1
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Kuna M, Soares MJ. Cited2 is a key regulator of placental development and plasticity. Bioessays 2024:e2300118. [PMID: 38922923 DOI: 10.1002/bies.202300118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
The biology of trophoblast cell lineage development and placentation is characterized by the involvement of several known transcription factors. Central to the action of a subset of these transcriptional regulators is CBP-p300 interacting transactivator with Glu/Asp-rich carboxy-terminal domain 2 (CITED2). CITED2 acts as a coregulator modulating transcription factor activities and affecting placental development and adaptations to physiological stressors. These actions of CITED2 on the trophoblast cell lineage and placentation are conserved across the mouse, rat, and human. Thus, aspects of CITED2 biology in hemochorial placentation can be effectively modeled in the mouse and rat. In this review, we present information on the conserved role of CITED2 in the biology of placentation and discuss the use of CITED2 as a tool to discover new insights into regulatory mechanisms controlling placental development.
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Affiliation(s)
- Marija Kuna
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Michael J Soares
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, Kansas, USA
- Center for Perinatal Research, Children's Mercy Research Institute, Children's Mercy, Kansas City, Missouri, USA
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2
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Bracken RC, Davison LM, Buehler DP, Fulton ME, Carson EE, Sheng Q, Stolze LK, Guillermier C, Steinhauser ML, Brown JD. Transcriptional synergy in human aortic endothelial cells is vulnerable to combination p300/CBP and BET bromodomain inhibition. iScience 2024; 27:110011. [PMID: 38868181 PMCID: PMC11167439 DOI: 10.1016/j.isci.2024.110011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 03/14/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024] Open
Abstract
Combinatorial signaling by proinflammatory cytokines synergizes to exacerbate toxicity to cells and tissue injury during acute infections. To explore synergism at the gene-regulatory level, we investigated the dynamics of transcription and chromatin signaling in response to dual cytokines by integrating nascent RNA imaging mass spectrometry, RNA sequencing, amplification-independent mRNA quantification, assay for transposase-accessible chromatin using sequencing (ATAC-seq), and transcription factor profiling. Costimulation with interferon-gamma (IFNγ) and tumor necrosis factor alpha (TNFα) synergistically induced a small subset of genes, including the chemokines CXCL9, -10, and -11. Gene induction coincided with increased chromatin accessibility at non-coding regions enriched for p65 and STAT1 binding sites. To discover coactivator dependencies, we conducted a targeted chemogenomic screen of transcriptional inhibitors followed by modeling of inhibitor dose-response curves. These results identified high efficacy of either p300/CREB-binding protein (CBP) or bromodomain and extra-terminal (BET) bromodomain inhibitors to disrupt induction of synergy genes. Combination p300/CBP and BET bromodomain inhibition at half-maximal inhibitory concentrations (subIC50) synergistically abrogated IFNγ/TNFα-induced chemokine gene and protein levels.
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Affiliation(s)
- Ronan C. Bracken
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Lindsay M. Davison
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Dennis P. Buehler
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Maci E. Fulton
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Emily E. Carson
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 3723, USA
| | - Lindsey K. Stolze
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 3723, USA
| | - Christelle Guillermier
- Harvard Medical School, Boston, MA 02115, USA
- Center for NanoImaging, Cambridge MA 02115, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | | | - Jonathan D. Brown
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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3
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Li T, Shahabi S, Biswas T, Tsodikov OV, Pan W, Huang DB, Wang VYF, Wang Y, Ghosh G. Transient interactions modulate the affinity of NF-κB transcription factors for DNA. Proc Natl Acad Sci U S A 2024; 121:e2405555121. [PMID: 38805268 PMCID: PMC11161749 DOI: 10.1073/pnas.2405555121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/09/2024] [Indexed: 05/30/2024] Open
Abstract
The dimeric nuclear factor kappa B (NF-κB) transcription factors (TFs) regulate gene expression by binding to a variety of κB DNA elements with conserved G:C-rich flanking sequences enclosing a degenerate central region. Toward defining mechanistic principles of affinity regulated by degeneracy, we observed an unusual dependence of the affinity of RelA on the identity of the central base pair, which appears to be noncontacted in the complex crystal structures. The affinity of κB sites with A or T at the central position is ~10-fold higher than with G or C. The crystal structures of neither the complexes nor the free κB DNAs could explain the differences in affinity. Interestingly, differential dynamics of several residues were revealed in molecular dynamics simulation studies, where simulation replicates totaling 148 μs were performed on NF-κB:DNA complexes and free κB DNAs. Notably, Arg187 and Arg124 exhibited selectivity in transient interactions that orchestrated a complex interplay among several DNA-interacting residues in the central region. Binding and simulation studies with mutants supported these observations of transient interactions dictating specificity. In combination with published reports, this work provides insights into the nuanced mechanisms governing the discriminatory binding of NF-κB family TFs to κB DNA elements and sheds light on cancer pathogenesis of cRel, a close homolog of RelA.
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Affiliation(s)
- Tianjie Li
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region999077, China
| | - Shandy Shahabi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
| | - Tapan Biswas
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
| | - Oleg V. Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY40536
| | - Wenfei Pan
- Faculty of Health Sciences, University of Macau, Taipa, Macau Special Administrative Region999078, China
| | - De-Bin Huang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
| | - Vivien Ya-Fan Wang
- Faculty of Health Sciences, University of Macau, Taipa, Macau Special Administrative Region999078, China
| | - Yi Wang
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region999077, China
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
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4
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Kochel B. Negative feedback systems for modelling NF-κB transcription factor oscillatory activity. Transcription 2024:1-32. [PMID: 38739365 DOI: 10.1080/21541264.2024.2331887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/13/2024] [Indexed: 05/14/2024] Open
Abstract
Low-dimensional negative feedback systems (NFSs) were developed within a signal flow model to describe the oscillatory activities of NF-κB caused by interactions with its inhibitor IκBα. The NFSs were established as 3rd- and 4th-order linear systems containing unperturbed and perturbed negative feedback (NF) loops with constant or time-varying NF strengths and a feed-forward loop. NF-related analytical solutions to the NFSs representing the time courses of NF-κB and IκBα were determined and their exact mathematical relationship was found. The NFS's parameters were determined to fit the experimental time courses of NF-κB in TNF-α-stimulated embryonic fibroblasts, rela-/- embryonic fibroblasts reconstituted with RelA, C9L cells, GFP-p65 knock-in embryonic fibroblasts and embryogenic fibroblasts lacking Iκβ and IκBε, LPS-stimulated IC-21 macrophages treated or not with DCPA, and anti-IgM-stimulated DT40 B-lymphocytes. The unperturbed and perturbed NFSs describing the above biosystems generated isochronous and non-isochronous solutions, depending on a constant or time-varying NF strength, respectively. The oscillation period of the NF-coupled solutions, the phase difference between them and the time delays in the appearance of cytoplasmic IκBα after stimulation of NF-κB were determined. A significant divergence between the IκBα solutions to the NFSs and the IκBα experimental courses led to a rejection of the NF coupling between NF-κB and IκBα in the above biosystems. It was shown that neither the linearity nor the low dimensionality of the NFSs altered the NF relationship and the divergence between the IκBα solutions to the NFS and IκBα experimental time courses. Although the NF relationship between IκBα and NF-κB was not confirmed in all the experimental data analyzed, delayed negative feedback was found in some cases.
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Affiliation(s)
- Bonawentura Kochel
- Immunotherapy Central Europe, Wroclaw Medical University, Wrocław, Poland
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5
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Inge MM, Miller R, Hook H, Bray D, Keenan JL, Zhao R, Gilmore TD, Siggers T. Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.05.588333. [PMID: 38617258 PMCID: PMC11014505 DOI: 10.1101/2024.04.05.588333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Transcription factor (TF)-cofactor (COF) interactions define dynamic, cell-specific networks that govern gene expression; however, these networks are understudied due to a lack of methods for high-throughput profiling of DNA-bound TF-COF complexes. Here we describe the Cofactor Recruitment (CoRec) method for rapid profiling of cell-specific TF-COF complexes. We define a lysine acetyltransferase (KAT)-TF network in resting and stimulated T cells. We find promiscuous recruitment of KATs for many TFs and that 35% of KAT-TF interactions are condition specific. KAT-TF interactions identify NF-κB as a primary regulator of acutely induced H3K27ac. Finally, we find that heterotypic clustering of CBP/P300-recruiting TFs is a strong predictor of total promoter H3K27ac. Our data supports clustering of TF sites that broadly recruit KATs as a mechanism for widespread co-occurring histone acetylation marks. CoRec can be readily applied to different cell systems and provides a powerful approach to define TF-COF networks impacting chromatin state and gene regulation.
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Affiliation(s)
- MM Inge
- Department of Biology, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- These authors contributed equally
| | - R Miller
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- These authors contributed equally
| | - H Hook
- Department of Biology, Boston University, Boston, MA, USA
| | - D Bray
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - JL Keenan
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - R Zhao
- Department of Biology, Boston University, Boston, MA, USA
| | - TD Gilmore
- Department of Biology, Boston University, Boston, MA, USA
| | - T Siggers
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
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6
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Wiggins DA, Maxwell JN, Nelson DE. Exploring the role of CITED transcriptional regulators in the control of macrophage polarization. Front Immunol 2024; 15:1365718. [PMID: 38646545 PMCID: PMC11032013 DOI: 10.3389/fimmu.2024.1365718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Macrophages are tissue resident innate phagocytic cells that take on contrasting phenotypes, or polarization states, in response to the changing combination of microbial and cytokine signals at sites of infection. During the opening stages of an infection, macrophages adopt the proinflammatory, highly antimicrobial M1 state, later shifting to an anti-inflammatory, pro-tissue repair M2 state as the infection resolves. The changes in gene expression underlying these transitions are primarily governed by nuclear factor kappaB (NF-κB), Janus kinase (JAK)/signal transducer and activation of transcription (STAT), and hypoxia-inducible factor 1 (HIF1) transcription factors, the activity of which must be carefully controlled to ensure an effective yet spatially and temporally restricted inflammatory response. While much of this control is provided by pathway-specific feedback loops, recent work has shown that the transcriptional co-regulators of the CBP/p300-interacting transactivator with glutamic acid/aspartic acid-rich carboxy-terminal domain (CITED) family serve as common controllers for these pathways. In this review, we describe how CITED proteins regulate polarization-associated gene expression changes by controlling the ability of transcription factors to form chromatin complexes with the histone acetyltransferase, CBP/p300. We will also cover how differences in the interactions between CITED1 and 2 with CBP/p300 drive their contrasting effects on pro-inflammatory gene expression.
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Affiliation(s)
| | | | - David E. Nelson
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, United States
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7
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Ang DA, Carter JM, Deka K, Tan JHL, Zhou J, Chen Q, Chng WJ, Harmston N, Li Y. Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma. Nat Commun 2024; 15:2513. [PMID: 38514625 PMCID: PMC10957915 DOI: 10.1038/s41467-024-46728-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 03/07/2024] [Indexed: 03/23/2024] Open
Abstract
In multiple myeloma, abnormal plasma cells establish oncogenic niches within the bone marrow by engaging the NF-κB pathway to nurture their survival while they accumulate pro-proliferative mutations. Under these conditions, many cases eventually develop genetic abnormalities endowing them with constitutive NF-κB activation. Here, we find that sustained NF-κB/p52 levels resulting from such mutations favours the recruitment of enhancers beyond the normal B-cell repertoire. Furthermore, through targeted disruption of p52, we characterise how such enhancers are complicit in the formation of super-enhancers and the establishment of cis-regulatory interactions with myeloma dependencies during constitutive activation of p52. Finally, we functionally validate the pathological impact of these cis-regulatory modules on cell and tumour phenotypes using in vitro and in vivo models, confirming RGS1 as a p52-dependent myeloma driver. We conclude that the divergent epigenomic reprogramming enforced by aberrant non-canonical NF-κB signalling potentiates transcriptional programs beneficial for multiple myeloma progression.
