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Pan S, Wang X, Jiao J, Zhang L. The role of histone deacetylases in inflammatory respiratory diseases: an update. Expert Rev Clin Immunol 2024:1-11. [PMID: 38823008 DOI: 10.1080/1744666x.2024.2363803] [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: 02/02/2024] [Accepted: 05/31/2024] [Indexed: 06/03/2024]
Abstract
INTRODUCTION Histone deacetylases (HDACs) catalyze the removal of acetyl groups from lysine residues of histones and other proteins, generally leading to a closed chromosomal configuration and transcriptional repression. Different HDACs have distinct substrate specificities and functions in different biological processes. Accumulating evidence indicates that HDACs play a key role in the pathogenesis of multiple respiratory diseases. AREAS COVERED After an extensive search of the PubMed database, Web of Science and ClinicalTrials.gov, covering the period from 1992 to 2024, this review summarizes recent advances in understanding the role of HDACs in inflammatory respiratory diseases, including allergic rhinitis (AR), chronic rhinosinusitis (CRS), asthma and chronic obstructive pulmonary disease (COPD). We also examine recent progress on the efficacy and potential use of histone deacetylase inhibitors (HDACi) for the treatment of these diseases. EXPERT OPINION Available data indicate that HDACs play an important role in the development of common inflammatory respiratory diseases, and HDACi have shown promise as treatments for these diseases. However, the exact roles and underlying mechanisms of specific HDACs in disease pathogenesis require further study. Additional work is necessary to develop novel potent HDACi with high isoform selectivity.
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Affiliation(s)
- Sicen Pan
- Department of Otolaryngology Head and Neck surgery and Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Otolaryngology, Beijing Laboratory of Allergic Diseases, Beijing Key Laboratory of Nasal Diseases, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China
| | - Xiangdong Wang
- Department of Otolaryngology Head and Neck surgery and Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Otolaryngology, Beijing Laboratory of Allergic Diseases, Beijing Key Laboratory of Nasal Diseases, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China
| | - Jian Jiao
- Department of Otolaryngology Head and Neck surgery and Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Otolaryngology, Beijing Laboratory of Allergic Diseases, Beijing Key Laboratory of Nasal Diseases, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China
| | - Luo Zhang
- Department of Otolaryngology Head and Neck surgery and Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China
- Beijing Institute of Otolaryngology, Beijing Laboratory of Allergic Diseases, Beijing Key Laboratory of Nasal Diseases, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China
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Chinellato M, Perin S, Carli A, Lastella L, Biondi B, Borsato G, Di Giorgio E, Brancolini C, Cendron L, Angelini A. Folding of Class IIa HDAC Derived Peptides into α-helices Upon Binding to Myocyte Enhancer Factor-2 in Complex with DNA. J Mol Biol 2024; 436:168541. [PMID: 38492719 DOI: 10.1016/j.jmb.2024.168541] [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: 10/15/2023] [Revised: 02/27/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Interaction of transcription factor myocyte enhancer factor-2 (MEF2) family members with class IIa histone deacetylases (HDACs) has been implicated in a wide variety of diseases. Though considerable knowledge on this topic has been accumulated over the years, a high resolution and detailed analysis of the binding mode of multiple class IIa HDAC derived peptides with MEF2D is still lacking. To fulfil this gap, we report here the crystal structure of MEF2D in complex with double strand DNA and four different class IIa HDAC derived peptides, namely HDAC4, HDAC5, HDAC7 and HDAC9. All class IIa HDAC derived peptides form extended amphipathic α-helix structures that fit snugly in the hydrophobic groove of MEF2D domain. Binding mode of class IIa HDAC derived peptides to MEF2D is very similar and occur primarily through nonpolar interactions mediated by highly conserved branched hydrophobic amino acids. Further studies revealed that class IIa HDAC derived peptides are unstructured in solution and appear to adopt a folded α-helix structure only upon binding to MEF2D. Comparison of our peptide-protein complexes with previously characterized structures of MEF2 bound to different co-activators and co-repressors, highlighted both differences and similarities, and revealed the adaptability of MEF2 in protein-protein interactions. The elucidation of the three-dimensional structure of MEF2D in complex with multiple class IIa HDAC derived peptides provide not only a better understanding of the molecular basis of their interactions but also have implications for the development of novel antagonist.
