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Evans MM, Liu S, Krautner JS, Seguin CG, Leung R, Ronald JA. Evaluation of DNA minicircles for delivery of adenine and cytosine base editors using activatable gene on "GO" reporter imaging systems. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102248. [PMID: 39040503 PMCID: PMC11260848 DOI: 10.1016/j.omtn.2024.102248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 06/07/2024] [Indexed: 07/24/2024]
Abstract
Over 30,000 point mutations are associated with debilitating diseases, including many cancer types, underscoring a critical need for targeted genomic solutions. CRISPR base editors, like adenine base editors (ABEs) and cytosine base editors (CBEs), enable precise modifications by converting adenine to guanine and cytosine to thymine, respectively. Challenges in efficiency and safety concerns regarding viral vectors used in delivery limit the scope of base editing. This study introduces non-viral minicircles, bacterial-backbone-free plasmids, as a delivery vehicle for ABEs and CBEs. The research uses cells engineered with the "Gene On" (GO) reporter gene systems for tracking minicircle-delivered ABEs, CBEs, or Cas9 nickase (control), using green fluorescent protein (GFPGO), bioluminescence reporter firefly luciferase (LUCGO), or a highly sensitive Akaluciferase (AkalucGO) designed in this study. The results show that transfection of minicircles expressing CBE or ABE resulted in significantly higher GFP expression and luminescence signals over controls, with minicircles demonstrating the most substantial editing. This study presents minicircles as a new strategy for base editor delivery and develops an enhanced bioluminescence imaging reporter system for tracking ABE activity. Future studies aim to evaluate the use of minicircles in preclinical cancer models, facilitating potential clinical applications.
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Affiliation(s)
- Melissa M. Evans
- Robarts Research Institute, University of Western Ontario, London, ON N6A 3K7, Canada
- Department of Medical Biophysics, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Shirley Liu
- Robarts Research Institute, University of Western Ontario, London, ON N6A 3K7, Canada
- Department of Medical Biophysics, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Joshua S. Krautner
- Robarts Research Institute, University of Western Ontario, London, ON N6A 3K7, Canada
- Department of Medical Biophysics, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Caroline G. Seguin
- Robarts Research Institute, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Rajan Leung
- Robarts Research Institute, University of Western Ontario, London, ON N6A 3K7, Canada
- Department of Medical Biophysics, University of Western Ontario, London, ON N6A 5C1, Canada
| | - John A. Ronald
- Robarts Research Institute, University of Western Ontario, London, ON N6A 3K7, Canada
- Department of Medical Biophysics, University of Western Ontario, London, ON N6A 5C1, Canada
- Lawson Health Research Institute, London, ON N6C 2R5, Canada
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Comeau ZJ, Lessard BH, Shuhendler AJ. The Need to Pair Molecular Monitoring Devices with Molecular Imaging to Personalize Health. Mol Imaging Biol 2022; 24:675-691. [PMID: 35257276 PMCID: PMC8901094 DOI: 10.1007/s11307-022-01714-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 12/11/2022]
Abstract
By enabling the non-invasive monitoring and quantification of biomolecular processes, molecular imaging has dramatically improved our understanding of disease. In recent years, non-invasive access to the molecular drivers of health versus disease has emboldened the goal of precision health, which draws on concepts borrowed from process monitoring in engineering, wherein hundreds of sensors can be employed to develop a model which can be used to preventatively detect and diagnose problems. In translating this monitoring regime from inanimate machines to human beings, precision health posits that continual and on-the-spot monitoring are the next frontiers in molecular medicine. Early biomarker detection and clinical intervention improves individual outcomes and reduces the societal cost of treating chronic and late-stage diseases. However, in current clinical settings, methods of disease diagnoses and monitoring are typically intermittent, based on imprecise risk factors, or self-administered, making optimization of individual patient outcomes an ongoing challenge. Low-cost molecular monitoring devices capable of on-the-spot biomarker analysis at high frequencies, and even continuously, could alter this paradigm of therapy and disease prevention. When these devices are coupled with molecular imaging, they could work together to enable a complete picture of pathogenesis. To meet this need, an active area of research is the development of sensors capable of point-of-care diagnostic monitoring with an emphasis on clinical utility. However, a myriad of challenges must be met, foremost, an integration of the highly specialized molecular tools developed to understand and monitor the molecular causes of disease with clinically accessible techniques. Functioning on the principle of probe-analyte interactions yielding a transducible signal, probes enabling sensing and imaging significantly overlap in design considerations and targeting moieties, however differing in signal interpretation and readout. Integrating molecular sensors with molecular imaging can provide improved data on the personal biomarkers governing disease progression, furthering our understanding of pathogenesis, and providing a positive feedback loop toward identifying additional biomarkers and therapeutics. Coupling molecular imaging with molecular monitoring devices into the clinical paradigm is a key step toward achieving precision health.
