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Goto R, Miyakawa S, Inomata E, Takami T, Yamaura J, Nakamura Y. De novo sequencing of highly modified therapeutic oligonucleotides by hydrophobic tag sequencing coupled with LC-MS. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:78-93. [PMID: 27935159 DOI: 10.1002/jms.3902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 11/23/2016] [Accepted: 11/24/2016] [Indexed: 06/06/2023]
Abstract
Correct sequences are prerequisite for quality control of therapeutic oligonucleotides. However, there is no definitive method available for determining sequences of highly modified therapeutic RNAs, and thereby, most of the oligonucleotides have been used clinically without direct sequence determination. In this study, we developed a novel sequencing method called 'hydrophobic tag sequencing'. Highly modified oligonucleotides are sequenced by partially digesting oligonucleotides conjugated with a 5'-hydrophobic tag, followed by liquid chromatography-mass spectrometry analysis. 5'-Hydrophobic tag-printed fragments (5'-tag degradates) can be separated in order of their molecular masses from tag-free oligonucleotides by reversed-phase liquid chromatography. As models for the sequencing, the anti-VEGF aptamer (Macugen) and the highly modified 38-mer RNA sequences were analyzed under blind conditions. Most nucleotides were identified from the molecular weight of hydrophobic 5'-tag degradates calculated from monoisotopic mass in simple full mass data. When monoisotopic mass could not be assigned, the nucleotide was estimated using the molecular weight of the most abundant mass. The sequences of Macugen and 38-mer RNA perfectly matched the theoretical sequences. The hydrophobic tag sequencing worked well to obtain simple full mass data, resulting in accurate and clear sequencing. The present study provides for the first time a de novo sequencing technology for highly modified RNAs and contributes to quality control of therapeutic oligonucleotides. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- R Goto
- Bioanalysis Business Department, CMIC Pharma Science Co., Ltd., 17-18, Nakahata-cho, Nishiwaki-shi, Hyogo, 677-0032, Japan
| | - S Miyakawa
- Exploratory Research Laboratory, RIBOMIC Inc., 3-16-13, Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
| | - E Inomata
- Exploratory Research Laboratory, RIBOMIC Inc., 3-16-13, Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
| | - T Takami
- Bioanalysis Department, CMIC, Inc., Hoffman Estates, Illinois, 60192-3702, USA
| | - J Yamaura
- Exploratory Research Laboratory, RIBOMIC Inc., 3-16-13, Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
| | - Y Nakamura
- Exploratory Research Laboratory, RIBOMIC Inc., 3-16-13, Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan
- Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
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52
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Mossanen JC, Krenkel O, Ergen C, Govaere O, Liepelt A, Puengel T, Heymann F, Kalthoff S, Lefebvre E, Eulberg D, Luedde T, Marx G, Strassburg CP, Roskams T, Trautwein C, Tacke F. Chemokine (C-C motif) receptor 2-positive monocytes aggravate the early phase of acetaminophen-induced acute liver injury. Hepatology 2016; 64:1667-1682. [PMID: 27302828 DOI: 10.1002/hep.28682] [Citation(s) in RCA: 236] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/09/2016] [Accepted: 05/25/2016] [Indexed: 12/12/2022]
Abstract
UNLABELLED Acetaminophen (APAP, paracetamol) poisoning is a leading cause of acute liver failure (ALF) in humans and induces hepatocyte necrosis, followed by activation of the innate immune system, further aggravating liver injury. The role of infiltrating monocytes during the early phase of ALF is still ambiguous. Upon experimental APAP overdose in mice, monocyte-derived macrophages (MoMFs) massively accumulated in injured liver within 12-24 hours, whereas the number of tissue-resident macrophages (Kupffer cells) decreased. Influx of MoMFs is dependent on the chemokine receptor, chemokine (C-C motif) receptor 2 (CCR2), given that Ccr2-/- mice display reduced