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Signal B, Phipps AJ, Giles KA, Huskins SN, Mercer TR, Robinson MD, Woodhouse A, Taberlay PC. Ageing-Related Changes to H3K4me3, H3K27ac, and H3K27me3 in Purified Mouse Neurons. Cells 2024; 13:1393. [PMID: 39195281 DOI: 10.3390/cells13161393] [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: 07/09/2024] [Revised: 08/19/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024] Open
Abstract
Neurons are central to lifelong learning and memory, but ageing disrupts their morphology and function, leading to cognitive decline. Although epigenetic mechanisms are known to play crucial roles in learning and memory, neuron-specific genome-wide epigenetic maps into old age remain scarce, often being limited to whole-brain homogenates and confounded by glial cells. Here, we mapped H3K4me3, H3K27ac, and H3K27me3 in mouse neurons across their lifespan. This revealed stable H3K4me3 and global losses of H3K27ac and H3K27me3 into old age. We observed patterns of synaptic function gene deactivation, regulated through the loss of the active mark H3K27ac, but not H3K4me3. Alongside this, embryonic development loci lost repressive H3K27me3 in old age. This suggests a loss of a highly refined neuronal cellular identity linked to global chromatin reconfiguration. Collectively, these findings indicate a key role for epigenetic regulation in neurons that is inextricably linked with ageing.
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Affiliation(s)
- Brandon Signal
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
| | - Andrew J Phipps
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
| | - Katherine A Giles
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
- Children's Medical Research Institute, University of Sydney, 214 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - Shannon N Huskins
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, Corner College and Cooper Roads, Brisbane, QLD 4072, Australia
| | - Mark D Robinson
- SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Adele Woodhouse
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
| | - Phillippa C Taberlay
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
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2
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Saha E, Guebila MB, Fanfani V, Shutta KH, DeMeo DL, Quackenbush J, Lopes-Ramos CM. Aging-associated Alterations in the Gene Regulatory Network Landscape Associate with Risk, Prognosis and Response to Therapy in Lung Adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601689. [PMID: 39005266 PMCID: PMC11244978 DOI: 10.1101/2024.07.02.601689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Aging is the primary risk factor for many individual cancer types, including lung adenocarcinoma (LUAD). To understand how aging-related alterations in the regulation of key cellular processes might affect LUAD risk and survival outcomes, we built individual (person)-specific gene regulatory networks integrating gene expression, transcription factor protein-protein interaction, and sequence motif data, using PANDA/LIONESS algorithms, for both non-cancerous lung tissue samples from the Genotype Tissue Expression (GTEx) project and LUAD samples from The Cancer Genome Atlas (TCGA). In GTEx, we found that pathways involved in cell proliferation and immune response are increasingly targeted by regulatory transcription factors with age; these aging-associated alterations are accelerated by tobacco smoking and resemble oncogenic shifts in the regulatory landscape observed in LUAD and suggests that dysregulation of aging pathways might be associated with an increased risk of LUAD. Comparing normal adjacent samples from individuals with LUAD with healthy lung tissue samples from those without LUAD, we found that aging-associated genes show greater aging-biased targeting patterns in younger individuals with LUAD compared to their healthy counterparts of similar age, a pattern suggestive of age acceleration. This implies that an accelerated aging process may be responsible for tumor incidence in younger individuals. Using drug repurposing tool CLUEreg, we found small molecule drugs with potential geroprotective effects that may alter the accelerating aging profiles we found. We also observed that, in contrast to chronological age, a network-informed aging signature was associated with survival and response to chemotherapy in LUAD.
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Affiliation(s)
- Enakshi Saha
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Marouen Ben Guebila
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Viola Fanfani
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Katherine H Shutta
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA 02115
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - John Quackenbush
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA 02115
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Camila M Lopes-Ramos
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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Kumar KK, Aburawi EH, Ljubisavljevic M, Leow MKS, Feng X, Ansari SA, Emerald BS. Exploring histone deacetylases in type 2 diabetes mellitus: pathophysiological insights and therapeutic avenues. Clin Epigenetics 2024; 16:78. [PMID: 38862980 PMCID: PMC11167878 DOI: 10.1186/s13148-024-01692-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/04/2024] [Indexed: 06/13/2024] Open
Abstract
Diabetes mellitus is a chronic disease that impairs metabolism, and its prevalence has reached an epidemic proportion globally. Most people affected are with type 2 diabetes mellitus (T2DM), which is caused by a decline in the numbers or functioning of pancreatic endocrine islet cells, specifically the β-cells that release insulin in sufficient quantity to overcome any insulin resistance of the metabolic tissues. Genetic and epigenetic factors have been implicated as the main contributors to the T2DM. Epigenetic modifiers, histone deacetylases (HDACs), are enzymes that remove acetyl groups from histones and play an important role in a variety of molecular processes, including pancreatic cell destiny, insulin release, insulin production, insulin signalling, and glucose metabolism. HDACs also govern other regulatory processes related to diabetes, such as oxidative stress, inflammation, apoptosis, and fibrosis, revealed by network and functional analysis. This review explains the current understanding of the function of HDACs in diabetic pathophysiology, the inhibitory role of various HDAC inhibitors (HDACi), and their functional importance as biomarkers and possible therapeutic targets for T2DM. While their role in T2DM is still emerging, a better understanding of the role of HDACi may be relevant in improving insulin sensitivity, protecting β-cells and reducing T2DM-associated complications, among others.
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Affiliation(s)
- Kukkala Kiran Kumar
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 15551, Al Ain, Abu Dhabi, United Arab Emirates
| | - Elhadi Husein Aburawi
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Milos Ljubisavljevic
- Department of Physiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
- Duke-NUS Medical School, Cardiovascular and Metabolic Disorders Program, Singapore, Singapore
| | - Melvin Khee Shing Leow
- LKC School of Medicine, Nanyang Technological University, Singapore, Singapore
- Dept of Endocrinology, Tan Tock Seng Hospital, Singapore, Singapore
- Duke-NUS Medical School, Cardiovascular and Metabolic Disorders Program, Singapore, Singapore
| | - Xu Feng
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - Suraiya Anjum Ansari
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
- ASPIRE Precision Medicine Research Institute, Abu Dhabi, United Arab Emirates
| | - Bright Starling Emerald
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 15551, Al Ain, Abu Dhabi, United Arab Emirates.
- Zayed Center for Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates.
- ASPIRE Precision Medicine Research Institute, Abu Dhabi, United Arab Emirates.
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4
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Castilho RM, Castilho LS, Palomares BH, Squarize CH. Determinants of Chromatin Organization in Aging and Cancer-Emerging Opportunities for Epigenetic Therapies and AI Technology. Genes (Basel) 2024; 15:710. [PMID: 38927646 PMCID: PMC11202709 DOI: 10.3390/genes15060710] [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: 03/31/2024] [Revised: 05/21/2024] [Accepted: 05/26/2024] [Indexed: 06/28/2024] Open
Abstract
This review article critically examines the pivotal role of chromatin organization in gene regulation, cellular differentiation, disease progression and aging. It explores the dynamic between the euchromatin and heterochromatin, coded by a complex array of histone modifications that orchestrate essential cellular processes. We discuss the pathological impacts of chromatin state misregulation, particularly in cancer and accelerated aging conditions such as progeroid syndromes, and highlight the innovative role of epigenetic therapies and artificial intelligence (AI) in comprehending and harnessing the histone code toward personalized medicine. In the context of aging, this review explores the use of AI and advanced machine learning (ML) algorithms to parse vast biological datasets, leading to the development of predictive models for epigenetic modifications and providing a framework for understanding complex regulatory mechanisms, such as those governing cell identity genes. It supports innovative platforms like CEFCIG for high-accuracy predictions and tools like GridGO for tailored ChIP-Seq analysis, which are vital for deciphering the epigenetic landscape. The review also casts a vision on the prospects of AI and ML in oncology, particularly in the personalization of cancer therapy, including early diagnostics and treatment optimization for diseases like head and neck and colorectal cancers by harnessing computational methods, AI advancements and integrated clinical data for a transformative impact on healthcare outcomes.
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Affiliation(s)
- Rogerio M. Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA; (L.S.C.); (C.H.S.)
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109-1078, USA
| | - Leonard S. Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA; (L.S.C.); (C.H.S.)
| | - Bruna H. Palomares
- Oral Diagnosis Department, Piracicaba School of Dentistry, State University of Campinas, Piracicaba 13414-903, Sao Paulo, Brazil;
| | - Cristiane H. Squarize
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA; (L.S.C.); (C.H.S.)
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109-1078, USA
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5
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Curcio A, Rocca R, Alcaro S, Artese A. The Histone Deacetylase Family: Structural Features and Application of Combined Computational Methods. Pharmaceuticals (Basel) 2024; 17:620. [PMID: 38794190 PMCID: PMC11124352 DOI: 10.3390/ph17050620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Histone deacetylases (HDACs) are crucial in gene transcription, removing acetyl groups from histones. They also influence the deacetylation of non-histone proteins, contributing to the regulation of various biological processes. Thus, HDACs play pivotal roles in various diseases, including cancer, neurodegenerative disorders, and inflammatory conditions, highlighting their potential as therapeutic targets. This paper reviews the structure and function of the four classes of human HDACs. While four HDAC inhibitors are currently available for treating hematological malignancies, numerous others are undergoing clinical trials. However, their non-selective toxicity necessitates ongoing research into safer and more efficient class-selective or isoform-selective inhibitors. Computational methods have aided the discovery of HDAC inhibitors with the desired potency and/or selectivity. These methods include ligand-based approaches, such as scaffold hopping, pharmacophore modeling, three-dimensional quantitative structure-activity relationships, and structure-based virtual screening (molecular docking). Moreover, recent developments in the field of molecular dynamics simulations, combined with Poisson-Boltzmann/molecular mechanics generalized Born surface area techniques, have improved the prediction of ligand binding affinity. In this review, we delve into the ways in which these methods have contributed to designing and identifying HDAC inhibitors.
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Affiliation(s)
- Antonio Curcio
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
| | - Roberta Rocca
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
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6
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Pozzo LD, Xu Z, Lin S, Wang J, Wang Y, Enechojo OS, Abankwah JK, Peng Y, Chu X, Zhou H, Bian Y. Role of epigenetics in the regulation of skin aging and geroprotective intervention: A new sight. Biomed Pharmacother 2024; 174:116592. [PMID: 38615608 DOI: 10.1016/j.biopha.2024.116592] [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: 02/15/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 04/16/2024] Open
Abstract
Multiple epigenetic factors play a regulatory role in maintaining the homeostasis of cutaneous components and are implicated in the aging process of the skin. They have been associated with the activation of the senescence program, which is the primary contributor to age-related decline in the skin. Senescent species drive a series of interconnected processes that impact the immediate surroundings, leading to structural changes, diminished functionality, and heightened vulnerability to infections. Geroprotective medicines that may restore the epigenetic balance represent valid therapeutic alliances against skin aging. Most of them are well-known Western medications such as metformin, nicotinamide adenine dinucleotide (NAD+), rapamycin, and histone deacetylase inhibitors, while others belong to Traditional Chinese Medicine (TCM) remedies for which the scientific literature provides limited information. With the help of the Geroprotectors.org database and a comprehensive analysis of the referenced literature, we have compiled data on compounds and formulae that have shown potential in preventing skin aging and have been identified as epigenetic modulators.
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Affiliation(s)
- Lisa Dal Pozzo
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zhe Xu
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Shan Lin
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jida Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Ying Wang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Ogbe Susan Enechojo
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Joseph Kofi Abankwah
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yanfei Peng
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xiaoqian Chu
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Huifang Zhou
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Yuhong Bian
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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7
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Olaniyi KS, Areloegbe SE. Acetate ameliorates ovarian mitochondrial dysfunction in letrozole-induced polycystic ovarian syndrome rat model by improving mitofusin-2. J Physiol Sci 2024; 74:22. [PMID: 38561673 PMCID: PMC10983676 DOI: 10.1186/s12576-024-00908-5] [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: 12/07/2023] [Accepted: 02/23/2024] [Indexed: 04/04/2024]
Abstract
Androgen excess and metabolic abnormality largely contribute to the pathogenesis of polycystic ovarian syndrome (PCOS), which primarily precipitates ovarian dysfunction and infertility in reproductive-age women. Impaired mitochondrial function and epigenetic alteration have been linked to the development of PCOS. However, it is unknown whether acetate would exert a therapeutic effect on ovarian mitochondrial dysfunction in PCOS. Herein, the study hypothesized that acetate reverses ovarian mitochondrial dysfunction in experimental PCOS rat model, possibly through modulation of mitofusin-2 (MFn2). Eight-week-old female Wistar rats were randomized into four groups (n = 5). Induction of PCOS was performed by 1 mg/kg letrozole (p.o.), administered for 21 days. Thereafter, the rats were treated with acetate (200 mg/kg; p.o.) for 6 weeks. The PCOS rats demonstrated androgen excess, multiple ovarian cysts, elevated anti-mullerian hormone and leptin and decreased SHBG, adiponectin and 17-β estradiol with corresponding increase in ovarian transforming growth factor-β1. Additionally, inflammation (tumor growth factor and nuclear factor-kB), elevated caspase-6, decreased hypoxia-inducible factor-1α and elevated histone deacetylase-2 (HDAC2) were observed in the ovaries of PCOS rats, while mitochondrial abnormality with evidence of decreased adenosine triphosphate synthase and MFn2 was observed in rats with PCOS. Treatment with acetate reversed the alterations. The present results collectively suggest that acetate ameliorates ovarian mitochondrial abnormality, a beneficial effect that is accompanied by MFn2 with consequent normalization of reproductive-endocrine profile and ovarian function. Perhaps, the present data provide hope for PCOS individuals that suffer infertility.