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Affiliation(s)
- Zachary J Comeau
- Department of Chemical and Biological Engineering, University of Ottawa, 161 Louis Pasteur, Ottawa, ON, K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 150 Louis Pasteur, Ottawa, ON, K1N 6N5, Canada
| | - Benoît H Lessard
- Department of Chemical and Biological Engineering, University of Ottawa, 161 Louis Pasteur, Ottawa, ON, K1N 6N5, Canada
- School of Electrical Engineering and Computer Science, University of Ottawa, 800 King Edward Ave., Ottawa, ON, K1N 6N5, Canada
| | - Adam J Shuhendler
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 150 Louis Pasteur, Ottawa, ON, K1N 6N5, Canada.
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, K1N 6N5, Canada.
- University of Ottawa Heart Institute, 40 Ruskin St, Ottawa, ON, K1Y 4W7, Canada.
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Kwong GA, Ghosh S, Gamboa L, Patriotis C, Srivastava S, Bhatia SN. Synthetic biomarkers: a twenty-first century path to early cancer detection. Nat Rev Cancer 2021; 21:655-668. [PMID: 34489588 PMCID: PMC8791024 DOI: 10.1038/s41568-021-00389-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/14/2021] [Indexed: 02/08/2023]
Abstract
Detection of cancer at an early stage when it is still localized improves patient response to medical interventions for most cancer types. The success of screening tools such as cervical cytology to reduce mortality has spurred significant interest in new methods for early detection (for example, using non-invasive blood-based or biofluid-based biomarkers). Yet biomarkers shed from early lesions are limited by fundamental biological and mass transport barriers - such as short circulation times and blood dilution - that limit early detection. To address this issue, synthetic biomarkers are being developed. These represent an emerging class of diagnostics that deploy bioengineered sensors inside the body to query early-stage tumours and amplify disease signals to levels that could potentially exceed those of shed biomarkers. These strategies leverage design principles and advances from chemistry, synthetic biology and cell engineering. In this Review, we discuss the rationale for development of biofluid-based synthetic biomarkers. We examine how these strategies harness dysregulated features of tumours to amplify detection signals, use tumour-selective activation to increase specificity and leverage natural processing of bodily fluids (for example, blood, urine and proximal fluids) for easy detection. Finally, we highlight the challenges that exist for preclinical development and clinical translation of synthetic biomarker diagnostics.
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Affiliation(s)
- Gabriel A Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, USA.
- Parker H. Petit Institute of Bioengineering and Bioscience, Atlanta, GA, USA.
- Institute for Electronics and Nanotechnology, Georgia Tech, Atlanta, GA, USA.
- The Georgia Immunoengineering Consortium, Emory University and Georgia Tech, Atlanta, GA, USA.
- Winship Cancer Institute, Emory University, Atlanta, GA, USA.
| | - Sharmistha Ghosh
- Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Lena Gamboa
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, USA
| | - Christos Patriotis
- Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sudhir Srivastava
- Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Sangeeta N Bhatia
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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4
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Gregg JR, Thompson TC. Considering the potential for gene-based therapy in prostate cancer. Nat Rev Urol 2021; 18:170-184. [PMID: 33637962 DOI: 10.1038/s41585-021-00431-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2021] [Indexed: 01/31/2023]
Abstract
Therapeutic gene manipulation has been at the forefront of popular scientific discussion and basic and clinical research for decades. Basic and clinical research applications of CRISPR-Cas9-based technologies and ongoing clinical trials in this area have demonstrated the potential of genome editing to cure human disease. Evaluation of research and clinical trials in gene therapy reveals a concentration of activity in prostate cancer research and practice. Multiple aspects of prostate cancer care - including anatomical considerations that enable direct tumour injections and sampling, the availability of preclinical immune-competent models and the delineation of tumour-related antigens that might provide targets for an induced immune system - make gene therapy an appealing treatment option for this common malignancy. Vaccine-based therapies that induce an immune response and new technologies exploiting CRISPR-Cas9-assisted approaches, including chimeric antigen receptor (CAR) T cell therapies, are very promising and are currently under investigation both in the laboratory and in the clinic. Although laboratory and preclinical advances have, thus far, not led to oncologically relevant outcomes in the clinic, future studies offer great promise for gene therapy to become established in prostate cancer care.
