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Zamperla MG, Illi B, Barbi V, Cencioni C, Santoni D, Gagliardi S, Garofalo M, Zingale GA, Pandino I, Sbardella D, Cipolla L, Sabbioneda S, Farsetti A, Ripamonti C, Fossati G, Steinkühler C, Gaetano C, Atlante S. HDAC6 inhibition disrupts HDAC6-P300 interaction reshaping the cancer chromatin landscape. Clin Epigenetics 2024; 16:109. [PMID: 39155390 PMCID: PMC11331611 DOI: 10.1186/s13148-024-01725-8] [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: 03/14/2024] [Accepted: 08/08/2024] [Indexed: 08/20/2024] Open
Abstract
BACKGROUND Histone deacetylases (HDACs) are crucial regulators of gene expression, DNA synthesis, and cellular processes, making them essential targets in cancer research. HDAC6, specifically, influences protein stability and chromatin dynamics. Despite HDAC6's potential therapeutic value, its exact role in gene regulation and chromatin remodeling needs further clarification. This study examines how HDAC6 inactivation influences lysine acetyltransferase P300 stabilization and subsequent effects on chromatin structure and function in cancer cells. METHODS AND RESULTS We employed the HDAC6 inhibitor ITF3756, siRNA, or CRISPR/Cas9 gene editing to inactivate HDAC6 in different epigenomic backgrounds. Constantly, this inactivation led to significant changes in chromatin accessibility, particularly increased acetylation of histone H3 lysines 9, 14, and 27 (ATAC-seq and H3K27Ac ChIP-seq analysis). Transcriptomics, proteomics, and gene ontology analysis revealed gene changes in cell proliferation, adhesion, migration, and apoptosis. Significantly, HDAC6 inactivation altered P300 ubiquitination, stabilizing P300 and leading to downregulating genes critical for cancer cell survival. CONCLUSIONS Our study highlights the substantial impact of HDAC6 inactivation on the chromatin landscape of cancer cells and suggests a role for P300 in contributing to the anticancer effects. The stabilization of P300 with HDAC6 inhibition proposes a potential shift in therapeutic focus from HDAC6 itself to its interaction with P300. This finding opens new avenues for developing targeted cancer therapies, improving our understanding of epigenetic mechanisms in cancer cells.
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Affiliation(s)
| | - Barbara Illi
- Institute of Molecular Biology and Pathology, National Research Council (CNR), c/o Sapienza University of Rome, 00185, Rome, Italy
| | - Veronica Barbi
- Laboratory of Epigenetics, Istituti Clinici Scientifici Maugeri IRCCS, 27100, Pavia, Italy
| | - Chiara Cencioni
- Institute for Systems Analysis and Computer Science, National Research Council (CNR)-IASI, 00185, Rome, Italy
| | - Daniele Santoni
- Institute for Systems Analysis and Computer Science, National Research Council (CNR)-IASI, 00185, Rome, Italy
| | - Stella Gagliardi
- Molecular Biology and Transcriptomics Unit, IRCCS Mondino Foundation, 27100, Pavia, Italy
| | - Maria Garofalo
- Molecular Biology and Transcriptomics Unit, IRCCS Mondino Foundation, 27100, Pavia, Italy
| | | | | | | | - Lina Cipolla
- Institute of Molecular Genetics, National Research Council (CNR), 27100, Pavia, Italy
| | - Simone Sabbioneda
- Institute of Molecular Genetics, National Research Council (CNR), 27100, Pavia, Italy
| | - Antonella Farsetti
- Institute for Systems Analysis and Computer Science, National Research Council (CNR)-IASI, 00185, Rome, Italy
| | - Chiara Ripamonti
- New Drug Incubator Department, Italfarmaco Group, 20092, Cinisello Balsamo, Italy
| | - Gianluca Fossati
- New Drug Incubator Department, Italfarmaco Group, 20092, Cinisello Balsamo, Italy
| | | | - Carlo Gaetano
- Laboratory of Epigenetics, Istituti Clinici Scientifici Maugeri IRCCS, 27100, Pavia, Italy.