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Affiliation(s)
- Monica Chinellato
- Department of Biology, University of Padua, Via U. Bassi 58, 35131 Padova, Italy
| | - Stefano Perin
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy
| | - Alberto Carli
- Department of Biology, University of Padua, Via U. Bassi 58, 35131 Padova, Italy
| | - Luana Lastella
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Via Marzolo 1, 35131 Padova, Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Via Marzolo 1, 35131 Padova, Italy
| | - Giuseppe Borsato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy
| | - Eros Di Giorgio
- Department of Medicine, Università Degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Claudio Brancolini
- Department of Medicine, Università Degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Laura Cendron
- Department of Biology, University of Padua, Via U. Bassi 58, 35131 Padova, Italy.
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy; European Centre for Living Technology (ECLT), Ca' Bottacin, Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy.
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Veerapaneni P, Goo B, Ahmadieh S, Shi H, Kim DS, Ogbi M, Cave S, Chouhaita R, Cyriac N, Fulton DJ, Verin AD, Chen W, Lei Y, Lu XY, Kim HW, Weintraub NL. Transgenic Overexpression of HDAC9 Promotes Adipocyte Hypertrophy, Insulin Resistance and Hepatic Steatosis in Aging Mice. Biomolecules 2024; 14:494. [PMID: 38672510 PMCID: PMC11048560 DOI: 10.3390/biom14040494] [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: 02/13/2024] [Revised: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Histone deacetylase (HDAC) 9 is a negative regulator of adipogenic differentiation, which is required for maintenance of healthy adipose tissues. We reported that HDAC9 expression is upregulated in adipose tissues during obesity, in conjunction with impaired adipogenic differentiation, adipocyte hypertrophy, insulin resistance, and hepatic steatosis, all of which were alleviated by global genetic deletion of Hdac9. Here, we developed a novel transgenic (TG) mouse model to test whether overexpression of Hdac9 is sufficient to induce adipocyte hypertrophy, insulin resistance, and hepatic steatosis in the absence of obesity. HDAC9 TG mice gained less body weight than wild-type (WT) mice when fed a standard laboratory diet for up to 40 weeks, which was attributed to reduced fat mass (primarily inguinal adipose tissue). There was no difference in insulin sensitivity or glucose tolerance in 18-week-old WT and HDAC9 TG mice; however, at 40 weeks of age, HDAC9 TG mice exhibited impaired insulin sensitivity and glucose intolerance. Tissue histology demonstrated adipocyte hypertrophy, along with reduced numbers of mature adipocytes and stromovascular cells, in the HDAC9 TG mouse adipose tissue. Moreover, increased lipids were detected in the livers of aging HDAC9 TG mice, as evaluated by oil red O staining. In conclusion, the experimental aging HDAC9 TG mice developed adipocyte hypertrophy, insulin resistance, and hepatic steatosis, independent of obesity. This novel mouse model may be useful in the investigation of the impact of Hdac9 overexpression associated with metabolic and aging-related diseases.
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Affiliation(s)
- Praneet Veerapaneni
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA; (P.V.); (B.G.); (S.A.); (H.S.); (D.S.K.); (M.O.); (S.C.); (R.C.); (N.C.); (D.J.F.); (A.D.V.); (H.W.K.)
| | - Brandee Goo
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA; (P.V.); (B.G.); (S.A.); (H.S.); (D.S.K.); (M.O.); (S.C.); (R.C.); (N.C.); (D.J.F.); (A.D.V.); (H.W.K.)
| | - Samah Ahmadieh
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA; (P.V.); (B.G.); (S.A.); (H.S.); (D.S.K.); (M.O.); (S.C.); (R.C.); (N.C.); (D.J.F.); (A.D.V.); (H.W.K.)
| | - Hong Shi
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA; (P.V.); (B.G.); (S.A.); (H.S.); (D.S.K.); (M.O.); (S.C.); (R.C.); (N.C.); (D.J.F.); (A.D.V.); (H.W.K.)
