1
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Maheden K, Hwang K, Egilmez I, Shakiba N. An Optimized Mouse Embryonic Stem Cell Based Reverse Poly-Transfection Technique for Rapid Exploration of Nucleic Acid Ratios. J Vis Exp 2023. [PMID: 38145374 DOI: 10.3791/65766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2023] Open
Abstract
Due to its relative simplicity and ease of use, transient transfection of mammalian cell lines with nucleic acids has become a mainstay in biomedical research. While most widely used cell lines have robust protocols for transfection in adherent two-dimensional culture, these protocols often do not translate well to less-studied lines or those with atypical, hard-to-transfect morphologies. Using mouse pluripotent stem cells grown in 2i/LIF media, a widely used culture model for regenerative medicine, this method outlines an optimized, rapid reverse transfection protocol capable of achieving higher transfection efficiency. Leveraging this protocol, a three-plasmid poly-transfection is performed, taking advantage of the higher-than-normal efficiency in plasmid delivery to study an expanded range of plasmid stoichiometry. This reverse poly-transfection protocol allows for a one-pot experimental method, enabling users to optimize plasmid ratios in a single well, rather than across several co-transfections. By facilitating the rapid exploration of the effect of DNA stoichiometry on the overall function of delivered genetic circuits, this protocol minimizes the time and cost of embryonic stem cell transfection.
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Affiliation(s)
- Kieran Maheden
- School of Biomedical Engineering, University of British Columbia
| | - Karen Hwang
- School of Biomedical Engineering, University of British Columbia
| | - Ipek Egilmez
- School of Biomedical Engineering, University of British Columbia
| | - Nika Shakiba
- School of Biomedical Engineering, University of British Columbia;
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2
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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. Sci Adv 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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Yachie N, Shakiba N. Tenure time loopers. Nat Biotechnol 2023; 41:1375-1377. [PMID: 37626232 DOI: 10.1038/s41587-023-01924-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Affiliation(s)
- Nozomu Yachie
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
- Premium Research Institute for Human Metaverse Medicine, Osaka University, Suita, Japan.
- Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.
| | - Nika Shakiba
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
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4
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Abstract
The dynamic nature of the COVID-19 pandemic has demanded a public health response that is constantly evolving due to the novelty of the virus. Many jurisdictions in the USA, Canada, and across the world have adopted social distancing and recommended the use of face masks. Considering these measures, it is prudent to understand the contributions of subpopulations—such as “silent spreaders”—to disease transmission dynamics in order to inform public health strategies in a jurisdiction-dependent manner. Additionally, we and others have shown that demographic and environmental stochasticity in transmission rates can play an important role in shaping disease dynamics. Here, we create a model for the COVID-19 pandemic by including two classes of individuals: silent spreaders, who either never experience a symptomatic phase or remain undetected throughout their disease course; and symptomatic spreaders, who experience symptoms and are detected. We fit the model to real-time COVID-19 confirmed cases and deaths to derive the transmission rates, death rates, and other relevant parameters for multiple phases of outbreaks in British Columbia (BC), Canada. We determine the extent to which SilS contributed to BC’s early wave of disease transmission as well as the impact of public health interventions on reducing transmission from both SilS and SymS. To do this, we validate our model against an existing COVID-19 parameterized framework and then fit our model to clinical data to estimate key parameter values for different stages of BC’s disease dynamics. We then use these parameters to construct a hybrid stochastic model that leverages the strengths of both a time-nonhomogeneous discrete process and a stochastic differential equation model. By combining these previously established approaches, we explore the impact of demographic and environmental variability on disease dynamics by simulating various scenarios in which a COVID-19 outbreak is initiated. Our results demonstrate that variability in disease transmission rate impacts the probability and severity of COVID-19 outbreaks differently in high- versus low-transmission scenarios.