infiltration of monocytes and attenuated liver injury post-APAP overdose at early time points. As evidenced by intravital multiphoton microscopy of Ccr2 reporter mice, CCR2+ monocytes infiltrate liver as early as 8-12 hours post-APAP overdose and form dense cellular clusters around necrotic areas. CCR2+ MoMFs express a distinct pattern of inflammatory, but also repair-associated, genes in injured livers. Adoptive transfer experiments revealed that MoMFs primarily exert proinflammatory functions early post-APAP, thereby aggravating liver injury. Consequently, early pharmacological inhibition of either chemokine (C-C motif) ligand (CCL2; by the inhibitor, mNOX-E36) or CCR2 (by the orally available dual CCR2/CCR5 inhibitor, cenicriviroc) reduces monocyte infiltration and APAP-induced liver injury (AILI) in mice. Importantly, neither the early nor continuous inhibition of CCR2 hinder repair processes during resolution from injury. In line with this, human livers of ALF patients requiring liver transplantation reveal increased CD68+ hepatic macrophage numbers with massive infiltrates of periportal CCR2+ macrophages that display a proinflammatory polarization. CONCLUSION Infiltrating monocyte-derived macrophages aggravate APAP hepatotoxicity, and the pharmacological inhibition of either CCL2 or CCR2 might bear therapeutic potential by reducing the inflammatory reaction during the early phase of AILI. (Hepatology 2016;64:1667-1682).
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Affiliation(s)
- Jana C Mossanen
- Department of Medicine III, University Hospital Aachen, Aachen, Germany.,Department of Intensive and Intermediate Care, University Hospital Aachen, Aachen, Germany
| | - Oliver Krenkel
- Department of Medicine III, University Hospital Aachen, Aachen, Germany
| | - Can Ergen
- Department of Medicine III, University Hospital Aachen, Aachen, Germany
| | - Olivier Govaere
- Department of Imaging & Pathology, University of Leuven, Leuven, Belgium
| | - Anke Liepelt
- Department of Medicine III, University Hospital Aachen, Aachen, Germany
| | - Tobias Puengel
- Department of Medicine III, University Hospital Aachen, Aachen, Germany
| | - Felix Heymann
- Department of Medicine III, University Hospital Aachen, Aachen, Germany
| | - Sandra Kalthoff
- Department of Medicine I, University Hospital Bonn, Bonn, Germany
| | | | | | - Tom Luedde
- Department of Medicine III, University Hospital Aachen, Aachen, Germany
| | - Gernot Marx
- Department of Intensive and Intermediate Care, University Hospital Aachen, Aachen, Germany
| | | | - Tania Roskams
- Department of Imaging & Pathology, University of Leuven, Leuven, Belgium
| | | | - Frank Tacke
- Department of Medicine III, University Hospital Aachen, Aachen, Germany.
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53
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Kufareva I. Chemokines and their receptors: insights from molecular modeling and crystallography. Curr Opin Pharmacol 2016; 30:27-37. [PMID: 27459124 PMCID: PMC5071139 DOI: 10.1016/j.coph.2016.07.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/07/2016] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
Abstract
Chemokines are small secreted proteins that direct cell migration in development, immunity, inflammation, and cancer. They do so by binding and activating specific G protein coupled receptors on the surface of migrating cells. Despite the importance of receptor:chemokine interactions, their structural basis remained unclear for a long time. In 2015, the first atomic resolution insights were obtained with the publication of X-ray structures for two distantly related receptors bound to chemokines. In conjunction with experiment-guided molecular modeling, the structures suggest a conserved receptor:chemokine complex architecture, while highlighting the diverse details and functional roles of individual interaction epitopes. Novel findings promote the development and detailed structural interpretation of the canonical two-site hypothesis of receptor:chemokine recognition, and suggest new avenues for pharmacological modulation of chemokine receptors.
