1
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Su F, Koeberle A. Regulation and targeting of SREBP-1 in hepatocellular carcinoma. Cancer Metastasis Rev 2024; 43:673-708. [PMID: 38036934 PMCID: PMC11156753 DOI: 10.1007/s10555-023-10156-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023]
Abstract
Hepatocellular carcinoma (HCC) is an increasing burden on global public health and is associated with enhanced lipogenesis, fatty acid uptake, and lipid metabolic reprogramming. De novo lipogenesis is under the control of the transcription factor sterol regulatory element-binding protein 1 (SREBP-1) and essentially contributes to HCC progression. Here, we summarize the current knowledge on the regulation of SREBP-1 isoforms in HCC based on cellular, animal, and clinical data. Specifically, we (i) address the overarching mechanisms for regulating SREBP-1 transcription, proteolytic processing, nuclear stability, and transactivation and (ii) critically discuss their impact on HCC, taking into account (iii) insights from pharmacological approaches. Emphasis is placed on cross-talk with the phosphatidylinositol-3-kinase (PI3K)-protein kinase B (Akt)-mechanistic target of rapamycin (mTOR) axis, AMP-activated protein kinase (AMPK), protein kinase A (PKA), and other kinases that directly phosphorylate SREBP-1; transcription factors, such as liver X receptor (LXR), peroxisome proliferator-activated receptors (PPARs), proliferator-activated receptor γ co-activator 1 (PGC-1), signal transducers and activators of transcription (STATs), and Myc; epigenetic mechanisms; post-translational modifications of SREBP-1; and SREBP-1-regulatory metabolites such as oxysterols and polyunsaturated fatty acids. By carefully scrutinizing the role of SREBP-1 in HCC development, progression, metastasis, and therapy resistance, we shed light on the potential of SREBP-1-targeting strategies in HCC prevention and treatment.
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Affiliation(s)
- Fengting Su
- Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Andreas Koeberle
- Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria.
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2
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Ghorbani R, Gharbavi M, Keshavarz B, Madanchi H, Johari B. Targeting c-Myc with decoy oligodeoxynucleotide-loaded polycationic nanoparticles inhibits cell growth and induces apoptosis in cancer stem-like cells (NTERA-2). Mol Biol Rep 2024; 51:623. [PMID: 38710891 DOI: 10.1007/s11033-024-09559-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 04/16/2024] [Indexed: 05/08/2024]
Abstract
BACKGROUND An increase in cancer stem cell (CSC) populations and their resistance to common treatments could be a result of c-Myc dysregulations in certain cancer cells. In the current study, we investigated anticancer effects of c-Myc decoy ODNs loaded-poly (methacrylic acid-co-diallyl dimethyl ammonium chloride) (PMA-DDA)-coated silica nanoparticles as carriers on cancer-like stem cells (NTERA-2). METHODS AND RESULTS The physicochemical characteristics of the synthesized nanocomposites (SiO2@PMA-DDA-DEC) were analyzed using FT-IR, DLS, and SEM techniques. UV-Vis spectrophotometer was applied to analyze the release pattern of decoy ODNs from the nanocomposite. Furthermore, uptake, cell viability, apoptosis, and cell cycle assays were used to investigate the anticancer effects of nanocomposites loaded with c-Myc decoy ODNs on NTERA-2 cancer cells. The results of physicochemical analytics demonstrated that SiO2@PMA-DDA-DEC nanocomposites were successfully synthesized. The prepared nanocomposites were taken up by NTERA-2 cells with high efficiency, and could effectively inhibit cell growth and increase apoptosis rate in the treated cells compared to the control group. Moreover, SiO2@PMA-DDA nanocomposites loaded with c-Myc decoy ODNs induced cell cycle arrest at the G0/G1 phase in the treated cells. CONCLUSIONS The conclusion drawn from this study is that c-Myc decoy ODN-loaded SiO2@PMA-DDA nanocomposites can effectively inhibit cell growth and induce apoptosis in NTERA-2 cancer cells. Moreover, given that a metal core is incorporated into this synthetic nanocomposite, it could potentially be used in conjunction with irradiation as part of a decoy-radiotherapy combinational therapy in future investigations.
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Affiliation(s)
- Roghayeh Ghorbani
- Department of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
- Student Research Committee, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mahmoud Gharbavi
- Nanotechnology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Pain Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Benyamin Keshavarz
- Student Research Committee, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Hamid Madanchi
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran.
- Department of Medical Biotechnology, School of Medicine, Semnan University of Medical Sciences, Semnan, 35131-38111, Iran.
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, 13198, Iran.
| | - Behrooz Johari
- Department of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran.
- Zanjan Pharmaceutical Biotechnology Research Center, Zanjan University of Medical Sciences, Zanjan, Iran.
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Choi HJ, Kim YA, Ryu J, Park KK, Lee SJ, Kim BS, Song JE, Kim JD. STAT3 Decoy Oligodeoxynucleotides Suppress Liver Inflammation and Fibrosis in Liver Cancer Cells and a DDC-Induced Liver Injury Mouse Model. Molecules 2024; 29:593. [PMID: 38338338 PMCID: PMC10856653 DOI: 10.3390/molecules29030593] [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: 11/22/2023] [Revised: 12/28/2023] [Accepted: 01/15/2024] [Indexed: 02/12/2024] Open
Abstract
Liver damage caused by various factors results in fibrosis and inflammation, leading to cirrhosis and cancer. Fibrosis results in the accumulation of extracellular matrix components. The role of STAT proteins in mediating liver inflammation and fibrosis has been well documented; however, approved therapies targeting STAT3 inhibition against liver disease are lacking. This study investigated the anti-fibrotic and anti-inflammatory effects of STAT3 decoy oligodeoxynucleotides (ODN) in hepatocytes and liver fibrosis mouse models. STAT3 decoy ODN were delivered into cells using liposomes and hydrodynamic tail vein injection into 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC)-fed mice in which liver injury was induced. STAT3 target gene expression changes were verified using qPCR and Western blotting. Liver tissue fibrosis and bile duct proliferation were assessed in animal experiments using staining techniques, and macrophage and inflammatory cytokine distribution was verified using immunohistochemistry. STAT3 decoy ODN reduced fibrosis and inflammatory factors in liver cancer cell lines and DDC-induced liver injury mouse model. These results suggest that STAT3 decoy ODN may effectively treat liver fibrosis and must be clinically investigated.
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Affiliation(s)
- Hye Jin Choi
- Department of Surgery, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea;
| | - Young-Ah Kim
- Seoul Clinical Laboratories of Daegu, Daegu 41238, Republic of Korea
| | - Junghwa Ryu
- Department of Radiology, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea;
| | - Kwan-Kyu Park
- Department of Pathology, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea; (K.-K.P.)
| | - Sun-Jae Lee
- Department of Pathology, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea; (K.-K.P.)
| | - Byung Seok Kim
- Department of Internal Medicine, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea; (B.S.K.)
| | - Jeong-En Song
- Department of Internal Medicine, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea; (B.S.K.)
| | - Joo Dong Kim
- Department of Surgery, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea;
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4
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Al-Tohamy A, Grove A. Targeting bacterial transcription factors for infection control: opportunities and challenges. Transcription 2023:1-28. [PMID: 38126125 DOI: 10.1080/21541264.2023.2293523] [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: 08/31/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
The rising threat of antibiotic resistance in pathogenic bacteria emphasizes the need for new therapeutic strategies. This review focuses on bacterial transcription factors (TFs), which play crucial roles in bacterial pathogenesis. We discuss the regulatory roles of these factors through examples, and we outline potential therapeutic strategies targeting bacterial TFs. Specifically, we discuss the use of small molecules to interfere with TF function and the development of transcription factor decoys, oligonucleotides that compete with promoters for TF binding. We also cover peptides that target the interaction between the bacterial TF and other factors, such as RNA polymerase, and the targeting of sigma factors. These strategies, while promising, come with challenges, from identifying targets to designing interventions, managing side effects, and accounting for changing bacterial resistance patterns. We also delve into how Artificial Intelligence contributes to these efforts and how it may be exploited in the future, and we touch on the roles of multidisciplinary collaboration and policy to advance this research domain.Abbreviations: AI, artificial intelligence; CNN, convolutional neural networks; DTI: drug-target interaction; HTH, helix-turn-helix; IHF, integration host factor; LTTRs, LysR-type transcriptional regulators; MarR, multiple antibiotic resistance regulator; MRSA, methicillin resistant Staphylococcus aureus; MSA: multiple sequence alignment; NAP, nucleoid-associated protein; PROTACs, proteolysis targeting chimeras; RNAP, RNA polymerase; TF, transcription factor; TFD, transcription factor decoying; TFTRs, TetR-family transcriptional regulators; wHTH, winged helix-turn-helix.
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Affiliation(s)
- Ahmed Al-Tohamy
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
- Department of Cell Biology, Biotechnology Research Institute, National Research Centre, Cairo, Egypt
| | - Anne Grove
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
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5
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Gwon MG, Leem J, An HJ, Gu H, Bae S, Kim JH, Park KK. The decoy oligodeoxynucleotide against HIF-1α and STAT5 ameliorates atopic dermatitis-like mouse model. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102036. [PMID: 37799329 PMCID: PMC10550406 DOI: 10.1016/j.omtn.2023.102036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 09/15/2023] [Indexed: 10/07/2023]
Abstract
Atopic dermatitis (AD) is a common inflammatory skin disease caused by an immune disorder. Mast cells are known to be activated and granulated to maintain an allergic reaction, including rhinitis, asthma, and AD. Although hypoxia-inducible factor-1 alpha (HIF-1α) and signal transducer and activator of transcription 5 (STAT5) play crucial roles in mast cell survival and granulation, their effects need to be clarified in allergic disorders. Thus, we designed decoy oligodeoxynucleotide (ODN) synthetic DNA, without open ends, containing complementary sequences for HIF-1α and STAT5 to suppress the transcriptional activities of HIF-1α and STAT5. In this study, we demonstrated the effects of HIF-1α/STAT5 ODN using AD-like in vivo and in vitro models. The HIF-1α/STAT5 decoy ODN significantly alleviated cutaneous symptoms similar to AD, including morphology changes, immune cell infiltration, skin barrier dysfunction, and inflammatory response. In the AD model, it also inhibited mast cell infiltration and degranulation in skin tissue. These results suggest that the HIF-1α/STAT5 decoy ODN ameliorates the AD-like disorder and immunoglobulin E (IgE)-induced mast cell activation by disrupting HIF-1α/STAT5 signaling pathways. Taken together, these findings suggest the possibility of HIF-1α/STAT5 as therapeutic targets and their decoy ODN as a potential therapeutic tool for AD.