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Affiliation(s)
- Karen K. L. Hwang
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC Canada
| | | | - Omar Saucedo
- Department of Mathematics, Virginia Tech, Blacksburg, VA USA
| | - Linda J. S. Allen
- Department of Mathematics and Statistics, Texas Tech University, Lubbock, TX USA
| | - Nika Shakiba
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC Canada
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6
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Maheden K, Zhang VW, Shakiba N. The Field of Cell Competition Comes of Age: Semantics and Technological Synergy. Front Cell Dev Biol 2022; 10:891569. [PMID: 35646896 PMCID: PMC9132545 DOI: 10.3389/fcell.2022.891569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
Stem cells experience many selective pressures which shape their cellular populations, potentially pushing them to skew towards dominance of a few break-through clones. An evolutionarily conserved answer to curb these aberrant selective pressures is cell competition, the elimination of a subset of cells by their neighbours in a seemingly homogenous population. Cell competition in mammalian systems is a relatively recent discovery that has now been observed across many tissue systems, such as embryonic, haematopoietic, intestinal, and epithelial compartments. With this rapidly growing field, there is a need to revisit and standardize the terminology used, much of which has been co-opted from evolutionary biology. Further, the implications of cell competition across biological scales in organisms have been difficult to capture. In this review, we make three key points. One, we propose new nomenclature to standardize concepts across dispersed studies of different types of competition, each of which currently use the same terminology to describe different phenomena. Second, we highlight the challenges in capturing information flow across biological scales. Third, we challenge the field to incorporate next generation technologies into the cell competition toolkit to bridge these gaps. As the field of cell competition matures, synergy between cutting edge tools will help elucidate the molecular events which shape cellular growth and death dynamics, allowing a deeper examination of this evolutionarily conserved mechanism at the core of multicellularity.
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Affiliation(s)
| | | | - Nika Shakiba
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
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7
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Shakiba N, Li C, Garcia-Ojalvo J, Cho KH, Patil K, Walczak A, Liu YY, Kuehn S, Nie Q, Klein A, Deco G, Kringelbach M, Iyer-Biswas S. How can Waddington-like landscapes facilitate insights beyond developmental biology? Cell Syst 2022; 13:4-9. [DOI: 10.1016/j.cels.2021.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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8
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Maheden K, Bashth OS, Shakiba N. Evening the playing field: microenvironmental control over stem cell competition during fate programming. Curr Opin Genet Dev 2021; 70:66-75. [PMID: 34153929 DOI: 10.1016/j.gde.2021.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 12/26/2022]
Abstract
Recent advancements in cellular engineering, including reprogramming of somatic cells into pluripotent stem cells, have opened the door to a new era of regenerative medicine. Given that cellular decisions are guided by microenvironmental cues, such as secreted factors and interactions with neighbouring cells, reproducible cell manufacturing requires robust control over cell-cell interactions. Cell competition has recently emerged as a previously unknown interaction that plays a significant role in shaping the growth and death dynamics of multicellular stem cell populations, both in vivo and in vitro. Although recent studies have largely focused on exploring how the differential expression of key genes mediate the competitive elimination of some cells, little is known about the impact of the microenvironment on cell competition, despite its critical role in shaping cell fate outcomes. Here, we explore recent findings that have brought cell competition into the spotlight, while dissecting the role of microenvironmental factors for controlling competition in cell fate programming applications.
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Affiliation(s)
- Kieran Maheden
- School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, University of British Columbia, Biomedical Research Centre, 2222 Health Sciences Mall, V6T 1Z3, Vancouver, Canada
| | - Omar S Bashth
- School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, University of British Columbia, Biomedical Research Centre, 2222 Health Sciences Mall, V6T 1Z3, Vancouver, Canada
| | - Nika Shakiba
- School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, University of British Columbia, Biomedical Research Centre, 2222 Health Sciences Mall, V6T 1Z3, Vancouver, Canada.
