1
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Caliendo F, Vitu E, Wang J, Kuo SH, Sandt H, Enghuus CN, Tordoff J, Estrada N, Collins JJ, Weiss R. Customizable gene sensing and response without altering endogenous coding sequences. Nat Chem Biol 2024:10.1038/s41589-024-01733-y. [PMID: 39266721 DOI: 10.1038/s41589-024-01733-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/20/2024] [Indexed: 09/14/2024]
Abstract
Synthetic biology aims to modify cellular behaviors by implementing genetic circuits that respond to changes in cell state. Integrating genetic biosensors into endogenous gene coding sequences using clustered regularly interspaced short palindromic repeats and Cas9 enables interrogation of gene expression dynamics in the appropriate chromosomal context. However, embedding a biosensor into a gene coding sequence may unpredictably alter endogenous gene regulation. To address this challenge, we developed an approach to integrate genetic biosensors into endogenous genes without modifying their coding sequence by inserting into their terminator region single-guide RNAs that activate downstream circuits. Sensor dosage responses can be fine-tuned and predicted through a mathematical model. We engineered a cell stress sensor and actuator in CHO-K1 cells that conditionally activates antiapoptotic protein BCL-2 through a downstream circuit, thereby increasing cell survival under stress conditions. Our gene sensor and actuator platform has potential use for a wide range of applications that include biomanufacturing, cell fate control and cell-based therapeutics.
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Affiliation(s)
- Fabio Caliendo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Elvira Vitu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Junmin Wang
- Bioinformatics Graduate Program, Boston University, Boston, MA, USA
| | - Shuo-Hsiu Kuo
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hayden Sandt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Casper Nørskov Enghuus
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jesse Tordoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Neslly Estrada
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - James J Collins
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
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2
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Love KS, Johnstone CP, Peterman EL, Gaglione S, Galloway KE. Model-guided design of microRNA-based gene circuits supports precise dosage of transgenic cargoes into diverse primary cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600629. [PMID: 38979370 PMCID: PMC11230401 DOI: 10.1101/2024.06.25.600629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
To realize the potential of engineered cells in therapeutic applications, transgenes must be expressed within the window of therapeutic efficacy. Differences in copy number and other sources of extrinsic noise generate variance in transgene expression and limit the performance of synthetic gene circuits. In a therapeutic context, supraphysiological expression of transgenes can compromise engineered phenotypes and lead to toxicity. To ensure a narrow range of transgene expression, we design and characterize Compact microRNA-Mediated Attenuator of Noise and Dosage (ComMAND), a single-transcript, microRNA-based incoherent feedforward loop. We experimentally tune the ComMAND output profile, and we model the system to explore additional tuning strategies. By comparing ComMAND to two-gene implementations, we highlight the precise control afforded by the single-transcript architecture, particularly at relatively low copy numbers. We show that ComMAND tightly regulates transgene expression from lentiviruses and precisely controls expression in primary human T cells, primary rat neurons, primary mouse embryonic fibroblasts, and human induced pluripotent stem cells. Finally, ComMAND effectively sets levels of the clinically relevant transgenes FMRP1 and FXN within a narrow window. Together, ComMAND is a compact tool well-suited to precisely specify expression of therapeutic cargoes.
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Affiliation(s)
- Kasey S. Love
- Department of Biological Engineering, MIT, 25 Ames St., Cambridge, MA 02139, USA
| | | | - Emma L. Peterman
- Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA 02139, USA
| | - Stephanie Gaglione
- Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA 02139, USA
| | - Kate E. Galloway
- Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA 02139, USA
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3
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Wang L, Xu W, Zhang S, Gundberg GC, Zheng CR, Wan Z, Mustafina K, Caliendo F, Sandt H, Kamm R, Weiss R. Sensing and guiding cell-state transitions by using genetically encoded endoribonuclease-mediated microRNA sensors. Nat Biomed Eng 2024:10.1038/s41551-024-01229-z. [PMID: 38982158 DOI: 10.1038/s41551-024-01229-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/11/2024] [Indexed: 07/11/2024]
Abstract
Precisely sensing and guiding cell-state transitions via the conditional genetic activation of appropriate differentiation factors is challenging. Here we show that desired cell-state transitions can be guided via genetically encoded sensors, whereby endogenous cell-state-specific miRNAs regulate the translation of a constitutively transcribed endoribonuclease, which, in turn, controls the translation of a gene of interest. We used this approach to monitor several cell-state transitions, to enrich specific cell types and to automatically guide the multistep differentiation of human induced pluripotent stem cells towards a haematopoietic lineage via endothelial cells as an intermediate state. Such conditional activation of gene expression is durable and resistant to epigenetic silencing and could facilitate the monitoring of cell-state transitions in physiological and pathological conditions and eventually the 'rewiring' of cell-state transitions for applications in organoid-based disease modelling, cellular therapies and regenerative medicine.
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Affiliation(s)
- Lei Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Bioengineering, Northeastern University, Boston, MA, USA.
- Department of Biology, Northeastern University, Boston, MA, USA.
| | - Wenlong Xu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shun Zhang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- State Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gregory C Gundberg
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christine R Zheng
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhengpeng Wan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kamila Mustafina
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fabio Caliendo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hayden Sandt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Roger Kamm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
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4
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Peterman EL, Ploessl DS, Galloway KE. Accelerating Diverse Cell-Based Therapies Through Scalable Design. Annu Rev Chem Biomol Eng 2024; 15:267-292. [PMID: 38594944 DOI: 10.1146/annurev-chembioeng-100722-121610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Augmenting cells with novel, genetically encoded functions will support therapies that expand beyond natural capacity for immune surveillance and tissue regeneration. However, engineering cells at scale with transgenic cargoes remains a challenge in realizing the potential of cell-based therapies. In this review, we introduce a range of applications for engineering primary cells and stem cells for cell-based therapies. We highlight tools and advances that have launched mammalian cell engineering from bioproduction to precision editing of therapeutically relevant cells. Additionally, we examine how transgenesis methods and genetic cargo designs can be tailored for performance. Altogether, we offer a vision for accelerating the translation of innovative cell-based therapies by harnessing diverse cell types, integrating the expanding array of synthetic biology tools, and building cellular tools through advanced genome writing techniques.