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Affiliation(s)
- Mi-Gyeong Gwon
- Department of Pathology, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea
| | - Jaechan Leem
- Department of Immunology, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea
| | - Hyun-Jin An
- Department of Pathology, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea
| | - Hyemin Gu
- Department of Pathology, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea
| | - Seongjae Bae
- Department of Pathology, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea
| | - Jong Hyun Kim
- Department of Biochemistry, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea
| | - Kwan-Kyu Park
- Department of Pathology, School of Medicine, Daegu Catholic University, Daegu 42472, Republic of Korea
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Thakur S, Sinhari A, Jain P, Jadhav HR. A perspective on oligonucleotide therapy: Approaches to patient customization. Front Pharmacol 2022; 13:1006304. [PMID: 36339619 PMCID: PMC9626821 DOI: 10.3389/fphar.2022.1006304] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/05/2022] [Indexed: 09/12/2023] Open
Abstract
It is estimated that the human genome encodes 15% of proteins that are considered to be disease-modifying. Only 2% of these proteins possess a druggable site that the approved clinical candidates target. Due to this disparity, there is an immense need to develop therapeutics that may better mitigate the disease or disorders aroused by non-druggable and druggable proteins or enzymes. The recent surge in approved oligonucleotide therapeutics (OT) indicates the imminent potential of these therapies. Oligonucleotide-based therapeutics are of intermediate size with much-improved selectivity towards the target and fewer off-target effects than small molecules. The OTs include Antisense RNAs, MicroRNA (MIR), small interfering RNA (siRNA), and aptamers, which are currently being explored for their use in neurodegenerative disorders, cancer, and even orphan diseases. The present review is a congregated effort to present the past and present of OTs and the current efforts to make OTs for plausible future therapeutics. The review provides updated literature on the challenges and bottlenecks of OT and recent advancements in OT drug delivery. Further, this review deliberates on a newly emerging approach to personalized treatment for patients with rare and fatal diseases with OT.
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Affiliation(s)
- Shikha Thakur
- Pharmaceutical Chemistry Laboratory, Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Pilani, RJ, India
| | - Apurba Sinhari
- Pharmaceutical Chemistry Laboratory, Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Pilani, RJ, India
| | - Priti Jain
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Hemant R. Jadhav
- Pharmaceutical Chemistry Laboratory, Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Pilani, RJ, India
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7
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Synthetic Non-Coding RNA for Suppressing mTOR Translation to Prevent Renal Fibrosis Related to Autophagy in UUO Mouse Model. Int J Mol Sci 2022; 23:ijms231911365. [PMID: 36232665 PMCID: PMC9569483 DOI: 10.3390/ijms231911365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 11/16/2022] Open
Abstract
The global burden of chronic kidney disease is increasing, and the majority of these diseases are progressive. Special site-targeted drugs are emerging as alternatives to traditional drugs. Oligonucleotides (ODNs) have been proposed as effective therapeutic tools in specific molecular target therapies for several diseases. We designed ring-type non-coding RNAs (ncRNAs), also called mTOR ODNs to suppress mammalian target rapamycin (mTOR) translation. mTOR signaling is associated with excessive cell proliferation and fibrogenesis. In this study, we examined the effects of mTOR suppression on chronic renal injury. To explore the regulation of fibrosis and inflammation in unilateral ureteral obstruction (UUO)-induced injury, we injected synthesized ODNs via the tail vein of mice. The expression of inflammatory-related markers (interleukin-1β, tumor necrosis factor-α), and that of fibrosis (α-smooth muscle actin, fibronectin), was decreased by synthetic ODNs. Additionally, ODN administration inhibited the expression of autophagy-related markers, microtubule-associated protein light chain 3, Beclin1, and autophagy-related gene 5-12. We confirmed that ring-type ODNs inhibited fibrosis, inflammation, and autophagy in a UUO mouse model. These results suggest that mTOR may be involved in the regulation of autophagy and fibrosis and that regulating mTOR signaling may be a therapeutic strategy against chronic renal injury.
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8
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Jung HJ, An HJ, Gwon MG, Gu H, Bae S, Lee SJ, Kim YA, Leem J, Park KK. Anti-Fibrotic Effect of Synthetic Noncoding Oligodeoxynucleotide for Inhibiting mTOR and STAT3 via the Regulation of Autophagy in an Animal Model of Renal Injury. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030766. [PMID: 35164031 PMCID: PMC8840279 DOI: 10.3390/molecules27030766] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/10/2022] [Accepted: 01/19/2022] [Indexed: 12/12/2022]
Abstract
Renal fibrosis is a common process of various kidney diseases. Autophagy is an important cell biology process to maintain cellular homeostasis. In addition, autophagy is involved in the pathogenesis of various renal disease, including acute kidney injury, glomerular diseases, and renal fibrosis. However, the functional role of autophagy in renal fibrosis remains poorly unclear. The mammalian target of rapamycin (mTOR) plays a negative regulatory role in autophagy. Signal transducer and activator of transcription 3 (STAT3) is an important intracellular signaling that may regulate a variety of inflammatory responses. In addition, STAT3 regulates autophagy in various cell types. Thus, we synthesized the mTOR/STAT3 oligodeoxynucleotide (ODN) to regulate the autophagy. The aim of this study was to investigate the beneficial effect of mTOR/STAT3 ODN via the regulation of autophagy appearance on unilateral ureteral obstruction (UUO)-induced renal fibrosis. This study showed that UUO induced inflammation, tubular atrophy, and tubular interstitial fibrosis. However, mTOR/STAT3 ODN suppressed UUO-induced renal fibrosis and inflammation. The autophagy markers have no statistically significant relation, whereas mTOR/STAT3 ODN suppressed the apoptosis in tubular cells. These results suggest the possibility of mTOR/STAT3 ODN for preventing renal fibrosis. However, the role of mTOR/STAT3 ODN on autophagy regulation needs to be further investigated.
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Affiliation(s)
- Hyun Jin Jung
- Department of Urology, College of Medicine, Catholic University of Daegu, Daegu 42472, Korea;
| | - Hyun-Jin An
- Department of Pathology, College of Medicine, Catholic University of Daegu, Daegu 42472, Korea; (H.-J.A.); (M.-G.G.); (H.G.); (S.B.); (S.-J.L.); (Y.-A.K.)
| | - Mi-Gyeong Gwon
- Department of Pathology, College of Medicine, Catholic University of Daegu, Daegu 42472, Korea; (H.-J.A.); (M.-G.G.); (H.G.); (S.B.); (S.-J.L.); (Y.-A.K.)
| | - Hyemin Gu
- Department of Pathology, College of Medicine, Catholic University of Daegu, Daegu 42472, Korea; (H.-J.A.); (M.-G.G.); (H.G.); (S.B.); (S.-J.L.); (Y.-A.K.)
| | - Seongjae Bae
- Department of Pathology, College of Medicine, Catholic University of Daegu, Daegu 42472, Korea; (H.-J.A.); (M.-G.G.); (H.G.); (S.B.); (S.-J.L.); (Y.-A.K.)
| | - Sun-Jae Lee
- Department of Pathology, College of Medicine, Catholic University of Daegu, Daegu 42472, Korea; (H.-J.A.); (M.-G.G.); (H.G.); (S.B.); (S.-J.L.); (Y.-A.K.)
| | - Young-Ah Kim
- Department of Pathology, College of Medicine, Catholic University of Daegu, Daegu 42472, Korea; (H.-J.A.); (M.-G.G.); (H.G.); (S.B.); (S.-J.L.); (Y.-A.K.)
| | - Jaechan Leem
- Department of Immunology, College of Medicine, Catholic University of Daegu, Daegu 42472, Korea;
| | - Kwan-Kyu Park
- Department of Pathology, College of Medicine, Catholic University of Daegu, Daegu 42472, Korea; (H.-J.A.); (M.-G.G.); (H.G.); (S.B.); (S.-J.L.); (Y.-A.K.)
- Correspondence: ; Tel.: +82-53-650-4149; Fax: +82-53-650-4834
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9
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Johari B, Moradi M. Application of Transcription Factor Decoy Oligodeoxynucleotides (ODNs) for Cancer Therapy. Methods Mol Biol 2022; 2521:207-230. [PMID: 35733000 DOI: 10.1007/978-1-0716-2441-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
As a method of gene therapy, application of decoy oligodeoxynucleotides (ODNs) could interfere at the pretranscription level, by blocking the transcription factors, and inhibiting their attachment to the corresponding sequences in genomic DNA. Some of the transcription factors including MYC, OCT4, SOX2, STAT3, and NANOG are associated with the stemness properties of cancer cells, and suppressing them could interfere with cellular differentiation, which synergizes the efficiency of other anticancer therapies. The use of decoy ODNs has shown to be an effective measure against various malignancies, and it has shown to have a synergic effect when it is used along with the other cancer therapy methods. Emergence of modern nanocarriers has shown to further improve the outcome of using decoy ODNs against some cancers, and it has the potential of being used for clinical applications. In this chapter, it was aimed to provide a glance of this method for cancer therapy.
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Affiliation(s)
- Behrooz Johari
- Department of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran.
- Cancer Gene Therapy Research Center, Zanjan University of Medical Sciences, Zanjan, Iran.
| | - Mohammad Moradi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
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Lim YX, Lin H, Seah SH, Lim YP. Reciprocal Regulation of Hippo and WBP2 Signalling-Implications in Cancer Therapy. Cells 2021; 10:cells10113130. [PMID: 34831354 PMCID: PMC8625973 DOI: 10.3390/cells10113130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/08/2021] [Accepted: 11/08/2021] [Indexed: 11/23/2022] Open
Abstract
Cancer is a global health problem. The delineation of molecular mechanisms pertinent to cancer initiation and development has spurred cancer therapy in the form of precision medicine. The Hippo signalling pathway is a tumour suppressor pathway implicated in a multitude of cancers. Elucidation of the Hippo pathway has revealed an increasing number of regulators that are implicated, some being potential therapeutic targets for cancer interventions. WW domain-binding protein 2 (WBP2) is an oncogenic transcriptional co-factor that interacts, amongst others, with two other transcriptional co-activators, YAP and TAZ, in the Hippo pathway. WBP2 was recently discovered to modulate the upstream Hippo signalling components by associating with LATS2 and WWC3. Exacerbating the complexity of the WBP2/Hippo network, WBP2 itself is reciprocally regulated by Hippo-mediated microRNA biogenesis, contributing to a positive feedback loop that further drives carcinogenesis. Here, we summarise the biological mechanisms of WBP2/Hippo reciprocal regulation and propose therapeutic strategies to overcome Hippo defects in cancers through targeting WBP2.
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Affiliation(s)
- Yvonne Xinyi Lim
- Integrative Sciences and Engineering Programme, National University of Singapore, Singapore 119077, Singapore; (Y.X.L.); (H.L.); (S.H.S.)
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore
| | - Hexian Lin
- Integrative Sciences and Engineering Programme, National University of Singapore, Singapore 119077, Singapore; (Y.X.L.); (H.L.); (S.H.S.)
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore
| | - Sock Hong Seah
- Integrative Sciences and Engineering Programme, National University of Singapore, Singapore 119077, Singapore; (Y.X.L.); (H.L.); (S.H.S.)
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Yoon Pin Lim
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore
- Correspondence:
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11
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Recent trends of NFκB decoy oligodeoxynucleotide-based nanotherapeutics in lung diseases. J Control Release 2021; 337:629-644. [PMID: 34375688 DOI: 10.1016/j.jconrel.2021.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 02/07/2023]
Abstract
Nuclear factor κB (NFκB) is a unique protein complex that plays a major role in lung inflammation and respiratory dysfunction. The NFκB signaling pathway, therefore becomes an avenue for the development of potential pharmacological interventions, especially in situations where chronic inflammation is often constitutively active and plays a key role in the pathogenesis and progression of the disease. NFκB decoy oligodeoxynucleotides (ODNs) are double-stranded and carry NFκB binding sequences. They prevent the formation of NFκB-mediated inflammatory cytokines and thus have been employed in the treatment of a variety of chronic inflammatory diseases. However, the systemic administration of naked decoy ODNs restricts their therapeutic effectiveness because of their poor pharmacokinetic profile, instability, degradation by cellular enzymes and their low cellular uptake. Both structural modification and nanotechnology have shown promising results in enhancing the pharmacokinetic profiles of potent therapeutic substances and have also shown great potential in the treatment of respiratory diseases such as asthma, chronic obstructive pulmonary disease and cystic fibrosis. In this review, we examine the contribution of NFκB activation in respiratory diseases and recent advancements in the therapeutic use of decoy ODNs. In addition, we also highlight the limitations and challenges in use of decoy ODNs as therapeutic molecules, cellular uptake of decoy ODNs, and the current need for novel delivery systems to provide efficient delivery of decoy ODNs. Furthermore, this review provides a common platform for discussion on the existence of decoy ODNs, as well as outlining perspectives on the latest generation of delivery systems that encapsulate decoy ODNs and target NFκB in respiratory diseases.