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Affiliation(s)
- Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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54
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Kahsai AW, Wisler JW, Lee J, Ahn S, Cahill TJ, Dennison SM, Staus DP, Thomsen ARB, Anasti KM, Pani B, Wingler LM, Desai H, Bompiani KM, Strachan RT, Qin X, Alam SM, Sullenger BA, Lefkowitz RJ. Conformationally selective RNA aptamers allosterically modulate the β2-adrenoceptor. Nat Chem Biol 2016; 12:709-16. [PMID: 27398998 PMCID: PMC4990464 DOI: 10.1038/nchembio.2126] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/09/2016] [Indexed: 01/08/2023]
Abstract
G-protein-coupled receptor (GPCR) ligands function by stabilizing multiple, functionally distinct receptor conformations. This property underlies the ability of 'biased agonists' to activate specific subsets of a given receptor's signaling profile. However, stabilizing distinct active GPCR conformations to enable structural characterization of mechanisms underlying GPCR activation remains difficult. These challenges have accentuated the need for receptor tools that allosterically stabilize and regulate receptor function through unique, previously unappreciated mechanisms. Here, using a highly diverse RNA library combined with advanced selection strategies involving state-of-the-art next-generation sequencing and bioinformatics analyses, we identify RNA aptamers that bind a prototypical GPCR, the β2-adrenoceptor (β2AR). Using biochemical, pharmacological, and biophysical approaches, we demonstrate that these aptamers bind with nanomolar affinity at defined surfaces of the receptor, allosterically stabilizing active, inactive, and ligand-specific receptor conformations. The discovery of RNA aptamers as allosteric GPCR modulators significantly expands the diversity of ligands available to study the structural and functional regulation of GPCRs.
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Affiliation(s)
- Alem W. Kahsai
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - James W. Wisler
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - Jungmin Lee
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Seungkirl Ahn
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - Thomas J. Cahill
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710
| | - S. Moses Dennison
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710
| | - Dean P. Staus
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - Alex R. B. Thomsen
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - Kara M. Anasti
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710
| | - Biswaranjan Pani
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - Laura M. Wingler
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - Hemant Desai
- The University of North Carolina School of Medicine, Chapel Hill, NC 27516
| | - Kristin M. Bompiani
- Department of Surgery, Duke University Medical Center, Durham, NC, 27710
- Duke Translational Research Institute, Duke University Medical Center, Durham, NC, 27710
- The University of California, San Diego, Moores Cancer Center, La Jolla, CA 92093
| | | | - Xiaoxia Qin
- Genome Sequencing and Analysis Core Resource, Duke University, Durham, NC, 27710
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710
| | - Bruce A. Sullenger
- Department of Surgery, Duke University Medical Center, Durham, NC, 27710
- Duke Translational Research Institute, Duke University Medical Center, Durham, NC, 27710
| | - Robert J. Lefkowitz
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC, 27710
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55
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Brenneman J, Hill J, Pullen S. Emerging therapeutics for the treatment of diabetic nephropathy. Bioorg Med Chem Lett 2016; 26:4394-4402. [PMID: 27520943 DOI: 10.1016/j.bmcl.2016.07.079] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 07/27/2016] [Accepted: 07/29/2016] [Indexed: 02/06/2023]
Abstract
Diabetic nephropathy (DN) is the most common pathology contributing to the development of chronic kidney disease (CKD). DN caused by hypertension and unmitigated inflammation in diabetics, renders the kidneys unable to perform normally, and leads to renal fibrosis and organ failure. The increasing global prevalence of DN has been directly attributed to rising incidences of Type II diabetes, and is now the largest non-communicable cause of death worldwide. Despite the high morbidity, successful new treatments for DN are lacking. This review seeks to provide new insight on emerging clinical candidates under investigation for the treatment of DN.