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Affiliation(s)
- Emma L Peterman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Deon S Ploessl
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Kate E Galloway
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
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5
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Lalanne JB, Regalado SG, Domcke S, Calderon D, Martin BK, Li X, Li T, Suiter CC, Lee C, Trapnell C, Shendure J. Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters. Nat Methods 2024; 21:983-993. [PMID: 38724692 PMCID: PMC11166576 DOI: 10.1038/s41592-024-02260-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/22/2024] [Indexed: 06/13/2024]
Abstract
The inability to scalably and precisely measure the activity of developmental cis-regulatory elements (CREs) in multicellular systems is a bottleneck in genomics. Here we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. Together with RNA barcode stabilization via circularization, these scalable single-cell quantitative expression reporters provide high-contrast readouts, analogous to classic in situ assays but entirely from sequencing. Screening >200 regions of accessible chromatin in a multicellular in vitro model of early mammalian development, we identify 13 (8 previously uncharacterized) autonomous and cell-type-specific developmental CREs. We further demonstrate that chimeric CRE pairs generate cognate two-cell-type activity profiles and assess gain- and loss-of-function multicellular expression phenotypes from CRE variants with perturbed transcription factor binding sites. Single-cell quantitative expression reporters can be applied in developmental and multicellular systems to quantitatively characterize native, perturbed and synthetic CREs at scale, with high sensitivity and at single-cell resolution.
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Affiliation(s)
| | - Samuel G Regalado
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Silvia Domcke
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Diego Calderon
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Xiaoyi Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Tony Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Chase C Suiter
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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6
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Eisenhut P, Marx N, Borsi G, Papež M, Ruggeri C, Baumann M, Borth N. Manipulating gene expression levels in mammalian cell factories: An outline of synthetic molecular toolboxes to achieve multiplexed control. N Biotechnol 2024; 79:1-19. [PMID: 38040288 DOI: 10.1016/j.nbt.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/06/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Mammalian cells have developed dedicated molecular mechanisms to tightly control expression levels of their genes where the specific transcriptomic signature across all genes eventually determines the cell's phenotype. Modulating cellular phenotypes is of major interest to study their role in disease or to reprogram cells for the manufacturing of recombinant products, such as biopharmaceuticals. Cells of mammalian origin, for example Chinese hamster ovary (CHO) and Human embryonic kidney 293 (HEK293) cells, are most commonly employed to produce therapeutic proteins. Early genetic engineering approaches to alter their phenotype have often been attempted by "uncontrolled" overexpression or knock-down/-out of specific genetic factors. Many studies in the past years, however, highlight that rationally regulating and fine-tuning the strength of overexpression or knock-down to an optimum level, can adjust phenotypic traits with much more precision than such "uncontrolled" approaches. To this end, synthetic biology tools have been generated that enable (fine-)tunable and/or inducible control of gene expression. In this review, we discuss various molecular tools used in mammalian cell lines and group them by their mode of action: transcriptional, post-transcriptional, translational and post-translational regulation. We discuss the advantages and disadvantages of using these tools for each cell regulatory layer and with respect to cell line engineering approaches. This review highlights the plethora of synthetic toolboxes that could be employed, alone or in combination, to optimize cellular systems and eventually gain enhanced control over the cellular phenotype to equip mammalian cell factories with the tools required for efficient production of emerging, more difficult-to-express biologics formats.
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Affiliation(s)
- Peter Eisenhut
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicolas Marx
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
| | - Giulia Borsi
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Maja Papež
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Caterina Ruggeri
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
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7
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Du R, Flynn MJ, Honsa M, Jungmann R, Elowitz MB. miRNA circuit modules for precise, tunable control of gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.583048. [PMID: 38559239 PMCID: PMC10979901 DOI: 10.1101/2024.03.12.583048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The ability to express transgenes at specified levels is critical for understanding cellular behaviors, and for applications in gene and cell therapy. Transfection, viral vectors, and other gene delivery methods produce varying protein expression levels, with limited quantitative control, while targeted knock-in and stable selection are inefficient and slow. Active compensation mechanisms can improve precision, but the need for additional proteins or lack of tunability have prevented their widespread use. Here, we introduce a toolkit of compact, synthetic miRNA-based circuit modules that provide precise, tunable control of transgenes across diverse cell types. These circuits, termed DIMMERs (Dosage-Invariant miRNA-Mediated Expression Regulators) use multivalent miRNA regulatory interactions within an incoherent feed-forward loop architecture to achieve nearly uniform protein expression over more than two orders of magnitude variation in underlying gene dosages or transcription rates. They also allow coarse and fine control of expression, and are portable, functioning across diverse cell types. In addition, a heuristic miRNA design algorithm enables the creation of orthogonal circuit variants that independently control multiple genes in the same cell. These circuits allowed dramatically improved CRISPR imaging, and super-resolution imaging of EGFR receptors with transient transfections. The toolbox provided here should allow precise, tunable, dosage-invariant expression for research, gene therapy, and other biotechnology applications.