- Department of Medicine, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA
| | - David S. Kim
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA; (P.V.); (B.G.); (S.A.); (H.S.); (D.S.K.); (M.O.); (S.C.); (R.C.); (N.C.); (D.J.F.); (A.D.V.); (H.W.K.)
| | - Mourad Ogbi
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA; (P.V.); (B.G.); (S.A.); (H.S.); (D.S.K.); (M.O.); (S.C.); (R.C.); (N.C.); (D.J.F.); (A.D.V.); (H.W.K.)
| | - Stephen Cave
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA; (P.V.); (B.G.); (S.A.); (H.S.); (D.S.K.); (M.O.); (S.C.); (R.C.); (N.C.); (D.J.F.); (A.D.V.); (H.W.K.)
| | - Ronnie Chouhaita
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA; (P.V.); (B.G.); (S.A.); (H.S.); (D.S.K.); (M.O.); (S.C.); (R.C.); (N.C.); (D.J.F.); (A.D.V.); (H.W.K.)
| | - Nicole Cyriac
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA; (P.V.); (B.G.); (S.A.); (H.S.); (D.S.K.); (M.O.); (S.C.); (R.C.); (N.C.); (D.J.F.); (A.D.V.); (H.W.K.)
| | - David J. Fulton
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA; (P.V.); (B.G.); (S.A.); (H.S.); (D.S.K.); (M.O.); (S.C.); (R.C.); (N.C.); (D.J.F.); (A.D.V.); (H.W.K.)
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA
| | - Alexander D. Verin
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA; (P.V.); (B.G.); (S.A.); (H.S.); (D.S.K.); (M.O.); (S.C.); (R.C.); (N.C.); (D.J.F.); (A.D.V.); (H.W.K.)
- Department of Medicine, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA
| | - Weiqin Chen
- Department of Physiology, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA;
| | - Yun Lei
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA; (Y.L.); (X.-Y.L.)
| | - Xin-Yun Lu
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA; (Y.L.); (X.-Y.L.)
| | - Ha Won Kim
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA; (P.V.); (B.G.); (S.A.); (H.S.); (D.S.K.); (M.O.); (S.C.); (R.C.); (N.C.); (D.J.F.); (A.D.V.); (H.W.K.)
- Department of Medicine, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA
| | - Neal L. Weintraub
- Vascular Biology Center, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA; (P.V.); (B.G.); (S.A.); (H.S.); (D.S.K.); (M.O.); (S.C.); (R.C.); (N.C.); (D.J.F.); (A.D.V.); (H.W.K.)
- Department of Medicine, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA 30912, USA
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Chen Y, Guo P, Dong Z. The role of histone acetylation in transcriptional regulation and seed development. PLANT PHYSIOLOGY 2024; 194:1962-1979. [PMID: 37979164 DOI: 10.1093/plphys/kiad614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/09/2023] [Accepted: 10/29/2023] [Indexed: 11/20/2023]
Abstract
Histone acetylation is highly conserved across eukaryotes and has been linked to gene activation since its discovery nearly 60 years ago. Over the past decades, histone acetylation has been evidenced to play crucial roles in plant development and response to various environmental cues. Emerging data indicate that histone acetylation is one of the defining features of "open chromatin," while the role of histone acetylation in transcription remains controversial. In this review, we briefly describe the discovery of histone acetylation, the mechanism of histone acetylation regulating transcription in yeast and mammals, and summarize the research progress of plant histone acetylation. Furthermore, we also emphasize the effect of histone acetylation on seed development and its potential use in plant breeding. A comprehensive knowledge of histone acetylation might provide new and more flexible research perspectives to enhance crop yield and stress resistance.
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Affiliation(s)
- Yan Chen
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Peiguo Guo
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Zhicheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
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Das T, Khatun S, Jha T, Gayen S. HDAC9 as a Privileged Target: Reviewing its Role in Different Diseases and Structure-activity Relationships (SARs) of its Inhibitors. Mini Rev Med Chem 2024; 24:767-784. [PMID: 37818566 DOI: 10.2174/0113895575267301230919165827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/17/2023] [Accepted: 08/11/2023] [Indexed: 10/12/2023]
Abstract
HDAC9 is a histone deacetylase enzyme belonging to the class IIa of HDACs which catalyses histone deacetylation. HDAC9 inhibit cell proliferation by repairing DNA, arresting the cell cycle, inducing apoptosis, and altering genetic expression. HDAC9 plays a significant part in human physiological system and are involved in various type of diseases like cancer, diabetes, atherosclerosis and CVD, autoimmune response, inflammatory disease, osteoporosis and liver fibrosis. This review discusses the role of HDAC9 in different diseases and structure-activity relationships (SARs) of various hydroxamate and non-hydroxamate-based inhibitors. SAR of compounds containing several scaffolds have been discussed in detail. Moreover, structural requirements regarding the various components of HDAC9 inhibitor (cap group, linker and zinc-binding group) has been highlighted in this review. Though, HDAC9 is a promising target for the treatment of a number of diseases including cancer, a very few research are available. Thus, this review may provide useful information for designing novel HDAC9 inhibitors to fight against different diseases in the future.
