1
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Hall J, Zhang Z, Bhattacharya S, Wang D, Alcantara M, Liang Y, Swiderski P, Forman S, Kwak L, Vaidehi N, Kortylewski M. Oligo-PROTAC strategy for cell-selective and targeted degradation of activated STAT3. Mol Ther Nucleic Acids 2024; 35:102137. [PMID: 38384444 PMCID: PMC10879796 DOI: 10.1016/j.omtn.2024.102137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024]
Abstract
Decoy oligodeoxynucleotides (ODNs) allow targeting undruggable transcription factors, such as STAT3, but their limited potency and lack of delivery methods hampered translation. To overcome these challenges, we conjugated a STAT3-specific decoy to thalidomide, a ligand to cereblon in E3 ubiquitin ligase complex, to generate a proteolysis-targeting chimera (STAT3DPROTAC). STAT3DPROTAC downregulated STAT3 in target cells, but not STAT1 or STAT5. Computational modeling of the STAT3DPROTAC ternary complex predicted two surface lysines, K601 and K626, in STAT3 as potential ubiquitination sites. Accordingly, K601/K626 point mutations in STAT3, as well as proteasome inhibition or cereblon deletion, alleviated STAT3DPROTAC effect. Next, we conjugated STAT3DPROTAC to a CpG oligonucleotide targeting Toll-like receptor 9 (TLR9) to generate myeloid/B cell-selective C-STAT3DPROTAC. Naked C-STAT3DPROTAC was spontaneously internalized by TLR9+ myeloid cells, B cells, and human and mouse lymphoma cells but not by T cells. C-STAT3DPROTAC effectively decreased STAT3 protein levels and also STAT3-regulated target genes critical for lymphoma cell proliferation and/or survival (BCL2L1, CCND2, and MYC). Finally, local C-STAT3DPROTAC administration to human Ly3 lymphoma-bearing mice triggered tumor regression, while control C-STAT3D and C-SCR treatments had limited effects. Our results underscore the feasibility of using a PROTAC strategy for cell-selective, decoy oligonucleotide-based STAT3 targeting of and potentially other tumorigenic transcription factors for cancer therapy.
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Affiliation(s)
- Jeremy Hall
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Zhuoran Zhang
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Supriyo Bhattacharya
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Dongfang Wang
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Marice Alcantara
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Yong Liang
- DNA/RNA Synthesis Core Facility, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Piotr Swiderski
- DNA/RNA Synthesis Core Facility, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Stephen Forman
- Department of Hematology & Hematopoietic Cell Transplantation, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Larry Kwak
- Department of Hematology & Hematopoietic Cell Transplantation, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Marcin Kortylewski
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
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2
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Mylonas KS, Peroulis M, Kapelouzou A. Transfection of Vein Grafts with Early Growth Response Factor-1 Oligodeoxynucleotide Decoy: Effects on Stem-Cell Genes and Toll-like Receptor-Mediated Inflammation. Int J Mol Sci 2023; 24:15866. [PMID: 37958848 PMCID: PMC10647335 DOI: 10.3390/ijms242115866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
The long-term patency of vein grafts is challenged by intimal hyperplasia. We sought to explore the intricate relationships between the transcription factor Egr-1, toll-like receptors (TLRs), and stem cell genes and also assessed oligodeoxynucleotide decoys (ODNs) as a strategy to prevent vein graft failures. A total of 42 New Zealand white rabbits were fed hyperlipidemic chow and classified into three groups. A double-stranded Egr-1 ODN was synthesized and infused in vein grafts prior to anastomosis with the common carotid artery. All vein grafts were retrieved at the conclusion of the predefined experimental period. Real-time quantitative polymerase chain reaction was performed to estimate expression patterns for several genes of interest. MYD88, TLR2-4, TLR8, NF-kB, TNF-α, IFNβ, and IFNγ; chemokines CCL4, CCL20, CCR2; numerous interleukins; and stem cell genes KFL4, NANOG, HOXA5, and HIF1α were universally downregulated in the ODN arm compared with the controls. By understanding these multifaceted interactions, our study offers actionable insights that may pave the way for innovative interventions in vascular reconstructions.
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Affiliation(s)
| | - Michail Peroulis
- Department of Surgery, Vascular Surgery Unit, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Alkistis Kapelouzou
- Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation Academy of Athens, 11527 Athens, Greece;
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3
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Renzi F, Seamann A, Ganguly K, Pandey K, Byrareddy SN, Batra S, Kumar S, Ghersi D. Engineering an ACE2-Derived Fragment as a Decoy for Novel SARS-CoV-2 Virus. ACS Pharmacol Transl Sci 2023; 6:857-867. [PMID: 37325447 PMCID: PMC10262318 DOI: 10.1021/acsptsci.2c00180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Indexed: 06/17/2023]
Abstract
Entry inhibitors are an important resource in the response against emerging pathogens like the novel SARS-CoV-2, which enters human cells via interaction between the surface spike glycoprotein and the cellular membrane receptor angiotensin-converting enzyme 2 (ACE2). Using a combination of comparative structural analyses of the binding surface of the spike to ACE2, docking experiments, and molecular dynamics simulations, we identified a stable fragment of ACE2 that binds to the spike, is soluble, and is not predicted to bind to its physiological ligand angiotensin II. From this fragment we computationally designed and experimentally validated a smaller, stable peptide that disrupts ACE2-spike interaction at nanomolar concentrations, suggesting its potential use as a decoy that could interfere with viral binding by competition.
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Affiliation(s)
- Fabiana Renzi
- Department
of Physics, Università di Roma ”La
Sapienza”, 00185 Rome, Italy
| | - Austin Seamann
- School
of Interdisciplinary Informatics, University
of Nebraska at Omaha, Omaha, Nebraska 68182, USA
| | - Koelina Ganguly
- Department
of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Kabita Pandey
- Department
of Pharmacology & Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Siddappa N. Byrareddy
- Department
of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
- Department
of Pharmacology & Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Surinder Batra
- Department
of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Sushil Kumar
- Department
of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Dario Ghersi
- School
of Interdisciplinary Informatics, University
of Nebraska at Omaha, Omaha, Nebraska 68182, USA
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4
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Greene LA, Zhou Q, Siegelin MD, Angelastro JM. Targeting Transcription Factors ATF5, CEBPB and CEBPD with Cell-Penetrating Peptides to Treat Brain and Other Cancers. Cells 2023; 12. [PMID: 36831248 DOI: 10.3390/cells12040581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Developing novel therapeutics often follows three steps: target identification, design of strategies to suppress target activity and drug development to implement the strategies. In this review, we recount the evidence identifying the basic leucine zipper transcription factors ATF5, CEBPB, and CEBPD as targets for brain and other malignancies. We describe strategies that exploit the structures of the three factors to create inhibitory dominant-negative (DN) mutant forms that selectively suppress growth and survival of cancer cells. We then discuss and compare four peptides (CP-DN-ATF5, Dpep, Bpep and ST101) in which DN sequences are joined with cell-penetrating domains to create drugs that pass through tissue barriers and into cells. The peptide drugs show both efficacy and safety in suppressing growth and in the survival of brain and other cancers in vivo, and ST101 is currently in clinical trials for solid tumors, including GBM. We further consider known mechanisms by which the peptides act and how these have been exploited in rationally designed combination therapies. We additionally discuss lacunae in our knowledge about the peptides that merit further research. Finally, we suggest both short- and long-term directions for creating new generations of drugs targeting ATF5, CEBPB, CEBPD, and other transcription factors for treating brain and other malignancies.
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Chintha N, Jupudi S, Palathoti N, Bharathi J J, Justin A. In-silico docking and molecular dynamic introspective study of multiple targets of AChE with Rivastigmine and NMDA receptors with Riluzole for Alzheimer's disease. J Biomol Struct Dyn 2023; 41:12620-12631. [PMID: 36644856 DOI: 10.1080/07391102.2023.2167119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023]
Abstract
The present study was initiated with PDB selection and validation where 11 acetylcholinesterase (AChE) and 4 N-methyl-D-aspartate receptor (NMDAR) proteins were considered for docking with Rivastigmine and Riluzole respectively. Out of the 15 proteins, selected significant binding was observed for AChE, with 5FPQ, and NMDA receptors with 5I2K. Molecular docking studies of 5FPQ/Rivastigmine complex displayed a binding score of -8.6 kcal/mol, and the predicted inhibitory concentration (Ki) was found to be 31 nM, whereas the 5I2K/Riluzole complex showed a binding score of -9.6 kcal/mol, with an inhibitory concentration (Ki) of 21 nM. Riluzole in complex with 5I2K formed predominant π-π stacking interactions with Tyr144, pi-alkyl interaction with Pro129, and conventional hydrogen bond with Phe130. In contrast, Rivastigmine in a complex with 5FPQ formed a hydrogen bond with Gln413 and pi-alkyl with Pro537. Molecular dynamics simulation study of both complexes 5FPQ/Rivastigmine and 5I2K/Riluzole exhibited stable RMSD, RMSF, Rg, and significant numbers of hydrogen bonds. From free energy landscape (FEL) analysis both complexes were observed to achieve global minima. Overall, molecular docking and MD simulation with subsequent binding free energies studies (MM-PBSA) elucidate the binding conformations and stability of these reprogrammed drugs in the AChE and NMDAR targets. From these in-silico predictions, it can be suggested that both Rivastigmine and Riluzole combination may provide better insights as a starting point combination therapy for the treatment of Alzheimer's disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Narendar Chintha
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamil Nadu, India
| | - Srikanth Jupudi
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamil Nadu, India
| | - Nagarjuna Palathoti
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamil Nadu, India
| | - Jeyaram Bharathi J
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamil Nadu, India
| | - Antony Justin
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamil Nadu, India
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Hatori T, Maeda T, Suzuki A, Takahashi K, Kato Y. SPARC is a decoy counterpart for c‑Fos and is associated with osteoblastic differentiation of bone marrow stromal cells by inhibiting adipogenesis. Mol Med Rep 2023; 27:50. [PMID: 36633137 DOI: 10.3892/mmr.2023.12937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/13/2022] [Indexed: 01/11/2023] Open
Abstract
Secreted protein acidic and rich in cysteine (SPARC), also called basement‑membrane protein 40 or osteonectin, is a matricellular protein that is abundant not only in bone tissue as a non‑collagenous protein but is also ubiquitously expressed in non‑calcified tissue. SPARC is located intracellularly and disruption of the Sparc gene has been reported to reduce bone formation and increase fat tissue; however, the mechanism by which SPARC inhibits adipogenesis remains unclear. The present study evaluated the intracellular function of SPARC in adipogenesis using the bone marrow stromal cell line ST2. When ST2 cells with low SPARC production were cloned, intrinsic activator protein‑1 (AP‑1) activity was markedly higher, mineralized nodule formation was significantly lower and lipid accumulation was significantly increased compared with in the parental ST2 cells. Forced expression of secreted SPARC with the signal peptide‑coding sequences of wild‑type Sparc or preprotrypsin in SPARC‑low ST2 cells significantly reduced AP‑1 transcription activity; however, these reductions were not observed in the absence of signal peptide sequences. Recombinant SPARC, produced using Brevibacillus brevis, specifically bound to c‑Fos but not c‑Jun and inhibited the binding of c‑Fos/c‑Jun to a TPA‑response element sequence. These data suggested that SPARC was incorporated into the cells from the extracellular spaces and serves an intracellular role as a decoy counterpart for c‑Fos, as well as being associated with osteoblastogenesis through the inhibition of adipogenesis. These findings may provide new insights into regenerative medicine.
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7
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Zhang L, Narayanan KK, Cooper L, Chan KK, Skeeters SS, Devlin CA, Aguhob A, Shirley K, Rong L, Rehman J, Malik AB, Procko E. An ACE2 decoy can be administered by inhalation and potently targets omicron variants of SARS-CoV-2. EMBO Mol Med 2022. [PMID: 36094679 DOI: 10.1101/2022.03.28.486075v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
Monoclonal antibodies targeting the SARS-CoV-2 spike (S) neutralize infection and are efficacious for the treatment of COVID-19. However, SARS-CoV-2 variants, notably sublineages of B.1.1.529/omicron, have emerged that escape antibodies in clinical use. As an alternative, soluble decoy receptors based on the host entry receptor ACE2 broadly bind and block S from SARS-CoV-2 variants and related betacoronaviruses. The high-affinity and catalytically active decoy sACE22 .v2.4-IgG1 was previously shown to be effective against SARS-CoV-2 variants when administered intravenously. Here, inhalation of aerosolized sACE22 .v2.4-IgG1 increased survival and ameliorated lung injury in K18-hACE2 mice inoculated with P.1/gamma virus. Loss of catalytic activity reduced the decoy's therapeutic efficacy, which was further confirmed by intravenous administration, supporting dual mechanisms of action: direct blocking of S and turnover of ACE2 substrates associated with lung injury and inflammation. Furthermore, sACE22 .v2.4-IgG1 tightly binds and neutralizes BA.1, BA.2, and BA.4/BA.5 omicron and protects K18-hACE2 mice inoculated with a high dose of BA.1 omicron virus. Overall, the therapeutic potential of sACE22 .v2.4-IgG1 is demonstrated by the inhalation route and broad neutralization potency persists against highly divergent SARS-CoV-2 variants.