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Involvement of Scratch2 in GalR1-mediated depression-like behaviors in the rat ventral periaqueductal gray. Proc Natl Acad Sci U S A 2021; 118:1922586118. [PMID: 34108238 DOI: 10.1073/pnas.1922586118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Galanin receptor1 (GalR1) transcript levels are elevated in the rat ventral periaqueductal gray (vPAG) after chronic mild stress (CMS) and are related to depression-like behavior. To explore the mechanisms underlying the elevated GalR1 expression, we carried out molecular biological experiments in vitro and in animal behavioral experiments in vivo. It was found that a restricted upstream region of the GalR1 gene, from -250 to -220, harbors an E-box and plays a negative role in the GalR1 promoter activity. The transcription factor Scratch2 bound to the E-box to down-regulate GalR1 promoter activity and lower expression levels of the GalR1 gene. The expression of Scratch2 was significantly decreased in the vPAG of CMS rats. Importantly, local knockdown of Scratch2 in the vPAG caused elevated expression of GalR1 in the same region, as well as depression-like behaviors. RNAscope analysis revealed that GalR1 mRNA is expressed together with Scratch2 in both GABA and glutamate neurons. Taking these data together, our study further supports the involvement of GalR1 in mood control and suggests a role for Scratch2 as a regulator of depression-like behavior by repressing the GalR1 gene in the vPAG.
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Remes A, Wagner AH, Schmiedel N, Heckmann M, Ruf T, Ding L, Jungmann A, Senger F, Katus HA, Ullrich ND, Frey N, Hecker M, Müller OJ. AAV-mediated expression of NFAT decoy oligonucleotides protects from cardiac hypertrophy and heart failure. Basic Res Cardiol 2021; 116:38. [PMID: 34089101 PMCID: PMC8178147 DOI: 10.1007/s00395-021-00880-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 05/18/2021] [Indexed: 01/08/2023]
Abstract
Previous studies have underlined the substantial role of nuclear factor of activated T cells (NFAT) in hypertension-induced myocardial hypertrophy ultimately leading to heart failure. Here, we aimed at neutralizing four members of the NFAT family of transcription factors as a therapeutic strategy for myocardial hypertrophy transiting to heart failure through AAV-mediated cardiac expression of a RNA-based decoy oligonucleotide (dON) targeting NFATc1-c4. AAV-mediated dON expression markedly decreased endothelin-1 induced cardiomyocyte hypertrophy in vitro and resulted in efficient expression of these dONs in the heart of adult mice as evidenced by fluorescent in situ hybridization. Cardiomyocyte-specific dON expression both before and after induction of transverse aortic constriction protected mice from development of cardiac hypertrophy, cardiac remodeling, and heart failure. Singular systemic administration of AAVs enabling a cell-specific expression of dONs for selective neutralization of a given transcription factor may thus represent a novel and powerful therapeutic approach.
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MESH Headings
- Animals
- Cells, Cultured
- Dependovirus/genetics
- Disease Models, Animal
- Endothelin-1/toxicity
- Genetic Therapy
- Genetic Vectors
- Heart Failure/genetics
- Heart Failure/metabolism
- Heart Failure/physiopathology
- Heart Failure/prevention & control
- Hypertrophy, Left Ventricular/genetics
- Hypertrophy, Left Ventricular/metabolism
- Hypertrophy, Left Ventricular/physiopathology
- Hypertrophy, Left Ventricular/prevention & control
- Mice, Inbred C57BL
- Myocytes, Cardiac/drug effects
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
- NFATC Transcription Factors/genetics
- NFATC Transcription Factors/metabolism
- Oligonucleotides/genetics
- Oligonucleotides/metabolism
- Rats, Wistar
- Ventricular Function, Left
- Ventricular Remodeling
- Mice
- Rats
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Affiliation(s)
- Anca Remes
- Department of Internal Medicine III, University Hospital Schleswig-Holstein and University of Kiel , Arnold-Heller-Str. 3 , Kiel, Germany
- Institute of Physiology and Pathophysiology, Heidelberg University, Heidelberg, Germany
- German Centre for Cardiovascular Research , Partner Site Hamburg/Kiel/Lübeck , Kiel, Germany
| | - Andreas H Wagner
- Institute of Physiology and Pathophysiology, Heidelberg University, Heidelberg, Germany
| | - Nesrin Schmiedel
- Department of Internal Medicine III, University Hospital Schleswig-Holstein and University of Kiel , Arnold-Heller-Str. 3 , Kiel, Germany
- German Centre for Cardiovascular Research , Partner Site Hamburg/Kiel/Lübeck , Kiel, Germany
| | - Markus Heckmann
- Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany
| | - Theresa Ruf
- Department of Internal Medicine III, University Hospital Schleswig-Holstein and University of Kiel , Arnold-Heller-Str. 3 , Kiel, Germany
- Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany
| | - Lin Ding
- Department of Internal Medicine III, University Hospital Schleswig-Holstein and University of Kiel , Arnold-Heller-Str. 3 , Kiel, Germany
- German Centre for Cardiovascular Research , Partner Site Hamburg/Kiel/Lübeck , Kiel, Germany
| | - Andreas Jungmann
- Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany
| | - Frauke Senger
- Department of Internal Medicine III, University Hospital Schleswig-Holstein and University of Kiel , Arnold-Heller-Str. 3 , Kiel, Germany
- German Centre for Cardiovascular Research , Partner Site Hamburg/Kiel/Lübeck , Kiel, Germany
| | - Hugo A Katus
- Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany
| | - Nina D Ullrich
- Institute of Physiology and Pathophysiology, Heidelberg University, Heidelberg, Germany
| | - Norbert Frey
- Department of Internal Medicine III, University Hospital Schleswig-Holstein and University of Kiel , Arnold-Heller-Str. 3 , Kiel, Germany
- Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany
- German Centre for Cardiovascular Research , Partner Site Hamburg/Kiel/Lübeck , Kiel, Germany
| | - Markus Hecker
- Institute of Physiology and Pathophysiology, Heidelberg University, Heidelberg, Germany
| | - Oliver J Müller
- Department of Internal Medicine III, University Hospital Schleswig-Holstein and University of Kiel , Arnold-Heller-Str. 3 , Kiel, Germany.
- German Centre for Cardiovascular Research , Partner Site Hamburg/Kiel/Lübeck , Kiel, Germany.
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14
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Kim YA, Kim HJ, Gwon MG, Gu H, An HJ, Bae S, Leem J, Jung HJ, Park KK. Inhibitory Effects of STAT3 Transcription Factor by Synthetic Decoy ODNs on Autophagy in Renal Fibrosis. Biomedicines 2021; 9:biomedicines9040331. [PMID: 33806080 PMCID: PMC8064438 DOI: 10.3390/biomedicines9040331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 01/04/2023] Open
Abstract
Autophagy in the proximal tubules may promote fibrosis by activating tubular cell death, interstitial inflammation, and the production of pro-fibrotic factors. The signal transducer and activator of transcription 3 (STAT3) is activated as a potential transcription factor, which mediates the stimulation of renal fibrosis. We investigated the role of the STAT3 in autophagy and its effect on the prevention of interstitial renal fibrosis. In this study, we use synthesized STAT3 decoy oligonucleotides (ODN), which were injected into the tail veins of unilateral ureteral obstruction (UUO) mice, to explore the regulation of autophagy in UUO-induced renal fibrosis. The expression of interleukin-6 (IL-6), interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α), and collagen were decreased by STAT3 decoy ODN. The autophagy markers microtubule-associated protein light chain 3 (LC3) and fibronectin, were identified through immunofluorescent staining, indicating that they were reduced in the group injected with ODN. The expressions of LC3, Beclin1, p62, and autophagy-related 5–12 (Atg5–12) and hypoxia inducible factor-1α (HIF-1α) were inhibited in the ODN injection group. We determined the inhibitory effect of autophagy in chronic kidney disease and confirmed that STAT3 decoy ODN effectively inhibited autophagy by inhibiting the expression of STAT3 transcription factors in the UUO group.
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Affiliation(s)
- Young-Ah Kim
- Department of Pathology, School of Medicine, Catholic University of Daegu, Daegu 42472, Korea; (Y.-A.K.); (H.-J.K.); (M.-G.G.); (H.G.); (H.-J.A.); (S.B.)
| | - Hyun-Ju Kim
- Department of Pathology, School of Medicine, Catholic University of Daegu, Daegu 42472, Korea; (Y.-A.K.); (H.-J.K.); (M.-G.G.); (H.G.); (H.-J.A.); (S.B.)
| | - Mi-Gyeong Gwon
- Department of Pathology, School of Medicine, Catholic University of Daegu, Daegu 42472, Korea; (Y.-A.K.); (H.-J.K.); (M.-G.G.); (H.G.); (H.-J.A.); (S.B.)
| | - Hyemin Gu
- Department of Pathology, School of Medicine, Catholic University of Daegu, Daegu 42472, Korea; (Y.-A.K.); (H.-J.K.); (M.-G.G.); (H.G.); (H.-J.A.); (S.B.)
| | - Hyun-Jin An
- Department of Pathology, School of Medicine, Catholic University of Daegu, Daegu 42472, Korea; (Y.-A.K.); (H.-J.K.); (M.-G.G.); (H.G.); (H.-J.A.); (S.B.)
| | - Seongjae Bae
- Department of Pathology, School of Medicine, Catholic University of Daegu, Daegu 42472, Korea; (Y.-A.K.); (H.-J.K.); (M.-G.G.); (H.G.); (H.-J.A.); (S.B.)
| | - Jaechan Leem
- Department of Immunology, School of Medicine, Catholic University of Daegu, Daegu 42472, Korea;
| | - Hyun Jin Jung
- Department of Urology, School of Medicine, Catholic University of Daegu, Daegu 42472, Korea;
| | - Kwan-Kyu Park
- Department of Pathology, School of Medicine, Catholic University of Daegu, Daegu 42472, Korea; (Y.-A.K.); (H.-J.K.); (M.-G.G.); (H.G.); (H.-J.A.); (S.B.)
- Correspondence: ; Tel.: +82-53-650-4149
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15
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Wang T, Tague N, Whelan SA, Dunlop MJ. Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites. Nucleic Acids Res 2021; 49:1163-1172. [PMID: 33367820 PMCID: PMC7826281 DOI: 10.1093/nar/gkaa1234] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 11/12/2020] [Accepted: 12/08/2020] [Indexed: 12/30/2022] Open
Abstract
Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia coli. We show that transcription factor decoys can effectively regulate expression of native and heterologous genes. Tunability of the decoy can be engineered via changes in copy number or modifications to the DNA decoy site sequence. Using arginine biosynthesis as a showcase, we observed a 16-fold increase in arginine production when we introduced the decoy system to steer metabolic flux towards increased arginine biosynthesis, with negligible growth differences compared to the wild type strain. The decoy-based production strain retains high genetic integrity; in contrast to a gene knock-out approach where mutations were common, we detected no mutations in the production system using the decoy-based strain. We further show that transcription factor decoys are amenable to multiplexed library screening by demonstrating enhanced tolerance to pinene with a combinatorial decoy library. Our study shows that transcription factor decoy binding sites are a powerful and compact tool for metabolic engineering.
