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Jin G, Ho JW, Keeney-Bonthrone TP, Pai MP, Wen B, Ober RA, Dimonte D, Chtraklin K, Joaquin TA, Latif Z, Vercruysse C, Alam HB. Prolonging the therapeutic window for valproic acid treatment in a swine model of traumatic brain injury and hemorrhagic shock. J Trauma Acute Care Surg 2023; 95:657-663. [PMID: 37314445 DOI: 10.1097/ta.0000000000004022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND It has previously been shown that administration of valproic acid (VPA) can improve outcomes if given within an hour following traumatic brain injury (TBI). This short therapeutic window (TW) limits its use in real-life situations. Based upon its pharmacokinetic data, we hypothesized that TW can be extended to 3 hours if a second dose of VPA is given 8 hours after the initial dose. METHOD Yorkshire swine (40-45 kg; n = 10) were subjected to TBI (controlled cortical impact) and 40% blood volume hemorrhage. After 2 hours of shock, they were randomized to either (1) normal saline resuscitation (control) or (2) normal saline-VPA (150 mg/kg × two doses). First dose of VPA was started 3 hours after the TBI, with a second dose 8 hours after the first dose. Neurologic severity scores (range, 0-36) were assessed daily for 14 days, and brain lesion size was measured via magnetic resonance imaging on postinjury day 3. RESULTS Hemodynamic and laboratory parameters of shock were similar in both groups. Valproic acid-treated animals had significantly less neurologic impairment on days 2 (16.3 ± 2.0 vs. 7.3 ± 2.8) and 3 (10.9 ± 3.6 vs. 2.8 ± 1.1) postinjury and returned to baseline levels 54% faster. Magnetic resonance imaging showed no differences in brain lesion size on day 3. Pharmacokinetic data confirmed neuroprotective levels of VPA in the circulation. CONCLUSION This is the first study to demonstrate that VPA can be neuroprotective even when given 3 hours after TBI. This expanded TW has significant implications for the design of the clinical trial.
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Affiliation(s)
- Guang Jin
- From the Department of Surgery (G.J., J.W.H., T.P.K.-B., K.C., T.A.J., Z.L., C.V., H.B.A.), Feinberg School of Medicine, Northwestern University, Chicago; Department of Clinical Pharmacy (M.P.P., B.W.), University of Michigan, Ann Arbor, Michigan; Center for Comparative Medicine (R.A.O.), Northwestern University, Chicago; and Electrical and Computer Engineering (D.D.), Robert R. McCormick School, Northwestern University, Evanston, Illinois
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Zu G, Sun Z, Chen Y, Geng J, Lv J, You Z, Jiang C, Sheng Q, Nie Z. The acetyltransferase BmCBP changes the acetylation modification of BmSP3 and affects its protein expression in silkworm, Bombyx mori. Mol Biol Rep 2023; 50:8509-8521. [PMID: 37642757 DOI: 10.1007/s11033-023-08699-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND Protein acetylation is an important post-translational modification (PTM) that widely exists in organisms. As a reversible PTM, acetylation modification can regulate the function of proteins with high efficiency. In the previous study, the acetylation sites of silkworm proteins were identified on a large scale by nano-HPLC/MS/MS (nanoscale high performance liquid chromatography-tandem secondary mass spectrometry), and a total of 11 acetylation sites were discovered on Bombyx mori nutrient-storage protein SP3 (BmSP3). The purpose of this study was to investigate the effect of acetylation level on BmSP3. METHODS AND RESULTS In this study, the acetylation of BmSP3 was further verified by immunoprecipitation (IP) and Western blotting. Then, it was confirmed that acetylation could up-regulate the expression of BmSP3 by improving its protein stability in BmN cells. Co-IP and RNAi experiments showed acetyltransferase BmCBP could bind to BmSP3 and catalyze its acetylation modification, then regulate the expression of BmSP3. Furthermore, the knock-down of BmCBP could improve the ubiquitination level of BmSP3. Both acetylation and ubiquitination occur on the side chain of lysine residues, therefore, we speculated that the acetylation of BmSP3 catalyzed by BmCBP could competitively inhibit its ubiquitination modification and improve its protein stability by inhibiting ubiquitin-mediated proteasome degradation pathway, and thereby increase the expression and intracellular accumulation. CONCLUSIONS BmCBP catalyzes the acetylation of BmSP3 and may improve the stability of BmSP3 by competitive ubiquitination. This conclusion provides a new functional basis for the extensive involvement of acetylation in the regulation of nutrient storage and utilization in silkworm, Bombyx mori.
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Affiliation(s)
- Guowei Zu
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Zihan Sun
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Yanmei Chen
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Jiasheng Geng
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Jiao Lv
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Zhengying You
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Caiying Jiang
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Qing Sheng
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Zuoming Nie
- College of Life Sciences and Medicine, Zhejiang provincial key laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China.
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Rajaraman S, Balakrishnan R, Deshmukh D, Ganorkar A, Biswas S, Pulya S, Ghosh B. HDAC8 as an emerging target in drug discovery with special emphasis on medicinal chemistry. Future Med Chem 2023; 15:885-908. [PMID: 37227732 DOI: 10.4155/fmc-2023-0054] [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: 02/22/2023] [Accepted: 05/04/2023] [Indexed: 05/26/2023] Open
Abstract
HDAC8 catalyzes the deacetylation of both histones and nonhistone proteins. The abnormal expression of HDAC8 is associated with various pathological conditions causing cancer and other diseases like myopathies, Cornelia de Lange syndrome, renal fibrosis, and viral and parasitic infections. The substrates of HDAC8 are involved in diverse molecular mechanisms of cancer such as cell proliferation, invasion, metastasis and drug resistance. Based on the crystal structures and the key residues at the active site, HDAC8 inhibitors have been designed along the canonical pharmacophore. This article details the importance, recent advancements, and the structural and functional aspects of HDAC8 with special emphasis on the medicinal chemistry aspect of HDAC8 inhibitors that will help in developing novel epigenetic therapeutics.
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Affiliation(s)
- Srinidhi Rajaraman
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Ranjani Balakrishnan
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Dhruv Deshmukh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Abhiram Ganorkar
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Swati Biswas
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Sravani Pulya
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
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Nazri JM, Oikonomopoulou K, de Araujo ED, Kraskouskaya D, Gunning PT, Chandran V. Histone deacetylase inhibitors as a potential new treatment for psoriatic disease and other inflammatory conditions. Crit Rev Clin Lab Sci 2023; 60:300-320. [PMID: 36846924 DOI: 10.1080/10408363.2023.2177251] [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: 03/01/2023]
Abstract
Collectively known as psoriatic disease, psoriasis and psoriatic arthritis (PsA) are immune-mediated inflammatory diseases in which patients present with cutaneous and musculoskeletal inflammation. Affecting roughly 2-3% of the world's total population, there remains unmet therapeutic needs in both psoriasis and PsA despite the availability of current immunomodulatory treatments. As a result, patients with psoriatic disease often experience reduced quality of life. Recently, a class of small molecules, commonly investigated as anti-cancer agents, called histone deacetylase (HDAC) inhibitors, have been proposed as a new promising anti-inflammatory treatment for immune- and inflammatory-related diseases. In inflammatory diseases, current evidence is derived from studies on diseases like rheumatoid arthritis (RA) and systematic lupus erythematosus (SLE), and while there are some reports studying psoriasis, data on PsA patients are not yet available. In this review, we provide a brief overview of psoriatic disease, psoriasis, and PsA, as well as HDACs, and discuss the rationale behind the potential use of HDAC inhibitors in the management of persistent inflammation to suggest its possible use in psoriatic disease.
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Affiliation(s)
- Jehan Mohammad Nazri
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | | | - Elvin D de Araujo
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, Canada
| | - Dziyana Kraskouskaya
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, Canada
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, Canada.,Department of Chemistry, University of Toronto, Toronto, Canada
| | - Vinod Chandran
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Schroeder Arthritis Institute, University Health Network, Toronto, Canada.,Department of Medicine, University of Toronto, Toronto, Canada.,Institute of Medical Science, University of Toronto, Toronto, Canada.,Department of Medicine, Memorial University, St. John's, Canada
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Chen Z, Liu X, Li F, Li C, Marquez-Lago T, Leier A, Webb GI, Xu D, Akutsu T, Song J. Systematic Characterization of Lysine Post-translational Modification Sites Using MUscADEL. Methods Mol Biol 2022; 2499:205-219. [PMID: 35696083 DOI: 10.1007/978-1-0716-2317-6_11] [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] [Indexed: 06/15/2023]
Abstract
Among various types of protein post-translational modifications (PTMs), lysine PTMs play an important role in regulating a wide range of functions and biological processes. Due to the generation and accumulation of enormous amount of protein sequence data by ongoing whole-genome sequencing projects, systematic identification of different types of lysine PTM substrates and their specific PTM sites in the entire proteome is increasingly important and has therefore received much attention. Accordingly, a variety of computational methods for lysine PTM identification have been developed based on the combination of various handcrafted sequence features and machine-learning techniques. In this chapter, we first briefly review existing computational methods for lysine PTM identification and then introduce a recently developed deep learning-based method, termed MUscADEL (Multiple Scalable Accurate Deep Learner for lysine PTMs). Specifically, MUscADEL employs bidirectional long short-term memory (BiLSTM) recurrent neural networks and is capable of predicting eight major types of lysine PTMs in both the human and mouse proteomes. The web server of MUscADEL is publicly available at http://muscadel.erc.monash.edu/ for the research community to use.
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Affiliation(s)
- Zhen Chen
- Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Xuhan Liu
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Fuyi Li
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Chen Li
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Tatiana Marquez-Lago
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - André Leier
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Geoffrey I Webb
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, Australia
| | - Dakang Xu
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Molecular and Translational Science, Faculty of Medicine, Hudson Institute of Medical Research, Monash University, Melbourne, VIC, Australia
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan.
| | - Jiangning Song
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia.
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, Australia.
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Wakam GK, Biesterveld BE, Pai MP, Kemp MT, O'Connell RL, Williams AM, Srinivasan A, Chtraklin K, Siddiqui AZ, Bhatti UF, Vercruysse CA, Alam HB. Administration of valproic acid in clinically approved dose improves neurologic recovery and decreases brain lesion size in swine subjected to hemorrhagic shock and traumatic brain injury. J Trauma Acute Care Surg 2021; 90:346-352. [PMID: 33230090 DOI: 10.1097/ta.0000000000003036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Traumatic brain injury (TBI) and hemorrhage remain the leading causes of death after trauma. We have previously shown that a dose of valproic acid (VPA) at (150 mg/kg) can decrease brain lesion size and hasten neurologic recovery. The current Food and Drug Administration-approved dose of VPA is 60 mg/kg. We evaluate neurologic outcomes and brain lesion size of a single dose of VPA at a level currently within Food and Drug Administration-approved dose in swine subjected to TBI and hemorrhagic shock. METHODS Swine (n = 5/group) were subjected to TBI and 40% blood volume hemorrhage. Animals remained in shock for 2 hours before randomization to normal saline (NS) resuscitation alone (control), NS-VPA 150 mg/kg (VPA 150), or NS-VPA 50 mg/kg (VPA 50). Neurologic severity scores (range, 0-32) were assessed daily for 14 days, and brain lesion size was measured via magnetic resonance imaging on postinjury day (PID) 3. RESULTS Shock severity and laboratory values were similar in all groups. Valproic acid-treated animals demonstrated significantly less neurologic impairment on PID 1 and returned to baseline faster (PID 1 mean neurologic severity score, control = 22 ± 3 vs. VPA 150 mg/kg = 8 ± 7 or VPA 50 mg/kg = 6 ± 6; p = 0.02 and 0.003). Valproic acid-treated animals had significantly smaller brain lesion sizes (mean volume in mm3, control = 1,268.0 ± 241.2 vs. VPA 150 mg/kg = 620.4 ± 328.0 or VPA 50 mg/kg = 438.6 ± 234.8; p = 0.007 and 0.001). CONCLUSION In swine subjected to TBI and hemorrhagic shock, VPA treatment, in a dose that is approved for clinical use, decreases brain lesion size and reduces neurologic impairment compared with resuscitation alone.