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Affiliation(s)
- Totan Das
- Department of Pharmaceutical Technology, Laboratory of Drug Design and Discovery, Jadavpur University, Kolkata, 700032, India
| | - Samima Khatun
- Department of Pharmaceutical Technology, Laboratory of Drug Design and Discovery, Jadavpur University, Kolkata, 700032, India
| | - Tarun Jha
- Department of Pharmaceutical Technology, Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Jadavpur University, Kolkata, 700032, India
| | - Shovanlal Gayen
- Department of Pharmaceutical Technology, Laboratory of Drug Design and Discovery, Jadavpur University, Kolkata, 700032, India
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Abstract
The identification of a variant in the HDAC9 gene as a risk factor for large-artery atherosclerotic stroke, and subsequently coronary artery disease, has opened novel treatment pathways for stroke and more widely atherosclerotic disease. This article describes the pathway from gene discovery to novel therapeutic approaches that are now entering man. HDAC9 expression is elevated in human atherosclerotic plaque, while in animal and cellular models, reducing HDAC9 (histone deacetylase 9) protein is associated with reduced disease. Several mechanisms have been proposed to account for the association between HDAC9 and atherosclerosis including alterations in the inflammatory response and cholesterol efflux and endothelial-mesenchymal transition. The association raises the possibility that inhibiting HDAC9 may provide a novel treatment approach for atherosclerotic cardiovascular disease. This is supported by intervention studies demonstrating HDAC9 inhibition reduces atherosclerosis in animal and cellular models. Indirect data support such an approach in man. The antiseizure drug sodium valproate, which has nonspecific HDAC inhibitory properties, both inhibits atherosclerosis in animal models and is epidemiologically associated with reduced stroke and myocardial infarction risk in man. It is now being trailed in phase 2 studies in large-artery stroke, while more specific HDAC9 inhibitors are being developed.
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Affiliation(s)
- Hugh S Markus
- Stroke Research Group, Department of Clinical Neurosciences, University of Cambridge, United Kingdom
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Drakontaeidi A, Pontiki E. A Review on Molecular Docking on HDAC Isoforms: Novel Tool for Designing Selective Inhibitors. Pharmaceuticals (Basel) 2023; 16:1639. [PMID: 38139766 PMCID: PMC10746130 DOI: 10.3390/ph16121639] [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: 10/08/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 12/24/2023] Open
Abstract
Research into histone deacetylases (HDACs) has experienced a remarkable surge in recent years. These enzymes are key regulators of several fundamental biological processes, often associated with severe and potentially fatal diseases. Inhibition of their activity represents a promising therapeutic approach and a prospective strategy for the development of new therapeutic agents. A critical aspect of their inhibition is to achieve selectivity in terms of enzyme isoforms, which is essential to improve treatment efficacy while reducing undesirable pleiotropic effects. The development of computational chemistry tools, particularly molecular docking, is greatly enhancing the precision of designing molecules with inherent potential for specific activity. Therefore, it was considered necessary to review the molecular docking studies conducted on the major isozymes of the enzyme in order to identify the specific interactions associated with each selective HDAC inhibitor. In particular, the most critical isozymes of HDAC (1, 2, 3, 6, and 8) have been thoroughly investigated within the scope of this review.
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Affiliation(s)
| | - Eleni Pontiki
- Department of Pharmaceutical Chemistry, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
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Kumari S, Gupta R, Ambasta RK, Kumar P. Emerging trends in post-translational modification: Shedding light on Glioblastoma multiforme. Biochim Biophys Acta Rev Cancer 2023; 1878:188999. [PMID: 37858622 DOI: 10.1016/j.bbcan.2023.188999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023]
Abstract
Recent multi-omics studies, including proteomics, transcriptomics, genomics, and metabolomics have revealed the critical role of post-translational modifications (PTMs) in the progression and pathogenesis of Glioblastoma multiforme (GBM). Further, PTMs alter the oncogenic signaling events and offer a novel avenue in GBM therapeutics research through PTM enzymes as potential biomarkers for drug targeting. In addition, PTMs are critical regulators of chromatin architecture, gene expression, and tumor microenvironment (TME), that play a crucial function in tumorigenesis. Moreover, the implementation of artificial intelligence and machine learning algorithms enhances GBM therapeutics research through the identification of novel PTM enzymes and residues. Herein, we briefly explain the mechanism of protein modifications in GBM etiology, and in altering the biologics of GBM cells through chromatin remodeling, modulation of the TME, and signaling pathways. In addition, we highlighted the importance of PTM enzymes as therapeutic biomarkers and the role of artificial intelligence and machine learning in protein PTM prediction.