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Affiliation(s)
- Tiebin Wang
- Molecular Biology, Cell Biology & Biochemistry, Boston University, Boston, MA 02215, USA.,Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Nathan Tague
- Biological Design Center, Boston University, Boston, MA 02215, USA.,Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | | | - Mary J Dunlop
- Molecular Biology, Cell Biology & Biochemistry, Boston University, Boston, MA 02215, USA.,Biological Design Center, Boston University, Boston, MA 02215, USA.,Biomedical Engineering, Boston University, Boston, MA 02215, USA
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16
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Tabatabaeian H, Rao A, Ramos A, Chu T, Sudol M, Lim YP. The emerging roles of WBP2 oncogene in human cancers. Oncogene 2020; 39:4621-4635. [PMID: 32393834 PMCID: PMC7286818 DOI: 10.1038/s41388-020-1318-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 12/15/2022]
Abstract
WW domain-binding protein 2 (WBP2) is an emerging oncoprotein. Over the past decade, WBP2 surfaced as a key node connecting key signaling pathways associated with ER/PR, EGFR, PI3K, Hippo, and Wnt in cancer. In addition to the oncogenic functions of WBP2, this review discusses the latest research regarding the multilevel regulation and modes of action of WBP2 and how they can be exploited for molecular medicine. In translational research, evidence supports the role of WBP2 as a biomarker for early detection, prognosis, and companion diagnostics in breast cancer. Finally, we envision new trends in WBP2 research in the space of molecular etiology of cancer, targeted therapeutics, and precision medicine.
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Affiliation(s)
- Hossein Tabatabaeian
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore
| | - Angad Rao
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore
| | - Alisha Ramos
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore
| | - Tinghine Chu
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 117456, Singapore
| | - Marius Sudol
- Department of Physiology, National University of Singapore, Mechanobiology Institute, Singapore, 117597, Singapore
- Institute for Molecular and Cell Biology (IMCB, A*STAR), Singapore, 138673, Singapore
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yoon Pin Lim
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore.
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 117456, Singapore.
- National University Cancer Institute, Singapore, 119082, Singapore.
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17
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Hibbitts A, Lucía A, Serrano-Sevilla I, De Matteis L, McArthur M, de la Fuente JM, Aínsa JA, Navarro F. Co-delivery of free vancomycin and transcription factor decoy-nanostructured lipid carriers can enhance inhibition of methicillin resistant Staphylococcus aureus (MRSA). PLoS One 2019; 14:e0220684. [PMID: 31479462 PMCID: PMC6719865 DOI: 10.1371/journal.pone.0220684] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 07/22/2019] [Indexed: 01/17/2023] Open
Abstract
Bacterial resistance to antibiotics is widely regarded as a major public health concern with last resort MRSA treatments like vancomycin now encountering resistant strains. TFDs (Transcription Factor Decoys) are oligonucleotide copies of the DNA-binding sites for transcription factors. They bind to and sequester the targeted transcription factor, thus inhibiting transcription of many genes. By developing TFDs with sequences aimed at inhibiting transcription factors controlling the expression of highly conserved bacterial cell wall proteins, TFDs present as a potential method for inhibiting microbial growth without encountering typical resistance mechanisms. However, the efficient protection and delivery of the TFDs inside the bacterial cells is a critical step for the success of this technology. Therefore, in our study, specific TFDs against S. aureus were complexed with two different types of nanocarriers: cationic nanostructured lipid carriers (cNLCs) and chitosan-based nanoparticles (CS-NCs). These TFD-carrier nanocomplexes were characterized for size, zeta potential and TFD complexation or loading efficiency in a variety of buffers. In vitro activity of the nanocomplexes was examined alone and in combination with vancomycin, first in methicillin susceptible strains of S. aureus with the lead candidate advancing to tests against MRSA cultures. Results found that both cNLCs and chitosan-based carriers were adept at complexing and protecting TFDs in a range of physiological and microbiological buffers up to 72 hours. From initial testing, chitosan-TFD particles demonstrated no visible improvements in effect when co-administered with vancomycin. However, co-delivery of cNLC-TFD with vancomycin reduced the MIC of vancomycin by over 50% in MSSA and resulted in significant decreases in viability compared with vancomycin alone in MRSA cultures. Furthermore, these TFD-loaded particles demonstrated very low levels of cytotoxicity and haemolysis in vitro. To our knowledge, this is the first attempt at a combined antibiotic/oligonucleotide-TFD approach to combatting MRSA and, as such, highlights a new avenue of MRSA treatment combining traditional small molecules drugs and bacterial gene inhibition.
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Affiliation(s)
- Alan Hibbitts
- University Grenoble Alpes, CEA, LETI, Technologies for Healthcare and Biology division, Microfluidic Systems and Bioengineering Lab, Grenoble, France
| | - Ainhoa Lucía
- Departamento de Microbiología, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Inés Serrano-Sevilla
- Instituto de Nanociencia de Aragón (INA), Universidad de Zaragoza, Zaragoza, Spain
- CIBER Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Laura De Matteis
- Instituto de Nanociencia de Aragón (INA), Universidad de Zaragoza, Zaragoza, Spain
- CIBER Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Michael McArthur
- University of East Anglia, Norwich Medical School, Norwich, United Kingdom
| | - Jesús M. de la Fuente
- Instituto de Nanociencia de Aragón (INA), Universidad de Zaragoza, Zaragoza, Spain
- CIBER Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, Madrid, Spain
| | - José A. Aínsa
- Departamento de Microbiología, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Fabrice Navarro
- University Grenoble Alpes, CEA, LETI, Technologies for Healthcare and Biology division, Microfluidic Systems and Bioengineering Lab, Grenoble, France
- * E-mail:
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18
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Johari B, Asadi Z, Rismani E, Maghsood F, Sheikh Rezaei Z, Farahani S, Madanchi H, Kadivar M. Inhibition of transcription factor T-cell factor 3 (TCF3) using the oligodeoxynucleotide strategy increases embryonic stem cell stemness: possible application in regenerative medicine. Cell Biol Int 2019; 43:852-862. [PMID: 31033094 DOI: 10.1002/cbin.11153] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 03/10/2019] [Accepted: 04/24/2019] [Indexed: 12/22/2022]
Abstract
The transcription factor T-cell factor 3 (TCF3), one component of the Wnt pathway, is known as a cell-intrinsic inhibitor of many pluripotency genes in embryonic stem cells (ESCs) that influences the balance between pluripotency and differentiation. In this study, the effects of inhibition of TCF3 transcription factor on the stemness of mouse ESCs (mESCs) were investigated using the decoy oligodeoxynucleotides (ODNs) strategy. The TCF3 decoy and its scramble ODNs were designed and synthesized. The interaction specificity of the TCF3 decoy with the TCF3 transcription factor was evaluated by the electrophoretic mobility shift assay. Subcellular localization was carried out using fluorescence and confocal microscopy. Self-renewal and pluripotency of mESCs were analyzed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT), cell cycle and apoptosis, alkaline phosphatase (ALP), embryoid body (EB) formation, and real-time assays. All experiments were performed in triplicate. The results showed that knockdown of TCF3 by decoy ODNs transfection in mESCs led to an increase in the cell proliferation, ALP enzyme activity, and master regulatory stemness genes and a decrease in the number and diameter of EBs. These results supported TCF3 as a potential target to maintain the pluripotency and self-renewal capacity of mESCs. Knockdown of the TCF3 transcription factor using decoy ODNs can be a promising method to maintain the stemness of stem cells in regenerative medicine and cell therapy researches.
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Affiliation(s)
- Behrooz Johari
- Student Research Committee, Zanjan University of Medical Sciences, Zanjan, Iran.,Department of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Zoleykha Asadi
- Department of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Elham Rismani
- Deartment of Molecular Medicine, Pasteur Institute of Iran, Tehran, Iran
| | - Faezeh Maghsood
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran
| | | | - Sima Farahani
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran
| | - Hamid Madanchi
- Department and Center for Biotechnology Research, Semnan University of Medical Sciences, Semnan, Iran
| | - Mehdi Kadivar
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran
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19
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Abstract
Post-transcriptional regulation is linked to the development of pain hypersensitivity. A growing body of evidence indicates that RNA-binding proteins are involved in pain. RNA-based inhibitors are a potential new source of pain therapeutics.
RNA-protein interactions permeate biology. Transcription, translation, processing, and mRNA decay all hinge on widespread use of regulatory information decoded by RNA-binding proteins. The final committed step of protein synthesis, translation, is intimately linked to nociceptor excitability. Understanding the factors that control translation is essential as nociceptor plasticity is a hallmark of persistent pain. Here, we review the growing body of evidence for widespread involvement of RNA-binding proteins in pain. Many of the relevant factors have been implicated in post-transcriptional and translational mechanisms of mRNA control. We propose that recent advances in the development of RNA-based therapeutics provide a potential means to exploit our current understanding of liaisons between RNAs and proteins for therapeutic purposes.
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Affiliation(s)
| | - Zachary T. Campbell
- Corresponding author at: Department of Biological Sciences, 800 W. Campbell Road, RL10 BSB 12.510, Richardson, TX 75080, United States.
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20
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Jin Y, Fei M, Rosenquist S, Jin L, Gohil S, Sandström C, Olsson H, Persson C, Höglund AS, Fransson G, Ruan Y, Åman P, Jansson C, Liu C, Andersson R, Sun C. A Dual-Promoter Gene Orchestrates the Sucrose-Coordinated Synthesis of Starch and Fructan in Barley. MOLECULAR PLANT 2017; 10:1556-1570. [PMID: 29126994 DOI: 10.1016/j.molp.2017.10.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 09/25/2017] [Accepted: 10/17/2017] [Indexed: 06/07/2023]
Abstract
Sequential carbohydrate synthesis is important for plant survival because it guarantees energy supplies for growth and development during plant ontogeny and reproduction. Starch and fructan are two important carbohydrates in many flowering plants and in human diets. Understanding this coordinated starch and fructan synthesis and unraveling how plants allocate photosynthates and prioritize different carbohydrate synthesis for survival could lead to improvements to cereals in agriculture for the purposes of greater food security and production quality. Here, we report a system from a single gene in barley employing two alternative promoters, one intronic/exonic, to generate two sequence-overlapping but functionally opposing transcription factors, in sensing sucrose, potentially via sucrose/glucose/fructose/trehalose 6-phosphate signaling. The system employs an autoregulatory mechanism in perceiving a sucrose-controlled trans activity on one promoter and orchestrating the coordinated starch and fructan synthesis by competitive transcription factor binding on the other promoter. As a case in point for the physiological roles of the system, we have demonstrated that this multitasking system can be exploited in breeding barley with tailored amounts of fructan to produce healthy food ingredients. The identification of an intron/exon-spanning promoter in a hosting gene, resulting in proteins with distinct functions, adds to the complexity of plant genomes.
