLC-50 arrested the cell cycle in the G2 phase and induced apoptosis in HCT-116 cells. Our findings present a novel avenue for further exploration of PARP-1 inhibitors and dual PARP-1/HDAC-1 inhibitors.
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Affiliation(s)
- Jie Wu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Xiaoqian Wang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Yaning Yao
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Nan Du
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China
| | - Liancheng Duan
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China.
| | - Ping Gong
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, China.
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13
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Zhang SY, Zhang LY, Wen R, Yang N, Zhang TN. Histone deacetylases and their inhibitors in inflammatory diseases. Biomed Pharmacother 2024; 179:117295. [PMID: 39146765 DOI: 10.1016/j.biopha.2024.117295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/03/2024] [Accepted: 08/09/2024] [Indexed: 08/17/2024] Open
Abstract
Despite considerable research efforts, inflammatory diseases remain a heavy burden on human health, causing significant economic losses annually. Histone deacetylases (HDACs) play a significant role in regulating inflammation (via histone and non-histone protein deacetylation) and chromatin structure and gene expression regulation. Herein, we present a detailed description of the different HDACs and their functions and analyze the role of HDACs in inflammatory diseases, including pro-inflammatory cytokine production reduction, immune cell function modulation, and anti-inflammatory cell activity enhancement. Although HDAC inhibitors have shown broad inflammatory disease treatment potentials, their clinical applicability remains limited because of their non-specific effects, adverse effects, and drug resistance. With further research and insight, these inhibitors are expected to become important tools for the treatment of a wide range of inflammatory diseases. This review aims to explore the mechanisms and application prospects of HDACs and their inhibitors in multiple inflammatory diseases.
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Affiliation(s)
- Sen-Yu Zhang
- Department of Pediatrics, PICU, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Li-Ying Zhang
- Department of Pediatrics, PICU, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Ri Wen
- Department of Pediatrics, PICU, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Ni Yang
- Department of Pediatrics, PICU, Shengjing Hospital of China Medical University, Shenyang 110004, China.
| | - Tie-Ning Zhang
- Department of Pediatrics, PICU, Shengjing Hospital of China Medical University, Shenyang 110004, China.
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14
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Bhat MF, Srdanović S, Sundberg LR, Einarsdóttir HK, Marjomäki V, Dekker FJ. Impact of HDAC inhibitors on macrophage polarization to enhance innate immunity against infections. Drug Discov Today 2024; 29:104193. [PMID: 39332483 DOI: 10.1016/j.drudis.2024.104193] [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: 05/31/2024] [Revised: 08/26/2024] [Accepted: 09/23/2024] [Indexed: 09/29/2024]
Abstract
Innate immunity plays an important role in host defense against pathogenic infections. It involves macrophage polarization into either the pro-inflammatory M1 or the anti-inflammatory M2 phenotype, influencing immune stimulation or suppression, respectively. Epigenetic changes during immune reactions contribute to long-term innate immunity imprinting on macrophage polarization. It is becoming increasingly evident that epigenetic modulators, such as histone deacetylase (HDAC) inhibitors (HDACi), enable the enhancement of innate immunity by tailoring macrophage polarization in response to immune stressors. In this review, we summarize current literature on the impact of HDACi and other epigenetic modulators on the functioning of macrophages during diseases that have a strong immune component, such as infections. Depending on the disease context and the chosen therapeutic intervention, HDAC1, HDAC2, HDAC3, HDAC6, or HDAC8 are particularly important in influencing macrophage polarization towards either M1 or M2 phenotypes. We anticipate that therapeutic strategies based on HDAC epigenetic mechanisms will provide a unique approach to boost immunity against disease challenges, including resistant infections.
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Affiliation(s)
- Mohammad Faizan Bhat
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, the Netherlands
| | - Sonja Srdanović
- Akthelia Pharmaceuticals, Grandagardi 16, 101 Reykjavik, Iceland
| | - Lotta-Riina Sundberg
- Department of Biological and Environmental Sciences and Nanoscience Center, 40014 University of Jyväskylä, Jyväskylä, Finland
| | | | - Varpu Marjomäki
- Department of Biological and Environmental Sciences and Nanoscience Center, 40014 University of Jyväskylä, Jyväskylä, Finland
| | - Frank J Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, the Netherlands.
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15
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Zhong X, Wu X, Zhou Y, Wu R, Yang J, Yin H, Meng H, Xie W, Liu G, Wang C, Bai P, Zhang W. PET imaging assist investigation of HDAC6 expression change in MDD and evaluating antidepressant efficacy of a newly developed HDAC6 inhibitor. Eur J Med Chem 2024; 280:116908. [PMID: 39366254 DOI: 10.1016/j.ejmech.2024.116908] [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: 08/15/2024] [Revised: 09/09/2024] [Accepted: 09/13/2024] [Indexed: 10/06/2024]
Abstract
The histone deacetylase 6 (HDAC6) is closely related to the pathogenesis of depression in epigenetic regulation. However, it remains unclear how HDAC6 expression changes in depression pathophysiology and whether it is a target for antidepressant treatment. Herein, we investigate the expression change of HDAC6 in major depressive disorder (MDD) and evaluate the efficacy of a novel HDAC6 inhibitor, PB200, using positron emission tomography (PET) imaging. PET imaging studies with an HDAC6 PET probe [18F]Bavarostat allied with in vitro experiments demonstrated significantly increased HDAC6 expression in the brains of MDD mice. To investigate if pharmacological inhibition of HDAC6 can exert antidepressant effects, a series of naphthyridine-based HDAC6 inhibitors were designed and synthesized, among which PB200 demonstrated high selectivity and inhibitory activity against HDAC6, favorable metabolic stability, and excellent brain uptake. Moreover, PB200 exhibited significant antidepressant effects by restoring abnormal HDAC6 expression level and alleviating neuroinflammation. These results imply that targeting HDAC6 shows promise as a therapeutic strategy for depression, and PB200 is a potential therapeutic option for treating MDD.
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Affiliation(s)
- Xiao Zhong
- Department of Nuclear Medicine, Laboratory of Clinical Nuclear Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiaoai Wu
- Department of Nuclear Medicine, Laboratory of Clinical Nuclear Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yanting Zhou
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Institute of Respiratory Health, Targeted Tracer Research and Development Laboratory, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Rui Wu
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Institute of Respiratory Health, Targeted Tracer Research and Development Laboratory, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jingyi Yang
- Mental Health Center and Psychiatric Laboratory, The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Honghai Yin
- Department of Nuclear Medicine, Laboratory of Clinical Nuclear Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Hui Meng
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Institute of Respiratory Health, Targeted Tracer Research and Development Laboratory, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Weiyao Xie
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Institute of Respiratory Health, Targeted Tracer Research and Development Laboratory, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Gang Liu
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Institute of Respiratory Health, Targeted Tracer Research and Development Laboratory, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Changning Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, United States
| | - Ping Bai
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Institute of Respiratory Health, Targeted Tracer Research and Development Laboratory, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Wei Zhang
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Mental Health Center and Psychiatric Laboratory, The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
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16
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Lin C, Sniezek CM, McGann CD, Karki R, Giglio RM, Garcia BA, McFaline-Figeroa JL, Schweppe DK. Defining the heterogeneous molecular landscape of lung cancer cell responses to epigenetic inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.592075. [PMID: 38853901 PMCID: PMC11160595 DOI: 10.1101/2024.05.23.592075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Epigenetic inhibitors exhibit powerful antiproliferative and anticancer activities. However, cellular responses to small-molecule epigenetic inhibition are heterogenous and dependent on factors such as the genetic background, metabolic state, and on-/off-target engagement of individual small-molecule compounds. The molecular study of the extent of this heterogeneity often measures changes in a single cell line or using a small number of compounds. To more comprehensively profile the effects of small-molecule perturbations and their influence on these heterogeneous cellular responses, we present a molecular resource based on the quantification of chromatin, proteome, and transcriptome remodeling due to histone deacetylase inhibitors (HDACi) in non-isogenic cell lines. Through quantitative molecular profiling of 10,621 proteins, these data reveal coordinated molecular remodeling of HDACi treated cancer cells. HDACi-regulated proteins differ greatly across cell lines with consistent (JUN, MAP2K3, CDKN1A) and divergent (CCND3, ASF1B, BRD7) cell-state effectors. Together these data provide valuable insight into cell-type driven and heterogeneous responses that must be taken into consideration when monitoring molecular perturbations in culture models.
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Affiliation(s)
- Chuwei Lin
- Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | | | | | - Rashmi Karki
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ross M. Giglio
- Biomedical Engineer, Columbia University, New York, NY 10027, USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Devin K. Schweppe
- Genome Sciences, University of Washington, Seattle, WA 98105, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA
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17
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Chen LY, Singha Roy SJ, Jadhav AM, Wang WW, Chen PH, Bishop T, Erb MA, Parker CG. Functional Investigations of p53 Acetylation Enabled by Heterobifunctional Molecules. ACS Chem Biol 2024; 19:1918-1929. [PMID: 39250704 PMCID: PMC11421428 DOI: 10.1021/acschembio.4c00438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 08/21/2024] [Accepted: 09/03/2024] [Indexed: 09/11/2024]
Abstract
Post-translational modifications (PTMs) dynamically regulate the critical stress response and tumor suppressive functions of p53. Among these, acetylation events mediated by multiple acetyltransferases lead to differential target gene activation and subsequent cell fate. However, our understanding of these events is incomplete due to, in part, the inability to selectively and dynamically control p53 acetylation. We recently developed a heterobifunctional small molecule system, AceTAG, to direct the acetyltransferase p300/CBP for targeted protein acetylation in cells. Here, we expand AceTAG to leverage the acetyltransferase PCAF/GCN5 and apply these tools to investigate the functional consequences of targeted p53 acetylation in human cancer cells. We demonstrate that the recruitment of p300/CBP or PCAF/GCN5 to p53 results in distinct acetylation events and differentiated transcriptional activities. Further, we show that chemically induced acetylation of multiple hotspot p53 mutants results in increased stabilization and enhancement of transcriptional activity. Collectively, these studies demonstrate the utility of AceTAG for functional investigations of protein acetylation.
