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Taylor AI, Wan CJK, Donde MJ, Peak-Chew SY, Holliger P. A modular XNAzyme cleaves long, structured RNAs under physiological conditions and enables allele-specific gene silencing. Nat Chem 2022; 14:1295-1305. [PMID: 36064973 PMCID: PMC7613789 DOI: 10.1038/s41557-022-01021-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 07/08/2022] [Indexed: 11/07/2022]
Abstract
Nucleic-acid catalysts (ribozymes, DNA- and XNAzymes) cleave target (m)RNAs with high specificity but have shown limited efficacy in clinical applications. Here we report on the in vitro evolution and engineering of a highly specific modular RNA endonuclease XNAzyme, FR6_1, composed of 2'-deoxy-2'-fluoro-β-D-arabino nucleic acid (FANA). FR6_1 overcomes the activity limitations of previous DNA- and XNAzymes and can be retargeted to cleave highly structured full-length (>5 kb) BRAF and KRAS mRNAs at physiological Mg2+ concentrations with allelic selectivity for tumour-associated (BRAF V600E and KRAS G12D) mutations. Phosphorothioate-FANA modification enhances FR6_1 biostability and enables rapid KRAS mRNA knockdown in cultured human adenocarcinoma cells with a G12D-allele-specific component provided by in vivo XNAzyme cleavage activity. These results provide a starting point for the development of improved gene-silencing agents based on FANA or other XNA chemistries.
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Affiliation(s)
- Alexander I Taylor
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK.
| | | | - Maria J Donde
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
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Wei Y, Elahy M, Friedhuber AM, Wong JY, Hughes JD, Doschak MR, Dass CR. Triple-threat activity of PEDF in bone tumors: Tumor inhibition, tissue preservation and cardioprotection against doxorubicin. Bone 2019; 124:103-117. [PMID: 31028961 DOI: 10.1016/j.bone.2019.04.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 04/20/2019] [Accepted: 04/23/2019] [Indexed: 12/31/2022]
Abstract
Pigment epithelium-derived factor (PEDF) is known for its osteogenic properties, but its effects against primary and secondary bone tumors have not comprehensively been demonstrated. We show the ubiquitous expression of PEDF in murine embryonic tissue. Continuous administration of PEDF in pregnant mice for five days did not adversely affect foetal health, despite PEDF's known potent antiangiogenic properties. In the case of the devastating childhood bone cancer osteosarcoma, PEDF has direct anticancer activity per se, and protects against the toxicity of doxorubicin in the heart, small intestine and testes. PEDF demonstrated anti-proliferative and pro-apoptotic effects against human prostate and breast cancer cells, tumors which are known to metastasize to bone as the preferred secondary site. Caspase-2 was activated in both tumor cell types by PEDF. In models of prostate and breast cancer in bone, PEDF significantly reduced tumor volumes. When combined with zoledronic acid, continuously-administered PEDF significantly reduced breast tumor volume at the bone, and was able to preserve the quality of bone better than the combination therapy. These multiple positive findings make PEDF an ideal endogenous and safe biological for possible future clinical testing.
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Affiliation(s)
- Yongzhong Wei
- Department of Orthopaedics, the First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China
| | - Mina Elahy
- School of Medical Sciences, University of New South Wales, Kensington, Sydney, NSW 2052, Australia
| | - Anna M Friedhuber
- Department of Pathology, University of Melbourne, Parkville, Melbourne, VIC 3050, Australia
| | - Jia Y Wong
- School of Pharmacy and Biomedical Science, Curtin University, Bentley, Perth, WA 6102, Australia
| | - Jeffery D Hughes
- School of Pharmacy and Biomedical Science, Curtin University, Bentley, Perth, WA 6102, Australia
| | - Michael R Doschak
- Department of Biomedical Engineering, University of Alberta, Alberta T6G 2E1, Canada; Department of Dentistry, University of Alberta, Alberta T6G 2E1, Canada
| | - Crispin R Dass
- School of Pharmacy and Biomedical Science, Curtin University, Bentley, Perth, WA 6102, Australia; Curtin Health Innovation Research Institute, Curtin University, Bentley, Perth, WA 6102, Australia; College of Health and Biomedicine, Victoria University, St Albans, Melbourne, VIC 3021, Australia.