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Affiliation(s)
- Kehinde S Olaniyi
- Cardio/Endo-metabolic and Microbiome Research Unit, Department of Physiology, College of Medicine and Health Sciences, Afe Babalola University, P.M.B. 5454, Ado-Ekiti, 360101, Nigeria.
| | - Stephanie E Areloegbe
- Cardio/Endo-metabolic and Microbiome Research Unit, Department of Physiology, College of Medicine and Health Sciences, Afe Babalola University, P.M.B. 5454, Ado-Ekiti, 360101, Nigeria
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8
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Jagaraj CJ, Shadfar S, Kashani SA, Saravanabavan S, Farzana F, Atkin JD. Molecular hallmarks of ageing in amyotrophic lateral sclerosis. Cell Mol Life Sci 2024; 81:111. [PMID: 38430277 PMCID: PMC10908642 DOI: 10.1007/s00018-024-05164-9] [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: 12/05/2023] [Revised: 01/21/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal, severely debilitating and rapidly progressing disorder affecting motor neurons in the brain, brainstem, and spinal cord. Unfortunately, there are few effective treatments, thus there remains a critical need to find novel interventions that can mitigate against its effects. Whilst the aetiology of ALS remains unclear, ageing is the major risk factor. Ageing is a slowly progressive process marked by functional decline of an organism over its lifespan. However, it remains unclear how ageing promotes the risk of ALS. At the molecular and cellular level there are specific hallmarks characteristic of normal ageing. These hallmarks are highly inter-related and overlap significantly with each other. Moreover, whilst ageing is a normal process, there are striking similarities at the molecular level between these factors and neurodegeneration in ALS. Nine ageing hallmarks were originally proposed: genomic instability, loss of telomeres, senescence, epigenetic modifications, dysregulated nutrient sensing, loss of proteostasis, mitochondrial dysfunction, stem cell exhaustion, and altered inter-cellular communication. However, these were recently (2023) expanded to include dysregulation of autophagy, inflammation and dysbiosis. Hence, given the latest updates to these hallmarks, and their close association to disease processes in ALS, a new examination of their relationship to pathophysiology is warranted. In this review, we describe possible mechanisms by which normal ageing impacts on neurodegenerative mechanisms implicated in ALS, and new therapeutic interventions that may arise from this.
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Affiliation(s)
- Cyril Jones Jagaraj
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Sina Shadfar
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Sara Assar Kashani
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Sayanthooran Saravanabavan
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Fabiha Farzana
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Julie D Atkin
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia.
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9
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Pereira B, Correia FP, Alves IA, Costa M, Gameiro M, Martins AP, Saraiva JA. Epigenetic reprogramming as a key to reverse ageing and increase longevity. Ageing Res Rev 2024; 95:102204. [PMID: 38272265 DOI: 10.1016/j.arr.2024.102204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/18/2023] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
The pursuit for the fountain of youth has long been a fascination amongst scientists and humanity. Ageing is broadly characterized by a cellular decline with increased susceptibility to age-related diseases, being intimately associated with epigenetic modifications. Recently, reprogramming-induced rejuvenation strategies have begun to greatly alter longevity research not only to tackle age-related defects but also to possibly reverse the cellular ageing process. Hence, in this review, we highlight the major epigenetic changes during ageing and the state-of-art of the current emerging epigenetic reprogramming strategies leveraging on transcription factors. Notably, partial reprogramming enables the resetting of the ageing clock without erasing cellular identity. Promising chemical-based rejuvenation strategies harnessing small molecules, including DNA methyltransferase and histone deacetylase inhibitors are also discussed. Moreover, in parallel to longevity interventions, the foundations of epigenetic clocks for accurate ageing assessment and evaluation of reprogramming approaches are briefly presented. Going further, with such scientific breakthroughs, we are witnessing a rise in the longevity biotech industry aiming to extend the health span and ideally achieve human rejuvenation one day. In this context, we overview the main scenarios proposed for the future of the socio-economic and ethical challenges associated with such an emerging field. Ultimately, this review aims to inspire future research on interventions that promote healthy ageing for all.
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Affiliation(s)
- Beatriz Pereira
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | | | - Inês A Alves
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Margarida Costa
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Mariana Gameiro
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Ana P Martins
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Jorge A Saraiva
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal.
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10
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Tammaro A, Daniels EG, Hu IM, ‘t Hart KC, Reid K, Juni RP, Butter LM, Vasam G, Kamble R, Jongejan A, Aviv RI, Roelofs JJ, Aronica E, Boon RA, Menzies KJ, Houtkooper RH, Janssens GE. HDAC1/2 inhibitor therapy improves multiple organ systems in aged mice. iScience 2024; 27:108681. [PMID: 38269100 PMCID: PMC10805681 DOI: 10.1016/j.isci.2023.108681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/25/2023] [Accepted: 12/05/2023] [Indexed: 01/26/2024] Open
Abstract
Aging increases the risk of age-related diseases, imposing substantial healthcare and personal costs. Targeting fundamental aging mechanisms pharmacologically can promote healthy aging and reduce this disease susceptibility. In this work, we employed transcriptome-based drug screening to identify compounds emulating transcriptional signatures of long-lived genetic interventions. We discovered compound 60 (Cmpd60), a selective histone deacetylase 1 and 2 (HDAC1/2) inhibitor, mimicking diverse longevity interventions. In extensive molecular, phenotypic, and bioinformatic assessments using various cell and aged mouse models, we found Cmpd60 treatment to improve age-related phenotypes in multiple organs. Cmpd60 reduces renal epithelial-mesenchymal transition and fibrosis in kidney, diminishes dementia-related gene expression in brain, and enhances cardiac contractility and relaxation for the heart. In sum, our two-week HDAC1/2 inhibitor treatment in aged mice establishes a multi-tissue, healthy aging intervention in mammals, holding promise for therapeutic translation to promote healthy aging in humans.
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Affiliation(s)
- Alessandra Tammaro
- Amsterdam UMC location University of Amsterdam, Department of Pathology, Amsterdam Infection & Immunity, Amsterdam, the Netherlands
| | - Eileen G. Daniels
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology and Metabolism Institute, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Iman M. Hu
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology and Metabolism Institute, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Kelly C. ‘t Hart
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology and Metabolism Institute, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Kim Reid
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Rio P. Juni
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Loes M. Butter
- Amsterdam UMC location University of Amsterdam, Department of Pathology, Amsterdam Infection & Immunity, Amsterdam, the Netherlands
| | - Goutham Vasam
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Rashmi Kamble
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Aldo Jongejan
- Deptartment of Epidemiology & Data Science (EDS), Bioinformatics Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Richard I. Aviv
- Department of Medical Imaging, The Ottawa Hospital, 1053 Carling Ave, Ottawa, ON K1Y 4E9, Canada
- Department of Radiology, University of Ottawa, Ottawa, ON, Canada
| | - Joris J.T.H. Roelofs
- Amsterdam UMC location University of Amsterdam, Department of Pathology, Amsterdam Infection & Immunity, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Reinier A. Boon
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Keir J. Menzies
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Riekelt H. Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology and Metabolism Institute, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Georges E. Janssens
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology and Metabolism Institute, Amsterdam University Medical Centers, Amsterdam, the Netherlands
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11
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Yang H, Hur G, Lee TK, Kim JE, Kim JH, Kim JR, Kim J, Park JHY, Lee KW. Sulforaphane Mitigates High-Fat Diet-Induced Obesity by Enhancing Mitochondrial Biogenesis in Skeletal Muscle via the HDAC8-PGC1α Axis. Mol Nutr Food Res 2023; 67:e2300149. [PMID: 37775334 DOI: 10.1002/mnfr.202300149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/13/2023] [Indexed: 10/01/2023]
Abstract
SCOPE Histone deacetylases (HDACs) play a crucial role in the transcriptional regulation of various genes which can contribute to metabolic disorders. Although sulforaphane (SFN), a natural HDAC inhibitor, has been reported to alleviate obesity in humans and mice, the specific mechanisms and how HDACs contribute to SFN's anti-obesity effects remain unclear. METHODS AND RESULTS Oral administration of SFN in mice fed high-fat diet increases peroxisome proliferator activating receptor γ coactivator (PGC1α)-induced mitochondrial biogenesis in skeletal muscle. Among HDACs, SFN specifically inhibits HDAC8 activity. SFN enhances mitochondrial DNA and adenosine triphosphate (ATP) production in C2C12 myotubes, similar to the action of PCI34051, a synthetic HDAC8-specific inhibitor. These effects are mediated by increased expression of PGC1α via upregulation of cAMP response element binding (CREB, Ser133 ) phosphorylation and p53 (Lys379 ) acetylation. These SFN-induced effects are not observed in cells with a genetic deletion of HDAC8, suggesting the existence of a regulatory loop between HDAC8 and PGC1α in SFN's action. CONCLUSION SFN prevents obesity-related metabolic dysregulation by enhancing mitochondrial biogenesis and function via targeting the HDAC8-PGCα axis. These results suggest SFN as a beneficial anti-obesity agent providing new insight into the role of HDAC8 in the PGC1α-mediated mitochondrial biogenesis, which may be a novel and promising drug target for metabolic diseases.
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Affiliation(s)
- Hee Yang
- Department of Food and Nutrition, Kookmin University, 77 Jeongneung-ro, Seongbuk-gu, Seoul, 02707, South Korea
| | - Gihyun Hur
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Tae Kyung Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jong-Eun Kim
- Department of Food Science and Technology, Korea National University of Transportation, Jeungpyeong, Republic of Korea
| | - Jong Hun Kim
- Department of Food Science and Biotechnology, Sungshin University, Seoul, 01133, Republic of Korea
- Basic Science Research Institute, Sungshin University, Seoul, 01133, Republic of Korea
| | - Jong Rhan Kim
- R&D Evaluation Center, Korea Institute of Science and Technology Evaluation and Planning, 1339 Eumseong-gun, Chungcheongbuk-do, Republic of Korea
| | - Jiyoung Kim
- Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Republic of Korea
| | | | - Ki Won Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
- Bio-MAX Institute, Seoul National University, Seoul, 08826, South Korea
- Advanced Institute of Convergence Technology, Seoul National University, Suwon, 16229, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Institutes of Green Bio Science & Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Republic of Korea
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12
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Nevi L, Pöllänen N, Penna F, Caretti G. Targeting Epigenetic Regulators with HDAC and BET Inhibitors to Modulate Muscle Wasting. Int J Mol Sci 2023; 24:16404. [PMID: 38003594 PMCID: PMC10671811 DOI: 10.3390/ijms242216404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Epigenetic changes contribute to the profound alteration in the transcriptional program associated with the onset and progression of muscle wasting in several pathological conditions. Although HDACs and their inhibitors have been extensively studied in the field of muscular dystrophies, the potential of epigenetic inhibitors has only been marginally explored in other disorders associated with muscle atrophy, such as in cancer cachexia and sarcopenia. BET inhibitors represent a novel class of recently developed epigenetic drugs that display beneficial effects in a variety of diseases beyond malignancies. Based on the preliminary in vitro and preclinical data, HDACs and BET proteins contribute to the pathogenesis of cancer cachexia and sarcopenia, modulating processes related to skeletal muscle mass maintenance and/or metabolism. Thus, epigenetic drugs targeting HDACs and BET proteins may emerge as promising strategies to reverse the catabolic phenotype associated with cachexia and sarcopenia. Further preclinical studies are warranted to delve deeper into the molecular mechanisms associated with the functions of HDACs and BET proteins in muscle atrophy and to establish whether their epigenetic inhibitors represent a prospective therapeutic avenue to alleviate muscle wasting.