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Affiliation(s)
- Smita Kumari
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological, University, India
| | - Rohan Gupta
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological, University, India; School of Medicine, University of South Carolina, Columbia, SC, United States of America
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological, University, India; Department of Biotechnology and Microbiology, SRM University, Sonepat, Haryana, India.
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological, University, India.
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Szczepanek J, Tretyn A. MicroRNA-Mediated Regulation of Histone-Modifying Enzymes in Cancer: Mechanisms and Therapeutic Implications. Biomolecules 2023; 13:1590. [PMID: 38002272 PMCID: PMC10669115 DOI: 10.3390/biom13111590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
In the past decade, significant advances in molecular research have provided a deeper understanding of the intricate regulatory mechanisms involved in carcinogenesis. MicroRNAs, short non-coding RNA sequences, exert substantial influence on gene expression by repressing translation or inducing mRNA degradation. In the context of cancer, miRNA dysregulation is prevalent and closely associated with various stages of carcinogenesis, including initiation, progression, and metastasis. One crucial aspect of the cancer phenotype is the activity of histone-modifying enzymes that govern chromatin accessibility for transcription factors, thus impacting gene expression. Recent studies have revealed that miRNAs play a significant role in modulating these histone-modifying enzymes, leading to significant implications for genes related to proliferation, differentiation, and apoptosis in cancer cells. This article provides an overview of current research on the mechanisms by which miRNAs regulate the activity of histone-modifying enzymes in the context of cancer. Both direct and indirect mechanisms through which miRNAs influence enzyme expression are discussed. Additionally, potential therapeutic implications arising from miRNA manipulation to selectively impact histone-modifying enzyme activity are presented. The insights from this analysis hold significant therapeutic promise, suggesting the utility of miRNAs as tools for the precise regulation of chromatin-related processes and gene expression. A contemporary focus on molecular regulatory mechanisms opens therapeutic pathways that can effectively influence the control of tumor cell growth and dissemination.
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Affiliation(s)
- Joanna Szczepanek
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, ul. Wilenska 4, 87-100 Torun, Poland
| | - Andrzej Tretyn
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, ul. Lwowska 1, 87-100 Torun, Poland;
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Deng SZ, Wu X, Tang J, Dai L, Cheng B. Integrative analysis of lysine acetylation-related genes and identification of a novel prognostic model for oral squamous cell carcinoma. Front Mol Biosci 2023; 10:1185832. [PMID: 37705968 PMCID: PMC10495994 DOI: 10.3389/fmolb.2023.1185832] [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: 03/28/2023] [Accepted: 08/17/2023] [Indexed: 09/15/2023] Open
Abstract
Introduction: Oral squamous cell carcinoma (OSCC), which accounts for a high proportion of oral cancers, is characterized by high aggressiveness and rising incidence. Lysine acetylation is associated with cancer pathogenesis. Lysine acetylation-related genes (LARGs) are therapeutic targets and potential prognostic indicators in various tumors, including oral squamous cell carcinoma. However, systematic bioinformatics analysis of the Lysine acetylation-related genes in Oral squamous cell carcinoma is still unexplored. Methods: We analyzed the expression of 33 Lysine acetylation-related genes in oral squamous cell carcinoma and the effects of their somatic mutations on oral squamous cell carcinoma prognosis. Consistent clustering analysis identified two lysine acetylation patterns and the differences between the two patterns were further evaluated. Least absolute shrinkage and selection operator (LASSO) regression analysis was used to develop a lysine acetylation-related prognostic model using TCGA oral squamous cell carcinoma datasets, which was then validated using gene expression omnibus (GEO) dataset GSE41613. Results: Patients with lower risk scores had better prognoses, in both the overall cohort and within the subgroups These patients also had "hot" immune microenvironments and were more sensitive to immunotherapy. Disscussion: Our findings offer a new model for classifying oral squamous cell carcinoma and determining its prognosis and offer novel insights into oral squamous cell carcinoma diagnosis and treatment.