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Affiliation(s)
- Glenn K Wakam
- From the Department of Surgery (G.K.W., B.E.B., M.T.K., R.L.O., A.M.W., K.C., A.Z.S., U.F.B., C.A.V., H.B.A.), Department of Clinical Pharmacy (M.P.P.), and Section of Neuroradiology, Department of Radiology (A.S.), Michigan Medicine, University of Michigan, Ann Arbor, Michigan
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Mullin NP, Varghese J, Colby D, Richardson JM, Findlay GM, Chambers I. Phosphorylation of NANOG by casein kinase I regulates embryonic stem cell self-renewal. FEBS Lett 2021; 595:14-25. [PMID: 33107035 PMCID: PMC7839479 DOI: 10.1002/1873-3468.13969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022]
Abstract
The self-renewal efficiency of mouse embryonic stem cells (ESCs) is determined by the concentration of the transcription factor NANOG. While NANOG binds thousands of sites in chromatin, the regulatory systems that control DNA binding are poorly characterised. Here, we show that NANOG is phosphorylated by casein kinase I, and identify target residues. Phosphomimetic substitutions at phosphorylation sites within the homeodomain (S130 and S131) have site-specific functional effects. Phosphomimetic substitution of S130 abolishes DNA binding by NANOG and eliminates LIF-independent self-renewal. In contrast, phosphomimetic substitution of S131 enhances LIF-independent self-renewal, without influencing DNA binding. Modelling the DNA-homeodomain complex explains the disparate effects of these phosphomimetic substitutions. These results indicate how phosphorylation may influence NANOG homeodomain interactions that underpin ESC self-renewal.
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Affiliation(s)
- Nicholas P. Mullin
- Centre for Regenerative MedicineInstitute for Stem Cell ResearchSchool of Biological SciencesUniversity of EdinburghUK
| | - Joby Varghese
- Protein Phosphorylation and Ubiquitylation UnitJames Black CentreSchool of Life SciencesDundeeUK
| | - Douglas Colby
- Centre for Regenerative MedicineInstitute for Stem Cell ResearchSchool of Biological SciencesUniversity of EdinburghUK
| | - Julia M. Richardson
- Institute of Quantitative Biology, Biochemistry and BiotechnologyEdinburghUK
| | - Greg M. Findlay
- Protein Phosphorylation and Ubiquitylation UnitJames Black CentreSchool of Life SciencesDundeeUK
| | - Ian Chambers
- Centre for Regenerative MedicineInstitute for Stem Cell ResearchSchool of Biological SciencesUniversity of EdinburghUK
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Pulya S, Amin SA, Adhikari N, Biswas S, Jha T, Ghosh B. HDAC6 as privileged target in drug discovery: A perspective. Pharmacol Res 2020; 163:105274. [PMID: 33171304 DOI: 10.1016/j.phrs.2020.105274] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/15/2020] [Accepted: 10/25/2020] [Indexed: 12/25/2022]
Abstract
HDAC6, a class IIB HDAC isoenzyme, stands unique in its structural and physiological functions. Besides histone modification, largely due to its cytoplasmic localization, HDAC6 also targets several non-histone proteins including Hsp90, α-tubulin, cortactin, HSF1, etc. Thus, it is one of the key regulators of different physiological and pathological disease conditions. HDAC6 is involved in different signaling pathways associated with several neurological disorders, various cancers at early and advanced stage, rare diseases and immunological conditions. Therefore, targeting HDAC6 has been found to be effective for various therapeutic purposes in recent years. Though several HDAC6 inhibitors (HDAC6is) have been developed till date, only two ACY-1215 (ricolinostat) and ACY-241 (citarinostat) are in the clinical trials. A lot of work is still needed to pinpoint strictly selective as well as potent HDAC6i. Considering the recent crystal structure of HDAC6, novel HDAC6is of significant therapeutic value can be designed. Notably, the canonical pharmacophore features of HDAC6is consist of a zinc binding group (ZBG), a linker function and a cap group. Significant modifications of cap function may lead to achieve better selectivity of the inhibitors. This review details the study about the structural biology of HDAC6, the physiological and pathological role of HDAC6 in several disease states and the detailed structure-activity relationships (SARs) of the known HDAC6is. This detailed review will provide key insights to design novel and highly effective HDAC6i in the future.
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Affiliation(s)
- Sravani Pulya
- Epigenetic Research Laboratory, Department of Pharmacy, BITS-Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India
| | - Sk Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P. O. Box 17020, Jadavpur University, Kolkata 700032, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P. O. Box 17020, Jadavpur University, Kolkata 700032, India
| | - Swati Biswas
- Epigenetic Research Laboratory, Department of Pharmacy, BITS-Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P. O. Box 17020, Jadavpur University, Kolkata 700032, India.
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, BITS-Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India.
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A New Therapeutic Strategy Targeting Protein Deacetylation for Spinal Cord Injury. Neuroscience 2020; 451:197-206. [PMID: 33039524 DOI: 10.1016/j.neuroscience.2020.09.060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/27/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023]
Abstract
Lysine acetylation is a post-translational modification that regulates a diversity of biological processes. However, its implication in spinal cord injury (SCI) remains unclear. Here we investigated the acetylation events in injured spinal cords on a proteomic scale for the first time. Additionally, whether promoting acetylation could mitigate SCI was evaluated. A total of 268 differentially acetylated peptides were identified. Among them, 2 peptides were up-acetylated and 141 peptides were down-acetylated in the injured spinal cord tissues (Fold change >2 and P < 0.05). There were also 116 unique acetylated peptides in the sham group and 9 unique acetylated peptides in the SCI group. Functional enrichment analysis revealed that differently acetylated proteins were involved in multiple cellular processes and metabolic processes. Kyoto Encyclopaedia of Genes and Genomes analysis showed that several pathways, including cGMP-PKG signaling pathway and hypoxia-inducible factor-1 (HIF-1) signaling pathway, were predominantly presented. Moreover, promoting acetylation using glycerol triacetate (GTA) showed a therapeutic effect on SCI, with improved Basso-Beattie-Bresnahan scores and histologic morphology, and decreased neuronal apoptosis and inflammation. In conclusion, our data indicated that protein deacetylation might play crucial roles in the development of secondary injury of SCI, and promoting acetylation by GTA effectively mitigated SCI. Our data not only enhance our understanding on acetylproteome dataset in the spinal cord tissues, but also provide novel insights for the treatment of SCI.
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Quagliano A, Gopalakrishnapillai A, Barwe SP. Understanding the Mechanisms by Which Epigenetic Modifiers Avert Therapy Resistance in Cancer. Front Oncol 2020; 10:992. [PMID: 32670880 PMCID: PMC7326773 DOI: 10.3389/fonc.2020.00992] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 05/19/2020] [Indexed: 12/19/2022] Open
Abstract
The development of resistance to anti-cancer therapeutics remains one of the core issues preventing the improvement of survival rates in cancer. Therapy resistance can arise in a multitude of ways, including the accumulation of epigenetic alterations in cancer cells. By remodeling DNA methylation patterns or modifying histone proteins during oncogenesis, cancer cells reorient their epigenomic landscapes in order to aggressively resist anti-cancer therapy. To combat these chemoresistant effects, epigenetic modifiers such as DNA hypomethylating agents, histone deacetylase inhibitors, histone demethylase inhibitors, along with others have been used. While these modifiers have achieved moderate success when used either alone or in combination with one another, the most positive outcomes were achieved when they were used in conjunction with conventional anti-cancer therapies. Epigenome modifying drugs have succeeded in sensitizing cancer cells to anti-cancer therapy via a variety of mechanisms: disrupting pro-survival/anti-apoptotic signaling, restoring cell cycle control and preventing DNA damage repair, suppressing immune system evasion, regulating altered metabolism, disengaging pro-survival microenvironmental interactions and increasing protein expression for targeted therapies. In this review, we explore different mechanisms by which epigenetic modifiers induce sensitivity to anti-cancer therapies and encourage the further identification of the specific genes involved with sensitization to facilitate development of clinical trials.
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Affiliation(s)
- Anthony Quagliano
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Anilkumar Gopalakrishnapillai
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Sonali P. Barwe
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
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Isoform 6-selective histone deacetylase inhibition reduces lesion size and brain swelling following traumatic brain injury and hemorrhagic shock. J Trauma Acute Care Surg 2020; 86:232-239. [PMID: 30399139 DOI: 10.1097/ta.0000000000002119] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND Nonselective histone deacetylase (pan-HDAC) inhibitors, such as valproic acid (VPA), have demonstrated neuroprotective properties in trauma models. However, isoform-specific HDAC inhibitors may provide opportunity for more effective drug administration with fewer adverse effects. We investigated HDAC6 inhibition with ACY-1083 in an in vitro and an in vivo large animal model of injury. METHODS Mouse hippocampal cells were subjected to oxygen-glucose deprivation (0% O2, glucose-free and serum-free medium, 18 hours) and reoxygenation (21% O2, normal culture media, 4 hours) with/without VPA (4 mmol/L) or ACY-1083 (30 nmol/L, 300 nmol/L). Cell viability was measured by methylthiazolyl tetrazolium assay. Expression of hypoxia-inducible factor-1α, heat shock protein 70, and effectors in the phosphoinositide-3 kinase/mammalian target of rapamycin pathway were measured by Western blot analysis. Additionally, swine were subjected to combined traumatic brain injury and hemorrhagic shock and randomized to three treatment groups (n = 5/group): (i) normal saline (NS; 3× hemorrhage volume); (ii) NS + VPA (NS; 3× hemorrhage volume, VPA; 150 mg/kg), and (iii) NS + ACY-1083 (NS; 3× hemorrhage volume, ACY-1083; 30 mg/kg). After 6 hours, brain tissue was harvested to assess lesion size and brain swelling. RESULTS Significant improvement in cell viability was seen with both HDAC inhibitors in the in vitro study. ACY-1083 suppressed hypoxia-inducible factor-1α expression and up-regulated phosphorylated mammalian target of rapamycin and heat shock protein 70 in a dose-dependent manner. Lesion size and brain swelling in animals treated with pharmacologic agents (VPA and ACY-1083) were both smaller than in the NS group. No differences were observed between the VPA and ACY-1083 treatment groups. CONCLUSIONS In conclusion, selective inhibition of HDAC6 is as neuroprotective as nonselective HDAC inhibition in large animal models of traumatic brain injury and hemorrhagic shock.
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Barbosa DM, Fahlbusch P, Herzfeld de Wiza D, Jacob S, Kettel U, Al-Hasani H, Krüger M, Ouwens DM, Hartwig S, Lehr S, Kotzka J, Knebel B. Rhein, a novel Histone Deacetylase (HDAC) inhibitor with antifibrotic potency in human myocardial fibrosis. Sci Rep 2020; 10:4888. [PMID: 32184434 PMCID: PMC7078222 DOI: 10.1038/s41598-020-61886-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/04/2020] [Indexed: 12/18/2022] Open
Abstract
Although fibrosis depicts a reparative mechanism, maladaptation of the heart due to excessive production of extracellular matrix accelerates cardiac dysfunction. The anthraquinone Rhein was examined for its anti-fibrotic potency to mitigate cardiac fibroblast-to-myofibroblast transition (FMT). Primary human ventricular cardiac fibroblasts were subjected to hypoxia and characterized with proteomics, transcriptomics and cell functional techniques. Knowledge based analyses of the omics data revealed a modulation of fibrosis-associated pathways and cell cycle due to Rhein administration during hypoxia, whereas p53 and p21 were identified as upstream regulators involved in the manifestation of cardiac fibroblast phenotypes. Mechanistically, Rhein acts inhibitory on HDAC classes I/II as enzymatic inhibitor. Rhein-mediated cellular effects were linked to the histone deacetylase (HDAC)-dependent protein stabilization of p53 under normoxic but not hypoxic conditions. Functionally, Rhein inhibited collagen contraction, indicating anti-fibrotic property in cardiac remodeling. This was accompanied by increased abundance of SMAD7, but not SMAD2/3, and consistently SMAD-specific E3 ubiquitin ligase SMURF2. In conclusion, this study identifies Rhein as a novel potent direct HDAC inhibitor that may contribute to the treatment of cardiac fibrosis as anti-fibrotic agent. As readily available drug with approved safety, Rhein constitutes a promising potential therapeutic approach in the supplemental and protective intervention of cardiac fibrosis.