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Affiliation(s)
- Li-Yun Chen
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Soumya Jyoti Singha Roy
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Appaso M. Jadhav
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Wesley W. Wang
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Pei-Hsin Chen
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Timothy Bishop
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Michael A. Erb
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Christopher G. Parker
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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18
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Berluti F, Baselious F, Hagemann S, Hilscher S, Schmidt M, Hüttelmaier S, Schutkowski M, Sippl W, Ibrahim HS. Development of new pyrazoles as class I HDAC inhibitors: Synthesis, molecular modeling, and biological characterization in leukemia cells. Arch Pharm (Weinheim) 2024:e2400437. [PMID: 39291901 DOI: 10.1002/ardp.202400437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/26/2024] [Accepted: 08/27/2024] [Indexed: 09/19/2024]
Abstract
Class I histone deacetylases (HDACs) are considered promising targets in current cancer research. To obtain subtype-selective and potent HDAC inhibitors, we used the aminobenzamide scaffold as the zinc-binding group and prepared new derivatives with a pyrazole ring as the linking group. The synthesized compounds were analyzed in vitro using an enzymatic assay against HDAC1, -2, and -3. Compounds 12b, 15b, and 15i were found to be potent HDAC1 inhibitors, also in comparison to the reference compounds entinostat and tacedinaline, with IC50 values of 0.93, 0.22, and 0.68 μM, respectively. The best compounds were measured for their cellular effect and target engagement in acute myeloid leukemia (AML) cells. In addition, we studied the interaction of the compounds with HDAC subtypes using docking and molecular dynamic simulations. In summary, we have developed a new chemotype of HDAC1 inhibitors that can be used for further structure-based optimization.
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Affiliation(s)
- Francesco Berluti
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Fady Baselious
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Sven Hagemann
- Department of Molecular Medicine, Faculty of Medicine, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Sebastian Hilscher
- Department of Enzymology, Institute of Biochemistry, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Matthias Schmidt
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Stefan Hüttelmaier
- Department of Molecular Medicine, Faculty of Medicine, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Hany S Ibrahim
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, Egypt
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19
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Zhang Z, Zeng Y, Hou J, Li L. Advances in understanding the roles of plant HAT and HDAC in non-histone protein acetylation and deacetylation. PLANTA 2024; 260:93. [PMID: 39264431 DOI: 10.1007/s00425-024-04518-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Accepted: 08/23/2024] [Indexed: 09/13/2024]
Abstract
MAIN CONCLUSION This review focuses on HATs and HDACs that modify non-histone proteins, summarizes functional mechanisms of non-histone acetylation as well as the roles of HATs and HDACs in rice and Arabidopsis. The growth and development of plants, as well as their responses to biotic and abiotic stresses, are governed by intricate gene and protein regulatory networks, in which epigenetic modifying enzymes play a crucial role. Histone lysine acetylation levels, modulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), are well-studied in the realm of transcriptional regulation. However, the advent of advanced proteomics has unveiled that non-histone proteins also undergo acetylation, with its underlying mechanisms now being clarified. Indeed, non-histone acetylation influences protein functionality through diverse pathways, such as modulating protein stability, adjusting enzymatic activity, steering subcellular localization, influencing interactions with other post-translational modifications, and managing protein-protein and protein-DNA interactions. This review delves into the recent insights into the functional mechanisms of non-histone acetylation in plants. We also provide a summary of the roles of HATs and HDACs in rice and Arabidopsis, and explore their potential involvement in the regulation of non-histone proteins.
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Affiliation(s)
- Zihan Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yan Zeng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jiaqi Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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20
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Tiwari V, Prajapati B, Asare Y, Damkou A, Ji H, Liu L, Naser N, Gouna G, Leszczyńska KB, Mieczkowski J, Dichgans M, Wang Q, Kawaguchi R, Shi Z, Swarup V, Geschwind DH, Prinz M, Gokce O, Simons M. Innate immune training restores pro-reparative myeloid functions to promote remyelination in the aged central nervous system. Immunity 2024; 57:2173-2190.e8. [PMID: 39053462 DOI: 10.1016/j.immuni.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 11/21/2023] [Accepted: 07/01/2024] [Indexed: 07/27/2024]
Abstract
The reduced ability of the central nervous system to regenerate with increasing age limits functional recovery following demyelinating injury. Previous work has shown that myelin debris can overwhelm the metabolic capacity of microglia, thereby impeding tissue regeneration in aging, but the underlying mechanisms are unknown. In a model of demyelination, we found that a substantial number of genes that were not effectively activated in aged myeloid cells displayed epigenetic modifications associated with restricted chromatin accessibility. Ablation of two class I histone deacetylases in microglia was sufficient to restore the capacity of aged mice to remyelinate lesioned tissue. We used Bacillus Calmette-Guerin (BCG), a live-attenuated vaccine, to train the innate immune system and detected epigenetic reprogramming of brain-resident myeloid cells and functional restoration of myelin debris clearance and lesion recovery. Our results provide insight into aging-associated decline in myeloid function and how this decay can be prevented by innate immune reprogramming.
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Affiliation(s)
- Vini Tiwari
- Institute of Neuronal Cell Biology, Technical University Munich, 81377 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany
| | - Bharat Prajapati
- Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Yaw Asare
- Institute for Stroke and Dementia Research, University Hospital of Munich, LMU Munich, 81377 Munich, Germany
| | - Alkmini Damkou
- Institute of Neuronal Cell Biology, Technical University Munich, 81377 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany
| | - Hao Ji
- Institute for Stroke and Dementia Research, University Hospital of Munich, LMU Munich, 81377 Munich, Germany
| | - Lu Liu
- German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Institute for Stroke and Dementia Research, University Hospital of Munich, LMU Munich, 81377 Munich, Germany
| | - Nawraa Naser
- Institute for Stroke and Dementia Research, University Hospital of Munich, LMU Munich, 81377 Munich, Germany
| | - Garyfallia Gouna
- Institute of Neuronal Cell Biology, Technical University Munich, 81377 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany
| | - Katarzyna B Leszczyńska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, 02093 Warsaw, Poland
| | - Jakub Mieczkowski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, 02093 Warsaw, Poland; 3P-Medicine Laboratory, Medical University of Gdańsk, 80211 Gdańsk, Poland
| | - Martin Dichgans
- German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Munich Cluster of Systems Neurology (SyNergy), 81377 Munich, Germany; Institute for Stroke and Dementia Research, University Hospital of Munich, LMU Munich, 81377 Munich, Germany
| | - Qing Wang
- Departments of Neurology and Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Riki Kawaguchi
- Departments of Neurology and Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Psychiatry, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zechuan Shi
- Department of Neurobiology and Behavior, University of California, Irvine, CA, USA
| | - Vivek Swarup
- Department of Neurobiology and Behavior, University of California, Irvine, CA, USA
| | - Daniel H Geschwind
- Departments of Neurology and Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marco Prinz
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, 79085 Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Ozgun Gokce
- Munich Cluster of Systems Neurology (SyNergy), 81377 Munich, Germany; Institute for Stroke and Dementia Research, University Hospital of Munich, LMU Munich, 81377 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany; Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, 53127 Bonn, Germany
| | - Mikael Simons
- Institute of Neuronal Cell Biology, Technical University Munich, 81377 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Munich Cluster of Systems Neurology (SyNergy), 81377 Munich, Germany; Institute for Stroke and Dementia Research, University Hospital of Munich, LMU Munich, 81377 Munich, Germany.
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21
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Ritika, Liao ZY, Chen PY, Rao NV, Mathew J, Sharma R, Grewal AS, Singh G, Mehan S, Liou JP, Pan CH, Nepali K. Rationally designed febuxostat-based hydroxamic acid and its pH-Responsive nanoformulation elicits anti-tumor activity. Eur J Med Chem 2024; 279:116866. [PMID: 39293244 DOI: 10.1016/j.ejmech.2024.116866] [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: 05/21/2024] [Revised: 08/29/2024] [Accepted: 09/08/2024] [Indexed: 09/20/2024]
Abstract
Attempts to furnish antitumor structural templates that can prevent the occurrence of drug-induced hyperuricemia spurred us to generate xanthine oxidase inhibitor-based hydroxamic acids and anilides. Specifically, the design strategy involved the insertion of febuxostat (xanthine oxidase inhibitor) as a surface recognition part of the HDAC inhibitor pharmacophore model. Investigation outcomes revealed that hydroxamic acid 4 elicited remarkable antileukemic effects mediated via HDAC isoform inhibition. Delightfully, the adduct retained xanthine oxidase inhibitory activity, though xanthine oxidase inhibition was not the underlying mechanism of its cell growth inhibitory effects. Also, compound 4 demonstrated significant in-vivo anti-hyperuricemic (PO-induced hyperuricemia model) and antitumor activity in an HL-60 xenograft mice model. Compound 4 was conjugated with poly (ethylene glycol) poly(aspartic acid) block copolymer to furnish pH-responsive nanoparticles (NPs) in pursuit of circumventing its cytotoxicity towards the normal cell lines. SEM analysis revealed that NPs had uniform size distributions, while TEM analysis ascertained the spherical shape of NPs, indicating their ability to undergo self-assembly. HDAC inhibitor 4 was liberated from the matrix due to the polymeric nanoformulation's pH-responsiveness, and the NPs demonstrated selective cancer cell targeting ability.