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Affiliation(s)
- Lianghui Zhang
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular Biology, The University of Illinois College of Medicine, Chicago, IL, USA
| | | | - Laura Cooper
- Department of Microbiology and Immunology, The University of Illinois College of Medicine, Chicago, IL, USA
| | - Kui K Chan
- Cyrus Biotechnology, Inc., Seattle, WA, USA
| | | | | | | | | | - Lijun Rong
- Department of Microbiology and Immunology, The University of Illinois College of Medicine, Chicago, IL, USA
| | - Jalees Rehman
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular Biology, The University of Illinois College of Medicine, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, The University of Illinois College of Medicine, Chicago, IL, USA
| | - Asrar B Malik
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular Biology, The University of Illinois College of Medicine, Chicago, IL, USA
| | - Erik Procko
- Department of Biochemistry, University of Illinois, Urbana, IL, USA
- Cyrus Biotechnology, Inc., Seattle, WA, USA
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8
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Zhang L, Narayanan KK, Cooper L, Chan KK, Skeeters SS, Devlin CA, Aguhob A, Shirley K, Rong L, Rehman J, Malik AB, Procko E. An ACE2 decoy can be administered by inhalation and potently targets omicron variants of SARS-CoV-2. EMBO Mol Med 2022; 14:e16109. [PMID: 36094679 PMCID: PMC9539395 DOI: 10.15252/emmm.202216109] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 11/09/2022] Open
Abstract
Monoclonal antibodies targeting the SARS-CoV-2 spike (S) neutralize infection and are efficacious for the treatment of COVID-19. However, SARS-CoV-2 variants, notably sublineages of B.1.1.529/omicron, have emerged that escape antibodies in clinical use. As an alternative, soluble decoy receptors based on the host entry receptor ACE2 broadly bind and block S from SARS-CoV-2 variants and related betacoronaviruses. The high-affinity and catalytically active decoy sACE22 .v2.4-IgG1 was previously shown to be effective against SARS-CoV-2 variants when administered intravenously. Here, inhalation of aerosolized sACE22 .v2.4-IgG1 increased survival and ameliorated lung injury in K18-hACE2 mice inoculated with P.1/gamma virus. Loss of catalytic activity reduced the decoy's therapeutic efficacy, which was further confirmed by intravenous administration, supporting dual mechanisms of action: direct blocking of S and turnover of ACE2 substrates associated with lung injury and inflammation. Furthermore, sACE22 .v2.4-IgG1 tightly binds and neutralizes BA.1, BA.2, and BA.4/BA.5 omicron and protects K18-hACE2 mice inoculated with a high dose of BA.1 omicron virus. Overall, the therapeutic potential of sACE22 .v2.4-IgG1 is demonstrated by the inhalation route and broad neutralization potency persists against highly divergent SARS-CoV-2 variants.
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Affiliation(s)
- Lianghui Zhang
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular BiologyThe University of Illinois College of MedicineChicagoILUSA
- Present address:
Division of Pulmonary, Allergy and Critical Care Medicine, Department of MedicineUniversity of Pittsburgh Medical CenterPittsburghPAUSA
| | | | - Laura Cooper
- Department of Microbiology and ImmunologyThe University of Illinois College of MedicineChicagoILUSA
| | | | | | | | | | | | - Lijun Rong
- Department of Microbiology and ImmunologyThe University of Illinois College of MedicineChicagoILUSA
| | - Jalees Rehman
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular BiologyThe University of Illinois College of MedicineChicagoILUSA
- Department of Biochemistry and Molecular GeneticsThe University of Illinois College of MedicineChicagoILUSA
| | - Asrar B Malik
- Department of Pharmacology and Regenerative Medicine and the Center for Lung and Vascular BiologyThe University of Illinois College of MedicineChicagoILUSA
| | - Erik Procko
- Department of BiochemistryUniversity of IllinoisUrbanaILUSA
- Cyrus Biotechnology, Inc.SeattleWAUSA
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Park SH, Choi U, Ryu SH, Lee HB, Lee JW, Lee CR. Divergent Effects of Peptidoglycan Carboxypeptidase DacA on Intrinsic β-Lactam and Vancomycin Resistance. Microbiol Spectr 2022;:e0173422. [PMID: 35758683 DOI: 10.1128/spectrum.01734-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Vancomycin and β-lactams are clinically important antibiotics that inhibit the formation of peptidoglycan cross-links, but their binding targets are different. The binding target of vancomycin is d-alanine-d-alanine (d-Ala-d-Ala), whereas that of β-lactam is penicillin-binding proteins (PBPs). In this study, we revealed the divergent effects of peptidoglycan (PG) carboxypeptidase DacA on vancomycin and β-lactam resistance in Escherichia coli and Bacillus subtilis. The deletion of DacA induced sensitivity to most β-lactams, whereas it induced strong resistance toward vancomycin. Notably, both phenotypes did not have a strong association with ld-transpeptidases, which are necessary for the formation of PG 3-3 cross-links and covalent bonds between PG and an Lpp outer membrane (OM) lipoprotein. Vancomycin resistance was induced by an increased amount of decoy d-Ala-d-Ala residues within PG, whereas β-lactam sensitivity was associated with physical interactions between DacA and PBPs. The presence of an OM permeability barrier strongly strengthened vancomycin resistance, but it significantly weakened β-lactam sensitivity. Collectively, our results revealed two distinct functions of DacA, which involved inverse modulation of bacterial resistance to clinically important antibiotics, β-lactams and vancomycin, and presented evidence for a link between DacA and PBPs. IMPORTANCE Bacterial PG hydrolases play important roles in various aspects of bacterial physiology, including cytokinesis, PG synthesis, quality control of PG, PG recycling, and stress adaptation. Of all the PG hydrolases, the role of PG carboxypeptidases is poorly understood, especially regarding their impacts on antibiotic resistance. We have revealed two distinct functions of PG carboxypeptidase DacA with respect to antibiotic resistance. The deletion of DacA led to sensitivity to most β-lactams, while it caused strong resistance to vancomycin. Our study provides novel insights into the roles of PG carboxypeptidases in the regulation of antibiotic resistance and a potential clue for the development of a drug to improve the clinical efficacy of β-lactam antibiotics.
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10
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Ao K, Li X. Indirect recognition of pathogen effectors by NLRs. Essays Biochem 2022:EBC20210097. [PMID: 35535995 DOI: 10.1042/EBC20210097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 12/11/2022]
Abstract
To perceive pathogen threats, plants utilize both plasma membrane-localized and intracellular receptors. Nucleotide-binding domain leucine-rich repeat containing (NLR) proteins are key receptors that can recognize pathogen-derived intracellularly delivered effectors and activate downstream defense. Exciting recent findings have propelled our understanding of the various recognition and activation mechanisms of plant NLRs. Some NLRs directly bind to effectors, but others can perceive effector-induced changes on targeted host proteins (guardees), or non-functional host protein mimics (decoys). Such guarding strategies are thought to afford the host more durable resistance to quick-evolving and diverse pathogens. Here, we review classic and recent examples of indirect effector recognition by NLRs and discuss strategies for the discovery and study of new NLR-decoy/guardee systems. We also provide a perspective on how executor NLRs and helper NLRs (hNLRs) provide recognition for a wider range of effectors through sensor NLRs and how this can be considered an expanded form of indirect recognition. Furthermore, we summarize recent structural findings on NLR activation and resistosome formation upon indirect recognition. Finally, we discuss existing and potential applications that harness NLR indirect recognition for plant disease resistance and crop resilience.
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11
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Cardozo T, Cardozo L, Boutjdir M. Autoantibody:Autoantigen Competitor Decoys: Application to Cardiac Phenotypes. Front Immunol 2022; 13:812649. [PMID: 35154130 PMCID: PMC8832015 DOI: 10.3389/fimmu.2022.812649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/12/2022] [Indexed: 01/05/2023] Open
Abstract
Autoimmune diseases are often associated with autoantibodies that abnormally target self-antigens (autoantigens). An intuitive therapeutic strategy for diseases caused by aAbs is to design decoys, or soluble molecules that target the antigen combining site of these aAbs, thereby blocking binding of aAb to self-antigen and subsequent tissue damage. Here, we review the known decoy molecules of these types, discuss newer technological opportunities afforded by monoclonal antibody and structural biology advances, and discuss the challenges to this approach. Recent opportunities relevant to this approach for cardiac phenotypes, specifically Ro-associated long QT syndrome, are discussed.
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Affiliation(s)
- Timothy Cardozo
- Department of Biochemistry and Molecular Pharmacology, New York University (NYU) Grossman School of Medicine, New York, NY, United States
| | - Lila Cardozo
- Department of Biochemistry and Molecular Pharmacology, New York University (NYU) Grossman School of Medicine, New York, NY, United States
| | - Mohamed Boutjdir
- Department of Medicine, New York University (NYU) Grossman School of Medicine, New York, NY, United States.,Department of Medicine, Cell Biology and Pharmacology, State University of New York Downstate Medical Center, New York, NY, United States.,Cardiovascular Research Program, VA New York Harbor Healthcare System, New York, NY, United States
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12
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Naganuma M, Ohoka N, Tsuji G, Tsujimura H, Matsuno K, Inoue T, Naito M, Demizu Y. Development of Chimeric Molecules That Degrade the Estrogen Receptor Using Decoy Oligonucleotide Ligands. ACS Med Chem Lett 2021; 13:134-139. [PMID: 35059133 PMCID: PMC8762735 DOI: 10.1021/acsmedchemlett.1c00629] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/14/2021] [Indexed: 01/16/2023] Open
Abstract
Targeted protein degradation using chimeric small molecules, such as proteolysis-targeting chimeras (PROTACs) and specific and nongenetic inhibitors of apoptosis protein (IAP)-dependent protein erasers (SNIPERs), has attracted attention as a method for degrading intracellular target proteins via the ubiquitin-proteasome system (UPS). These chimeric molecules target a variety of proteins using small molecules that can bind to the proteins. However, it is difficult to develop such degraders in the absence of suitable small-molecule ligands for the target proteins, such as for transcription factors (TFs). Therefore, we constructed the chimeric molecule LCL-ER(dec), which consists of a decoy oligonucleotide that can bind to estrogen receptor α (ERα) and an IAP ligand, LCL161 (LCL), in a click reaction. LCL-ER(dec) was found to selectively degrade ERα via the UPS. These findings will be applicable to the development of other oligonucleotide-type degraders that target different TFs.
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Affiliation(s)
- Miyako Naganuma
- Division
of Organic Chemistry, National Institute
of Health Sciences, Kanagawa 210-9501, Japan,Graduate
School of Medical Life Science, Yokohama
City University, Kanagawa 236-0027, Japan,Department
of Chemistry and Life Science, Kogakuin
University, Tokyo 192-0015, Japan
| | - Nobumichi Ohoka
- Division
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kanagawa 158-8501, Japan,Tel: +81-44-270-6537.
| | - Genichiro Tsuji
- Division
of Organic Chemistry, National Institute
of Health Sciences, Kanagawa 210-9501, Japan
| | - Haruna Tsujimura
- Division
of Organic Chemistry, National Institute
of Health Sciences, Kanagawa 210-9501, Japan,Graduate
School of Medical Life Science, Yokohama
City University, Kanagawa 236-0027, Japan
| | - Kenji Matsuno
- Department
of Chemistry and Life Science, Kogakuin
University, Tokyo 192-0015, Japan
| | - Takao Inoue
- Division
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kanagawa 158-8501, Japan
| | - Mikihiko Naito
- Laboratory
of Targeted Protein Degradation, Graduate School of Pharmaceutical
Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yosuke Demizu
- Division
of Organic Chemistry, National Institute
of Health Sciences, Kanagawa 210-9501, Japan,Graduate
School of Medical Life Science, Yokohama
City University, Kanagawa 236-0027, Japan,Tel: +81-44-270-6578. Fax: +81-44-270-6578.