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Affiliation(s)
- Lorenzo Nevi
- Department of Biosciences, University of Milan, 20133 Milan, Italy;
| | - Noora Pöllänen
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Fabio Penna
- Department of Clinical and Biological Sciences, University of Torino, 10125 Torino, Italy
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13
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Jain A, Casanova D, Padilla AV, Paniagua Bojorges A, Kotla S, Ko KA, Samanthapudi VSK, Chau K, Nguyen MTH, Wen J, Hernandez Gonzalez SL, Rodgers SP, Olmsted-Davis EA, Hamilton DJ, Reyes-Gibby C, Yeung SCJ, Cooke JP, Herrmann J, Chini EN, Xu X, Yusuf SW, Yoshimoto M, Lorenzi PL, Hobbs B, Krishnan S, Koutroumpakis E, Palaskas NL, Wang G, Deswal A, Lin SH, Abe JI, Le NT. Premature senescence and cardiovascular disease following cancer treatments: mechanistic insights. Front Cardiovasc Med 2023; 10:1212174. [PMID: 37781317 PMCID: PMC10540075 DOI: 10.3389/fcvm.2023.1212174] [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: 04/25/2023] [Accepted: 08/03/2023] [Indexed: 10/03/2023] Open
Abstract
Cardiovascular disease (CVD) is a leading cause of morbidity and mortality, especially among the aging population. The "response-to-injury" model proposed by Dr. Russell Ross in 1999 emphasizes inflammation as a critical factor in atherosclerosis development, with atherosclerotic plaques forming due to endothelial cell (EC) injury, followed by myeloid cell adhesion and invasion into the blood vessel walls. Recent evidence indicates that cancer and its treatments can lead to long-term complications, including CVD. Cellular senescence, a hallmark of aging, is implicated in CVD pathogenesis, particularly in cancer survivors. However, the precise mechanisms linking premature senescence to CVD in cancer survivors remain poorly understood. This article aims to provide mechanistic insights into this association and propose future directions to better comprehend this complex interplay.
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Affiliation(s)
- Ashita Jain
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Diego Casanova
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | | | - Sivareddy Kotla
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Kyung Ae Ko
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | - Khanh Chau
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
| | - Minh T. H. Nguyen
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
| | - Jake Wen
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | - Shaefali P. Rodgers
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
| | | | - Dale J. Hamilton
- Department of Medicine, Center for Bioenergetics, Houston Methodist Research Institute, Houston, TX, United States
| | - Cielito Reyes-Gibby
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Sai-Ching J. Yeung
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - John P. Cooke
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
| | - Joerg Herrmann
- Cardio Oncology Clinic, Division of Preventive Cardiology, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, United States
| | - Eduardo N. Chini
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Jacksonville, FL, United States
| | - Xiaolei Xu
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, United States
| | - Syed Wamique Yusuf
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Momoko Yoshimoto
- Center for Stem Cell & Regenerative Medicine, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Philip L. Lorenzi
- Department of Bioinformatics and Computational Biology, Division of VP Research, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Brain Hobbs
- Department of Population Health, The University of Texas at Austin, Austin, TX, United States
| | - Sunil Krishnan
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Efstratios Koutroumpakis
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Nicolas L. Palaskas
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Guangyu Wang
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
| | - Anita Deswal
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Steven H. Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jun-ichi Abe
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Nhat-Tu Le
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
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14
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Wang H, Zhang Y, Wang Z, Zhang L, Guo M, Cao C, Xiao H. Deciphering Nucleic Acid Binding Proteome of Mouse Immune Organs Reveals Hub Proteins for Aging. Mol Cell Proteomics 2023; 22:100611. [PMID: 37391046 PMCID: PMC10412848 DOI: 10.1016/j.mcpro.2023.100611] [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: 02/23/2023] [Revised: 05/24/2023] [Accepted: 06/26/2023] [Indexed: 07/02/2023] Open
Abstract
Profiling the nucleic acid-binding proteins (NABPs) during aging process is critical to elucidate its roles in biological systems as well as transcriptional and translational regulation. Here, we developed a comprehensive strategy to survey the NABPs of mouse immune organs by using single cell preparation and selective capture technology-based proteomics. Our approach provided a global view of tissue NABPs from different organs under normal physiological conditions with extraction specificity of 70 to 90%. Through quantitative proteomics analysis of mouse spleen and thymus at 1, 4, 12, 24, 48, and 72 weeks, we investigated the molecular features of aging-related NABPs. A total of 2674 proteins were quantified in all six stages, demonstrating distinct and time-specific expression pattern of NABPs. Thymus and spleen exhibited unique aging signatures, and differential proteins and pathways were enriched across the mouse lifespan. Three core modules and 16 hub proteins associated with aging were revealed through weighted gene correlation network analysis. Significant candidates were screened for immunoassay verification, and six hub proteins were confirmed. The integrated strategy pertains the capability to decipher the dynamic functions of NABPs in aging physiology and benefit further mechanism research.
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Affiliation(s)
- Huiyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Zeyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lu Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Miao Guo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chengxi Cao
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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15
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Bazan N, Bhattacharjee S, Kala-Bhattacharjee S, Ledet A, Mukherjee P. Elovanoids are neural resiliency epigenomic regulators targeting histone modifications, DNA methylation, tau phosphorylation, telomere integrity, senescence programming, and dendrite integrity. RESEARCH SQUARE 2023:rs.3.rs-3185942. [PMID: 37502897 PMCID: PMC10371143 DOI: 10.21203/rs.3.rs-3185942/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Cellular identity, developmental reorganization, genomic structure modulation, and susceptibility to diseases are determined by epigenomic regulation by multiple signaling interplay. Here we demonstrate that elovanoids (ELVs), mediators derived from very-long-chain polyunsaturated fatty acids (VLC-PUFAs, n-3, C > 28), and their precursors in neurons in culture overcome the damage triggered by oligomeric amyloid-beta (OAβ), erastin (ferroptosis-dependent cell death), or other insults that target epigenomic signaling. We uncover that ELVs counteract damage targeting histones H3K9 and H3K27 methylation and acetylation; tau hyperphosphorylation (pThr181, pThr217, pThr231, and pSer202/pThr205 (AT8)); senescence gene programming (p16INK4a, p27KIP, p21CIP1, and p53); DNA methylation (DNAm) modifying enzymes: TET (DNA hydroxymethylase), DNA methyltransferase, DNA demethylase, and DNAm (5mC) phenotype. Moreover, ELVs revert OAβ-triggered telomere length (TL) attrition as well as upregulation of telomerase reverse transcriptase (TERT) expression fostering dendrite protection and neuronal survival. Thus, ELVs modulate epigenomic resiliency by pleiotropic interrelated signaling.
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16
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Islam R, Dash D, Singh R. An antioxidant ameliorates allergic airway inflammation by inhibiting HDAC 1 via HIF-1α/VEGF axis suppression in mice. Sci Rep 2023; 13:9637. [PMID: 37316684 DOI: 10.1038/s41598-023-36678-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023] Open
Abstract
Histone deacetylase inhibitors (HDACi) are novel class of drugs as they are involved in post translational modification of several proteins involved in signaling pathways related to asthma. HDACi have been reported to elicit protective effects on asthma but the signaling pathways associated with it have not been investigated much. Recently, we have demonstrated that intranasal administrations of Pan-HDAC inhibitors, sodium butyrate and curcumin, which have effectively reduced asthma severity via HDAC1 inhibition in Ovalbumin induced mouse model. Present study aimed to investigate possible pathways by which curcumin and sodium butyrate may minimize asthma pathogenesis via HDAC 1 inhibition. Balb/c mice were exposed (sensitized and challenged) with Ovalbumin to establish allergic asthma model followed by pretreatment of curcumin (5 mg/kg) and sodium butyrate (50 mg/kg) through intranasal route. Effects of curcumin and sodium butyrate on HIF-1α/VEGF signaling through activation of PI3K/Akt axis has been investigated using protein expressions followed by chromatin immunoprecipitation of BCL2 and CCL2 against HDAC1. Molecular docking analysis was also performed to investigate effects of curcumin and butyrate on mucus hypersecretion, goblet cell hyperplasia and airway hyperresponsiveness. Augmented expressions of HDAC-1, HIF-1α, VEGF, p-Akt and p-PI3K were observed in asthmatic group which was suppressed in both the treatments. NRF-2 level was significantly restored by curcumin and butyrate treatments. Protein expressions of p-p38, IL-5 and mRNA expressions of GATA-3 were also reduced in curcumin and butyrate treatment groups. Our findings suggest that curcumin and sodium butyrate may attenuate airway inflammation via down regulation of p-Akt/p-PI3K/HIF-1α/VEGF axis.
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Affiliation(s)
- Ramiya Islam
- Department of Zoology, MMV, Banaras Hindu University, Varanasi, 221005, India
| | - D Dash
- Department of Biochemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Rashmi Singh
- Department of Biochemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India.
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17
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Peters JD, Peters MP, Bradshaw PC. Nicotinamide riboside functions during development while beta-hydroxybutyrate functions during adulthood to extend C. elegans lifespan. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000841. [PMID: 37325193 PMCID: PMC10267727 DOI: 10.17912/micropub.biology.000841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/24/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023]
Abstract
Nicotinamide riboside (NR), a form of vitamin B3 and a nicotinamide adenine dinucleotide (NAD + ) precursor, has been shown to activate the mitochondrial unfolded protein response (UPR mt ) and extend the lifespan when supplemented to C. elegans. The ketone body and histone deacetylase (HDAC) inhibitor beta-hydroxybutyrate (BHB) has also been shown to extend C. elegans lifespan. Experiments were performed that showed that NR extended lifespan by acting almost exclusively during larval development, while BHB extended lifespan by acting during adulthood, and the combination of NR during development and BHB during adulthood unexpectedly decreased lifespan. This suggests that hormesis is involved in the lifespan-altering effects of BHB and NR and that they are inducing parallel longevity pathways that converge on a common downstream target.
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Affiliation(s)
- J. Dylan Peters
- James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee, USA
| | | | - Patrick C. Bradshaw
- Department of Biomedical Sciences, East Tennessee State University, Johnson City, Tennessee, USA
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18
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Shen C, Li M, Duan Y, Jiang X, Hou X, Xue F, Zhang Y, Luo Y. HDAC inhibitors enhance the anti-tumor effect of immunotherapies in hepatocellular carcinoma. Front Immunol 2023; 14:1170207. [PMID: 37304265 PMCID: PMC10250615 DOI: 10.3389/fimmu.2023.1170207] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023] Open
Abstract
Hepatocellular carcinoma (HCC), the most common liver malignancy with a poor prognosis and increasing incidence, remains a serious health problem worldwide. Immunotherapy has been described as one of the ideal ways to treat HCC and is transforming patient management. However, the occurrence of immunotherapy resistance still prevents some patients from benefiting from current immunotherapies. Recent studies have shown that histone deacetylase inhibitors (HDACis) can enhance the efficacy of immunotherapy in a variety of tumors, including HCC. In this review, we present current knowledge and recent advances in immunotherapy-based and HDACi-based therapies for HCC. We highlight the fundamental dynamics of synergies between immunotherapies and HDACis, further detailing current efforts to translate this knowledge into clinical benefits. In addition, we explored the possibility of nano-based drug delivery system (NDDS) as a novel strategy to enhance HCC treatment.
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Affiliation(s)
- Chen Shen
- Department of Laboratory Medicine, Medical Equipment Innovation Research Center/Medical Device Regulatory Research and Evaluation Center, West China Hospital, Sichuan University, Chengdu, China
| | - Mei Li
- Department of Laboratory Medicine, Medical Equipment Innovation Research Center/Medical Device Regulatory Research and Evaluation Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yujuan Duan
- School of Chemical Science and Engineering, Tongji University, Shanghai, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Jiang
- Department of Laboratory Medicine, Medical Equipment Innovation Research Center/Medical Device Regulatory Research and Evaluation Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoming Hou
- Department of Laboratory Medicine, Medical Equipment Innovation Research Center/Medical Device Regulatory Research and Evaluation Center, West China Hospital, Sichuan University, Chengdu, China
| | - Fulai Xue
- Department of Laboratory Medicine, Medical Equipment Innovation Research Center/Medical Device Regulatory Research and Evaluation Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yinan Zhang
- School of Chemical Science and Engineering, Tongji University, Shanghai, China
| | - Yao Luo
- Department of Laboratory Medicine, Medical Equipment Innovation Research Center/Medical Device Regulatory Research and Evaluation Center, West China Hospital, Sichuan University, Chengdu, China
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19
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Liang S, Liu D, Xiao Z, Greenbaum J, Shen H, Xiao H, Deng H. Repurposing Approved Drugs for Sarcopenia Based on Transcriptomics Data in Humans. Pharmaceuticals (Basel) 2023; 16:ph16040607. [PMID: 37111364 PMCID: PMC10145476 DOI: 10.3390/ph16040607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/31/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Sarcopenia, characterized by age-related loss of muscle mass, strength, and decreased physical performance, is a growing public health challenge amid the rapidly ageing population. As there are no approved drugs that target sarcopenia, it has become increasingly urgent to identify promising pharmacological interventions. In this study, we conducted an integrative drug repurposing analysis utilizing three distinct approaches. Firstly, we analyzed skeletal muscle transcriptomic sequencing data in humans and mice using gene differential expression analysis, weighted gene co-expression analysis, and gene set enrichment analysis. Subsequently, we employed gene expression profile similarity assessment, hub gene expression reversal, and disease-related pathway enrichment to identify and repurpose candidate drugs, followed by the integration of findings with rank aggregation algorithms. Vorinostat, the top-ranking drug, was also validated in an in vitro study, which demonstrated its efficacy in promoting muscle fiber formation. Although still requiring further validation in animal models and human clinical trials, these results suggest a promising drug repurposing prospect in the treatment and prevention of sarcopenia.