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Affiliation(s)
- Ritika
- International Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taiwan
| | - Zi-Yi Liao
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, 110031, Taiwan
| | - Pin-Yu Chen
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, 110031, Taiwan
| | - N Vijayakamasewara Rao
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taiwan
| | - Jacob Mathew
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, 106335, Taiwan
| | - Ram Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, 110031, Taiwan
| | - Ajmer Singh Grewal
- Department of Pharmaceutical Sciences, Guru Gobind Singh College of Pharmacy, Near Guru Nanak Khalsa College, Yamuna Nagar, 135001, Haryana, India
| | - Gurpreet Singh
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, India
| | - Sidharth Mehan
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, India; Department of Pharmacology, ISF College of Pharmacy, Moga, Punjab, India
| | - Jing Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, 110031, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taiwan
| | - Chun Hsu Pan
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taiwan.
| | - Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, 110031, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taiwan.
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22
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Wu CS, Sun X, Liu L, Cheng L. A Live-Cell Epigenome Manipulation by Photo-Stimuli-Responsive Histone Methyltransferase Inhibitor. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2404608. [PMID: 39250325 DOI: 10.1002/advs.202404608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/23/2024] [Indexed: 09/11/2024]
Abstract
Post-translational modifications on the histone H3 tail regulate chromatin structure, impact epigenetics, and hence the gene expressions. Current chemical modulation tools, such as unnatural amino acid incorporation, protein splicing, and sortase-based editing, have allowed for the modification of histones with various PTMs in cellular contexts, but are not applicable for editing native chromatin. The use of small organic molecules to manipulate histone-modifying enzymes alters endogenous histone PTMs but lacks precise temporal and spatial control. To date, there has been no achievement in modulating histone methylation in living cells with spatiotemporal resolution. In this study, a new method is presented for temporally manipulating histone dimethylation H3K9me2 using a photo-responsive inhibitor that specifically targets the methyltransferase G9a on demand. The photo-caged molecule is stable under physiological conditions and cellular environments, but rapidly activated upon exposure to light, releasing the bioactive component that can immediately inhibit the catalytic ability of the G9a in vitro. Besides, this masked compound could also efficiently reactivate the inhibition of methyltransferase activity in living cells, subsequently suppress H3K9me2, a mark that regulates various chromatin functions. Therefore, the chemical system will be a valuable tool for manipulating the epigenome for therapeutic purposes and furthering the understanding of epigenetic mechanisms.
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Affiliation(s)
- Chuan-Shuo Wu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
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23
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Josa-Culleré L, Aira Rodríguez C, Llebaria A. Hemithioindigo-based histone deacetylase inhibitors induce a light-dependent anticancer effect. Eur J Med Chem 2024; 279:116846. [PMID: 39270453 DOI: 10.1016/j.ejmech.2024.116846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 08/14/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024]
Abstract
Photoswitchable molecules exhibit light-dependent biological activity which allow us to control the therapeutic effect of drugs with high precision. Such molecules could solve some of the limitations of anticancer drugs by providing a localised effect in the tumour. Histone deacetylase inhibitors (HDACis) constitute a promising drug class for oncology whose application is often limited by a lack of selectivity. Herein, we developed photoswitchable HDACis based on a hemithioindigo scaffold. We established synthetic routes to access them and determined the optimal conditions for isomerisation and their thermal stability. We then optimised their enzyme activity through three rounds of re-design to identify examples that are up to 6-fold more active under illumination than in the dark. We also confirmed that our best derivative reduces the viability of HeLa cells only under illumination. All in all, we disclose a series of derivatives containing a hemithioindigo moiety, which display a light-dependent effect on both HDAC inhibition and cancer cell viability.
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Affiliation(s)
- Laia Josa-Culleré
- MCS, Laboratory of Medicinal Chemistry & Synthesis, Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain.
| | - Carla Aira Rodríguez
- MCS, Laboratory of Medicinal Chemistry & Synthesis, Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Amadeu Llebaria
- MCS, Laboratory of Medicinal Chemistry & Synthesis, Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain.
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24
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Yang L, Wei Q, Chen X, Yang Y, Huang Q, Wang B, Ma X. Identification of HDAC10 as a candidate oncogene in clear cell renal carcinoma that facilitates tumor proliferation and metastasis. Diagn Pathol 2024; 19:120. [PMID: 39237939 PMCID: PMC11378624 DOI: 10.1186/s13000-024-01493-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/06/2024] [Indexed: 09/07/2024] Open
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) remains one of the most lethal urological malignancies even though a great number of improvements in diagnosis and management have achieved over the past few decades. Accumulated evidence revealed that histone deacetylases (HDACs) play vital role in cell proliferation, differentiation and apoptosis. Nevertheless, the biological functions of histone deacetylation modification related genes in ccRCC remains poorly understood. METHOD Bulk transcriptomic data and clinical information of ccRCC patients were obtained from the TCGA database and collected from the Chinese PLA General Hospital. A total of 36 histone deacetylation genes were selected and studied in our research. Univariate cox regression analysis, least absolute shrinkage and selection operator (LASSO) regression, random forest (RF) analysis, and protein-protein interaction (PPI) network analysis were applied to identify key genes affecting the prognosis of ccRCC. The 'oncoPredict' algorithm was utilized for drug-sensitive analysis. Gene Set Enrichment Analysis (GSEA) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was used to explore the potential biological function. The ssGSEA algorithm was used for tumor immune microenvironment analysis. The expression levels of HDAC10 were validated by RT-PCR and immunohistochemistry (IHC). 5-ethynyl-2'-deoxyuridine (EdU assay), CCK-8 assay, cell transwell migration and invasion assay and colony formation assay were performed to detect the proliferation and invasion ability of ccRCC cells. A nomogram incorporating HDAC10 and clinicopathological characteristics was established to predict the prognosis of ccRCC patients. RESULT Two machine learning algorithms and PPI analysis identified four histone deacetylation genes that have a significant association with the prognosis of ccRCC, with HDAC10 being the key gene among them. HDAC10 is highly expressed in ccRCC and its high expression is associated with poor prognosis for ccRCC patients. Pathway enrichment and the experiments of EdU staining, CCK-8 assay, cell transwell migration and invasion assay and colony formation assay demonstrated that HDAC10 mediated the proliferation and metastasis of ccRCC cells and involved in reshaping the tumor microenvironment (TME) of ccRCC. A clinically reliable prognostic predictive model was established by incorporating HDAC10 and other clinicopathological characteristics ( https://nomogramhdac10.shinyapps.io/HDAC10_Nomogram/ ). CONCLUSION Our study found the increased expression of HDAC10 was closely associated with poor prognosis of ccRCC patients. HDAC10 showed a pro-tumorigenic effect on ccRCC and promote the proliferation and metastasis of ccRCC, which may provide new light on targeted therapy for ccRCC.
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Affiliation(s)
- Luojia Yang
- Medical School of Chinese PLA, Beijing, 100853, China
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Qin Wei
- The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, China
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200125, China
| | - Xinran Chen
- Medical School of Chinese PLA, Beijing, 100853, China
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yang Yang
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Qingbo Huang
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Baojun Wang
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
| | - Xin Ma
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
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25
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Dunaway LS, Cook AK, Kellum CE, Edell C, Botta D, Molina PA, Sedaka RS, d’Uscio LV, Katusic ZS, Pollock DM, Inscho EW, Pollock JS. Endothelial histone deacetylase 1 activity impairs kidney microvascular NO signaling in rats fed a high-salt diet. Acta Physiol (Oxf) 2024; 240:e14201. [PMID: 39007513 PMCID: PMC11329346 DOI: 10.1111/apha.14201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/12/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024]
Abstract
AIM We aimed to test the hypothesis that a high-salt diet (HS) impairs NO signaling in kidney microvascular endothelial cells through a histone deacetylase 1 (HDAC1)-dependent mechanism. METHODS Male Sprague Dawley rats were fed normal salt diet (NS; 0.49% NaCl) or HS (4% NaCl) for 2 weeks. NO signaling was assessed by measuring L-NAME induced vasoconstriction of the afferent arteriole using the blood perfused juxtamedullary nephron (JMN) preparation. In this preparation, kidneys were perfused with blood from a donor rat on a matching or different diet to that of the kidney donor. Kidney endothelial cells were isolated with magnetic activated cell sorting and HDAC1 activity was measured. RESULTS We found HS-induced impaired NO signaling in the afferent arteriole. This was restored by inhibition of HDAC1 with MS-275. Consistent with these findings, HDAC1 activity was increased in kidney endothelial cells. We further found the loss of NO to be dependent upon the diet of the blood donor rather than the diet of the kidney donor and the plasma from HS-fed rats to be sufficient to induce impaired NO signaling. This indicates the presence of a humoral factor we termed plasma-derived endothelial dysfunction mediator (PDEM). Pretreatment with the antioxidants, PEG-SOD and PEG-catalase, as well as the NOS cofactor, tetrahydrobiopterin, restored NO signaling. CONCLUSION We conclude that HS activates endothelial HDAC1 through PDEM leading to decreased NO signaling. This study provides novel insights into the molecular mechanisms by which a HS decreases renal microvascular endothelial NO signaling.