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14
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Gunnels TF, Stranford DM, Mitrut RE, Kamat NP, Leonard JN. Elucidating design principles for engineering cell-derived vesicles to inhibit SARS-CoV-2 infection. bioRxiv 2021:2021.12.04.471153. [PMID: 34909773 PMCID: PMC8669840 DOI: 10.1101/2021.12.04.471153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The ability of pathogens to develop drug resistance is a global health challenge. The SARS-CoV-2 virus presents an urgent need wherein several variants of concern resist neutralization by monoclonal antibody therapies and vaccine-induced sera. Decoy nanoparticles-cell-mimicking particles that bind and inhibit virions-are an emerging class of therapeutics that may overcome such drug resistance challenges. To date, we lack quantitative understanding as to how design features impact performance of these therapeutics. To address this gap, here we perform a systematic, comparative evaluation of various biologically-derived nanoscale vesicles, which may be particularly well-suited to sustained or repeated administration in the clinic due to low toxicity, and investigate their potential to inhibit multiple classes of model SARS-CoV-2 virions. A key finding is that such particles exhibit potent antiviral efficacy across multiple manufacturing methods, vesicle subclasses, and virus-decoy binding affinities. In addition, these cell-mimicking vesicles effectively inhibit model SARS-CoV-2 variants that evade monoclonal antibodies and recombinant protein-based decoy inhibitors. This study provides a foundation of knowledge that may guide the design of decoy nanoparticle inhibitors for SARS-CoV-2 and other viral infections.
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Affiliation(s)
- Taylor F. Gunnels
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Devin M. Stranford
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Roxana E. Mitrut
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Neha P. Kamat
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Joshua N. Leonard
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA
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15
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Lua J, Ekanayake K, Fangman M, Doré S. Potential Role of Soluble Toll-like Receptors 2 and 4 as Therapeutic Agents in Stroke and Brain Hemorrhage. Int J Mol Sci 2021; 22:ijms22189977. [PMID: 34576137 PMCID: PMC8470802 DOI: 10.3390/ijms22189977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/29/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
Hemolysis is a physiological condition in which red blood cells (RBCs) lyse, releasing their contents into the extracellular environment. Hemolysis can be a manifestation of several diseases and conditions, such as sickle cell disease, hemorrhagic stroke, and trauma. Heme and hemoglobin are among the unique contents of RBCs that are released into the environment. Although these contents can cause oxidative stress, especially when oxidized in the extracellular environment, they can also initiate a proinflammatory response because they bind to receptors such as the Toll-like receptor (TLR) family. This review seeks to clarify the mechanism by which TLRs initiate a proinflammatory response to heme, hemoglobin, and their oxidized derivatives, as well as the possibility of using soluble TLRs (sTLRs) as therapeutic agents. Furthermore, this review explores the possibility of using sTLRs in hemorrhagic disorders in which mitigating inflammation is essential for clinical outcomes, including hemorrhagic stroke and its subtypes, intracerebral hemorrhage (ICH), and subarachnoid hemorrhage (SAH).
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Affiliation(s)
- Josh Lua
- Department of Anesthesiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (J.L.); (K.E.); (M.F.)
| | - Kanishka Ekanayake
- Department of Anesthesiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (J.L.); (K.E.); (M.F.)
| | - Madison Fangman
- Department of Anesthesiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (J.L.); (K.E.); (M.F.)
| | - Sylvain Doré
- Department of Anesthesiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (J.L.); (K.E.); (M.F.)
- Center for Translational Research in Neurodegenerative Disease, Departments of Psychiatry, Pharmaceutics and Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
- Correspondence: ; Tel.: +1-352-273-9663
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16
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Deshpande MS, Banerjee T. A decoy strategy to activate the immune system. IUBMB Life 2021; 73:1205-1209. [PMID: 34455696 DOI: 10.1002/iub.2548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 12/13/2022]
Abstract
An approach comprising a novel fusion protein and inactivated virus, as a more efficacious vaccine against invading viruses is presented, using SARS-CoV-2 as a most prominent example. The fusion protein consists of the Hepatitis B surface antigen (HBsAg) conjugated to the N-terminal helix (NTH) of Angiotensin-Converting Enzyme 2 (ACE2), which is the receptor for SARS-CoV-2. For vaccination, this fusion protein is to be administered together with the whole killed virus. The NTH would bind to the Receptor Binding Domain (RBD) of the Spike protein of the killed virus. Due to HBsAg acting as a decoy, immune responses would be mounted. Neutralizing antibodies (NAbs) pre-existing in people already vaccinated with the recombinant Hepatitis B vaccine, fresh production of NAbs, and NAbs produced by memory B cells would bind to the HBsAg. This would lead to "presentation" of the killed virus to elements of the immune system at close range. Also, there would be enhanced opsonization and effective antigen presentation. This two-component vaccine could be a platform strategy, wherein HBsAg could be linked to the part of the cellular receptor that any new intractable virus binds to, and is administered together with whole inactivated virus. Now, the same fusion protein, administered by itself to persons with infection, would have therapeutic action, yet by harnessing elements of the immune system. NAbs would bind to the fusion protein as above, the NTH of which would bind to the RBDs of the infecting virus, which, in effect would be neutralized.
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Affiliation(s)
- Manisha S Deshpande
- Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Tanushree Banerjee
- Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, India.,Molecular Neuroscience Research Laboratory, Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra, India
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17
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Mahjoubin-Tehran M, Atkin SL, Bezsonov EE, Jamialahmadi T, Sahebkar A. Harnessing the Therapeutic Potential of Decoys in Non-Atherosclerotic Cardiovascular Diseases: State of the Art. J Cardiovasc Dev Dis 2021; 8:jcdd8090103. [PMID: 34564121 PMCID: PMC8467637 DOI: 10.3390/jcdd8090103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/06/2021] [Accepted: 08/20/2021] [Indexed: 01/30/2023] Open
Abstract
Cardiovascular disease (CVD) is the main cause of global death, highlighting the fact that conventional therapeutic approaches for the treatment of CVD patients are insufficient, and there is a need to develop new therapeutic approaches. In recent years, decoy technology, decoy oligodeoxynucleotides (ODN), and decoy peptides show promising results for the future treatment of CVDs. Decoy ODN inhibits transcription by binding to the transcriptional factor, while decoy peptide neutralizes receptors by binding to the ligands. This review focused on studies that have investigated the effects of decoy ODN and decoy peptides on non-atherosclerotic CVD.
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Affiliation(s)
- Maryam Mahjoubin-Tehran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran;
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Evgeny E. Bezsonov
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 8 Baltiiskaya Street, 125315 Moscow, Russia;
- Laboratory of Cellular and Molecular Pathology of Cardiovascular System, Institute of Human Morphology, Moscow, Russia
- Department of Biology and General Genetics, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Tannaz Jamialahmadi
- Department of Food Science and Technology, Quchan Branch, Islamic Azad University, Quchan, Iran;
- Department of Nutrition, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- School of Medicine, The University of Western Australia, Perth, Australia
- School of Pharmacy, Mashhad University of Medical Sciences, Mashhad 9177948954, Iran
- Correspondence: or
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18
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Abstract
Circular RNAs (circRNAs) are emerging as novel regulators of gene expression in various biological processes. CircRNAs regulate gene expression by interacting with cellular regulators such as microRNAs and RNA binding proteins (RBPs) to regulate downstream gene expression. The accumulation of high-throughput RNA-protein interaction data revealed the interaction of RBPs with the coding and noncoding RNAs, including recently discovered circRNAs. RBPs are a large family of proteins known to play a critical role in gene expression by modulating RNA splicing, nuclear export, mRNA stability, localization, and translation. However, the interaction of RBPs with circRNAs and their implications on circRNA biogenesis and function has been emerging in the last few years. Recent studies suggest that circRNA interaction with target proteins modulates the interaction of the protein with downstream target mRNAs or proteins. This review outlines the emerging mechanisms of circRNA-protein interactions and their functional role in cell physiology.
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Affiliation(s)
- Arundhati Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar 751023, India; (A.D.); (T.S.); (S.S.)
- School of Biotechnology, KIIT University, Bhubaneswar 751024, India
| | - Tanvi Sinha
- Institute of Life Sciences, Nalco Square, Bhubaneswar 751023, India; (A.D.); (T.S.); (S.S.)
| | - Sharmishtha Shyamal
- Institute of Life Sciences, Nalco Square, Bhubaneswar 751023, India; (A.D.); (T.S.); (S.S.)
| | - Amaresh Chandra Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar 751023, India; (A.D.); (T.S.); (S.S.)
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19
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Troyer Z, Alhusaini N, Tabler CO, Sweet T, de Carvalho KIL, Schlatzer DM, Carias L, King CL, Matreyek K, Tilton JC. Extracellular vesicles carry SARS-CoV-2 spike protein and serve as decoys for neutralizing antibodies. J Extracell Vesicles 2021; 10:e12112. [PMID: 34188786 PMCID: PMC8213968 DOI: 10.1002/jev2.12112] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/17/2021] [Accepted: 05/28/2021] [Indexed: 01/05/2023] Open
Abstract
In late 2019, a novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China. SARS-CoV-2 and the disease it causes, coronavirus disease 2019 (COVID-19), spread rapidly and became a global pandemic in early 2020. SARS-CoV-2 spike protein is responsible for viral entry and binds to angiotensin converting enzyme 2 (ACE2) on host cells, making it a major target of the immune system - particularly neutralizing antibodies (nAbs) that are induced by infection or vaccines. Extracellular vesicles (EVs) are small membraned particles constitutively released by cells, including virally-infected cells. EVs and viruses enclosed within lipid membranes share some characteristics: they are small, sub-micron particles and they overlap in cellular biogenesis and egress routes. Given their shared characteristics, we hypothesized that EVs released from spike-expressing cells could carry spike and serve as decoys for anti-spike nAbs, promoting viral infection. Here, using mass spectrometry and nanoscale flow cytometry (NFC) approaches, we demonstrate that SARS-CoV-2 spike protein can be incorporated into EVs. Furthermore, we show that spike-carrying EVs act as decoy targets for convalescent patient serum-derived nAbs, reducing their effectiveness in blocking viral entry. These findings have important implications for the pathogenesis of SARS-CoV-2 infection in vivo and highlight the complex interplay between viruses, extracellular vesicles, and the immune system that occurs during viral infections.
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Affiliation(s)
- Zach Troyer
- Center for Proteomics and BioinformaticsDepartment of NutritionSchool of MedicineCase Western Reserve UniversityClevelandOhioUSA
| | - Najwa Alhusaini
- Center for Proteomics and BioinformaticsDepartment of NutritionSchool of MedicineCase Western Reserve UniversityClevelandOhioUSA
| | - Caroline O. Tabler
- Center for Proteomics and BioinformaticsDepartment of NutritionSchool of MedicineCase Western Reserve UniversityClevelandOhioUSA
| | - Thomas Sweet
- Center for Proteomics and BioinformaticsDepartment of NutritionSchool of MedicineCase Western Reserve UniversityClevelandOhioUSA
| | | | - Daniela M. Schlatzer
- Center for Proteomics and BioinformaticsDepartment of NutritionSchool of MedicineCase Western Reserve UniversityClevelandOhioUSA
| | - Lenore Carias
- Division of General Medical SciencesSchool of MedicineCase Western Reserve UniversityClevelandOhioUSA
| | - Christopher L. King
- Division of General Medical SciencesSchool of MedicineCase Western Reserve UniversityClevelandOhioUSA
| | - Kenneth Matreyek
- Department of PathologySchool of MedicineCase Western Reserve UniversityClevelandOhioUSA
| | - John C. Tilton
- Center for Proteomics and BioinformaticsDepartment of NutritionSchool of MedicineCase Western Reserve UniversityClevelandOhioUSA
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20
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Zhou Q, Sun X, Pasquier N, Jefferson P, Nguyen TTT, Siegelin MD, Angelastro JM, Greene LA. Cell-Penetrating CEBPB and CEBPD Leucine Zipper Decoys as Broadly Acting Anti-Cancer Agents. Cancers (Basel) 2021; 13:cancers13102504. [PMID: 34065488 PMCID: PMC8161188 DOI: 10.3390/cancers13102504] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary The gene-regulatory factors ATF5, CEBPB and CEBPD promote survival, growth, metastasis and treatment resistance of a range of cancer cell types. Presently, no drugs target all three at once. Here, with the aim of treating cancers, we designed novel cell-penetrating peptides that interact with and inactivate all three. The peptides Bpep and Dpep kill a range of cancer cell types in culture and in animals. In animals with tumors, they also significantly increase survival time. In contrast, they do not affect survival of non-cancer cells and have no apparent side effects in animals. The peptides work in combination with other anti-cancer treatments. Mechanism studies of how the peptides kill cancer cells indicate a decrease in survival proteins and increase in death proteins. These studies support the potential of Bpep and Dpep as novel, safe agents for the treatment of a variety of cancer types, both as mono- and combination therapies. Abstract Transcription factors are key players underlying cancer formation, growth, survival, metastasis and treatment resistance, yet few drugs exist to directly target them. Here, we characterized the in vitro and in vivo anti-cancer efficacy of novel synthetic cell-penetrating peptides (Bpep and Dpep) designed to interfere with the formation of active leucine-zipper-based dimers by CEBPB and CEBPD, transcription factors implicated in multiple malignancies. Both peptides similarly promoted apoptosis of multiple tumor lines of varying origins, without such effects on non-transformed cells. Combined with other treatments (radiation, Taxol, chloroquine, doxorubicin), the peptides acted additively to synergistically and were fully active on Taxol-resistant cells. The peptides suppressed expression of known direct CEBPB/CEBPD targets IL6, IL8 and asparagine synthetase (ASNS), supporting their inhibition of transcriptional activation. Mechanisms by which the peptides trigger apoptosis included depletion of pro-survival survivin and a required elevation of pro-apoptotic BMF. Bpep and Dpep significantly slowed tumor growth in mouse models without evident side effects. Dpep significantly prolonged survival in xenograft models. These findings indicate the efficacy and potential of Bpep and Dpep as novel agents to treat a variety of cancers as mono- or combination therapies.