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Affiliation(s)
- Rongrong Du
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael J. Flynn
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Monique Honsa
- Max Planck Institute of Biochemistry, Martinsried, Germany; Faculty of Physics, Ludwig Maximilian University, Munich, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Martinsried, Germany; Faculty of Physics, Ludwig Maximilian University, Munich, Germany
| | - Michael B. Elowitz
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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8
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Mumford TR, Rae D, Brackhahn E, Idris A, Gonzalez-Martinez D, Pal AA, Chung MC, Guan J, Rhoades E, Bugaj LJ. Simple visualization of submicroscopic protein clusters with a phase-separation-based fluorescent reporter. Cell Syst 2024; 15:166-179.e7. [PMID: 38335954 PMCID: PMC10947474 DOI: 10.1016/j.cels.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/06/2023] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
Protein clustering plays numerous roles in cell physiology and disease. However, protein oligomers can be difficult to detect because they are often too small to appear as puncta in conventional fluorescence microscopy. Here, we describe a fluorescent reporter strategy that detects protein clusters with high sensitivity called CluMPS (clusters magnified by phase separation). A CluMPS reporter detects and visually amplifies even small clusters of a binding partner, generating large, quantifiable fluorescence condensates. We use computational modeling and optogenetic clustering to demonstrate that CluMPS can detect small oligomers and behaves rationally according to key system parameters. CluMPS detected small aggregates of pathological proteins where the corresponding GFP fusions appeared diffuse. CluMPS also detected and tracked clusters of unmodified and tagged endogenous proteins, and orthogonal CluMPS probes could be multiplexed in cells. CluMPS provides a powerful yet straightforward approach to observe higher-order protein assembly in its native cellular context. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Thomas R Mumford
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Diarmid Rae
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Emily Brackhahn
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Abbas Idris
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Ayush Aditya Pal
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael C Chung
- Department of Physics, University of Florida, Gainesville, FL 32611, USA
| | - Juan Guan
- Department of Physics, University of Florida, Gainesville, FL 32611, USA; Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32611, USA
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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9
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Ilia K, Shakiba N, Bingham T, Jones RD, Kaminski MM, Aravera E, Bruno S, Palacios S, Weiss R, Collins JJ, Del Vecchio D, Schlaeger TM. Synthetic genetic circuits to uncover the OCT4 trajectories of successful reprogramming of human fibroblasts. SCIENCE ADVANCES 2023; 9:eadg8495. [PMID: 38019912 PMCID: PMC10686568 DOI: 10.1126/sciadv.adg8495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023]
Abstract
Reprogramming human fibroblasts to induced pluripotent stem cells (iPSCs) is inefficient, with heterogeneity among transcription factor (TF) trajectories driving divergent cell states. Nevertheless, the impact of TF dynamics on reprogramming efficiency remains uncharted. We develop a system that accurately reports OCT4 protein levels in live cells and use it to reveal the trajectories of OCT4 in successful reprogramming. Our system comprises a synthetic genetic circuit that leverages noise to generate a wide range of OCT4 trajectories and a microRNA targeting endogenous OCT4 to set total cellular OCT4 protein levels. By fusing OCT4 to a fluorescent protein, we are able to track OCT4 trajectories with clonal resolution via live-cell imaging. We discover that a supraphysiological, stable OCT4 level is required, but not sufficient, for efficient iPSC colony formation. Our synthetic genetic circuit design and high-throughput live-imaging pipeline are generalizable for investigating TF dynamics for other cell fate programming applications.
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Affiliation(s)
- Katherine Ilia
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nika Shakiba
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3 Canada
| | - Trevor Bingham
- Stem Cell Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard University, Boston, MA 02115, USA
| | - Ross D. Jones
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3 Canada
| | - Michael M. Kaminski
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz-Association, Berlin 10115, Germany
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Medizinische Klinik m.S. Nephrologie und Intensivmedizin, Berlin 10117, Germany
- Berlin Institute of Health, Berlin 13125, Germany
| | - Eliezer Aravera
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Simone Bruno
- Department of Mechanical Engineering, MIT, Cambridge, MA 02139, USA
| | - Sebastian Palacios
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Mechanical Engineering, MIT, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - James J. Collins
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Domitilla Del Vecchio
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Mechanical Engineering, MIT, Cambridge, MA 02139, USA
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10
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Yde Ohki CM, Walter NM, Rickli M, Salazar Campos JM, Werling AM, Döring C, Walitza S, Grünblatt E. Protocol for a Wnt reporter assay to measure its activity in human neural stem cells derived from induced pluripotent stem cells. CURRENT RESEARCH IN NEUROBIOLOGY 2023; 5:100095. [PMID: 37426743 PMCID: PMC10329100 DOI: 10.1016/j.crneur.2023.100095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/24/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023] Open
Abstract
The canonical Wnt signaling is an essential pathway that regulates cellular proliferation, maturation, and differentiation during neurodevelopment and maintenance of adult tissue homeostasis. This pathway has been implicated with the pathophysiology of neuropsychiatric disorders and was associated with cognitive processes, such as learning and memory. However, the molecular investigation of the Wnt signaling in functional human neural cell lines might be challenging since brain biopsies are not possible and animal models may not represent the polygenic profile of some neurological and neurodevelopmental disorders. In this context, using induced pluripotent stem cells (iPSCs) has become a powerful tool to model disorders that affect the Central Nervous System (CNS) in vitro, by maintaining patients' genetic backgrounds. In this method paper, we report the development of a virus-free Wnt reporter assay in neural stem cells (NSCs) derived from human iPSCs from two healthy individuals, by using a vector containing a reporter gene (luc2P) under the control of a TCF/LEF (T-cell factor/lymphoid enhancer factor) responsive element. Dose-response curve analysis from this luciferase-based method might be useful when testing the activity of the Wnt signaling pathway after agonists (e.g. Wnt3a) or antagonists (e.g. DKK1) administration, comparing activity between cases and controls in distinct disorders. Using such a reporter assay method may help to elucidate whether neurological or neurodevelopmental mental disorders show alterations in this pathway, and testing whether targeted treatment may reverse these. Therefore, our established assay aims to help researchers on the functional and molecular investigation of the Wnt pathway in patient-specific cell types comprising several neuropsychiatric disorders.