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Affiliation(s)
- Jehrod Brenneman
- Small Molecule Discovery Research, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Rd., Ridgefield, CT 06877, USA.
| | - Jon Hill
- Research Networking, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Rd., Ridgefield, CT 06877, USA
| | - Steve Pullen
- Cardiometabolic Disease Research, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Rd., Ridgefield, CT 06877, USA
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56
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Menger M, Yarman A, Erdőssy J, Yildiz HB, Gyurcsányi RE, Scheller FW. MIPs and Aptamers for Recognition of Proteins in Biomimetic Sensing. BIOSENSORS 2016; 6:E35. [PMID: 27438862 PMCID: PMC5039654 DOI: 10.3390/bios6030035] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/04/2016] [Accepted: 07/11/2016] [Indexed: 12/12/2022]
Abstract
Biomimetic binders and catalysts have been generated in order to substitute the biological pendants in separation techniques and bioanalysis. The two major approaches use either "evolution in the test tube" of nucleotides for the preparation of aptamers or total chemical synthesis for molecularly imprinted polymers (MIPs). The reproducible production of aptamers is a clear advantage, whilst the preparation of MIPs typically leads to a population of polymers with different binding sites. The realization of binding sites in the total bulk of the MIPs results in a higher binding capacity, however, on the expense of the accessibility and exchange rate. Furthermore, the readout of the bound analyte is easier for aptamers since the integration of signal generating labels is well established. On the other hand, the overall negative charge of the nucleotides makes aptamers prone to non-specific adsorption of positively charged constituents of the sample and the "biological" degradation of non-modified aptamers and ionic strength-dependent changes of conformation may be challenging in some application.
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Affiliation(s)
- Marcus Menger
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, Potsdam D-14476, Germany.
| | - Aysu Yarman
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 25-26, Potsdam D-14476, Germany.
- Turkish-German University, Faculty of Science, Molecular Biotechnology, Sahinkaya Cad. No. 86, Bekoz, Istanbul 34820, Turkey.
| | - Júlia Erdőssy
- MTA-BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, Budapest H-1111, Hungary.
| | - Huseyin Bekir Yildiz
- Department of Materials Science and Nanotechnology Engineering, KTO Karatay University, Konya 42020, Turkey.
| | - Róbert E Gyurcsányi
- MTA-BME "Lendület" Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, Budapest H-1111, Hungary.
| | - Frieder W Scheller
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, Potsdam D-14476, Germany.
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 25-26, Potsdam D-14476, Germany.
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57
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Reautschnig P, Vogel P, Stafforst T. The notorious R.N.A. in the spotlight - drug or target for the treatment of disease. RNA Biol 2016; 14:651-668. [PMID: 27415589 PMCID: PMC5449091 DOI: 10.1080/15476286.2016.1208323] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
mRNA is an attractive drug target for therapeutic interventions. In this review we highlight the current state, clinical trials, and developments in antisense therapy, including the classical approaches like RNaseH-dependent oligomers, splice-switching oligomers, aptamers, and therapeutic RNA interference. Furthermore, we provide an overview on emerging concepts for using RNA in therapeutic settings including protein replacement by in-vitro-transcribed mRNAs, mRNA as vaccines and anti-allergic drugs. Finally, we give a brief outlook on early-stage RNA repair approaches that apply endogenous or engineered proteins in combination with short RNAs or chemically stabilized oligomers for the re-programming of point mutations, RNA modifications, and frame shift mutations directly on the endogenous mRNA.
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Affiliation(s)
- Philipp Reautschnig
- a Interfaculty Institute of Biochemistry, University of Tübingen Auf der Morgenstelle , Tübingen , Germany
| | - Paul Vogel
- a Interfaculty Institute of Biochemistry, University of Tübingen Auf der Morgenstelle , Tübingen , Germany
| | - Thorsten Stafforst
- a Interfaculty Institute of Biochemistry, University of Tübingen Auf der Morgenstelle , Tübingen , Germany
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58
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Heiat M, Ranjbar R, Fasihi-Ramandi M, Latifi AM, Rasaee MJ. Characterization of pharmacological properties of isolated single-stranded DNA aptamers against angiotensin II. Mol Cell Probes 2016; 30:238-245. [PMID: 27346721 DOI: 10.1016/j.mcp.2016.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 06/19/2016] [Accepted: 06/20/2016] [Indexed: 11/28/2022]
Abstract
Nucleic acid aptamers can be served as drugs, carriers and diagnostic probes in living systems. Before recruiting aptamers, their pharmacological characteristics should be determined. Here we intended to investigate four important properties of isolated ssDNA anti-angiotensin II aptamers (FLC112 and FLC125) including hemolytic activity, cytotoxicity, immunogenicity and serum stability through in vitro and in vivo models. The hemolytic effect and cytotoxicity potential of aptamers were measured through hemolysis test and MTT assay respectively. In the following test, the humoral immune responses to aptamers in BALB/c mice were assessed. The human serum stability of aptamers was also determined using real-time PCR (qPCR). The results of this study revealed that the FLC112 aptamer with its unique structure had slightly higher cytotoxicity and hemolysis effect (9.14% and 0.1 ± 0.037% respectively) relative to FLC125 (8.07% and 0.08 ± 0.045% respectively) at the highest concentration (5 μM). FLC112 showed ignorable immune response in mice and barely higher than FLC125. Serum stability test confirmed that FLC112 with 12 h had more nuclease stability than FLC125 with 8 h. Aptamer molecule analysis revealed that the structure, sequense composition and motifs are the determinative parameters in aptamer pharmacological properties.