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Affiliation(s)
- Qing Zhou
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; (Q.Z.); (X.S.); (N.P.); (P.J.); (T.T.T.N.); (M.D.S.)
| | - Xiotian Sun
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; (Q.Z.); (X.S.); (N.P.); (P.J.); (T.T.T.N.); (M.D.S.)
| | - Nicolas Pasquier
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; (Q.Z.); (X.S.); (N.P.); (P.J.); (T.T.T.N.); (M.D.S.)
| | - Parvaneh Jefferson
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; (Q.Z.); (X.S.); (N.P.); (P.J.); (T.T.T.N.); (M.D.S.)
| | - Trang T. T. Nguyen
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; (Q.Z.); (X.S.); (N.P.); (P.J.); (T.T.T.N.); (M.D.S.)
| | - Markus D. Siegelin
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; (Q.Z.); (X.S.); (N.P.); (P.J.); (T.T.T.N.); (M.D.S.)
| | - James M. Angelastro
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA;
| | - Lloyd A. Greene
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; (Q.Z.); (X.S.); (N.P.); (P.J.); (T.T.T.N.); (M.D.S.)
- Correspondence:
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21
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Mahjoubin-Tehran M, Teng Y, Jalili A, Aghaee-Bakhtiari SH, Markin AM, Sahebkar A. Decoy Technology as a Promising Therapeutic Tool for Atherosclerosis. Int J Mol Sci 2021; 22:4420. [PMID: 33922585 DOI: 10.3390/ijms22094420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 12/26/2022] Open
Abstract
Cardiovascular diseases (CVDs) have been classified into several types of disease, of which atherosclerosis is the most prevalent. Atherosclerosis is characterized as an inflammatory chronic disease which is caused by the formation of lesions in the arterial wall. Subsequently, lesion progression and disruption ultimately lead to heart disease and stroke. The development of atherosclerosis is the underlying cause of approximately 50% of all deaths in westernized societies. Countless studies have aimed to improve therapeutic approaches for atherosclerosis treatment; however, it remains high on the global list of challenges toward healthy and long lives. Some patients with familial hypercholesterolemia could not get intended LDL-C goals even with high doses of traditional therapies such as statins, with many of them being unable to tolerate statins because of the harsh side effects. Furthermore, even in patients achieving target LDL-C levels, the residual risk of traditional therapies is still significant thus highlighting the necessity of ongoing research for more effective therapeutic approaches with minimal side effects. Decoy-based drug candidates represent an opportunity to inhibit regulatory pathways that promote atherosclerosis. In this review, the potential roles of decoys in the treatment of atherosclerosis were described based on the in vitro and in vivo findings.
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22
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Yano S, Tazawa H, Kagawa S, Fujiwara T, Hoffman RM. FUCCI Real-Time Cell-Cycle Imaging as a Guide for Designing Improved Cancer Therapy: A Review of Innovative Strategies to Target Quiescent Chemo-Resistant Cancer Cells. Cancers (Basel) 2020; 12:cancers12092655. [PMID: 32957652 PMCID: PMC7563319 DOI: 10.3390/cancers12092655] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/03/2020] [Accepted: 09/09/2020] [Indexed: 01/06/2023] Open
Abstract
Simple Summary Chemotherapy of solid tumors has made very slow progress over many decades. A major problem has been that solid tumors very often contain non-dividing cells due to lack of oxygen deep in the tumor and these non-dividing cells resist most currently-used chemotherapy which usually only targets dividing cells. The present review demonstrates how a unique imaging system, FUCCI, which color codes cells depending on whether they are in a dividing or non-dividing phase, is being used to design very novel therapy that targets non-dividing cancer cells which can greatly improve the efficacy of cancer chemotherapy. Abstract Progress in chemotherapy of solid cancer has been tragically slow due, in large part, to the chemoresistance of quiescent cancer cells in tumors. The fluorescence ubiquitination cell-cycle indicator (FUCCI) was developed in 2008 by Miyawaki et al., which color-codes the phases of the cell cycle in real-time. FUCCI utilizes genes linked to different color fluorescent reporters that are only expressed in specific phases of the cell cycle and can, thereby, image the phases of the cell cycle in real-time. Intravital real-time FUCCI imaging within tumors has demonstrated that an established tumor comprises a majority of quiescent cancer cells and a minor population of cycling cancer cells located at the tumor surface or in proximity to tumor blood vessels. In contrast to most cycling cancer cells, quiescent cancer cells are resistant to cytotoxic chemotherapy, most of which target cells in S/G2/M phases. The quiescent cancer cells can re-enter the cell cycle after surviving treatment, which suggests the reason why most cytotoxic chemotherapy is often ineffective for solid cancers. Thus, quiescent cancer cells are a major impediment to effective cancer therapy. FUCCI imaging can be used to effectively target quiescent cancer cells within tumors. For example, we review how FUCCI imaging can help to identify cell-cycle-specific therapeutics that comprise decoy of quiescent cancer cells from G1 phase to cycling phases, trapping the cancer cells in S/G2 phase where cancer cells are mostly sensitive to cytotoxic chemotherapy and eradicating the cancer cells with cytotoxic chemotherapy most active against S/G2 phase cells. FUCCI can readily image cell-cycle dynamics at the single cell level in real-time in vitro and in vivo. Therefore, visualizing cell cycle dynamics within tumors with FUCCI can provide a guide for many strategies to improve cell-cycle targeting therapy for solid cancers.
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Affiliation(s)
- Shuya Yano
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; (H.T.); (S.K.); (T.F.)
- Center for Graduate Medical Education, Okayama University Hospital, Okayama 700-8558, Japan
- Correspondence: ; Tel.: +81-86-235-7257; Fax: +81-86-221-8775
| | - Hiroshi Tazawa
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; (H.T.); (S.K.); (T.F.)
- Center of Innovative Clinical Medicine, Okayama University Hospital, Okayama 700-8558, Japan
| | - Shunsuke Kagawa
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; (H.T.); (S.K.); (T.F.)
- Minimally Invasive Therapy Center, Okayama University Hospital, Okayama 700-8558, Japan
| | - Toshiyoshi Fujiwara
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan; (H.T.); (S.K.); (T.F.)
| | - Robert M. Hoffman
- AntiCancer, Inc., San Diego, CA 92111, USA;
- Department of Surgery, University of California, San Diego, CA 92093, USA
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Ohlhausen P, Langen N. When a Combination of Nudges Decreases Sustainable Food Choices Out-Of-Home-The Example of Food Decoys and Descriptive Name Labels. Foods 2020; 9:E557. [PMID: 32370148 DOI: 10.3390/foods9050557] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 12/18/2022] Open
Abstract
This paper reports results from three consecutive studies focusing on the comparison of the effectiveness of different nudges and their combinations to increase sustainable food choices out of the home. The nudges compared are the use of descriptive name labels (DNLs) for the most sustainable dish of a choice set (menu) and the decoy effect (DE), created by adding a less attractive decoy dish to a more attractive target dish with the goal of increasing the choice frequency of the target dish. In the literature, both nudges have been found to influence consumers’ choices. In the first study, six category names of sustainability indicators were deduced from a focus group. These were tested with 100 students to identify the most attractive DNLs. Study II, a randomized choice study (n = 420), tested the DE, the DNLs and a combination of the DNLs and the DE used on four different dishes in a university canteen. In study III, 820 guests of a business canteen voted during four weeks for the special meals of the following week (identical to the four choice sets displayed in study II). Results indicate that the combination of DNLs and the DE is not recommended for fostering sustainable food choices. Pure DNLs were more efficient in increasing the choice frequency of the more sustainable meal, whereas the decoy effect resulted in decreased choice frequencies. Regional and sustainable DNLs were favoured by consumers.
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24
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Emmerich AC, Wellstein J, Ossipova E, Baumann I, Lengqvist J, Kultima K, Jakobsson PJ, Steinhilber D, Saul MJ. Proteomics-Based Characterization of miR-574-5p Decoy to CUGBP1 Suggests Specificity for mPGES-1 Regulation in Human Lung Cancer Cells. Front Pharmacol 2020; 11:196. [PMID: 32231562 PMCID: PMC7082395 DOI: 10.3389/fphar.2020.00196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/13/2020] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRs) are one of the most important post-transcriptional repressors of gene expression. However, miR-574-5p has recently been shown to positively regulate the expression of microsomal prostaglandin E-synthase-1 (mPGES-1), a key enzyme in the prostaglandin E2 (PGE2) biosynthesis, by acting as decoy to the RNA-binding protein CUG-RNA binding protein 1 (CUGBP1) in human lung cancer. miR-574-5p exhibits oncogenic properties and promotes lung tumor growth in vivo via induction of mPGES-1-derived PGE2 synthesis. In a mass spectrometry-based proteomics study, we now attempted to characterize this decoy mechanism in A549 lung cancer cells at a cellular level. Besides the identification of novel CUGBP1 targets, we identified that the interaction between miR-574-5p and CUGBP1 specifically regulates mPGES-1 expression. This is supported by the fact that CUGBP1 and miR-574-5p are located in the nucleus, where CUGBP1 regulates alternative splicing. Further, in a bioinformatical approach we showed that the decoy-dependent mPGES-1 splicing pattern is unique. The specificity of miR-574-5p/CUGBP1 regulation on mPGES-1 expression supports the therapeutic strategy of pharmacological inhibition of PGE2 formation, which may provide significant therapeutic value for NSCLC patients with high miR-574-5p levels.
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Affiliation(s)
- Anne C Emmerich
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany.,Institute of Pharmaceutical Chemistry, Goethe-Universität Frankfurt, Frankfurt, Germany
| | - Julia Wellstein
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany.,Institute of Pharmaceutical Chemistry, Goethe-Universität Frankfurt, Frankfurt, Germany
| | - Elena Ossipova
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Isabell Baumann
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany.,Institute of Pharmaceutical Chemistry, Goethe-Universität Frankfurt, Frankfurt, Germany
| | - Johan Lengqvist
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kim Kultima
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden
| | - Per-Johan Jakobsson
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe-Universität Frankfurt, Frankfurt, Germany
| | - Meike J Saul
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany.,Institute of Pharmaceutical Chemistry, Goethe-Universität Frankfurt, Frankfurt, Germany
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25
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Klingler C, Ashley J, Shi K, Stiefvater A, Kyba M, Sinnreich M, Aihara H, Kinter J. DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD. FASEB J 2020; 34:4573-4590. [PMID: 32020675 PMCID: PMC7079142 DOI: 10.1096/fj.201902696] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/17/2020] [Indexed: 01/13/2023]
Abstract
Aberrant expression of the transcription factor double homeobox protein 4 (DUX4) can lead to a number of diseases including facio‐scapulo‐humeral muscular dystrophy (FSHD), acute lymphoblastic leukemia, and sarcomas. Inhibition of DUX4 may represent a therapeutic strategy for these diseases. By applying Systematic Evolution of Ligands by EXponential Enrichment (SELEX), we identified aptamers against DUX4 with specific secondary structural elements conveying high affinity to DUX4 as assessed by fluorescence resonance energy transfer and fluorescence polarization techniques. Sequences analysis of these aptamers revealed the presence of two consensus DUX4 motifs in a reverse complementary fashion forming hairpins interspersed with bulge loops at distinct positions that enlarged the binding surface with the DUX4 protein, as determined by crystal structure analysis. We demonstrate that insertion of specific structural elements into transcription factor binding oligonucleotides can enhance specificity and affinity.