| | - Sandra Atlante
- Institute for Systems Analysis and Computer Science, National Research Council (CNR)-IASI, 00185, Rome, Italy
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Ma Y, Lai J, Wan Q, Sun L, Wang Y, Li X, Zhang Q, Wu J. Exploring the common mechanisms and biomarker ST8SIA4 of atherosclerosis and ankylosing spondylitis through bioinformatics analysis and machine learning. Front Cardiovasc Med 2024; 11:1421071. [PMID: 39131703 PMCID: PMC11310936 DOI: 10.3389/fcvm.2024.1421071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 07/08/2024] [Indexed: 08/13/2024] Open
Abstract
Background Atherosclerosis (AS) is a major contributor to cerebrovascular and cardiovascular events. There is growing evidence that ankylosing spondylitis is closely linked to AS, often co-occurring with it; however, the shared pathogenic mechanisms between the two conditions are not well understood. This study employs bioinformatics approaches to identify common biomarkers and pathways between AS and ankylosing spondylitis. Methods Gene expression datasets for AS (GSE100927, GSE28829, GSE155512) and ankylosing spondylitis (GSE73754, GSE25101) were obtained from the Gene Expression Omnibus (GEO). Differential expression genes (DEGs) and module genes for AS and ankylosing spondylitis were identified using the Limma R package and weighted gene co-expression network analysis (WGCNA) techniques, respectively. The machine learning algorithm SVM-RFE was applied to pinpoint promising biomarkers, which were then validated in terms of their expression levels and diagnostic efficacy in AS and ankylosing spondylitis, using two separate GEO datasets. Furthermore, the interaction of the key biomarker with the immune microenvironment was investigated via the CIBERSORT algorithm, single-cell analysis was used to identify the locations of common diagnostic markers. Results The dataset GSE100927 contains 524 DEGs associated with AS, whereas dataset GSE73754 includes 1,384 genes categorized into modules specific to ankylosing spondylitis. Analysis of these datasets revealed an overlap of 71 genes between the DEGs of AS and the modular genes of ankylosing spondylitis. Utilizing the SVM-RFE algorithm, 15 and 24 central diagnostic genes were identified in datasets GSE100927 and GSE73754, respectively. Further validation of six key genes using external datasets confirmed ST8SIA4 as a common diagnostic marker for both conditions. Notably, ST8SIA4 is upregulated in samples from both diseases. Additionally, ROC analysis confirmed the robust diagnostic utility of ST8SIA4. Moreover, analysis through CIBERSORT suggested an association of the ST8SIA4 gene with the immune microenvironment in both disease contexts. Single-cell analysis revealed that ST8SIA4 is primarily expressed in Macrophages, Monocytes, T cells, and CMPs. Conclusion This study investigates the role of ST8SIA4 as a common diagnostic gene and the involvement of the lysosomal pathway in both AS and ankylosing spondylitis. The findings may yield potential diagnostic biomarkers and offer new insights into the shared pathogenic mechanisms underlying these conditions.
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Affiliation(s)
- Yirong Ma
- Department of Postgraduate, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Junyu Lai
- Cardiology Department, Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Qiang Wan
- Cardiology Department, Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Liqiang Sun
- Cardiology Department, Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Yang Wang
- Department of Postgraduate, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Xingliang Li
- Department of Postgraduate, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Qinhe Zhang
- Department of Acupuncture and Tuina, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Jianguang Wu
- Cardiology Department, Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, China
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3
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Sun Y, Li F, Liu Y, Qiao D, Yao X, Liu GS, Li D, Xiao C, Wang T, Chi W. Targeting inflammasomes and pyroptosis in retinal diseases-molecular mechanisms and future perspectives. Prog Retin Eye Res 2024; 101:101263. [PMID: 38657834 DOI: 10.1016/j.preteyeres.2024.101263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
Retinal diseases encompass various conditions associated with sight-threatening immune responses and are leading causes of blindness worldwide. These diseases include age-related macular degeneration, diabetic retinopathy, glaucoma and uveitis. Emerging evidence underscores the vital role of the innate immune response in retinal diseases, beyond the previously emphasized T-cell-driven processes of the adaptive immune system. In particular, pyroptosis, a newly discovered programmed cell death process involving inflammasome formation, has been implicated in the loss of membrane integrity and the release of inflammatory cytokines. Several disease-relevant animal models have provided evidence that the formation of inflammasomes and the induction of pyroptosis in innate immune cells contribute to inflammation in various retinal diseases. In this review article, we summarize current knowledge about the innate immune system and pyroptosis in retinal diseases. We also provide insights into translational targeting approaches, including novel drugs countering pyroptosis, to improve the diagnosis and treatment of retinal diseases.