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Affiliation(s)
- Mohammad Heiat
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Mahdi Fasihi-Ramandi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Mohammad Latifi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Rasaee
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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59
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Aptamers: A Feasible Technology in Cancer Immunotherapy. J Immunol Res 2016; 2016:1083738. [PMID: 27413756 PMCID: PMC4931050 DOI: 10.1155/2016/1083738] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/22/2016] [Indexed: 12/21/2022] Open
Abstract
Aptamers are single-chained RNA or DNA oligonucleotides (ODNs) with three-dimensional folding structures which allow them to bind to their targets with high specificity. Aptamers normally show affinities comparable to or higher than that of antibodies. They are chemically synthesized and therefore less expensive to manufacture and produce. A variety of aptamers described to date have been shown to be reliable in modulating immune responses against cancer by either blocking or activating immune receptors. Some of them have been conjugated to other molecules to target the immune system and reduce off-target side effects. Despite the success of first-line treatments against cancer, the elevated number of relapsing cases and the tremendous side effects shown by the commonly used agents hinder conventional treatments against cancer. The advantages provided by aptamers could enhance the therapeutic index of a given strategy and therefore enhance the antitumor effect. Here we recapitulate the provided benefits of aptamers with immunomodulatory activity described to date in cancer therapy and the benefits that aptamer-based immunotherapy could provide either alone or combined with first-line treatments in cancer therapy.
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60
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Perez-Gomez MV, Sanchez-Niño MD, Sanz AB, Zheng B, Martín-Cleary C, Ruiz-Ortega M, Ortiz A, Fernandez-Fernandez B. Targeting inflammation in diabetic kidney disease: early clinical trials. Expert Opin Investig Drugs 2016; 25:1045-58. [PMID: 27268955 DOI: 10.1080/13543784.2016.1196184] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION The age-standardized death rate from diabetic kidney disease increased by 106% from 1990 to 2013, indicating that novel therapeutic approaches are needed, in addition to the renin-angiotensin system (RAS) blockers currently in use. Clinical trial results of anti-fibrotic therapy have been disappointing. However, promising anti-inflammatory drugs are currently on phase 1 and 2 randomized controlled trials. AREAS COVERED The authors review the preclinical, phase 1 and 2 clinical trial information of drugs tested for diabetic kidney disease that directly target inflammation as a main or key mode of action. Agents mainly targeting other pathways, such as endothelin receptor or mineralocorticoid receptor blockers and vitamin D receptor activators are not discussed. EXPERT OPINION Agents targeting inflammation have shown promising results in the treatment of diabetic kidney disease when added on top of RAS blockade. The success of pentoxifylline in open label trials supports the concept of targeting inflammation. In early clinical trials, the pentoxifylline derivative CTP-499, the CCR2 inhibitor CCX140-B, the CCL2 inhibitor emapticap pegol and the JAK1/JAK2 inhibitor baricitinib were the most promising drugs for diabetic kidney disease. The termination of trials testing the anti-IL-1β antibody gevokizumab in 2015 will postpone the evaluation of therapies targeting inflammatory cytokines.