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Affiliation(s)
- Christian Klingler
- Neuromuscular Research Group, Department of Neurology, University Hospital Basel, Basel, Switzerland.,Neuromuscular Research Group, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Jon Ashley
- Neuromuscular Research Group, Department of Neurology, University Hospital Basel, Basel, Switzerland.,Neuromuscular Research Group, Department of Biomedicine, University Hospital Basel, Basel, Switzerland.,Department of Health Technology, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Adeline Stiefvater
- Neuromuscular Research Group, Department of Neurology, University Hospital Basel, Basel, Switzerland.,Neuromuscular Research Group, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Michael Kyba
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, USA.,Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Michael Sinnreich
- Neuromuscular Research Group, Department of Neurology, University Hospital Basel, Basel, Switzerland.,Neuromuscular Research Group, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Jochen Kinter
- Neuromuscular Research Group, Department of Neurology, University Hospital Basel, Basel, Switzerland.,Neuromuscular Research Group, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
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26
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Pittarello A, Caserotti M, Rubaltelli E. 'Three is better than two': Increasing donations with the attraction effect. Br J Psychol 2019; 111:805-822. [PMID: 31617591 DOI: 10.1111/bjop.12428] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/24/2019] [Indexed: 11/29/2022]
Abstract
Five experiments (Ntotal = 2,503) tested the attraction effect and its boundary conditions in the context of helping behaviour. Participants could choose one donation appeal in a set of either two or three alternatives. The three alternatives set included a decoy - an alternative that resembled but was clearly inferior to a target (i.e., the most beneficial) alternative. A clear and consistent pattern emerged: Participants chose the target alternative more frequently and perceived it as more beneficial (and somewhat less costly) when the decoy was present compared to when it was absent. This finding was robust when the attribute ratings of the alternatives were unclear, when the target alternative offered a bundle of unrelated products, and when participants could refrain from donating altogether, or contribute any amount they wished. Our findings offer concrete and simple strategies that charities can implement at zero cost to increase giving and the perceived benefits that people's good deed bring about to those in need.
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Affiliation(s)
- Andrea Pittarello
- Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
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27
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Takakura K, Kawamura A, Torisu Y, Koido S, Yahagi N, Saruta M. The Clinical Potential of Oligonucleotide Therapeutics against Pancreatic Cancer. Int J Mol Sci 2019; 20:ijms20133331. [PMID: 31284594 PMCID: PMC6651255 DOI: 10.3390/ijms20133331] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/03/2019] [Accepted: 07/03/2019] [Indexed: 02/07/2023] Open
Abstract
Although many diagnostic and therapeutic modalities for pancreatic cancer have been proposed, an urgent need for improved therapeutic strategies remains. Oligonucleotide therapeutics, such as those based on antisense RNAs, small interfering RNA (siRNA), microRNA (miRNA), aptamers, and decoys, are promising agents against pancreatic cancer, because they can identify a specific mRNA fragment of a given sequence or protein, and interfere with gene expression as molecular-targeted agents. Within the past 25 years, the diversity and feasibility of these drugs as diagnostic or therapeutic tools have dramatically increased. Several clinical and preclinical studies of oligonucleotides have been conducted for patients with pancreatic cancer. To support the discovery of effective diagnostic or therapeutic options using oligonucleotide-based strategies, in the absence of satisfactory therapies for long-term survival and the increasing trend of diseases, we summarize the current clinical trials of oligonucleotide therapeutics for pancreatic cancer patients, with underlying preclinical and scientific data, and focus on the possibility of oligonucleotides for targeting pancreatic cancer in clinical implications.
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Affiliation(s)
- Kazuki Takakura
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo 105-8461, Japan.
| | - Atsushi Kawamura
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Yuichi Torisu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Shigeo Koido
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Naohisa Yahagi
- Division of Research and Development for Minimally Invasive Treatment, Cancer Center, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masayuki Saruta
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo 105-8461, Japan
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28
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Askitas N. Selfish altruism, fierce cooperation and the predator. J Biol Dyn 2018; 12:471-485. [PMID: 29774800 DOI: 10.1080/17513758.2018.1473645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
This paper suggests a new way to think about a famous question: what explains cooperation in nature and in particular in humans? I argue that, for an evolutionary biologist as well as a quantitative social scientist, the triangle of two 'teammates' in the presence of a predator (passing and shooting in two-on-one situations) is one of the fundamental conceptual building-blocks for understanding these phenomena because in such a situation the fact that life is packaged in many distinct enclosures (and not in one big monolithic blob) can unfold its comparative advantage. I show how, in the presence of a predator, cooperative equilibria emerge among entirely selfish teammates if we infinitesimally bias the lead player in the selfish direction or assign a computational burden on the predator due to the presence of a teammate. I argue that 'predators' are common in the biological jungle but also in everyday human settings. Intuitively, this paper builds on the simple idea - a familiar one to a biologist observing the natural world but perhaps less so to social scientists - that everybody has enemies.
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29
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Wang SS, Gao X, Solar VD, Yu X, Antonopoulos A, Friedman AE, Matich EK, Atilla-Gokcumen GE, Nasirikenari M, Lau JT, Dell A, Haslam SM, Laine RA, Matta KL, Neelamegham S. Thioglycosides Are Efficient Metabolic Decoys of Glycosylation that Reduce Selectin Dependent Leukocyte Adhesion. Cell Chem Biol 2018; 25:1519-1532.e5. [PMID: 30344053 DOI: 10.1016/j.chembiol.2018.09.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 08/14/2018] [Accepted: 09/25/2018] [Indexed: 12/24/2022]
Abstract
Metabolic decoys are synthetic analogs of naturally occurring biosynthetic acceptors. These compounds divert cellular biosynthetic pathways by acting as artificial substrates that usurp the activity of natural enzymes. While O-linked glycosides are common, they are only partially effective even at millimolar concentrations. In contrast, we report that N-acetylglucosamine (GlcNAc) incorporated into various thioglycosides robustly truncate cell surface N- and O-linked glycan biosynthesis at 10-100 μM concentrations. The >10-fold greater inhibition is in part due to the resistance of thioglycosides to hydrolysis by intracellular hexosaminidases. The thioglycosides reduce β-galactose incorporation into lactosamine chains, cell surface sialyl Lewis-X expression, and leukocyte rolling on selectin substrates including inflamed endothelial cells under fluid shear. Treatment of granulocytes with thioglycosides prior to infusion into mouse inhibited neutrophil homing to sites of acute inflammation and bone marrow by ∼80%-90%. Overall, thioglycosides represent an easy to synthesize class of efficient metabolic inhibitors or decoys. They reduce N-/O-linked glycan biosynthesis and inflammatory leukocyte accumulation.
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Affiliation(s)
- Shuen-Shiuan Wang
- Department of Chemical and Biological Engineering, State University of New York, 906 Furnas Hall, Buffalo, NY 14260, USA
| | - Xuefeng Gao
- TumorEnd LLC, Louisiana Emerging Technology Center, 340 East Parker Drive, Suite 246, Baton Rouge, LA 70803, USA
| | - Virginia Del Solar
- Department of Chemical and Biological Engineering, State University of New York, 906 Furnas Hall, Buffalo, NY 14260, USA; Clinical & Translational Research Center and State University of New York, Buffalo, NY 14260, USA
| | - Xinheng Yu
- Department of Chemical and Biological Engineering, State University of New York, 906 Furnas Hall, Buffalo, NY 14260, USA
| | | | - Alan E Friedman
- Department of Chemistry, State University of New York, Buffalo, NY 14260, USA
| | - Eryn K Matich
- Department of Chemistry, State University of New York, Buffalo, NY 14260, USA
| | | | - Mehrab Nasirikenari
- Department of Cellular and Molecular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Joseph T Lau
- Department of Cellular and Molecular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Anne Dell
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Roger A Laine
- TumorEnd LLC, Louisiana Emerging Technology Center, 340 East Parker Drive, Suite 246, Baton Rouge, LA 70803, USA
| | - Khushi L Matta
- Department of Chemical and Biological Engineering, State University of New York, 906 Furnas Hall, Buffalo, NY 14260, USA; TumorEnd LLC, Louisiana Emerging Technology Center, 340 East Parker Drive, Suite 246, Baton Rouge, LA 70803, USA.
| | - Sriram Neelamegham
- Department of Chemical and Biological Engineering, State University of New York, 906 Furnas Hall, Buffalo, NY 14260, USA; Clinical & Translational Research Center and State University of New York, Buffalo, NY 14260, USA.
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30
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Gwon MG, Kim JY, An HJ, Kim WH, Gu H, Kim MK, Park SC, Park KK. Antifibrotic Effect of Smad Decoy Oligodeoxynucleotide in a CCl₄-Induced Hepatic Fibrosis Animal Model. Molecules 2018; 23:E1991. [PMID: 30103395 DOI: 10.3390/molecules23081991] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/08/2018] [Accepted: 08/08/2018] [Indexed: 01/18/2023] Open
Abstract
Hepatic fibrosis is the wound-healing process of chronic hepatic disease that leads to the end-stage of hepatocellular carcinoma and demolition of hepatic structures. Epithelial–mesenchymal transition (EMT) has been identified to phenotypic conversion of the epithelium to mesenchymal phenotype that occurred during fibrosis. Smad decoy oligodeoxynucleotide (ODN) is a synthetic DNA fragment containing a complementary sequence of Smad transcription factor. Thus, this study evaluated the antifibrotic effects of Smad decoy ODN on carbon tetrachloride (CCl4)-induced hepatic fibrosis in mice. As shown in histological results, CCl4 treatment triggered hepatic fibrosis and increased Smad expression. On the contrary, Smad decoy ODN administration suppressed fibrogenesis and EMT process. The expression of Smad signaling and EMT-associated protein was markedly decreased in Smad decoy ODN-treated mice compared with CCl4-injured mice. In conclusion, these data indicate the practicability of Smad decoy ODN administration for preventing hepatic fibrosis and EMT processes.
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31
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Basilico C, Modica C, Maione F, Vigna E, Comoglio PM. Targeting the MET oncogene by concomitant inhibition of receptor and ligand via an antibody-" decoy" strategy. Int J Cancer 2018; 143:1774-1785. [PMID: 29693242 DOI: 10.1002/ijc.31550] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 02/07/2018] [Accepted: 03/01/2018] [Indexed: 12/18/2022]
Abstract
MET, a master gene sustaining "invasive growth," is a relevant target for cancer precision therapy. In the vast majority of tumors, wild-type MET behaves as a "stress-response" gene and relies on the ligand (HGF) to sustain cell "scattering," invasive growth and apoptosis protection (oncogene "expedience"). In this context, concomitant targeting of MET and HGF could be crucial to reach effective inhibition. To test this hypothesis, we combined an anti-MET antibody (MvDN30) inducing "shedding" (i.e., removal of MET from the cell surface), with a "decoy" (i.e., the soluble extracellular domain of the MET receptor) endowed with HGF-sequestering ability. To avoid antibody/decoy interaction-and subsequent neutralization-we identified a single aminoacid in the extracellular domain of MET-lysine 842-that is critical for MvDN30 binding and engineered the corresponding recombinant decoyMET (K842E). DecoyMETK842E retains the ability to bind HGF with high affinity and inhibits HGF-induced MET phosphorylation. In HGF-dependent cellular models, MvDN30 antibody and decoyMETK842E used in combination cooperate in restraining invasive growth, and synergize in blocking cancer cell "scattering." The antibody and the decoy unbridle apoptosis of colon cancer stem cells grown in vitro as spheroids. In a preclinical model, built by orthotopic transplantation of a human pancreatic carcinoma in SCID mice engineered to express human HGF, concomitant treatment with antibody and decoy significantly reduces metastatic spread. The data reported indicate that vertical targeting of the MET/HGF axis results in powerful inhibition of ligand-dependent MET activation, providing proof of concept in favor of combined target therapy of MET "expedience."