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Affiliation(s)
- Yunkai Jin
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, China; Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007 Uppsala, Sweden
| | - Mingliang Fei
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, China; Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007 Uppsala, Sweden; Key Laboratory of Education, Department of Hunan Province on Plant Genetics and Molecular Biology, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Sara Rosenquist
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007 Uppsala, Sweden
| | - Lu Jin
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, China; Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007 Uppsala, Sweden
| | - Suresh Gohil
- Department of Chemistry and Biotechnology, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, 750 07 Uppsala, Sweden
| | - Corine Sandström
- Department of Chemistry and Biotechnology, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, 750 07 Uppsala, Sweden
| | - Helena Olsson
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007 Uppsala, Sweden
| | - Cecilia Persson
- The Swedish NMR Centre at University of Gothenburg, Box 465, 405 30 Gothenburg, Sweden
| | - Anna-Stina Höglund
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007 Uppsala, Sweden
| | - Gunnel Fransson
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7051, 750 07 Uppsala, Sweden
| | - Ying Ruan
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, China; Key Laboratory of Education, Department of Hunan Province on Plant Genetics and Molecular Biology, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Per Åman
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7051, 750 07 Uppsala, Sweden
| | - Christer Jansson
- The Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory, P.O. Box 999, K8-93, Richland, WA 99352, USA
| | - Chunlin Liu
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, China.
| | - Roger Andersson
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7051, 750 07 Uppsala, Sweden
| | - Chuanxin Sun
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007 Uppsala, Sweden.
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21
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Laughlin-Toth S, Carter EK, Ivanov I, Wilson WD. DNA microstructure influences selective binding of small molecules designed to target mixed-site DNA sequences. Nucleic Acids Res 2017; 45:1297-1306. [PMID: 28180310 PMCID: PMC5388402 DOI: 10.1093/nar/gkw1232] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/18/2016] [Accepted: 11/23/2016] [Indexed: 12/18/2022] Open
Abstract
Specific targeting of protein–nucleic acid interactions is an area of current interest, for example, in the regulation of gene-expression. Most transcription factor proteins bind in the DNA major groove; however, we are interested in an approach using small molecules to target the minor groove to control expression by an allosteric mechanism. In an effort to broaden sequence recognition of DNA-targeted-small-molecules to include both A·T and G·C base pairs, we recently discovered that the heterocyclic diamidine, DB2277, forms a strong monomer complex with a DNA sequence containing 5΄-AAAGTTT-3΄. Competition mass spectrometry and surface plasmon resonance identified new monomer complexes, as well as unexpected binding of two DB2277 with certain sequences. Inherent microstructural differences within the experimental DNAs were identified through computational analyses to understand the molecular basis for recognition. These findings emphasize the critical nature of the DNA minor groove microstructure for sequence-specific recognition and offer new avenues to design synthetic small molecules for effective regulation of gene-expression.
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Affiliation(s)
- Sarah Laughlin-Toth
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - E Kathleen Carter
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Ivaylo Ivanov
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - W David Wilson
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
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22
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Arif R, Zaradzki M, Remes A, Seppelt P, Kunze R, Schröder H, Schwill S, Ensminger SM, Robinson PN, Karck M, Müller OJ, Hecker M, Wagner AH, Kallenbach K. AP-1 Oligodeoxynucleotides Reduce Aortic Elastolysis in a Murine Model of Marfan Syndrome. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 9:69-79. [PMID: 29246325 PMCID: PMC5608502 DOI: 10.1016/j.omtn.2017.08.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 11/28/2022]
Abstract
Marfan syndrome is characterized by high expression of matrix metalloproteinases (MMPs) in aortic smooth muscle cells (AoSMCs) associated with medial elastolysis and aortic root aneurysm. We aimed to reduce aortic elastolysis through decrease of MMP expression with decoy oligodeoxynucleotides (dODNs) neutralizing the transcription factor activating factor-1 (AP-1). AP-1 abundance in nuclear extracts as well as MMP-2 and MMP-9 expression were significantly increased in isolated mAoSMC of mgR/mgR Marfan mice compared to wild-type cells. Exposure to AP-1 neutralizing dODNs resulted in a significant reduction of basal and interleukin-1β-stimulated MMP expression and activity in mAoSMCs. Moreover, increased migration and formation of superoxide radical anions was substantially decreased in mAoSMCs by AP-1 dODN treatment. Aortic grafts from donor Marfan mice were treated with AP-1- dODN ex vivo and implanted as infrarenal aortic interposition grafts in mgR/mgR mice. Pretreatment of aortic grafts with AP-1 dODN led to reduced elastolysis, macrophage infiltration, and MMP activity. Permeability of the endothelial monolayer was increased for dODN in mgR/mgR aortae with observed loss of tight junction proteins ZO-1 and occludin, enabling dODN to reach the tunica media. Targeting AP-1 activity offers a new potential strategy to treat the vascular phenotype associated with Marfan syndrome.
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Affiliation(s)
- Rawa Arif
- Department of Cardiac Surgery, University Hospital Heidelberg, Heidelberg, Germany.
| | - Marcin Zaradzki
- Department of Cardiac Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Anca Remes
- Institute of Physiology and Pathophysiology, Heidelberg University, Heidelberg, Germany
| | - Philipp Seppelt
- Department of Cardiac Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Reiner Kunze
- Institute of Physiology and Pathophysiology, Heidelberg University, Heidelberg, Germany
| | - Hannes Schröder
- Institute of Physiology and Pathophysiology, Heidelberg University, Heidelberg, Germany
| | - Simon Schwill
- Department of Cardiac Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Stephan M Ensminger
- Department of Cardiovascular Surgery, Heart and Cardiovascular Centre North Rhine-Westphalia, Ruhr University, Bochum, Germany
| | - Peter N Robinson
- Institute for Medical Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Karck
- Department of Cardiac Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Oliver J Müller
- Department of Internal Medicine III, University Hospital Heidelberg and DZHK (German Center for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Markus Hecker
- Institute of Physiology and Pathophysiology, Heidelberg University, Heidelberg, Germany
| | - Andreas H Wagner
- Institute of Physiology and Pathophysiology, Heidelberg University, Heidelberg, Germany
| | - Klaus Kallenbach
- Department of Cardiac Surgery, University Hospital Heidelberg, Heidelberg, Germany; INCCI HaerzZenter, Department of Cardiac Surgery, Luxembourg, Luxembourg
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Kim JY, An HJ, Kim WH, Gwon MG, Gu H, Park YY, Park KK. Anti-fibrotic Effects of Synthetic Oligodeoxynucleotide for TGF-β1 and Smad in an Animal Model of Liver Cirrhosis. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 8:250-263. [PMID: 28918026 PMCID: PMC5511593 DOI: 10.1016/j.omtn.2017.06.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/29/2017] [Accepted: 06/29/2017] [Indexed: 12/12/2022]
Abstract
Liver fibrosis is characterized by changes in tissue architecture and extracellular matrix composition. Liver fibrosis affects not only hepatocytes but also the non-parenchymal cells such as hepatic stellate cells (HSCs), which are essential for maintaining an intact liver structure and function. Transforming growth factor β1 (TGF-β1) is a multifunctional cytokine that induces liver fibrosis through activation of Smad signaling pathways. To improve a new therapeutic approach, synthetic TGF-β1/Smad oligodeoxynucleotide (ODN) was used to suppress both TGF-β1 expression and Smad transcription factor using a combination of antisense ODN and decoy ODN. The aims of this study are to investigate the anti-fibrotic effects of TGF-β1/Smad ODN on simultaneous suppressions of both Smad transcription factor and TGF-β1 mRNA expression in the hepatic fibrosis model in vitro and in vivo. Synthetic TGF-β1/Smad ODN effectively inhibits Smad binding activity and TGF-β1 expression. TGF-β1/Smad ODN attenuated the epithelial mesenchymal transition (EMT) and activation of HSCs in TGF-β1-induced AML12 and HSC-T6 cells. TGF-β1/Smad ODN prevented the fibrogenesis and deposition of collagen in CCl4-treated mouse model. Synthetic TGF-β1/Smad ODN demonstrates anti-fibrotic effects that are mediated by the suppression of fibrogenic protein and inflammatory cytokines. Therefore, synthetic TGF-β1/Smad ODN has substantial therapeutic feasibility for the treatment of liver fibrotic diseases.
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Affiliation(s)
- Jung-Yeon Kim
- Department of Pathology, College of Medicine, Catholic University of Daegu, Daegu 42472, Republic of Korea
| | - Hyun-Jin An
- Department of Pathology, College of Medicine, Catholic University of Daegu, Daegu 42472, Republic of Korea
| | - Woon-Hae Kim
- Department of Pathology, College of Medicine, Catholic University of Daegu, Daegu 42472, Republic of Korea
| | - Mi-Gyeong Gwon
- Department of Pathology, College of Medicine, Catholic University of Daegu, Daegu 42472, Republic of Korea
| | - Hyemin Gu
- Department of Pathology, College of Medicine, Catholic University of Daegu, Daegu 42472, Republic of Korea
| | - Yoon-Yub Park
- Department of Physiology, College of Medicine, Catholic University of Daegu, Daegu 42472, Republic of Korea
| | - Kwan-Kyu Park
- Department of Pathology, College of Medicine, Catholic University of Daegu, Daegu 42472, Republic of Korea.
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24
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Hackl EV, Khutoryanskiy VV, Ermolina I. Hydrogels based on copolymers of 2-hydroxyethylmethacrylate and 2-hydroxyethylacrylate as a delivery system for proteins: Interactions with lysozyme. J Appl Polym Sci 2017. [DOI: 10.1002/app.44768] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ellen V. Hackl
- Leicester School of Pharmacy; De Montfort University; Leicester United Kingdom
| | | | - Irina Ermolina
- Leicester School of Pharmacy; De Montfort University; Leicester United Kingdom
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25
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Antimicrobial Nanoplexes meet Model Bacterial Membranes: the key role of Cardiolipin. Sci Rep 2017; 7:41242. [PMID: 28120892 PMCID: PMC5264643 DOI: 10.1038/srep41242] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 11/28/2016] [Indexed: 02/05/2023] Open
Abstract
Antimicrobial resistance to traditional antibiotics is a crucial challenge of medical research. Oligonucleotide therapeutics, such as antisense or Transcription Factor Decoys (TFDs), have the potential to circumvent current resistance mechanisms by acting on novel targets. However, their full translation into clinical application requires efficient delivery strategies and fundamental comprehension of their interaction with target bacterial cells. To address these points, we employed a novel cationic bolaamphiphile that binds TFDs with high affinity to form self-assembled complexes (nanoplexes). Confocal microscopy revealed that nanoplexes efficiently transfect bacterial cells, consistently with biological efficacy on animal models. To understand the factors affecting the delivery process, liposomes with varying compositions, taken as model synthetic bilayers, were challenged with nanoplexes and investigated with Scattering and Fluorescence techniques. Thanks to the combination of results on bacteria and synthetic membrane models we demonstrate for the first time that the prokaryotic-enriched anionic lipid Cardiolipin (CL) plays a key-role in the TFDs delivery to bacteria. Moreover, we can hypothesize an overall TFD delivery mechanism, where bacterial membrane reorganization with permeability increase and release of the TFD from the nanoplexes are the main factors. These results will be of great benefit to boost the development of oligonucleotides-based antimicrobials of superior efficacy.
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26
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Bharadwaj U, Kasembeli MM, Tweardy DJ. STAT3 Inhibitors in Cancer: A Comprehensive Update. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-3-319-42949-6_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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27
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Nguyen D, Zandarashvili L, White MA, Iwahara J. Stereospecific Effects of Oxygen-to-Sulfur Substitution in DNA Phosphate on Ion Pair Dynamics and Protein-DNA Affinity. Chembiochem 2016; 17:1636-42. [PMID: 27271797 DOI: 10.1002/cbic.201600265] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Indexed: 02/05/2023]
Abstract
Oxygen-to-sulfur substitutions in DNA phosphate often enhance affinity for DNA-binding proteins. Our previous studies have suggested that this effect of sulfur substitution of both OP1 and OP2 atoms is due to an entropic gain associated with enhanced ion pair dynamics. In this work, we studied stereospecific effects of single sulfur substitution of either the OP1 or OP2 atom in DNA phosphate at the Lys57 interaction site of the Antennapedia homeodomain-DNA complex. Using crystallography, we obtained structural information on the RP and SP diastereomers of the phosphoromonothioate and their interaction with Lys57. Using fluorescence-based assays, we found significant affinity enhancement upon sulfur substitution of the OP2 atom. Using NMR spectroscopy, we found significant mobilization of the Lys57 side-chain NH3 (+) group upon sulfur substitution of the OP2 atom. These data provide further mechanistic insights into the affinity enhancement by oxygen-to-sulfur substitution in DNA phosphate.