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Affiliation(s)
- Yimeng Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Fan Li
- Eye Center, Zhongshan City People's Hospital, Zhongshan, 528403, China
| | - Yunfei 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
| | - Dijie Qiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Xinyu Yao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Guei-Sheung Liu
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia; Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, 3002, Australia
| | - Dequan Li
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chuanle Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Tao Wang
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Guangming District, Shenzhen, 518132, China; School of Basic Medical Sciences, Capital Medical University, 10 Xitoutiao You'anMen Street, Beijing, 100069, China
| | - Wei Chi
- 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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Bahram Sangani N, Koetsier J, Mélius J, Kutmon M, Ehrhart F, Evelo CT, Curfs LMG, Reutelingsperger CP, Eijssen LMT. A novel insight into neurological disorders through HDAC6 protein-protein interactions. Sci Rep 2024; 14:14666. [PMID: 38918466 PMCID: PMC11199618 DOI: 10.1038/s41598-024-65094-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
Due to its involvement in physiological and pathological processes, histone deacetylase 6 (HDAC6) is considered a promising pharmaceutical target for several neurological manifestations. However, the exact regulatory role of HDAC6 in the central nervous system (CNS) is still not fully understood. Hence, using a semi-automated literature screening technique, we systematically collected HDAC6-protein interactions that are experimentally validated and reported in the CNS. The resulting HDAC6 network encompassed 115 HDAC6-protein interactions divided over five subnetworks: (de)acetylation, phosphorylation, protein complexes, regulatory, and aggresome-autophagy subnetworks. In addition, 132 indirect interactions identified through HDAC6 inhibition were collected and categorized. Finally, to display the application of our HDAC6 network, we mapped transcriptomics data of Alzheimer's disease, Parkinson's disease, and Amyotrophic Lateral Sclerosis on the network and highlighted that in the case of Alzheimer's disease, alterations predominantly affect the HDAC6 phosphorylation subnetwork, whereas differential expression within the deacetylation subnetwork is observed across all three neurological disorders. In conclusion, the HDAC6 network created in the present study is a novel and valuable resource for the understanding of the HDAC6 regulatory mechanisms, thereby providing a framework for the integration and interpretation of omics data from neurological disorders and pharmacodynamic assessments.
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Affiliation(s)
- Nasim Bahram Sangani
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200 MD, Maastricht, The Netherlands.
- GKC, Maastricht University Medical Centre, 6229 ER, Maastricht, The Netherlands.