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Affiliation(s)
- Shuang Liang
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Danyang Liu
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha 410013, China
| | - Zhengwu Xiao
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Jonathan Greenbaum
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA 999039, USA
| | - Hui Shen
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA 999039, USA
| | - Hongmei Xiao
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Hongwen Deng
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA 999039, USA
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20
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Zhao L, Liang Q, He Y, Liu M, Tong R, Jiang Z, Wang W, Shi J. HDAC/JAK dual target inhibitors of cancer-related targets: The success of nonclearable linked pharmacophore mode. Bioorg Chem 2022; 129:106181. [DOI: 10.1016/j.bioorg.2022.106181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/18/2022] [Accepted: 09/25/2022] [Indexed: 11/24/2022]
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21
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Epigenetic regulation of aging: implications for interventions of aging and diseases. Signal Transduct Target Ther 2022; 7:374. [PMID: 36336680 PMCID: PMC9637765 DOI: 10.1038/s41392-022-01211-8] [Citation(s) in RCA: 127] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022] Open
Abstract
Aging is accompanied by the decline of organismal functions and a series of prominent hallmarks, including genetic and epigenetic alterations. These aging-associated epigenetic changes include DNA methylation, histone modification, chromatin remodeling, non-coding RNA (ncRNA) regulation, and RNA modification, all of which participate in the regulation of the aging process, and hence contribute to aging-related diseases. Therefore, understanding the epigenetic mechanisms in aging will provide new avenues to develop strategies to delay aging. Indeed, aging interventions based on manipulating epigenetic mechanisms have led to the alleviation of aging or the extension of the lifespan in animal models. Small molecule-based therapies and reprogramming strategies that enable epigenetic rejuvenation have been developed for ameliorating or reversing aging-related conditions. In addition, adopting health-promoting activities, such as caloric restriction, exercise, and calibrating circadian rhythm, has been demonstrated to delay aging. Furthermore, various clinical trials for aging intervention are ongoing, providing more evidence of the safety and efficacy of these therapies. Here, we review recent work on the epigenetic regulation of aging and outline the advances in intervention strategies for aging and age-associated diseases. A better understanding of the critical roles of epigenetics in the aging process will lead to more clinical advances in the prevention of human aging and therapy of aging-related diseases.
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22
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Therapeutic Antiaging Strategies. Biomedicines 2022; 10:biomedicines10102515. [PMID: 36289777 PMCID: PMC9599338 DOI: 10.3390/biomedicines10102515] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/21/2022] [Accepted: 09/24/2022] [Indexed: 11/17/2022] Open
Abstract
Aging constitutes progressive physiological changes in an organism. These changes alter the normal biological functions, such as the ability to manage metabolic stress, and eventually lead to cellular senescence. The process itself is characterized by nine hallmarks: genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, and altered intercellular communication. These hallmarks are risk factors for pathologies, such as cardiovascular diseases, neurodegenerative diseases, and cancer. Emerging evidence has been focused on examining the genetic pathways and biological processes in organisms surrounding these nine hallmarks. From here, the therapeutic approaches can be addressed in hopes of slowing the progression of aging. In this review, data have been collected on the hallmarks and their relative contributions to aging and supplemented with in vitro and in vivo antiaging research experiments. It is the intention of this article to highlight the most important antiaging strategies that researchers have proposed, including preventive measures, systemic therapeutic agents, and invasive procedures, that will promote healthy aging and increase human life expectancy with decreased side effects.
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Auzmendi-Iriarte J, Moreno-Cugnon L, Saenz-Antoñanzas A, Grassi D, de Pancorbo MM, Arevalo MA, Wood IC, Matheu A. High levels of HDAC expression correlate with microglial aging. Expert Opin Ther Targets 2022; 26:911-922. [PMID: 36503367 DOI: 10.1080/14728222.2022.2158081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Cellular damage gradually accumulates with aging, promoting a time-dependent functional decline of the brain. Microglia play an essential regulatory role in maintaining cognitive activity by phagocytosing cell debris and apoptotic cells during neurogenesis. The activities of different histone deacetylases (HDACs) regulate microglial function during development and neurodegeneration. However, no studies have described the role of HDACs in microglia during physiological aging. RESEARCH DESIGN AND METHODS HDAC and microglial marker levels were examined in microglial cells after inducing senescence in vitro and in mouse and human hippocampal biopsies in vivo, using quantitative real-time PCR. Publicly available datasets were used to determine HDAC expression in different brain areas during physiological aging. RESULTS HDAC expression increased upon the induction of senescence with bleomycin or serial passage in microglial cultures. High levels of HDACs were detected in mice and aged human brain samples. Human hippocampal samples showed a positive correlation between the expression of HDAC1, 3, and 7 and microglial and senescence markers. HDAC1 and 3 levels are enriched in the purified aged microglial population. CONCLUSIONS Several HDACs, particularly HDAC1, are elevated in microglia upon senescence induction in vitro and with aging in vivo, and correlate with microglial and senescence biomarkers.
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Affiliation(s)
| | - Leire Moreno-Cugnon
- Cellular Oncology Group, Biodonostia Health Research Institute, San Sebastian, Spain
| | | | - Daniela Grassi
- Department of Anatomy, Histology and Neuroscience, Autonoma University of Madrid, Madrid, Spain.,Consejo Superior de Investigaciones Científicas (CSIC), Instituto Cajal, Madrid, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country, Vitoria, Spain
| | - Maria-Angeles Arevalo
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto Cajal, Madrid, Spain.,CIBER de Fragilidad y Envejecimiento Saludable (CIBERfes), Madrid, Spain
| | - Ian C Wood
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Ander Matheu
- Cellular Oncology Group, Biodonostia Health Research Institute, San Sebastian, Spain.,CIBER de Fragilidad y Envejecimiento Saludable (CIBERfes), Madrid, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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24
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Jeon M, Xie Z, Evangelista JE, Wojciechowicz ML, Clarke DJB, Ma’ayan A. Transforming L1000 profiles to RNA-seq-like profiles with deep learning. BMC Bioinformatics 2022; 23:374. [PMID: 36100892 PMCID: PMC9472394 DOI: 10.1186/s12859-022-04895-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/17/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractThe L1000 technology, a cost-effective high-throughput transcriptomics technology, has been applied to profile a collection of human cell lines for their gene expression response to > 30,000 chemical and genetic perturbations. In total, there are currently over 3 million available L1000 profiles. Such a dataset is invaluable for the discovery of drug and target candidates and for inferring mechanisms of action for small molecules. The L1000 assay only measures the mRNA expression of 978 landmark genes while 11,350 additional genes are computationally reliably inferred. The lack of full genome coverage limits knowledge discovery for half of the human protein coding genes, and the potential for integration with other transcriptomics profiling data. Here we present a Deep Learning two-step model that transforms L1000 profiles to RNA-seq-like profiles. The input to the model are the measured 978 landmark genes while the output is a vector of 23,614 RNA-seq-like gene expression profiles. The model first transforms the landmark genes into RNA-seq-like 978 gene profiles using a modified CycleGAN model applied to unpaired data. The transformed 978 RNA-seq-like landmark genes are then extrapolated into the full genome space with a fully connected neural network model. The two-step model achieves 0.914 Pearson’s correlation coefficients and 1.167 root mean square errors when tested on a published paired L1000/RNA-seq dataset produced by the LINCS and GTEx programs. The processed RNA-seq-like profiles are made available for download, signature search, and gene centric reverse search with unique case studies.
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25
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Abbotto E, Scarano N, Piacente F, Millo E, Cichero E, Bruzzone S. Virtual Screening in the Identification of Sirtuins’ Activity Modulators. Molecules 2022; 27:molecules27175641. [PMID: 36080416 PMCID: PMC9457788 DOI: 10.3390/molecules27175641] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
Sirtuins are NAD+-dependent deac(et)ylases with different subcellular localization. The sirtuins’ family is composed of seven members, named SIRT-1 to SIRT-7. Their substrates include histones and also an increasing number of different proteins. Sirtuins regulate a wide range of different processes, ranging from transcription to metabolism to genome stability. Thus, their dysregulation has been related to the pathogenesis of different diseases. In this review, we discussed the pharmacological approaches based on sirtuins’ modulators (both inhibitors and activators) that have been attempted in in vitro and/or in in vivo experimental settings, to highlight the therapeutic potential of targeting one/more specific sirtuin isoform(s) in cancer, neurodegenerative disorders and type 2 diabetes. Extensive research has already been performed to identify SIRT-1 and -2 modulators, while compounds targeting the other sirtuins have been less studied so far. Beside sections dedicated to each sirtuin, in the present review we also included sections dedicated to pan-sirtuins’ and to parasitic sirtuins’ modulators. A special focus is dedicated to the sirtuins’ modulators identified by the use of virtual screening.
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Affiliation(s)
- Elena Abbotto
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy
| | - Naomi Scarano
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Francesco Piacente
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy
| | - Enrico Millo
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy
| | - Elena Cichero
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Santina Bruzzone
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy
- Correspondence:
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26
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Goo B, Ahmadieh S, Zarzour A, Yiew NKH, Kim D, Shi H, Greenway J, Cave S, Nguyen J, Aribindi S, Wendolowski M, Veerapaneni P, Ogbi M, Chen W, Lei Y, Lu XY, Kim HW, Weintraub NL. Sex-Dependent Role of Adipose Tissue HDAC9 in Diet-Induced Obesity and Metabolic Dysfunction. Cells 2022; 11:2698. [PMID: 36078104 PMCID: PMC9454798 DOI: 10.3390/cells11172698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Obesity is a major risk factor for both metabolic and cardiovascular disease. We reported that, in obese male mice, histone deacetylase 9 (HDAC9) is upregulated in adipose tissues, and global deletion of HDAC9 protected against high fat diet (HFD)-induced obesity and metabolic disease. Here, we investigated the impact of adipocyte-specific HDAC9 gene deletion on diet-induced obesity in male and female mice. The HDAC9 gene expression was increased in adipose tissues of obese male and female mice and HDAC9 expression correlated positively with body mass index in humans. Interestingly, female, but not male, adipocyte-specific HDAC9 KO mice on HFD exhibited reduced body weight and visceral adipose tissue mass, adipocyte hypertrophy, and improved insulin sensitivity, glucose tolerance and adipogenic differentiation gene expression. Furthermore, adipocyte-specific HDAC9 gene deletion in female mice improved metabolic health as assessed by whole body energy expenditure, oxygen consumption, and adaptive thermogenesis. Mechanistically, compared to female mice, HFD-fed male mice exhibited preferential HDAC9 expression in the stromovascular fraction, which may have offset the impact of adipocyte-specific HDAC9 gene deletion in male mice. These results suggest that HDAC9 expressed in adipocytes is detrimental to obesity in female mice and provides novel evidence of sex-related differences in HDAC9 cellular expression and contribution to obesity-related metabolic disease.