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Affiliation(s)
- Daniel A Ang
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jean-Michel Carter
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Kamalakshi Deka
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Joel H L Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Jianbiao Zhou
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Republic of Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore
- NUS Centre for Cancer Research, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Qingfeng Chen
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Republic of Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore
- NUS Centre for Cancer Research, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS), 1E, Kent Ridge Road, Singapore, 119228, Republic of Singapore
| | - Nathan Harmston
- Division of Science, Yale-NUS College, Singapore, 138527, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
- Molecular Biosciences Division, Cardiff School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Yinghui Li
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Singapore.
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore.
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8
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Maurya SK, Rehman AU, Zaidi MAA, Khan P, Gautam SK, Santamaria-Barria JA, Siddiqui JA, Batra SK, Nasser MW. Epigenetic alterations fuel brain metastasis via regulating inflammatory cascade. Semin Cell Dev Biol 2024; 154:261-274. [PMID: 36379848 PMCID: PMC10198579 DOI: 10.1016/j.semcdb.2022.11.001] [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: 09/09/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
Brain metastasis (BrM) is a major threat to the survival of melanoma, breast, and lung cancer patients. Circulating tumor cells (CTCs) cross the blood-brain barrier (BBB) and sustain in the brain microenvironment. Genetic mutations and epigenetic modifications have been found to be critical in controlling key aspects of cancer metastasis. Metastasizing cells confront inflammation and gradually adapt in the unique brain microenvironment. Currently, it is one of the major areas that has gained momentum. Researchers are interested in the factors that modulate neuroinflammation during BrM. We review here various epigenetic factors and mechanisms modulating neuroinflammation and how this helps CTCs to adapt and survive in the brain microenvironment. Since epigenetic changes could be modulated by targeting enzymes such as histone/DNA methyltransferase, deacetylases, acetyltransferases, and demethylases, we also summarize our current understanding of potential drugs targeting various aspects of epigenetic regulation in BrM.
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Affiliation(s)
- Shailendra Kumar Maurya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Asad Ur Rehman
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Mohd Ali Abbas Zaidi
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Parvez Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Shailendra K Gautam
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | | | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68108, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68108, USA.
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9
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Dogsom O, Hamza A, Mahmud S, Min JK, Lee YB, Park JB. The Complex of p-Tyr42 RhoA and p-p65/RelA in Response to LPS Regulates the Expression of Phosphoglycerate Kinase 1. Antioxidants (Basel) 2023; 12:2090. [PMID: 38136210 PMCID: PMC10740983 DOI: 10.3390/antiox12122090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/24/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Inflammation plays a crucial role in tumorigenesis, primarily mediated by NF-κB. RhoA GTPases are instrumental in regulating the activation of NF-κB. Specifically, the phosphorylation of Tyrosine 42 on RhoA ensures the activation of NF-κB by directly activating the IKKβ associated with IKKγ (NEMO). This study aimed to uncover the molecular mechanism through which p-Tyrosine 42 RhoA, in conjunction with NF-κB, promotes tumorigenesis. Notably, we observed that p-Tyrosine 42 RhoA co-immunoprecipitated with the p-Ser 536 p65/RelA subunit in NF-κB in response to LPS. Moreover, both p-Tyrosine 42 RhoA and p-p65/RelA translocated to the nucleus, where they formed a protein complex associated with the promoter of phosphoglycerate kinase 1 (PGK1) and regulated the expression of PGK1. In addition, p-p65/RelA and p-Tyr42 RhoA co-immunoprecipitated with p300 histone acetyltransferase. Intriguingly, PGK1 exhibited an interaction with β-catenin, PKM1 and PKM2. Of particular interest, si-PGK1 led to a reduction in the levels of β-catenin and phosphorylated pyruvate dehydrogenase A1 (p-PDHA1). We also found that PGK1 phosphorylated β-catenin at the Thr551 and Ser552 residues. These findings discovered that PGK1 may play a role in transcriptional regulation, alongside other transcription factors.
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Affiliation(s)
- Oyungerel Dogsom
- Department of Biochemistry, Hallym University College of Medicine, Hallymdaehag-Gil 1, Chuncheon 24252, Kangwon-do, Republic of Korea; (O.D.); (A.H.); (S.M.); (J.-K.M.); (Y.-B.L.)
- Department of Biology, School of Bio-Medicine, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia
| | - Amir Hamza
- Department of Biochemistry, Hallym University College of Medicine, Hallymdaehag-Gil 1, Chuncheon 24252, Kangwon-do, Republic of Korea; (O.D.); (A.H.); (S.M.); (J.-K.M.); (Y.-B.L.)
| | - Shohel Mahmud
- Department of Biochemistry, Hallym University College of Medicine, Hallymdaehag-Gil 1, Chuncheon 24252, Kangwon-do, Republic of Korea; (O.D.); (A.H.); (S.M.); (J.-K.M.); (Y.-B.L.)
- National Institute of Biotechnology, Ganakbari, Ashulia, Savar 1349, Dhaka, Bangladesh
| | - Jung-Ki Min
- Department of Biochemistry, Hallym University College of Medicine, Hallymdaehag-Gil 1, Chuncheon 24252, Kangwon-do, Republic of Korea; (O.D.); (A.H.); (S.M.); (J.-K.M.); (Y.-B.L.)
| | - Yoon-Beom Lee
- Department of Biochemistry, Hallym University College of Medicine, Hallymdaehag-Gil 1, Chuncheon 24252, Kangwon-do, Republic of Korea; (O.D.); (A.H.); (S.M.); (J.-K.M.); (Y.-B.L.)
| | - Jae-Bong Park
- Department of Biochemistry, Hallym University College of Medicine, Hallymdaehag-Gil 1, Chuncheon 24252, Kangwon-do, Republic of Korea; (O.D.); (A.H.); (S.M.); (J.-K.M.); (Y.-B.L.)
- Institute of Cell Differentiation and Aging, Hallym University College of Medicine, Hallymdaehag-Gil 1, Chuncheon 24252, Kangwon-do, Republic of Korea
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10
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Wang T, Qin Y, Qiao J, Liu Y, Wang L, Zhang X. Overexpression of SIRT6 regulates NRF2/HO-1 and NF-κB signaling pathways to alleviate UVA-induced photoaging in skin fibroblasts. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2023; 249:112801. [PMID: 37897855 DOI: 10.1016/j.jphotobiol.2023.112801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/02/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023]
Abstract
Skin photoaging, resulting from prolonged exposure to sunlight, especially UVA rays, has been identified as a key contributor to age-related skin degeneration. However, the mechanism by which UVA radiation induces skin cell senescence has not been fully elucidated. In this investigation, bioinformatics technology was employed to identify SIRT6 as the core hub gene involved in the progression of skin photoaging. The study evinced that prolonged exposure of cutaneous fibroblasts to UVA radiation results in a marked reduction in the expression of SIRT6, both in vivo and in vitro. Knockdown of SIRT6 in skin fibroblasts resulted in the upregulation of genes associated with cellular aging, thereby exacerbating the effects of UVA radiation-induced photoaging. Conversely, overexpression of SIRT6 decreased the expression of cell aging-related genes, indicating that SIRT6 plays a role in the regulation of senescence in skin fibroblasts induced by UVA radiation. We proffer substantiation that overexpression of SIRT6 protects skin fibroblasts from UVA-induced oxidative stress by activating the NRF2/HO-1 signaling cascade. Moreover, SIRT6 overexpression also reduced UVA-induced type I collagen degradation by inhibiting NF-κB signaling cascade. In summary, our findings showed that overexpression of SIRT6 inhibits UVA-induced senescence phenotype and type I collagen degradation in skin fibroblasts by modulating the NRF2/HO-1 and NF-κB signaling pathways. And the regulation of these signaling pathways by SIRT6 may be achieved through its deacetylase activity. Therefore, SIRT6 is a novel and promising therapeutic target for skin aging related to age and UV.
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Affiliation(s)
- Tao Wang
- Department of Plastic Surgery, Lanzhou University Second Hospital, Lanzhou City 730000, Gansu Province, China
| | - Yonghong Qin
- Department of Plastic Surgery, Lanzhou University Second Hospital, Lanzhou City 730000, Gansu Province, China
| | - Jianxiong Qiao
- Department of Plastic Surgery, Lanzhou University Second Hospital, Lanzhou City 730000, Gansu Province, China
| | - Yang Liu
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, the Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu 610000, China
| | - Lerong Wang
- Department of Plastic Surgery, Lanzhou University Second Hospital, Lanzhou City 730000, Gansu Province, China
| | - Xuanfen Zhang
- Department of Plastic Surgery, Lanzhou University Second Hospital, Lanzhou City 730000, Gansu Province, China.
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11
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Chiou JT, Lee YC, Chang LS. Hydroquinone-selected chronic myelogenous leukemia cells are sensitive to chloroquine-induced cytotoxicity via MCL1 suppression and glycolysis inhibition. Biochem Pharmacol 2023; 218:115934. [PMID: 37989415 DOI: 10.1016/j.bcp.2023.115934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/12/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023]
Abstract
Previous studies have provided evidence that repeated exposure to the benzene metabolite hydroquinone (HQ) induces malignant transformation and increases basal autophagy in the chronic myeloid leukemia (CML) cell line K562. This study explored the cytotoxicity of the autophagy inhibitor chloroquine (CQ) on parental and HQ-selected K562 (K562/HQ) cells. CQ triggered apoptosis in these cells independently of inhibiting autophagic flux; however, in K562/HQ cells, CQ-induced cytotoxicity was higher than in K562 cells. Mechanistically, CQ-induced NOXA upregulation led to MCL1 downregulation and mitochondrial depolarization in K562/HQ cells. MCL1 overexpression or NOXA silencing attenuated CQ-mediated cytotoxicity in K562/HQ cells. CQ triggered ERK inactivation to increase Sp1, NFκB, and p300 expression, and co-assembly of Sp1, NFκB, and p300 in the miR-29a promoter region coordinately upregulated miR-29a transcription. CQ-induced miR-29a expression destabilized tristetraprolin (TTP) mRNA, which in turn reduced TTP-mediated NOXA mRNA decay, thereby increasing NOXA protein expression. A similar mechanism explained the CQ-induced downregulation of MCL1 in K562 cells. K562/HQ cells relied more on glycolysis for ATP production than K562 cells, whereas inhibition of glycolysis by CQ was greater in K562/HQ cells than in K562 cells. Likewise, CQ-induced MCL1 suppression and glycolysis inhibition resulted in higher cytotoxicity in CML KU812/HQ cells than in KU812 cells. Taken together, our data confirm that CQ inhibits MCL1 expression through the ERK/miR-29a/TTP/NOXA pathway, and that inhibition of glycolysis is positively correlated to higher cytotoxicity of CQ on HQ-selected CML cells.
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Affiliation(s)
- Jing-Ting Chiou
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Yuan-Chin Lee
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Long-Sen Chang
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan; Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
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12
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Strachowska M, Gronkowska K, Sobczak M, Grodzicka M, Michlewska S, Kołacz K, Sarkar T, Korszun J, Ionov M, Robaszkiewicz A. I-CBP112 declines overexpression of ATP-binding cassette transporters and sensitized drug-resistant MDA-MB-231 and A549 cell lines to chemotherapy drugs. Biomed Pharmacother 2023; 168:115798. [PMID: 37913733 DOI: 10.1016/j.biopha.2023.115798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/15/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023] Open
Abstract
Despite extensive efforts and ongoing progress in personalized anticancer approaches, chemotherapy remains the first line or the only treatment for some tumors that may develop resistance to chemotherapeutics in time due to inter alia overexpression of ATP-binding cassette transporters. Using clinically-relevant resistant models of triple negative breast cancer (MDA-MB-231; TNBC) as well as non-small cell lung cancer (A549; NSCLC), we tested the efficacy of I-CBP112 - CBP/EP300 bromodomain inhibitor to overcome drug resistance by declining ABC gene transcription. I-CBP112 significantly reduced ABCB1, ABCC1, ABCC2, ABCC3, ABCC5 and ABCG2 in all resistant lines, as well as ABCC10 in TNBC and ABCC4 in paclitaxel-resistant NSCLC, thereby increasing intracellular drug accumulation and cytotoxicity in 2D and 3D cultures. This was phenocopied only by the joint effect of ABC inhibitors such as tariquidar (ABCB1 - P-glycoprotein and ABCG2) and MK-571 (ABCC), whereas single inhibition of ABCB1/ABCG2 or ABCC proteins did not affect drug accumulation, thereby implying the need of simultaneous deficiency in activity of majority of drug pumps for enhanced drug retention. I-CBP112 failed to directly inhibit activity of ABCB1, ABCG2 and ABCC subfamily members at the same time. Importantly, I-CBP112 treated cancer cells polarized human macrophages into proinflammatory phenotypes. Moreover, I-CBP112 remained non-toxic to primary cell lines, nor did it enhance anticancer drug toxicity to blood-immune cells. In silico assay of ADMET properties confirmed the desired pharmacokinetic features of I-CBP112. The results suggest that the CBP/p300 inhibitor is a promising co-adjuvant to chemotherapy in drug-resistant cancer phenotypes, capable of decreasing ABC transporter expression.