| | - Jarno Koetsier
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200 MD, Maastricht, The Netherlands
- GKC, Maastricht University Medical Centre, 6229 ER, Maastricht, The Netherlands
| | - Jonathan Mélius
- DataHub, Maastricht University & Maastricht UMC+, P. Debyelaan 15, 6229 HX, Maastricht, The Netherlands
| | - Martina Kutmon
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, 6200 MD, Maastricht, The Netherlands
| | - Friederike Ehrhart
- Department of Bioinformatics - BiGCaT, Research Institute of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD, Maastricht, The Netherlands
- Department of Psychiatry and Neuropsychology, Research Institute for Mental Health and Neuroscience (MHeNs), Maastricht University, 6200 MD, Maastricht, The Netherlands
| | - Chris T Evelo
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, 6200 MD, Maastricht, The Netherlands
- Department of Bioinformatics - BiGCaT, Research Institute of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD, Maastricht, The Netherlands
| | - Leopold M G Curfs
- GKC, Maastricht University Medical Centre, 6229 ER, Maastricht, The Netherlands
| | - Chris P Reutelingsperger
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200 MD, Maastricht, The Netherlands
- GKC, Maastricht University Medical Centre, 6229 ER, Maastricht, The Netherlands
| | - Lars M T Eijssen
- Department of Bioinformatics - BiGCaT, Research Institute of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6200 MD, Maastricht, The Netherlands
- Department of Psychiatry and Neuropsychology, Research Institute for Mental Health and Neuroscience (MHeNs), Maastricht University, 6200 MD, Maastricht, The Netherlands
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5
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Chen J, Gao Y, Liu N, Hai D, Wei W, Liu Y, Lan X, Jin X, Yu J, Ma L. Mechanism of NLRP3 Inflammasome in Epilepsy and Related Therapeutic Agents. Neuroscience 2024; 546:157-177. [PMID: 38574797 DOI: 10.1016/j.neuroscience.2024.03.029] [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: 12/31/2023] [Revised: 03/05/2024] [Accepted: 03/27/2024] [Indexed: 04/06/2024]
Abstract
Epilepsy is one of the most widespread and complex diseases in the central nervous system (CNS), affecting approximately 65 million people globally, an important factor resulting in neurological disability-adjusted life year (DALY) and progressive cognitive dysfunction. Medication is the most essential treatment. The currently used drugs have shown drug resistance in some patients and only control symptoms; the development of novel and more efficacious pharmacotherapy is imminent. Increasing evidence suggests neuroinflammation is involved in the occurrence and development of epilepsy, and high expression of NLRP3 inflammasome has been observed in the temporal lobe epilepsy (TLE) brain tissue of patients and animal models. The inflammasome is a crucial cause of neuroinflammation by activating IL-1β and IL-18. Many preclinical studies have confirmed that regulating NLRP3 inflammasome pathway can prevent the development of epilepsy, reduce the severity of epilepsy, and play a neuroprotective role. Therefore, regulating NLRP3 inflammasome could be a potential target for epilepsy treatment. In summary, this review describes the priming and activation of inflammasome and its biological function in the progression of epilepsy. In addition, we reviewes the current pharmacological researches for epilepsy based on the regulation of NLRP3 inflammasome, aiming to provide a basis and reference for developing novel antiepileptic drugs.
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Affiliation(s)
- Juan Chen
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, China
| | - Yuan Gao
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, China
| | - Ning Liu
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, China
| | - Dongmei Hai
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, China
| | - Wei Wei
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, China
| | - Yue Liu
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, China
| | - Xiaobing Lan
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, China
| | - Xueqin Jin
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, China.
| | - Jianqiang Yu
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, China.
| | - Lin Ma
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, China.
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6
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Zhao L, Gao N, Peng X, Chen L, Meng T, Jiang C, Jin J, Zhang J, Duan Q, Tian H, Weng L, Wang X, Tan X, Li Y, Qin H, Yuan J, Ge X, Deng L, Wang P. TRAF4-Mediated LAMTOR1 Ubiquitination Promotes mTORC1 Activation and Inhibits the Inflammation-Induced Colorectal Cancer Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2301164. [PMID: 38229144 DOI: 10.1002/advs.202301164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 11/28/2023] [Indexed: 01/18/2024]
Abstract
Mechanistic target of rapamycin complex 1 (mTORC1) is a conserved serine/threonine kinase that integrates various environmental signals to regulate cell growth and metabolism. mTORC1 activation requires tethering to lysosomes by the Ragulator-Rag complex. However, the dynamic regulation of the interaction between Ragulator and Rag guanosine triphosphatase (GTPase) remains unclear. In this study, that LAMTOR1, an essential component of Ragulator, is dynamically ubiquitinated depending on amino acid abundance is reported. It is found that the E3 ligase TRAF4 directly interacts with LAMTOR1 and catalyzes the K63-linked polyubiquitination of LAMTOR1 at K151. Ubiquitination of LAMTOR1 by TRAF4 promoted its binding to Rag GTPases and enhanced mTORC1 activation, K151R knock-in or TRAF4 knock-out blocks amino acid-induced mTORC1 activation and accelerates the development of inflammation-induced colon cancer. This study revealed that TRAF4-mediated LAMTOR1 ubiquitination is a regulatory mechanism for mTORC1 activation and provides a therapeutic target for diseases involving mTORC1 dysregulation.