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Affiliation(s)
| | - Chiara Modica
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy.,Department of Oncology, University of Turin, Torino, Italy
| | - Federica Maione
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Elisa Vigna
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy.,Department of Oncology, University of Turin, Torino, Italy
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32
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Igarashi K, Kawaguchi K, Kiyuna T, Miyake K, Miyake M, Li S, Han Q, Tan Y, Zhao M, Li Y, Nelson SD, Dry SM, Singh AS, Elliott IA, Russell TA, Eckardt MA, Yamamoto N, Hayashi K, Kimura H, Miwa S, Tsuchiya H, Eilber FC, Hoffman RM. Tumor-targeting Salmonella typhimurium A1-R combined with recombinant methioninase and cisplatinum eradicates an osteosarcoma cisplatinum-resistant lung metastasis in a patient-derived orthotopic xenograft (PDOX) mouse model: decoy, trap and kill chemotherapy moves toward the clinic. Cell Cycle 2018; 17:801-809. [PMID: 29374999 DOI: 10.1080/15384101.2018.1431596] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In the present study, a patient-derived orthotopic xenograft (PDOX) model of recurrent cisplatinum (CDDP)-resistant metastatic osteosarcoma was treated with Salmonella typhimurium A1-R (S. typhimurium A1-R), which decoys chemoresistant quiescent cancer cells to cycle, and recombinant methioninase (rMETase), which selectively traps cancer cells in late S/G2, and chemotherapy. The PDOX models were randomized into the following groups 14 days after implantation: G1, control without treatment; G2, CDDP (6 mg/kg, intraperitoneal (i.p.) injection, weekly, for 2 weeks); G3, rMETase (100 unit/mouse, i.p., daily, for 2 weeks). G4, S. typhimurium A1-R (5 × 107 CFU/100 μl, i.v., weekly, for 2 weeks); G5, S. typhimurium A1-R (5 × 107 CFU/100 μl, i.v., weekly, for 2 weeks) combined with rMETase (100 unit/mouse, i.p., daily, for 2 weeks); G6, S. typhimurium A1-R (5 × 107 CFU/100 μl, i.v., weekly, for 2 weeks) combined with rMETase (100 unit/mouse, i.p., daily, for 2 weeks) and CDDP (6 mg/kg, i.p. injection, weekly, for 2 weeks). On day 14 after initiation, all treatments except CDDP alone, significantly inhibited tumor growth compared to untreated control: (CDDP: p = 0.586; rMETase: p = 0.002; S. typhimurium A1-R: p = 0.002; S. typhimurium A1-R combined with rMETase: p = 0.0004; rMETase combined with both S. typhimurium A1-R and CDDP: p = 0.0001). The decoy, trap and kill combination of S. typhimurium A1-R, rMETase and CDDP was the most effective of all therapies and was able to eradicate the metastatic osteosarcoma PDOX.
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Affiliation(s)
- Kentaro Igarashi
- a AntiCancer, Inc. , San Diego , CA, USA.,b Department of Surgery , University of California , San Diego , CA, USA.,c Department of Orthopaedic Surgery , Kanazawa University , Kanazawa , Japan
| | - Kei Kawaguchi
- a AntiCancer, Inc. , San Diego , CA, USA.,b Department of Surgery , University of California , San Diego , CA, USA
| | - Tasuku Kiyuna
- a AntiCancer, Inc. , San Diego , CA, USA.,b Department of Surgery , University of California , San Diego , CA, USA
| | - Kentaro Miyake
- a AntiCancer, Inc. , San Diego , CA, USA.,b Department of Surgery , University of California , San Diego , CA, USA
| | - Masuyo Miyake
- a AntiCancer, Inc. , San Diego , CA, USA.,b Department of Surgery , University of California , San Diego , CA, USA
| | - Shukuan Li
- a AntiCancer, Inc. , San Diego , CA, USA
| | | | - Yuying Tan
- a AntiCancer, Inc. , San Diego , CA, USA
| | - Ming Zhao
- a AntiCancer, Inc. , San Diego , CA, USA
| | - Yunfeng Li
- d Dept. of Pathology , University of California , Los Angeles , CA , USA
| | - Scott D Nelson
- d Dept. of Pathology , University of California , Los Angeles , CA , USA
| | - Sarah M Dry
- d Dept. of Pathology , University of California , Los Angeles , CA , USA
| | - Arun S Singh
- e Division of Hematology-Oncology , University of California , Los Angeles , CA , USA
| | - Irmina A Elliott
- f Division of Surgical Oncology , University of California , Los Angeles , CA , USA
| | - Tara A Russell
- f Division of Surgical Oncology , University of California , Los Angeles , CA , USA
| | - Mark A Eckardt
- g Department of Surgery, Yale School of Medicine , New Haven , CT, USA
| | - Norio Yamamoto
- c Department of Orthopaedic Surgery , Kanazawa University , Kanazawa , Japan
| | - Katsuhiro Hayashi
- c Department of Orthopaedic Surgery , Kanazawa University , Kanazawa , Japan
| | - Hiroaki Kimura
- c Department of Orthopaedic Surgery , Kanazawa University , Kanazawa , Japan
| | - Shinji Miwa
- c Department of Orthopaedic Surgery , Kanazawa University , Kanazawa , Japan
| | - Hiroyuki Tsuchiya
- c Department of Orthopaedic Surgery , Kanazawa University , Kanazawa , Japan
| | - Fritz C Eilber
- f Division of Surgical Oncology , University of California , Los Angeles , CA , USA
| | - Robert M Hoffman
- a AntiCancer, Inc. , San Diego , CA, USA.,b Department of Surgery , University of California , San Diego , CA, USA
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Réau M, Langenfeld F, Zagury JF, Lagarde N, Montes M. Decoys Selection in Benchmarking Datasets: Overview and Perspectives. Front Pharmacol 2018; 9:11. [PMID: 29416509 PMCID: PMC5787549 DOI: 10.3389/fphar.2018.00011] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/05/2018] [Indexed: 11/24/2022] Open
Abstract
Virtual Screening (VS) is designed to prospectively help identifying potential hits, i.e., compounds capable of interacting with a given target and potentially modulate its activity, out of large compound collections. Among the variety of methodologies, it is crucial to select the protocol that is the most adapted to the query/target system under study and that yields the most reliable output. To this aim, the performance of VS methods is commonly evaluated and compared by computing their ability to retrieve active compounds in benchmarking datasets. The benchmarking datasets contain a subset of known active compounds together with a subset of decoys, i.e., assumed non-active molecules. The composition of both the active and the decoy compounds subsets is critical to limit the biases in the evaluation of the VS methods. In this review, we focus on the selection of decoy compounds that has considerably changed over the years, from randomly selected compounds to highly customized or experimentally validated negative compounds. We first outline the evolution of decoys selection in benchmarking databases as well as current benchmarking databases that tend to minimize the introduction of biases, and secondly, we propose recommendations for the selection and the design of benchmarking datasets.
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Affiliation(s)
- Manon Réau
- Laboratoire GBA, EA4627, Conservatoire National des Arts et Métiers, Paris, France
| | - Florent Langenfeld
- Laboratoire GBA, EA4627, Conservatoire National des Arts et Métiers, Paris, France
| | - Jean-François Zagury
- Laboratoire GBA, EA4627, Conservatoire National des Arts et Métiers, Paris, France
| | - Nathalie Lagarde
- Laboratoire GBA, EA4627, Conservatoire National des Arts et Métiers, Paris, France
| | - Matthieu Montes
- Laboratoire GBA, EA4627, Conservatoire National des Arts et Métiers, Paris, France
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Hollensen AK, Thomsen R, Bak RO, Petersen CC, Ermegaard ER, Aagaard L, Damgaard CK, Mikkelsen JG. Improved microRNA suppression by WPRE-linked tough decoy microRNA sponges. RNA 2017; 23:1247-1258. [PMID: 28487381 PMCID: PMC5513069 DOI: 10.1261/rna.061192.117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 04/26/2017] [Indexed: 05/02/2023]
Abstract
Our genes are post-transcriptionally regulated by microRNAs (miRNAs) inducing translational suppression and degradation of targeted mRNAs. Strategies to inhibit miRNAs in a spatiotemporal manner in a desired cell type or tissue, or at a desired developmental stage, can be crucial for understanding miRNA function and for pushing forward miRNA suppression as a feasible rationale for genetic treatment of disease. For such purposes, RNA polymerase II (RNA Pol II)-transcribed tough decoy (TuD) miRNA inhibitors are particularly attractive. Here, we demonstrate augmented miRNA suppression capacity of TuD RNA hairpins linked to the Woodchuck hepatitis virus post-transcriptional regulatory element (WPRE). This effect is position-dependent and evident only when the WPRE is positioned upstream of the TuD. In accordance, inclusion of the WPRE does not change nuclear export, translation, total levels of TuD-containing RNA transcripts, or cytoplasmic P-body localization, suggesting that previously reported WPRE functions are negligible for improved TuD function. Notably, deletion analysis of TuD-fused WPRE unveils truncated WPRE variants resulting in optimized miRNA suppression. Together, our findings add to the guidelines for production of WPRE-supported anti-miRNA TuDs.
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Affiliation(s)
- Anne Kruse Hollensen
- Department of Biomedicine, HEALTH, Aarhus University, DK-8000 Aarhus C, Denmark
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Rune Thomsen
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Rasmus O Bak
- Department of Biomedicine, HEALTH, Aarhus University, DK-8000 Aarhus C, Denmark
- Department of Pediatrics, Stanford University, Stanford, California 94305, USA
| | | | - Eva R Ermegaard
- Department of Biomedicine, HEALTH, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Lars Aagaard
- Department of Biomedicine, HEALTH, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Christian Kroun Damgaard
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-8000 Aarhus C, Denmark
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Esch L, Schaffrath U. An Update on Jacalin-Like Lectins and Their Role in Plant Defense. Int J Mol Sci 2017; 18:ijms18071592. [PMID: 28737678 PMCID: PMC5536079 DOI: 10.3390/ijms18071592] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/17/2017] [Accepted: 07/20/2017] [Indexed: 12/11/2022] Open
Abstract
Plant lectins are proteins that reversibly bind carbohydrates and are assumed to play an important role in plant development and resistance. Through the binding of carbohydrate ligands, lectins are involved in the perception of environmental signals and their translation into phenotypical responses. These processes require down-stream signaling cascades, often mediated by interacting proteins. Fusing the respective genes of two interacting proteins can be a way to increase the efficiency of this process. Most recently, proteins containing jacalin-related lectin (JRL) domains became a subject of plant resistance responses research. A meta-data analysis of fusion proteins containing JRL domains across different kingdoms revealed diverse partner domains ranging from kinases to toxins. Among them, proteins containing a JRL domain and a dirigent domain occur exclusively within monocotyledonous plants and show an unexpected high range of family member expansion compared to other JRL-fusion proteins. Rice, wheat, and barley plants overexpressing OsJAC1, a member of this family, are resistant against important fungal pathogens. We discuss the possibility that JRL domains also function as a decoy in fusion proteins and help to alert plants of the presence of attacking pathogens.
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Affiliation(s)
- Lara Esch
- Department of Plant Physiology, RWTH Aachen University, 52056 Aachen, Germany.
| | - Ulrich Schaffrath
- Department of Plant Physiology, RWTH Aachen University, 52056 Aachen, Germany.
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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. Mol Ther 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Yano S, Takehara K, Tazawa H, Kishimoto H, Urata Y, Kagawa S, Fujiwara T, Hoffman RM. Cell-cycle-dependent drug-resistant quiescent cancer cells induce tumor angiogenesis after chemotherapy as visualized by real-time FUCCI imaging. Cell Cycle 2017; 16:406-414. [PMID: 27715464 PMCID: PMC5351920 DOI: 10.1080/15384101.2016.1220461] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 07/31/2016] [Indexed: 01/26/2023] Open
Abstract
We previously demonstrated that quiescent cancer cells in a tumor are resistant to conventional chemotherapy as visualized with a fluorescence ubiquitination cell cycle indicator (FUCCI). We also showed that proliferating cancer cells exist in a tumor only near nascent vessels or on the tumor surface as visualized with FUCCI and green fluorescent protein (GFP)-expressing tumor vessels. In the present study, we show the relationship between cell-cycle phase and chemotherapy-induced tumor angiogenesis using in vivo FUCCI real-time imaging of the cell cycle and nestin-driven GFP to detect nascent blood vessels. We observed that chemotherapy-treated tumors, consisting of mostly of quiescent cancer cells after treatment, had much more and deeper tumor vessels than untreated tumors. These newly-vascularized cancer cells regrew rapidly after chemotherapy. In contrast, formerly quiescent cancer cells decoyed to S/G2 phase by a telomerase-dependent adenovirus did not induce tumor angiogenesis. The present results further demonstrate the importance of the cancer-cell position in the cell cycle in order that chemotherapy be effective and not have the opposite effect of stimulating tumor angiogenesis and progression.