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Affiliation(s)
- Maria Vanessa Perez-Gomez
- a Division of Nephrology and Hypertension and FRIAT, IIS-Fundacion Jimenez Diaz, School of Medicine , UAM , Madrid , Spain.,b REDINREN , Madrid , Spain
| | - Maria Dolores Sanchez-Niño
- a Division of Nephrology and Hypertension and FRIAT, IIS-Fundacion Jimenez Diaz, School of Medicine , UAM , Madrid , Spain.,b REDINREN , Madrid , Spain
| | - Ana Belen Sanz
- a Division of Nephrology and Hypertension and FRIAT, IIS-Fundacion Jimenez Diaz, School of Medicine , UAM , Madrid , Spain.,b REDINREN , Madrid , Spain
| | - Binbin Zheng
- a Division of Nephrology and Hypertension and FRIAT, IIS-Fundacion Jimenez Diaz, School of Medicine , UAM , Madrid , Spain
| | - Catalina Martín-Cleary
- a Division of Nephrology and Hypertension and FRIAT, IIS-Fundacion Jimenez Diaz, School of Medicine , UAM , Madrid , Spain.,b REDINREN , Madrid , Spain
| | - Marta Ruiz-Ortega
- a Division of Nephrology and Hypertension and FRIAT, IIS-Fundacion Jimenez Diaz, School of Medicine , UAM , Madrid , Spain.,b REDINREN , Madrid , Spain
| | - Alberto Ortiz
- a Division of Nephrology and Hypertension and FRIAT, IIS-Fundacion Jimenez Diaz, School of Medicine , UAM , Madrid , Spain.,b REDINREN , Madrid , Spain
| | - Beatriz Fernandez-Fernandez
- a Division of Nephrology and Hypertension and FRIAT, IIS-Fundacion Jimenez Diaz, School of Medicine , UAM , Madrid , Spain.,b REDINREN , Madrid , Spain
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61
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Abstract
Aptamers are single strand DNA or RNA molecules, selected by an iterative process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Due to various advantages of aptamers such as high temperature stability, animal free, cost effective production and its high affinity and selectivity for its target make them attractive alternatives to monoclonal antibody for use in diagnostic and therapeutic purposes. Aptamer has been generated against vesicular endothelial growth factor 165 involved in age related macular degeneracy. Macugen was the first FDA approved aptamer based drug that was commercialized. Later other aptamers were also developed against blood clotting proteins, cancer proteins, antibody E, agents involved in diabetes nephropathy, autoantibodies involved in autoimmune disorders, etc. Aptamers have also been developed against viruses and could work with other antiviral agents in treating infections.
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Affiliation(s)
- Abhishek Parashar
- Research Scholar, Animal Biochemistry Division, National Dairy Research Institute , Karnal, India
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62
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Bjerregaard N, Andreasen PA, Dupont DM. Expected and unexpected features of protein-binding RNA aptamers. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:744-757. [PMID: 27173731 DOI: 10.1002/wrna.1360] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/03/2016] [Accepted: 04/04/2016] [Indexed: 12/28/2022]
Abstract
RNA molecules with high affinity to specific proteins can be isolated from libraries of up to 1016 different RNA sequences by systematic evolution of ligands by exponential enrichment (SELEX). These so-called protein-binding RNA aptamers are often interesting, e.g., as modulators of protein function for therapeutic use, for probing the conformations of proteins, for studies of basic aspects of nucleic acid-protein interactions, etc. Studies on the interactions between RNA aptamers and proteins display a number of expected and unexpected features, including the chemical nature of the interacting RNA-protein surfaces, the conformation of protein-bound aptamer versus free aptamer, the conformation of aptamer-bound protein versus free protein, and the effects of aptamers on protein function. Here, we review current insights into the details of RNA aptamer-protein interactions. WIREs RNA 2016, 7:744-757. doi: 10.1002/wrna.1360 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Nils Bjerregaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Peter A Andreasen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Daniel M Dupont
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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63