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Affiliation(s)
- Linlin Zhao
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Ni Gao
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Xiaoping Peng
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Lei Chen
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Tong Meng
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
- Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200940, P. R. China
| | - Cong Jiang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Jiali Jin
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Jiawen Zhang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Qiuhui Duan
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Hongling Tian
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Linjun Weng
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Xinbo Wang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Xiao Tan
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Yaxu Li
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Huanlong Qin
- Department of Gastrointestinal Surgery, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 200092, P. R. China
- Research Institute of Intestinal Diseases, Tongji University School of Medicine, Shanghai, 200092, P. R. China
| | - Jian Yuan
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200092, P. R. China
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, P. R. China
| | - Xin Ge
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
| | - Lu Deng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Ping Wang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai, 200092, P. R. China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200092, P. R. China
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Wang L, Shi S, Unterreiner A, Kapetanovic R, Ghosh S, Sanchez J, Aslani S, Xiong Y, Hsu CL, Donovan KA, Farady CJ, Fischer ES, Bornancin F, Matthias P. HDAC6/aggresome processing pathway importance for inflammasome formation is context-dependent. J Biol Chem 2024; 300:105638. [PMID: 38199570 PMCID: PMC10850954 DOI: 10.1016/j.jbc.2024.105638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/19/2023] [Accepted: 12/31/2023] [Indexed: 01/12/2024] Open
Abstract
The inflammasome is a large multiprotein complex that assembles in the cell cytoplasm in response to stress or pathogenic infection. Its primary function is to defend the cell and promote the secretion of pro-inflammatory cytokines, including IL-1β and IL-18. Previous research has shown that in immortalized bone marrow-derived macrophages (iBMDMs) inflammasome assembly is dependent on the deacetylase HDAC6 and the aggresome processing pathway (APP), a cellular pathway involved in the disposal of misfolded proteins. Here we used primary BMDMs from mice in which HDAC6 is ablated or impaired and found that inflammasome activation was largely normal. We also used human peripheral blood mononuclear cells and monocyte cell lines expressing a synthetic protein blocking the HDAC6-ubiquitin interaction and impairing the APP and found that inflammasome activation was moderately affected. Finally, we used a novel HDAC6 degrader and showed that inflammasome activation was partially impaired in human macrophage cell lines with depleted HDAC6. Our results therefore show that HDAC6 importance in inflammasome activation is context-dependent.
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Affiliation(s)
- Longlong Wang
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | - Shihua Shi
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Ronan Kapetanovic
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Sucheta Ghosh
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Jacint Sanchez
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Selma Aslani
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Yuan Xiong
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Chi-Lin Hsu
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Eric S Fischer
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Sciences, University of Basel, Basel, Switzerland.
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8
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Bonam SR, Mastrippolito D, Georgel P, Muller S. Pharmacological targets at the lysosomal autophagy-NLRP3 inflammasome crossroads. Trends Pharmacol Sci 2024; 45:81-101. [PMID: 38102020 DOI: 10.1016/j.tips.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023]
Abstract
Many aspects of cell homeostasis and integrity are maintained by the nucleotide-binding oligomerization domain (NOD)-like receptor (NLR) family pyrin domain-containing 3 (NLRP3) inflammasome. The NLRP3 oligomeric protein complex assembles in response to exogenous and endogenous danger signals. This inflammasome has also been implicated in the pathogenesis of a range of disease conditions, particularly chronic inflammatory diseases. Given that NLRP3 modulates autophagy, which is also a key regulator of inflammasome activity, excessive inflammation may be controlled by targeting this intersecting pathway. However, specific niche areas of NLRP3-autophagy interactions and their reciprocal regulatory mechanisms remain underexplored. Consequently, we lack treatment methods specifically targeting this pivotal axis. Here, we discuss the potential of such strategies in the context of autoimmune and metabolic diseases and propose some research avenues.