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Affiliation(s)
- David Monteiro Barbosa
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany.,Medical Faculty, Institute of Cardiovascular Physiology, Heinrich-Heine-University, Duesseldorf, Germany
| | - Pia Fahlbusch
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Daniella Herzfeld de Wiza
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Sylvia Jacob
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Ulrike Kettel
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Hadi Al-Hasani
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany.,Medical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Heinrich-Heine-University, Duesseldorf, Germany
| | - Martina Krüger
- Medical Faculty, Institute of Cardiovascular Physiology, Heinrich-Heine-University, Duesseldorf, Germany
| | - D Margriet Ouwens
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany.,Department of Endocrinology, Ghent University Hospital, Ghent, Belgium
| | - Sonja Hartwig
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Stefan Lehr
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Jorg Kotzka
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Birgit Knebel
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany. .,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany.
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13
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Concise Review: The Regulatory Mechanism of Lysine Acetylation in Mesenchymal Stem Cell Differentiation. Stem Cells Int 2020; 2020:7618506. [PMID: 32399051 PMCID: PMC7204305 DOI: 10.1155/2020/7618506] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022] Open
Abstract
Nowadays, the use of MSCs has attracted considerable attention in the global science and technology field, with the self-renewal and multidirectional differentiation potential for diabetes, obesity treatment, bone repair, nerve repair, myocardial repair, and so on. Epigenetics plays an important role in the regulation of mesenchymal stem cell differentiation, which has become a research hotspot in the medical field. This review focuses on the role of lysine acetylation modification on the determination of MSC differentiation direction. During this progress, the recruitment of lysine acetyltransferases (KATs) and lysine deacetylases (KDACs) is the crux of transcriptional mechanisms in the dynamic regulation of key genes controlling MSC multidirectional differentiation.
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14
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Li B, Li M, Li X, Li H, Lai Y, Huang S, He X, Si X, Zheng H, Liao W, Liao Y, Bin J. Sirt1-inducible deacetylation of p21 promotes cardiomyocyte proliferation. Aging (Albany NY) 2019; 11:12546-12567. [PMID: 31881009 PMCID: PMC6949046 DOI: 10.18632/aging.102587] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/26/2019] [Indexed: 12/17/2022]
Abstract
Inducing cardiomyocyte proliferation is a hopeful approach for cardiac regeneration following myocardial infarction. Previous studies have shown that p21 inhibits the cardiomyocyte proliferation and cardiac regeneration. Deacetylation of p21 by Sirt1 deacetylase may reduce p21 abundance and remove p21-induced cell cycle arrest. However, whether p21 deacetylation and Sirt1 deacetylate control cardiomyocyte proliferation is unclear. Here, we show that acetylation of p21 induces cardiomyocyte proliferation arrest, whereas blocking the acetylation of p21 increases cardiomyocyte proliferation. P21 can be acetylated by Sirt1, and Sirt1 activate p21 ubiquitination through deacetylation. Additionally, overexpression of Sirt1 induces EdU-, pH3-, and Aurora B-positive cardiomyocytes in neonatal and adult mice. In contrast, depletion of Sirt1 reduces cardiomyocyte proliferation in vitro and in vivo. Moreover, Sirt1 protects cardiac function, reduces cardiac remodeling, inhibits cardiomyocyte apoptosis, and attenuates cardiomyocyte hypertrophy post-myocardial infarction. These results suggest that Sirt1-induced p21 deacetylation plays an essential role in cardiomyocyte proliferation and that it could be a novel therapeutic strategy for myocardial infarction.
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Affiliation(s)
- Bing Li
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,School of Medicine, Guizhou University, Guiyang, Guizhou 550025, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
| | - Mengsha Li
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xinzhong Li
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
| | - Hairui Li
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yanxian Lai
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Senlin Huang
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
| | - Xiang He
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
| | - Xiaoyun Si
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Hao Zheng
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
| | - Wangjun Liao
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yulin Liao
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
| | - Jianping Bin
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
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15
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Chen Z, Liu X, Li F, Li C, Marquez-Lago T, Leier A, Akutsu T, Webb GI, Xu D, Smith AI, Li L, Chou KC, Song J. Large-scale comparative assessment of computational predictors for lysine post-translational modification sites. Brief Bioinform 2019; 20:2267-2290. [PMID: 30285084 PMCID: PMC6954452 DOI: 10.1093/bib/bby089] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/17/2018] [Accepted: 08/18/2018] [Indexed: 12/22/2022] Open
Abstract
Lysine post-translational modifications (PTMs) play a crucial role in regulating diverse functions and biological processes of proteins. However, because of the large volumes of sequencing data generated from genome-sequencing projects, systematic identification of different types of lysine PTM substrates and PTM sites in the entire proteome remains a major challenge. In recent years, a number of computational methods for lysine PTM identification have been developed. These methods show high diversity in their core algorithms, features extracted and feature selection techniques and evaluation strategies. There is therefore an urgent need to revisit these methods and summarize their methodologies, to improve and further develop computational techniques to identify and characterize lysine PTMs from the large amounts of sequence data. With this goal in mind, we first provide a comprehensive survey on a large collection of 49 state-of-the-art approaches for lysine PTM prediction. We cover a variety of important aspects that are crucial for the development of successful predictors, including operating algorithms, sequence and structural features, feature selection, model performance evaluation and software utility. We further provide our thoughts on potential strategies to improve the model performance. Second, in order to examine the feasibility of using deep learning for lysine PTM prediction, we propose a novel computational framework, termed MUscADEL (Multiple Scalable Accurate Deep Learner for lysine PTMs), using deep, bidirectional, long short-term memory recurrent neural networks for accurate and systematic mapping of eight major types of lysine PTMs in the human and mouse proteomes. Extensive benchmarking tests show that MUscADEL outperforms current methods for lysine PTM characterization, demonstrating the potential and power of deep learning techniques in protein PTM prediction. The web server of MUscADEL, together with all the data sets assembled in this study, is freely available at http://muscadel.erc.monash.edu/. We anticipate this comprehensive review and the application of deep learning will provide practical guide and useful insights into PTM prediction and inspire future bioinformatics studies in the related fields.
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Affiliation(s)
- Zhen Chen
- School of Basic Medical Science, Qingdao University, Dengzhou Road, Qingdao, Shandong, China
| | - Xuhan Liu
- Medicinal Chemistry, Leiden Academic Centre for Drug Research,Einsteinweg, Leiden, The Netherlands
| | - Fuyi Li
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Melbourne, VIC, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, Australia
| | - Chen Li
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Melbourne, VIC, Australia
- Institute of Molecular Systems Biology, ETH Zürich,Auguste-Piccard-Hof, Zürich, Switzerland
| | - Tatiana Marquez-Lago
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, AL, USA
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, AL, USA
| | - André Leier
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, AL, USA
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, AL, USA
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research,Kyoto University, Uji, Kyoto, Japan
| | - Geoffrey I Webb
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, Australia
| | - Dakang Xu
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Molecular and Translational Science, Faculty of Medicine, Hudson Institute of Medical Research, Monash University, Melbourne, VIC, Australia
| | - Alexander Ian Smith
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Melbourne, VIC, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, Australia
| | - Lei Li
- School of Basic Medical Science, Qingdao University, Dengzhou Road, Qingdao, Shandong, China
| | - Kuo-Chen Chou
- Gordon Life Science Institute, Boston, MA, USA
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Melbourne, VIC, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, Australia
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, Australia
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16
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Monick S, Mohanty V, Khan M, Yerneni G, Kumar R, Cantu J, Ichi S, Xi G, Singh BR, Tomita T, Mayanil CS. A Phenotypic Switch of Differentiated Glial Cells to Dedifferentiated Cells Is Regulated by Folate Receptor α. Stem Cells 2019; 37:1441-1454. [PMID: 31381815 PMCID: PMC6899875 DOI: 10.1002/stem.3067] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/05/2019] [Accepted: 07/09/2019] [Indexed: 12/18/2022]
Abstract
In a previous study, we showed that folate receptor‐α (FRα) translocates to the nucleus where it acts as a transcription factor and upregulates Hes1, Oct4, Sox2, and Klf4 genes responsible for pluripotency. Here, we show that acetylation and phosphorylation of FRα favor its nuclear translocation in the presence of folate and can cause a phenotypic switch from differentiated glial cells to dedifferentiated cells. shRNA‐FRα mediated knockdown of FRα was used to confirm the role of FRα in dedifferentiation. Ocimum sanctum hydrophilic fraction‐1 treatment not only blocks the folate mediated dedifferentiation of glial cells but also promotes redifferentiation of dedifferentiated glial cells, possibly by reducing the nuclear translocation of ~38 kDa FRα and subsequent interaction with chromatin assembly factor‐1. stem cells2019;37:1441–1454
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Affiliation(s)
- Sarah Monick
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Vineet Mohanty
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Mariam Khan
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Gowtham Yerneni
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Raj Kumar
- Institute of Advanced Sciences, Dartmouth, Massachusetts, USA
| | - Jorge Cantu
- Department of Biology, Northeastern Illinois University, Chicago, Illinois, USA
| | - Shunsuke Ichi
- Department of Neurosurgery, Japanese Red Cross Medical Center, Tokyo, Japan
| | - Guifa Xi
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Bal Ram Singh
- Institute of Advanced Sciences, Dartmouth, Massachusetts, USA
| | - Tadanori Tomita
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Chandra Shekhar Mayanil
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.,Institute of Advanced Sciences, Dartmouth, Massachusetts, USA
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17
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Montgomery MR, Hull EE. Alterations in the glycome after HDAC inhibition impact oncogenic potential in epigenetically plastic SW13 cells. BMC Cancer 2019; 19:79. [PMID: 30651077 PMCID: PMC6335691 DOI: 10.1186/s12885-018-5129-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/23/2018] [Indexed: 02/07/2023] Open
Abstract
Background Defects in the type and degree of cellular glycosylation impact oncogenesis on multiple levels. Although the type of glycosylation is determined by protein sequence encoded by the genome, the extent and modifications of glycosylation depends on the activity of biosynthetic enzymes and recent data suggests that the glycome is also subject to epigenetic regulation. This study focuses on the ability of HDAC inhibition to alter glycosylation and to lead to pro-oncogenic alterations in the glycome as assessed by metastatic potential and chemoresistance. Methods Epigenetically plastic SW13 adrenocortical carcinoma cells were treated with FK228, an HDAC inhibitor with high affinity for HDAC1 and, to a lesser extent, HDAC2. In comparing HDAC inhibitor treated and control cells, differential expression of glycome-related genes were assessed by microarray. Differential glycosylation was then assessed by lectin binding arrays and the ability of cellular proteins to bind to glycans was assessed by glycan binding arrays. Differential sensitivity to paclitaxel, proliferation, and MMP activity were also assessed. Results Treatment with FK228 alters expression of enzymes in the biosynthetic pathways for a large number of glycome related genes including enzymes in all major glycosylation pathways and several glycan binding proteins. 84% of these differentially expressed glycome-related genes are linked to cancer, some as prognostic markers and others contributing basic oncogenic functions such as metastasis or chemoresistance. Glycan binding proteins also appear to be differentially expressed as protein extracts from treated and untreated cells show differential binding to glycan arrays. The impact of differential mRNA expression of glycosylation enzymes was documented by differential lectin binding. However, the assessment of changes in the glycome is complicated by the fact that detection of differential glycosylation through lectin binding is dependent on the methods used to prepare samples as protein-rich lysates show different binding than fixed cells in several cases. Paralleling the alterations in the glycome, treatment of SW13 cells with FK228 increases metastatic potential and reduces sensitivity to paclitaxel. Conclusions The glycome is substantially altered by HDAC inhibition and these changes may have far-reaching impacts on oncogenesis. Electronic supplementary material The online version of this article (10.1186/s12885-018-5129-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- McKale R Montgomery
- College of Human Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Elizabeth E Hull
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, Glendale, AZ, 85308, USA.