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Affiliation(s)
- Shi-Zhou Deng
- Department of Hepatobiliary Surgery, Xi-Jing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Xuechen Wu
- Department of Stomatology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiezhang Tang
- Department of Burn and Plastic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi’an, China
| | - Lin Dai
- Department of Stomatology, The First Hospital of Wuhan, Wuhan, China
| | - Bo Cheng
- Department of Stomatology, Zhongnan Hospital of Wuhan University, Wuhan, China
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Lin Y, Jing X, Chen Z, Pan X, Xu D, Yu X, Zhong F, Zhao L, Yang C, Wang B, Wang S, Ye Y, Shen Z. Histone deacetylase-mediated tumor microenvironment characteristics and synergistic immunotherapy in gastric cancer. Theranostics 2023; 13:4574-4600. [PMID: 37649598 PMCID: PMC10465215 DOI: 10.7150/thno.86928] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/07/2023] [Indexed: 09/01/2023] Open
Abstract
Background: Studies have shown that the expression of histone deacetylases (HDACs) is significantly related to the tumor microenvironment (TME) in gastric cancer. However, the expression of a single molecule or several molecules does not accurately reflect the TME characteristics or guide immunotherapy in gastric cancer. Methods: We constructed an HDAC score (HDS) based on the expression level of HDACs. The single-cell transcriptome was used to analyze the underlying factors contributing to differences in immune infiltration between patients with a high and low HDS. In vitro and in vivo experiments validated the strategy of transforming cold tumors into hot tumors to guide immunotherapy. Results: According to the expression characteristics of HDACs, we constructed an HDS model to characterize the TME. We found that patients with a high HDS had stronger immunogenicity and could benefit more from immunotherapy than those with a low score. The AUC value of the HDS combined with the combined positive score (CPS)for predicting the efficacy of immunotherapy was as high as 0.96. By single-cell and paired bulk transcriptome sequencing analysis, we found that the infiltration levels of CD4+ T cells, CD8+ T cells and NK cells were significantly decreased in the low HDS group, which may be induced by MYH11+ fibroblasts, CD234+ endothelial cells and CCL17+ pDCs via the MIF signaling pathway. Inhibition of the MIF signaling pathway was confirmed to potentially enhance immune infiltration. In addition, our analysis revealed that GPX4 inhibitors might be effective for patients with a low HDS. GPX4 knockout significantly inhibited PD-L1 expression and promoted the infiltration and activation of CD8+ T cells. Conclusion: We constructed an HDS model based on the HDAC expression characteristics of gastric cancer. This model was used to evaluate TME characteristics and predict immunotherapy efficacy. Inhibition of the MIF signaling pathway in the TME and GPX4 expression in tumor cells may be an important strategy for cold tumor synergistic immunotherapy for gastric cancer.
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Affiliation(s)
- Yilin Lin
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing 100044, PR China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing 100044, PR China
| | - Xiangxiang Jing
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing 100044, PR China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing 100044, PR China
| | - Zhihua Chen
- Department of Gastrointestinal surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, 350000, PR China
| | - Xiaoxian Pan
- Department of Radiotherapy, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, 350000, PR China
| | - Duo Xu
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing 100044, PR China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing 100044, PR China
| | - Xiang Yu
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing 100044, PR China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing 100044, PR China
| | - Fengyun Zhong
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing 100044, PR China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing 100044, PR China
| | - Long Zhao
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing 100044, PR China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing 100044, PR China
| | - Changjiang Yang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing 100044, PR China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing 100044, PR China
| | - Bo Wang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing 100044, PR China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing 100044, PR China
| | - Shan Wang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing 100044, PR China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing 100044, PR China
| | - Yingjiang Ye
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing 100044, PR China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing 100044, PR China
| | - Zhanlong Shen
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing 100044, PR China
- Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing 100044, PR China
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12
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He Y, Liu T. Oxidized low-density lipoprotein regulates macrophage polarization in atherosclerosis. Int Immunopharmacol 2023; 120:110338. [PMID: 37210916 DOI: 10.1016/j.intimp.2023.110338] [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: 02/28/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
Atherosclerosis is the pathological basis of acute cardiovascular and cerebrovascular diseases. Oxidized LDL has been recognized as a major atherogenic factor in the vessel wall for decades. A growing body of evidence suggests that oxidized LDL modulates macrophage phenotypes in atherosclerosis. This article reviews the research progress on the regulation of macrophage polarization by oxidized LDL. Mechanistically, oxidized LDL induces macrophage polarization via cell signaling, metabolic reprogramming, epigenetic regulation, and intercellular regulation. This review is expected to provide new targets for the treatment of atherosclerosis.