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Affiliation(s)
- Luke S. Dunaway
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL USA
| | - Anthony K. Cook
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL USA
| | - Cailin E. Kellum
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL USA
| | - Claudia Edell
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL USA
| | - Davide Botta
- Department of Microbiology, Immunology Institute, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Patrick A. Molina
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL USA
| | - Randee S. Sedaka
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL USA
| | - Livius V. d’Uscio
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - Zvonimir S. Katusic
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - David M. Pollock
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL USA
| | - Edward W. Inscho
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL USA
| | - Jennifer S. Pollock
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL USA
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26
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Kadier K, Niu T, Ding B, Chen B, Qi X, Chen D, Cheng X, Fang Y, Zhou J, Zhao W, Liu Z, Yuan Y, Zhou Z, Dong X, Yang B, He Q, Cao J, Jiang L, Zhu CL. PROTAC-Mediated HDAC7 Protein Degradation Unveils Its Deacetylase-Independent Proinflammatory Function in Macrophages. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309459. [PMID: 39049738 PMCID: PMC11423193 DOI: 10.1002/advs.202309459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 04/25/2024] [Indexed: 07/27/2024]
Abstract
Class IIa histone deacetylases (Class IIa HDACs) play critical roles in regulating essential cellular metabolism and inflammatory pathways. However, dissecting the specific roles of each class IIa HDAC isoform is hindered by the pan-inhibitory effect of current inhibitors and a lack of tools to probe their functions beyond epigenetic regulation. In this study, a novel PROTAC-based compound B4 is developed, which selectively targets and degrades HDAC7, resulting in the effective attenuation of a specific set of proinflammatory cytokines in both lipopolysaccharide (LPS)-stimulated macrophages and a mouse model. By employing B4 as a molecular probe, evidence is found for a previously explored role of HDAC7 that surpasses its deacetylase function, suggesting broader implications in inflammatory processes. Mechanistic investigations reveal the critical involvement of HDAC7 in the Toll-like receptor 4 (TLR4) signaling pathway by directly interacting with the TNF receptor-associated factor 6 and TGFβ-activated kinase 1 (TRAF6-TAK1) complex, thereby initiating the activation of the downstream mitogen-activated protein kinase/nuclear factor-κB (MAPK/NF-κB) signaling cascade and subsequent gene transcription. This study expands the insight into HDAC7's role within intricate inflammatory networks and highlights its therapeutic potential as a novel target for anti-inflammatory treatments.
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Affiliation(s)
- Kailibinuer Kadier
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Tian Niu
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Baoli Ding
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Boya Chen
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Xuxin Qi
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Danni Chen
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Xirui Cheng
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Yizheng Fang
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Jiahao Zhou
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Wenyi Zhao
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
| | - Zeqi Liu
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Yi Yuan
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Zhan Zhou
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
| | - Xiaowu Dong
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Engineering Research Center of Innovative Anticancer Drugs, Ministry of Education, Hangzhou, 310058, P. R. China
- Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Cancer Center, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Bo Yang
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Engineering Research Center of Innovative Anticancer Drugs, Ministry of Education, Hangzhou, 310058, P. R. China
- Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Cancer Center, Zhejiang University, Hangzhou, 310058, P. R. China
- Center for Medical Research and Innovation in Digestive System Tumors, Ministry of Education, Hangzhou, 310058, P. R. China
- School of Medicine, Hangzhou City University, Hangzhou, 310015, P. R. China
| | - Qiaojun He
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Engineering Research Center of Innovative Anticancer Drugs, Ministry of Education, Hangzhou, 310058, P. R. China
- Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Cancer Center, Zhejiang University, Hangzhou, 310058, P. R. China
- Center for Medical Research and Innovation in Digestive System Tumors, Ministry of Education, Hangzhou, 310058, P. R. China
- Center for Drug Safety Evaluation and Research of Zhejiang University, Hangzhou, 310058, P. R. China
| | - Ji Cao
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Engineering Research Center of Innovative Anticancer Drugs, Ministry of Education, Hangzhou, 310058, P. R. China
- Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Cancer Center, Zhejiang University, Hangzhou, 310058, P. R. China
- Center for Medical Research and Innovation in Digestive System Tumors, Ministry of Education, Hangzhou, 310058, P. R. China
| | - Li Jiang
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
| | - Cheng-Liang Zhu
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Engineering Research Center of Innovative Anticancer Drugs, Ministry of Education, Hangzhou, 310058, P. R. China
- Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, 310018, P. R. China
- Cancer Center, Zhejiang University, Hangzhou, 310058, P. R. China
- Center for Drug Safety Evaluation and Research of Zhejiang University, Hangzhou, 310058, P. R. China
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Raouf YS. Targeting histone deacetylases: Emerging applications beyond cancer. Drug Discov Today 2024; 29:104094. [PMID: 38997001 DOI: 10.1016/j.drudis.2024.104094] [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: 05/03/2024] [Revised: 06/25/2024] [Accepted: 07/04/2024] [Indexed: 07/14/2024]
Abstract
Histone deacetylases (HDACs) are a special class of hydrolase enzymes, which through epigenetic control of cellular acetylation, play regulatory roles in various processes including chromatin packing, cytokine signaling, and gene expression. Widespread influence on cell function has implicated dysregulated HDAC activity in human disease. While traditionally an oncology target, in the past decade, there has been a notable rise in inhibition strategies within several therapeutic areas beyond cancer. This review highlights advances in four of these indications, neurodegenerative disease, metabolic disorders, cardiovascular disease, and viral infections, focusing on the role of deacetylases in disease, small molecule drug discovery, and clinical progress.
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Affiliation(s)
- Yasir S Raouf
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, P.O. Box 15551, United Arab Emirates.
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Lill A, Schweipert M, Nehls T, Wurster E, Lermyte F, Meyer-Almes FJ, Schmitz K. Design and synthesis of peptides as stabilizers of histone deacetylase 4. J Pept Sci 2024; 30:e3603. [PMID: 38623824 DOI: 10.1002/psc.3603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/17/2024]
Abstract
Histone deacetylase 4 (HDAC4) contributes to gene repression by complex formation with HDAC3 and the corepressor silencing mediator for retinoid or thyroid hormone receptors (SMRT). We hypothesized that peptides derived from the class IIa specific binding site of SMRT would stabilize a specific conformation of its target protein and modulate its activity. Based on the SMRT-motif 1 (SM1) involved in the interaction of SMRT with HDAC4, we systematically developed cyclic peptides that exhibit Ki values that are 9 to 56 times lower than that of the linear SMRT peptide. The peptide macrocycles stabilize the wildtype of the catalytic domain of HDAC4 (cHDAC4) considerably better than its thermally more stable 'gain-of-function' (GOF) variant, cHDAC4-H976Y. Molecular docking and mutagenesis studies indicated that the cyclic peptides bind in a similar but not identical manner as the linear SMRT peptide to a discontinuous binding site. Ion mobility mass spectrometry showed no major changes in the protein fold upon peptide binding. Consistent with these results, preliminary hydrogen-deuterium exchange mass spectrometry measurements indicated only minor conformational changes. Taken together, the cyclic SMRT peptides most likely stabilize the apo form of cHDAC4.
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Affiliation(s)
- Annika Lill
- Biological Chemistry, Clemens-Schöpf-Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Markus Schweipert
- Physical Biochemistry, Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Darmstadt, Germany
| | - Thomas Nehls
- Conformation-Sensitive Mass Spectrometry Laboratory, Clemens-Schöpf-Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Eva Wurster
- Physical Biochemistry, Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Darmstadt, Germany
| | - Frederik Lermyte
- Conformation-Sensitive Mass Spectrometry Laboratory, Clemens-Schöpf-Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Franz-Josef Meyer-Almes
- Physical Biochemistry, Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Darmstadt, Germany
| | - Katja Schmitz
- Biological Chemistry, Clemens-Schöpf-Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
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29
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Thej C, Kishore R. Epigenetic regulation of sex dimorphism in cardiovascular health. Can J Physiol Pharmacol 2024; 102:498-510. [PMID: 38427976 DOI: 10.1139/cjpp-2023-0406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Cardiovascular diseases (CVDs) remain the leading cause of morbidity and mortality, affecting people of all races, ages, and sexes. Substantial sex dimorphism exists in the prevalence, manifestation, and outcomes of CVDs. Understanding the role of sex hormones as well as sex-hormone-independent epigenetic mechanisms could play a crucial role in developing effective and sex-specific cardiovascular therapeutics. Existing research highlights significant disparities in sex hormones, epigenetic regulators, and gene expression related to cardiac health, emphasizing the need for a nuanced understanding of these variations between men and women. Despite these differences, current treatment approaches for CVDs often lack sex-specific considerations. A pivotal shift toward personalized medicine, informed by comprehensive insights into sex-specific DNA methylation, histone modifications, and non-coding RNA dynamics, holds the potential to revolutionize CVD management. By understanding sex-specific epigenetic complexities, independent of sex hormone influence, future cardiovascular research can be tailored to achieve effective diagnostic and therapeutic interventions for both men and women. This review summarizes the current knowledge and gaps in epigenetic mechanisms and sex dimorphism implicated in CVDs.
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Affiliation(s)
- Charan Thej
- Aging and Cardiovascular Discovery Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Raj Kishore
- Aging and Cardiovascular Discovery Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
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30
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Liu Y, Wai AP, Zolzaya T, Iida Y, Okada S, Iizasa H, Yoshiyama H. Exploring the anti-EBV potential of suberoylanilide hydroxamic acid: Induction of apoptosis in infected cells through suppressing BART gene expression and inducing lytic infection. Virology 2024; 597:110161. [PMID: 38981317 DOI: 10.1016/j.virol.2024.110161] [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: 03/29/2024] [Revised: 06/09/2024] [Accepted: 06/24/2024] [Indexed: 07/11/2024]
Abstract
Epstein-Barr virus (EBV) is linked to lymphoma and epithelioma but lacks drugs specifically targeting EBV-positive tumors. BamHI A Rightward Transcript (BART) miRNAs are expressed in all EBV-positive tumors, suppressing both lytic infection and host cell apoptosis. We identified suberoylanilide hydroxamic acid (SAHA), an inhibitor of histone deacetylase enzymes, as an agent that suppresses BART promoter activity and transcription of BART miRNAs. SAHA treatment demonstrated a more pronounced inhibition of cell proliferation in EBV-positive cells compared to EBV-negative cells, affecting both p53 wild-type and mutant gastric epithelial cells. SAHA treatment enhanced lytic infection in wild-type EBV-infected cells, while also enhancing cell death in BZLF1-deficient EBV-infected cells. It reduced BART gene expression by 85% and increased the expression of proapoptotic factors targeted by BART miRNAs. These findings suggest that SAHA not only induces lytic infection but also leads to cell death by suppressing BART miRNA transcription and promoting the apoptotic program.