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18
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Ahmed MS, Shahjaman M, Kabir E, Kamruzzaman M. Prediction of Protein Acetylation Sites using Kernel Naive Bayes Classifier Based on Protein Sequences Profiling. Bioinformation 2018; 14:213-218. [PMID: 30108418 PMCID: PMC6077816 DOI: 10.6026/97320630014213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 04/29/2018] [Accepted: 04/29/2018] [Indexed: 12/11/2022] Open
Abstract
Lysine acetylation is one of the decisive categories of protein post-translational modification (PTM), it is convoluted in many significant cellular developments and severe diseases in the biological system. The experimental identification of protein-acetylated sites is painstaking, time-consuming and expensive. Hence, there is significant interest in the development of computational approaches for consistent prediction of acetylation sites using protein sequences. Features selection from protein sequences plays a significant role for acetylation sites prediction. We describe an improved feature selection approach for acetylation sites prediction based on kernel naive Bayes classifier (KNBC). We have shown that KNBC generated from selected features by a new feature selection method outperforms than the existing methods for identification of acetylation sites. The sensitivity, specificity, ACC (Accuracy), MCC (Matthews Correlation Coefficient) and AUC (Area under Curve of ROC) in our proposed method are as follows 80.71%, 93.39%, 76.73%, 41.37% and 83.0% with the optimum window size is 47. Thus the kernel naive Bayes classifier finds application in acetylation site prediction.
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Affiliation(s)
- Md. Shakil Ahmed
- Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh
| | - Md. Shahjaman
- Department of Statistics, Begum Rokeya University, Rangpur-5400, Bangladesh
| | - Enamul Kabir
- School of Agricultural, Computational and Environmental Sciences, University of Southern Queensland, Australia
| | - Md. Kamruzzaman
- Data Science for Knowledge Creation Research Center, Seoul National University, Korea
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19
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Weykamp M, Nikolian VC, Dennahy IS, Higgins GA, Georgoff PE, Remmer H, Ghandour MH, Alam HB. Rapid valproic acid-induced modulation of the traumatic proteome in a porcine model of traumatic brain injury and hemorrhagic shock. J Surg Res 2018; 228:84-92. [PMID: 29907235 DOI: 10.1016/j.jss.2018.02.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/10/2018] [Accepted: 02/22/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Histone deacetylase inhibitors such as valproic acid (VPA) improve survival in lethal models of hemorrhagic shock and polytrauma. Although VPA is known to modulate transcription, its ability to reduce mortality within minutes of administration suggests involvement of a rapid, posttranslational mechanism. We hypothesized that VPA treatment would cause proteomic changes within minutes of treatment including quantitative and/or posttranslational differences in structural and/or effector proteins. MATERIALS AND METHODS We used a porcine model of traumatic brain injury (computer-controlled cortical impact, 12 mm depth) and hemorrhagic shock (40% hemorrhage). Animals were kept in shock for 2 h and randomized to two groups (n = 3): normal saline (volume = 3:1 hemorrhage volume) or normal saline + VPA (150 mg/kg, single dose). Peripheral blood mononuclear cells were collected at baseline, postshock, and postresuscitation. Intracellular protein profiles were assessed using 1 dimensional gel electrophoresis, liquid chromatography, mass spectrometry, and analyzed with Ingenuity Pathway Analysis software. RESULTS Animals treated with VPA demonstrated significant proteomic changes. Quantitative differences were found in over 200 proteins including effector, regulatory, and structural proteins in critical cell signaling pathways. Posttranslational modification analysis demonstrated differential VPA-induced acetylation of lysine residues in histone and nonhistone proteins. Pathway analysis correlated these changes with significant increases in numerous prosurvival and cytoskeletal intracellular pathways, including Rho GTPase signaling (P = 1.66E-11), integrin signaling (P = 4.19E-21), and a decrease in Rho guanosine nucleotide dissociation inhibitor signaling (P = 4.83E-12). CONCLUSIONS In a porcine model of severe injuries, a single dose of VPA is associated with protective changes in the proteome that are measurable within minutes of treatment.
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Affiliation(s)
- Michael Weykamp
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan
| | - Vahagn C Nikolian
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan
| | - Isabel S Dennahy
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan
| | - Gerald A Higgins
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Patrick E Georgoff
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan
| | - Henriette Remmer
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan
| | - Mohamed H Ghandour
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan
| | - Hasan B Alam
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan.
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20
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Nikolian VC, Pan B, Mesar T, Dennahy IS, Georgoff PE, Duan X, Liu B, Wu X, Duggan MJ, Alam HB, Li Y. Lung Protective Effects of Low-Volume Resuscitation and Pharmacologic Treatment of Swine Subjected to Polytrauma and Hemorrhagic Shock. Inflammation 2018; 40:1264-1274. [PMID: 28493077 DOI: 10.1007/s10753-017-0569-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Hemorrhage is a common cause of death in the battlefield. Valproic acid (VPA) has been associated with improved outcomes in multiple models of trauma, when combined with isotonic fluid resuscitation. However, isotonic fluid administered in this setting is logistically impractical and may be associated with complications. In this study, we sought to evaluate the feasibility and immunologic impact of combining VPA treatment with low-volume hypertonic saline (HTS). In vivo: female Yorkshire swine were subjected to hemorrhage (40% total blood volume) and polytrauma (rib fracture and delayed liver injury). Animals were kept in shock for 30 minutes and resuscitated with (1) normal saline (NS, 3× hemorrhaged volume), (2) HTS (7.5% saline, 4 mL/kg), or (3) HTS + VPA (4 mg/kg; 150 mg/kg; n = 3/cohort). After 18 hours of observation, animals were euthanized and the lungs evaluated for acute injury and expression of myeloperoxidase (MPO) and caveolin-1 (Cav-1). In vitro: human umbilical vein endothelial cells (HUVECs) were exposed to anoxic conditions (5% CO2, 95% N2) for 16 hours in (1) normosmotic, (2) hyperosmotic (400 mOsm), or (3) hyperosmotic + VPA (4 mM) media. Immunohistochemistry and Western blots were performed to determine Cav-1 expression. Lungs from VPA-treated animals demonstrated decreased acute injury, MPO expression, and endothelial expression of Cav-1 when compared to lungs from animals resuscitated with NS or HTS alone. Similarly, HUVECs cultured in hyperosmotic media containing VPA demonstrated decreased expression of Cav-1. This study demonstrates that combined treatment with VPA and HTS is a viable strategy in hemorrhagic shock and polytrauma. Attenuation of lung injury following VPA treatment may be related to modulation of the inflammatory response.
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Affiliation(s)
- Vahagn C Nikolian
- Department of Surgery, University of Michigan Health System, NCRC Building 26 Room 363N, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Baihong Pan
- Department of Surgery, University of Michigan Health System, NCRC Building 26 Room 363N, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA.,Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Tomaz Mesar
- Division of Trauma, Emergency Surgery and Surgical Critical Care, Department of Surgery, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Isabel S Dennahy
- Department of Surgery, University of Michigan Health System, NCRC Building 26 Room 363N, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Patrick E Georgoff
- Department of Surgery, University of Michigan Health System, NCRC Building 26 Room 363N, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Xiuzhen Duan
- Department of Pathology, Loyola University Medical Center, Maywood, IL, USA
| | - Baoling Liu
- Department of Surgery, University of Michigan Health System, NCRC Building 26 Room 363N, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Xizi Wu
- Emergency Department, The First Hospital of China Medical University, Shenyang, China
| | - Michael J Duggan
- Division of Trauma, Emergency Surgery and Surgical Critical Care, Department of Surgery, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Hasan B Alam
- Department of Surgery, University of Michigan Health System, NCRC Building 26 Room 363N, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Yongqing Li
- Department of Surgery, University of Michigan Health System, NCRC Building 26 Room 363N, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA.
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21
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He P, Li K, Li SB, Hu TT, Guan M, Sun FY, Liu WW. Upregulation of AKAP12 with HDAC3 depletion suppresses the progression and migration of colorectal cancer. Int J Oncol 2018; 52:1305-1316. [PMID: 29484387 DOI: 10.3892/ijo.2018.4284] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 02/16/2018] [Indexed: 11/05/2022] Open
Abstract
A-kinase anchor protein 12 (AKAP12; also known as Gravin) functions as a tumor suppressor in several human primary cancers. However, the potential correlation between histone deacetylase 3 (HDAC3) and AKAP12 and the underlying mechanisms remain unclear. Thus, in this study, in an aim to shed light into this matter, the expression levels of HDAC3 and AKAP12 in 96 colorectal cancer (CRC) and adjacent non-cancerous tissues, as well as in SW480 cells were examined by immunohistochemical, RT-qPCR and western blot analyses. The effects of HDAC3 and AKAP12 on the proliferation, apoptosis and metastasis of CRC cells were examined by cell counting kit-8 (CCK-8) assay, colony formation assays, flow cytometry, cell cycle analysis and Transwell assays. The results revealed that the reduction or loss of AKAP12 expression was detected in 69 (71.8%) of the 96 tissue specimens, whereas HDAC3 was upregulated in 50 (52.1%) of the 96 tumor tissue specimens. AKAP12 expression was markedly increased upon treatment with the HDAC3 inhibitors, trichostatin A (TSA) and RGFP966, at both the mRNA and protein level. Mechanistically, the direct binding of HDAC3 within the intron-1 region of AKAP12 was identified to be indispensable for the inhibition of AKAP12 expression. Moreover, the proliferation, colony-forming ability, cell cycle progression and the migration of the CRC cells were found to be promoted in response to AKAP12 silencing or AKAP12/HDAC3 co-silencing, whereas transfection with si-HDAC3 yielded opposite effects. Apart from the elevated expression of the anti-apoptotic protein, Bcl-2, after AKAP12 knockdown, the increased activity of PI3K/AKT signaling was found to be indispensable for AKAP12-mediated colony formation and migration. On the whole, these findings indicate that AKAP12 may be a potential prognostic predictor and therapeutic target for the treatment of CRC in combination with HDAC3.
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Affiliation(s)
- Ping He
- Central Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200070, P.R. China
| | - Ke Li
- Central Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200070, P.R. China
| | - Shi-Bao Li
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical College, Xuzhou, Jiangsu 221100, P.R. China
| | - Ting-Ting Hu
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, P.R. China
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, P.R. China
| | - Fen-Yong Sun
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200070, P.R. China
| | - Wei-Wei Liu
- Central Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200070, P.R. China
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22
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Valproic acid decreases brain lesion size and improves neurologic recovery in swine subjected to traumatic brain injury, hemorrhagic shock, and polytrauma. J Trauma Acute Care Surg 2017; 83:1066-1073. [PMID: 28697014 DOI: 10.1097/ta.0000000000001612] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND We have previously shown that treatment with valproic acid (VPA) decreases brain lesion size in swine models of traumatic brain injury (TBI) and controlled hemorrhage. To translate this treatment into clinical practice, validation of drug efficacy and evaluation of pharmacologic properties in clinically realistic models of injury are necessary. In this study, we evaluate neurologic outcomes and perform pharmacokinetic analysis of a single dose of VPA in swine subjected to TBI, hemorrhagic shock, and visceral hemorrhage. METHODS Yorkshire swine (n = 5/cohort) were subjected to TBI, hemorrhagic shock, and polytrauma (liver and spleen injury, rib fracture, and rectus abdominis crush). Animals remained in hypovolemic shock for 2 hours before resuscitation with isotonic sodium chloride solution (ISCS; volume = 3× hemorrhage) or ISCS + VPA (150 mg/kg). Neurologic severity scores were assessed daily for 30 days, and brain lesion size was measured via magnetic resonance imaging on postinjury days (PID) 3 and 10. Serum samples were collected for pharmacokinetic analysis. RESULTS Shock severity and response to resuscitation were similar in both groups. Valproic acid-treated animals demonstrated significantly less neurologic impairment between PID 1 to 5 and smaller brain lesions on PID 3 (mean lesion size ± SEM, mm: ISCS = 4,956 ± 1,511 versus ISCS + VPA = 828 ± 279; p = 0.047). No significant difference in lesion size was identified between groups at PID 10 and all animals recovered to baseline neurologic function during the 30-day observation period. Animals treated with VPA had faster neurocognitive recovery (days to initiation of testing, mean ± SD: ISCS = 6.2 ± 1.6 vs ISCS + VPA = 3.6 ± 1.5; p = 0.002; days to task mastery: ISCS = 7.0 ± 1.0 vs ISCS + VPA = 4.8 ± 0.5; p = 0.03). The mean ± SD maximum VPA concentrations, area under the curve, and half-life were 145 ± 38.2 mg/L, 616 ± 150 hour·mg/L, and 1.70 ± 0.12 hours. CONCLUSIONS In swine subjected to TBI, hemorrhagic shock, and polytrauma, VPA treatment is safe, decreases brain lesion size, and reduces neurologic injury compared to resuscitation with ISCS alone. These benefits are achieved at clinically translatable serum concentrations of VPA. LEVEL OF EVIDENCE Therapeutic (preclinical study).