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Affiliation(s)
- Cristine Marie Yde Ohki
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland
- Biomedicine PhD Program, University of Zurich, Winterthurerstrasse 11, 8057, Zurich, Switzerland
| | - Natalie Monet Walter
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland
| | - Michelle Rickli
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland
| | - José Maria Salazar Campos
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland
| | - Anna Maria Werling
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland
| | - Christian Döring
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland
- Neuroscience Center Zurich, University of Zurich and the ETH Zurich, Winterthurerstrasse 11, 8057, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Winterthurerstrasse 11, 8057, Zurich, Switzerland
| | - Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland
- Neuroscience Center Zurich, University of Zurich and the ETH Zurich, Winterthurerstrasse 11, 8057, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Winterthurerstrasse 11, 8057, Zurich, Switzerland
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11
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Autocatalytic base editing for RNA-responsive translational control. Nat Commun 2023; 14:1339. [PMID: 36906659 PMCID: PMC10008589 DOI: 10.1038/s41467-023-36851-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 02/20/2023] [Indexed: 03/13/2023] Open
Abstract
Genetic circuits that control transgene expression in response to pre-defined transcriptional cues would enable the development of smart therapeutics. To this end, here we engineer programmable single-transcript RNA sensors in which adenosine deaminases acting on RNA (ADARs) autocatalytically convert target hybridization into a translational output. Dubbed DART VADAR (Detection and Amplification of RNA Triggers via ADAR), our system amplifies the signal from editing by endogenous ADAR through a positive feedback loop. Amplification is mediated by the expression of a hyperactive, minimal ADAR variant and its recruitment to the edit site via an orthogonal RNA targeting mechanism. This topology confers high dynamic range, low background, minimal off-target effects, and a small genetic footprint. We leverage DART VADAR to detect single nucleotide polymorphisms and modulate translation in response to endogenous transcript levels in mammalian cells.
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12
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Ilia K, Shakiba N, Bingham T, Jones RD, Kaminski MM, Aravera E, Bruno S, Palacios S, Weiss R, Collins JJ, Del Vecchio D, Schlaeger TM. Synthetic genetic circuits to uncover and enforce the OCT4 trajectories of successful reprogramming of human fibroblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525529. [PMID: 36747813 PMCID: PMC9900859 DOI: 10.1101/2023.01.25.525529] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Reprogramming human fibroblasts to induced pluripotent stem cells (iPSCs) is inefficient, with heterogeneity among transcription factor (TF) trajectories driving divergent cell states. Nevertheless, the impact of TF dynamics on reprogramming efficiency remains uncharted. Here, we identify the successful reprogramming trajectories of the core pluripotency TF, OCT4, and design a genetic controller that enforces such trajectories with high precision. By combining a genetic circuit that generates a wide range of OCT4 trajectories with live-cell imaging, we track OCT4 trajectories with clonal resolution and find that a distinct constant OCT4 trajectory is required for colony formation. We then develop a synthetic genetic circuit that yields a tight OCT4 distribution around the identified trajectory and outperforms in terms of reprogramming efficiency other circuits that less accurately regulate OCT4. Our synthetic biology approach is generalizable for identifying and enforcing TF dynamics for cell fate programming applications.
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Affiliation(s)
- Katherine Ilia
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Nika Shakiba
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, V6T 1Z3 Canada
| | - Trevor Bingham
- Boston Children’s Hospital Stem Cell Program, Boston Children’s Hospital, Boston, MA, 02115, USA
- Harvard University, Boston, MA, 02115, USA
| | - Ross D. Jones
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, V6T 1Z3 Canada
| | - Michael M. Kaminski
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany
| | - Eliezer Aravera
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- College of Engineering and Applied Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Simone Bruno
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sebastian Palacios
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - James J. Collins
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02139, USA
| | - Domitilla Del Vecchio
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Thorsten M. Schlaeger
- Boston Children’s Hospital Stem Cell Program, Boston Children’s Hospital, Boston, MA, 02115, USA
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13
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Oliynyk RT, Church GM. Efficient modification and preparation of circular DNA for expression in cell culture. Commun Biol 2022; 5:1393. [PMID: 36543890 PMCID: PMC9772414 DOI: 10.1038/s42003-022-04363-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
DNA plasmids are an essential tool for delivery and expression of RNAs and proteins in cell culture experiments. The preparation of plasmids typically involves a laborious process of bacterial cloning, validation, and purification. While the expression plasmids can be designed and ordered from the contract manufacturers, the cost may be prohibitive when a large number of plasmids is required. We have developed an efficient fully synthetic method and protocol that enables the production of circularized DNA containing expression elements ready for transfection in as little as 3 hours, thereby eliminating the bacterial cloning steps. The protocol describes how to take a linear double-stranded DNA fragment and efficiently circularize and purify this DNA fragment with minimal hands-on time. As proof of the principle, we applied Circular Vector expressing engineered prime editing guide RNA (epegRNA) in cell culture, and demonstrated matching and even exceeding performance of this method as compared to guides expressed by plasmids. The method's speed of preparation, low cost, and ease of use will make it a useful tool in applications requiring the expression of short RNAs and proteins.
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Affiliation(s)
- Roman Teo Oliynyk
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Computer Science, University of Auckland, Auckland, New Zealand.
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
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14
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A Possible Explanation for the Low Penetrance of Pathogenic KCNE1 Variants in Long QT Syndrome Type 5. Pharmaceuticals (Basel) 2022; 15:ph15121550. [PMID: 36559002 PMCID: PMC9782992 DOI: 10.3390/ph15121550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Long QT syndrome (LQTS) is an inherited cardiac rhythm disorder associated with increased incidence of cardiac arrhythmias and sudden death. LQTS type 5 (LQT5) is caused by dominant mutant variants of KCNE1, a regulatory subunit of the voltage-gated ion channels generating the cardiac potassium current IKs. While mutant LQT5 KCNE1 variants are known to inhibit IKs amplitudes in heterologous expression systems, cardiomyocytes from a transgenic rabbit LQT5 model displayed unchanged IKs amplitudes, pointing towards the critical role of additional factors in the development of the LQT5 phenotype in vivo. In this study, we demonstrate that KCNE3, a candidate regulatory subunit of IKs channels minimizes the inhibitory effects of LQT5 KCNE1 variants on IKs amplitudes, while current deactivation is accelerated. Such changes recapitulate IKs properties observed in LQT5 transgenic rabbits. We show that KCNE3 accomplishes this by displacing the KCNE1 subunit within the IKs ion channel complex, as evidenced by a dedicated biophysical assay. These findings depict KCNE3 as an integral part of the IKs channel complex that regulates IKs function in cardiomyocytes and modifies the development of the LQT5 phenotype.