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Affiliation(s)
- Dan Nguyen
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Medical Research Building 5.104C, Galveston, TX, 77555-1068, USA
| | - Levani Zandarashvili
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Medical Research Building 5.104C, Galveston, TX, 77555-1068, USA
| | - Mark A White
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Medical Research Building 5.104C, Galveston, TX, 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Boulevard, Medical Research Building 5.104C, Galveston, TX, 77555-1068, USA.
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28
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Mamusa M, Resta C, Barbero F, Carta D, Codoni D, Hatzixanthis K, McArthur M, Berti D. Interaction between a cationic bolaamphiphile and DNA: The route towards nanovectors for oligonucleotide antimicrobials. Colloids Surf B Biointerfaces 2016; 143:139-147. [PMID: 26998876 DOI: 10.1016/j.colsurfb.2016.03.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 12/12/2022]
Abstract
Bacterial resistance to antimicrobials is a global threat that requires development of innovative therapeutics that circumvent its onset. The use of Transcription Factor Decoys (TFDs), DNA fragments that act by blocking essential transcription factors in microbes, represents a very promising approach. TFDs require appropriate carriers to protect them from degradation in biological fluids and transfect them through the bacterial cell wall into the cytoplasm, their site of action. Here we report on a bolaform cationic surfactant, [12-bis-THA]Cl2, with proven transfection activity in vivo. By studying the physical-chemical properties of its aqueous solutions with light scattering, cryo-TEM, ζ-potential, absorption and fluorescence spectroscopies, we prove that the bolaamphiphiles associate into transient vesicles which convert into one-dimensional elongated structures over time. These surfactant assemblies complex TFDs with extremely high efficiency, if compared to common cationic amphiphiles. At Z+/-=11, the nanoplexes are stable and have a size of 120nm, and they form independently of the original morphology of the [12-bis-THA]Cl2 aggregate. DNA is compacted in the nanoplexes, as shown through CD spectroscopy and fluorescence, but is readily released in its native form if sodium taurocholate is added.
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Affiliation(s)
- Marianna Mamusa
- Department of Chemistry "Ugo Schiff" and CSGI, University of Florence. Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Claudio Resta
- Department of Chemistry "Ugo Schiff" and CSGI, University of Florence. Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | | | - Davide Carta
- Procarta Biosystems Ltd. Innovation Centre, Norwich Research Park, Norwich NR4 7GJ, UK; Biological Chemistry Department, John Innes Centre, Norwich NR4 7UH, UK
| | - Doroty Codoni
- Procarta Biosystems Ltd. Innovation Centre, Norwich Research Park, Norwich NR4 7GJ, UK; Kuecept Ltd. 16/17 Station Close, Potters Bar EN6 1TL, UK
| | - Kostas Hatzixanthis
- Procarta Biosystems Ltd. Innovation Centre, Norwich Research Park, Norwich NR4 7GJ, UK; School of Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK
| | - Michael McArthur
- Procarta Biosystems Ltd. Innovation Centre, Norwich Research Park, Norwich NR4 7GJ, UK; Norwich Medical School, University of East Anglia, Norwich NR4 7UQ, UK
| | - Debora Berti
- Department of Chemistry "Ugo Schiff" and CSGI, University of Florence. Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy.
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29
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Klaus M, Prokoph N, Girbig M, Wang X, Huang YH, Srivastava Y, Hou L, Narasimhan K, Kolatkar PR, Francois M, Jauch R. Structure and decoy-mediated inhibition of the SOX18/Prox1-DNA interaction. Nucleic Acids Res 2016; 44:3922-35. [PMID: 26939885 PMCID: PMC4856986 DOI: 10.1093/nar/gkw130] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 02/22/2016] [Indexed: 12/25/2022] Open
Abstract
The transcription factor (TF) SOX18 drives lymphatic vessel development in both embryogenesis and tumour-induced neo-lymphangiogenesis. Genetic disruption of Sox18 in a mouse model protects from tumour metastasis and established the SOX18 protein as a molecular target. Here, we report the crystal structure of the SOX18 DNA binding high-mobility group (HMG) box bound to a DNA element regulating Prox1 transcription. The crystals diffracted to 1.75Å presenting the highest resolution structure of a SOX/DNA complex presently available revealing water structure, structural adjustments at the DNA contact interface and non-canonical conformations of the DNA backbone. To explore alternatives to challenging small molecule approaches for targeting the DNA-binding activity of SOX18, we designed a set of five decoys based on modified Prox1-DNA. Four decoys potently inhibited DNA binding of SOX18 in vitro and did not interact with non-SOX TFs. Serum stability, nuclease resistance and thermal denaturation assays demonstrated that a decoy circularized with a hexaethylene glycol linker and terminal phosphorothioate modifications is most stable. This SOX decoy also interfered with the expression of a luciferase reporter under control of a SOX18-dependent VCAM1 promoter in COS7 cells. Collectively, we propose SOX decoys as potential strategy for inhibiting SOX18 activity to disrupt tumour-induced neo-lymphangiogenesis.
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Affiliation(s)
- Miriam Klaus
- Genome Regulation Laboratory, Drug Discovery Pipeline, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China Institut für Chemie und Biochemie, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Nina Prokoph
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, 60 Biopolis Street, 138672 Singapore
| | - Mathias Girbig
- Genome Regulation Laboratory, Drug Discovery Pipeline, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China Institut für Chemie und Biochemie, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Xuecong Wang
- Genome Regulation Laboratory, Drug Discovery Pipeline, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yong-Heng Huang
- Genome Regulation Laboratory, Drug Discovery Pipeline, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yogesh Srivastava
- Genome Regulation Laboratory, Drug Discovery Pipeline, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Linlin Hou
- Genome Regulation Laboratory, Drug Discovery Pipeline, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Kamesh Narasimhan
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, 60 Biopolis Street, 138672 Singapore
| | - Prasanna R Kolatkar
- Qatar Biomedical Research Institute, Hamad Bin Khalifa Unversity, QatarFoundation, PO Box 5825, Doha, Qatar
| | - Mathias Francois
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Ralf Jauch
- Genome Regulation Laboratory, Drug Discovery Pipeline, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
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30
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Roopmani P, Sethuraman S, Satheesh S, Maheswari Krishnan U. The metamorphosis of vascular stents: passive structures to smart devices. RSC Adv 2016. [DOI: 10.1039/c5ra19109b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The role of nanotechnology enabled techniques in the evolution of vascular stents.
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Affiliation(s)
- Purandhi Roopmani
- Centre for Nanotechnology and Advanced Biomaterials (CeNTAB)
- School of Chemical and Biotechnology
- SASTRA University
- Thanjavur-613 401
- India
| | - Swaminathan Sethuraman
- Centre for Nanotechnology and Advanced Biomaterials (CeNTAB)
- School of Chemical and Biotechnology
- SASTRA University
- Thanjavur-613 401
- India
| | - Santhosh Satheesh
- Jawaharlal Institute of Post Graduate Medical Education and Research (JIPMER)
- Department of Cardiology
- Pondicherry-605 006
- India
| | - Uma Maheswari Krishnan
- Centre for Nanotechnology and Advanced Biomaterials (CeNTAB)
- School of Chemical and Biotechnology
- SASTRA University
- Thanjavur-613 401
- India
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31
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Affiliation(s)
- Andrei L Gartel
- a Department of Medicine ; University of Illinois at Chicago ; Chicago , IL USA
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32
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Mondragón E, Maher LJ. Anti-Transcription Factor RNA Aptamers as Potential Therapeutics. Nucleic Acid Ther 2015; 26:29-43. [PMID: 26509637 PMCID: PMC4753637 DOI: 10.1089/nat.2015.0566] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Transcription factors (TFs) are DNA-binding proteins that play critical roles in regulating gene expression. These proteins control all major cellular processes, including growth, development, and homeostasis. Because of their pivotal role, cells depend on proper TF function. It is, therefore, not surprising that TF deregulation is linked to disease. The therapeutic drug targeting of TFs has been proposed as a frontier in medicine. RNA aptamers make interesting candidates for TF modulation because of their unique characteristics. The products of in vitro selection, aptamers are short nucleic acids (DNA or RNA) that bind their targets with high affinity and specificity. Aptamers can be expressed on demand from transgenes and are intrinsically amenable to recognition by nucleic acid-binding proteins such as TFs. In this study, we review several natural prokaryotic and eukaryotic examples of RNAs that modulate the activity of TFs. These examples include 5S RNA, 6S RNA, 7SK, hepatitis delta virus-RNA (HDV-RNA), neuron restrictive silencer element (NRSE)-RNA, growth arrest-specific 5 (Gas5), steroid receptor RNA activator (SRA), trophoblast STAT utron (TSU), the 3' untranslated region of caudal mRNA, and heat shock RNA-1 (HSR1). We then review examples of unnatural RNA aptamers selected to inhibit TFs nuclear factor-kappaB (NF-κB), TATA-binding protein (TBP), heat shock factor 1 (HSF1), and runt-related transcription factor 1 (RUNX1). The field of RNA aptamers for DNA-binding proteins continues to show promise.
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Affiliation(s)
- Estefanía Mondragón
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine , Rochester, Minnesota
| | - Louis James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine , Rochester, Minnesota
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33
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Youn SW, Park KK. Small-nucleic-acid-based therapeutic strategy targeting the transcription factors regulating the vascular inflammation, remodeling and fibrosis in atherosclerosis. Int J Mol Sci 2015; 16:11804-33. [PMID: 26006249 PMCID: PMC4463731 DOI: 10.3390/ijms160511804] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/15/2015] [Accepted: 05/18/2015] [Indexed: 12/20/2022] Open
Abstract
Atherosclerosis arises when injury to the arterial wall induces an inflammatory cascade that is sustained by a complex network of cytokines, together with accumulation of lipids and fibrous material. Inflammatory cascades involve leukocyte adherence and chemotaxis, which are coordinated by the local secretion of adhesion molecules, chemotactic factors, and cytokines. Transcription factors are critical to the integration of the various steps of the cascade response to mediators of vascular injury, and are induced in a stimulus-dependent and cell-type-specific manner. Several small-nucleic-acid-based therapeutic strategies have recently been developed to target transcription factors: antisense oligodeoxynucleotides, RNA interference, microRNA, and decoy oligodeoxynucleotides. The aim of this review was to provide an overview of these particular targeted therapeutic strategies, toward regulation of the vascular inflammation, remodeling and fibrosis associated with atherosclerosis.
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Affiliation(s)
- Sung Won Youn
- Department of Radiology, Catholic University of Daegu Medical Center, School of Medicine, Catholic University of Daegu, Daegu 705-718, Korea.
| | - Kwan-Kyu Park
- Department of Pathology, Catholic University of Daegu Medical Center, School of Medicine, Catholic University of Daegu, Daegu 705-718, Korea.