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Affiliation(s)
- Yuxin Liu
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Aung Phyo Wai
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Tumurgan Zolzaya
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Yuichi Iida
- Department of Immunology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Shunpei Okada
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Hisashi Iizasa
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Hironori Yoshiyama
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
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van Eyll J, Prior R, Celanire S, Van Den Bosch L, Rombouts F. Therapeutic indications for HDAC6 inhibitors in the peripheral and central nervous disorders. Expert Opin Ther Targets 2024; 28:719-737. [PMID: 39305025 DOI: 10.1080/14728222.2024.2404571] [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: 04/16/2024] [Accepted: 09/06/2024] [Indexed: 09/26/2024]
Abstract
INTRODUCTION Inhibition of the enzymatic function of HDAC6 is currently being explored in clinical trials ranging from peripheral neuropathies to cancers. Advances in selective HDAC6 inhibitor discovery allowed studying highly efficacious brain penetrant and peripheral restrictive compounds for treating PNS and CNS indications. AREAS COVERED This review explores the multifactorial role of HDAC6 in cells, the common pathological hallmarks of PNS and CNS disorders, and how HDAC6 modulates these mechanisms. Pharmacological inhibition of HDAC6 and genetic knockout/knockdown studies as a therapeutic strategy in PNS and CNS indications were analyzed. Furthermore, we describe the recent developments in HDAC6 PET tracers and their utility in CNS indications. Finally, we explore the advancements and challenges with HDAC6 inhibitor compounds, such as hydroxamic acid, fluoromethyl oxadiazoles, HDAC6 degraders, and thiol-based inhibitors. EXPERT OPINION Based on extensive preclinical evidence, pharmacological inhibition of HDAC6 is a promising approach for treating both PNS and CNS disorders, given its involvement in neurodegeneration and aging-related cellular processes. Despite the progress in the development of selective HDAC6 inhibitors, safety concerns remain regarding their chronic administration in PNS and CNS indications, and the development of novel compound classes and modalities inhibiting HDAC6 function offer a way to mitigate some of these safety concerns.
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Affiliation(s)
| | | | - Sylvain Celanire
- Augustine Therapeutics, Research and Development, Leuven, Belgium
| | - Ludo Van Den Bosch
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven - University of Leuven, Leuven, Belgium
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
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Niharika, Ureka L, Roy A, Patra SK. Dissecting SOX2 expression and function reveals an association with multiple signaling pathways during embryonic development and in cancer progression. Biochim Biophys Acta Rev Cancer 2024; 1879:189136. [PMID: 38880162 DOI: 10.1016/j.bbcan.2024.189136] [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: 05/09/2023] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024]
Abstract
SRY (Sex Determining Region) box 2 (SOX2) is an essential transcription factor that plays crucial roles in activating genes involved in pre- and post-embryonic development, adult tissue homeostasis, and lineage specifications. SOX2 maintains the self-renewal property of stem cells and is involved in the generation of induced pluripotency stem cells. SOX2 protein contains a particular high-mobility group domain that enables SOX2 to achieve the capacity to participate in a broad variety of functions. The information about the involvement of SOX2 with gene regulatory elements, signaling networks, and microRNA is gradually emerging, and the higher expression of SOX2 is functionally relevant to various cancer types. SOX2 facilitates the oncogenic phenotype via cellular proliferation and enhancement of invasive tumor properties. Evidence are accumulating in favor of three dimensional (higher order) folding of chromatin and epigenetic control of the SOX2 gene by chromatin modifications, which implies that the expression level of SOX2 can be modulated by epigenetic regulatory mechanisms, specifically, via DNA methylation and histone H3 modification. In view of this, and to focus further insights into the roles SOX2 plays in physiological functions, involvement of SOX2 during development, precisely, the advances of our knowledge in pre- and post-embryonic development, and interactions of SOX2 in this scenario with various signaling pathways in tumor development and cancer progression, its potential as a therapeutic target against many cancers are summarized and discussed in this article.
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Affiliation(s)
- Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Lina Ureka
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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33
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Zhang ZX, Tian Y, Li S, Jing HB, Cai J, Li M, Xing GG. Involvement of HDAC2-mediated kcnq2/kcnq3 genes transcription repression activated by EREG/EGFR-ERK-Runx1 signaling in bone cancer pain. Cell Commun Signal 2024; 22:416. [PMID: 39192337 PMCID: PMC11350972 DOI: 10.1186/s12964-024-01797-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 08/18/2024] [Indexed: 08/29/2024] Open
Abstract
Bone cancer pain (BCP) represents a prevalent symptom among cancer patients with bone metastases, yet its underlying mechanisms remain elusive. This study investigated the transcriptional regulation mechanism of Kv7(KCNQ)/M potassium channels in DRG neurons and its involvement in the development of BCP in rats. We show that HDAC2-mediated transcriptional repression of kcnq2/kcnq3 genes, which encode Kv7(KCNQ)/M potassium channels in dorsal root ganglion (DRG), contributes to the sensitization of DRG neurons and the pathogenesis of BCP in rats. Also, HDAC2 requires the formation of a corepressor complex with MeCP2 and Sin3A to execute transcriptional regulation of kcnq2/kcnq3 genes. Moreover, EREG is identified as an upstream signal molecule for HDAC2-mediated kcnq2/kcnq3 genes transcription repression. Activation of EREG/EGFR-ERK-Runx1 signaling, followed by the induction of HDAC2-mediated transcriptional repression of kcnq2/kcnq3 genes in DRG neurons, leads to neuronal hyperexcitability and pain hypersensitivity in tumor-bearing rats. Consequently, the activation of EREG/EGFR-ERK-Runx1 signaling, along with the subsequent transcriptional repression of kcnq2/kcnq3 genes by HDAC2 in DRG neurons, underlies the sensitization of DRG neurons and the pathogenesis of BCP in rats. These findings uncover a potentially targetable mechanism contributing to bone metastasis-associated pain in cancer patients.
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Affiliation(s)
- Zi-Xian Zhang
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center and Neuroscience Research Institute, Peking University, Beijing, China
| | - Yue Tian
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center and Neuroscience Research Institute, Peking University, Beijing, China
- Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, Beijing, 100191, China
| | - Song Li
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center and Neuroscience Research Institute, Peking University, Beijing, China
| | - Hong-Bo Jing
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center and Neuroscience Research Institute, Peking University, Beijing, China
| | - Jie Cai
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center and Neuroscience Research Institute, Peking University, Beijing, China
- Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, Beijing, 100191, China
| | - Min Li
- Department of Anesthesiology, Peking University Third Hospital, Beijing, 100191, China.
| | - Guo-Gang Xing
- Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center and Neuroscience Research Institute, Peking University, Beijing, China.
- Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, Beijing, 100191, China.
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34
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Yuan D, Zhang X, Yang Y, Wei L, Li H, Zhao T, Guo M, Li Z, Huang Z, Wang M, Dai Z, Li P, Xia Q, Qian W, Cheng D. Schlank orchestrates insect developmental transition by switching H3K27 acetylation to trimethylation in the prothoracic gland. Proc Natl Acad Sci U S A 2024; 121:e2401861121. [PMID: 39167603 PMCID: PMC11363265 DOI: 10.1073/pnas.2401861121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/22/2024] [Indexed: 08/23/2024] Open
Abstract
Insect developmental transitions are precisely coordinated by ecdysone and juvenile hormone (JH). We previously revealed that accumulated H3K27 trimethylation (H3K27me3) at the locus encoding JH signal transducer Hairy is involved in the larval-pupal transition in insects, but the underlying mechanism remains to be fully defined. Here, we show in Drosophila and Bombyx that Rpd3-mediated H3K27 deacetylation in the prothoracic gland during the last larval instar promotes ecdysone biosynthesis and the larval-pupal transition by enabling H3K27me3 accumulation at the Hairy locus to induce its transcriptional repression. Importantly, we find that the homeodomain transcription factor Schlank acts to switch active H3K27 acetylation (H3K27ac) to repressive H3K27me3 at the Hairy locus by directly binding to the Hairy promoter and then recruiting the histone deacetylase Rpd3 and the histone methyltransferase PRC2 component Su(z)12 through physical interactions. Moreover, Schlank inhibits Hairy transcription to facilitate the larval-pupal transition, and the Schlank signaling cascade is suppressed by JH but regulated in a positive feedback manner by ecdysone. Together, our data uncover that Schlank mediates epigenetic reprogramming of H3K27 modifications in hormone actions during insect developmental transition.
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Affiliation(s)
- Dongqin Yuan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Xing Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Yan Yang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Ling Wei
- School of Life Sciences, Southwest University, Chongqing400715, China
| | - Hao Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Tujing Zhao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Mengge Guo
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Zheng Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Zhu Huang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Min Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Zongcai Dai
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Peixin Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Wenliang Qian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Daojun Cheng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
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Taylor CA, Maor-Nof M, Metzl-Raz E, Hidalgo A, Yee C, Gitler AD, Shen K. Histone deacetylase inhibition expands cellular proteostasis repertoires to enhance neuronal stress resilience. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.21.608176. [PMID: 39229034 PMCID: PMC11370365 DOI: 10.1101/2024.08.21.608176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Neurons are long-lived, terminally differentiated cells with limited regenerative capacity. Cellular stressors such as endoplasmic reticulum (ER) protein folding stress and membrane trafficking stress accumulate as neurons age and accompany age-dependent neurodegeneration. Current strategies to improve neuronal resilience are focused on using factors to reprogram neurons or targeting specific proteostasis pathways. We discovered a different approach. In an unbiased screen for modifiers of neuronal membrane trafficking defects, we unexpectedly identified a role for histone deacetylases (HDACs) in limiting cellular flexibility in choosing cellular pathways to respond to diverse types of stress. Genetic or pharmacological inactivation of HDACs resulted in improved neuronal health in response to ER protein folding stress and endosomal membrane trafficking stress in C. elegans and mammalian neurons. Surprisingly, HDAC inhibition enabled neurons to activate latent proteostasis pathways tailored to the nature of the individual stress, instead of generalized transcriptional upregulation. These findings shape our understanding of neuronal stress responses and suggest new therapeutic strategies to enhance neuronal resilience.