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Affiliation(s)
- Magdalena Strachowska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska St.141/143, 90-236 Lodz, Poland; Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, University of Lodz, Banacha St. 12/16, 90-237 Lodz, Poland.
| | - Karolina Gronkowska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska St.141/143, 90-236 Lodz, Poland; Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, University of Lodz, Banacha St. 12/16, 90-237 Lodz, Poland
| | - Maciej Sobczak
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska St.141/143, 90-236 Lodz, Poland; Department of Internal Diseases, Diabetology and Clinical Pharmacology, Medical University of Lodz, Pomorska St. 251, 92-213 Lodz, Poland
| | - Marika Grodzicka
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska St.141/143, 90-236 Lodz, Poland; Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, University of Lodz, Banacha St. 12/16, 90-237 Lodz, Poland
| | - Sylwia Michlewska
- Laboratory of Microscopic Imaging and Specialized Biological Techniques, Faculty of Biology and Environmental Protection, University of Lodz, Banacha St. 12/16, 90-237 Lodz, Poland
| | - Kinga Kołacz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska St.141/143, 90-236 Lodz, Poland; Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, University of Lodz, Banacha St. 12/16, 90-237 Lodz, Poland
| | - Tuhin Sarkar
- Department of Microbiology, University of Kalyani, West Bengal 741245, India
| | - Joanna Korszun
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska St.141/143, 90-236 Lodz, Poland; Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, University of Lodz, Banacha St. 12/16, 90-237 Lodz, Poland; Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine - National Research Institute, Szaserow St. 128, 04-349 Warsaw, Poland
| | - Maksim Ionov
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska St.141/143, 90-236 Lodz, Poland; Faculty of Medicine, Collegium Medicum, Mazovian Academy in Plock, 2 Dabrowskiego Sq, 09-402, Plock, Poland
| | - Agnieszka Robaszkiewicz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska St.141/143, 90-236 Lodz, Poland.
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Ghare SS, Charpentier BT, Ghooray DT, Zhang J, Vadhanam MV, Reddy S, Joshi-Barve S, McClain CJ, Barve SS. Tributyrin Mitigates Ethanol-Induced Lysine Acetylation of Histone-H3 and p65-NFκB Downregulating CCL2 Expression and Consequent Liver Inflammation and Injury. Nutrients 2023; 15:4397. [PMID: 37892472 PMCID: PMC10610222 DOI: 10.3390/nu15204397] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 09/27/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
PURPOSE Chemokine-driven leukocyte infiltration and sustained inflammation contribute to alcohol-associated liver disease (ALD). Elevated hepatic CCL2 expression, seen in ALD, is associated with disease severity. However, mechanisms of CCL2 regulation are not completely elucidated. Post-translational modifications (PTMs) of proteins, particularly acetylation, modulate gene expression. This study examined the acetylation changes of promoter-associated histone-H3 and key transcription factor-NFκB in regulating hepatic CCL2 expression and subsequent inflammation and injury. Further, the effect of therapeutic modulation of the acetylation state by tributyrin (TB), a butyrate prodrug, was assessed. METHODS Hepatic CCL2 expression was assessed in mice fed control (PF) or an ethanol-containing Lieber-DeCarli (5% v/v, EF) diet for 7 weeks with or without oral administration of tributyrin (TB, 2 g/kg, 5 days/week). A chromatin immunoprecipitation (ChIP) assay evaluated promoter-associated modifications. Nuclear association between SIRT1, p300, and NFκB-p65 and acetylation changes of p65 were determined using immunoprecipitation and Western blot analyses. A Student's t-test and one-way ANOVA determined the significance. RESULTS Ethanol significantly increased promoter-associated histone-H3-lysine-9 acetylation (H3K9Ac), reflecting a transcriptionally permissive state with a resultant increase in hepatic CCL2 mRNA and protein expression. Moreover, increased lysine-310-acetylation of nuclear RelA/p65 decreased its association with SIRT1, a class III HDAC, but concomitantly increased with p300, a histone acetyltransferase. This further led to enhanced recruitment of NF-κB/p65 and RNA polymerase-II to the CCL2 promoter. Oral TB administration prevented ethanol-associated acetylation changes, thus downregulating CCL2 expression, hepatic neutrophil infiltration, and inflammation/ injury. CONCLUSION The modulation of a protein acetylation state via ethanol or TB mechanistically regulates hepatic CCL2 upregulation in ALD.
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Affiliation(s)
- Smita S. Ghare
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- UofL Alcohol Center, University of Louisville, Louisville, KY 40202, USA
- UofL Hepatobiology COBRE, University of Louisville, Louisville, KY 40202, USA
| | - Benjamin T. Charpentier
- UofL Alcohol Center, University of Louisville, Louisville, KY 40202, USA
- Department of Anatomical Science and Neurobiology, University of Louisville, Louisville, KY 40202, USA
| | - Dushan T. Ghooray
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- UofL Alcohol Center, University of Louisville, Louisville, KY 40202, USA
- UofL Hepatobiology COBRE, University of Louisville, Louisville, KY 40202, USA
| | - Jingwen Zhang
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- UofL Alcohol Center, University of Louisville, Louisville, KY 40202, USA
- UofL Hepatobiology COBRE, University of Louisville, Louisville, KY 40202, USA
| | - Manicka V. Vadhanam
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- UofL Alcohol Center, University of Louisville, Louisville, KY 40202, USA
- UofL Hepatobiology COBRE, University of Louisville, Louisville, KY 40202, USA
| | - Sreelatha Reddy
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- UofL Alcohol Center, University of Louisville, Louisville, KY 40202, USA
- UofL Hepatobiology COBRE, University of Louisville, Louisville, KY 40202, USA
| | - Swati Joshi-Barve
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- UofL Alcohol Center, University of Louisville, Louisville, KY 40202, USA
- UofL Hepatobiology COBRE, University of Louisville, Louisville, KY 40202, USA
| | - Craig J. McClain
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- UofL Alcohol Center, University of Louisville, Louisville, KY 40202, USA
- UofL Hepatobiology COBRE, University of Louisville, Louisville, KY 40202, USA
- Robley Rex VA Medical Center, University of Louisville, Louisville, KY 40202, USA
| | - Shirish S. Barve
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- UofL Alcohol Center, University of Louisville, Louisville, KY 40202, USA
- UofL Hepatobiology COBRE, University of Louisville, Louisville, KY 40202, USA
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14
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Hasegawa Y, Asada S. DNA-dependent protein kinase catalytic subunit binds to the transactivation domain 1 of NF-κB p65. Biochem Biophys Rep 2023; 35:101538. [PMID: 37674974 PMCID: PMC10477060 DOI: 10.1016/j.bbrep.2023.101538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
Nuclear factor-kappa B (NF-κB) is a transcriptional factor that binds to the ∼10-base-pair κB motif on target genes and acts as an inflammatory regulator. Since dysregulation of NF-κB is thought to be related to various diseases, it would be very important to elucidate its post-translational modifications and binding partners in detail and to deeply understand mechanisms of the NF-κB dysregulation. NF-κB p65 is known to interact with the basic transcription factor TFIID subunit hTAFII31/TAF9 through the ФXXФФ (Ф, hydrophobic amino acid; X, any amino acid) motif in a similar fashion to p53. MDM2 is known to inhibit p53 from binding to hTAFII31/TAF9 by masking p53's ФXXФФ motif. Here, as can be rationalized from this observation, we searched for novel nuclear proteins that interact with the transactivation domain 1 (TA1) of NF-κB p65 containing a ФXXФФ motif. We prepared a GST-tagged polypeptide, GST-p65532-550, from Phe532-Ser550 of the TA1 domain and found various U937 cell nuclear proteins that bound to GST-p65532-550. The largest bound protein the size of ∼400 kDa was subjected to mass spectrometric analysis and found to be DNA-dependent protein kinase catalytic subunit (DNA-PKcs). An immunoprecipitation experiment with an antibody against p65 and nuclear extracts from TNF-α-treated A549 cells suggested that NF-κB p65 indeed binds to DNA-PKcs in human cells. Furthermore, binding assays with a series of His-tagged DNA-PKcs fragments suggested that DNA-PKcs can bind to NF-κB p65 through the interaction of the TA1 domain with the region 541-750 in the N-HEAT domain or the region 2485-2576 in the M-HEAT domain.
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Affiliation(s)
- Yuta Hasegawa
- Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akiha-ku, Niigata, Niigata, 956-8603, Japan
| | - Shinichi Asada
- Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Applied Life Sciences, Higashijima 265-1, Akiha-ku, Niigata, Niigata, 956-8603, Japan
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15
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Brown AD, Cranstone C, Dupré DJ, Langelaan DN. β-Catenin interacts with the TAZ1 and TAZ2 domains of CBP/p300 to activate gene transcription. Int J Biol Macromol 2023; 238:124155. [PMID: 36963539 DOI: 10.1016/j.ijbiomac.2023.124155] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 03/26/2023]
Abstract
The transcriptional co-regulator β-catenin is a critical member of the canonical Wnt signaling pathway, which plays an important role in regulating cell fate. Deregulation of the Wnt/β-catenin pathway is characteristic in the development of major types of cancer, where accumulation of β-catenin promotes cancer cell proliferation and renewal. β-catenin gene expression is facilitated through recruitment of co-activators such as histone acetyltransferases CBP/p300; however, the mechanism of their interaction is not fully understood. Here we investigate the interaction between the C-terminal transactivation domain of β-catenin and CBP/p300. Using a combination of pulldown assays, isothermal titration calorimetry, and nuclear resonance spectroscopy we determine the disordered C-terminal region of β-catenin binds promiscuously to the TAZ1 and TAZ2 domains of CBP/p300. We then map the interaction site of the C-terminal β-catenin transactivation domain onto TAZ1 and TAZ2 using chemical-shift perturbation studies. Luciferase-based gene reporter assays indicate Asp750-Leu781 is critical to β-catenin gene activation, and mutagenesis revealed that acidic and hydrophobic residues within this region are necessary to maintain TAZ1 binding. These results outline a mechanism of Wnt/β-catenin gene regulation that underlies cell development and provides a framework to develop methods to block β-catenin dependent signaling.