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15
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Evans CW, Ho D, Marlow JB, King JJ, Hee C, Wong LN, Atkin R, Smith NM, Warr GG, Norret M, Iyer KS. Intracellular Communication between Synthetic Macromolecules. J Am Chem Soc 2022; 144:14112-14120. [PMID: 35901278 DOI: 10.1021/jacs.2c02793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Non-viral delivery is an important strategy for selective and efficient gene therapy, immunization, and RNA interference, which overcomes problems of genotoxicity and inherent immunogenicity associated with viral vectors. Liposomes and polymers are compelling candidates as carriers for intracellular, non-viral delivery, but maximal efficiencies of around 1% have been reported for the most advanced non-viral carriers. Here, we develop a library of dendronized bottlebrush polymers with controlled defects, displaying a level of precision surpassed only by biological molecules like DNA, RNA, and proteins. We test concurrent and competitive delivery of DNA and show for the first time that, while intracellular communication is thought to be an exclusively biomolecular phenomenon, such communication between synthetic macromolecular complexes can also take place. Our findings challenge the assumption that delivery agents behave as bystanders that enable transfection by passive intracellular release of genetic cargo and improve upon coarse strategies in intracellular carrier design lacking control over polymer sequence, architecture, and composition, leading to a hit-or-miss outcome. Understanding the communication that takes place between macromolecules will help improve the design of non-viral delivery agents and facilitate translation of genome engineering, vaccines, and nucleic acid-based therapies.
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Affiliation(s)
- Cameron W Evans
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Diwei Ho
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Joshua B Marlow
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jessica J King
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Charmaine Hee
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Lucas N Wong
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Rob Atkin
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Nicole M Smith
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Gregory G Warr
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Marck Norret
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - K Swaminathan Iyer
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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16
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DiAndreth B, Wauford N, Hu E, Palacios S, Weiss R. PERSIST platform provides programmable RNA regulation using CRISPR endoRNases. Nat Commun 2022; 13:2582. [PMID: 35562172 PMCID: PMC9095627 DOI: 10.1038/s41467-022-30172-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/20/2022] [Indexed: 12/26/2022] Open
Abstract
Regulated transgene expression is an integral component of gene therapies, cell therapies and biomanufacturing. However, transcription factor-based regulation, upon which most applications are based, suffers from complications such as epigenetic silencing that limit expression longevity and reliability. Constitutive transgene transcription paired with post-transcriptional gene regulation could combat silencing, but few such RNA- or protein-level platforms exist. Here we develop an RNA-regulation platform we call "PERSIST" which consists of nine CRISPR-specific endoRNases as RNA-level activators and repressors as well as modular OFF- and ON-switch regulatory motifs. We show that PERSIST-regulated transgenes exhibit strong OFF and ON responses, resist silencing for at least two months, and can be readily layered to construct cascades, logic functions, switches and other sophisticated circuit topologies. The orthogonal, modular and composable nature of this platform as well as the ease in constructing robust and predictable gene circuits promises myriad applications in gene and cell therapies.
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Affiliation(s)
- Breanna DiAndreth
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Noreen Wauford
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Eileen Hu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sebastian Palacios
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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17
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Florio F, Accordini S, Libergoli M, Biressi S. Targeting Muscle-Resident Single Cells Through in vivo Electro-Enhanced Plasmid Transfer in Healthy and Compromised Skeletal Muscle. Front Physiol 2022; 13:834705. [PMID: 35431987 PMCID: PMC9010744 DOI: 10.3389/fphys.2022.834705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Skeletal muscle is composed of syncytial muscle fibers, and by various mononucleated cellular types, such as muscle stem cells, immune cells, interstitial and stromal progenitors. These cell populations play a crucial role during muscle regeneration, and alterations of their phenotypic properties have been associated with defective repair and fibrosis in aging and dystrophic muscle. Studies involving in vivo gene modulation are valuable to investigate the mechanisms underlining cell function and dysfunction in complex pathophysiological settings. Electro-enhanced transfer of plasmids using square-wave generating devices represents a cost-effective approach that is widely used to transport DNA to muscle fibers efficiently. Still, it is not clear if this method can also be applied to mononuclear cells present in muscle. We demonstrate here that it is possible to efficiently deliver DNA into different muscle–resident cell populations in vivo. We evaluated the efficiency of this approach not only in healthy muscle but also in muscles of aging and dystrophic animal models. As an exemplificative application of this method, we used a strategy relying on a reporter gene-based plasmid containing regulatory sequences from the collagen 1 locus, and we determined collagen expression in various cell types reportedly involved in the production of fibrotic tissue in the dystrophic settings. The results enclosed in this manuscript reveal the suitability in applying electro-enhanced transfer of plasmid DNA to mononucleated muscle-resident cells to get insights into the molecular events governing diseased muscle physiology.