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Affiliation(s)
- Brandee Goo
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1120 15th St., CB3940, Augusta, GA 30912, USA
| | - Samah Ahmadieh
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1120 15th St., CB3940, Augusta, GA 30912, USA
- Department of Medicine, Medical College of Georgia, Augusta University, 1120 15th St., BI5076, Augusta, GA 30912, USA
| | - Abdalrahman Zarzour
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1120 15th St., CB3940, Augusta, GA 30912, USA
- Department of Medicine, Medical College of Georgia, Augusta University, 1120 15th St., BI5076, Augusta, GA 30912, USA
| | - Nicole K. H. Yiew
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1120 15th St., CB3940, Augusta, GA 30912, USA
| | - David Kim
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1120 15th St., CB3940, Augusta, GA 30912, USA
| | - Hong Shi
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1120 15th St., CB3940, Augusta, GA 30912, USA
- Department of Medicine, Medical College of Georgia, Augusta University, 1120 15th St., BI5076, Augusta, GA 30912, USA
| | - Jacob Greenway
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1120 15th St., CB3940, Augusta, GA 30912, USA
| | - Stephen Cave
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1120 15th St., CB3940, Augusta, GA 30912, USA
| | - Jenny Nguyen
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1120 15th St., CB3940, Augusta, GA 30912, USA
| | - Swetha Aribindi
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1120 15th St., CB3940, Augusta, GA 30912, USA
| | - Mark Wendolowski
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1120 15th St., CB3940, Augusta, GA 30912, USA
| | - Praneet Veerapaneni
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1120 15th St., CB3940, Augusta, GA 30912, USA
| | - Mourad Ogbi
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1120 15th St., CB3940, Augusta, GA 30912, USA
| | - Weiqin Chen
- Departments of Physiology and Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th St., CA3126, Augusta, GA 30912, USA
| | - Yun Lei
- Departments of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th St., CA3008, Augusta, GA 30912, USA
| | - Xin-Yun Lu
- Departments of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th St., CA3008, Augusta, GA 30912, USA
| | - Ha Won Kim
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1120 15th St., CB3940, Augusta, GA 30912, USA
- Department of Medicine, Medical College of Georgia, Augusta University, 1120 15th St., BI5076, Augusta, GA 30912, USA
| | - Neal L. Weintraub
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1120 15th St., CB3940, Augusta, GA 30912, USA
- Department of Medicine, Medical College of Georgia, Augusta University, 1120 15th St., BI5076, Augusta, GA 30912, USA
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27
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Design, Synthesis, and biological evaluation of HDAC6 inhibitors based on Cap modification strategy. Bioorg Chem 2022; 125:105874. [DOI: 10.1016/j.bioorg.2022.105874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/05/2022] [Accepted: 05/11/2022] [Indexed: 11/22/2022]
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Ebert T, Tran N, Schurgers L, Stenvinkel P, Shiels PG. Ageing - Oxidative stress, PTMs and disease. Mol Aspects Med 2022; 86:101099. [PMID: 35689974 DOI: 10.1016/j.mam.2022.101099] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/10/2022] [Indexed: 12/15/2022]
Abstract
Post-translational modifications (PTMs) have been proposed as a link between the oxidative stress-inflammation-ageing trinity, thereby affecting several hallmarks of ageing. Phosphorylation, acetylation, and ubiquitination cover >90% of all the reported PTMs. Several of the main PTMs are involved in normal "healthy" ageing and in different age-related diseases, for instance neurodegenerative, metabolic, cardiovascular, and bone diseases, as well as cancer and chronic kidney disease. Ultimately, data from human rare progeroid syndromes, but also from long-living animal species, imply that PTMs are critical regulators of the ageing process. Mechanistically, PTMs target epigenetic and non-epigenetic pathways during ageing. In particular, epigenetic histone modification has critical implications for the ageing process and can modulate lifespan. Therefore, PTM-based therapeutics appear to be attractive pharmaceutical candidates to reduce the burden of ageing-related diseases. Several phosphorylation and acetylation inhibitors have already been FDA-approved for the treatment of other diseases and offer a unique potential to investigate both beneficial effects and possible side-effects. As an example, the most well-studied senolytic compounds dasatinib and quercetin, which have already been tested in Phase 1 pilot studies, also act as kinase inhibitors, targeting cellular senescence and increasing lifespan. Future studies need to carefully determine the best PTM-based candidates for the treatment of the "diseasome of ageing".
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Affiliation(s)
- Thomas Ebert
- Karolinska Institute, Department of Clinical Science, Intervention and Technology, Division of Renal Medicine, Stockholm, Sweden; University of Leipzig Medical Center, Medical Department III - Endocrinology, Nephrology, Rheumatology, Leipzig, Germany.
| | - Ngoc Tran
- University of Glasgow, Wolfson Wohl Cancer Research Centre, College of Medical, Veterinary & Life Sciences, Institute of Cancer Sciences, Glasgow, UK
| | - Leon Schurgers
- Department of Biochemistry, Cardiovascular Research School Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands
| | - Peter Stenvinkel
- Karolinska Institute, Department of Clinical Science, Intervention and Technology, Division of Renal Medicine, Stockholm, Sweden
| | - Paul G Shiels
- University of Glasgow, Wolfson Wohl Cancer Research Centre, College of Medical, Veterinary & Life Sciences, Institute of Cancer Sciences, Glasgow, UK
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29
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Liu F, Chen J, Li Z, Meng X. Recent Advances in Epigenetics of Age-Related Kidney Diseases. Genes (Basel) 2022; 13:genes13050796. [PMID: 35627181 PMCID: PMC9142069 DOI: 10.3390/genes13050796] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 02/03/2023] Open
Abstract
Renal aging has attracted increasing attention in today’s aging society, as elderly people with advanced age are more susceptible to various kidney disorders such as acute kidney injury (AKI) and chronic kidney disease (CKD). There is no clear-cut universal mechanism for identifying age-related kidney diseases, and therefore, they pose a considerable medical and public health challenge. Epigenetics refers to the study of heritable modifications in the regulation of gene expression that do not require changes in the underlying genomic DNA sequence. A variety of epigenetic modifiers such as histone deacetylases (HDAC) inhibitors and DNA methyltransferase (DNMT) inhibitors have been proposed as potential biomarkers and therapeutic targets in numerous fields including cardiovascular diseases, immune system disease, nervous system diseases, and neoplasms. Accumulating evidence in recent years indicates that epigenetic modifications have been implicated in renal aging. However, no previous systematic review has been performed to systematically generalize the relationship between epigenetics and age-related kidney diseases. In this review, we aim to summarize the recent advances in epigenetic mechanisms of age-related kidney diseases as well as discuss the application of epigenetic modifiers as potential biomarkers and therapeutic targets in the field of age-related kidney diseases. In summary, the main types of epigenetic processes including DNA methylation, histone modifications, non-coding RNA (ncRNA) modulation have all been implicated in the progression of age-related kidney diseases, and therapeutic targeting of these processes will yield novel therapeutic strategies for the prevention and/or treatment of age-related kidney diseases.
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Affiliation(s)
- Feng Liu
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China;
| | - Jiefang Chen
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China;
| | - Zhenqiong Li
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China;
- Correspondence: (Z.L.); (X.M.)
| | - Xianfang Meng
- Department of Neurobiology, Institute of Brain Research, School of Basic Medical Sciences, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Correspondence: (Z.L.); (X.M.)
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30
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Moskalev A, Guvatova Z, Lopes IDA, Beckett CW, Kennedy BK, De Magalhaes JP, Makarov AA. Targeting aging mechanisms: pharmacological perspectives. Trends Endocrinol Metab 2022; 33:266-280. [PMID: 35183431 DOI: 10.1016/j.tem.2022.01.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/18/2022] [Accepted: 01/22/2022] [Indexed: 12/12/2022]
Abstract
Geroprotectors slow down aging and promote healthy longevity in model animals. Although hundreds of compounds have been shown to extend the life of laboratory model organisms, clinical studies on potential geroprotectors are exceedingly rare, especially in healthy elders. This review aims to classify potential geroprotectors based on the mechanisms by which they influence aging. These pharmacological interventions can be classified into the following groups: those that prevent oxidation; proteostasis regulators; suppressors of genomic instability; epigenetic drugs; those that preserve mitochondrial function; inhibitors of aging-associated signaling pathways; hormetins; senolytics/senostatics; anti-inflammatory drugs; antifibrotic agents; neurotrophic factors; factors preventing the impairment of barrier function; immunomodulators; and prebiotics, metabiotics, and enterosorbents.
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Affiliation(s)
- Alexey Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; Institute of Biology of the Federal Research Center of Komi Science Center, Ural Branch of the Russian Academy of Sciences, 28 Kommunisticheskaya Street, Syktyvkar 167982, Russia.
| | - Zulfiya Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Ines De Almeida Lopes
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Charles W Beckett
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK
| | - Brian K Kennedy
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Centre for Healthy Longevity, National University Health System, Singapore; Singapore Institute of Clinical Sciences, A*STAR, Singapore
| | - Joao Pedro De Magalhaes
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK.
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.
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Zheng W. The Zinc-Dependent HDACs: Non-Histone Substrates and Catalytic Deacylation Beyond Deacetylation. Mini Rev Med Chem 2022; 22:2478-2485. [PMID: 35362374 DOI: 10.2174/1389557522666220330144151] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/24/2021] [Accepted: 02/16/2022] [Indexed: 11/22/2022]
Abstract
Protein lysine side chain Nε-acylation and -deacylation play an important regulatory role in both epigenetic and non-epigenetic processes via a structural and functional regulation of histone and non-histone proteins. The enzymes catalyzing deacylation were traditionally termed as the histone deacetylases (HDACs) since histone proteins were the first substrates identified and the deacetylation was the first type of deacylation identified. However, it has now been known that, besides the seven sirtuins (i.e. SIRT1-7, theβ-nicotinamide adenine dinucleotide (β-NAD+)-dependent class III HDACs), several of the other eleven members of the mammalian HDAC family (i.e. HDAC1-11, the zinc-dependent classes I, II, and IV HDACs) have been found to also accept non-histone proteins as native substrates and to also catalyze the removal of the acyl groups other than acetyl, such as formyl, crotonyl, and myristoyl. In this mini-review, I will first integrate the current literature coverage on the non-histone substrates and the catalytic deacylation (beyond deacetylation) of the zinc-dependent HDACs, which will be followed by an address on the functional interrogation and pharmacological exploitation (inhibitor design) of the zinc-dependent HDAC-catalyzed deacylation (beyond deacetylation).
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Affiliation(s)
- Weiping Zheng
- School of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, P. R. China
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32
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Fischer F, Grigolon G, Benner C, Ristow M. Evolutionarily conserved transcription factors as regulators of longevity and targets for geroprotection. Physiol Rev 2022; 102:1449-1494. [PMID: 35343830 DOI: 10.1152/physrev.00017.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aging is the single largest risk factor for many debilitating conditions, including heart diseases, stroke, cancer, diabetes, and neurodegenerative disorders. While far from understood in its full complexity, it is scientifically well-established that aging is influenced by genetic and environmental factors, and can be modulated by various interventions. One of aging's early hallmarks are aberrations in transcriptional networks, controlling for example metabolic homeostasis or the response to stress. Evidence in different model organisms abounds that a number of evolutionarily conserved transcription factors, which control such networks, can affect lifespan and healthspan across species. These transcription factors thus potentially represent conserved regulators of longevity and are emerging as important targets in the challenging quest to develop treatments to mitigate age-related diseases, and possibly even to slow aging itself. This review provides an overview of evolutionarily conserved transcription factors that impact longevity or age-related diseases in at least one multicellular model organism (nematodes, flies, or mice), and/or are tentatively linked to human aging. Discussed is the general evidence for transcriptional regulation of aging and disease, followed by a more detailed look at selected transcription factor families, the common metabolic pathways involved, and the targeting of transcription factors as a strategy for geroprotective interventions.
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Affiliation(s)
- Fabian Fischer
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Giovanna Grigolon
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Christoph Benner
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Michael Ristow
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
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Gomez-Sanchez JA, Patel N, Martirena F, Fazal SV, Mutschler C, Cabedo H. Emerging Role of HDACs in Regeneration and Ageing in the Peripheral Nervous System: Repair Schwann Cells as Pivotal Targets. Int J Mol Sci 2022; 23:ijms23062996. [PMID: 35328416 PMCID: PMC8951080 DOI: 10.3390/ijms23062996] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/04/2022] [Accepted: 03/09/2022] [Indexed: 02/07/2023] Open
Abstract
The peripheral nervous system (PNS) has a remarkable regenerative capacity in comparison to the central nervous system (CNS), a phenomenon that is impaired during ageing. The ability of PNS axons to regenerate after injury is due to Schwann cells (SC) being reprogrammed into a repair phenotype called Repair Schwann cells. These repair SCs are crucial for supporting axonal growth after injury, myelin degradation in a process known as myelinophagy, neurotropic factor secretion, and axonal growth guidance through the formation of Büngner bands. After regeneration, repair SCs can remyelinate newly regenerated axons and support nonmyelinated axons. Increasing evidence points to an epigenetic component in the regulation of repair SC gene expression changes, which is necessary for SC reprogramming and regeneration. One of these epigenetic regulations is histone acetylation by histone acetyl transferases (HATs) or histone deacetylation by histone deacetylases (HDACs). In this review, we have focused particularly on three HDAC classes (I, II, and IV) that are Zn2+-dependent deacetylases. These HDACs are important in repair SC biology and remyelination after PNS injury. Another key aspect explored in this review is HDAC genetic compensation in SCs and novel HDAC inhibitors that are being studied to improve nerve regeneration.