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Affiliation(s)
- Alexandra D Brown
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Connor Cranstone
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Denis J Dupré
- Department of Pharmacology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - David N Langelaan
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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16
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Lou LQ, Zhou WQ, Song X, Chen Z. Elevation of hsa-miR-7-5p level mediated by CtBP1-p300-AP1 complex targets ATXN1 to trigger NF-κB-dependent inflammation response. J Mol Med (Berl) 2023; 101:223-235. [PMID: 36629882 DOI: 10.1007/s00109-022-02274-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 10/18/2022] [Accepted: 11/15/2022] [Indexed: 01/12/2023]
Abstract
Nuclear factor-κB (NF-κB)-mediated inflammation is a major cause of acute respiratory distress syndrome (ARDS). However, the regulatory mechanisms by which NF-κB transactivates proinflammatory cytokines remain unclear in the pathogenesis of ARDS. Herein, we report that the activating protein 1 (AP1) transcription factor recruits a histone acetyltransferase p300 and a transcriptional regulator C-terminal binding protein 1 (CtBP1) to assemble the CtBP1-p300-AP1 complex, which transactivates the expression of hsa-miR-7-5p in ARDS biopsies. Overexpressed hsa-miR-7-5p binds to the three prime untranslated regions (3'-UTRs) of ataxin 1 (ATXN1), suppressing its expression. Decreased ATXN1 expression relieves its repression of NF-κB, causing the induction of proinflammatory cytokine genes and triggering an inflammatory response. Depletion of CtBP1 or treatments with two CtBP1 inhibitors (NSC95397 and 4-methylthio-2-oxobutanoate (MTOB)) in human macrophages impairs the assembly of the CtBP2-p300-AP1 complex, resulting in decreased hsa-miR-7-5p levels, upregulation of ATXN1, and attenuation of proinflammatory cytokines. A similar regulatory mechanism was observed in lipopolysaccharide-treated mice. Our results reveal that increased hsa-miR-7-5p level mediated by the CtBP1-p300-AP1 complex targets ATXN1 to trigger an NF-κB-dependent inflammatory response. Interfering with this signaling pathway to block the inflammatory response may be a strategy for treating ARDS. KEY MESSAGES : The transcription factor AP1 recruits p300 and CtBP1 to form a transcriptional complex, which transactivates the expression of hsa-miR-7-5p in ARDS biopsies. Overexpressed hsa-miR-7-5p binds to the 3'-UTR of ATXN1, suppressing its expression. The decreased ATXN1 impaired its suppression of NF-κB, causing the induction of proinflammatory cytokine genes and triggering inflammation response. Disruption of the assembly of CtBP2-p300-AP1 complex upregulates ATXN1 and attenuates inflammation.
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Affiliation(s)
- Li-Qiong Lou
- Central Supply Service Department, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, 330006, Jiangxi, China
| | - Wen-Qiang Zhou
- Medical Department of Graduate School, Nanchang University, Nanchang, 330006, Jiangxi, China
- Department of Emergency, Donghu District, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, 92 Aiguo Rd, Nanchang, 330006, Jiangxi, China
| | - Xin Song
- Medical Department of Graduate School, Nanchang University, Nanchang, 330006, Jiangxi, China
- Department of Emergency, Donghu District, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, 92 Aiguo Rd, Nanchang, 330006, Jiangxi, China
| | - Zhi Chen
- Department of Emergency, Donghu District, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, 92 Aiguo Rd, Nanchang, 330006, Jiangxi, China.
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17
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Targeting IKKβ Activity to Limit Sterile Inflammation in Acetaminophen-Induced Hepatotoxicity in Mice. Pharmaceutics 2023; 15:pharmaceutics15020710. [PMID: 36840032 PMCID: PMC9959252 DOI: 10.3390/pharmaceutics15020710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/02/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
The kinase activity of inhibitory κB kinase β (IKKβ) acts as a signal transducer in the activating pathway of nuclear factor-κB (NF-κB), a master regulator of inflammation and cell death in the development of numerous hepatocellular injuries. However, the importance of IKKβ activity on acetaminophen (APAP)-induced hepatotoxicity remains to be defined. Here, a derivative of caffeic acid benzylamide (CABA) inhibited the kinase activity of IKKβ, as did IMD-0354 and sulfasalazine which show therapeutic efficacy against inflammatory diseases through a common mechanism: inhibiting IKKβ activity. To understand the importance of IKKβ activity in sterile inflammation during hepatotoxicity, C57BL/6 mice were treated with CABA, IMD-0354, or sulfasalazine after APAP overdose. These small-molecule inhibitors of IKKβ activity protected the APAP-challenged mice from necrotic injury around the centrilobular zone in the liver, and rescued the mice from hepatic damage-associated lethality. From a molecular perspective, IKKβ inhibitors directly interrupted sterile inflammation in the Kupffer cells of APAP-challenged mice, such as damage-associated molecular pattern (DAMP)-induced activation of NF-κB activity via IKKβ, and NF-κB-regulated expression of cytokines and chemokines. However, CABA did not affect the upstream pathogenic events, including oxidative stress with glutathione depletion in hepatocytes after APAP overdose. N-acetyl cysteine (NAC), the only FDA-approved antidote against APAP overdose, replenishes cellular levels of glutathione, but its limited efficacy is concerning in late-presenting patients who have already undergone oxidative stress in the liver. Taken together, we propose a novel hypothesis that chemical inhibition of IKKβ activity in sterile inflammation could mitigate APAP-induced hepatotoxicity in mice, and have the potential to complement NAC treatment in APAP overdoses.
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18
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Mbonye U, Kizito F, Karn J. New insights into transcription elongation control of HIV-1 latency and rebound. Trends Immunol 2023; 44:60-71. [PMID: 36503686 DOI: 10.1016/j.it.2022.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 12/13/2022]
Abstract
Antiretroviral therapy reduces circulating HIV-1 to undetectable amounts but does not eliminate the virus due to the persistence of a stable reservoir of latently infected cells. The reservoir is maintained both by proliferation of latently infected cells and by reseeding from reactivated cells. A major challenge for the field is to find safe and effective methods to eliminate this source of rebounding HIV-1. Studies on the molecular mechanisms leading to HIV-1 latency and reactivation are being transformed using latency models in primary and patient CD4+ T cells. These studies have revealed the central role played by the biogenesis of the transcription elongation factor P-TEFb (Positive Transcription Elongation Factor b) and its recruitment to proviral HIV-1, for the maintenance of viral latency and the control of viral reactivation.
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Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Fredrick Kizito
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA.
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19
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Nuclear receptor coactivator 3 transactivates proinflammatory cytokines in collagen-induced arthritis. Cytokine 2023; 161:156074. [PMID: 36323191 DOI: 10.1016/j.cyto.2022.156074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/24/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
Rheumatoid arthritis (RA) is an autoimmune disorder in which the immune system mistakenly attacks joints. The molecular mechanisms underlying RA pathology are still under investigation. In this study, we discovered overexpression of nuclear receptor coactivator 3 (NCOA3) in the joint tissues of type II collagen-induced arthritis (CIA) mice, an important autoimmune model of human RA. Administration of two NCOA3 inhibitors, gossypol (GSP) and SI-2 hydrochloride (SHC), significantly alleviated inflammation and improved the outcomes of CIA mice. In vivo and in vitro experiments revealed that NCOA3 assembled a transcriptional complex with a histone acetyltransferase p300 and two subunits of nuclear factor kappa B (NF-κB). This complex specifically controlled the expression of proinflammatory cytokine genes by binding to their promoters. Knockdown of NCOA3 or in vitro treatments with GSP and SHC impaired the assembly of NCOA3-p300-NF-κB complex and decreased the expression of proinflammatory cytokine genes. Taken together, our results demonstrated that NCOA3 acts as a mediator of proinflammatory cytokine genes in CIA mice and that inhibition of the NCOA3-p300-NF-κB complex may represent a new avenue for improving RA outcomes.
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20
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Ibrahim Z, Wang T, Destaing O, Salvi N, Hoghoughi N, Chabert C, Rusu A, Gao J, Feletto L, Reynoird N, Schalch T, Zhao Y, Blackledge M, Khochbin S, Panne D. Structural insights into p300 regulation and acetylation-dependent genome organisation. Nat Commun 2022; 13:7759. [PMID: 36522330 PMCID: PMC9755262 DOI: 10.1038/s41467-022-35375-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Histone modifications are deposited by chromatin modifying enzymes and read out by proteins that recognize the modified state. BRD4-NUT is an oncogenic fusion protein of the acetyl lysine reader BRD4 that binds to the acetylase p300 and enables formation of long-range intra- and interchromosomal interactions. We here examine how acetylation reading and writing enable formation of such interactions. We show that NUT contains an acidic transcriptional activation domain that binds to the TAZ2 domain of p300. We use NMR to investigate the structure of the complex and found that the TAZ2 domain has an autoinhibitory role for p300. NUT-TAZ2 interaction or mutations found in cancer that interfere with autoinhibition by TAZ2 allosterically activate p300. p300 activation results in a self-organizing, acetylation-dependent feed-forward reaction that enables long-range interactions by bromodomain multivalent acetyl-lysine binding. We discuss the implications for chromatin organisation, gene regulation and dysregulation in disease.
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Affiliation(s)
- Ziad Ibrahim
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Tao Wang
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Olivier Destaing
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Nicola Salvi
- Institut de Biologie Structurale, CNRS, CEA, UGA, Grenoble, France
| | - Naghmeh Hoghoughi
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Clovis Chabert
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Alexandra Rusu
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Jinjun Gao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL, 60637, USA
| | - Leonardo Feletto
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Nicolas Reynoird
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Thomas Schalch
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL, 60637, USA
| | | | - Saadi Khochbin
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Daniel Panne
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK.
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21
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Baughman HER, Narang D, Chen W, Villagrán Suárez AC, Lee J, Bachochin MJ, Gunther TR, Wolynes PG, Komives EA. An intrinsically disordered transcription activation domain increases the DNA binding affinity and reduces the specificity of NFκB p50/RelA. J Biol Chem 2022; 298:102349. [PMID: 35934050 PMCID: PMC9440430 DOI: 10.1016/j.jbc.2022.102349] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 12/03/2022] Open
Abstract
Many transcription factors contain intrinsically disordered transcription activation domains (TADs), which mediate interactions with coactivators to activate transcription. Historically, DNA-binding domains and TADs have been considered as modular units, but recent studies have shown that TADs can influence DNA binding. Whether these results can be generalized to more TADs is not clear. Here, we biophysically characterized the NFκB p50/RelA heterodimer including the RelA TAD and investigated the TAD's influence on NFκB-DNA interactions. In solution, we show the RelA TAD is disordered but compact, with helical tendency in two regions that interact with coactivators. We determined that the presence of the TAD increased the stoichiometry of NFκB-DNA complexes containing promoter DNA sequences with tandem κB recognition motifs by promoting the binding of NFκB dimers in excess of the number of κB sites. In addition, we measured the binding affinity of p50/RelA for DNA containing tandem κB sites and single κB sites. While the presence of the TAD enhanced the binding affinity of p50/RelA for all κB sequences tested, it also increased the affinity for nonspecific DNA sequences by over 10-fold, leading to an overall decrease in specificity for κB DNA sequences. In contrast, previous studies have generally reported that TADs decrease DNA-binding affinity and increase sequence specificity. Our results reveal a novel function of the RelA TAD in promoting binding to nonconsensus DNA, which sheds light on previous observations of extensive nonconsensus DNA binding by NFκB in vivo in response to strong inflammatory signals.
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Affiliation(s)
- Hannah E R Baughman
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Dominic Narang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Wei Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Amalia C Villagrán Suárez
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Joan Lee
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Maxwell J Bachochin
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Tristan R Gunther
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Peter G Wolynes
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas, USA
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA.
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22
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Ayanwale A, Trapp S, Guabiraba R, Caballero I, Roesch F. New Insights in the Interplay Between African Swine Fever Virus and Innate Immunity and Its Impact on Viral Pathogenicity. Front Microbiol 2022; 13:958307. [PMID: 35875580 PMCID: PMC9298521 DOI: 10.3389/fmicb.2022.958307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/14/2022] [Indexed: 12/18/2022] Open
Abstract
The continuous spread of African swine fever virus (ASFV) in Europe and Asia represents a major threat to livestock health, with billions of dollars of income losses and major perturbations of the global pig industry. One striking feature of African swine fever (ASF) is the existence of different forms of the disease, ranging from acute with mortality rates approaching 100% to chronic, with mild clinical manifestations. These differences in pathogenicity have been linked to genomic alterations present in attenuated ASFV strains (and absent in virulent ones) and differences in the immune response of infected animals. In this mini-review, we summarized current knowledge on the connection between ASFV pathogenicity and the innate immune response induced in infected hosts, with a particular focus on the pathways involved in ASFV detection. Indeed, recent studies have highlighted the key role of the DNA sensor cGAS in ASFV sensing. We discussed what other pathways may be involved in ASFV sensing and inflammasome activation and summarized recent findings on the viral ASFV genes involved in the modulation of the interferon (IFN) and nuclear factor kappa B (NF-κB) pathways.