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Affiliation(s)
- Srinivasa Reddy Bonam
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Dylan Mastrippolito
- CNRS-University of Strasbourg, Biotechnology and Cell Signaling, Illkirch, France; Strasbourg Institute of Drug Discovery and Development (IMS), Strasbourg, France
| | - Philippe Georgel
- CNRS-University of Strasbourg, Biotechnology and Cell Signaling, Illkirch, France; Strasbourg Institute of Drug Discovery and Development (IMS), Strasbourg, France; Fédération Hospitalo-Universitaire (FHU) OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg University, Strasbourg, France
| | - Sylviane Muller
- CNRS-University of Strasbourg, Biotechnology and Cell Signaling, Illkirch, France; Strasbourg Institute of Drug Discovery and Development (IMS), Strasbourg, France; Fédération Hospitalo-Universitaire (FHU) OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg University, Strasbourg, France; University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France.
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Yang Y, Zhang G. Lysosome-Related Diagnostic Biomarkers for Pediatric Sepsis Integrated by Machine Learning. J Inflamm Res 2023; 16:5575-5583. [PMID: 38034045 PMCID: PMC10685105 DOI: 10.2147/jir.s437110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/21/2023] [Indexed: 12/02/2023] Open
Abstract
Background There is currently no biomarker that can reliably identify sepsis, despite recent scientific advancements. We systematically evaluated the value of lysosomal genes for the diagnosis of pediatric sepsis. Methods Three datasets (GSE13904, GSE26378, and GSE26440) were obtained from the gene expression omnibus (GEO) database. LASSO regression analysis and random forest analysis were employed for screening pivotal genes to construct a diagnostic model between the differentially expressed genes (DEGs) and lysosomal genes. The efficacy of the diagnostic model for pediatric sepsis identification in the three datasets was validated through receiver operating characteristic curve (ROC) analysis. Furthermore, a total of 30 normal samples and 35 pediatric sepsis samples were gathered to detect the expression levels of crucial genes and assess the diagnostic model's efficacy in diagnosing pediatric sepsis in real clinical samples through real-time quantitative PCR (qRT-PCR). Results Among the 83 differentially expressed genes (DEGs) related to lysosomes, four key genes (STOM, VNN1, SORT1, and RETN) were identified to develop a diagnostic model for pediatric sepsis. The expression levels of these four key genes were consistently higher in the sepsis group compared to the normal group across all three cohorts. The diagnostic model exhibited excellent diagnostic performance, as evidenced by area under the curve (AUC) values of 1, 0.971, and 0.989. Notably, the diagnostic model also demonstrated strong diagnostic ability with an AUC of 0.917 when applied to the 65 clinical samples, surpassing the efficacy of conventional inflammatory indicators such as procalcitonin (PCT), white blood cell (WBC) count, C-reactive protein (CRP), and neutrophil percentage (NEU%). Conclusion A four-gene diagnostic model of lysosomal function was devised and validated, aiming to accurately detect pediatric sepsis cases and propose potential target genes for lysosomal intervention in affected children.
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Affiliation(s)
- Yang Yang
- Department of Nuclear Medicine, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, Henan, 450003, People’s Republic of China
| | - Genhao Zhang
- Department of Blood Transfusion, Zhengzhou University First Affiliated Hospital, Zhengzhou, Henan, 450052, People’s Republic of China
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10
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Bornancin F, Dekker C. A phospho-harmonic orchestra plays the NLRP3 score. Front Immunol 2023; 14:1281607. [PMID: 38022631 PMCID: PMC10654991 DOI: 10.3389/fimmu.2023.1281607] [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: 08/22/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
NLRP3 is a prototypical sensor protein connecting cellular stress to pro-inflammatory signaling. A complex array of regulatory steps is required to switch NLRP3 from an inactive state into a primed entity that is poised to assemble an inflammasome. Accumulating evidence suggests that post-translational mechanisms are critical. In particular, phosphorylation/dephosphorylation and ubiquitylation/deubiquitylation reactions have been reported to regulate NLRP3. Taken individually, several post-translational modifications appear to be essential. However, it remains difficult to understand how they may be coordinated, whether there is a unique sequence of regulatory steps accounting for the functional maturation of NLRP3, or whether the sequence is subject to variations depending on cell type, the stimulus, and other parameters such as the cellular context. This review will focus on the regulation of the NLRP3 inflammasome by phosphorylation and dephosphorylation, and on kinases and phosphatases that have been reported to modulate NLRP3 activity. The aim is to try to integrate the current understanding and highlight potential gaps for further studies.