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Affiliation(s)
- Caitlin A Taylor
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, 94305 USA
| | - Maya Maor-Nof
- Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, 94305 USA
| | - Eyal Metzl-Raz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aaron Hidalgo
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Callista Yee
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, 94305 USA
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, 94158, USA
| | - Kang Shen
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, 94305 USA
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Carreiras MDC, Marco-Contelles J. Hydrazides as Inhibitors of Histone Deacetylases. J Med Chem 2024; 67:13512-13533. [PMID: 39092855 DOI: 10.1021/acs.jmedchem.4c00541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
In this Perspective, we have brought together available biological evidence on hydrazides as histone deacetylase inhibitors (HDACis) and as a distinct type of Zn-binding group (ZBG) to be reviewed for the first time in the literature. N-Alkyl hydrazides have transformed the field, providing innovative and practical chemical tools for selective and effective inhibition of specific histone deacetylase (HDAC) enzymes, in addition to the usual hydroxamic acid and o-aminoanilide ZBG-bearing HDACis. This has enabled efficient targeting of neurodegenerative diseases such as Alzheimer's disease, cancer, cardiovascular diseases, and protozoal pathologies.
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Affiliation(s)
- Maria do Carmo Carreiras
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisbon, Portugal
| | - José Marco-Contelles
- Laboratory of Medicinal Chemistry, Institute of Organic Chemistry CSIC, Juan de la Cierva, 3, 28006 Madrid, Spain
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Gupta I, Badrzadeh F, Tsentalovich Y, Gaykalova DA. Connecting the dots: investigating the link between environmental, genetic, and epigenetic influences in metabolomic alterations in oral squamous cell carcinoma. J Exp Clin Cancer Res 2024; 43:239. [PMID: 39169426 PMCID: PMC11337877 DOI: 10.1186/s13046-024-03141-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 07/28/2024] [Indexed: 08/23/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) accounts for around 90% of all oral cancers and is the eighth most common cancer worldwide. Despite progress in managing OSCC, the overall prognosis remains poor, with a survival rate of around 50-60%, largely due to tumor size and recurrence. The challenges of late-stage diagnosis and limitations in current methods emphasize the urgent need for less invasive techniques to enable early detection and treatment, crucial for improving outcomes in this aggressive form of oral cancer. Research is currently aimed at unraveling tumor-specific metabolite profiles to identify candidate biomarkers as well as discover underlying pathways involved in the onset and progression of cancer that could be used as new targets for diagnostic and therapeutic purposes. Metabolomics is an advanced technological approach to identify metabolites in different sample types (biological fluids and tissues). Since OSCC promotes metabolic reprogramming influenced by a combination of genetic predisposition and environmental factors, including tobacco and alcohol consumption, and viral infections, the identification of distinct metabolites through screening may aid in the diagnosis of this condition. Moreover, studies have shown the use of metabolites during the catalysis of epigenetic modification, indicating a link between epigenetics and metabolism. In this review, we will focus on the link between environmental, genetic, and epigenetic influences in metabolomic alterations in OSCC. In addition, we will discuss therapeutic targets of tumor metabolism, which may prevent oral tumor growth, metastasis, and drug resistance.
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Affiliation(s)
- Ishita Gupta
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA
| | - Fariba Badrzadeh
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA
| | - Yuri Tsentalovich
- International tomography center CB RAS, Institutskaya str. 3a, Novosibirsk, 630090, Russia
| | - Daria A Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA.
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
- Institute for Genome Sciences, 670 West Baltimore Street, Baltimore, MD, 21201, USA.
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Wang J, Feng J, Ni Y, Wang Y, Zhang T, Cao Y, Zhou M, Zhao C. Histone modifications and their roles in macrophage-mediated inflammation: a new target for diabetic wound healing. Front Immunol 2024; 15:1450440. [PMID: 39229271 PMCID: PMC11368794 DOI: 10.3389/fimmu.2024.1450440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 08/02/2024] [Indexed: 09/05/2024] Open
Abstract
Impaired wound healing is one of the main clinical complications of type 2 diabetes (T2D) and a major cause of lower limb amputation. Diabetic wounds exhibit a sustained inflammatory state, and reducing inflammation is crucial to diabetic wounds management. Macrophages are key regulators in wound healing, and their dysfunction would cause exacerbated inflammation and poor healing in diabetic wounds. Gene regulation caused by histone modifications can affect macrophage phenotype and function during diabetic wound healing. Recent studies have revealed that targeting histone-modifying enzymes in a local, macrophage-specific manner can reduce inflammatory responses and improve diabetic wound healing. This article will review the significance of macrophage phenotype and function in wound healing, as well as illustrate how histone modifications affect macrophage polarization in diabetic wounds. Targeting macrophage phenotype with histone-modifying enzymes may provide novel therapeutic strategies for the treatment of diabetic wound healing.
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Affiliation(s)
- Jing Wang
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jiawei Feng
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yiming Ni
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuqing Wang
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ting Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yemin Cao
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Mingmei Zhou
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Cheng Zhao
- Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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McClarty BM, Rodriguez G, Dong H. Class 1 histone deacetylases differentially modulate memory and synaptic genes in a spatial and temporal manner in aged and APP/PS1 mice. Brain Res 2024; 1837:148951. [PMID: 38642789 PMCID: PMC11182336 DOI: 10.1016/j.brainres.2024.148951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
Epigenetics plays a vital role in aging and Alzheimer's disease (AD); however, whether epigenetic alterations during aging can initiate AD and exacerbate AD progression remains unclear. In this study, using 3-, 12- and 18- month-old APP/PS1 mice and age matched WT littermates, we conducted a series of memory tests, measured synapse-related gene expression, class 1 histone deacetylases (HDACs) abundance, and H3K9ac levels at target gene promoters in the hippocampus and prefrontal cortex (PFC). Our results showed impaired recognition and long-term spatial memory in 18-month-old WT mice and impaired recognition, short-term working, and long-term spatial reference memory in 12-and 18- month-old APP/PS1 mice. These memory impairments are associated with changes of synapse-related gene (nr2a, glur1, glur2, psd95) expression, HDAC abundance, and H3K9ac levels; more specifically, increased HDAC2 was associated with synapse-related gene expression changes through modulation of H3K9ac at the gene promoters during aging and AD progression in the hippocampus. Conversely, increased HDAC3 was associated with synapse-related gene expression changes through modulation of H3K9ac at the gene promoters during AD progression in the PFC. These findings suggest memory impairments in aging and AD may associated with a differential HDAC modulation of synapse-related gene expression in the brain.
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Affiliation(s)
- Bryan M McClarty
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, Ward 7-103, Chicago, IL 60611, USA
| | - Guadalupe Rodriguez
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, Ward 7-103, Chicago, IL 60611, USA
| | - Hongxin Dong
- Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, Ward 7-103, Chicago, IL 60611, USA.
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Zhang F, Cui Y, Zhang T, Yin W. Epigenetic regulation of macrophage activation in chronic obstructive pulmonary disease. Front Immunol 2024; 15:1445372. [PMID: 39206196 PMCID: PMC11349576 DOI: 10.3389/fimmu.2024.1445372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024] Open
Abstract
Macrophages in the innate immune system play a vital role in various lung diseases such as asthma, chronic obstructive pulmonary disease (COPD), acute lung injury and pulmonary fibrosis. Macrophages involved in the process of immunity need to go through a process of activation, including changes in gene expression and cell metabolism. Epigenetic modifications are key factors of macrophage activation including DNA methylation, histone modification and non-coding RNA regulation. Understanding the role and mechanisms of epigenetic regulation of macrophage activation can provide insights into the function of macrophages in lung diseases and help identification of potential therapeutic targets. This review summarizes the latest progress in the epigenetic changes and regulation of macrophages in their development process and in normal physiological states, and the epigenetic regulation of macrophages in COPD as well as the influence of macrophage activation on COPD development.
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Affiliation(s)
- Feng Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University (GMU) - Guangzhou Institutes of Biomedicine and Health (GIBH) Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong, China
| | - Yachao Cui
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University (GMU) - Guangzhou Institutes of Biomedicine and Health (GIBH) Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong, China
| | - Tiejun Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University (GMU) - Guangzhou Institutes of Biomedicine and Health (GIBH) Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
- The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, State Key Laboratory of Respiratory Disease, Guangzhou Medical University Affiliated Qingyuan Hospital, Qingyuan People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wenguang Yin
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University (GMU) - Guangzhou Institutes of Biomedicine and Health (GIBH) Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong, China
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41
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Ou X, Yang J, Yang L, Zeng H, Shao L. Histone acetylation regulated by histone deacetylases during spermatogenesis. Andrology 2024. [PMID: 39132925 DOI: 10.1111/andr.13723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/03/2024] [Accepted: 07/23/2024] [Indexed: 08/13/2024]
Abstract
BACKGROUND Physical, chemical, and biological factors in the environment constantly influence in vivo and in vitro biological processes, including diverse histone modifications involved in cancer and metabolism. However, the intricate mechanisms of acetylation regulation remain poorly elucidated. In mammalian spermatogenesis, acetylation plays a crucial role in repairing double-strand DNA breaks, regulating gene transcription, and modulating various signaling pathways. RESULTS This review summarizes the histone acetylation sites in the mouse testis and provides a comprehensive overview of how histone acetylation is involved in different stages of spermatogenesis under the regulation by histone deacetylases. The regulatory functions of various class histone deacetylases during spermatogenesis and the crossroad between histone acetylation and other histone modifications are highlighted. It is imperative to understand the mechanisms of histone acetylation regulated by histone deacetylases in spermatogenesis, which facilitates to prevent and treat infertility-related diseases.