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Affiliation(s)
| | - Sascha Trapp
- UMR 1282 ISP, INRAE Centre Val de Loire, Nouzilly, France
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23
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Tan SYX, Zhang J, Tee WW. Epigenetic Regulation of Inflammatory Signaling and Inflammation-Induced Cancer. Front Cell Dev Biol 2022; 10:931493. [PMID: 35757000 PMCID: PMC9213816 DOI: 10.3389/fcell.2022.931493] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/23/2022] [Indexed: 01/10/2023] Open
Abstract
Epigenetics comprise a diverse array of reversible and dynamic modifications to the cell’s genome without implicating any DNA sequence alterations. Both the external environment surrounding the organism, as well as the internal microenvironment of cells and tissues, contribute to these epigenetic processes that play critical roles in cell fate specification and organismal development. On the other hand, dysregulation of epigenetic activities can initiate and sustain carcinogenesis, which is often augmented by inflammation. Chronic inflammation, one of the major hallmarks of cancer, stems from proinflammatory cytokines that are secreted by tumor and tumor-associated cells in the tumor microenvironment. At the same time, inflammatory signaling can establish positive and negative feedback circuits with chromatin to modulate changes in the global epigenetic landscape. In this review, we provide an in-depth discussion of the interconnected crosstalk between epigenetics and inflammation, specifically how epigenetic mechanisms at different hierarchical levels of the genome control inflammatory gene transcription, which in turn enact changes within the cell’s epigenomic profile, especially in the context of inflammation-induced cancer.
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Affiliation(s)
- Shawn Ying Xuan Tan
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Jieqiong Zhang
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wee-Wei Tee
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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24
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Amarante ADM, da Silva ICDA, Carneiro VC, Vicentino ARR, Pinto MDA, Higa LM, Moharana KC, Talyuli OAC, Venancio TM, de Oliveira PL, Fantappié MR. Zika virus infection drives epigenetic modulation of immunity by the histone acetyltransferase CBP of Aedes aegypti. PLoS Negl Trop Dis 2022; 16:e0010559. [PMID: 35759510 PMCID: PMC9269902 DOI: 10.1371/journal.pntd.0010559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 07/08/2022] [Accepted: 06/03/2022] [Indexed: 11/18/2022] Open
Abstract
Epigenetic mechanisms are responsible for a wide range of biological phenomena in insects, controlling embryonic development, growth, aging and nutrition. Despite this, the role of epigenetics in shaping insect-pathogen interactions has received little attention. Gene expression in eukaryotes is regulated by histone acetylation/deacetylation, an epigenetic process mediated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). In this study, we explored the role of the Aedes aegypti histone acetyltransferase CBP (AaCBP) after infection with Zika virus (ZIKV), focusing on the two main immune tissues, the midgut and fat body. We showed that the expression and activity of AaCBP could be positively modulated by blood meal and ZIKV infection. Nevertheless, Zika-infected mosquitoes that were silenced for AaCBP revealed a significant reduction in the acetylation of H3K27 (CBP target marker), followed by downmodulation of the expression of immune genes, higher titers of ZIKV and lower survival rates. Importantly, in Zika-infected mosquitoes that were treated with sodium butyrate, a histone deacetylase inhibitor, their capacity to fight virus infection was rescued. Our data point to a direct correlation among histone hyperacetylation by AaCBP, upregulation of antimicrobial peptide genes and increased survival of Zika-infected-A. aegypti.
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Affiliation(s)
- Anderson de Mendonça Amarante
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Isabel Caetano de Abreu da Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Vitor Coutinho Carneiro
- Division of Epigenetics, German Cancer Research Center, Im Neuenheimer Feld, Heidelberg, Germany
| | - Amanda Roberta Revoredo Vicentino
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Marcia de Amorim Pinto
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Luiza Mendonça Higa
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Kanhu Charan Moharana
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brasil
| | - Octavio A. C. Talyuli
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Thiago Motta Venancio
- Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brasil
| | - Pedro Lagerblad de Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Marcelo Rosado Fantappié
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Instituto Nacional de Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- * E-mail:
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25
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Feoktistov AV, Georgieva SG, Soshnikova NV. Role of the SWI/SNF Chromatin Remodeling Complex in Regulation of Inflammation Gene Expression. Mol Biol 2022. [DOI: 10.1134/s0026893322020054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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26
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Zhang R, Geng GJ, Guo JG, Mi YJ, Zhu XL, Li N, Liu HM, Lin JF, Wang JW, Zhao G, Ye GZ, Li BA, Luo QC, Jiang J. An NF-κB/OVOL2 circuit regulates glucose import and cell survival in non-small cell lung cancer. Cell Commun Signal 2022; 20:40. [PMID: 35346238 PMCID: PMC8962559 DOI: 10.1186/s12964-022-00845-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/11/2022] [Indexed: 11/24/2022] Open
Abstract
Background Tumor cells tend to utilize glycolysis rather than aerobic respiration even under aerobic conditions. OVOL2, an inhibitory C2H2 zinc finger transcription factor, is a potential tumor suppressor in cancers. However, the association between OVOL2 and tumor energy metabolism is unknown. Methods Western blotting was used to determine the expression of OVOL2 in different non-small cell lung cancer (NSCLC) cell lines and mouse models. The metabolic parameters in NSCLC cells following overexpression or knockdown OVOL2 were examined. To define the mechanism by which OVOL2 regulates aerobic glycolysis, interacting protein of OVOl2 and downstream molecular events were identified by luciferase assay and co-immunoprecipitation. We documented the regulatory mechanism in mouse xenograft models. Finally, clinical relevance of OVOL2, NF-κB signaling and GLUT1 was measured by immunostaining.
Results OVOL2 is downregulated in NSCLC and overexpression of OVOL2 inhibits the survival of cancer cells. Moreover, OVOL2 directly binds to P65 and inhibits the recruitment of P300 but facilitates the binding of HDAC1 to P65, which in turn negatively regulates NF-κB signaling to suppress GLUT1 translocation and glucose import. In contrast, OVOL2 expression is negatively regulated by NF-κB signaling in NSCLC cells via the ubiquitin–proteasome pathway. Re-expression of OVOL2 significantly compromise NF-κB signaling-induced GLUT1 translocation, aerobic glycolysis in NSCLC cells and mouse models. Immunostaining revealed inverse correlations between the OVOL2 and phosphorylated P65 levels and between the OVOL2 and membrane GLUT1 levels, and a strong correlation between the phosphorylated P65 and membrane GLUT1 levels.
Conclusions These results suggest a regulatory circuit linking NF-κB and OVOL2, which highlights the role of NF-κB signaling and OVOL2 in the modulation of glucose metabolism in NSCLC. Video Abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-022-00845-z.
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27
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Tabassum S, Ghosh MK. DEAD-box RNA helicases with special reference to p68: Unwinding their biology, versatility, and therapeutic opportunity in cancer. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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28
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Salutari I, Caflisch A. Dynamics of the Histone Acetyltransferase Lysine-Rich Loop in the Catalytic Core of the CREB-Binding Protein. J Chem Inf Model 2022; 62:1014-1024. [PMID: 35119862 DOI: 10.1021/acs.jcim.1c01423] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The tight control of transcriptional coactivators is a fundamental aspect of gene expression in cells. The regulation of the CREB-binding protein (CBP) and p300 coactivators, two paralog multidomain proteins, involves an autoinhibitory loop (AIL) of the histone acetyltransferase (HAT) domain. There is experimental evidence for the AIL engaging with the HAT binding site, thus interrupting the acetylation of histone tails or other proteins. Both CBP and p300 contain a domain of about 110 residues (called the bromodomain) that recognizes histone tails with one or more acetylated lysine side chains. Here, we investigate by molecular dynamics simulations whether the AIL of CBP (residues 1556-1618) acetylated at the side chain of Lys1595 can bind to the bromodomain. The structural instability and fast unbinding kinetics of the AIL from the bromodomain pocket suggest that the AIL is not a ligand of the bromodomain on the same protein chain. This is further supported by the absence of strong and persistent contacts at the binding interface. Furthermore, the simulations of unbinding show an initial fast detachment of the acetylated lysine and a slower phase necessary for complete AIL dissociation. We provide further evidence for the instability of the AIL intramolecular binding by comparison with a natural ligand, the histone peptide H3K56ac, which shows higher stability in the pocket.
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Affiliation(s)
- Ilaria Salutari
- Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
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29
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Albarnaz JD, Ren H, Torres AA, Shmeleva EV, Melo CA, Bannister AJ, Brember MP, Chung BYW, Smith GL. Molecular mimicry of NF-κB by vaccinia virus protein enables selective inhibition of antiviral responses. Nat Microbiol 2022; 7:154-168. [PMID: 34949827 PMCID: PMC7614822 DOI: 10.1038/s41564-021-01004-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 10/21/2021] [Indexed: 12/16/2022]
Abstract
Infection of mammalian cells with viruses activates NF-κB to induce the expression of cytokines and chemokines and initiate an antiviral response. Here, we show that a vaccinia virus protein mimics the transactivation domain of the p65 subunit of NF-κB to inhibit selectively the expression of NF-κB-regulated genes. Using co-immunoprecipitation assays, we found that the vaccinia virus protein F14 associates with NF-κB co-activator CREB-binding protein (CBP) and disrupts the interaction between p65 and CBP. This abrogates CBP-mediated acetylation of p65, after which it reduces promoter recruitment of the transcriptional regulator BRD4 and diminishes stimulation of NF-κB-regulated genes CXCL10 and CCL2. Recruitment of BRD4 to the promoters of NFKBIA and CXCL8 remains unaffected by either F14 or JQ1 (a competitive inhibitor of BRD4 bromodomains), indicating that BRD4 recruitment is acetylation-independent. Unlike other viral proteins that are general antagonists of NF-κB, F14 is a selective inhibitor of NF-κB-dependent gene expression. An in vivo model of infection demonstrated that F14 promotes virulence. Molecular mimicry of NF-κB may be conserved because other orthopoxviruses, including variola, monkeypox and cowpox viruses, encode orthologues of F14.
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Affiliation(s)
- Jonas D Albarnaz
- Department of Pathology, University of Cambridge, Cambridge, UK.
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
| | - Hongwei Ren
- Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, London, UK
| | - Alice A Torres
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Evgeniya V Shmeleva
- Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
| | - Carlos A Melo
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | | | | | - Betty Y-W Chung
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Geoffrey L Smith
- Department of Pathology, University of Cambridge, Cambridge, UK.
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30
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Hóbor F, Hegedüs Z, Ibarra AA, Petrovicz VL, Bartlett GJ, Sessions RB, Wilson AJ, Edwards TA. Understanding p300-transcription factor interactions using sequence variation and hybridization. RSC Chem Biol 2022; 3:592-603. [PMID: 35656479 PMCID: PMC9092470 DOI: 10.1039/d2cb00026a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/10/2022] [Indexed: 11/21/2022] Open
Abstract
The hypoxic response is central to cell function and plays a significant role in the growth and survival of solid tumours. HIF-1 regulates the hypoxic response by activating over 100...
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Affiliation(s)
- Fruzsina Hóbor
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Zsófia Hegedüs
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H-6720 Szeged Hungary
| | - Amaurys Avila Ibarra
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Vencel L Petrovicz
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H-6720 Szeged Hungary
| | - Gail J Bartlett
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
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31
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Stati G, Passaretta F, Gindraux F, Centurione L, Di Pietro R. The Role of the CREB Protein Family Members and the Related Transcription Factors in Radioresistance Mechanisms. Life (Basel) 2021; 11:life11121437. [PMID: 34947968 PMCID: PMC8706059 DOI: 10.3390/life11121437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/02/2021] [Accepted: 12/16/2021] [Indexed: 02/05/2023] Open
Abstract
In the framework of space flight, the risk of radiation carcinogenesis is considered a "red" risk due to the high likelihood of occurrence as well as the high potential impact on the quality of life in terms of disease-free survival after space missions. The cyclic AMP response element-binding protein (CREB) is overexpressed both in haematological malignancies and solid tumours and its expression and function are modulated following irradiation. The CREB protein is a transcription factor and member of the CREB/activating transcription factor (ATF) family. As such, it has an essential role in a wide range of cell processes, including cell survival, proliferation, and differentiation. Among the CREB-related nuclear transcription factors, NF-κB and p53 have a relevant role in cell response to ionising radiation. Their expression and function can decide the fate of the cell by choosing between death or survival. The aim of this review was to define the role of the CREB/ATF family members and the related transcription factors in the response to ionising radiation of human haematological malignancies and solid tumours.