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23
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Hsu FF, Chiang MT, Li FA, Yeh CT, Lee WH, Chau LY. Acetylation is essential for nuclear heme oxygenase-1-enhanced tumor growth and invasiveness. Oncogene 2017; 36:6805-6814. [PMID: 28846111 DOI: 10.1038/onc.2017.294] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 06/19/2017] [Accepted: 07/17/2017] [Indexed: 12/12/2022]
Abstract
Overexpression of heme oxygenase-1 (HO-1), an endoplasmic reticulum-anchored enzyme, is observed in many cancers. HO-1 nuclear translocation has been shown to correlate with progression of several cancers. We recently reported that HO-1 is susceptible to intramembrane proteolysis and translocates to the nucleus to promote cancer growth and invasiveness without depending on its enzymatic activity. In the present study, we show that the HO-1 lacking C-terminal transmembrane segment (t-HO-1) was susceptible to acetylation by p300 and CREB-binding protein (CBP) histone acetyltransferase in the nucleus. Mass spectrometry analysis of HO-1 isolated from human embryonic kidney cells 293T (HEK293T) cells overexpressing CBP and t-HO-1 revealed two acetylation sites located at K243 and K256. Mutation of both lysine residues to arginine (R) abolished t-HO-1-enhanced tumor cell growth, migration and invasion. However, mutation of the lysine residues to glutamine (Q), a mimic of acetylated lysine, had no significant effect on t-HO-1-mediated tumorigenicity. Mechanistic studies demonstrated that transcriptional factor JunD interacted with wild-type (WT) t-HO-1 and mutant carrying K243/256Q but not K243/256 R mutation. Moreover, JunD-induced AP-1 transcriptional activity was significantly enhanced by coexpression with WT and acetylation-mimic but not acetylation-defective t-HO-1. Consistent with the in vitro observations, the implication of K243/256 acetylation in t-HO-1-enhanced tumorigenicity was also demonstrated in xenograft models. Immunohistochemistry performed with a specific antibody against acetyl-HO-1 showed the positive acetyl-HO-1 nuclear staining in human lung cancer tissues but not in the corresponding non-tumor tissues, supporting its clinical significance. Collectively, our findings highlight the importance of nuclear HO-1 post-translational modification in the induction of cancer progression.
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Affiliation(s)
- F-F Hsu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - M-T Chiang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - F-A Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - C-T Yeh
- Cancer Center, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
| | - W-H Lee
- Cancer Center, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
| | - L-Y Chau
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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Kohlgrüber S, Upadhye A, Dyballa-Rukes N, McNamara CA, Altschmied J. Regulation of Transcription Factors by Reactive Oxygen Species and Nitric Oxide in Vascular Physiology and Pathology. Antioxid Redox Signal 2017; 26:679-699. [PMID: 27841660 PMCID: PMC5421514 DOI: 10.1089/ars.2016.6946] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
SIGNIFICANCE Cardiovascular diseases are the main cause of death worldwide and pose an immense economical burden. In most cases, the underlying problem is vascular occlusion by atherosclerotic plaques. Importantly, different cell types of the vascular wall and the immune system play crucial roles in atherosclerosis at different stages of the disease. Furthermore, atherosclerosis and conditions recognized as risk factors are characterized by a reduced availability of the vasoprotective molecule nitric oxide and an increase in reactive oxygen species, so-called oxidative stress. Transcription factors function as intracellular signal integrators and relays and thus, play a central role in cellular responses to changing conditions. Recent Advances: Work on specific transcriptional regulators has uncovered many of their functions and the upstream pathways modulating their activity in response to reactive oxygen and nitrogen species. Here, we have reviewed for a few selected examples how this can contribute not only to protection against atherosclerosis development but also to disease progression and the occurrence of clinical manifestations, such as plaque rupture. CRITICAL ISSUES Transcription factors have pleiotropic outputs and often also divergent functions in different cell types and tissues. Thus, in light of potential severe adverse side effects, a global activation or inhibition of particular transcriptions factors does not seem a feasible therapeutic option. FUTURE DIRECTIONS A further in-depth characterization of the cell- and stage-specific actions and regulation of transcription factors in atherosclerosis with respect to protein-protein interactions and target genes could open up new avenues for prevention or therapeutic interventions in this vascular disease. Antioxid. Redox Signal. 26, 679-699.
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Affiliation(s)
- Stefanie Kohlgrüber
- 1 IUF-Leibniz Research Institute for Environmental Medicine , Düsseldorf, Germany
| | - Aditi Upadhye
- 2 Department of Microbiology, Immunology, Cancer Biology, University of Virginia , Charlottesville, Virginia
| | - Nadine Dyballa-Rukes
- 1 IUF-Leibniz Research Institute for Environmental Medicine , Düsseldorf, Germany
| | - Coleen A McNamara
- 3 Cardiovascular Division, Department of Medicine and Robert M. Berne Cardiovascular Research Center, University of Virginia-School of Medicine , Charlottesville, Virginia
| | - Joachim Altschmied
- 1 IUF-Leibniz Research Institute for Environmental Medicine , Düsseldorf, Germany
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25
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Gilardini Montani MS, Granato M, Santoni C, Del Porto P, Merendino N, D'Orazi G, Faggioni A, Cirone M. Histone deacetylase inhibitors VPA and TSA induce apoptosis and autophagy in pancreatic cancer cells. Cell Oncol (Dordr) 2017; 40:167-180. [PMID: 28160167 DOI: 10.1007/s13402-017-0314-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2017] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Histone deacetylase inhibitors (HDACi) are anti-neoplastic agents that are known to affect the growth of different cancer types, but their underlying mechanisms are still incompletely understood. Here, we compared the effects of two HDACi, i.e., Trichostatin A (TSA) and Valproic Acid (VPA), on the induction of cell death and autophagy in pancreatic cancer-derived cells that exhibit a high metastatic capacity and carry KRAS/p53 double mutations. METHODS Cell viability and proliferation tests were carried out using Trypan blue dye exclusion, MTT and BrdU assays. FACS analyses were carried out to assess cell cycle progression, apoptosis, reactive oxygen species (ROS) production and mitochondrial depolarization, while Western blot and immunoprecipitation analyses were employed to detect proteins involved in apoptosis and autophagy. RESULTS We found that both VPA and TSA can induce apoptosis in Panc1 and PaCa44 pancreatic cancer-derived cells by triggering mitochondrial membrane depolarization, Cytochrome c release and Caspase 3 activation, although VPA was more effective than TSA, especially in Panc1 cells. As underlying molecular events, we found that ERK1/2 was de-phosphorylated and that the c-Myc and mutant p53 protein levels were reduced after VPA and, to a lesser extent, after TSA treatment. Up-regulation of p21 and Puma was also observed, concomitantly with mutant p53 degradation. In addition, we found that in both cell lines VPA increased the pro-apoptotic Bim level, reduced the anti-apoptotic Mcl-1 level and increased ROS production and autophagy, while TSA was able to induce these effects only in PaCA44 cells. CONCLUSIONS From our results we conclude that both VPA and TSA can induce pancreatic cancer cell apoptosis and autophagy. VPA appears have a stronger and broader cytotoxic effect than TSA and, thus, may represent a better choice for anti-pancreatic cancer therapy.
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Affiliation(s)
| | - Marisa Granato
- Department of Experimental Medicine, La Sapienza University of Rome, V.le Regina Elena 324, 00161, Rome, Italy
| | - Claudio Santoni
- Department of Ecological and Biological Sciences (DEB), Tuscia University, Viterbo, Italy
| | - Paola Del Porto
- Department of Biology and Biotechnology 'Charles Darwin', La Sapienza University of Rome, Rome, Italy
| | - Nicolò Merendino
- Department of Ecological and Biological Sciences (DEB), Tuscia University, Viterbo, Italy
| | - Gabriella D'Orazi
- Department of Research, Advanced Diagnostic and Technological Innovation, Regina Elena National Cancer Institute, Rome, Italy.,Department of Medical Sciences, Tumor Biology Unit, University "G. D'Annunzio", Chieti, Italy
| | - Alberto Faggioni
- Department of Experimental Medicine, La Sapienza University of Rome, V.le Regina Elena 324, 00161, Rome, Italy.
| | - Mara Cirone
- Department of Experimental Medicine, La Sapienza University of Rome, V.le Regina Elena 324, 00161, Rome, Italy.
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26
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Nalawansha DA, Pflum MKH. LSD1 Substrate Binding and Gene Expression Are Affected by HDAC1-Mediated Deacetylation. ACS Chem Biol 2017; 12:254-264. [PMID: 27977115 DOI: 10.1021/acschembio.6b00776] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lysine Specific Demethylase 1 (LSD1) catalyzes the demethylation of histone 3 to regulate gene expression. With a fundamental role in gene regulation, LSD1 is involved in multiple cellular processes, including embryonic development, cell proliferation, and metastasis. Significantly, LSD1 is overexpressed in multiple cancers and has emerged as a potential anticancer drug target. LSD1 is typically found in association with another epigenetic enzyme, histone deacetylase (HDAC). HDAC and LSD1 inhibitor compounds have been tested as combination anticancer agents. However, the functional link between LSD1 and HDAC has yet to be understood in detail. Here, we used a substrate trapping strategy to identify cellular substrates of HDAC1. Using inactive HDAC1 mutants, we identified LSD1 as an HDAC1 substrate. HDAC1 mediated deacetylation of LSD1 at K374 in the substrate binding lobe, which affected the histone 3 binding and gene expression activity of LSD1. The mechanistic link between HDAC1 and LSD1 established here suggests that HDAC inhibitors influence LSD1 activity, which will ultimately guide drug design targeting epigenetic enzymes.
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Affiliation(s)
- Dhanusha A. Nalawansha
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Mary Kay H. Pflum
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
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27
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Abstract
Cancer remains one of the leading causes of death around the world. Initially it is recognized as a genetic disease, but now it is known to involve epigenetic abnormalities along with genetic alterations. Epigenetics refers to heritable changes that are not encoded in the DNA sequence itself, but play an important role in the control of gene expression. It includes changes in DNA methylation, histone modifications, and RNA interference. Although it is heritable, environmental factors such as diet could directly influence epigenetic mechanisms in humans. This article will focus on the role of dietary patterns and phytochemicals that have been demonstrated to influence the epigenome and more precisely histone and non-histone proteins modulation by acetylation that helps to induce apoptosis and phosphorylation inhibition, which counteracts with cells proliferation. Recent developments discussed here enhance our understanding of how dietary intervention could be beneficial in preventing or treating cancer and improving health outcomes.
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Affiliation(s)
- Wissam Zam
- a Department of Analytical and Food Chemistry , Faculty of Pharmacy, Al-Andalus University for Medical Sciences, Al-Quadmous , Tartous , Syrian Arab Republic
| | - Aziz Khadour
- b Department of Microbiology , Faculty of Pharmacy, Al-Andalus University for Medical Sciences, Al-Quadmous , Tartous , Syrian Arab Republic
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28
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Kentache T, Jouenne T, Dé E, Hardouin J. Proteomic characterization of Nα- and Nε-acetylation in Acinetobacter baumannii. J Proteomics 2016; 144:148-58. [PMID: 27222042 DOI: 10.1016/j.jprot.2016.05.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/12/2016] [Accepted: 05/18/2016] [Indexed: 12/25/2022]
Abstract
Nα- and Nε-acetylation represent a pivotal post-translational modification used by both eukaryotes and prokaryotes to modulate diverse biological processes. Acinetobacter baumannii has been described as an important nosocomial pathogen for the past 30 years, frequently involved in ventilator-associated pneumonia, bloodstream and urinary tract infections. Many aspects of the biology of A. baumannii remain elusive, in particular the extent and function of N-acetylation. We investigated here N-acetylation in A. baumannii strain ATCC 17978 by proteomic analysis, and we showed the usefulness of using different analytical approaches. Overall, we identified 525 N-acetylated proteins in which, 145 were Nα-acetylated and 411 were Nε-acetylated. Among them, 41 proteins carried both types of N-acetylation. We found that N-acetylation may play a role in biofilm formation, bacterial virulence (e.g. in several iron acquisition pathways), as well as a number of phenotypes, such as, stress adaptation and drug resistance. BIOLOGICAL SIGNIFICANCE This study is the first to perform the N-acetylome of A. baumannii using different analytical approaches. Each analytical tool permitted to characterize distinctive modified peptides. The combination of all these methods allowed us to identify 145 and 411 Nα- and Nε-acetylated proteins. Besides the fact that acetylation was involved in central metabolism as previously described in other bacteria, some N-acetylated proteins showed interesting role in bacterial virulence (iron acquisition), biofilm formation, stress adaptation and drug resistance of A. baumannii.