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Affiliation(s)
- Francesca Florio
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Dulbecco Telethon Institute at University of Trento, Trento, Italy
| | - Silvia Accordini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Michela Libergoli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Dulbecco Telethon Institute at University of Trento, Trento, Italy
| | - Stefano Biressi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Dulbecco Telethon Institute at University of Trento, Trento, Italy
- *Correspondence: Stefano Biressi,
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18
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Jones RD, Qian Y, Ilia K, Wang B, Laub MT, Del Vecchio D, Weiss R. Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles. Nat Commun 2022; 13:1720. [PMID: 35361767 PMCID: PMC8971529 DOI: 10.1038/s41467-022-29338-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
Engineered signaling networks can impart cells with new functionalities useful for directing differentiation and actuating cellular therapies. For such applications, the engineered networks must be tunable, precisely regulate target gene expression, and be robust to perturbations within the complex context of mammalian cells. Here, we use bacterial two-component signaling proteins to develop synthetic phosphoregulation devices that exhibit these properties in mammalian cells. First, we engineer a synthetic covalent modification cycle based on kinase and phosphatase proteins derived from the bifunctional histidine kinase EnvZ, enabling analog tuning of gene expression via its response regulator OmpR. By regulating phosphatase expression with endogenous miRNAs, we demonstrate cell-type specific signaling responses and a new strategy for accurate cell type classification. Finally, we implement a tunable negative feedback controller via a small molecule-stabilized phosphatase, reducing output expression variance and mitigating the context-dependent effects of off-target regulation and resource competition. Our work lays the foundation for establishing tunable, precise, and robust control over cell behavior with synthetic signaling networks.
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Affiliation(s)
- Ross D Jones
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yili Qian
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Katherine Ilia
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Benjamin Wang
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Michael T Laub
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Domitilla Del Vecchio
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Electrical Engineering and Computer Science Department, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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19
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Moradian H, Gossen M, Lendlein A. Co-delivery of genes can be confounded by bicistronic vector design. MRS COMMUNICATIONS 2022; 12:145-153. [PMID: 35223145 PMCID: PMC8856875 DOI: 10.1557/s43579-021-00128-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/26/2021] [Indexed: 06/14/2023]
Abstract
UNLABELLED Maximizing the efficiency of nanocarrier-mediated co-delivery of genes for co-expression in the same cell is critical for many applications. Strategies to maximize co-delivery of nucleic acids (NA) focused largely on carrier systems, with little attention towards payload composition itself. Here, we investigated the effects of different payload designs: co-delivery of two individual "monocistronic" NAs versus a single bicistronic NA comprising two genes separated by a 2A self-cleavage site. Unexpectedly, co-delivery via the monocistronic design resulted in a higher percentage of co-expressing cells, while predictive co-expression via the bicistronic design remained elusive. Our results will aid the application-dependent selection of the optimal methodology for co-delivery of genes. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1557/s43579-021-00128-7.
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Affiliation(s)
- Hanieh Moradian
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Manfred Gossen
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany
| | - Andreas Lendlein
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
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20
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Shakiba N, Jones RD, Weiss R, Del Vecchio D. Context-aware synthetic biology by controller design: Engineering the mammalian cell. Cell Syst 2021; 12:561-592. [PMID: 34139166 PMCID: PMC8261833 DOI: 10.1016/j.cels.2021.05.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/19/2021] [Accepted: 05/14/2021] [Indexed: 12/25/2022]
Abstract
The rise of systems biology has ushered a new paradigm: the view of the cell as a system that processes environmental inputs to drive phenotypic outputs. Synthetic biology provides a complementary approach, allowing us to program cell behavior through the addition of synthetic genetic devices into the cellular processor. These devices, and the complex genetic circuits they compose, are engineered using a design-prototype-test cycle, allowing for predictable device performance to be achieved in a context-dependent manner. Within mammalian cells, context effects impact device performance at multiple scales, including the genetic, cellular, and extracellular levels. In order for synthetic genetic devices to achieve predictable behaviors, approaches to overcome context dependence are necessary. Here, we describe control systems approaches for achieving context-aware devices that are robust to context effects. We then consider cell fate programing as a case study to explore the potential impact of context-aware devices for regenerative medicine applications.
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Affiliation(s)
- Nika Shakiba
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Ross D Jones
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Domitilla Del Vecchio
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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21
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Chong ZX, Yeap SK, Ho WY. Transfection types, methods and strategies: a technical review. PeerJ 2021; 9:e11165. [PMID: 33976969 PMCID: PMC8067914 DOI: 10.7717/peerj.11165] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/05/2021] [Indexed: 12/17/2022] Open
Abstract
Transfection is a modern and powerful method used to insert foreign nucleic acids into eukaryotic cells. The ability to modify host cells' genetic content enables the broad application of this process in studying normal cellular processes, disease molecular mechanism and gene therapeutic effect. In this review, we summarized and compared the findings from various reported literature on the characteristics, strengths, and limitations of various transfection methods, type of transfected nucleic acids, transfection controls and approaches to assess transfection efficiency. With the vast choices of approaches available, we hope that this review will help researchers, especially those new to the field, in their decision making over the transfection protocol or strategy appropriate for their experimental aims.