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Affiliation(s)
- Jose A. Gomez-Sanchez
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández—Consejo Superior de Investigaciones Científicas, 03550 San Juan de Alicante, Spain; (N.P.); (H.C.)
- Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 03010 Alicante, Spain
- Correspondence: ; Tel.: +34-965-919-594
| | - Nikiben Patel
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández—Consejo Superior de Investigaciones Científicas, 03550 San Juan de Alicante, Spain; (N.P.); (H.C.)
- Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 03010 Alicante, Spain
| | - Fernanda Martirena
- Department of Hematology, General University Hospital of Elda, 03600 Elda, Spain;
| | - Shaline V. Fazal
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0PY, UK; (S.V.F.); (C.M.)
- Wellcome—MRC Cambridge Stem Cell Institute, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Clara Mutschler
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0PY, UK; (S.V.F.); (C.M.)
| | - Hugo Cabedo
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández—Consejo Superior de Investigaciones Científicas, 03550 San Juan de Alicante, Spain; (N.P.); (H.C.)
- Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), 03010 Alicante, Spain
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Addicks GC, Zhang H, Ryu D, Vasam G, Green AE, Marshall PL, Patel S, Kang BE, Kim D, Katsyuba E, Williams EG, Renaud JM, Auwerx J, Menzies KJ. GCN5 maintains muscle integrity by acetylating YY1 to promote dystrophin expression. J Cell Biol 2022; 221:e202104022. [PMID: 35024765 PMCID: PMC8931935 DOI: 10.1083/jcb.202104022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 11/04/2021] [Accepted: 12/08/2021] [Indexed: 12/12/2022] Open
Abstract
Protein lysine acetylation is a post-translational modification that regulates protein structure and function. It is targeted to proteins by lysine acetyltransferases (KATs) or removed by lysine deacetylases. This work identifies a role for the KAT enzyme general control of amino acid synthesis protein 5 (GCN5; KAT2A) in regulating muscle integrity by inhibiting DNA binding of the transcription factor/repressor Yin Yang 1 (YY1). Here we report that a muscle-specific mouse knockout of GCN5 (Gcn5skm-/-) reduces the expression of key structural muscle proteins, including dystrophin, resulting in myopathy. GCN5 was found to acetylate YY1 at two residues (K392 and K393), disrupting the interaction between the YY1 zinc finger region and DNA. These findings were supported by human data, including an observed negative correlation between YY1 gene expression and muscle fiber diameter. Collectively, GCN5 positively regulates muscle integrity through maintenance of structural protein expression via acetylation-dependent inhibition of YY1. This work implicates the role of protein acetylation in the regulation of muscle health and for consideration in the design of novel therapeutic strategies to support healthy muscle during myopathy or aging.
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Affiliation(s)
- Gregory C Addicks
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Hongbo Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Dongryeol Ryu
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Goutham Vasam
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Alexander E Green
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology and the Éric Poulin Centre for Neuromuscular Disease, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Philip L Marshall
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Sonia Patel
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Baeki E Kang
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Doyoun Kim
- Division of Therapeutics and Biotechnology, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | - Elena Katsyuba
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Evan G Williams
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jean-Marc Renaud
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Keir J Menzies
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology and the Éric Poulin Centre for Neuromuscular Disease, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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Liu S, Cai X, Wang T, Xu J, Cheng W, Wang X, Wei G, Yan S. Downregulation of ALDH6A1 is a New Marker of Muscle Insulin Resistance in Type 2 Diabetes Mellitus. Int J Gen Med 2022; 15:2137-2147. [PMID: 35241929 PMCID: PMC8887615 DOI: 10.2147/ijgm.s343727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/21/2022] [Indexed: 12/23/2022] Open
Abstract
Purpose Skeletal muscle insulin resistance (IR) is an important etiology of type 2 diabetes mellitus (T2DM); however, its molecular mechanism is yet to be fully defined. This study attempted to identify the gene expression patterns and molecular disorders in T2DM patients’ skeletal muscle samples. Methods First, the difference in genetic expression among GSE25462 data was analyzed. Next, PPI network analysis of differential genes was carried out, after which the maladjustment module was identified. Then, an enrichment analysis and gene set enrichment analysis (GSEA) were carried out. Finally, the transcription factors that regulate the modular genes by raid were predicted. Results Most differentially expressed genes were found to be able to form an interaction network and cluster into 9 modules. These modular genes were shown to possess a significant correlation with immune inflammation and metabolic response. Importantly, the top 15 genes of area under receiver operating characteristic curve (AUC) were identified, and the expression of 10 genes by GSE12643, GSE18732 and GSE29221 was confirmed. The expression and AUC value of ALDH6A1 were then verified according to three sets of data, where ALDH6A1 was found to be negatively correlated with follicular helper T cells. However, among the predicted transcription regulators, HDAC was shown to have a better regulatory effect. Conclusion The findings highlight that the dysregulation of ALDH6A1 expression in IR of T2DM may serve as a potential therapeutic target. ALDH6A1 is involved in the immune inflammation and metabolic pathways.
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Affiliation(s)
- Song Liu
- Endocrinology Department, Traditional Chinese Medicine Academy of Heilongjiang, Harbin, Heilongjiang Province, People’s Republic of China
| | - Xiaojun Cai
- Endocrinology Department, Traditional Chinese Medicine Academy of Heilongjiang, Harbin, Heilongjiang Province, People’s Republic of China
| | - Tao Wang
- Endocrinology Department, Traditional Chinese Medicine Academy of Heilongjiang, Harbin, Heilongjiang Province, People’s Republic of China
| | - Jiwen Xu
- Anatomy, Histology and Embryology Teaching and Research Section, School of Basic Medicine, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, People’s Republic of China
| | - Weilun Cheng
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People’s Republic of China
| | - Xuling Wang
- Endocrinology Department, Traditional Chinese Medicine Academy of Heilongjiang, Harbin, Heilongjiang Province, People’s Republic of China
| | - Gangjie Wei
- Medical Department, Traditional Chinese Medicine Academy of Heilongjiang, Harbin, Heilongjiang Province, People’s Republic of China
| | - Shuang Yan
- Department of Endocrinology and Metabolism, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People’s Republic of China
- Correspondence: Shuang Yan, Email
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Grigolon G, Araldi E, Erni R, Wu JY, Thomas C, La Fortezza M, Laube B, Pöhlmann D, Stoffel M, Zarse K, Carreira EM, Ristow M, Fischer F. Grainyhead 1 acts as a drug-inducible conserved transcriptional regulator linked to insulin signaling and lifespan. Nat Commun 2022; 13:107. [PMID: 35013237 PMCID: PMC8748497 DOI: 10.1038/s41467-021-27732-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022] Open
Abstract
Aging is impacted by interventions across species, often converging on metabolic pathways. Transcription factors regulate longevity yet approaches for their pharmacological modulation to exert geroprotection remain sparse. We show that increased expression of the transcription factor Grainyhead 1 (GRH-1) promotes lifespan and pathogen resistance in Caenorhabditis elegans. A compound screen identifies FDA-approved drugs able to activate human GRHL1 and promote nematodal GRH-1-dependent longevity. GRHL1 activity is regulated by post-translational lysine methylation and the phosphoinositide (PI) 3-kinase C2A. Consistently, nematodal longevity following impairment of the PI 3-kinase or insulin/IGF-1 receptor requires grh-1. In BXD mice, Grhl1 expression is positively correlated with lifespan and insulin sensitivity. In humans, GRHL1 expression positively correlates with insulin receptor signaling and also with lifespan. Fasting blood glucose levels, including in individuals with type 2 diabetes, are negatively correlated with GRHL1 expression. Thereby, GRH-1/GRHL1 is identified as a pharmacologically malleable transcription factor impacting insulin signaling and lifespan. Life- and healthspan of organisms can be modulated by dietary, genetic, or pharmacological interventions, which often affect metabolic pathways. Here the authors report that Grainyhead 1 is an evolutionarily conserved, drug-inducible transcription factor that promotes longevity in C. elegans, and thus a potential target for the development of geroprotective drugs.
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Affiliation(s)
- Giovanna Grigolon
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Elisa Araldi
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland.,Metabolism and Metabolic Disease Laboratory, Institute for Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, CH-8093, Switzerland
| | - Reto Erni
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, CH-8093, Switzerland
| | - Jia Yee Wu
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Carolin Thomas
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Marco La Fortezza
- Evolutionary Biology Laboratory, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, CH-8092, Switzerland
| | - Beate Laube
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Doris Pöhlmann
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Markus Stoffel
- Metabolism and Metabolic Disease Laboratory, Institute for Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, CH-8093, Switzerland
| | - Kim Zarse
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Erick M Carreira
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, CH-8093, Switzerland
| | - Michael Ristow
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland.
| | - Fabian Fischer
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
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Lei H, Huffman DM, Salmon AB, LeBrasseur NK, Carter C, Richardson A, Austad S, Ladiges W. Resilience to aging is a heterogeneous characteristic defined by physical stressors. AGING PATHOBIOLOGY AND THERAPEUTICS 2022; 4:19-22. [PMID: 35475259 PMCID: PMC9038086 DOI: 10.31491/apt.2022.03.076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Physical resilience, the capacity to respond to and recover from a stressful event, declines with advancing age. Individuals respond differently to physical stressors across their lifespans. While the biological underpinnings of resilience remain unclear, a plausible determinant is the capacity of an individual's cellular and molecular levels to return to homeostasis after a physical challenge. Impaired resilience may not only be a consequence of aging but could also be a contributing factor to the aging process. Therefore, resilience at relatively younger ages could be predictive of future health and lifespan. By utilizing standardized physical challenges and measuring stress response patterns, the relative resilience of individuals can be quantified and classified. Current preclinical research suggests that several physical stressors could be used to measure resilience in clinical aging studies. A mechanistic understanding of why some individuals are more resilient to physical stressors than others could help identify protective factors and therapeutic ways to promote healthy aging.
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Affiliation(s)
- Haoyi Lei
- Department of Comparative Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | - Derek M. Huffman
- Departments of Molecular Pharmacology, Medicine and Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Adam B. Salmon
- San Antonio Sam and Ann Barshop Institute for Longevity and Aging Studies and Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, Department of Molecular Medicine, South Texas Veterans Health Care System, Geriatric Research Education and Clinical Center, San Antonio, TX, USA
| | - Nathan K. LeBrasseur
- Department of Physical Medicine & Rehabilitation, Mayo Clinic, Rochester, MN, USA
| | - Christy Carter
- Department of Medicine, Division of Gerontology, Geriatrics and Palliative Care, School of Medicine, University of Alabama Birmingham, Birmingham, AL, USA
| | - Arlan Richardson
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Science Center. Oklahoma City VA Medical Center, Oklahoma City, OK, USA
| | - Steve Austad
- Department of Biology, University of Alabama Birmingham, Birmingham, AL, USA
| | - Warren Ladiges
- Department of Comparative Medicine, School of Medicine, University of Washington, Seattle, WA, USA
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Zhou M, Yuan M, Zhang M, Lei C, Aras O, Zhang X, An F. Combining histone deacetylase inhibitors (HDACis) with other therapies for cancer therapy. Eur J Med Chem 2021; 226:113825. [PMID: 34562854 DOI: 10.1016/j.ejmech.2021.113825] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/30/2022]
Abstract
Histone deacetylases (HDACs) play an important role in regulating the expression of genes involved in tumorigenesis and tumor maintenance, and hence they have been considered as key targets in cancer therapy. As a novel category of antitumor agents, histone deacetylase inhibitors (HDACis) can induce cell cycle arrest, apoptosis, and differentiation in cancer cells, ultimately combating cancer. Although in the United States, the use of HDACis for the treatment of certain cancers has been approved, the therapeutic efficacy of HDACis as a single therapeutic agent in solid tumorshas been unsatisfactory and drug resistance may yet occur. To enhance therapeutic efficacy and limit drug resistance, numerous combination therapies involving HDACis in synergy with other antitumor therapies have been studied. In this review, we describe the classification of HDACs. Moreover, we summarize the antitumor mechanism of the HDACis for targeting key cellular processes of cancers (cell cycle, apoptosis, angiogenesis, DNA repair, and immune response). In addition, we outline the major developments of other antitumor therapies in combination with HDACis, including chemotherapy, radiotherapy, phototherapy, targeted therapy, and immunotherapy. Finally, we discuss the current state and challenges of HDACis-drugs combinations in future clinical studies, with the aim of optimizing the antitumor effect of such combinations.