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Affiliation(s)
- Takfarinas Kentache
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France
| | - Thierry Jouenne
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France
| | - Emmanuelle Dé
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France
| | - Julie Hardouin
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France.
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29
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Wagner W, Ciszewski W, Kania K, Dastych J. Lactate Stimulates IL-4 and IL-13 Production in Activated HuT-78 T Lymphocytes Through a Process That Involves Monocarboxylate Transporters and Protein Hyperacetylation. J Interferon Cytokine Res 2016; 36:317-27. [DOI: 10.1089/jir.2015.0086] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Waldemar Wagner
- Laboratory of Cellular Immunology, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland
| | - Wojciech Ciszewski
- Laboratory of Cellular Immunology, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland
| | - Katarzyna Kania
- Laboratory of Transcriptional Regulation, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland
| | - Jarosław Dastych
- Laboratory of Cellular Immunology, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland
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30
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Aftabi Y, Colagar AH, Mehrnejad F. An in silico approach to investigate the source of the controversial interpretations about the phenotypic results of the human AhR-gene G1661A polymorphism. J Theor Biol 2016; 393:1-15. [PMID: 26776670 DOI: 10.1016/j.jtbi.2016.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 12/11/2015] [Accepted: 01/01/2016] [Indexed: 12/21/2022]
Abstract
Aryl hydrocarbon receptor (AhR) acts as an enhancer binding ligand-activated intracellular receptor. Chromatin remodeling components and general transcription factors such as TATA-binding protein (TBP) are evoked on AhR-target genes by interaction with its flexible transactivation domain (TAD). AhR-G1661A single nucleotide polymorphism (SNP: rs2066853) causes an arginine to lysine substitution in the acidic sub-domain of TAD at position 554 (R554K). Although, numerous studies associate the SNP with some abnormalities such as cancer, other reliable investigations refuse the associations. Consequently, the interpretation of the phenotypic results of G1661A-transition has been controversial. In this study, an in silico analysis were performed to investigate the possible effects of the transition on AhR-mRNA, protein structure, interaction properties and modifications. The analysis revealed that the R554K substitution affects secondary structure and solvent accessibility of adjacent residues. Also, it causes to decreasing of the AhR stability; altering the hydropathy features of the local sequence and changing the pattern of the residues at the binding site of the TAD-acidic sub-domain. Generating of new sites for ubiquitination and acetylation for AhR-K554 variant respectively at positions 544 and 560 was predicted. Our findings intensify the idea that the AhR-G1661A transition may affects AhR-TAD interactions, especially with the TBP, which influence AhR-target genes expression. However, the previously reported flexibility of the modular TAD could act as an intervening factor, moderate the SNP effects and causes distinct outcomes in different individuals and tissues.
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Affiliation(s)
- Younes Aftabi
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Post Code: 47416-95447, Mazandaran, Iran
| | - Abasalt Hosseinzadeh Colagar
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Post Code: 47416-95447, Mazandaran, Iran.
| | - Faramarz Mehrnejad
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, P.O. Box: 14395-1561, Tehran, Iran
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31
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Pinto G, Shtaif B, Phillip M, Gat-Yablonski G. Growth attenuation is associated with histone deacetylase 10-induced autophagy in the liver. J Nutr Biochem 2015; 27:171-80. [PMID: 26462881 DOI: 10.1016/j.jnutbio.2015.08.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 08/26/2015] [Accepted: 08/26/2015] [Indexed: 11/26/2022]
Abstract
Our previous data suggested that the histone deacetylase (HDAC) SIRT1 is involved in mediating the effect of nutrition on growth. The aim of the present research was to study the mechanism by which additional HDACs may be involved in nutrition-induced linear growth. The in vivo studies were performed in young male Sprague-Dawley rats that were either fed ad libitum (AL) or subjected to 10days of 40% food restriction (RES) and then refed (CU). For in vitro studies, Huh7 hepatoma cells were used. Food restriction led to significant reduction in liver weight, concomitant with increased autophagy (i.e., a decrease in the level of P62 and an increase in the expression level of Ambra1 and Atg16L2 genes in the RES group). At the same time, we found that the level of HDAC10 was significantly increased. Overexpression of HDAC10 in Huh7 hepatoma cells led to reduced cell viability and increased autophagy as shown by increased conversion of LC3-I to LC3-II. An increase in the level of HDAC10 was also obtained when mTOR was inhibited by Rapamycin. siRNA directed against HDAC10 abolished the effect of Rapamycin on cell viability and Ambra1 and Atg16L2 increased expression. These results suggest that increased levels of HDAC10 may mediate the effect of malnutrition on growth attenuation and autophagy. Deciphering the role of epigenetic regulation in the nutrition-growth connection may pave the way for the development of new forms of treatment for children with growth disorders.
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Affiliation(s)
- Galit Pinto
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Felsenstein Medical Research Center, Petach Tikva, Israel.
| | - Biana Shtaif
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Felsenstein Medical Research Center, Petach Tikva, Israel.
| | - Moshe Phillip
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Felsenstein Medical Research Center, Petach Tikva, Israel; The Jesse Z and Sara Lea Shafer Institute for Endocrinology and Diabetes, National Center for Childhood Diabetes, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.
| | - Galia Gat-Yablonski
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Felsenstein Medical Research Center, Petach Tikva, Israel; The Jesse Z and Sara Lea Shafer Institute for Endocrinology and Diabetes, National Center for Childhood Diabetes, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.
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32
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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Rumberger JM, Arch JRS, Green A. Butyrate and other short-chain fatty acids increase the rate of lipolysis in 3T3-L1 adipocytes. PeerJ 2014; 2:e611. [PMID: 25320679 PMCID: PMC4193401 DOI: 10.7717/peerj.611] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 09/16/2014] [Indexed: 12/15/2022] Open
Abstract
We determined the effect of butyrate and other short-chain fatty acids (SCFA) on rates of lipolysis in 3T3-L1 adipocytes. Prolonged treatment with butyrate (5 mM) increased the rate of lipolysis approximately 2–3-fold. Aminobutyric acid and acetate had little or no effect on lipolysis, however propionate stimulated lipolysis, suggesting that butyrate and propionate act through their shared activity as histone deacetylase (HDAC) inhibitors. Consistent with this, the HDAC inhibitor trichostatin A (1 µM) also stimulated lipolysis to a similar extent as did butyrate. Western blot data suggested that neither mitogen-activated protein kinase (MAPK) activation nor perilipin down-regulation are necessary for SCFA-induced lipolysis. Stimulation of lipolysis with butyrate and trichostatin A was glucose-dependent. Changes in AMP-activated protein kinase (AMPK) phosphorylation mediated by glucose were independent of changes in rates of lipolysis. The glycolytic inhibitor iodoacetate prevented both butyrate- and tumor necrosis factor-alpha-(TNF-α) mediated increases in rates of lipolysis indicating glucose metabolism is required. However, unlike TNF-α– , butyrate-stimulated lipolysis was not associated with increased lactate release or inhibited by activation of pyruvate dehydrogenase (PDH) with dichloroacetate. These data demonstrate an important relationship between lipolytic activity and reported HDAC inhibitory activity of butyrate, other short-chain fatty acids and trichostatin A. Given that HDAC inhibitors are presently being evaluated for the treatment of diabetes and other disorders, more work will be essential to determine if these effects on lipolysis are due to inhibition of HDAC.
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Affiliation(s)
- John M Rumberger
- Bassett Healthcare , Cooperstown, NY , USA ; Clore Laboratory, University of Buckingham , Buckingham , UK
| | | | - Allan Green
- Department of Chemistry and Biochemistry, SUNY Oneonta , Oneonta, NY , USA
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Sprow GM, Rinker JA, Thiele TE. Histone acetylation in the nucleus accumbens shell modulates ethanol-induced locomotor activity in DBA/2J mice. Alcohol Clin Exp Res 2014; 38:2377-86. [PMID: 25130590 DOI: 10.1111/acer.12502] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 05/20/2014] [Indexed: 02/05/2023]
Abstract
BACKGROUND A growing body of literature suggests that epigenetic mechanisms, including histone acetylation, may play key roles in drug abuse and the development of addiction. Experiments in this study were designed to investigate the role of histone acetylation in ethanol (EtOH)-induced locomotor sensitization. METHODS Immunohistochemical, Western blotting, and site-directed pharmacological techniques were used to explore the roles of histone acetylation at histone H3 (acH3K9) in both the expression of and acquisition of EtOH-induced locomotor sensitization. A commonly used sensitization protocol, in which animals were exposed to repeated injections of a low dose of EtOH while in their home cage, was used to examine this behavioral phenomenon. Additionally, site-directed administration of the histone deacetylase inhibitor (HDACi) Trichostatin A (TSA), in the absence of repeated EtOH injections, was used to examine the role of hyperacetylation in the nucleus accumbens (NAC) shell in EtOH-induced locomotor sensitization. RESULTS Sensitized mice displayed elevated acH3K9 immunoreactivity (IR) localized to the shell of the NAC. This augmentation in acH3K9 IR was confirmed, in a separate experiment, using Western blot analyses. Next, repeated intra-accumbal infusions of TSA, in the absence of repeated EtOH injections, were sufficient to induce an augmented locomotor response to a later injection of a low dose (2.0 g/kg, intraperitoneally) of EtOH, indicative of cross-sensitization to this locomotor stimulation between TSA and EtOH. Finally, a local infusion of TSA into the shell of the accumbens was also associated with a significant increase in acH3K9 IR within this region. CONCLUSIONS Together, the present observations suggest that histone acetylation, particularly within the shell of the NAC, is important for the development and expression of EtOH-induced locomotor sensitization.
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Affiliation(s)
- Gretchen M Sprow
- Department of Psychology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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Hou T, Zheng G, Zhang P, Jia J, Li J, Xie L, Wei C, Li Y. LAceP: lysine acetylation site prediction using logistic regression classifiers. PLoS One 2014; 9:e89575. [PMID: 24586884 PMCID: PMC3930742 DOI: 10.1371/journal.pone.0089575] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 01/22/2014] [Indexed: 11/19/2022] Open
Abstract
Background Lysine acetylation is a crucial type of protein post-translational modification, which is involved in many important cellular processes and serious diseases. However, identification of protein acetylated sites through traditional experiment methods is time-consuming and laborious. Those methods are not suitable to identify a large number of acetylated sites quickly. Therefore, computational methods are still very valuable to accelerate lysine acetylated site finding. Result In this study, many biological characteristics of acetylated sites have been investigated, such as the amino acid sequence around the acetylated sites, the physicochemical property of the amino acids and the transition probability of adjacent amino acids. A logistic regression method was then utilized to integrate these information for generating a novel lysine acetylation prediction system named LAceP. When compared with existing methods, LAceP overwhelms most of state-of-the-art methods. Especially, LAceP has a more balanced prediction capability for positive and negative datasets. Conclusion LAceP can integrate different biological features to predict lysine acetylation with high accuracy. An online web server is freely available at http://www.scbit.org/iPTM/.