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Affiliation(s)
- Gianmarco Stati
- Department of Medicine and Ageing Sciences, G. d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.P.); (L.C.); (R.D.P.)
- Correspondence: ; Tel.: +39-08713554567
| | - Francesca Passaretta
- Department of Medicine and Ageing Sciences, G. d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.P.); (L.C.); (R.D.P.)
| | - Florelle Gindraux
- Laboratoire de Nanomédecine, Imagerie, Thérapeutique EA 4662, Université Bourgogne Franche-Comté, 25030 Besançon, France;
- Service de Chirurgie Orthopédique, Traumatologique et Plastique, CHU, 25030 Besançon, France
| | - Lucia Centurione
- Department of Medicine and Ageing Sciences, G. d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.P.); (L.C.); (R.D.P.)
| | - Roberta Di Pietro
- Department of Medicine and Ageing Sciences, G. d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.P.); (L.C.); (R.D.P.)
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32
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Lin YT, Lin J, Liu YE, Hsu KW, Hsieh CC, Chen DR, Wu HT. Nafamostat mesylate overcomes endocrine resistance of breast cancer through epigenetic regulation of CDK4 and CDK6 expression. Transl Oncol 2021; 15:101302. [PMID: 34890965 PMCID: PMC8665409 DOI: 10.1016/j.tranon.2021.101302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 11/30/2022] Open
Abstract
Nafamostat mesylate (NM) causes apoptosis and suppresses metastasis of endocrine-resistant ER-positive breast cancer (ERPBC). Epigenetic downregulation of CDK4/CDK6 by NM in endocrine-resistant ERPBC via disruption of binding of H3K27Ac on promoter region. Combination of nafamostat mesylate and CDK4/6 inhibitor synergistically overcomes endocrine resistance of breast cancer. Nafamostat mesylate would be a well-efficient drug for endocrine-resistant ERPBC.
Breast cancer is common worldwide, and the estrogen receptor-positive subtype accounts for approximately 70% of breast cancer in women. Tamoxifen and fulvestrant are drugs currently used for endocrinal therapy. Breast cancer exhibiting endocrine resistance can undergo metastasis and lead to the death of breast cancer patients. Drug repurposing is an active area of research in clinical medicine. We found that nafamostat mesylate, clinically used for patients with pancreatitis and disseminated intravascular coagulation, acts as an anti-cancer drug for endocrine-resistant estrogen receptor-positive breast cancer (ERPBC). Epigenetic repression of CDK4 and CDK6 by nafamostat mesylate induced apoptosis and suppressed the metastasis of ERPBC through the deacetylation of Histone 3 Lysine 27. A combination of nafamostat mesylate and CDK4/6 inhibitor synergistically overcame endocrine resistance in ERPBC. Nafamostat mesylate might be an essential adjuvant or alternative drug for the treatment of endocrine-resistant ERPBC due to the low cost-efficiency of the CDK4/6 inhibitor.
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Affiliation(s)
- Yueh-Te Lin
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Gueishan Dist., Taoyuan 333, Taiwan
| | - Joseph Lin
- Comprehensive Breast Cancer Center, Changhua Christian Hospital, Changhua 500, Taiwan; Department of Animal Science and Biotechnology, Tunghai University, Taichung 407, Taiwan
| | - Yi-En Liu
- Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan
| | - Kai-Wen Hsu
- Research Center for Cancer Biology, Institute of New Drug Development, China Medical University, Taichung 404, Taiwan
| | - Chang-Chi Hsieh
- Department of Animal Science and Biotechnology, Tunghai University, Taichung 407, Taiwan
| | - Dar-Ren Chen
- Comprehensive Breast Cancer Center, Changhua Christian Hospital, Changhua 500, Taiwan; Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan; School of Medicine, Chung Shan Medical University, Taichung 402, Taiwan.
| | - Han-Tsang Wu
- Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan.
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Conserved Structure and Evolution of DPF Domain of PHF10-The Specific Subunit of PBAF Chromatin Remodeling Complex. Int J Mol Sci 2021; 22:ijms222011134. [PMID: 34681795 PMCID: PMC8538644 DOI: 10.3390/ijms222011134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 11/17/2022] Open
Abstract
Transcription activation factors and multisubunit coactivator complexes get recruited at specific chromatin sites via protein domains that recognize histone modifications. Single PHDs (plant homeodomains) interact with differentially modified H3 histone tails. Double PHD finger (DPF) domains possess a unique structure different from PHD and are found in six proteins: histone acetyltransferases MOZ and MORF; chromatin remodeling complex BAF (DPF1–3); and chromatin remodeling complex PBAF (PHF10). Among them, PHF10 stands out due to the DPF sequence, structure, and functions. PHF10 is ubiquitously expressed in developing and adult organisms as four isoforms differing in structure (the presence or absence of DPF) and transcription regulation functions. Despite the importance of the DPF domain of PHF10 for transcription activation, its structure remains undetermined. We performed homology modeling of the human PHF10 DPF domain and determined common and distinct features in structure and histone modifications recognition capabilities, which can affect PBAF complex chromatin recruitment. We also traced the evolution of DPF1–3 and PHF10 genes from unicellular to vertebrate organisms. The data reviewed suggest that the DPF domain of PHF10 plays an important role in SWI/SNF-dependent chromatin remodeling during transcription activation.
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Lin X, Tago K, Okazaki N, So T, Takahashi K, Mashino T, Tamura H, Funakoshi-Tago M. The indole-hydantoin derivative exhibits anti-inflammatory activity by preventing the transactivation of NF-κB through the inhibition of NF-κB p65 phosphorylation at Ser276. Int Immunopharmacol 2021; 100:108092. [PMID: 34474272 DOI: 10.1016/j.intimp.2021.108092] [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: 04/21/2021] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 01/17/2023]
Abstract
Indole- and hydantoin-based derivatives both exhibit anti-inflammatory activity, suggesting that the structures of indole and hydantoin are functional for this activity. In the present study, we synthesized two types of indole-hydantoin derivatives, IH-1 (5-(1H-indole-3-ylmethylene) imidazolidine-2,4-dione) and IH-2 (5-(1H-indole-3-ylmethyl) imidazolidine-2,4-dione) and examined their effects on LPS-induced inflammatory responses in murine macrophage-like RAW264.7 cells. LPS-induced inflammatory responses were not affected by indole, hydantoin, or IH-2. In contrast, IH-1 significantly inhibited the LPS-induced production of nitric oxide (NO) and secretion of CCL2 and CXCL1 by suppressing the mRNA expression of inducible NO synthase (iNOS), CCL2, and CXCL1. IH-1 markedly inhibited the LPS-induced activation of NF-κB without affecting the degradation of IκBα or nuclear translocation of NF-κB. IH-1 markedly attenuated the transcriptional activity of NF-κB by suppressing the LPS-induced phosphorylation of the NF-κB p65 subunit at Ser276. Furthermore, IH-1 prevented the LPS-induced interaction of NF-κB p65 subunit with a transcriptional coactivator, cAMP response element-binding protein (CBP). Collectively, these results revealed the potential of the novel indole-hydantoin derivative, IH-1 as an anti-inflammatory drug.
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Affiliation(s)
- Xin Lin
- Division of Hygienic Chemistry, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Kenji Tago
- Division of Structural Biochemistry, Department of Biochemistry, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi-ken 329-0498, Japan.
| | - Nozomi Okazaki
- Division of Bio-organic and Medicinal Chemistry, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Takanori So
- Division of Bio-organic and Medicinal Chemistry, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Kyoko Takahashi
- Division of Bio-organic and Medicinal Chemistry, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Tadahiko Mashino
- Division of Bio-organic and Medicinal Chemistry, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Hiroomi Tamura
- Division of Hygienic Chemistry, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Megumi Funakoshi-Tago
- Division of Hygienic Chemistry, Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan.
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35
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Tan D, Chen R, Mo Y, Gu S, Ma J, Xu W, Lu X, He H, Jiang F, Fan W, Wang Y, Chen X, Huang W. Quantitative control of noise in mammalian gene expression by dynamic histone regulation. eLife 2021; 10:65654. [PMID: 34379055 PMCID: PMC8357418 DOI: 10.7554/elife.65654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/23/2021] [Indexed: 12/11/2022] Open
Abstract
Fluctuation ('noise') in gene expression is critical for mammalian cellular processes. Numerous mechanisms contribute to its origins, yet the mechanisms behind large fluctuations that are induced by single transcriptional activators remain elusive. Here, we probed putative mechanisms by studying the dynamic regulation of transcriptional activator binding, histone regulator inhibitors, chromatin accessibility, and levels of mRNAs and proteins in single cells. Using a light-induced expression system, we showed that the transcriptional activator could form an interplay with dual functional co-activator/histone acetyltransferases CBP/p300. This interplay resulted in substantial heterogeneity in H3K27ac, chromatin accessibility, and transcription. Simultaneous attenuation of CBP/p300 and HDAC4/5 reduced heterogeneity in the expression of endogenous genes, suggesting that this mechanism is universal. We further found that the noise was reduced by pulse-wide modulation of transcriptional activator binding possibly as a result of alternating the epigenetic states. Our findings suggest a mechanism for the modulation of noise in synthetic and endogenous gene expression systems.
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Affiliation(s)
- Deng Tan
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Chemistry, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Rui Chen
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yuejian Mo
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Shu Gu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jiao Ma
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wei Xu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xibin Lu
- Core Research Facilities, Southern University of Science and Technology, Shenzhen, China
| | - Huiyu He
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Fan Jiang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Weimin Fan
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yili Wang
- Core Research Facilities, Southern University of Science and Technology, Shenzhen, China
| | - Xi Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wei Huang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
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36
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Wang N, Lefaudeux D, Mazumder A, Li JJ, Hoffmann A. Identifying the combinatorial control of signal-dependent transcription factors. PLoS Comput Biol 2021; 17:e1009095. [PMID: 34166361 PMCID: PMC8263068 DOI: 10.1371/journal.pcbi.1009095] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 07/07/2021] [Accepted: 05/18/2021] [Indexed: 12/13/2022] Open
Abstract
The effectiveness of immune responses depends on the precision of stimulus-responsive gene expression programs. Cells specify which genes to express by activating stimulus-specific combinations of stimulus-induced transcription factors (TFs). Their activities are decoded by a gene regulatory strategy (GRS) associated with each response gene. Here, we examined whether the GRSs of target genes may be inferred from stimulus-response (input-output) datasets, which remains an unresolved model-identifiability challenge. We developed a mechanistic modeling framework and computational workflow to determine the identifiability of all possible combinations of synergistic (AND) or non-synergistic (OR) GRSs involving three transcription factors. Considering different sets of perturbations for stimulus-response studies, we found that two thirds of GRSs are easily distinguishable but that substantially more quantitative data is required to distinguish the remaining third. To enhance the accuracy of the inference with timecourse experimental data, we developed an advanced error model that avoids error overestimates by distinguishing between value and temporal error. Incorporating this error model into a Bayesian framework, we show that GRS models can be identified for individual genes by considering multiple datasets. Our analysis rationalizes the allocation of experimental resources by identifying most informative TF stimulation conditions. Applying this computational workflow to experimental data of immune response genes in macrophages, we found that a much greater fraction of genes are combinatorially controlled than previously reported by considering compensation among transcription factors. Specifically, we revealed that a group of known NFκB target genes may also be regulated by IRF3, which is supported by chromatin immuno-precipitation analysis. Our study provides a computational workflow for designing and interpreting stimulus-response gene expression studies to identify underlying gene regulatory strategies and further a mechanistic understanding.