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Affiliation(s)
- Yonghang He
- The Second Clinical Medical College, Guangdong Medical University, Dongguan, 523808, China
| | - Tingting Liu
- The First Dongguan Affiliated Hospital, Guangdong Medical University, No. 42 Jiaoping Road, Tangxia Town, Dongguan City, Guangdong Province 523710, China; The Second Clinical Medical College, Guangdong Medical University, Dongguan, 523808, China.
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13
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Sehgal M, Jakhete SM, Manekar AG, Sasikumar S. Specific epigenetic regulators serve as potential therapeutic targets in idiopathic pulmonary fibrosis. Heliyon 2022; 8:e09773. [PMID: 36061031 PMCID: PMC9434059 DOI: 10.1016/j.heliyon.2022.e09773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/27/2022] [Accepted: 06/17/2022] [Indexed: 12/15/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF), a disorder observed mostly in older human beings, is characterised by chronic and progressive lung scarring leading to an irreversible decline in lung function. This health condition has a dismal prognosis and the currently available drugs only delay but fail to reverse the progression of lung damage. Consequently, it becomes imperative to discover improved therapeutic compounds and their cellular targets to cure IPF. In this regard, a number of recent studies have targeted the epigenetic regulation by histone deacetylases (HDACs) to develop and categorise antifibrotic drugs for lungs. Therefore, this review focuses on how aberrant expression or activity of Classes I, II and III HDACs alter TGF-β signalling to promote events such as epithelial-mesenchymal transition, differentiation of activated fibroblasts into myofibroblasts, and excess deposition of the extracellular matrix to propel lung fibrosis. Further, this study describes how certain chemical compounds or dietary changes modulate dysregulated HDACs to attenuate five faulty TGF-β-dependent profibrotic processes, both in animal models and cell lines replicating IPF, thereby identifying promising means to treat this lung disorder.
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Affiliation(s)
- Manas Sehgal
- Genetics and Molecular Biology Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Tathawade, Pune, Maharashtra, PIN - 411033, India
| | - Sharayu Manish Jakhete
- Genetics and Molecular Biology Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Tathawade, Pune, Maharashtra, PIN - 411033, India
| | - Amruta Ganesh Manekar
- Genetics and Molecular Biology Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Tathawade, Pune, Maharashtra, PIN - 411033, India
| | - Satish Sasikumar
- Genetics and Molecular Biology Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Tathawade, Pune, Maharashtra, PIN - 411033, India
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14
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Jafarzadeh A, Noori M, Sarrafzadeh S, Tamehri Zadeh SS, Nemati M, Chatrabnous N, Jafarzadeh S, Hamblin MR, Jafari Najaf Abadi MH, Mirzaei H. MicroRNA-383: A tumor suppressor miRNA in human cancer. Front Cell Dev Biol 2022; 10:955486. [PMID: 36313570 PMCID: PMC9608775 DOI: 10.3389/fcell.2022.955486] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/23/2022] [Indexed: 02/05/2023] Open
Abstract
Downregulated expression of anti-tumor miR-383 has been found in many kinds of cancer. MiR-383 family members can directly target the 3'-untranslated region (3'-UTR) of the mRNA of some pro-tumor genes to attenuate several cancer-related processes, including cell proliferation, invasion, migration, angiogenesis, immunosuppression, epithelial-mesenchymal transition, glycolysis, chemoresistance, and the development of cancer stem cells, whilst promoting apoptosis. Functionally, miR-383 operates as a tumor inhibitor miRNA in many types of cancer, including breast cancer, hepatocellular carcinoma, gastric cancer, pancreatic cancer, colorectal cancer, esophageal cancer, lung cancer, head and neck cancer, glioma, medulloblastoma, melanoma, prostate cancer, cervical cancer, oral squamous cell carcinoma, thyroid cancer, and B-cell lymphoma. Both pro-tumor and anti-tumor effects have been attributed to miR-383 in ovarian cancer. However, only the pro-tumor effects of miR-383 were reported in cholangiocarcinoma. The restoration of miR-383 expression could be considered a possible treatment for cancer. This review discusses the anti-tumor effects of miR-383 in human cancers, emphasizing their downstream target genes and potential treatment approaches.