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Affiliation(s)
- Zhi Xiong Chong
- School of Pharmacy, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Selangor, Malaysia
| | - Wan Yong Ho
- School of Pharmacy, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
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22
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Linnik DS, Tarakanchikova YV, Zyuzin MV, Lepik KV, Aerts JL, Sukhorukov G, Timin AS. Layer-by-Layer technique as a versatile tool for gene delivery applications. Expert Opin Drug Deliv 2021; 18:1047-1066. [DOI: 10.1080/17425247.2021.1879790] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Dmitrii S. Linnik
- Laboratory of Micro-Encapsulation and Targeted Delivery of Biologically Active Compounds, Peter The Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Yana V. Tarakanchikova
- Laboratory of Micro-Encapsulation and Targeted Delivery of Biologically Active Compounds, Peter The Great St. Petersburg Polytechnic University, St. Petersburg, Russia
- Nanobiotechnology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia
| | - Mikhail V. Zyuzin
- Department of Physics and Engineering, ITMO University, St. Petersburg, Russia
| | - Kirill V. Lepik
- Department of Hematology, Transfusion, and Transplantation, First I. P. Pavlov State Medical University of St. Petersburg, Saint-Petersburg, Russia
| | - Joeri L. Aerts
- Laboratory of Micro-Encapsulation and Targeted Delivery of Biologically Active Compounds, Peter The Great St. Petersburg Polytechnic University, St. Petersburg, Russia
- Neuro-Aging & Viro-Immunotherapy Lab (NAVI), Vrije Universiteit Brussel, Brussels, Belgium
| | - Gleb Sukhorukov
- Laboratory of Micro-Encapsulation and Targeted Delivery of Biologically Active Compounds, Peter The Great St. Petersburg Polytechnic University, St. Petersburg, Russia
- School of Engineering and Material Science, Queen Mary University of London, London, UK
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Moscow, Russia
| | - Alexander S. Timin
- Laboratory of Micro-Encapsulation and Targeted Delivery of Biologically Active Compounds, Peter The Great St. Petersburg Polytechnic University, St. Petersburg, Russia
- Research School of Chemical and Biomedical Engineering, National Research Tomsk Polytechnic University, Tomsk, Russia
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23
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Chieca M, Torrini S, Conticello SG. Live-Cell Quantification of APOBEC1-Mediated RNA Editing: A Comparison of RNA Editing Assays. Methods Mol Biol 2021; 2181:69-81. [PMID: 32729075 DOI: 10.1007/978-1-0716-0787-9_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
APOBEC1 is a member of the AID/APOBECs, a group of deaminases responsible for the editing of C>U in both DNA and RNA. APOBEC1 is physiologically involved in C>U RNA editing: while hundreds of targets have been discovered in mice, in humans the only well-characterized target of APOBEC1 is the apolipoprotein B (ApoB) transcript. APOBEC1 edits a CAA codon into a stop codon, which causes the translation of a truncated form of ApoB. A number of assays have been developed to investigate this process. Early assays, poisoned primer extension and Sanger sequencing, have focused on accuracy and sensitivity but rely on extraction of the RNA from tissues and cells. More recently, the need to visualize the RNA editing process directly in live cells have led to the development of fluorescence-based tools. These assays detect RNA editing through reporters whose editing causes a change in cellular localization or a change in fluorescent properties. Here we review the available assays to quantify RNA editing, and we present the protocol for cytofluorimetric analysis using a double-fluorescent reporter.
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Affiliation(s)
- Martina Chieca
- Core Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, Firenze, Italy.,Department of Medical Biotechnologies, Università di Siena, Siena, Italy
| | - Serena Torrini
- Core Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, Firenze, Italy.,Department of Medical Biotechnologies, Università di Siena, Siena, Italy
| | - Silvestro G Conticello
- Core Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, Firenze, Italy. .,Institute of Clinical Physiology, CNR, Pisa, Italy.
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24
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Slobodkina E, Boldyreva M, Karagyaur M, Eremichev R, Alexandrushkina N, Balabanyan V, Akopyan Z, Parfyonova Y, Tkachuk V, Makarevich P. Therapeutic Angiogenesis by a "Dynamic Duo": Simultaneous Expression of HGF and VEGF165 by Novel Bicistronic Plasmid Restores Blood Flow in Ischemic Skeletal Muscle. Pharmaceutics 2020; 12:E1231. [PMID: 33353116 PMCID: PMC7766676 DOI: 10.3390/pharmaceutics12121231] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/07/2020] [Accepted: 12/16/2020] [Indexed: 12/21/2022] Open
Abstract
Therapeutic angiogenesis is a promising strategy for relief of ischemic conditions, and gene delivery was used to stimulate blood vessels' formation and growth. We have previously shown that intramuscular injection of a mixture containing plasmids encoding vascular endothelial growth factor (VEGF)165 and hepatocyte growth factor (HGF) leads to restoration of blood flow in mouse ischemic limb, and efficacy of combined delivery was superior to each plasmid administered alone. In this work, we evaluated different approaches for co-expression of HGF and VEGF165 genes in a panel of candidate plasmid DNAs (pDNAs) with internal ribosome entry sites (IRESs), a bidirectional promoter or two independent promoters for each gene of interest. Studies in HEK293T culture showed that all plasmids provided synthesis of HGF and VEGF165 proteins and stimulated capillary formation by human umbilical vein endothelial cells (HUVEC), indicating the biological potency of expressed factors. Tests in skeletal muscle explants showed a dramatic difference and most plasmids failed to express HGF and VEGF165 in a significant quantity. However, a bicistronic plasmid with two independent promoters (cytomegalovirus (CMV) for HGF and chicken b-actin (CAG) for VEGF165) provided expression of both grow factors in skeletal muscle at an equimolar ratio. Efficacy tests of bicistronic plasmid were performed in a mouse model of hind limb ischemia. Intramuscular administration of plasmid induced significant restoration of perfusion compared to an empty vector and saline. These findings were supported by increased CD31+ capillary density in animals that received pHGF/VEGF. Overall, our study reports a first-in-class candidate gene therapy drug to deliver two pivotal angiogenic growth factors (HGF and VEGF165) with properties that provide basis for future development of treatment for an unmet medical need-peripheral artery disease and associated limb ischemia.
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Affiliation(s)
- Ekaterina Slobodkina
- Faculty of Medicine, Lomonosov Moscow State University, 117192 Moscow, Russia; (M.K.); (N.A.); (V.B.); (Z.A.); (Y.P.); (V.T.); (P.M.)
- Institute for Regenerative Medicine, Medical Research and Education Centre, Lomonosov Moscow State University, 119192 Moscow, Russia;
| | - Maria Boldyreva
- National Medical Research Center of Cardiology Russian Ministry of Health, 121552 Moscow, Russia;
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics (HSE), 109028 Moscow, Russia
| | - Maxim Karagyaur
- Faculty of Medicine, Lomonosov Moscow State University, 117192 Moscow, Russia; (M.K.); (N.A.); (V.B.); (Z.A.); (Y.P.); (V.T.); (P.M.)
- Institute for Regenerative Medicine, Medical Research and Education Centre, Lomonosov Moscow State University, 119192 Moscow, Russia;
| | - Roman Eremichev
- Institute for Regenerative Medicine, Medical Research and Education Centre, Lomonosov Moscow State University, 119192 Moscow, Russia;
| | - Natalia Alexandrushkina
- Faculty of Medicine, Lomonosov Moscow State University, 117192 Moscow, Russia; (M.K.); (N.A.); (V.B.); (Z.A.); (Y.P.); (V.T.); (P.M.)