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Affiliation(s)
| | - Carien Dekker
- Discovery Sciences Department, Novartis Biomedical Research, Basel, Switzerland
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11
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Pang J, Vince JE. The role of caspase-8 in inflammatory signalling and pyroptotic cell death. Semin Immunol 2023; 70:101832. [PMID: 37625331 DOI: 10.1016/j.smim.2023.101832] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/20/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023]
Abstract
The programmed cell death machinery exhibits surprising flexibility, capable of crosstalk and non-apoptotic roles. Much of this complexity arises from the diverse functions of caspase-8, a cysteine-aspartic acid protease typically associated with activating caspase-3 and - 7 to induce apoptosis. However, recent research has revealed that caspase-8 also plays a role in regulating the lytic gasdermin cell death machinery, contributing to pyroptosis and immune responses in contexts such as infection, autoinflammation, and T-cell signalling. In mice, loss of caspase-8 results in embryonic lethality from unrestrained necroptotic killing, while in humans caspase-8 deficiency can lead to an autoimmune lymphoproliferative syndrome, immunodeficiency, inflammatory bowel disease or, when it can't cleave its substrate RIPK1, early onset periodic fevers. This review focuses on non-canonical caspase-8 signalling that drives immune responses, including its regulation of inflammatory gene transcription, activation within inflammasome complexes, and roles in pyroptotic cell death. Ultimately, a deeper understanding of caspase-8 function will aid in determining whether, and when, targeting caspase-8 pathways could be therapeutically beneficial in human diseases.
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Affiliation(s)
- Jiyi Pang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - James E Vince
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia.
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12
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Wang L, Unterreiner A, Kapetanovic R, Aslani S, Xiong Y, Donovan KA, Farady CJ, Fischer ES, Bornancin F, Matthias P. HDAC6/aggresome processing pathway importance for inflammasome formation is context dependent. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553363. [PMID: 37645730 PMCID: PMC10461986 DOI: 10.1101/2023.08.15.553363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The inflammasome is a large multiprotein complex that assembles in the cell cytoplasm in response to stress or pathogenic infection. Its primary function is to defend the cell and promote the secretion of pro-inflammatory cytokines, including IL-1β and IL-18. It was shown that in immortalized bone marrow derived macrophages (iBMDMs) inflammasome assembly is dependent on the deacetylase HDAC6 and the aggresome processing pathway (APP), a cellular pathway involved in the disposal of misfolded proteins. Here we used primary BMDMs from mice in which HDAC6 is ablated or impaired and found that inflammasome activation was largely normal. We also used human peripheral blood mononuclear cells and monocytes cell lines expressing a synthetic protein blocking HDAC6-ubiquitin interaction and impairing the APP and found that inflammasome activation was moderately affected. Finally, we used a novel HDAC6 degrader and showed that inflammasome activation was partially impaired in human macrophage cell lines with depleted HDAC6. Our results therefore show that HDAC6 importance in inflammasome activation is context dependent.