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Affiliation(s)
- Ning Wang
- Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, United States of America
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California, United States of America
| | - Diane Lefaudeux
- Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Anup Mazumder
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Jingyi Jessica Li
- Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, California, United States of America
- Department of Statistics, University of California, Los Angeles, California, United States of America
| | - Alexander Hoffmann
- Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, United States of America
- * E-mail:
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37
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Villarreal A, Vidos C, Monteverde Busso M, Cieri MB, Ramos AJ. Pathological Neuroinflammatory Conversion of Reactive Astrocytes Is Induced by Microglia and Involves Chromatin Remodeling. Front Pharmacol 2021; 12:689346. [PMID: 34234677 PMCID: PMC8255379 DOI: 10.3389/fphar.2021.689346] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/25/2021] [Indexed: 01/06/2023] Open
Abstract
Following brain injury or in neurodegenerative diseases, astrocytes become reactive and may suffer pathological remodeling, features of which are the loss of their homeostatic functions and a pro-inflammatory gain of function that facilitates neurodegeneration. Pharmacological intervention to modulate this astroglial response and neuroinflammation is an interesting new therapeutic research strategy, but it still requires a deeper understanding of the underlying cellular and molecular mechanisms of the phenomenon. Based on the known microglial–astroglial interaction, the prominent role of the nuclear factor kappa B (NF-κB) pathway in mediating astroglial pathological pro-inflammatory gain of function, and its ability to recruit chromatin-remodeling enzymes, we first explored the microglial role in the initiation of astroglial pro-inflammatory conversion and then monitored the progression of epigenetic changes in the astrocytic chromatin. Different configurations of primary glial culture were used to modulate microglia–astrocyte crosstalk while inducing pro-inflammatory gain of function by lipopolysaccharide (LPS) exposure. In vivo, brain ischemia by cortical devascularization (pial disruption) was performed to verify the presence of epigenetic marks in reactive astrocytes. Our results showed that 1) microglia is required to initiate the pathological conversion of astrocytes by triggering the NF-κB signaling pathway; 2) this interaction is mediated by soluble factors and induces stable astroglial phenotypic changes; 3) the pathological conversion promotes chromatin remodeling with stable increase in H3K9K14ac, temporary increase in H3K27ac, and temporary reduction in heterochromatin mark H3K9me3; and 4) in vivo reactive astrocytes show increased H3K27ac mark in the neuroinflammatory milieu from the ischemic penumbra. Our findings indicate that astroglial pathological pro-inflammatory gain of function is associated with profound changes in the configuration of astrocytic chromatin, which in turn are initiated by microglia-derived cues. These results open a new avenue in the study of potential pharmacological interventions that modify the initiation and stabilization of astroglial pathological remodeling, which would be useful in acute and chronic CNS injury. Epigenetic changes represent a plausible pharmacological target to interfere with the stabilization of the pathological astroglial phenotype.
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Affiliation(s)
- Alejandro Villarreal
- Laboratorio de Neuropatología Molecular, Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis" UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Camila Vidos
- Laboratorio de Neuropatología Molecular, Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis" UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Matías Monteverde Busso
- Laboratorio de Neuropatología Molecular, Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis" UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina.,Primera Unidad Académica de Histología, Embriología, Biología Celular y Genética, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Belén Cieri
- Laboratorio de Neuropatología Molecular, Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis" UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina.,Primera Unidad Académica de Histología, Embriología, Biología Celular y Genética, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alberto Javier Ramos
- Laboratorio de Neuropatología Molecular, Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis" UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina.,Primera Unidad Académica de Histología, Embriología, Biología Celular y Genética, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
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38
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Overview of Evidence-Based Chemotherapy for Oral Cancer: Focus on Drug Resistance Related to the Epithelial-Mesenchymal Transition. Biomolecules 2021; 11:biom11060893. [PMID: 34208465 PMCID: PMC8234904 DOI: 10.3390/biom11060893] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/12/2021] [Accepted: 06/13/2021] [Indexed: 12/12/2022] Open
Abstract
The increasing incidence of resistance to chemotherapeutic agents has become a major issue in the treatment of oral cancer (OC). Epithelial-mesenchymal transition (EMT) has attracted a great deal of attention in recent years with regard to its relation to the mechanism of chemotherapy drug resistance. EMT-activating transcription factors (EMT-ATFs), such as Snail, TWIST, and ZEB, can activate several different molecular pathways, e.g., PI3K/AKT, NF-κB, and TGF-β. In contrast, the activated oncological signal pathways provide reciprocal feedback that affects the expression of EMT-ATFs, resulting in a peritumoral extracellular environment conducive to cancer cell survival and evasion of the immune system, leading to resistance to multiple chemotherapeutic agents. We present an overview of evidence-based chemotherapy for OC treatment based on the National Comprehensive Cancer Network (NCCN) Chemotherapy Order Templates. We focus on the molecular pathways involved in drug resistance related to the EMT and highlight the signal pathways and transcription factors that may be important for EMT-regulated drug resistance. Rapid progress in antitumor regimens, together with the application of powerful techniques such as high-throughput screening and microRNA technology, will facilitate the development of therapeutic strategies to augment chemotherapy.
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39
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Aspirin modulates 2-hydroxyisobutyrylation of ENO1K281 to attenuate the glycolysis and proliferation of hepatoma cells. Biochem Biophys Res Commun 2021; 560:172-178. [PMID: 34000466 DOI: 10.1016/j.bbrc.2021.04.083] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 11/21/2022]
Abstract
Aspirin can efficiently inhibit the glycolysis and proliferation of cancer cells, however, the underlying mechanism is poorly understood. Here, we report that aspirin attenuates the glycolysis and proliferation of hepatoma cells through modulating the levels of lysine 2-hydroxyisobutyrylation (Khib) of enolase 1 (ENO1). We found that aspirin decreased the levels of glucose consumption and lactate production in hepatoma cells. Moreover, 4 mM aspirin reduced the activities of ENO1, a key enzyme of glycolysis, and decreased the levels of ENO1 Khib in the cells. Interestingly, we identified that 4 mM aspirin could decrease the levels of Khib on many proteins by using pan Khib antibody in the cells. Interestingly, the activities of ENO1 could be rescued by the transient overexpression of ENO1, but not by ENO1 mutant (K281R). Moreover, we identified that the C646, an inhibitor of p300 which is a writer of Khib, could reduce the levels of ENO1 Khib, resulting in the decrease of ENO1 activities. The treatment with PDTC, an inhibitor of NF-κB which is a target of aspirin, could work well as C646 in the cells. Both of aspirin and C646 (or PDTC) displayed a stronger effect than the single treatment in the system. Functionally, ENO1, but not ENO1 mutant (K281R), could rescue the aspirin-induced inhibition of proliferation of liver cancer cells in vitro, suggesting that ENO1K281 is involved in the aspirin-mediated inhibition of liver cancer. Our finding provides new insights into the mechanism by which aspirin attenuates the glycolysis and proliferation of hepatoma cells.
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40
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Chang M, Wilson CJ, Karunatilleke NC, Moselhy MH, Karttunen M, Choy WY. Exploring the Conformational Landscape of the Neh4 and Neh5 Domains of Nrf2 Using Two Different Force Fields and Circular Dichroism. J Chem Theory Comput 2021; 17:3145-3156. [PMID: 33861593 DOI: 10.1021/acs.jctc.0c01243] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The nuclear factor erythroid 2-related factor 2 (Nrf2)-ARE transcriptional response pathway plays a critical role in protecting the cell from oxidative stresses via the upregulation of cytoprotective genes. Aberrant activation of Nrf2 in cancer cells can confer this cytoprotectivity, thereby reducing the efficacy of both chemotherapeutics and radiotherapies. Key to this antioxidant pathway is the interaction between Nrf2 and CREB binding protein (CBP), mediated by the Neh4 and Neh5 domains of Nrf2. Disruption of this interaction via small-molecule therapeutics could negate the effects of aberrant Nrf2 upregulation. Due to the disordered nature of these domains, there remains no three-dimensional structure of Neh4 or Neh5, making structure-based drug design a challenge. Here, we performed 48 μs of unbiased molecular dynamics (MD) simulations with the Amber99SB*-ILDNP and CHARMM36m force fields and circular dichroism (CD) spectropolarimetry experiments to elucidate the free-state structures of these domains; no previous data regarding their conformational landscapes exists. There are two main findings: First, we find Neh5 to be markedly more disordered than Neh4, which has nine residues in the middle of the domain showing α-helical propensity, thus pointing to Neh4 and Neh5 having different binding mechanisms. Second, the two force fields show strong differences for the glutamic acid-rich Neh5 peptide but are in reasonable agreement for Neh4, which has no glutamic acid. The CHARMM36m force field agrees more closely with the CD results.
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Affiliation(s)
- Megan Chang
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada
| | - Carter J Wilson
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada.,Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Nadun Chanaka Karunatilleke
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada
| | - Mohamed Hesham Moselhy
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada.,Department of Computer Science, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Mikko Karttunen
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada.,Centre for Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada
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41
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Xue Y, Nie D, Wang LJ, Qiu HC, Ma L, Dong MX, Tu WJ, Zhao J. Microglial Polarization: Novel Therapeutic Strategy against Ischemic Stroke. Aging Dis 2021; 12:466-479. [PMID: 33815877 PMCID: PMC7990355 DOI: 10.14336/ad.2020.0701] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 07/01/2020] [Indexed: 12/12/2022] Open
Abstract
Ischemic stroke, which is the second highest cause of death and the leading cause of disability, represents ~71% of all strokes globally. Some studies have found that the key elements of the pathobiology of stroke is immunity and inflammation. Microglia are the first line of defense in the nervous system. After stroke, the activated microglia become a double-edged sword, with distinct phenotypic changes to the deleterious M1 types and neuroprotective M2 types. Therefore, ways to promote microglial polarization toward M2 phenotype after stroke have become the focus of attention in recent years. In this review, we discuss the process of microglial polarization, summarize the alternation of signaling pathways and epigenetic regulation that control microglial polarization in ischemic stroke, aiming to find the potential mechanisms by which microglia can be transformed into the M2 polarized phenotype.
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Affiliation(s)
- Yimeng Xue
- 1Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,2Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Ding Nie
- 1Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lin-Jian Wang
- 1Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,2Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Han-Cheng Qiu
- 1Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Long Ma
- 1Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ming-Xin Dong
- 3Institute of Radiation Medicine, Chinese Academy of Medical Science & Peking Union Medical College, Tianjin, China
| | - Wen-Jun Tu
- 1Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,3Institute of Radiation Medicine, Chinese Academy of Medical Science & Peking Union Medical College, Tianjin, China
| | - Jizong Zhao
- 1Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,2Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.,4China National Clinical Research Center for Neurological Diseases, Beijing, China.,5Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China.,6Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
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42
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Ngo KA, Kishimoto K, Davis-Turak J, Pimplaskar A, Cheng Z, Spreafico R, Chen EY, Tam A, Ghosh G, Mitchell S, Hoffmann A. Dissecting the Regulatory Strategies of NF-κB RelA Target Genes in the Inflammatory Response Reveals Differential Transactivation Logics. Cell Rep 2021; 30:2758-2775.e6. [PMID: 32101750 PMCID: PMC7061728 DOI: 10.1016/j.celrep.2020.01.108] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/23/2019] [Accepted: 01/30/2020] [Indexed: 01/22/2023] Open
Abstract
Nuclear factor κB (NF-κB) RelA is the potent transcriptional activator of inflammatory response genes. We stringently defined a list of direct RelA target genes by integrating physical (chromatin immunoprecipitation sequencing [ChIP-seq]) and functional (RNA sequencing [RNA-seq] in knockouts) datasets. We then dissected each gene’s regulatory strategy by testing RelA variants in a primary-cell genetic-complementation assay. All endogenous target genes require RelA to make DNA-base-specific contacts, and none are activatable by the DNA binding domain alone. However, endogenous target genes differ widely in how they employ the two transactivation domains. Through model-aided analysis of the dynamic time-course data, we reveal the gene-specific synergy and redundancy of TA1 and TA2. Given that post-translational modifications control TA1 activity and intrinsic affinity for coactivators determines TA2 activity, the differential TA logics suggests context-dependent versus context-independent control of endogenous RelA-target genes. Although some inflammatory initiators appear to require co-stimulatory TA1 activation, inflammatory resolvers are a part of the NF-κB RelA core response. Ngo et al. developed a genetic complementation system for NF-κB RelA that reveals that NF-κB target-gene selection requires high-affinity RelA binding and transcriptional activation domains for gene induction. The synergistic and redundant functions of two transactivation domains define pro-inflammatory and inflammation-response genes.