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Sharaf El Din UAA, Salem MM, Abdulazim DO. Stop chronic kidney disease progression: Time is approaching. World J Nephrol 2016; 5:258-273. [PMID: 27152262 PMCID: PMC4848149 DOI: 10.5527/wjn.v5.i3.258] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 01/26/2016] [Accepted: 02/24/2016] [Indexed: 02/06/2023] Open
Abstract
Progression of chronic kidney disease (CKD) is inevitable. However, the last decade has witnessed tremendous achievements in this field. Today we are optimistic; the dream of withholding this progression is about to be realistic. The recent discoveries in the field of CKD management involved most of the individual diseases leading the patients to end-stage renal disease. Most of these advances involved patients suffering diabetic kidney disease, chronic glomerulonephritis, polycystic kidney disease, renal amyloidosis and chronic tubulointerstitial disease. The chronic systemic inflammatory status and increased oxidative stress were also investigated. This inflammatory status influences the anti-senescence Klotho gene expression. The role of Klotho in CKD progression together with its therapeutic value are explored. The role of gut as a major source of inflammation, the pathogenesis of intestinal mucosal barrier damage, the role of intestinal alkaline phosphatase and the dietary and therapeutic implications add a novel therapeutic tool to delay CKD progression.
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64
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Structural basis for specific inhibition of Autotaxin by a DNA aptamer. Nat Struct Mol Biol 2016; 23:395-401. [PMID: 27043297 DOI: 10.1038/nsmb.3200] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/10/2016] [Indexed: 12/14/2022]
Abstract
ATX is a plasma lysophospholipase D that hydrolyzes lysophosphatidylcholine (LPC) and produces lysophosphatidic acid. To date, no ATX-inhibition-mediated treatment strategies for human diseases have been established. Here, we report anti-ATX DNA aptamers that inhibit ATX with high specificity and efficacy. We solved the crystal structure of ATX in complex with the anti-ATX aptamer RB011, at 2.0-Å resolution. RB011 binds in the vicinity of the active site through base-specific interactions, thus preventing the access of the choline moiety of LPC substrates. Using the structural information, we developed the modified anti-ATX DNA aptamer RB014, which exhibited in vivo efficacy in a bleomycin-induced pulmonary fibrosis mouse model. Our findings reveal the structural basis for the specific inhibition of ATX by the anti-ATX aptamer and highlight the therapeutic potential of anti-ATX aptamers for the treatment of human diseases, such as pulmonary fibrosis.
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65
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Gelinas AD, Davies DR, Janjic N. Embracing proteins: structural themes in aptamer-protein complexes. Curr Opin Struct Biol 2016; 36:122-32. [PMID: 26919170 DOI: 10.1016/j.sbi.2016.01.009] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/13/2016] [Accepted: 01/15/2016] [Indexed: 01/17/2023]
Abstract
Understanding the structural rules that govern specific, high-affinity binding characteristic of aptamer-protein interactions is important in view of the increasing use of aptamers across many applications. From the modest number of 16 aptamer-protein structures currently available, trends are emerging. The flexible phosphodiester backbone allows folding into precise three-dimensional structures using known nucleic acid motifs as scaffolds that orient specific functional groups for target recognition. Still, completely novel motifs essential for structure and function are found in modified aptamers with diversity-enhancing side chains. Aptamers and antibodies, two classes of macromolecules used as affinity reagents with entirely different backbones and composition, recognize protein epitopes of similar size and with comparably high shape complementarity.
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Affiliation(s)
- Amy D Gelinas
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, United States
| | - Douglas R Davies
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Nebojsa Janjic
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, United States.