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Affiliation(s)
- Mengjiao Zhou
- Department of Pharmacology, School of Pharmacy, Nantong University, 226000, Nantong, Jiangsu, PR China
| | - Minjian Yuan
- Department of Pharmacology, School of Pharmacy, Nantong University, 226000, Nantong, Jiangsu, PR China
| | - Meng Zhang
- Institute of Medical Engineering, Department of Biophysics, School of Basic Medical Science, Health Science Center, Xi'an Jiaotong University, No.76 Yanta West Road, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Chenyi Lei
- Institute of Medical Engineering, Department of Biophysics, School of Basic Medical Science, Health Science Center, Xi'an Jiaotong University, No.76 Yanta West Road, Xi'an, 710061, Shaanxi, People's Republic of China
| | - Omer Aras
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
| | - Xiaohong Zhang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Collaborative Innovation Center of Suzhou Nano Science & Technology, Soochow University, 199 Ren'ai Road, Suzhou, 215123, Jiangsu, PR China.
| | - Feifei An
- Institute of Medical Engineering, Department of Biophysics, School of Basic Medical Science, Health Science Center, Xi'an Jiaotong University, No.76 Yanta West Road, Xi'an, 710061, Shaanxi, People's Republic of China; Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Collaborative Innovation Center of Suzhou Nano Science & Technology, Soochow University, 199 Ren'ai Road, Suzhou, 215123, Jiangsu, PR China.
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Lammers M. Post-translational Lysine Ac(et)ylation in Bacteria: A Biochemical, Structural, and Synthetic Biological Perspective. Front Microbiol 2021; 12:757179. [PMID: 34721364 PMCID: PMC8556138 DOI: 10.3389/fmicb.2021.757179] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/10/2021] [Indexed: 12/21/2022] Open
Abstract
Ac(et)ylation is a post-translational modification present in all domains of life. First identified in mammals in histones to regulate RNA synthesis, today it is known that is regulates fundamental cellular processes also in bacteria: transcription, translation, metabolism, cell motility. Ac(et)ylation can occur at the ε-amino group of lysine side chains or at the α-amino group of a protein. Furthermore small molecules such as polyamines and antibiotics can be acetylated and deacetylated enzymatically at amino groups. While much research focused on N-(ε)-ac(et)ylation of lysine side chains, much less is known about the occurrence, the regulation and the physiological roles on N-(α)-ac(et)ylation of protein amino termini in bacteria. Lysine ac(et)ylation was shown to affect protein function by various mechanisms ranging from quenching of the positive charge, increasing the lysine side chains’ size affecting the protein surface complementarity, increasing the hydrophobicity and by interfering with other post-translational modifications. While N-(ε)-lysine ac(et)ylation was shown to be reversible, dynamically regulated by lysine acetyltransferases and lysine deacetylases, for N-(α)-ac(et)ylation only N-terminal acetyltransferases were identified and so far no deacetylases were discovered neither in bacteria nor in mammals. To this end, N-terminal ac(et)ylation is regarded as being irreversible. Besides enzymatic ac(et)ylation, recent data showed that ac(et)ylation of lysine side chains and of the proteins N-termini can also occur non-enzymatically by the high-energy molecules acetyl-coenzyme A and acetyl-phosphate. Acetyl-phosphate is supposed to be the key molecule that drives non-enzymatic ac(et)ylation in bacteria. Non-enzymatic ac(et)ylation can occur site-specifically with both, the protein primary sequence and the three dimensional structure affecting its efficiency. Ac(et)ylation is tightly controlled by the cellular metabolic state as acetyltransferases use ac(et)yl-CoA as donor molecule for the ac(et)ylation and sirtuin deacetylases use NAD+ as co-substrate for the deac(et)ylation. Moreover, the accumulation of ac(et)yl-CoA and acetyl-phosphate is dependent on the cellular metabolic state. This constitutes a feedback control mechanism as activities of many metabolic enzymes were shown to be regulated by lysine ac(et)ylation. Our knowledge on lysine ac(et)ylation significantly increased in the last decade predominantly due to the huge methodological advances that were made in fields such as mass-spectrometry, structural biology and synthetic biology. This also includes the identification of additional acylations occurring on lysine side chains with supposedly different regulatory potential. This review highlights recent advances in the research field. Our knowledge on enzymatic regulation of lysine ac(et)ylation will be summarized with a special focus on structural and mechanistic characterization of the enzymes, the mechanisms underlying non-enzymatic/chemical ac(et)ylation are explained, recent technological progress in the field are presented and selected examples highlighting the important physiological roles of lysine ac(et)ylation are summarized.
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Affiliation(s)
- Michael Lammers
- Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Greifswald, Germany
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40
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Lee TW, Liu HW, Lin YF, Lee TI, Kao YH, Chen YJ. Histone deacetylase inhibition improves metabolism and mitochondrial dynamics: A potential novel therapeutic strategy for sarcopenia coexisting with diabetes mellitus. Med Hypotheses 2021; 158:110724. [PMID: 34753007 DOI: 10.1016/j.mehy.2021.110724] [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: 06/02/2021] [Revised: 09/14/2021] [Accepted: 10/10/2021] [Indexed: 11/16/2022]
Abstract
Sarcopenia, the age-associated-fragility with loss of skeletal muscle mass and function, often coexists with type 2 diabetes (T2D) in older individuals. Derangement of muscle metabolism and mitochondrial dynamics is critical, particularly in high-energy-demand organs in patients with metabolic disorder. However, targeted therapies to halt or reverse the pathological progression of sarcopenia coexisting with T2D are unavailable. Studies have identified the pathological roles of class I histone deacetylases (HDACs) in both T2D and sarcopenia. In addition to their proinflammatory properties, HDACs are known to modify muscle metabolism and mitochondrial dynamics in both the development of sarcopenia and pathogenesis of diabetes. Proper quality control of mitochondrial dynamics through protein degradation and the synthesis of new proteins may improve skeletal muscle function in sarcopenia. Class I HDAC inhibitors improve energy metabolism and modulate autophagy-related genes in skeletal muscle. However, class IIa HDAC4 plays a protective role in preserving skeletal muscle structure following long-term denervation, and selective inhibition of class IIa HDAC activity had no impact on oxidative metabolism of muscle mitochondria. These findings suggest the vital role of class I HDAC modulation in bioenergetics and mitochondria quality control, and may lead to a novel therapeutic strategy targeting sarcopenia that coexists with T2D. HDAC inhibitors have been approved for clinical applications, and interventions targeting on HDACs may be promising for the treatment of sarcopenia.
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Affiliation(s)
- Ting-Wei Lee
- Division of Endocrinology and Metabolism, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Endocrinology and Metabolism, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Han-Wen Liu
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Yuan-Feng Lin
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ting-I Lee
- Division of Endocrinology and Metabolism, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Endocrinology and Metabolism, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; Department of General Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
| | - Yu-Hsun Kao
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Department of Medical Education and Research, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; Taipei Heart Institute, Taipei Medical University, Taipei, Taiwan.
| | - Yi-Jen Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Cardiovascular Medicine, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; Cardiovascular Research Center, Wan Fan Hospital, Taipei Medical University, Taipei, Taiwan; Taipei Heart Institute, Taipei Medical University, Taipei, Taiwan
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Zhang L, Cao W. Histone deacetylase 3 (HDAC3) as an important epigenetic regulator of kidney diseases. J Mol Med (Berl) 2021; 100:43-51. [PMID: 34698870 DOI: 10.1007/s00109-021-02141-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/18/2021] [Accepted: 09/09/2021] [Indexed: 12/18/2022]
Abstract
Development and progression of many kidney diseases are substantially influenced by aberrant protein acetylation modifications of gene expression crucial for kidney functions. Histone deacetylase (HDAC) expression alterations are detected from renal samples of patients and animal models of various kidney diseases, and the administrations of HDAC inhibitors display impressive renal protective effects in vitro and in vivo. However, when the expression alterations of multiple HDACs occur, not all the HDACs causally affect the disease onset or progression. Identification of a single HDAC as a disease-causing factor will allow subtype-targeted intervention with less side effect. HDAC3 is a unique HDAC with distinct structural and subcellular distribution features and co-repressor dependency. HDAC3 is required for kidney development and its aberrations actively participate in many pathological processes, such as cancer, cardiovascular diseases, diabetes, and neurodegenerative disorders, and contribute significantly to the pathogenesis of kidney diseases. This review will discuss the recent studies that investigate the critical roles of HDAC3 aberrations in kidney development, renal aging, renal cell carcinoma, renal fibrosis, chronic kidney disease, polycystic kidney disease, glomerular podocyte injury, and diabetic nephropathy. These studies reveal the distinct characters of HDAC3 aberrations that act on different molecules/signaling pathways under various renal pathological conditions, which might shed lights into the epigenetic mechanisms of renal diseases and the potentially therapeutic strategies.
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Affiliation(s)
- Lijun Zhang
- Department of Nephrology, Northern Jiangsu People's Hospital, Nanjing University School of Medicine, Yangzhou, 225001, China
- Jiangsu Key Lab of Molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China
| | - Wangsen Cao
- Department of Nephrology, Northern Jiangsu People's Hospital, Nanjing University School of Medicine, Yangzhou, 225001, China.
- Jiangsu Key Lab of Molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China.
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Dai Y, Wei T, Shen Z, Bei Y, Lin H, Dai H. Classical HDACs in the regulation of neuroinflammation. Neurochem Int 2021; 150:105182. [PMID: 34509559 DOI: 10.1016/j.neuint.2021.105182] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/22/2021] [Accepted: 09/07/2021] [Indexed: 12/15/2022]
Abstract
Neuroinflammation is a key factor of the pathology of various neurological diseases (brain injury, depression, neurodegenerative diseases). It is a complex and orderly process that relies on various types of glial cells and peripheral immune cells. Inhibition of neuroinflammation can reduce the severity of neurological diseases. The initiation, progression, and termination of inflammation require gene activation, epigenetic modification, transcriptional translation, and post-translational regulation, all of which are tightly regulated by different enzymes. Epigenetics refers to the regulation of epigenetic gene expression by epigenetic changes (DNA methylation, histone modification, and non-coding RNAs such as miRNA) that are not dependent on changes in gene sequence and are heritable. Histone deacetylases (HDACs) are a group of important enzymes that regulate epigenetics. They can remove the acetyl group on the lysine ϵ-amino group of the target protein, thereby affecting gene transcription or altering protein activity. HDACs are involved in the regulation of immunity and inflammation. HDAC inhibitor (HDACi) has also become a new hotspot in the research of anti-inflammatory drugs. Therefore, the aim of the current review is to discuss and summarize the role and mechanism of different HDACs in neuroinflammation and the corresponding role of HDACi in neurological diseases, and to providing new ideas for future research on neuroinflammation-related diseases and drug development.
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Affiliation(s)
- Yunjian Dai
- Department of Pharmacy, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang Province, China
| | - Taofeng Wei
- Department of Pharmacy, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang Province, China
| | - Zexu Shen
- Department of Pharmacy, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang Province, China
| | - Yun Bei
- Department of Pharmacy, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang Province, China
| | - Haoran Lin
- Department of Pharmacy, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang Province, China
| | - Haibin Dai
- Department of Pharmacy, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang Province, China.
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Bieszczad B, Garbicz D, Świtalska M, Dudek MK, Warszycki D, Wietrzyk J, Grzesiuk E, Mieczkowski A. Improved HDAC Inhibition, Stronger Cytotoxic Effect and Higher Selectivity against Leukemias and Lymphomas of Novel, Tricyclic Vorinostat Analogues. Pharmaceuticals (Basel) 2021; 14:851. [PMID: 34577551 PMCID: PMC8470702 DOI: 10.3390/ph14090851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 11/23/2022] Open
Abstract
Histone deacetylase (HDAC) inhibitors are a class of drugs used in the cancer treatment. Here, we developed a library of 19 analogues of Vorinostat, an HDAC inhibitor used in lymphomas treatment. In Vorinostat, we replaced the hydrophobic phenyl group with various tricyclic 'caps' possessing a central, eight-membered, heterocyclic ring, and investigated the HDAC activity and cytotoxic effect on the cancer and normal cell lines. We found that 3 out of the 19 compounds, based on dibenzo[b,f]azocin-6(5H)-one, 11,12-dihydrodibenzo[b,f]azocin-6(5H)-one, and benzo[b]naphtho[2,3-f][1,5]diazocine-6,14(5H,13H)-dione scaffolds, showed better HDACs inhibition than the referenced Vorinostat. In leukemic cell line MV4-11 and in the lymphoma cell line Daudi, three compounds showed lower IC50 values than Vorinostat. These compounds had higher activity and selectivity against MV4-11 and Daudi cell lines than reference Vorinostat. We also observed a strong correlation between HDACs inhibition and the cytotoxic effect. Cell lines derived from solid tumours: A549 (lung carcinoma) and MCF-7 (breast adenocarcinoma) as well as reference BALB/3T3 (normal murine fibroblasts) were less susceptible to compounds tested. Developed derivatives show improved properties than Vorinostat, thus they could be considered as possible agents for leukemia and lymphoma treatment.