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34
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Rad SMAH, Langroudi L, Kouhkan F, Yazdani L, Koupaee AN, Asgharpour S, Shojaei Z, Bamdad T, Arefian E. Transcription factor decoy: a pre-transcriptional approach for gene downregulation purpose in cancer. Tumour Biol 2015; 36:4871-81. [PMID: 25835969 DOI: 10.1007/s13277-015-3344-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/15/2015] [Indexed: 12/13/2022] Open
Abstract
Gene therapy as a therapeutic approach has been the dream for many scientists around the globe. Many strategies have been proposed and applied for this purpose, yet the void for a functional safe method is still apparent. Since most of the diseases are caused by undesirable upregulation (oncogenes) or downregulation (tumor suppressor genes) of genes, major gene therapy's techniques affect gene expression. Most of the methods are used in post-transcriptional level such as RNA inhibitory (RNAi) and splice-switching oligonucleotides (SSOs). RNAi blocks messenger RNA (mRNA) translation by mRNA degradation or interruption between attachments of mRNA with ribosomes' subunits. However, one of the novel methods is the usage of transcription factor targeted decoys. DNA decoys are the new generation of functional gene downregulatory oligonucleotides which compete with specific binding sites of transcription factors. Considering the exponential growth of this technique in both in vitro and in vivo studies, in this paper, we aim to line out the description, design, and application of decoys in research and therapy.
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35
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Xiao X, Gang Y, Wang H, Wang J, Zhao L, Xu L, Liu Z. Double-stranded RNA transcribed from vector-based oligodeoxynucleotide acts as transcription factor decoy. Biochem Biophys Res Commun 2014; 457:221-6. [PMID: 25550185 DOI: 10.1016/j.bbrc.2014.12.091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/20/2014] [Indexed: 12/24/2022]
Abstract
In this study, we designed a short hairpin RNA vector-based oligodeoxynucleotide (VB-ODN) carrying transcription factor (TF) consensus sequence which could function as a decoy to block TF activity. Specifically, VB-ODN for Nuclear factor-κB (NF-κB) could inhibit cell viability and decrease downstream gene expression in HEK293 cells without affecting expression of NF-κB itself. The specific binding between VB-ODN produced double-stranded RNA and NF-κB was evidenced by electrophoretic mobility shift assay. Moreover, similar VB-ODNs designed for three other TFs also inhibit their downstream gene expression but not that of themselves. Our study provides a new design of decoy for blocking TF activity.
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Affiliation(s)
- Xiao Xiao
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, PR China
| | - Yi Gang
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, PR China; Department of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, Shaanxi Province, PR China
| | - Honghong Wang
- No. 518 Hospital of Chinese People's Liberation Army, Xi'an 710043, Shaanxi Province, PR China
| | - Jiayin Wang
- The Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Lina Zhao
- Department of Radiation Oncology, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, PR China
| | - Li Xu
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, PR China.
| | - Zhiguo Liu
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, PR China.
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Rad SMAH, Bamdad T, Sadeghizadeh M, Arefian E, Lotfinia M, Ghanipour M. Transcription factor decoy against stem cells master regulators, Nanog and Oct-4: a possible approach for differentiation therapy. Tumour Biol 2014; 36:2621-9. [PMID: 25464862 DOI: 10.1007/s13277-014-2884-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 11/21/2014] [Indexed: 01/31/2023] Open
Abstract
Transcription factor decoys (TFDs) are exogenous oligonucleotides which can compete by cis-elements in promoters or enhancers for binding to TFs and downregulating gene expression in a specific manner. It is believed that tumor mass originates from cancer stem cells (CSCs) which the same with embryonic stem cells (ESCs) have the properties of both pluripotency and self-renewal (stemness). Many transcription factors such as Nanog, Oct-4, Sox2, Klf4, and Sall4 act as master regulators in the maintenance of stemness in both cell types. Differentiation therapy is based on this theory that by differentiation of CSCs, tumor mass can be eliminated with common cancer therapy methods. To our knowledge, the present study is the first report of a TFD approach against master regulator of stemness, Nanog, Oct-4, and Klf4, for downregulation purposes in P19 embryonic carcinoma stem cell. Different simple and complex decoys against Nanog, OCT-4, Sox2, and Klf4 were designed and used for this purpose. The results showed that the applied decoys especially Nanog-specific decoy decreased the expression of downstream genes.
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Kim KH, Park KK. Small RNA- and DNA-based gene therapy for the treatment of liver cirrhosis, where we are? World J Gastroenterol 2014; 20:14696-14705. [PMID: 25356032 PMCID: PMC4209535 DOI: 10.3748/wjg.v20.i40.14696] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 04/03/2014] [Accepted: 06/05/2014] [Indexed: 02/06/2023] Open
Abstract
Chronic liver diseases with different aetiologies rely on the chronic activation of liver injuries which result in a fibrogenesis progression to the end stage of cirrhosis and liver failure. Based on the underlying cellular and molecular mechanisms of a liver fibrosis, there has been proposed several kinds of approaches for the treatment of liver fibrosis. Recently, liver gene therapy has been developed as an alternative way to liver transplantation, which is the only effective therapy for chronic liver diseases. The activation of hepatic stellate cells, a subsequent release of inflammatory cytokines and an accumulation of extracellular matrix during the liver fibrogenesis are the major obstacles to the treatment of liver fibrosis. Several targeted strategies have been developed, such as antisense oligodeoxynucleotides, RNA interference and decoy oligodeoxynucleotides to overcome this barriers. With this report an overview will be provided of targeted strategies for the treatment of liver cirrhosis, and particularly, of the targeted gene therapy using short RNA and DNA segments.
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Higuchi Y, Furukawa K, Miyazawa T, Minakawa N. Development of a new dumbbell-shaped decoy DNA using a combination of the unnatural base pair ImO(N):NaN(O) and a CuAAC reaction. Bioconjug Chem 2014; 25:1360-9. [PMID: 24965879 DOI: 10.1021/bc500225r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We describe the synthesis and potential application of a new dumbbell-shaped decoy DNA prepared using a combination of the base pair ImO(N):NaN(O) and a copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction. The CuAAC reaction between the azido group on the 5'-end of oligodeoxynucleotide (ODN) and the ethynyl group on the NaN(O) base of the opposite strand did not proceed, whereas that between the azido group and the flexible hexynyl group on the NaN(O) base of the opposite strand proceeded smoothly to give a new dumbbell-shaped double-stranded ODN (dsODN). The resulting dsODN had extremely high thermal stability and exhibited exonuclease resistance. In addition, the terminal modification did not affect its helical structure, and thus, the dumbbell-shaped dsODN displayed promising in vitro activity in a competition assay with the NF-kB p50 transcription factor homodimer.
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Affiliation(s)
- Yosuke Higuchi
- Graduate School of Pharmaceutical Sciences, The University of Tokushima , Shomachi 1-78-1, Tokushima 770-8505, Japan
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Abstract
Silencing of abnormally activated genes can be accomplished in a highly specific manner using nucleic acid based approaches. The focus of this review includes the different nucleic acid based inhibition strategies such as antisense oligodeoxynucleotides, small interfering RNA (siRNA), dominant-negative constructs, G-quartet oligonucleotides and decoy oligonucleotides, their mechanism of action and the effectiveness of these approaches to targeting the STAT (signal transducer and activator of transcription) proteins in cancer. Among the STAT proteins, especially STAT3, followed by STAT5, are the most frequently activated oncogenic STATs, which have emerged as plausible therapeutic cancer targets. Both STAT3 and STAT5 have been shown to regulate numerous oncogenic signaling pathways including proliferation, survival, angiogenesis and migration/invasion.
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Affiliation(s)
- Malabika Sen
- Department of Otolaryngology; University of Pittsburgh School of Medicine; Pittsburgh, PA USA
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Metelev VG, Kubareva EA, Oretskaya TS. Regulation of activity of transcription factor NF-κB by synthetic oligonucleotides. BIOCHEMISTRY (MOSCOW) 2014; 78:867-78. [PMID: 24228874 DOI: 10.1134/s0006297913080026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Eukaryotic dimeric nuclear factor-κB (NF-κB) is one of the main transcription factors that activate expression of genes, products of which play the key role in development of cardiovascular pathologies, carcinogenesis, and inflammatory and viral diseases. In this review, the main attention is given to modulation of the transcription factor NF-κB activity by antisense oligonucleotides and oligonucleotide decoys. Also, current concepts about interactions between NF-κB dimers and DNA and general problems that arise in experimental use of synthetic oligonucleotides in vivo are discussed.
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Affiliation(s)
- V G Metelev
- Faculty of Chemistry, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninsky Gory 1, Moscow, 119991, Russia.
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Kasparkova J, Thibault T, Kostrhunova H, Stepankova J, Vojtiskova M, Muchova T, Midoux P, Malinge JM, Brabec V. Different affinity of nuclear factor-kappa B proteins to DNA modified by antitumor cisplatin and its clinically ineffective trans isomer. FEBS J 2014; 281:1393-1408. [PMID: 24418212 DOI: 10.1111/febs.12711] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 11/06/2013] [Accepted: 12/13/2013] [Indexed: 01/06/2023]
Abstract
Nuclear factor-kappa B (NF-кB) comprises a family of protein transcription factors that have a regulatory function in numerous cellular processes and are implicated in the cancer cell response to antineoplastic drugs, including cisplatin. We characterized the effects of DNA adducts of cisplatin and ineffective transplatin on the affinity of NF-кB proteins to their consensus DNA sequence (кB site). Although the кB site-NF-κB protein interaction was significantly perturbed by DNA adducts of cisplatin, transplatin adducts were markedly less effective both in cell-free media and in cellulo using a decoy strategy derivatized-approach. Moreover, NF-κB inhibitor JSH-23 [4-methyl-N¹-(3-phenylpropyl)benzene-1,2-diamine] augmented cisplatin cytotoxicity in ovarian cancer cells and the data showed strong synergy with JSH-23 for cisplatin. The distinctive structural features of DNA adducts of the two platinum complexes suggest a unique role for conformational distortions induced in DNA by the adducts of cisplatin with respect to inhibition of the binding of NF-кB to the platinated кB sites. Because thousands of κB sites are present in the DNA, the mechanisms underlying the antitumor efficiency of cisplatin in some tumor cells may involve downstream processes after inhibition of the binding of NF-κB to κB site(s) by DNA adducts of cisplatin, including enhanced programmed cell death in response to drug treatment.
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Affiliation(s)
- Jana Kasparkova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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Concomitant targeting of multiple key transcription factors effectively disrupts cancer stem cells enriched in side population of human pancreatic cancer cells. PLoS One 2013; 8:e73942. [PMID: 24040121 PMCID: PMC3770686 DOI: 10.1371/journal.pone.0073942] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 07/24/2013] [Indexed: 12/17/2022] Open
Abstract
Background A major challenge in the treatment of pancreatic ductal adenocarcinoma is the failure of chemotherapy, which is likely due to the presence of the cancer stem cells (CSCs). Objective To identify side population (SP) cells and characterize s-like properties in human pancreatic cancer cell lines (h-PCCLs) and to exploit the efficacy of concomitant targeting of multiple key transcription factors governing the stemness of pancreatic CSCs in suppressing CSC-like phenotypes. Methods Flow cytometry and Hoechst 33342 DNA-binding dye efflux assay were used to sort SP and non-SP (NSP) cells from three h-PCCLs: PANC-1, SW1990, and BxPc-3. The self-renewal ability, invasiveness, migration and drug resistance of SP cells were evaluated. Expression of CSC marker genes was analyzed. Tumorigenicity was assessed using a xenograft model in nude mice. Effects of a complex decoy oligonucleotide (cdODN-SCO) designed to simultaneously targeting Sox2, Oct4 and c-Myc were assessed. Results CSCs were enriched in the side proportion (SP) cells contained in the h-PCCLs and they possessed aggressive growth, invasion, migration and drug-resistance properties, compared with NSP cells. SP cells overexpressed stem cell markers CD133 and ALDH1, pluripotency maintaining factors Nanog, Sox2 and Oct4, oncogenic transcription factor c-Myc, signaling molecule Notch1, and drug resistant gene ABCG2. Moreover, SP cells consistently demonstrated significantly greater tumorigenicity than NSP cells in xenograft model of nude mice. CdODN–SOC efficiently suppressed all CSC properties and phenotypes, and minimized the tumorigenic capability of the SP cells and the resistance to chemotherapy. By comparison, the negative control failed to do so. Conclusion The findings indicate that targeting the key genes conferring the stemness of CSCs can efficiently eliminate CSC-like phenotypes, and thus may be considered a new approach for cancer therapy. Specifically, the present study establishes the combination of Sox2/Oct4/c-Myc targeting as a potential anti-pancreatic cancer agent worthy of further studies in preclinical settings.