- Institute for Regenerative Medicine, Medical Research and Education Centre, Lomonosov Moscow State University, 119192 Moscow, Russia;
| | - Vadim Balabanyan
- Faculty of Medicine, Lomonosov Moscow State University, 117192 Moscow, Russia; (M.K.); (N.A.); (V.B.); (Z.A.); (Y.P.); (V.T.); (P.M.)
- Institute for Regenerative Medicine, Medical Research and Education Centre, Lomonosov Moscow State University, 119192 Moscow, Russia;
| | - Zhanna Akopyan
- Faculty of Medicine, Lomonosov Moscow State University, 117192 Moscow, Russia; (M.K.); (N.A.); (V.B.); (Z.A.); (Y.P.); (V.T.); (P.M.)
- Institute for Regenerative Medicine, Medical Research and Education Centre, Lomonosov Moscow State University, 119192 Moscow, Russia;
| | - Yelena Parfyonova
- Faculty of Medicine, Lomonosov Moscow State University, 117192 Moscow, Russia; (M.K.); (N.A.); (V.B.); (Z.A.); (Y.P.); (V.T.); (P.M.)
- National Medical Research Center of Cardiology Russian Ministry of Health, 121552 Moscow, Russia;
| | - Vsevolod Tkachuk
- Faculty of Medicine, Lomonosov Moscow State University, 117192 Moscow, Russia; (M.K.); (N.A.); (V.B.); (Z.A.); (Y.P.); (V.T.); (P.M.)
- Institute for Regenerative Medicine, Medical Research and Education Centre, Lomonosov Moscow State University, 119192 Moscow, Russia;
- National Medical Research Center of Cardiology Russian Ministry of Health, 121552 Moscow, Russia;
| | - Pavel Makarevich
- Faculty of Medicine, Lomonosov Moscow State University, 117192 Moscow, Russia; (M.K.); (N.A.); (V.B.); (Z.A.); (Y.P.); (V.T.); (P.M.)
- Institute for Regenerative Medicine, Medical Research and Education Centre, Lomonosov Moscow State University, 119192 Moscow, Russia;
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25
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Jones RD, Qian Y, Siciliano V, DiAndreth B, Huh J, Weiss R, Del Vecchio D. An endoribonuclease-based feedforward controller for decoupling resource-limited genetic modules in mammalian cells. Nat Commun 2020; 11:5690. [PMID: 33173034 PMCID: PMC7656454 DOI: 10.1038/s41467-020-19126-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/18/2020] [Indexed: 12/17/2022] Open
Abstract
Synthetic biology has the potential to bring forth advanced genetic devices for applications in healthcare and biotechnology. However, accurately predicting the behavior of engineered genetic devices remains difficult due to lack of modularity, wherein a device's output does not depend only on its intended inputs but also on its context. One contributor to lack of modularity is loading of transcriptional and translational resources, which can induce coupling among otherwise independently-regulated genes. Here, we quantify the effects of resource loading in engineered mammalian genetic systems and develop an endoribonuclease-based feedforward controller that can adapt the expression level of a gene of interest to significant resource loading in mammalian cells. Near-perfect adaptation to resource loads is facilitated by high production and catalytic rates of the endoribonuclease. Our design is portable across cell lines and enables predictable tuning of controller function. Ultimately, our controller is a general-purpose device for predictable, robust, and context-independent control of gene expression.
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Affiliation(s)
- Ross D Jones
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yili Qian
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Velia Siciliano
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Instituto Italiano di Tecnologia, Napoli, 80125, Italy
| | - Breanna DiAndreth
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jin Huh
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Domitilla Del Vecchio
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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26
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Moradian H, Lendlein A, Gossen M. Strategies for simultaneous and successive delivery of RNA. J Mol Med (Berl) 2020; 98:1767-1779. [PMID: 33146744 PMCID: PMC7679312 DOI: 10.1007/s00109-020-01956-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 01/05/2023]
Abstract
Advanced non-viral gene delivery experiments often require co-delivery of multiple nucleic acids. Therefore, the availability of reliable and robust co-transfection methods and defined selection criteria for their use in, e.g., expression of multimeric proteins or mixed RNA/DNA delivery is of utmost importance. Here, we investigated different co- and successive transfection approaches, with particular focus on in vitro transcribed messenger RNA (IVT-mRNA). Expression levels and patterns of two fluorescent protein reporters were determined, using different IVT-mRNA doses, carriers, and cell types. Quantitative parameters determining the efficiency of co-delivery were analyzed for IVT-mRNAs premixed before nanocarrier formation (integrated co-transfection) and when simultaneously transfecting cells with separately formed nanocarriers (parallel co-transfection), which resulted in a much higher level of expression heterogeneity for the two reporters. Successive delivery of mRNA revealed a lower transfection efficiency in the second transfection round. All these differences proved to be more pronounced for low mRNA doses. Concurrent delivery of siRNA with mRNA also indicated the highest co-transfection efficiency for integrated method. However, the maximum efficacy was shown for successive delivery, due to the kinetically different peak output for the two discretely operating entities. Our findings provide guidance for selection of the co-delivery method best suited to accommodate experimental requirements, highlighting in particular the nucleic acid dose-response dependence on co-delivery on the single-cell level.
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Affiliation(s)
- Hanieh Moradian
- Institute of Biomaterial Science, Helmholtz-Zentrum Geesthacht, Kantstr. 55, 14513, Teltow, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353, Berlin, Germany
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Andreas Lendlein
- Institute of Biomaterial Science, Helmholtz-Zentrum Geesthacht, Kantstr. 55, 14513, Teltow, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353, Berlin, Germany
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Manfred Gossen
- Institute of Biomaterial Science, Helmholtz-Zentrum Geesthacht, Kantstr. 55, 14513, Teltow, Germany.
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353, Berlin, Germany.
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