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Khachigian LM. Deoxyribozymes as Catalytic Nanotherapeutic Agents. Cancer Res 2019; 79:879-888. [DOI: 10.1158/0008-5472.can-18-2474] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/24/2018] [Accepted: 12/14/2018] [Indexed: 11/16/2022]
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Fokina AA, Stetsenko DA, François JC. DNA enzymes as potential therapeutics: towards clinical application of 10-23 DNAzymes. Expert Opin Biol Ther 2015; 15:689-711. [PMID: 25772532 DOI: 10.1517/14712598.2015.1025048] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Ongoing studies on the inhibition of gene expression at the mRNA level have identified several types of specific inhibitors such as antisense oligonucleotides, small interfering RNA, ribozymes and DNAzymes (Dz). After its discovery in 1997, the 10-23 Dz (which can cleave RNA efficiently and site-specifically, has flexible design, is independent from cell mechanisms, does not require expensive chemical modifications for effective use in vivo) has been employed to downregulate a range of therapeutically important genes. Recently, 10-23 Dzs have taken their first steps into clinical trials. AREAS COVERED This review focuses predominantly on Dz applications as potential antiviral, antibacterial, anti-cancer and anti-inflammatory agents as well as for the treatment of cardiovascular disease and diseases of CNS, summarizing results of their clinical trials up to the present day. EXPERT OPINION In comparison with antisense oligonucleotides and small interfering RNAs, Dzs do not usually show off-target effects due to their high specificity and lack of immunogenicity in vivo. As more results of clinical trials carried out so far are gradually becoming available, Dzs may turn out to be safe and well-tolerated therapeutics in humans. Therefore, there is a good chance that we may witness a deoxyribozyme drug reaching the clinic in the near future.
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Affiliation(s)
- Alesya A Fokina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue, Novosibirsk 630090 , Russia
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Tinzl M, Chen B, Chen SY, Semenas J, Abrahamsson PA, Dizeyi N. Interaction between c-jun and androgen receptor determines the outcome of taxane therapy in castration resistant prostate cancer. PLoS One 2013; 8:e79573. [PMID: 24260253 PMCID: PMC3832643 DOI: 10.1371/journal.pone.0079573] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 09/25/2013] [Indexed: 12/12/2022] Open
Abstract
Taxane based chemotherapy is the standard of care treatment in castration resistant prostate cancer (CRPC). There is convincing evidence that taxane therapy affects androgen receptor (AR) but the exact mechanisms have to be further elucidated. Our studies identified c-jun as a crucial key player which interacts with AR and thus determines the outcome of the taxane therapy given. Docetaxel (Doc) and paclitaxel (Pac) agents showed different effects on LNCaP and LNb4 evidenced by alteration in the protein and mRNA levels of c-jun, AR and PSA. Docetaxel-induced phophorylation of c-jun occurred before JNK phosphorylation which suggests that c-jun phosphorylation is independent of JNK pathways in prostate cancer cells. A xenograft study showed that mice treated with Pac and bicalutamide showed worse outcome supporting our hypothesis that upregulation of c-jun might act as a potent antiapoptotic factor. We observed in our in vitro studies an inverse regulation of PSA- and AR-mRNA levels in Doc treated LNb4 cells. This was also seen for kallikrein 2 (KLK 2) which followed the same pattern. Given the fact that response to taxane therapy is measured by PSA decrease we have to consider that this might not reflect the true activity of AR in CRPC patients.
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Affiliation(s)
- Martina Tinzl
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Binshen Chen
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Shao-Yong Chen
- Department of Hematology-Oncology, BIDMC, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Julius Semenas
- Department of Laboratory Medicine, Lund University, Malmö, Sweden
| | | | - Nishtman Dizeyi
- Department of Clinical Sciences, Lund University, Malmö, Sweden
- * E-mail:
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Hallett MA, Dalal P, Sweatman TW, Pourmotabbed T. The distribution, clearance, and safety of an anti-MMP-9 DNAzyme in normal and MMTV-PyMT transgenic mice. Nucleic Acid Ther 2013; 23:379-88. [PMID: 24083396 DOI: 10.1089/nat.2012.0348] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Catalytic oligonucleotides, known as DNAzymes, are a new class of nucleic acid-based gene therapy that have recently been used in preclinical animal studies to treat various cancers. In this study the systemic distribution, pharmacokinetics, and safety of intravenously administered anti-MMP (matrix metalloproteinase)-9 DNAzyme (AM9D) were determined in healthy FVB and in MMTV-polyoma virus middle T (PyMT) transgenic mice bearing mammary tumors. MMP-9 is known to be involved in tumor cell development, angiogenesis, invasion, and metastasis. Sulfur-35 ((35)S) labeled ([(35)S]-AM9D) administered intravenously, without the use of carrier molecules, to healthy and mammary tumor bearing MMTV-PyMT transgenic mice distributed to all major organs. The order of percentages of [(35)S]-AM9D accumulation in different organs of healthy and MMTV-PyMT mice were blood>liver>kidney>lung>spleen>heart and mammary tumor>blood≈liver>kidney>spleen>lung>heart, respectively. The amount of AM9D accumulated in mammary tumors 2 hours post injection was 0.6% and 0.2% higher than in either blood or liver, respectively, and its rate of initial clearance from mammary tissue was at least 50% slower than the other organs. Approximately 43% of the delivered dosage of [(35)S]-AM9D was cleared from the system via feces and urine over a period of 72 hours. No evidence of acute or chronic cytotoxicity, local or widespread, associated with AM9D treatment (up to 75 mg AM9D /kg of body weight) was observed in the organs examined. These data suggest that DNAzyme in general and AM9D in particular can be used systemically as a therapeutic agent to treat patients with breast cancer or other metastatic and surgically inaccessible tumors.