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Affiliation(s)
- Ting Hou
- School of Biological Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Center for Bioinformation Technology, Shanghai, China
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guangyong Zheng
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (GZ); (CCW); (YXL)
| | - Pingyu Zhang
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jia Jia
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Jing Li
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Chaochun Wei
- Shanghai Center for Bioinformation Technology, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (GZ); (CCW); (YXL)
| | - Yixue Li
- School of Biological Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Center for Bioinformation Technology, Shanghai, China
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (GZ); (CCW); (YXL)
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Abstract
BACKGROUND Neonatal total parenteral nutrition (TPN) is associated with animals with low glucose tolerance, body weight, and physical activity at adulthood. The early life origin of adult metabolic perturbations suggests a reprogramming of metabolism following epigenetic modifications induced by a change in the pattern of DNA expression. We hypothesized that peroxides contaminating TPN inhibit the activity of DNA methyltransferase (DNMT), leading to a modified DNA methylation state. METHODS Three groups of 3-d-old guinea pigs with catheters in their jugular veins were compared: (i) control: enterally fed with regular chow; (ii) TPN: fed exclusively with TPN (dextrose, amino acids, lipids, multivitamins, contaminated with 350 ± 29 μmol/l peroxides); (iii) H2O2: control + 350 μmol/l H2O2 intravenously. After 4 d, infusions were stopped and animals enterally fed. Half the animals were killed immediately after treatments and half were killed 8 wk later (n = 4-6 per group) for hepatic determination of DNMT activities and of 5'-methyl-2'-deoxycytidine (5MedCyd) levels, a marker of DNA methylation. RESULTS At 1 wk, DNMT and 5MedCyd were lower in the TPN and H2O2 groups as compared with controls. At 9 wk, DNMT remained lower in the TPN group, whereas 5MedCyd was lower in the TPN and H2O2 groups. CONCLUSION Administration of TPN or H2O2 early in life in guinea pigs induces a sustained hypomethylation of DNA following inhibition of DNMT activity.
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Kaluarachchi Duffy S, Friesen H, Baryshnikova A, Lambert JP, Chong YT, Figeys D, Andrews B. Exploring the yeast acetylome using functional genomics. Cell 2012; 149:936-48. [PMID: 22579291 DOI: 10.1016/j.cell.2012.02.064] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 01/24/2012] [Accepted: 02/24/2012] [Indexed: 10/28/2022]
Abstract
Lysine acetylation is a dynamic posttranslational modification with a well-defined role in regulating histones. The impact of acetylation on other cellular functions remains relatively uncharacterized. We explored the budding yeast acetylome with a functional genomics approach, assessing the effects of gene overexpression in the absence of lysine deacetylases (KDACs). We generated a network of 463 synthetic dosage lethal (SDL) interactions involving class I and II KDACs, revealing many cellular pathways regulated by different KDACs. A biochemical survey of genes interacting with the KDAC RPD3 identified 72 proteins acetylated in vivo. In-depth analysis of one of these proteins, Swi4, revealed a role for acetylation in G1-specific gene expression. Acetylation of Swi4 regulates interaction with its partner Swi6, both components of the SBF transcription factor. This study expands our view of the yeast acetylome, demonstrates the utility of functional genomic screens for exploring enzymatic pathways, and provides functional information that can be mined for future studies.
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Affiliation(s)
- Supipi Kaluarachchi Duffy
- Department of Molecular Genetics, The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada
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Wang L, Du Y, Lu M, Li T. ASEB: a web server for KAT-specific acetylation site prediction. Nucleic Acids Res 2012; 40:W376-9. [PMID: 22600735 PMCID: PMC3394258 DOI: 10.1093/nar/gks437] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Protein lysine acetylation plays an important role in the normal functioning of cells, including gene expression regulation, protein stability and metabolism regulation. Although large amounts of lysine acetylation sites have been identified via large-scale mass spectrometry or traditional experimental methods, the lysine (K)-acetyl-transferase (KAT) responsible for the acetylation of a given protein or lysine site remains largely unknown due to the experimental limitations of KAT substrate identification. Hence, the in silico prediction of KAT-specific acetylation sites may provide direction for further experiments. In our previous study, we developed the acetylation set enrichment based (ASEB) computer program to predict which KAT-families are responsible for the acetylation of a given protein or lysine site. In this article, we provide KAT-specific acetylation site prediction as a web service. This web server not only provides the online tool and R package for the method in our previous study, but several useful services are also included, such as the integration of protein–protein interaction information to enhance prediction accuracy. This web server can be freely accessed at http://cmbi.bjmu.edu.cn/huac.
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Affiliation(s)
- Likun Wang
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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Escobar J, Pereda J, López-Rodas G, Sastre J. Redox signaling and histone acetylation in acute pancreatitis. Free Radic Biol Med 2012; 52:819-37. [PMID: 22178977 DOI: 10.1016/j.freeradbiomed.2011.11.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 11/08/2011] [Accepted: 11/09/2011] [Indexed: 12/22/2022]
Abstract
Histone acetylation via CBP/p300 coordinates the expression of proinflammatory cytokines in the activation phase of inflammation, particularly through mitogen-activated protein kinases (MAPKs), nuclear factor-κB (NF-κB), and signal transducers and activators of transcription (STAT) pathways. In contrast, histone deacetylases (HDACs) and protein phosphatases are mainly involved in the attenuation phase of inflammation. The role of reactive oxygen species (ROS) in the inflammatory cascade is much more important than expected. Mitochondrial ROS act as signal-transducing molecules that trigger proinflammatory cytokine production via inflammasome-independent and inflammasome-dependent pathways. The major source of ROS in acute inflammation seems to be NADPH oxidases, whereas NF-κB, protein phosphatases, and HDACs are the major targets of ROS and redox signaling in this process. There is a cross-talk between oxidative stress and proinflammatory cytokines through serine/threonine protein phosphatases, tyrosine protein phosphatases, and MAPKs that greatly contributes to amplification of the uncontrolled inflammatory cascade and tissue injury in acute pancreatitis. Chromatin remodeling during induction of proinflammatory genes would depend primarily on phosphorylation of transcription factors and their binding to gene promoters together with recruitment of histone acetyltransferases. PP2A should be considered a key modulator of the inflammatory cascade in acute pancreatitis through the ERK/NF-κB pathway and histone acetylation.
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Affiliation(s)
- Javier Escobar
- Department of Physiology, School of Pharmacy, University of Valencia, Burjasot, Valencia, Spain
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Li T, Du Y, Wang L, Huang L, Li W, Lu M, Zhang X, Zhu WG. Characterization and prediction of lysine (K)-acetyl-transferase specific acetylation sites. Mol Cell Proteomics 2011; 11:M111.011080. [PMID: 21964354 DOI: 10.1074/mcp.m111.011080] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lysine acetylation is a well-studied post-translational modification on both histone and nonhistone proteins. More than 2000 acetylated proteins and 4000 lysine acetylation sites have been identified by large scale mass spectrometry or traditional experimental methods. Although over 20 lysine (K)-acetyl-transferases (KATs) have been characterized, which KAT is responsible for a given protein or lysine site acetylation is mostly unknown. In this work, we collected KAT-specific acetylation sites manually and analyzed sequence features surrounding the acetylated lysine of substrates from three main KAT families (CBP/p300, GCN5/PCAF, and the MYST family). We found that each of the three KAT families acetylates lysines with different sequence features. Based on these differences, we developed a computer program, Acetylation Set Enrichment Based method to predict which KAT-families are responsible for acetylation of a given protein or lysine site. Finally, we evaluated the efficiency of our method, and experimentally detected four proteins that were predicted to be acetylated by two KAT families when one representative member of the KAT family is over expressed. We conclude that our approach, combined with more traditional experimental methods, may be useful for identifying KAT families responsible for acetylated substrates proteome-wide.
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Affiliation(s)
- Tingting Li
- Department of Biomedical Informatics, Peking University Health Science Center, Beijing 100191, China; Institute of Systems Biomedicine, Peking University Health Science Center, Beijing 100191, China.
| | - Yipeng Du
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Likun Wang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China; College of Computer Science and Technology, Jilin University, Changchun 130012, China
| | - Lei Huang
- Advanced Computing Research Laboratory, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China; Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenlin Li
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Ming Lu
- Department of Biomedical Informatics, Peking University Health Science Center, Beijing 100191, China
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Wei-Guo Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China; The Center for Life Science, Peking University, Beijing 100871, China.
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Lombardi PM, Cole KE, Dowling DP, Christianson DW. Structure, mechanism, and inhibition of histone deacetylases and related metalloenzymes. Curr Opin Struct Biol 2011; 21:735-43. [PMID: 21872466 DOI: 10.1016/j.sbi.2011.08.004] [Citation(s) in RCA: 195] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 08/01/2011] [Indexed: 10/17/2022]
Abstract
Metal-dependent histone deacetylases (HDACs) catalyze the hydrolysis of acetyl-L-lysine side chains in histone and nonhistone proteins to yield l-lysine and acetate. This chemistry plays a critical role in the regulation of numerous biological processes. Aberrant HDAC activity is implicated in various diseases, and HDACs are validated targets for drug design. Two HDAC inhibitors are currently approved for cancer chemotherapy, and other inhibitors are in clinical trials. To date, X-ray crystal structures are available for four human HDACs (2, 4, 7, and 8) and three HDAC-related deacetylases from bacteria (histone deacetylase-like protein (HDLP); histone deacetylase-like amidohydrolase (HDAH); acetylpolyamine amidohydrolase (APAH)). Structural comparisons among these enzymes reveal a conserved constellation of active site residues, suggesting a common mechanism for the metal-dependent hydrolysis of acetylated substrates. Structural analyses of HDACs and HDAC-related deacetylases guide the design of tight-binding inhibitors, and future prospects for developing isozyme-specific inhibitors are quite promising.
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Affiliation(s)
- Patrick M Lombardi
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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Wan Y, Chen W, Xing J, Tan J, Li B, Chen H, Lin Z, Chiang JH, Ramsey S. Transcriptome profiling reveals a novel role for trichostatin A in antagonizing histone chaperone Chz1 mediated telomere anti-silencing. FEBS Lett 2011; 585:2519-25. [DOI: 10.1016/j.febslet.2011.06.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Revised: 06/12/2011] [Accepted: 06/20/2011] [Indexed: 01/06/2023]
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Raman and surface enhanced Raman spectroscopic studies of specific, small molecule activator of histone acetyltransferase p300. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.03.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Histone deacetylase inhibitors attenuate acute lung injury during cecal ligation and puncture-induced polymicrobial sepsis. World J Surg 2011; 34:1676-83. [PMID: 20177680 DOI: 10.1007/s00268-010-0493-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND The histone deacetylase (HDAC) inhibitors have emerged as the useful reagents that epigenetically modulate the expression of various genes. In the present study, the effects of HDAC inhibitors on the expression of inflammation-related genes and lung injury during sepsis were investigated. METHODS Mice were pretreated with two structurally unrelated HDAC inhibitors, Trichostatin A (TSA) and sodium butyrate (SB). Thirty minutes later, mice underwent cecal ligation and puncture (CLP)-induced sepsis. Lung injury and the expression of inflammation-related molecules were determined. In addition, survival was assessed post-CLP. RESULTS Our results indicated that administration of TSA or SB alleviated sepsis-induced lung injury. This was accompanied by reduced neutrophil infiltration, decreased intercellular adhesion molecule-1 (ICAM-1) and E-selectin expression in lung tissue, and lower interleukin-6 (IL-6) level in plasma. In addition, treatment with HDAC inhibitors significantly prolonged the survival time of CLP mice. CONCLUSIONS These data indicated that the HDAC inhibitors, based on modulating the key enzymes linked to acetylation modification, effectively attenuate intrapulmonary inflammatory response, thus significantly alleviating lung injury during sepsis.
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Ichi S, Boshnjaku V, Shen YW, Mania-Farnell B, Ahlgren S, Sapru S, Mansukhani N, McLone DG, Tomita T, Mayanil CSK. Role of Pax3 acetylation in the regulation of Hes1 and Neurog2. Mol Biol Cell 2010; 22:503-12. [PMID: 21169561 PMCID: PMC3038648 DOI: 10.1091/mbc.e10-06-0541] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Pax3 plays a role in regulating Hes1 and Neurog2 activity and thereby stem cell maintenance and neurogenesis. A mechanism for Pax3 regulation of these two opposing events, during caudal neural tube development, is examined in this study. Pax3 acetylation on C-terminal lysine residues K437 and K475 may be critical for proper regulation of Hes1 and Neurog2. Removal of these lysine residues increased Hes1 but decreased Neurog2 promoter activity. SIRT1 deacetylase may be a key component in regulating Pax3 acetylation. Chromatin immunoprecipitation assays showed that SIRT1 is associated with Hes1 and Neurog2 promoters during murine embryonic caudal neural tube development at E9.5, but not at E12.5. Overexpression of SIRT1 decreased Pax3 acetylation, Neurog2 and Brn3a positive staining. Conversely, siRNA-mediated silencing of SIRT1 increased these factors. These studies suggest that Pax3 acetylation results in decreased Hes1 and increased Neurog2 activity, thereby promoting sensory neuron differentiation.