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Affiliation(s)
- Bartosz Bieszczad
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; (B.B.); (D.G.)
| | - Damian Garbicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; (B.B.); (D.G.)
| | - Marta Świtalska
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.Ś.); (J.W.)
| | - Marta K. Dudek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland;
| | - Dawid Warszycki
- Maj Institute of Pharmacology, Polish Academy of Sciences, 31-343 Cracow, Poland;
| | - Joanna Wietrzyk
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland; (M.Ś.); (J.W.)
| | - Elżbieta Grzesiuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; (B.B.); (D.G.)
| | - Adam Mieczkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; (B.B.); (D.G.)
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Blasl AT, Schulze S, Qin C, Graf LG, Vogt R, Lammers M. Post-translational lysine ac(et)ylation in health, ageing and disease. Biol Chem 2021; 403:151-194. [PMID: 34433238 DOI: 10.1515/hsz-2021-0139] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022]
Abstract
The acetylation/acylation (ac(et)ylation) of lysine side chains is a dynamic post-translational modification (PTM) regulating fundamental cellular processes with implications on the organisms' ageing process: metabolism, transcription, translation, cell proliferation, regulation of the cytoskeleton and DNA damage repair. First identified to occur on histones, later studies revealed the presence of lysine ac(et)ylation in organisms of all kingdoms of life, in proteins covering all essential cellular processes. A remarkable finding showed that the NAD+-dependent sirtuin deacetylase Sir2 has an impact on replicative lifespan in Saccharomyces cerevisiae suggesting that lysine acetylation has a direct role in the ageing process. Later studies identified sirtuins as mediators for beneficial effects of caloric/dietary restriction on the organisms' health- or lifespan. However, the molecular mechanisms underlying these effects are only incompletely understood. Progress in mass-spectrometry, structural biology, synthetic and semi-synthetic biology deepened our understanding of this PTM. This review summarizes recent developments in the research field. It shows how lysine ac(et)ylation regulates protein function, how it is regulated enzymatically and non-enzymatically, how a dysfunction in this post-translational machinery contributes to disease development. A focus is set on sirtuins and lysine acyltransferases as these are direct sensors and mediators of the cellular metabolic state. Finally, this review highlights technological advances to study lysine ac(et)ylation.
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Affiliation(s)
- Anna-Theresa Blasl
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Sabrina Schulze
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Chuan Qin
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Leonie G Graf
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Robert Vogt
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Michael Lammers
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
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Schmitt HM, Fehrman RL, Maes ME, Yang H, Guo LW, Schlamp CL, Pelzel HR, Nickells RW. Increased Susceptibility and Intrinsic Apoptotic Signaling in Neurons by Induced HDAC3 Expression. Invest Ophthalmol Vis Sci 2021; 62:14. [PMID: 34398198 PMCID: PMC8375002 DOI: 10.1167/iovs.62.10.14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 07/05/2021] [Indexed: 12/12/2022] Open
Abstract
Purpose Inhibition or targeted deletion of histone deacetylase 3 (HDAC3) is neuroprotective in a variety neurodegenerative conditions, including retinal ganglion cells (RGCs) after acute optic nerve damage. Consistent with this, induced HDAC3 expression in cultured cells shows selective toxicity to neurons. Despite an established role for HDAC3 in neuronal pathology, little is known regarding the mechanism of this pathology. Methods Induced expression of an HDAC3-mCherry fusion protein in mouse RGCs was accomplished by transduction with AAV2/2-Pgk-HDAC3-mCherry. Increased susceptibility to optic nerve damage in HDAC3-mCherry expressing RGCs was evaluated in transduced mice that received acute optic nerve crush surgery. Expression of HDAC3-FLAG or HDAC3-mCherry was induced by nucleofection or transfection of plasmids into differentiated or undifferentiated 661W tissue culture cells. Immunostaining for cleaved caspase 3, localization of a GFP-BAX fusion protein, and quantitative RT-PCR was used to evaluate HDAC3-induced damage. Results Induced expression of exogenous HDAC3 in RGCs by viral-mediated gene transfer resulted in modest levels of cell death but significantly increased the sensitivity of these neurons to axonal damage. Undifferentiated 661W retinal precursor cells were resilient to induced HDAC3 expression, but after differentiation, HDAC3 induced GFP-BAX recruitment to the mitochondria and BAX/BAK dependent activation of caspase 3. This was accompanied by an increase in accumulation of transcripts for the JNK2/3 kinases and the p53-regulated BH3-only gene Bbc3/Puma. Cell cycle arrest of undifferentiated 661W cells did not increase their sensitivity to HDAC3 expression. Conclusions Collectively, these results indicate that HDAC3-induced toxicity to neurons is mediated by the intrinsic apoptotic pathway.
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Affiliation(s)
- Heather M. Schmitt
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison WI, United States
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, United States
- Department of Ophthalmology, Duke University, Durham, NC, United States
| | - Rachel L. Fehrman
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison WI, United States
| | - Margaret E. Maes
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Huan Yang
- Department of Surgery, University of Wisconsin-Madison, Madison, WI, United States
| | - Lian-Wang Guo
- Department of Surgery, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - Cassandra L. Schlamp
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison WI, United States
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Heather R. Pelzel
- Department of Biological Sciences, University of Wisconsin-Whitewater, Whitewater, WI, United States
| | - Robert W. Nickells
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison WI, United States
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, United States
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Stietz J, Pollerhoff L, Kurtz M, Li SC, Reiter AMF, Kanske P. The ageing of the social mind: replicating the preservation of socio-affective and the decline of socio-cognitive processes in old age. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210641. [PMID: 34457343 PMCID: PMC8386516 DOI: 10.1098/rsos.210641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 08/04/2021] [Indexed: 05/06/2023]
Abstract
Anticipating population ageing to reach a historically unprecedented level in this century and considering the public goal of promoting well-being until old age, research in many fields has started to focus on processes and factors that contribute to healthy ageing. Since human interactions have a tremendous impact on our mental and physical well-being, scientists are increasingly investigating the basic processes that enable successful social interactions such as social affect (empathy, compassion) and social cognition (Theory of Mind). However, regarding the replication crisis in psychological science it is crucial to probe the reproducibility of findings revealed by each specific method. To this end, we aimed to replicate the effect of age on empathy, compassion and Theory of Mind observed in Reiter and colleagues' study (Reiter et al. 2017 Sci. Rep. 7, 11046 (doi:10.1038/s41598-017-10669-4)) by using the same ecologically valid paradigm in an independent sample with similar age ranges. We were able to replicate the previously observed results of a preservation or even enhancement in socio-affective processes, but a decline in socio-cognitive processes for older adults. Our findings add to the understanding of how social affect and cognition change across the adult lifespan and may suggest targets for intervention studies aiming to foster successful social interactions and well-being until advanced old age.
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Affiliation(s)
- Julia Stietz
- Clinical Psychology and Behavioral Neuroscience, Faculty of Psychology, Technische Universität Dresden, Dresden, Germany
| | - Lena Pollerhoff
- Lifespan Developmental Neuroscience, Faculty of Psychology, Technische Universität Dresden, Dresden, Germany
| | - Marcel Kurtz
- Clinical Psychology and Behavioral Neuroscience, Faculty of Psychology, Technische Universität Dresden, Dresden, Germany
| | - Shu-Chen Li
- Lifespan Developmental Neuroscience, Faculty of Psychology, Technische Universität Dresden, Dresden, Germany
- Centre for Tactile Internet with Human-in-the-Loop, Faculty of Psychology, Technische Universität Dresden, Dresden, Germany
| | - Andrea M. F. Reiter
- Lifespan Developmental Neuroscience, Faculty of Psychology, Technische Universität Dresden, Dresden, Germany
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Philipp Kanske
- Clinical Psychology and Behavioral Neuroscience, Faculty of Psychology, Technische Universität Dresden, Dresden, Germany
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
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Gupta K, Yadav P, Maryam S, Ahuja G, Sengupta D. Quantification of Age-Related Decline in Transcriptional Homeostasis. J Mol Biol 2021; 433:167179. [PMID: 34339725 DOI: 10.1016/j.jmb.2021.167179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 10/20/2022]
Abstract
Age-dependent dysregulation of transcription regulatory machinery triggers modulations in the gene expression levels leading to the decline in cellular fitness. Tracking of these transcripts along the temporal axis in multiple species revealed a spectrum of evolutionarily conserved pathways, such as electron transport chain, translation regulation, DNA repair, etc. Recent shreds of evidence suggest that aging deteriorates the transcription machinery itself, indicating the hidden complexity of the aging transcriptomes. This reinforces the need for devising novel computational methods to view aging through the lens of transcriptomics. Here, we present Homeostatic Divergence Score (HDS) to quantify the extent of messenger RNA (mRNA) homeostasis by assessing the balance between spliced and unspliced mRNA repertoire in single cells. We validated its utility in two independent aging datasets, and identified sets of genes undergoing age-related breakdown of transcriptional homeostasis. Moreover, testing of our method on a subpopulation of human embryonic stem cells revealed a set of differentially processed transcripts segregating these subpopulations. Our preliminary analyses in this direction suggest that mRNA processing level information offered by single-cell RNA sequencing (scRNA-seq) data is a superior determinant of chronological age as compared to transcriptional noise.
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Affiliation(s)
- Krishan Gupta
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India
| | - Princey Yadav
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India
| | - Sidrah Maryam
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India
| | - Gaurav Ahuja
- Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India.
| | - Debarka Sengupta
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India; Department of Computational Biology, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India; Centre for Artificial Intelligence, Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi), Okhla, Phase III, New Delhi 110020, India; Institute of Health and Biomedical Innovation, Queensland University of Technology, Australia.
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Abstract
Infections caused by protozoans remain a public health issue, especially in tropical countries. Serious adverse events, lack of efficacy at the different stages of the infection and routes of administration that have a negative impact on treatment adherence are some of the problems with currently available therapy against these diseases. Here we describe an epigenetic target, sirtuin 2 and its related proteins, that is promising given the results in phenotypic assays and in vivo models against Sir2 of Plasmodium falciparum, Leishmania donovani, Leishmania infantum, Schistosoma mansoni, Trypanosoma brucei and Trypanosoma cruzi parasites. The results we present highlight how this target can be extensively explored and how its inhibitors might be employed in the clinic.
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Pedro Ferreira J, Pitt B, Zannad F. Histone deacetylase inhibitors for cardiovascular conditions and healthy longevity. THE LANCET. HEALTHY LONGEVITY 2021; 2:e371-e379. [DOI: 10.1016/s2666-7568(21)00061-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/19/2021] [Accepted: 03/11/2021] [Indexed: 10/21/2022] Open
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50
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Leite JA, Ghirotto B, Targhetta VP, de Lima J, Câmara NOS. Sirtuins as pharmacological targets in neurodegenerative and neuropsychiatric disorders. Br J Pharmacol 2021; 179:1496-1511. [PMID: 34029375 DOI: 10.1111/bph.15570] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 12/16/2022] Open
Abstract
Histone deacetylases (HDACs) are enzymes that regulate several processes, such as transcription, cell proliferation, differentiation and development. HDACs are classified as either Zn2+ -dependent or NAD+ -dependent enzymes. Over the years, experimental and clinical evidence has demonstrated that HDAC modulation is a critical process in neurodegenerative and psychiatric disorders. Nevertheless, most of the studies have focused on the role of Zn2+ -dependent HDACs in the development of these diseases, although there is growing evidence showing that the NAD+ -dependent HDACs, known as sirtuins, are also very promising targets. This possibility has been strengthened by reports of decreased levels of NAD+ in CNS disorders, which can lead to alterations in sirtuin activation and therefore result in increased pathology. In this review, we discuss the role of sirtuins in neurodegenerative and neuropsychiatric disorders as well the possible rationale for them to be considered as pharmacological targets in future therapeutic interventions.
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Affiliation(s)
- Jefferson A Leite
- Department of Biochemistry and Immunology, Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.,Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Bruno Ghirotto
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Vitor P Targhetta
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jean de Lima
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Niels O S Câmara
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Division of Nephrology, School of Medicine, Federal University of São Paulo, São Paulo, Brazil
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