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Affiliation(s)
- Xiangying Ou
- Department of Occupational Health and Toxicology, Jiangxi Provincial Key Laboratory of Disease Prevention and Public Health, School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, P. R. China
| | - Juan Yang
- Department of Occupational Health and Toxicology, Jiangxi Provincial Key Laboratory of Disease Prevention and Public Health, School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, P. R. China
| | - Linfeng Yang
- Department of Occupational Health and Toxicology, Jiangxi Provincial Key Laboratory of Disease Prevention and Public Health, School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, P. R. China
| | - Huihong Zeng
- Department of Histology and Embryology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, P. R. China
| | - Lijian Shao
- Department of Occupational Health and Toxicology, Jiangxi Provincial Key Laboratory of Disease Prevention and Public Health, School of Public Health, Jiangxi Medical College, Nanchang University, Nanchang, P. R. China
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Mbatha SZ, Back CR, Devine AJ, Mulliner HM, Johns ST, Lewin H, Cheung KA, Zorn K, Stach JEM, Hayes MA, van der Kamp MW, Race PR, Willis CL. Antibiotic origami: selective formation of spirotetronates in abyssomicin biosynthesis. Chem Sci 2024:d4sc03253e. [PMID: 39144453 PMCID: PMC11318650 DOI: 10.1039/d4sc03253e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 07/25/2024] [Indexed: 08/16/2024] Open
Abstract
The abyssomicins are a structurally intriguing family of bioactive natural products that include compounds with potent antibacterial, antitumour and antiviral activities. The biosynthesis of the characteristic abyssomicin spirotetronate core occurs via an enzyme-catalysed intramolecular Diels-Alder reaction, which proceeds via one of two distinct stereochemical pathways to generate products differing in configuration at the C15 spirocentre. Using the purified spirotetronate cyclases AbyU (from abyssomicin C/atrop-abyssomicin C biosynthesis) and AbmU (from abyssomicin 2/neoabyssomicin biosynthesis), in combination with synthetic substrate analogues, here we show that stereoselectivity in the spirotetronate-forming [4 + 2]-cycloaddition is controlled by a combination of factors attributable to both the enzyme and substrate. Furthermore, an achiral substrate was enzymatically cyclised to a single enantiomer of a spirocyclic product. X-ray crystal structures, molecular dynamics simulations, and assessment of substrate binding affinity and reactivity in both AbyU and AbmU establish the molecular determinants of stereochemical control in this important class of biocatalysts.
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Affiliation(s)
| | - Catherine R Back
- School of Biochemistry, University of Bristol Bristol BS8 1TD UK
| | - Andrew J Devine
- School of Chemistry, University of Bristol Bristol BS8 1TS UK
| | | | - Samuel T Johns
- School of Biochemistry, University of Bristol Bristol BS8 1TD UK
| | - Harry Lewin
- School of Biochemistry, University of Bristol Bristol BS8 1TD UK
| | - Kaiman A Cheung
- School of Chemistry, University of Bristol Bristol BS8 1TS UK
| | - Katja Zorn
- Compound Synthesis and Management, Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca Pepparedsleden 1 431 83 Mölndal Sweden
| | - James E M Stach
- School of Natural and Environmental Sciences, Newcastle University Newcastle Upon Tyne NE1 7RU UK
| | - Martin A Hayes
- Compound Synthesis and Management, Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca Pepparedsleden 1 431 83 Mölndal Sweden
| | | | - Paul R Race
- School of Biochemistry, University of Bristol Bristol BS8 1TD UK
- School of Natural and Environmental Sciences, Newcastle University Newcastle Upon Tyne NE1 7RU UK
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Ma M, Fei X, Jiang D, Chen H, Xie X, Wang Z, Huang Q. Research Progress on the Mechanism of Histone Deacetylases in Ferroptosis of Glioma. Oncol Rev 2024; 18:1432131. [PMID: 39193375 PMCID: PMC11348391 DOI: 10.3389/or.2024.1432131] [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: 05/13/2024] [Accepted: 08/02/2024] [Indexed: 08/29/2024] Open
Abstract
Glioma is the most prevalent primary malignant tumor of the central nervous system. While traditional treatment modalities such as surgical resection, radiotherapy, and chemotherapy have made significant advancements in glioma treatment, the prognosis for glioma patients remains often unsatisfactory. Ferroptosis, a novel form of programmed cell death, plays a crucial role in glioma and is considered to be the most functionally rich programmed cell death process. Histone deacetylases have emerged as a key focus in regulating ferroptosis in glioma. By inhibiting the activity of histone deacetylases, histone deacetylase inhibitors elevate acetylation levels of both histones and non-histone proteins, thereby influencing various cellular processes. Numerous studies have demonstrated that histone deacetylases are implicated in the development of glioma and hold promise for its treatment. This article provides an overview of research progress on the mechanism by which histone deacetylases contribute to ferroptosis in glioma.
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Affiliation(s)
- Meng Ma
- Department of Neurosurgery, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, China
| | - Xifeng Fei
- Department of Neurosurgery, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou, China
| | - Dongyi Jiang
- Department of Neurosurgery, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou, China
| | - Hanchun Chen
- Department of Neurosurgery, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou, China
| | - Xiangtong Xie
- Department of Neurosurgery, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou, China
| | - Zhimin Wang
- Department of Neurosurgery, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, China
| | - Qiang Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
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Zhang C, Liu X, Gu C, Su Y, Lv J, Liu Y, Gao Y, Chen H, Xu N, Xiao J, Xu Z, Su W. Histone deacetylases facilitate Th17-cell differentiation and pathogenicity in autoimmune uveitis via CDK6/ID2 axis. J Adv Res 2024:S2090-1232(24)00313-8. [PMID: 39107200 DOI: 10.1016/j.jare.2024.07.029] [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: 05/03/2024] [Revised: 07/25/2024] [Accepted: 07/28/2024] [Indexed: 08/09/2024] Open
Abstract
INTRODUCTION Autoimmune uveitis (AU) is a prevalent ocular autoimmune disease leading to significant visual impairment. However, underlying pathogenesis of AU required to develop more efficient therapy remain unclear. METHODS We isolated peripheral blood mononuclear cells (PBMCs) from AU patients and performed single-cell RNA sequencing (scRNA-seq). Besides, experimental autoimmune uveitis (EAU) model was established and treated with histone deacetylase inhibitor (HDACi) Belinostat or vehicle. We extracted immune cells from Blank, EAU, and HDACi-treated EAU mice and used scRNA-seq, flow cytometry, siRNA, specific inhibitors, and adoptive transfer experiments to explore the role of HDACs and its downstream potential molecular mechanisms in the immune response of EAU and AU. RESULTS We found highly expressed histone deacetylases (HDACs) family in AU patients and identified it as a key factor related to CD4+ effector T cell differentiation in the pathogenesis of AU. Our further studies showed that targeted inhibition of HDACs effectively alleviated EAU, restored its Th17/Treg balance, and reduced inflammatory gene expression, especially in CD4+ T cells. Post-HDACs inhibition, Treg proportions increased with enhanced immunomodulatory effects. Importantly, HDACs exhibited a positive promoting role on Th17 cells. Based on scRNA-seq screening and application of knock-down siRNAs and specific inhibitors in vitro and vivo, we identified CDK6 as a key downstream molecule regulated by HDAC1/3/6 through acetyl-histone H3/p53/p21 axis, which is involved in Th17 pathogenicity and EAU development. Additionally, HDACs-regulated CDK6 formed a positive loop with ID2, inducing PIM1 upregulation, promoting Th17 cell differentiation and pathogenicity, and correlates with AU progression. CONCLUSION Based on the screening of clinical samples and downstream molecular functional validation experiments, we revealed a driving role for HDACs and the HDACs-regulated CDK6/ID2 axis in Th17 cell differentiation and pathogenicity in AU, proposing a promising therapeutic strategy.
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Affiliation(s)
- Chun Zhang
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xiuxing Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China.
| | - Chenyang Gu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Yuhan Su
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China; Department of Clinical Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510060, China
| | - Jianjie Lv
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Yidan Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Yuehan Gao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Hui Chen
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Nanwei Xu
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Clinical Medicine (Eight-Year Program), West China School of Medicine, Sichuan University, Chengdu 610044, China
| | - Jing Xiao
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zhuping Xu
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Wenru Su
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China.
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Ozgencil F, Gunindi HB, Eren G. Dual-targeted NAMPT inhibitors as a progressive strategy for cancer therapy. Bioorg Chem 2024; 149:107509. [PMID: 38824699 DOI: 10.1016/j.bioorg.2024.107509] [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: 03/09/2024] [Revised: 04/29/2024] [Accepted: 05/28/2024] [Indexed: 06/04/2024]
Abstract
In mammals, nicotinamide phosphoribosyltransferase (NAMPT) is a crucial enzyme in the nicotinamide adenine dinucleotide (NAD+) synthesis pathway catalyzing the condensation of nicotinamide (NAM) with 5-phosphoribosyl-1-pyrophosphate (PRPP) to produce nicotinamide mononucleotide (NMN). Given the pivotal role of NAD+ in a range of cellular functions, including DNA synthesis, redox reactions, cytokine generation, metabolism, and aging, NAMPT has become a promising target for many diseases, notably cancer. Therefore, various NAMPT inhibitors have been reported and classified as first and second-generation based on their chemical structures and design strategies, dual-targeted being one. However, most NAMPT inhibitors suffer from several limitations, such as dose-dependent toxicity and poor pharmacokinetic properties. Consequently, there is no clinically approved NAMPT inhibitor. Hence, research on discovering more effective and less toxic dual-targeted NAMPT inhibitors with desirable pharmacokinetic properties has drawn attention recently. This review summarizes the previously reported dual-targeted NAMPT inhibitors, focusing on their design strategies and advantages over the single-targeted therapies.