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Affiliation(s)
- Shuya Yano
- AntiCancer, Inc., San Diego, CA, USA
- Department of Surgery, University of California San Diego, CA, USA
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kiyoto Takehara
- AntiCancer, Inc., San Diego, CA, USA
- Department of Surgery, University of California San Diego, CA, USA
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Hiroshi Tazawa
- Center for Innovative Clinical Medicine, Okayama University Hospital, Okayama, Japan
| | - Hiroyuki Kishimoto
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | | | - Shunsuke Kagawa
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Toshiyoshi Fujiwara
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Robert M. Hoffman
- AntiCancer, Inc., San Diego, CA, USA
- Department of Surgery, University of California San Diego, CA, USA
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Kemme CA, Nguyen D, Chattopadhyay A, Iwahara J. Regulation of transcription factors via natural decoys in genomic DNA. Transcription 2016; 7:115-20. [PMID: 27384377 PMCID: PMC4984682 DOI: 10.1080/21541264.2016.1188873] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 05/05/2016] [Accepted: 05/06/2016] [Indexed: 01/24/2023] Open
Abstract
Eukaryotic genomic DNA contains numerous high-affinity sites for transcription factors. Only a small fraction of these sites directly regulates target genes. Other high-affinity sites can serve as naturally present decoys that sequester transcription factors. Such natural decoys in genomic DNA may provide novel regulatory mechanisms for transcription factors.
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Affiliation(s)
- Catherine A. Kemme
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Dan Nguyen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Abhijnan Chattopadhyay
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
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Yano S, Takehara K, Zhao M, Tan Y, Han Q, Li S, Bouvet M, Fujiwara T, Hoffman RM. Tumor-specific cell-cycle decoy by Salmonella typhimurium A1-R combined with tumor-selective cell-cycle trap by methioninase overcome tumor intrinsic chemoresistance as visualized by FUCCI imaging. Cell Cycle 2016; 15:1715-23. [PMID: 27152859 DOI: 10.1080/15384101.2016.1181240] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We previously reported real-time monitoring of cell cycle dynamics of cancer cells throughout a live tumor intravitally using a fluorescence ubiquitination cell cycle indicator (FUCCI). Approximately 90% of cancer cells in the center and 80% of total cells of an established tumor are in G0/G1 phase. Longitudinal real-time FUCCI imaging demonstrated that cytotoxic agents killed only proliferating cancer cells at the surface and, in contrast, and had little effect on the quiescent cancer cells. Resistant quiescent cancer cells restarted cycling after the cessation of chemotherapy. Thus cytotoxic chemotherapy which targets cells in S/G2/M, is mostly ineffective on solid tumors, but causes toxic side effects on tissues with high fractions of cycling cells, such as hair follicles, bone marrow and the intestinal lining. We have termed this phenomenon tumor intrinsic chemoresistance (TIC). We previously demonstrated that tumor-targeting Salmonella typhimurium A1-R (S. typhimurium A1-R) decoyed quiescent cancer cells in tumors to cycle from G0/G1 to S/G2/M demonstrated by FUCCI imaging. We have also previously shown that when cancer cells were treated with recombinant methioninase (rMETase), the cancer cells were selectively trapped in S/G2, shown by cell sorting as well as by FUCCI. In the present study, we show that sequential treatment of FUCCI-expressing stomach cancer MKN45 in vivo with S. typhimurium A1-R to decoy quiescent cancer cells to cycle, with subsequent rMETase to selectively trap the decoyed cancer cells in S/G2 phase, followed by cisplatinum (CDDP) or paclitaxel (PTX) chemotherapy to kill the decoyed and trapped cancer cells completely prevented or regressed tumor growth. These results demonstrate the effectiveness of the praradigm of "decoy, trap and shoot" chemotherapy.
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Affiliation(s)
- Shuya Yano
- a AntiCancer Inc. , San Diego , CA.,b Department of Surgery , University of California , San Diego , CA.,c Department of Gastroenterological Surgery , Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences , Okayama , Japan
| | - Kiyoto Takehara
- a AntiCancer Inc. , San Diego , CA.,b Department of Surgery , University of California , San Diego , CA.,c Department of Gastroenterological Surgery , Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences , Okayama , Japan
| | | | | | | | | | - Michael Bouvet
- b Department of Surgery , University of California , San Diego , CA
| | - Toshiyoshi Fujiwara
- c Department of Gastroenterological Surgery , Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences , Okayama , Japan
| | - Robert M Hoffman
- a AntiCancer Inc. , San Diego , CA.,b Department of Surgery , University of California , San Diego , CA
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40
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Kroj T, Chanclud E, Michel‐Romiti C, Grand X, Morel J. Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread. New Phytol 2016; 210:618-26. [PMID: 26848538 PMCID: PMC5067614 DOI: 10.1111/nph.13869] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 12/16/2015] [Indexed: 05/18/2023]
Abstract
Plant immune receptors of the class of nucleotide-binding and leucine-rich repeat domain (NLR) proteins can contain additional domains besides canonical NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC)) and leucine-rich repeat (LRR) domains. Recent research suggests that these additional domains act as integrated decoys recognizing effectors from pathogens. Proteins homologous to integrated decoys are suspected to be effector targets and involved in disease or resistance. Here, we scrutinized 31 entire plant genomes to identify putative integrated decoy domains in NLR proteins using the Interpro search. The involvement of the Zinc Finger-BED type (ZBED) protein containing a putative decoy domain, called BED, in rice (Oryza sativa) resistance was investigated by evaluating susceptibility to the blast fungus Magnaporthe oryzae in rice over-expression and knock-out mutants. This analysis showed that all plants tested had integrated various atypical protein domains into their NLR proteins (on average 3.5% of all NLR proteins). We also demonstrated that modifying the expression of the ZBED gene modified disease susceptibility. This study suggests that integration of decoy domains in NLR immune receptors is widespread and frequent in plants. The integrated decoy model is therefore a powerful concept to identify new proteins involved in disease resistance. Further in-depth examination of additional domains in NLR proteins promises to unravel many new proteins of the plant immune system.
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Affiliation(s)
- Thomas Kroj
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
| | - Emilie Chanclud
- Université Montpellier2 Place Eugène Bataillon34095Montpellier Cedex 5France
| | - Corinne Michel‐Romiti
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
| | - Xavier Grand
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
| | - Jean‐Benoit Morel
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
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41
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Yano S, Zhang Y, Zhao M, Hiroshima Y, Miwa S, Uehara F, Kishimoto H, Tazawa H, Bouvet M, Fujiwara T, Hoffman RM. Tumor-targeting Salmonella typhimurium A1-R decoys quiescent cancer cells to cycle as visualized by FUCCI imaging and become sensitive to chemotherapy. Cell Cycle 2015; 13:3958-63. [PMID: 25483077 DOI: 10.4161/15384101.2014.964115] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Quiescent cancer cells are resistant to cytotoxic agents which target only proliferating cancer cells. Time-lapse imaging demonstrated that tumor-targeting Salmonella typhimurium A1-R (A1-R) decoyed cancer cells in monolayer culture and in tumor spheres to cycle from G0/G1 to S/G2/M, as demonstrated by fluorescence ubiquitination-based cell cycle indicator (FUCCI) imaging. A1-R infection of FUCCI-expressing subcutaneous tumors growing in nude mice also decoyed quiescent cancer cells, which were the majority of the cells in the tumors, to cycle from G0/G1 to S/G2/M, thereby making them sensitive to cytotoxic agents. The combination of A1-R and cisplatinum or paclitaxel reduced tumor size compared with A1-R monotherapy or cisplatinum or paclitaxel alone. The results of this study demonstrate that A1-R can decoy quiescent cancer cells to cycle to S/G2/M and sensitize them to cytotoxic chemotherapy. These results suggest a new paradigm of bacterial-decoy chemotherapy of cancer.
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Fujisaki K, Abe Y, Ito A, Saitoh H, Yoshida K, Kanzaki H, Kanzaki E, Utsushi H, Yamashita T, Kamoun S, Terauchi R. Rice Exo70 interacts with a fungal effector, AVR-Pii, and is required for AVR-Pii-triggered immunity. Plant J 2015; 83:875-87. [PMID: 26186703 DOI: 10.1111/tpj.12934] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/26/2015] [Accepted: 06/26/2015] [Indexed: 05/03/2023]
Abstract
Vesicle trafficking including the exocytosis pathway is intimately associated with host immunity against pathogens. However, we still have insufficient knowledge about how it contributes to immunity, and how pathogen factors affect it. In this study, we explore host factors that interact with the Magnaporthe oryzae effector AVR-Pii. Gel filtration chromatography and co-immunoprecipitation assays identified a 150 kDa complex of proteins in the soluble fraction comprising AVR-Pii and OsExo70-F2 and OsExo70-F3, two rice Exo70 proteins presumably involved in exocytosis. Simultaneous knockdown of OsExo70-F2 and F3 totally abrogated Pii immune receptor-dependent resistance, but had no effect on Pia- and Pik-dependent resistance. Knockdown levels of OsExo70-F3 but not OsExo70-F2 correlated with reduction of Pii function, suggesting that OsExo70-F3 is specifically involved in Pii-dependent resistance. Under our current experimental conditions, over-expression of AVR-Pii or knockdown of OsExo70-F2 and -F3 genes in rice did not affect the virulence of compatible isolates of M. oryzae. AVR-Pii interaction with OsExo70-F3 appears to play a crucial role in immunity triggered by Pii, suggesting a role for OsExo70 as a decoy or helper in Pii/AVR-Pii interactions.
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Affiliation(s)
- Koki Fujisaki
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Yoshiko Abe
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Akiko Ito
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | | | - Kentaro Yoshida
- Organization of Advanced Science and Technology, Kobe University, Kobe, Hyogo, Japan
| | | | - Eiko Kanzaki
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Hiroe Utsushi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | | | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
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An HJ, Lee WR, Kim KH, Kim JY, Kim WH, Park KK, Youn SW. Effects of Smad decoy ODN on shear stress-induced atherosclerotic ApoE-/-mouse. Int J Clin Exp Pathol 2015; 8:3971-3978. [PMID: 26097583 PMCID: PMC4466970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/23/2015] [Indexed: 06/04/2023]
Abstract
Atherosclerosis is a complex disease which involves both genetic and environmental factors in its development and progression. Shear stress is the drag force per unit area acting on the endothelium as a result of blood flow, and it plays a critical role in plaque location and progression. TGF-β1 is often regarded to have pro-atherosclerotic effect on vascular disease. TGF-β1 downstream targets Smad, for regulating a set of genes associated with atherosclerosis. Therefore, modulation of TGF-β1 and Smad expression may be the important targets for the prevention and treatment of shear stress-induced vascular disease. However, the precise mechanism of the anti-atherosclerotic effects of novel therapeutic approach has not been elucidated by using animal models regarding the shear stress-induced vascular disease. Therefore, we designed to test whether Smad decoy ODN would prevent the development of atherosclerosis in the shear stress-induced ApoE-/-mice on a western diet. We examined the effect of cast placement on the development of atherosclerosis, and the carotid artery was harvested at the sacrifice to observe histological changes. Also, we evaluated the impact of Smad decoy ODN in the regulation of genes expression related to atherosclerosis, including TGF-β1, PAI-1, and α-SMA. Our results showed that western diet with cast placement developed atherosclerosis in ApoE-/-mouse. Also, administration of Smad decoy ODN decreases the expression of TGF-β1, PAI-1, and α-SMA. These results demonstrate the potential of Smad decoy ODN to prevent the progression of atherosclerosis in ApoE-/-mouse model with western diet and shear stress.