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66
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Cui L, Peng R, Fu T, Zhang X, Wu C, Chen H, Liang H, Yang C, Tan W. Biostable L-DNAzyme for Sensing of Metal Ions in Biological Systems. Anal Chem 2016; 88:1850-5. [PMID: 26691677 PMCID: PMC4892185 DOI: 10.1021/acs.analchem.5b04170] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/22/2015] [Indexed: 12/13/2022]
Abstract
DNAzymes, an important type of metal ion-dependent functional nucleic acid, are widely applied in bioanalysis and biomedicine. However, the use of DNAzymes in practical applications has been impeded by the intrinsic drawbacks of natural nucleic acids, such as interferences from nuclease digestion and protein binding, as well as undesired intermolecular interactions with other nucleic acids. On the basis of reciprocal chiral substrate specificity, the enantiomer of D-DNAzyme, L-DNAzyme, could initiate catalytic cleavage activity with the same achiral metal ion as a cofactor. Meanwhile, by using the advantage of nonbiological L-DNAzyme, which is not subject to the interferences of biological matrixes, as recognition units, a facile and stable L-DNAzyme sensor was proposed for sensing metal ions in complex biological samples and live cells.
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Affiliation(s)
- Liang Cui
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Ruizi Peng
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Ting Fu
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Xiaobing Zhang
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Cuichen Wu
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
- Department
of Chemistry and Department of Physiology and Functional Genomics,
Center for Research at the Bio/Nano Interface, Health Cancer Center, University
of Florida, Gainesville, Florida 32611-7200, United States
| | - Huapei Chen
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Hao Liang
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Chaoyong
James Yang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory
for Chemical Biology of Fujian Province, The MOE Key Laboratory of
Spectrochemical Analysis & Instrumentation, Department of Chemical
Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Weihong Tan
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio
Sensing and Chemometrics, College of Chemistry and Chemical Engineering,
College of Biology, and Collaborative Research Center of Molecular
Engineering for Theranostics, Hunan University, Changsha 410082, China
- Department
of Chemistry and Department of Physiology and Functional Genomics,
Center for Research at the Bio/Nano Interface, Health Cancer Center, University
of Florida, Gainesville, Florida 32611-7200, United States
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67
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Ye X, Shi H, He X, Yu Y, He D, Tang J, Lei Y, Wang K. Cu-Au alloy nanostructures coated with aptamers: a simple, stable and highly effective platform for in vivo cancer theranostics. NANOSCALE 2016; 8:2260-2267. [PMID: 26743815 DOI: 10.1039/c5nr07017a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
As a star material in cancer theranostics, photoresponsive gold (Au) nanostructures may still have drawbacks, such as low thermal conductivity, irradiation-induced melting effect and high cost. To solve the problem, copper (Cu) with a much higher thermal conductivity and lower cost was introduced to generate a novel Cu-Au alloy nanostructure produced by a simple, gentle and one-pot synthetic method. Having the good qualities of both Cu and Au, the irregularly-shaped Cu-Au alloy nanostructures showed several advantages over traditional Au nanorods, including a broad and intense near-infrared (NIR) absorption band from 400 to 1100 nm, an excellent heating performance under laser irradiation at different wavelengths and even a notable photostability against melting. Then, via a simple conjugation of fluorophore-labeled aptamers on the Cu-Au alloy nanostructures, active targeting and signal output were simultaneously introduced, thus constructing a theranostic platform based on fluorophore-labeled, aptamer-coated Cu-Au alloy nanostructures. By using human leukemia CCRF-CEM cancer and Cy5-labeled aptamer Sgc8c (Cy5-Sgc8c) as the model, a selective fluorescence imaging and NIR photothermal therapy was successfully realized for both in vitro cancer cells and in vivo tumor tissues. It was revealed that Cy5-Sgc8c-coated Cu-Au alloy nanostructures were not only capable of robust target recognition and stable signal output for molecular imaging in complex biological systems, but also killed target cancer cells in mice with only five minutes of 980 nm irradiation. The platform was found to be simple, stable, biocompatible and highly effective, and shows great potential as a versatile tool for cancer theranostics.
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Affiliation(s)
- Xiaosheng Ye
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China.
| | - Hui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China.
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China.
| | - Yanru Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China.
| | - Dinggeng He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China.
| | - Jinlu Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China.
| | - Yanli Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China.
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Biology, Hunan University, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Changsha 410082, China.
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