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Affiliation(s)
- Shunsuke Ichi
- Developmental Neurobiology Laboratory, Department of Pediatric Neurosurgery, Children's Memorial Hospital, Chicago, IL 60614, USA
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Kim HC, Choi KC, Choi HK, Kang HB, Kim MJ, Lee YH, Lee OH, Lee J, Kim YJ, Jun W, Jeong JW, Yoon HG. HDAC3 selectively represses CREB3-mediated transcription and migration of metastatic breast cancer cells. Cell Mol Life Sci 2010; 67:3499-510. [PMID: 20473547 PMCID: PMC11115716 DOI: 10.1007/s00018-010-0388-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Revised: 04/19/2010] [Accepted: 04/23/2010] [Indexed: 12/19/2022]
Abstract
We identified CREB3 as a novel HDAC3-interacting protein in a yeast two-hybrid screen for HDAC3-interacting proteins. Among all class I HDACs, CREB3 specifically interacts with HDAC3, in vitro and in vivo. HDAC3 efficiently inhibited CREB3-enhanced NF-κB activation, whereas the other class I HDACs did not alter NF-κB-dependent promoter activities or the expression of NF-κB target genes. Importantly, both knock-down of CREB3 and overexpression of HDAC3 suppressed the transcriptional activation of the novel CREB3-regulated gene, CXCR4. Furthermore, CREB3 was shown to bind to the CRE element in the CXCR4 promoter and to activate the transcription of the CXCR4 gene by causing dissociation of HDAC3 and subsequently increasing histone acetylation. Importantly, both the depletion of HDAC3 and the overexpression of CREB3 substantially increased the migration of MDA-MB-231 metastatic breast cancer cells. Taken together, these findings suggest that HDAC3 selectively represses CREB3-mediated transcriptional activation and chemotactic signalling in human metastatic breast cancer cells.
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Affiliation(s)
- Han-Cheon Kim
- Department of Biochemistry and Molecular Biology, Center for Chronic Metabolic Disease Research, Brain Korea 21 Project for Medical Sciences, Severance Medical Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Kyung-Chul Choi
- Department of Biochemistry and Molecular Biology, Center for Chronic Metabolic Disease Research, Brain Korea 21 Project for Medical Sciences, Severance Medical Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Hyo-Kyoung Choi
- Department of Biochemistry and Molecular Biology, Center for Chronic Metabolic Disease Research, Brain Korea 21 Project for Medical Sciences, Severance Medical Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Hee-Bum Kang
- Department of Biochemistry and Molecular Biology, Center for Chronic Metabolic Disease Research, Brain Korea 21 Project for Medical Sciences, Severance Medical Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Mi-Jeong Kim
- Department of Biochemistry and Molecular Biology, Center for Chronic Metabolic Disease Research, Brain Korea 21 Project for Medical Sciences, Severance Medical Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Yoo-Hyun Lee
- Department of Food and Nutrition, The University of Suwon, Suwon, Korea
| | - Ok-Hee Lee
- Severance Hospital Integrative Research Institute for Cerebral and Cardiovascular Disease, Yonsei University Health System, Seoul, Korea
| | - Jeongmin Lee
- Department of Medical Nutrition, Kyung Hee University, Yongin-si, Kyunggi-do 446-701 South Korea
| | - Young Jun Kim
- Department of Food and Biotechnology, Korea University, Jochiwon-eup, Yeongi-gun, Chungnam Korea
| | - Woojin Jun
- Department of Food and Nutrition, Chonnam National University, Gwangju, Korea
| | - Jae-Wook Jeong
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Ho-Geun Yoon
- Department of Biochemistry and Molecular Biology, Center for Chronic Metabolic Disease Research, Brain Korea 21 Project for Medical Sciences, Severance Medical Research Institute, Yonsei University College of Medicine, Seoul, Korea
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Singh BN, Zhang G, Hwa YL, Li J, Dowdy SC, Jiang SW. Nonhistone protein acetylation as cancer therapy targets. Expert Rev Anticancer Ther 2010; 10:935-54. [PMID: 20553216 DOI: 10.1586/era.10.62] [Citation(s) in RCA: 216] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Acetylation and deacetylation are counteracting, post-translational modifications that affect a large number of histone and nonhistone proteins. The significance of histone acetylation in the modification of chromatin structure and dynamics, and thereby gene transcription regulation, has been well recognized. A steadily growing number of nonhistone proteins have been identified as acetylation targets and reversible lysine acetylation in these proteins plays an important role(s) in the regulation of mRNA stability, protein localization and degradation, and protein-protein and protein-DNA interactions. The recruitment of histone acetyltransferases (HATs) and histone deacetylases (HDACs) to the transcriptional machinery is a key element in the dynamic regulation of genes controlling cellular proliferation, differentiation and apoptosis. Many nonhistone proteins targeted by acetylation are the products of oncogenes or tumor-suppressor genes and are directly involved in tumorigenesis, tumor progression and metastasis. Aberrant activity of HDACs has been documented in several types of cancers and HDAC inhibitors (HDACi) have been employed for therapeutic purposes. Here we review the published literature in this field and provide updated information on the regulation and function of nonhistone protein acetylation. While concentrating on the molecular mechanism and pathways involved in the addition and removal of the acetyl moiety, therapeutic modalities of HDACi are also discussed.
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Affiliation(s)
- Brahma N Singh
- Department of Mycology & Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
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Kim SH, Kang HJ, Na H, Lee MO. Trichostatin A enhances acetylation as well as protein stability of ERalpha through induction of p300 protein. Breast Cancer Res 2010; 12:R22. [PMID: 20388208 PMCID: PMC2879569 DOI: 10.1186/bcr2562] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Revised: 01/30/2010] [Accepted: 04/13/2010] [Indexed: 12/20/2022] Open
Abstract
Introduction Trichostatin A (TSA) is a well-characterized histone deacetylase (HDAC) inhibitor. TSA modifies the balance between HDAC and histone acetyltransferase activities that is important in chromatin remodeling and gene expression. Although several previous studies have demonstrated the role of TSA in regulation of estrogen receptor alpha (ERα), the precise mechanism by which TSA affects ERα activity remains unclear. Methods Transient transfection was performed using the Welfect-EX™Plus procedure. The mRNA expression was determined using RT-PCR. Protein expression and interaction were determined by western blotting and immunoprecipitation. The transfection of siRNAs was performed using the Oligofectamine™ reagent procedure. Results TSA treatment increased acetylation of ERα in a dose-dependent manner. The TSA-induced acetylation of ERα was accompanied by an increased stability of ERα protein. Interestingly, TSA also increased the acetylation and the stability of p300 protein. Overexpression of p300 induced acetylation and stability of ERα by blocking ubiquitination. Knockdown of p300 by RNA interference decreased acetylation as well as the protein level of ERα, indicating that p300 mediated the TSA-induced stabilization of ERα. Conclusions We report that TSA enhanced acetylation as well as the stability of the ERα protein by modulating stability of p300. These results may provide the molecular basis for pharmacological functions of HDAC inhibitors in the treatment of human breast cancer.
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Affiliation(s)
- Sung-Hye Kim
- College of Pharmacy, Seoul National University, San 56-1, Sillim-dong, Kwanak-gu, Seoul, Republic of Korea.
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Taura A, Taura K, Choung YH, Masuda M, Pak K, Chavez E, Ryan AF. Histone deacetylase inhibition enhances adenoviral vector transduction in inner ear tissue. Neuroscience 2010; 166:1185-93. [PMID: 20060033 DOI: 10.1016/j.neuroscience.2009.12.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 12/16/2009] [Accepted: 12/23/2009] [Indexed: 10/20/2022]
Abstract
Adenovirus vectors (AdVs) are efficient tools for gene therapy in many tissues. Several studies have demonstrated successful transgene transduction with AdVs in the inner ear of rodents [Kawamoto K, Ishimoto SI, Minoda R, Brough DE, Raphael Y (2003) J Neurosci 23:4395-4400]. However, toxicity of AdVs [Morral N, O'Neal WK, Rice K, Leland MM, Piedra PA, Aguilar-Cordova E, Carey KD, Beaudet AL, Langston C (2002) Hum Gene Ther 13:143-154.] or lack of tropism to important cell types such as hair cells [Shou J, Zheng JL, Gao WQ (2003) Mol Cell Neurosci 23:169-179] appears to limit their experimental and potential clinical utility. Histone deacetylase inhibitors (HDIs) are known to enhance AdV-mediated transgene expression in various organs [Dion LD, Goldsmith KT, Tang DC, Engler JA, Yoshida M, Garver RI Jr (1997) Virology 231:201-209], but their effects in the inner ear have not been documented. We investigated the ability of one HDI, trichostatin A (TSA), to enhance AdV-mediated transgene expression in inner ear tissue. We cultured neonatal rat macular and cochlear explants, and transduced them with an AdV encoding green fluorescent protein (Ad-GFP) under the control of a constitutive promoter for 24 h. In the absence of TSA, GFP expression was limited, and very few hair cells were transduced. TSA did not enhance transduction when applied at the onset of Ad-GFP transduction. However, administration of TSA during or just after Ad-GFP application increased GFP expression in supporting cells approximately fourfold. Moreover, vestibular hair cell transduction was enhanced approximately sixfold, and that of inner hair cells by more than 17-fold. These results suggest that TSA increases AdV-mediated transgene expression in the inner ear, including the successful transduction of hair cells. HDIs, some of which are currently under clinical trials (Sandor et al., 2002), could be useful tools in overcoming current limitations of gene therapy in the inner ear using Ad-GFP.
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Affiliation(s)
- A Taura
- Division of Otolaryngology, Departments of Surgery, UCSD School of Medicine, San Diego, CA 92093, USA
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Koshikawa N, Hayashi JI, Nakagawara A, Takenaga K. Reactive oxygen species-generating mitochondrial DNA mutation up-regulates hypoxia-inducible factor-1alpha gene transcription via phosphatidylinositol 3-kinase-Akt/protein kinase C/histone deacetylase pathway. J Biol Chem 2009; 284:33185-94. [PMID: 19801684 PMCID: PMC2785161 DOI: 10.1074/jbc.m109.054221] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 09/20/2009] [Indexed: 11/06/2022] Open
Abstract
Lewis lung carcinoma-derived high metastatic A11 cells constitutively overexpress hypoxia-inducible factor (HIF)-1alpha mRNA compared with low metastatic P29 cells. Because A11 cells exclusively possess a G13997A mutation in the mitochondrial NADH dehydrogenase subunit 6 (ND6) gene, we addressed here a causal relationship between the ND6 mutation and the activation of HIF-1alpha transcription, and we investigated the potential mechanism. Using trans-mitochondrial cybrids between A11 and P29 cells, we found that the ND6 mutation was directly involved in HIF-1alpha mRNA overexpression. Stimulation of HIF-1alpha transcription by the ND6 mutation was mediated by overproduction of reactive oxygen species (ROS) and subsequent activation of phosphatidylinositol 3-kinase (PI3K)-Akt and protein kinase C (PKC) signaling pathways. The up-regulation of HIF-1alpha transcription was abolished by mithramycin A, an Sp1 inhibitor, but luciferase reporter and chromatin immunoprecipitation assays indicated that Sp1 was necessary but not sufficient for HIF-1alpha mRNA overexpression in A11 cells. On the other hand, trichostatin A, a histone deacetylase (HDAC) inhibitor, markedly suppressed HIF-1alpha transcription in A11 cells. In accordance with this, HDAC activity was high in A11 cells but low in P29 cells and in A11 cells treated with the ROS scavenger ebselene, the PI3K inhibitor LY294002, and the PKC inhibitor Ro31-8220. These results suggest that the ROS-generating ND6 mutation increases HIF-1alpha transcription via the PI3K-Akt/PKC/HDAC pathway, leading to HIF-1alpha protein accumulation in hypoxic tumor cells.
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Affiliation(s)
| | - Jun-Ichi Hayashi
- the Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, and
| | - Akira Nakagawara
- Division of Biochemistry and Innovative Cancer Therapeutics, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuoh-ku, Chiba 260-8717
| | - Keizo Takenaga
- From the Laboratory of Cancer Metastasis and
- the Laboratory of Tumor Biology, Division of Life Science, Shimane University Faculty of Medicine, 89-1 Enya, Izumo, Shimane 693-8501, Japan
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