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Affiliation(s)
- Hyun-Jin An
- Department of Pathology, College of Medicine, Catholic University of DaeguDaegu, South Korea
| | - Woo-Ram Lee
- Department of Pathology, College of Medicine, Catholic University of DaeguDaegu, South Korea
| | - Kyung-Hyun Kim
- Department of Pathology, College of Medicine, Catholic University of DaeguDaegu, South Korea
| | - Jung-Yeon Kim
- Department of Pathology, College of Medicine, Catholic University of DaeguDaegu, South Korea
| | - Woon-Hae Kim
- Department of Pathology, College of Medicine, Catholic University of DaeguDaegu, South Korea
| | - Kwan-Kyu Park
- Department of Pathology, College of Medicine, Catholic University of DaeguDaegu, South Korea
| | - Sung Won Youn
- Department of Radiology, College of Medicine, Catholic University of DaeguDaegu, South Korea
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Wu CH, Krasileva KV, Banfield MJ, Terauchi R, Kamoun S. The "sensor domains" of plant NLR proteins: more than decoys? Front Plant Sci 2015; 6:134. [PMID: 25798142 PMCID: PMC4350390 DOI: 10.3389/fpls.2015.00134] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 02/19/2015] [Indexed: 05/18/2023]
Affiliation(s)
- Chih-Hang Wu
- The Sainsbury Laboratory, Norwich Research ParkNorwich, UK
| | - Ksenia V. Krasileva
- The Sainsbury Laboratory, Norwich Research ParkNorwich, UK
- The Genome Analysis Centre, Norwich Research ParkNorwich, UK
| | - Mark J. Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research ParkNorwich, UK
| | | | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research ParkNorwich, UK
- *Correspondence: Sophien Kamoun,
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Strobel BN, Butler MJ. Monitoring Whooping Crane Abundance Using Aerial Surveys: Influences on Detectability. WILDLIFE SOC B 2014; 38:188-195. [PMID: 26388657 PMCID: PMC4571528 DOI: 10.1002/wsb.374] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 06/30/2013] [Indexed: 11/10/2022]
Abstract
The whooping crane (Grus americana), an endangered species, has been counted on its winter grounds in Texas, USA, since 1950 using fixed-wing aircraft. Many shortcomings of the traditional survey technique have been identified, calling into question its efficacy, defensibility, repeatability, and usefulness into the future. To improve and standardize monitoring effort, we began investigating new survey techniques. Here we focus on efficacy of line transect-based distance sampling during aerial surveys. We conducted a preliminary test of distance sampling during winter 2010-2011 while flying the traditional survey, which indicated that detectability within 500 m of transects was 0.558 (SE = 0.031). We then used an experimental decoy survey to evaluate impacts of observer experience, sun position, distance from transect, and group size on detectability. Our results indicated decoy detectability increased with group size and exhibited a quadratic relationship with distance likely due to pontoons on the aircraft. We found that detectability was 2.704 times greater when the sun was overhead and 3.912 times greater when the sun was at the observer's back than when it was in the observer's eyes. We found that an inexperienced observer misclassified non-target objects more often than an experienced observer. During the decoy experiment we used marks on the struts to categorize distances into intervals, but we found that observers misclassified distances 46.7% of the time (95% CI = 37.0-56.6%). Also, we found that detectability of individuals within detected groups was affected by group size and distance from transect. We discuss how these results inform design and implementation of future whooping crane monitoring efforts. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.
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Abstract
The role of non-coding RNAs (ncRNAs), both short and long ncRNAs, in the regulation of gene expression has become evident in recent years. Non-coding RNA-based regulation is achieved through a variety of mechanisms; some are relatively well-characterized, while others are much less understood. MicroRNAs (miRNAs), a class of endogenous small RNAs, function as master regulators of gene expression in eukaryotic organisms. A notable, recently discovered role for long ncRNAs is that of miRNA decoys, also referred to as target mimics or sponges, in which long ncRNAs carry a short stretch of sequence sharing homology to miRNA-binding sites in endogenous targets. As a consequence, miRNA decoys are able to sequester and inactivate miRNA function. Engineered miRNA decoys are also efficacious and useful tools for studying gene function. We recently demonstrated that the potential of miRNA decoys to inactivate miRNAs in the model plants Arabidopsis thaliana and Nicotiana benthamiana is dependent on the level of sequence complementarity to miRNAs of interest. The flexibility of the miRNA decoy approach in sequence-dependent miRNA inactivation, backbone choice, ability to simultaneously inactivate multiple miRNAs, and more importantly, to achieve a desirable level of miRNA inactivation, makes it a potentially useful tool for crop improvement. This research addendum reports the functional extension of miRNA decoys from model plants to crops. Furthermore, endogenous miRNA decoys, first described in plants, have been proposed to play a significant role in regulating the transcriptome in eukaryotes. Using computational analysis, we have identified numerous endogenous sequences with potential miRNA decoy activity for conserved miRNAs in several plant species. Our data suggest that endogenous miRNA decoys can be widespread in plants and may be a component of the global gene expression regulatory network in plants.
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Yu HP, Wang ZT, Xiao K, Shao L, Li GQ. The presence of conspecific decoys enhances the attractiveness of an NaCl resource to the yellow-spined locust, Ceracris kiangsu. J Insect Sci 2011; 11:45. [PMID: 21539416 PMCID: PMC3281467 DOI: 10.1673/031.011.0145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2010] [Accepted: 05/20/2010] [Indexed: 05/30/2023]
Abstract
Adults of the yellow-spined bamboo locust, Ceracris kiangsu Tsai (Orthoptera: Oedipodidae), aggregate and gnaw at human urine-contaminated materials, a phenomenon termed puddling. Several urine-borne chemicals, including NaCl, are known to stimulate adult C. kiangsu to consume filter paper. Because in nature C. kiangsu adults may use cues to locate puddling resources, we tested the influence of conspecific decoys (dried C. kiangsu) on foraging and consumption of 3% NaCl-treated filter paper. In a two-choice test experiment in the laboratory, female adults showed no preference for filter papers (not treated with NaCl) with or without decoys. In contrast, C. kiangsu females consumed significantly more NaCl-treated filter paper on which conspecific decoys were attached than those without decoys in both the laboratory and in a bamboo forest. When the bait was changed to 3% NaCl plus the insecticide bisultap, significantly more C. kiangsu were killed in the bamboo forest when decoys were present, however the results were not significant when the experiment was done in the laboratory. Hence, moving towards conspecifics seems to facilitate NaCl resource foraging in C. kiangsu, suggesting that the presence of conspecifics promotes feeding on puddling resources.
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Affiliation(s)
- Hai-Ping Yu
- Department of Entomology, Key Laboratory of Monitoring and Management of Plant Diseases and Pests, Ministry of Agriculture, Nanjing Agricultural University; Nanjing, China, 210095
- These authors contributed equally to the research
| | - Zhi-Tian Wang
- Department of Entomology, Key Laboratory of Monitoring and Management of Plant Diseases and Pests, Ministry of Agriculture, Nanjing Agricultural University; Nanjing, China, 210095
- These authors contributed equally to the research
| | - Kai Xiao
- Department of Entomology, Key Laboratory of Monitoring and Management of Plant Diseases and Pests, Ministry of Agriculture, Nanjing Agricultural University; Nanjing, China, 210095
| | - Lin Shao
- Department of Entomology, Key Laboratory of Monitoring and Management of Plant Diseases and Pests, Ministry of Agriculture, Nanjing Agricultural University; Nanjing, China, 210095
| | - Guo-Qing Li
- Department of Entomology, Key Laboratory of Monitoring and Management of Plant Diseases and Pests, Ministry of Agriculture, Nanjing Agricultural University; Nanjing, China, 210095
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Abstract
The microRNA (miRNA) "sponge" method was introduced three years ago as a means to create continuous miRNA loss of function in cell lines and transgenic organisms. Sponge RNAs contain complementary binding sites to a miRNA of interest, and are produced from transgenes within cells. As with most miRNA target genes, a sponge's binding sites are specific to the miRNA seed region, which allows them to block a whole family of related miRNAs. This transgenic approach has proven to be a useful tool to probe miRNA functions in a variety of experimental systems. Here we will discuss the ways sponge and related constructs can be optimized and review recent applications of this method with particular emphasis on stable expression in cancer studies and in transgenic animals.
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Affiliation(s)
- Margaret S Ebert
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Gupta S, Chakraborti D, Basu D, Das S. In search of decoy/guardee to R genes: deciphering the role of sugars in defense against Fusarium wilt in chickpea. Plant Signal Behav 2010; 5:1081-7. [PMID: 20855953 PMCID: PMC3115073 DOI: 10.4161/psb.5.9.12234] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Plant responses are coordinately controlled by both external and internal signals. Apt perception of pathogen attack and its appropriate conversion to internal signals ultimately determine the outcome of innate immunity. The present review predicts the involvement of unconventional 'Guard/Decoy Model' in chickpea-Fusarium encounter. Rapid alkalinization factor is predicted to act as initial 'Gatekeeper decoy' counteracting fungal entry. Phospholipases and cystatins probably function as 'Guardees' being shielded by R gene(s). Serine Threonine Kinases decodes external pathogenic signals to in planta defense alarms. 14.3.3 provides clues to the wilt mechanism. The versatile sugars serve as signal generators and transmitters maintaining intra and inter cellular connectivity during stress.
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Affiliation(s)
- Sumanti Gupta
- Division of Plant Biology; Bose Institute; Centenary Campus; Kankurgachi, Kolkata India
| | - Dipankar Chakraborti
- Division of Plant Biology; Bose Institute; Centenary Campus; Kankurgachi, Kolkata India
- P.G. Department of Biotechnology; St. Xavier's College; Kolkata, India
| | - Debabrata Basu
- Division of Plant Biology; Bose Institute; Centenary Campus; Kankurgachi, Kolkata India
| | - Sampa Das
- Division of Plant Biology; Bose Institute; Centenary Campus; Kankurgachi, Kolkata India
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Zariñán T, Perez-Solís MA, Maya-Núñez G, Casas-González P, Conn PM, Dias JA, Ulloa-Aguirre A. Dominant negative effects of human follicle-stimulating hormone receptor expression-deficient mutants on wild-type receptor cell surface expression. Rescue of oligomerization-dependent defective receptor expression by using cognate decoys. Mol Cell Endocrinol 2010; 321:112-22. [PMID: 20206665 PMCID: PMC2854281 DOI: 10.1016/j.mce.2010.02.027] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 02/22/2010] [Accepted: 02/22/2010] [Indexed: 12/31/2022]
Abstract
Current evidence indicates that G protein-coupled receptors form dimers that may affect biogenesis and membrane targeting of the complexed receptors. We here analyzed whether expression-deficient follicle-stimulating hormone receptor (FSHR) mutants exert dominant negative actions on wild-type FSHR cell surface membrane expression. Co-transfection of constant amounts of wild-type receptor cDNA and increasing quantities of mutant (R556A or R618A) FSHR cDNAs progressively decreased agonist-stimulated cAMP accumulation, [(125)I]-FSH binding, and plasma membrane expression of the mature wild-type FSHR species. Co-transfection of wild-type FSHR fragments involving transmembrane domains 5-6, or transmembrane domain 7 and/or the carboxyl-terminus specifically rescued wild-type FSHR expression from the transdominant inhibition by the mutants. Mutant FSHRs also inhibited function of the luteinizing hormone receptor but not that of the thyrotropin receptor or non-related receptors. Defective intracellular transport and/or interference with proper maturation due to formation of misfolded mutant:wild-type receptor complexes may explain the negative effects provoked by the altered FSHRs.
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Affiliation(s)
- Teresa Zariñán
- Research Unit in Reproductive Medicine, Hospital de Ginecobstetricia “Luis Castelazo Ayala”, Instituto Mexicano del Seguro Social, Mexico D.F., Mexico
| | - Marco A. Perez-Solís
- Research Unit in Reproductive Medicine, Hospital de Ginecobstetricia “Luis Castelazo Ayala”, Instituto Mexicano del Seguro Social, Mexico D.F., Mexico
| | - Guadalupe Maya-Núñez
- Research Unit in Reproductive Medicine, Hospital de Ginecobstetricia “Luis Castelazo Ayala”, Instituto Mexicano del Seguro Social, Mexico D.F., Mexico
| | - Patricia Casas-González
- Research Unit in Reproductive Medicine, Hospital de Ginecobstetricia “Luis Castelazo Ayala”, Instituto Mexicano del Seguro Social, Mexico D.F., Mexico
| | - P. Michael Conn
- Research Unit in Reproductive Medicine, Hospital de Ginecobstetricia “Luis Castelazo Ayala”, Instituto Mexicano del Seguro Social, Mexico D.F., Mexico
- Oregon National Primate Research Center, Oregon Health Sciences University, Beaverton, Oregon, USA
| | - James A. Dias
- Wadsworth Center, New York State Dept of Health, Albany, NY, and Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY, USA
| | - Alfredo Ulloa-Aguirre
- Research Unit in Reproductive Medicine, Hospital de Ginecobstetricia “Luis Castelazo Ayala”, Instituto Mexicano del Seguro Social, Mexico D.F., Mexico
- Oregon National Primate Research Center, Oregon Health Sciences University, Beaverton, Oregon, USA
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