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Affiliation(s)
- Fikriye Ozgencil
- SIRTeam Group, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Ankara, Türkiye
| | - Habibe Beyza Gunindi
- SIRTeam Group, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Ankara, Türkiye
| | - Gokcen Eren
- SIRTeam Group, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Ankara, Türkiye.
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46
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Li C, Liang S, Huang Q, Zhou Z, Ding Z, Long N, Wi K, Li L, Jiang X, Fan Y, Xu Y. Minor Spliceosomal 65K/RNPC3 Interacts with ANKRD11 and Mediates HDAC3-Regulated Histone Deacetylation and Transcription. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307804. [PMID: 38837887 PMCID: PMC11304329 DOI: 10.1002/advs.202307804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/12/2024] [Indexed: 06/07/2024]
Abstract
RNA splicing is crucial in the multilayer regulatory networks for gene expression, making functional interactions with DNA- and other RNA-processing machineries in the nucleus. However, these established couplings are all major spliceosome-related; whether the minor spliceosome is involved remains unclear. Here, through affinity purification using Drosophila lysates, an interaction is identified between the minor spliceosomal 65K/RNPC3 and ANKRD11, a cofactor of histone deacetylase 3 (HDAC3). Using a CRISPR/Cas9 system, Deletion strains are constructed and found that both Dm65KΔ/Δ and Dmankrd11Δ/Δ mutants have reduced histone deacetylation at Lys9 of histone H3 (H3K9) and Lys5 of histone H4 (H4K5) in their heads, exhibiting various neural-related defects. The 65K-ANKRD11 interaction is also conserved in human cells, and the HsANKRD11 middle-uncharacterized domain mediates Hs65K association with HDAC3. Cleavage under targets and tagmentation (CUT&Tag) assays revealed that HsANKRD11 is a bridging factor, which facilitates the synergistic common chromatin-binding of HDAC3 and Hs65K. Knockdown (KD) of HsANKRD11 simultaneously decreased their common binding, resulting in reduced deacetylation of nearby H3K9. Ultimately, this study demonstrates that expression changes of many genes caused by HsANKRD11-KD are due to the decreased common chromatin-binding of HDAC3 and Hs65K and subsequently reduced deacetylation of H3K9, illustrating a novel and conserved coupling mechanism that links the histone deacetylation with minor spliceosome for the regulation of gene expression.
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Affiliation(s)
- Chen‐Hui Li
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Shao‐Bo Liang
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Qi‐Wei Huang
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Zhen‐Zhen Zhou
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Zhan Ding
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
- Key Laboratory of Insect Developmental and Evolutionary BiologyCenter for Excellence in Molecular Plant SciencesChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai200032China
| | - Ni Long
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Kwang‐Chon Wi
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Liang Li
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Xi‐Ping Jiang
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Yu‐Jie Fan
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Yong‐Zhen Xu
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
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Abdelilah-Seyfried S. Epigenetics enters the stage in vascular malformations. J Clin Invest 2024; 134:e182904. [PMID: 39087470 PMCID: PMC11290957 DOI: 10.1172/jci182904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024] Open
Abstract
Cerebral arteriovenous malformations represent the most common form of vascular malformations and can cause recurrent bleeding and hemorrhagic stroke. The current issue of the JCI features an article by Zhao et al. describing a mouse model of cerebral arteriovenous malformations. Endothelial cells lacking matrix Gla protein, a BMP inhibitor, underwent epigenetic changes characteristic of an endothelial-to-mesenchymal fate transition. The authors uncovered a two-step process for this transition controlled by the epigenetic regulator histone deacetylase 2 (HDAC2), which controls endothelial cell differentiation, and by enhancer of zeste homolog 1 (EZH1), which suppressed mesenchymal fate. This discovery provides a promising entry point for preventive pharmacological interventions.
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Zhou H, Wu R, Li H. Downregulation of HDAC6 mitigates lung ischemia/reperfusion injury depending on activation of Nrf2/HO-1 signaling pathway and inactivation of ERK/NF-κB signaling pathway. Tissue Cell 2024; 89:102446. [PMID: 38936199 DOI: 10.1016/j.tice.2024.102446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 05/22/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024]
Abstract
INTRODUCTION Lung ischemia/reperfusion injury (LIRI) is a pathological process caused by the deficiency and subsequent reperfusion of oxygen and blood to the lung. Literature reports that the catalytic activity and expression of HDAC6 can be induced in response to IRI. HDAC6 inhibition confers protective effects against a series of IRI and also exerts pulmonary protection against various lung damage. The present study was formulated to investigate the functional role of HDAC6 inhibitor in LIRI and to probe into the intrinsic mechanisms underlying the protective role of HDAC6 inhibitor against LIRI. METHODS Lung epithelial cell line MLE-12 cells were subjected to H/R injury to construct in vitro cell culture model of LIRI. For functional experiments, MLE-12 cells were pre-treated with various concentrations of selective HDAC6 inhibitor ACY-1215 (1, 5, 10 μM) to evaluate the biological role of HDAC6 in LIRI. For rescue experiments, MLE-12 cells were pre-treated with Nrf2 inhibitor ML385 (10 μM) or ERK activator LM22B-10 (50 μM) to discuss the molecular mechanisms. RESULTS It was verified that HDAC6 inhibition repressed H/R-induced apoptosis, oxidative stress, inflammation and mitochondrial dysfunction of MLE-12 cells. HDAC6 inhibition activated Nrf2/HO-1 signaling pathway and inactivated ERK/NF-κB signaling pathway in MLE-12 cells. The repressing effects of HDAC6 inhibition on H/R-induced apoptosis, oxidative stress, inflammation and mitochondrial dysfunction of MLE-12 cells were partially abolished upon pre-treatment with Nrf2 inhibitor ML385 or ERK activator LM22B-10. CONCLUSION HDAC6 inhibition may mitigate H/R-induced lung epithelial cell injury depending on activation of Nrf2/HO-1 signaling pathway and inactivation of ERK/NF-κB signaling pathway.
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Affiliation(s)
- Hong Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province 710065, PR China
| | - Rui Wu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province 710065, PR China
| | - Hong Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province 710065, PR China.
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Abubakar M, Hajjaj M, Naqvi ZEZ, Shanawaz H, Naeem A, Padakanti SSN, Bellitieri C, Ramar R, Gandhi F, Saleem A, Abdul Khader AHS, Faraz MA. Non-Coding RNA-Mediated Gene Regulation in Cardiovascular Disorders: Current Insights and Future Directions. J Cardiovasc Transl Res 2024; 17:739-767. [PMID: 38092987 DOI: 10.1007/s12265-023-10469-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/23/2023] [Indexed: 09/04/2024]
Abstract
Cardiovascular diseases (CVDs) pose a significant burden on global health. Developing effective diagnostic, therapeutic, and prognostic indicators for CVDs is critical. This narrative review explores the role of select non-coding RNAs (ncRNAs) and provides an in-depth exploration of the roles of miRNAs, lncRNAs, and circRNAs in different aspects of CVDs, offering insights into their mechanisms and potential clinical implications. The review also sheds light on the diverse functions of ncRNAs, including their modulation of gene expression, epigenetic modifications, and signaling pathways. It comprehensively analyzes the interplay between ncRNAs and cardiovascular health, paving the way for potential novel interventions. Finally, the review provides insights into the methodologies used to investigate ncRNA-mediated gene regulation in CVDs, as well as the implications and challenges associated with translating ncRNA research into clinical applications. Considering the broader implications, this research opens avenues for interdisciplinary collaborations, enhancing our understanding of CVDs across scientific disciplines.
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Affiliation(s)
- Muhammad Abubakar
- Department of Internal Medicine, Ameer-Ud-Din Medical College, Lahore General Hospital, Lahore, Punjab, Pakistan.
| | - Mohsin Hajjaj
- Department of Internal Medicine, Jinnah Hospital, Lahore, Punjab, Pakistan
| | - Zil E Zehra Naqvi
- Department of Internal Medicine, Jinnah Hospital, Lahore, Punjab, Pakistan
| | - Hameed Shanawaz
- Department of Internal Medicine, Windsor University School of Medicine, Cayon, Saint Kitts and Nevis
| | - Ammara Naeem
- Department of Cardiology, Heart & Vascular Institute, Dearborn, Michigan, USA
| | | | | | - Rajasekar Ramar
- Department of Internal Medicine, Rajah Muthiah Medical College, Chidambaram, Tamil Nadu, India
| | - Fenil Gandhi
- Department of Family Medicine, Lower Bucks Hospital, Bristol, PA, USA
| | - Ayesha Saleem
- Department of Internal Medicine, Jinnah Hospital, Lahore, Punjab, Pakistan
| | | | - Muhammad Ahmad Faraz
- Department of Forensic Medicine, Postgraduate Medical Institute, Lahore, Punjab, Pakistan
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Liu R, Zhang L, Zhang K. Histone modification in psoriasis: Molecular mechanisms and potential therapeutic targets. Exp Dermatol 2024; 33:e15151. [PMID: 39090854 DOI: 10.1111/exd.15151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 06/24/2024] [Accepted: 07/19/2024] [Indexed: 08/04/2024]
Abstract
Psoriasis is an immune-mediated, inflammatory disease. Genetic and environmental elements are involved in the nosogenesis of this illness. Epigenetic inheritance serves as the connection between genetic and environmental factors. Histone modification, an epigenetic regulatory mechanism, is implicated in the development of numerous diseases. The basic function of histone modification is to regulate cellular functions by modifying gene expression. Modulation of histone modification, such as regulation of enzymes pertinent to histone modification, can be an alternative approach for treating some diseases, including psoriasis. Herein, we reviewed the regulatory mechanisms and biological effects of histone modifications and their roles in the pathogenesis of psoriasis.
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Affiliation(s)
- Ruifeng Liu
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
| | - Luyao Zhang
- Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kaiming Zhang
- Shanxi Key Laboratory of Stem Cells for Immunological Dermatosis, Institute of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, China
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