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Affiliation(s)
- Abdollah Jafarzadeh
- Department of Immunology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
- Immunology of Infectious Diseases Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
- *Correspondence: Abdollah Jafarzadeh, ; Mohammad Hassan Jafari Najaf Abadi, ; Hamed Mirzaei,
| | - Majid Noori
- Golestan Hospital Research Center, AJA University of Medical Sciences, Tehran, Iran
| | - Shaghayegh Sarrafzadeh
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Maryam Nemati
- Department of Immunology, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
- Department of Hematology and Laboratory Sciences, School of Para-Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Nazanin Chatrabnous
- Endocrinology and Metabolism Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sara Jafarzadeh
- Student Research Committee, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Johannesburg, South Africa
| | - Mohammad Hassan Jafari Najaf Abadi
- Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- *Correspondence: Abdollah Jafarzadeh, ; Mohammad Hassan Jafari Najaf Abadi, ; Hamed Mirzaei,
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
- *Correspondence: Abdollah Jafarzadeh, ; Mohammad Hassan Jafari Najaf Abadi, ; Hamed Mirzaei,
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15
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Yang J, Song C, Zhan X. The role of protein acetylation in carcinogenesis and targeted drug discovery. Front Endocrinol (Lausanne) 2022; 13:972312. [PMID: 36171897 PMCID: PMC9510633 DOI: 10.3389/fendo.2022.972312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/23/2022] [Indexed: 12/01/2022] Open
Abstract
Protein acetylation is a reversible post-translational modification, and is involved in many biological processes in cells, such as transcriptional regulation, DNA damage repair, and energy metabolism, which is an important molecular event and is associated with a wide range of diseases such as cancers. Protein acetylation is dynamically regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs) in homeostasis. The abnormal acetylation level might lead to the occurrence and deterioration of a cancer, and is closely related to various pathophysiological characteristics of a cancer, such as malignant phenotypes, and promotes cancer cells to adapt to tumor microenvironment. Therapeutic modalities targeting protein acetylation are a potential therapeutic strategy. This article discussed the roles of protein acetylation in tumor pathology and therapeutic drugs targeting protein acetylation, which offers the contributions of protein acetylation in clarification of carcinogenesis, and discovery of therapeutic drugs for cancers, and lays the foundation for precision medicine in oncology.
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Affiliation(s)
- Jingru Yang
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Cong Song
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Xianquan Zhan
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
- *Correspondence: Xianquan Zhan,
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16
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Lu J, He X, Zhang L, Zhang R, Li W. Acetylation in Tumor Immune Evasion Regulation. Front Pharmacol 2021; 12:771588. [PMID: 34880761 PMCID: PMC8645962 DOI: 10.3389/fphar.2021.771588] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/05/2021] [Indexed: 12/24/2022] Open
Abstract
Acetylation is considered as one of the most common types of epigenetic modifications, and aberrant histone acetylation modifications are associated with the pathological process of cancer through the regulation of oncogenes and tumor suppressors. Recent studies have shown that immune system function and tumor immunity can also be affected by acetylation modifications. A comprehensive understanding of the role of acetylation function in cancer is essential, which may help to develop new therapies to improve the prognosis of cancer patients. In this review, we mainly discussed the functions of acetylase and deacetylase in tumor, immune system and tumor immunity, and listed the information of drugs targeting these enzymes in tumor immunotherapy.
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Affiliation(s)
- Jun Lu
- Hunan Normal University School of Medicine, Changsha, China.,Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China
| | - Xiang He
- Key Laboratory of Molecular Radiation Oncology Hunan Province, Changsha, China.,Xiangya Cancer Center, Xiangya Hospital, Central South University, Changsha, China
| | - Lijuan Zhang
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, China
| | - Ran Zhang
- Hunan Normal University School of Medicine, Changsha, China
| | - Wenzheng Li
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, China
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