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Affiliation(s)
- Miranda A Hallett
- 1 Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center , Memphis Tennessee
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Dicke T, Pali-Schöll I, Kaufmann A, Bauer S, Renz H, Garn H. Absence of unspecific innate immune cell activation by GATA-3-specific DNAzymes. Nucleic Acid Ther 2012; 22:117-26. [PMID: 22428550 DOI: 10.1089/nat.2011.0294] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
DNAzymes of the 10-23 family represent an important class of antisense molecules with implications for therapeutic treatment of diseases. These molecules are single-stranded oligodeoxynucleotides combining the high specificity of oligonucleotide base pairing with an inherent RNA-cleaving enzymatic activity. However, like other oligonucleotide-based molecules these substances might exert so-called off-target effects, which have not been investigated so far for this molecule class. Therefore, the present study investigates putative off-target effects of DNAzymes on innate immune mechanisms using GATA-3-specific DNAzymes that have recently been developed as novel therapeutic approach for the treatment of allergic diseases including allergic asthma. The conserved catalytic domain of 10-23 DNAzymes contains a CpG motif that may stimulate innate immune cells via Toll-like receptor 9 (TLR-9). Therefore, potential TLR-9-mediated as well as TLR-9 independent cell activation was investigated using TLR-9-transfected HEK293 cells, macrophage cell lines and primary innate immune cells. Furthermore, putative effects of GATA-3-specific DNAzymes on the activation of neutrophil granulocytes and degranulation of mast cells/basophils were analyzed. In summary, no innate immune cell-stimulating activities of the tested DNAzymes were observed in any of the systems. Consequently, use of GATA-3-specific DNAzymes may represent a novel and highly specific approach for the treatment of allergic diseases.
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Affiliation(s)
- Tanja Dicke
- Sterna Biologicals GmbH & Co. KG, Marburg, Germany
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Kim SH, Dass CR. Induction of Caspase-2 Activation by a DNA Enzyme Evokes Tumor Cell Apoptosis. DNA Cell Biol 2012; 31:1-7. [DOI: 10.1089/dna.2011.1323] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Soo-Hyun Kim
- Department of Biomedical Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Crispin R. Dass
- Department of Biomedical and Health Sciences, Victoria University, St. Albans, Victoria, Australia
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Grimpe B. Deoxyribozymes and bioinformatics: complementary tools to investigate axon regeneration. Cell Tissue Res 2011; 349:181-200. [PMID: 22190188 PMCID: PMC7087747 DOI: 10.1007/s00441-011-1291-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 11/17/2011] [Indexed: 11/28/2022]
Abstract
For over 100 years, scientists have tried to understand the mechanisms that lead to the axonal growth seen during development or the lack thereof during regeneration failure after spinal cord injury (SCI). Deoxyribozyme technology as a potential therapeutic to treat SCIs or other insults to the brain, combined with a bioinformatics approach to comprehend the complex protein-protein interactions that occur after such trauma, is the focus of this review. The reader will be provided with information on the selection process of deoxyribozymes and their catalytic sequences, on the mechanism of target digestion, on modifications, on cellular uptake and on therapeutic applications and deoxyribozymes are compared with ribozymes, siRNAs and antisense technology. This gives the reader the necessary knowledge to decide which technology is adequate for the problem at hand and to design a relevant agent. Bioinformatics helps to identify not only key players in the complex processes that occur after SCI but also novel or less-well investigated molecules against which new knockdown agents can be generated. These two tools used synergistically should facilitate the pursuit of a treatment for insults to the central nervous system.
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Affiliation(s)
- Barbara Grimpe
- Applied Neurobiology, Department of Neurology, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany.
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Grimpe B. Deoxyribozymes: new therapeutics to treat central nervous system disorders. Front Mol Neurosci 2011; 4:25. [PMID: 21977013 PMCID: PMC3178805 DOI: 10.3389/fnmol.2011.00025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 09/02/2011] [Indexed: 12/13/2022] Open
Abstract
This mini-review focuses on a knockdown technology called deoxyribozymes, which has rarely been utilized in the field of neurobiology/neuroscience. Deoxyribozymes are catalytic DNA molecules, which are also entitled DNA enzyme or DNAzyme. This mini-review presents a description of their development, structure, function, and therapeutic application. In addition, information on siRNA, ribozymes, and antisense are given. Further information on two deoxyribozymes against c-Jun and xylosyltransferase (XT) mRNA are summarized of which the first is important to influence many neurological disorders and the last potentially treats spinal cord injuries (SCIs). In particular, insults to the central nervous system (CNS) such as SCI generate an inhibitory environment (lesion scar) at the injury site that prevents the endogenous and therapy-induced axonal regeneration and thereby limits repair strategies. Presently, there are no treatments available. Hence, deoxyribozymes provide an opportunity for new therapeutics that alter the inhibitory nature of the lesion scar and thus promote axonal growth in the injured spinal cord. When used cautiously and within the limits of its ability the deoxyribozyme technology holds promise to become a major contributing factor in repair strategies of the CNS.
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Affiliation(s)
- Barbara Grimpe
- Department of Neurology, Applied Neurobiology Group, University Medical Center of the Heinrich Heine University Düsseldorf Düsseldorf, Germany
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