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Affiliation(s)
- Kim A Ngo
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kensei Kishimoto
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jeremy Davis-Turak
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aditya Pimplaskar
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhang Cheng
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Roberto Spreafico
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Emily Y Chen
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amy Tam
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92037, USA
| | - Simon Mitchell
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alexander Hoffmann
- Signaling Systems Laboratory, Department of Microbiology Immunology, and Molecular Genetics (MIMG), Institute for Quantitative and Computational Biosciences (QCB), Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA.
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43
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Ding L, Wen Y, Zhang X, Zhao F, Lv K, Shi JH, Shen S, Pan X. Transcriptional network constituted of CBP, Ku70, NOX2, and BAX prevents the cell death of necrosis, paraptosis, and apoptosis in human melanoma. Cell Death Discov 2021; 7:40. [PMID: 33637687 PMCID: PMC7910564 DOI: 10.1038/s41420-021-00417-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 01/03/2021] [Accepted: 02/03/2021] [Indexed: 11/20/2022] Open
Abstract
CREB-binding protein (CBP) is an acetyltransferase known to play multiple roles in the transcriptions of genes involving oxidative metabolism, cell cycle, DNA damage checkpoints, and cell death. In this study, CBP was found to positively regulate the expression of Ku70, and both CBP and Ku70 were found to negatively regulate the expression of NOX2, therefore, mitigating the intracellular ROS in human melanoma. Knocking down CBP or Ku70 induced necrotic and paraptotic cell death as indicated by high-level intracellular ROS, cytoplasmic vacuolization, and cell cycle arrest in the S phase. In addition, chromosomal condensations were also observed in the cells proceeding necrotic and paraptotic cell death, which was found to be related to the BAX-associated intrinsic pathway of apoptotic cell death, when Ku70 was decreased either by CBP depletion or by Ku70 depletion directly. Our results, therefore, supported the idea that CBP, Ku70, BAX, and NOX2 have formed a transcriptional network in the prevention of cell death of necrosis, paraptosis, and apoptosis in human melanoma.
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Affiliation(s)
- Liang Ding
- School of Medicine, Hebei University, Baoding, 071002, China
| | - Yalei Wen
- School of Medicine, Hebei University, Baoding, 071002, China
| | - Xin Zhang
- School of Medicine, Hebei University, Baoding, 071002, China
| | - Fang Zhao
- School of Medicine, Hebei University, Baoding, 071002, China
| | - Kenao Lv
- School of Life Science, Beijing Institute of Technology, Beijin, 100081, China
| | - Jian-Hong Shi
- Central Laboratory, Affiliated Hospital of Hebei University, Baoding, 071002, China
| | - Shigang Shen
- School of Chemistry and environmental Science, Hebei University, Baodin, 071002, China
| | - Xuefeng Pan
- School of Medicine, Hebei University, Baoding, 071002, China. .,School of Life Science, Beijing Institute of Technology, Beijin, 100081, China. .,School of Chemistry and environmental Science, Hebei University, Baodin, 071002, China.
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Abstract
Despite high mortality rates, molecular understanding of metastasis remains limited. It can be regulated by both pro- and anti-metastasis genes. The metastasis suppressor, breast cancer metastasis suppressor 1 (BRMS1), has been positively correlated with patient outcomes, but molecular functions are still being characterized. BRMS1 has been implicated in focal adhesion kinase (FAK), epidermal growth factor receptor (EGFR), and NF-κB signaling pathways. We review evidence that BRMS1 regulates these vast signaling pathways through chromatin remodeling as a member of mSin3 histone deacetylase complexes.
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45
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The Landscape of AhR Regulators and Coregulators to Fine-Tune AhR Functions. Int J Mol Sci 2021; 22:ijms22020757. [PMID: 33451129 PMCID: PMC7828596 DOI: 10.3390/ijms22020757] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/09/2021] [Accepted: 01/11/2021] [Indexed: 01/04/2023] Open
Abstract
The aryl-hydrocarbon receptor (AhR) is a ligand-activated transcription factor that mediates numerous cellular responses. Originally investigated in toxicology because of its ability to bind environmental contaminants, AhR has attracted enormous attention in the field of immunology in the last 20 years. In addition, the discovery of endogenous and plant-derived ligands points to AhR also having a crucial role in normal cell physiology. Thus, AhR is emerging as a promiscuous receptor that can mediate either toxic or physiologic effects upon sensing multiple exogenous and endogenous molecules. Within this scenario, several factors appear to contribute to the outcome of gene transcriptional regulation by AhR, including the nature of the ligand as such and its further metabolism by AhR-induced enzymes, the local tissue microenvironment, and the presence of coregulators or specific transcription factors in the cell. Here, we review the current knowledge on the array of transcription factors and coregulators that, by interacting with AhR, tune its transcriptional activity in response to endogenous and exogenous ligands.
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46
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LncRNA HOTAIR regulates glucose transporter Glut1 expression and glucose uptake in macrophages during inflammation. Sci Rep 2021; 11:232. [PMID: 33420270 PMCID: PMC7794310 DOI: 10.1038/s41598-020-80291-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 12/17/2020] [Indexed: 12/11/2022] Open
Abstract
Inflammation plays central roles in the immune response. Inflammatory response normally requires higher energy and therefore is associated with glucose metabolism. Our recent study demonstrates that lncRNA HOTAIR plays key roles in NF-kB activation, cytokine expression, and inflammation. Here, we investigated if HOTAIR plays any role in the regulation of glucose metabolism in immune cells during inflammation. Our results demonstrate that LPS-induced inflammation induces the expression of glucose transporter isoform 1 (Glut1) which controls the glucose uptake in macrophages. LPS-induced Glut1 expression is regulated via NF-kB activation. Importantly, siRNA-mediated knockdown of HOTAIR suppressed the LPS-induced expression of Glut1 suggesting key roles of HOTAIR in LPS-induced Glut1 expression in macrophage. HOTAIR induces NF-kB activation, which in turn increases Glut1 expression in response to LPS. We also found that HOTAIR regulates glucose uptake in macrophages during LPS-induced inflammation and its knockdown decreases LPS-induced increased glucose uptake. HOTAIR also regulates other upstream regulators of glucose metabolism such as PTEN and HIF1α, suggesting its multimodal functions in glucose metabolism. Overall, our study demonstrated that lncRNA HOTAIR plays key roles in LPS-induced Glut1 expression and glucose uptake by activating NF-kB and hence HOTAIR regulates metabolic programming in immune cells potentially to meet the energy needs during the immune response.
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Santhakumar P, Roy A, Ganesh MK, Selvaraj J, Prathap L, Babu KY. Ethanolic extract of Capparis decidua fruit ameliorates methotrexate-induced hepatotoxicity by suppressing oxidative stress and inflammation by modulating nuclear factor-kappa B signaling pathway. Pharmacogn Mag 2021. [DOI: 10.4103/pm.pm_402_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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48
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Andrews C, Xu Y, Kirberger M, Yang JJ. Structural Aspects and Prediction of Calmodulin-Binding Proteins. Int J Mol Sci 2020; 22:ijms22010308. [PMID: 33396740 PMCID: PMC7795363 DOI: 10.3390/ijms22010308] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 11/19/2022] Open
Abstract
Calmodulin (CaM) is an important intracellular protein that binds Ca2+ and functions as a critical second messenger involved in numerous biological activities through extensive interactions with proteins and peptides. CaM’s ability to adapt to binding targets with different structures is related to the flexible central helix separating the N- and C-terminal lobes, which allows for conformational changes between extended and collapsed forms of the protein. CaM-binding targets are most often identified using prediction algorithms that utilize sequence and structural data to predict regions of peptides and proteins that can interact with CaM. In this review, we provide an overview of different CaM-binding proteins, the motifs through which they interact with CaM, and shared properties that make them good binding partners for CaM. Additionally, we discuss the historical and current methods for predicting CaM binding, and the similarities and differences between these methods and their relative success at prediction. As new CaM-binding proteins are identified and classified, we will gain a broader understanding of the biological processes regulated through changes in Ca2+ concentration through interactions with CaM.
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Affiliation(s)
- Corey Andrews
- Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (C.A.); (Y.X.)
| | - Yiting Xu
- Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (C.A.); (Y.X.)
| | - Michael Kirberger
- Chemistry Division, Georgia Gwinnett College, Lawrenceville, GA 30043, USA;
| | - Jenny J. Yang
- Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (C.A.); (Y.X.)
- Correspondence: ; Tel.: +1-4044135520
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49
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Gulliver C, Hoffmann R, Baillie GS. The enigmatic helicase DHX9 and its association with the hallmarks of cancer. Future Sci OA 2020; 7:FSO650. [PMID: 33437516 PMCID: PMC7787180 DOI: 10.2144/fsoa-2020-0140] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/20/2020] [Indexed: 12/16/2022] Open
Abstract
Much interest has been expended lately in characterizing the association between DExH-Box helicase 9 (DHX9) dysregulation and malignant development, however, the enigmatic nature of DHX9 has caused conflict as to whether it regularly functions as an oncogene or tumor suppressor. The impact of DHX9 on malignancy appears to be cell-type specific, dependent upon the availability of binding partners and activation of inter-connected signaling pathways. Realization of DHX9's pivotal role in the development of several hallmarks of cancer has boosted the enzyme's potential as a cancer biomarker and therapeutic target, opening up novel avenues for exploring DHX9 in precision medicine applications. Our review discusses the ascribed functions of DHX9 in cancer, explores its enigmatic nature and potential as an antineoplastic target.
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Affiliation(s)
- Chloe Gulliver
- Institute of Cardiovascular & Medical Science, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Ralf Hoffmann
- Institute of Cardiovascular & Medical Science, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
- Philips Research Europe, High Tech Campus, Eindhoven, The Netherlands
| | - George S Baillie
- Institute of Cardiovascular & Medical Science, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
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50
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Wang Y, Li D, Song L, Ding H. Ophiopogonin D attenuates PM2.5-induced inflammation via suppressing the AMPK/NF-κB pathway in mouse pulmonary epithelial cells. Exp Ther Med 2020; 20:139. [PMID: 33093877 PMCID: PMC7571316 DOI: 10.3892/etm.2020.9268] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 07/24/2020] [Indexed: 12/11/2022] Open
Abstract
Exposure to fine particulate matter, such as particulate matter of ≤2.5 µm in diameter (PM2.5), causes pulmonary inflammation and injury to other organs. It has been reported that Ophiopogonin D (OP-D) has anti-inflammatory activity. The aim of the present study was to investigate this anti-inflammatory activity of OP-D on PM2.5-induced acute airway inflammation and its underlying mechanisms. The viability of PM2.5-treated mouse lung epithelial (MLE-12) cells with or without OP-D treatment was determined using a Cell Counting Kit-8 assay. The corresponding levels of IL-1β, IL-6, IL-8 and TNF-α were examined via ELISA. Subcellular localization of NF-κBp65 was detected using immunofluorescence staining. The expression levels of AMP-activated protein kinase (AMPK), phosphorylated (p)-AMPK, NF-κBp65 and p-NF-κBp65 were analyzed using western blotting. The selective AMPK inhibitor Compound C (CC) was utilized to investigate the involvement of AMPK in the protection against PM2.5-induced cell inflammation by OP-D treatment. The results demonstrated that OP-D significantly ameliorated the PM2.5-stimulated release of proinflammatory cytokines (TNF-α, IL-1β, IL-6 and IL-8) and inhibited the translocation of NF-κBp65 from the cytoplasm to the nucleus in MLE-12 cells. Moreover, OP-D significantly prevented the PM2.5-triggered phosphorylation of NF-κBp65 and upregulated AMPK activity. The anti-inflammatory activity of OP-D could also be attenuated by the AMPK-specific inhibitor CC. The present results suggested that the anti-inflammatory activity of OP-D was mediated via AMPK activation and NF-κB signaling pathway downregulation, which ameliorated the expression of proinflammatory cytokines. Therefore, OP-D could be a candidate drug to treat PM2.5-induced airway inflammation.
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Affiliation(s)
- Ying Wang
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China.,Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing 100191, P.R. China
| | - Dan Li
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Lei Song
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Hui Ding
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
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