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Kohli S, Ahuja S, Rani V. Transcription factors in heart: promising therapeutic targets in cardiac hypertrophy. Curr Cardiol Rev 2013; 7:262-71. [PMID: 22758628 PMCID: PMC3322445 DOI: 10.2174/157340311799960618] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 01/08/2012] [Accepted: 01/08/2011] [Indexed: 12/16/2022] Open
Abstract
Regulation of gene expression is central to cell growth, differentiation and diseases. Context specific and signal dependent regulation of gene expression is achieved to a large part by transcription factors. Cardiac transcription factors regulate heart development and are also involved in stress regulation of the adult heart, which may lead to cardiac hypertrophy. Hypertrophy of cardiac myocytes is an outcome of the imbalance between prohypertrophic factors and anti-hypertrophic factors. This is initially a compensatory mechanism but sustained hypertrophy may lead to heart failure. The growing knowledge of transcriptional control mechanisms is helpful in the development of novel therapies. This review summarizes the role of cardiac transcription factors in cardiac hypertrophy, emphasizing their potential as attractive therapeutic targets to prevent the onset of heart failure and sudden death as they can be converging targets for current therapy.
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Affiliation(s)
- Shrey Kohli
- Department of Biotechnology, Jaypee Institute of Information Technology University, NOIDA 210307, India
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Cao L, Xi Z. Fast thiol–maleamic methyl ester addition for facile covalent cross-linking of oligonucleotides. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.01.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Koppikar P, Bromberg J. STATe-of-the-art approach: using oligonucleotide decoys to target the "undruggable". Cancer Discov 2013; 2:670-2. [PMID: 22886660 DOI: 10.1158/2159-8290.cd-12-0310] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Sen and colleagues have shown for the first time the clinical application of an oligonucleotide decoy targeting the oncogenic transcription factor STAT3 for the treatment of head and neck tumors. Intratumoral injection of decoy effectively reduced the activity of STAT3 as evidenced by a decrease in several of its transcriptional targets. However, its low bioavailability makes them unacceptable for systemic therapy. Cyclization of the STAT3 decoy markedly increased its half-life while preserving specificity and showed significant antitumor activity upon systemic delivery in preclinical models of head and neck cancer. These findings have broad therapeutic implications for the treatment of many malignancies.
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Affiliation(s)
- Priya Koppikar
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, USA
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Kucukguven A, Khalil RA. Matrix metalloproteinases as potential targets in the venous dilation associated with varicose veins. Curr Drug Targets 2013; 14:287-324. [PMID: 23316963 PMCID: PMC3584231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 11/20/2012] [Accepted: 01/01/2012] [Indexed: 06/01/2023]
Abstract
Varicose veins (VVs) are a common venous disease of the lower extremity characterized by incompetent valves, venous reflux, and dilated and tortuous veins. If untreated, VVs could lead to venous thrombosis, thrombophlebitis and chronic venous leg ulcers. Various genetic, hormonal and environmental factors may lead to structural changes in the vein valves and make them incompetent, leading to venous reflux, increased venous pressure and vein wall dilation. Prolonged increases in venous pressure and vein wall tension are thought to increase the expression/activity of matrix metalloproteinases (MMPs). Members of the MMPs family include collagenases, gelatinases, stromelysins, matrilysins, membrane- type MMPs and others. MMPs are known to degrade various components of the extracellular matrix (ECM). MMPs may also affect the endothelium and vascular smooth muscle, causing changes in the vein relaxation and contraction mechanisms. Endothelial cell injury also triggers leukocyte infiltration, activation and inflammation, which lead to further vein wall damage. The vein wall dilation and valve dysfunction, and the MMP activation and superimposed inflammation and fibrosis would lead to progressive venous dilation and VVs formation. Surgical ablation is an effective treatment for VVs, but may be associated with high recurrence rate, and other less invasive approaches that target the cause of the disease are needed. MMP inhibitors including endogenous tissue inhibitors (TIMPs) and pharmacological inhibitors such as zinc chelators, doxycycline, batimastat and marimastat, have been used as diagnostic and therapeutic tools in cancer, autoimmune and cardiovascular disease. However, MMP inhibitors may have side effects especially on the musculoskeletal system. With the advent of new genetic and pharmacological tools, specific MMP inhibitors with fewer undesirable effects could be useful to retard the progression and prevent the recurrence of VVs.
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Affiliation(s)
- Arda Kucukguven
- Vascular Surgery Research Laboratory, Division of Vascular and Endovascular Surgery, Brigham and Women’s Hospital, and Harvard Medical School, Boston, MA 02115, USA
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Transcriptional repression of VEGF by ZNF24: mechanistic studies and vascular consequences in vivo. Blood 2012; 121:707-15. [PMID: 23212515 DOI: 10.1182/blood-2012-05-433045] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
VEGF is a key regulator of normal and pathologic angiogenesis. Although many trans-activating factors of VEGF have been described, the transcriptional repression of VEGF remains much less understood. We have previously reported the identification of a SCAN domain-containing C2H2 zinc finger protein, ZNF24, that represses the transcription of VEGF. In the present study, we identify the mechanism by which ZNF24 represses VEGF transcription. Using reporter gene and electrophoretic mobility shift assays, we identify an 11-bp fragment of the proximal VEGF promoter as the ZNF24-binding site that is essential for ZNF24-mediated repression. We demonstrate in 2 in vivo models the potent inhibitory effect of ZNF24 on the vasculature. Expression of human ZNF24 induced in vivo vascular defects consistent with those induced by VEGF knockdown using a transgenic zebrafish model. These defects could be rescued by VEGF overexpression. Overexpression of ZNF24 in human breast cancer cells also inhibited tumor angiogenesis in an in vivo tumor model. Analyses of human breast cancer tissues showed that ZNF24 and VEGF levels were inversely correlated in malignant compared with normal tissues. These data demonstrate that ZNF24 represses VEGF transcription through direct binding to an 11-bp fragment of the VEGF proximal promoter and that it functions as a negative regulator of tumor growth by inhibiting angiogenesis.
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Ma LL, O'Byrne PM. The pharmacological modulation of allergen-induced asthma. Inflammopharmacology 2012; 21:113-24. [PMID: 23096484 DOI: 10.1007/s10787-012-0155-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 10/09/2012] [Indexed: 12/16/2022]
Abstract
Aeroallergens are the most common triggers for the development of asthma. Recent birth cohort studies have identified viral infections occurring against a background of aeroallergen sensitization as a potent risk factor for initiation of asthma. Viral infection enhances immunopathogenic potential of pre-existing inhalant allergy via modulating airway mucosal dendritic cells. By using an allergen inhalation challenge clinical model, studies have shown that the late asthma response (LAR) is associated with more pronounced allergen-induced airway inflammation and airway hyperresponsiveness. The degree of airway eosinophilia, regulated by bone marrow progenitor cells and interleukin-5 level, correlates with the magnitude of the LAR and the increase in hyperresponsiveness. Both myeloid and plasmacytoid dendritic cell subsets have been involved in the pathogenesis of allergen-induced LAR. Myeloid dendritic cells are responsible for the allergen presentation and induction of inflammation and plasmacytoid dendritic cells play a role in the resolution of allergen-induced inflammation. A variety of potential new classes of asthma medication has also been evaluated with the allergen inhalation challenge in mild asthmatic subjects. Examples are TPI ASM8, an inhaled anti-sense oligonucleotide drug product, which attenuated both early and LARs via inhibition of the target gene mRNA of chemokine receptor 3, and the common β chain of interleukin-3, interleukin-5 and granulocyte-macrophage colony-stimulating factor receptor. Anti-human antibody interleukin-13 (IM-638) significantly attenuated both early and late allergen-induced asthma response. Pitrakinra, which targets both interleukin-4 and interleukin-13, substantially diminishes allergen-induced airway responses. Allergen-induced airway responses are a valuable way to evaluate the activity of possible new therapies in asthmatic airways.
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Affiliation(s)
- L L Ma
- Firestone Institute of Respiratory Health, St. Joseph's Healthcare, Department of Medicine, McMaster University, Hamilton, ON, Canada
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Lampronti I, Khan MTH, Borgatti M, Bianchi N, Gambari R. Inhibitory Effects of Bangladeshi Medicinal Plant Extracts on Interactions between Transcription Factors and Target DNA Sequences. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2012; 5:303-12. [PMID: 18830455 PMCID: PMC2529391 DOI: 10.1093/ecam/nem042] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2006] [Accepted: 03/14/2007] [Indexed: 01/04/2023]
Abstract
Several transcription factors (TFs) play crucial roles in governing the expression of different genes involved in the immune response, embryo or cell lineage development, cell apoptosis, cell cycle progression, oncogenesis, repair and fibrosis processes and inflammation. As far as inflammation, TFs playing pivotal roles are nuclear factor kappa B (NF-kB), activator protein (AP-1), signal transducer and activator of transcription (STATs), cAMP response element binding protein (CREB) and GATA-1 factors. All these TFs regulate the expression of pro-inflammatory cytokines and are involved in the pathogenesis of a number of human disorders, particularly those with an inflammatory component. Since several medicinal plants can be employed to produce extracts exhibiting biological effects and because alteration of gene transcription represents a very interesting approach to control the expression of selected genes, this study sought to verify the ability of several extracts derived from Bangladeshi medicinal plants in interfering with molecular interactions between different TFs and specific DNA sequences. We first analyzed the antiproliferative activity of 19 medicinal plants on different human cell lines, including erythroleukemia K562, B lymphoid Raji and T lymphoid Jurkat cell lines. Secondly, we employed the electrophoretic mobility shift assay as a suitable technique for a fast screening of plant extracts altering the binding between NF-kB, AP-1, GATA-1, STAT-3, CREB and the relative target DNA elements.
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Affiliation(s)
- Ilaria Lampronti
- ER-GenTech, Department of Biochemistry and Molecular Biology, University of Ferrara, Italy, University of Science and Technology of Chittagong, Bangladesh, Laboratory for the Development of Pharmacologic and Pharmacogenomic Therapy of Thalassemia, Biothecnology Center and Center of Excellence on Inflammation, University of Ferrara, Italy
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50
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Abstract
The promise of short RNA or DNA segments such as siRNAs, antisense oligonucleotides, and transcription factor decoys to treat disease has prompted nearly 40 clinical trials for RNA interference (RNAi)-based therapeutics and more than 100 clinical trials for antisense oligonucleotide-based technologies; in fact, there are promising in vivo and preclinical studies for many hundreds of technologies. Current treatment strategies are largely injection-based, so effective oral delivery platforms for oligonucleotides may result in improved patient comfort and compliance. We analyze recently developed oral delivery methods for short RNA and DNA segments.
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