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Affiliation(s)
- Justin R Gregg
- Department of Urology and Health Disparities Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Timothy C Thompson
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Wang T, Chen Y, Goodale D, Allan AL, Ronald JA. A survivin-driven, tumor-activatable minicircle system for prostate cancer theranostics. MOLECULAR THERAPY-ONCOLYTICS 2021; 20:209-219. [PMID: 33665359 PMCID: PMC7889447 DOI: 10.1016/j.omto.2021.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 01/13/2021] [Indexed: 12/12/2022]
Abstract
Gene vectors regulated by tumor-specific promoters to express transgenes specifically in cancer cells are an emerging approach for cancer diagnosis and treatment. Minicircles are shortened plasmids stripped of prokaryotic sequences that have potency and safety characteristics beneficial for clinical translation. Previously, we developed minicircles driven by the tumor-specific survivin promoter, which exhibits elevated transcriptional activity in aggressive cancers, to express a secreted reporter for blood-based cancer detection. Here we present the first activatable, cancer theranostic minicircle system featuring a pair of diagnostic and therapeutic minicircles expressing Gaussia luciferase for urine-based cancer detection or cytosine deaminase:uracil phosphoribosyltransferase for gene-directed enzyme prodrug therapy. Diagnostic minicircles revealed urinary reporter output related to cellular survivin levels. Notably, mice with aggressive prostate tumors exhibited significantly higher urine reporter activity than mice with non-aggressive tumors and healthy mice after intratumoral minicircle administration. Therapeutic minicircles displayed specific cytotoxicity in survivin-rich cancer cells and significantly attenuated growth of aggressive orthotopic prostate tumors in mice. Use of these minicircles together creates a theranostic system that can first identify individuals carrying aggressive prostate cancer via a urinary test, followed by stringent control of tumor progression in stratified individuals who carry high-risk prostate lesions.
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Affiliation(s)
- TianDuo Wang
- Department of Medical Biophysics, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 5B7, Canada.,Robarts Research Institute - Imaging Research Laboratories, London, ON N6A 3K7, Canada
| | - Yuanxin Chen
- Robarts Research Institute - Imaging Research Laboratories, London, ON N6A 3K7, Canada
| | - David Goodale
- London Regional Cancer Program, London Health Science Centre, London, ON N6C 2R5, Canada
| | - Alison L Allan
- Department of Anatomy & Cell Biology, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 5B7, Canada.,Department of Oncology, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 5B7, Canada.,London Regional Cancer Program, London Health Science Centre, London, ON N6C 2R5, Canada.,Lawson Health Research Institute, London, ON N6C 2R5, Canada
| | - John A Ronald
- Department of Medical Biophysics, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 5B7, Canada.,Robarts Research Institute - Imaging Research Laboratories, London, ON N6A 3K7, Canada.,Lawson Health Research Institute, London, ON N6C 2R5, Canada
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Kelly JJ, Saee-Marand M, Nyström NN, Evans MM, Chen Y, Martinez FM, Hamilton AM, Ronald JA. Safe harbor-targeted CRISPR-Cas9 homology-independent targeted integration for multimodality reporter gene-based cell tracking. SCIENCE ADVANCES 2021; 7:eabc3791. [PMID: 33523917 PMCID: PMC7817109 DOI: 10.1126/sciadv.abc3791] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 11/25/2020] [Indexed: 05/12/2023]
Abstract
Imaging reporter genes provides longitudinal information on the biodistribution, growth, and survival of engineered cells in vivo. A translational bottleneck to using reporter genes is the necessity to engineer cells with randomly integrating vectors. Here, we built homology-independent targeted integration (HITI) CRISPR-Cas9 minicircle donors for precise safe harbor-targeted knock-in of fluorescence, bioluminescence, and MRI (Oatp1a1) reporter genes. Our results showed greater knock-in efficiency using HITI vectors compared to homology-directed repair vectors. HITI clones demonstrated functional fluorescence and bioluminescence reporter activity as well as significant Oatp1a1-mediated uptake of the clinically approved MRI agent gadolinium ethoxybenzyl diethylenetriamine pentaacetic acid. Contrast-enhanced MRI improved the conspicuity of both subcutaneous and metastatic Oatp1a1-expressing tumors before they became palpable or even readily visible on precontrast images. Our work demonstrates the first CRISPR-Cas9 HITI system for knock-in of large DNA donor constructs at a safe harbor locus, enabling multimodal longitudinal in vivo imaging of cells.
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Affiliation(s)
- John J Kelly
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
- Department of Medical Biophysics, University of Western Ontario, London, Ontario, Canada
| | - Moe Saee-Marand
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Nivin N Nyström
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
- Department of Medical Biophysics, University of Western Ontario, London, Ontario, Canada
| | - Melissa M Evans
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Yuanxin Chen
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Francisco M Martinez
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Amanda M Hamilton
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
| | - John A Ronald
- Robarts Research Institute, University of Western Ontario, London, Ontario, Canada.
- Department of Medical Biophysics, University of Western Ontario, London, Ontario, Canada
- Lawson Health Research Institute, London, Ontario, Canada
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