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Affiliation(s)
- Longlong Wang
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | | | - Ronan Kapetanovic
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Selma Aslani
- Novartis Institutes for Biomedical Research, 4056 Basel Switzerland
| | - Yuan Xiong
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States
| | - Katherine A Donovan
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States
| | | | - Eric S Fischer
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States
| | | | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- Faculty of Sciences, University of Basel, 4031 Basel, Switzerland
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13
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Tsujimoto K, Takamatsu H, Kumanogoh A. The Ragulator complex: delving its multifunctional impact on metabolism and beyond. Inflamm Regen 2023; 43:28. [PMID: 37173755 PMCID: PMC10175929 DOI: 10.1186/s41232-023-00278-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023] Open
Abstract
Our understanding of lysosomes has undergone a significant transformation in recent years, from the view that they are static organelles primarily responsible for the disposal and recycling of cellular waste to their recognition as highly dynamic structures. Current research posits that lysosomes function as a signaling hub that integrates both extracellular and intracellular stimuli, thereby regulating cellular homeostasis. The dysregulation of lysosomal function has been linked to a wide range of diseases. Of note, lysosomes contribute to the activation of mammalian target of rapamycin complex 1 (mTORC1), a key regulator of cellular metabolism. The Ragulator complex, a protein complex anchored on the lysosomal membrane, was initially shown to tether the mTORC1 complex to lysosomes. Recent research has substantially expanded our understanding of the roles of the Ragulator complex in lysosomes, including roles in the regulation of metabolism, inflammation, cell death, cell migration, and the maintenance of homeostasis, via interactions with various proteins. This review summarizes our current knowledge on the diverse functions of the Ragulator complex, highlighting important protein interactions.
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Affiliation(s)
- Kohei Tsujimoto
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Department of Immunopathology, Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Hyota Takamatsu
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan.
- Department of Immunopathology, Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan.
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Department of Immunopathology, Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
- Center for Infectious Diseases Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
- Japan Agency for Medical Research and Development - Core Research for Evolutional Science and Technology (AMED-CREST), Osaka University, Osaka, Japan
- Center for Advanced Modalities and DDS (CAMaD), Osaka University, Osaka, Japan
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14
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Devant P, Boršić E, Ngwa EM, Xiao H, Chouchani ET, Thiagarajah JR, Hafner-Bratkovič I, Evavold CL, Kagan JC. Gasdermin D pore-forming activity is redox-sensitive. Cell Rep 2023; 42:112008. [PMID: 36662620 PMCID: PMC9947919 DOI: 10.1016/j.celrep.2023.112008] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 11/21/2022] [Accepted: 12/31/2022] [Indexed: 01/21/2023] Open
Abstract
Reactive oxygen species (ROS) regulate the activities of inflammasomes, which are innate immune signaling organelles that induce pyroptosis. The mechanisms by which ROS control inflammasome activities are unclear and may be multifaceted. Herein, we report that the protein gasdermin D (GSDMD), which forms membrane pores upon cleavage by inflammasome-associated caspases, is a direct target of ROS. Exogenous and endogenous sources of ROS, and ROS-inducing stimuli that prime cells for pyroptosis induction, promote oligomerization of cleaved GSDMD, leading to membrane rupture and cell death. We find that ROS enhance GSDMD activities through oxidative modification of cysteine 192 (C192). Within macrophages, GSDMD mutants lacking C192 show impaired ability to form membrane pores and induce pyroptosis. Reciprocal mutagenesis studies reveal that C192 is the only cysteine within GSDMD that mediates ROS responsiveness. Cellular redox state is therefore a key determinant of GSDMD activities.
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Affiliation(s)
- Pascal Devant
- Division of Gastroenterology, Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Elvira Boršić
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; Graduate School of Biomedicine, University of Ljubljana, Kongresni trg 12, 1000 Ljubljana, Slovenia
| | - Elsy M Ngwa
- Division of Gastroenterology, Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Haopeng Xiao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Edward T Chouchani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Jay R Thiagarajah
- Division of Gastroenterology, Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
| | - Iva Hafner-Bratkovič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; EN-FIST Centre of Excellence, Trg Osvobodilne fronte 13, 1000 Ljubljana, Slovenia.
| | - Charles L Evavold
- Ragon Institute of MGH, MIT and Harvard, 400 Technology Square, Cambridge, MA 02139, USA.
| | - Jonathan C Kagan
- Division of Gastroenterology, Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
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