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9
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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: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Shakiba N, Edholm CJ, Emerenini BO, Murillo AL, Peace A, Saucedo O, Wang X, Allen LJ. Effects of environmental variability on superspreading transmission events in stochastic epidemic models. Infect Dis Model 2021; 6:560-583. [PMID: 33754134 PMCID: PMC7969833 DOI: 10.1016/j.idm.2021.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 11/02/2022] Open
Abstract
Superspreaders (individuals with a high propensity for disease spread) have played a pivotal role in recent emerging and re-emerging diseases. In disease outbreak studies, host heterogeneity based on demographic (e.g. age, sex, vaccination status) and environmental (e.g. climate, urban/rural residence, clinics) factors are critical for the spread of infectious diseases, such as Ebola and Middle East Respiratory Syndrome (MERS). Transmission rates can vary as demographic and environmental factors are altered naturally or due to modified behaviors in response to the implementation of public health strategies. In this work, we develop stochastic models to explore the effects of demographic and environmental variability on human-to-human disease transmission rates among superspreaders in the case of Ebola and MERS. We show that the addition of environmental variability results in reduced probability of outbreak occurrence, however the severity of outbreaks that do occur increases. These observations have implications for public health strategies that aim to control environmental variables.
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Affiliation(s)
- Nika Shakiba
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | | | - Blessing O. Emerenini
- Department of Mathematics, Oregon State University, Corvallis, OR, USA
- School of Mathematical Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Anarina L. Murillo
- Department of Pediatrics and Center for Statistical Sciences, Brown University, Providence, RI, USA
| | - Angela Peace
- Department of Mathematics and Statistics, Texas Tech University, Lubbock, TX, USA
| | - Omar Saucedo
- Department of Mathematics, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Xueying Wang
- Department of Mathematics and Statistics, Washington State University, Pullman, WA, USA
| | - Linda J.S. Allen
- Department of Mathematics and Statistics, Texas Tech University, Lubbock, TX, USA
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11
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Padervand S, Khoei SMM, Shakiba N. Access to Optimum Working Voltage of Plasma Electrolytic Nitridation of Tantalum Alloys. Surf Engin Appl Electrochem 2020. [DOI: 10.3103/s1068375520060125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Sarihi S, Padervand S, Mousavi khoei SM, Shakiba N. The effect of nitrogen concentration on N-doped diamond-like carbon films prepared by plasma-electrolytic method. INORG NANO-MET CHEM 2020. [DOI: 10.1080/24701556.2020.1852422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- S. Sarihi
- Mining and Metallurgical Engineering Department, Amirkabir University of Technology, Tehran, Iran
| | - S. Padervand
- Mining and Metallurgical Engineering Department, Amirkabir University of Technology, Tehran, Iran
| | - S. M. Mousavi khoei
- Mining and Metallurgical Engineering Department, Amirkabir University of Technology, Tehran, Iran
| | - N. Shakiba
- Mining and Metallurgical Engineering Department, Amirkabir University of Technology, Tehran, Iran
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13
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Tewary M, Dziedzicka D, Ostblom J, Prochazka L, Shakiba N, Heydari T, Aguilar-Hidalgo D, Woodford C, Piccinini E, Becerra-Alonso D, Vickers A, Louis B, Rahman N, Danovi D, Geens M, Watt FM, Zandstra PW. High-throughput micropatterning platform reveals Nodal-dependent bisection of peri-gastrulation-associated versus preneurulation-associated fate patterning. PLoS Biol 2019; 17:e3000081. [PMID: 31634368 PMCID: PMC6822778 DOI: 10.1371/journal.pbio.3000081] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 10/31/2019] [Accepted: 09/25/2019] [Indexed: 12/22/2022] Open
Abstract
In vitro models of postimplantation human development are valuable to the fields of regenerative medicine and developmental biology. Here, we report characterization of a robust in vitro platform that enabled high-content screening of multiple human pluripotent stem cell (hPSC) lines for their ability to undergo peri-gastrulation–like fate patterning upon bone morphogenetic protein 4 (BMP4) treatment of geometrically confined colonies and observed significant heterogeneity in their differentiation propensities along a gastrulation associable and neuralization associable axis. This cell line–associated heterogeneity was found to be attributable to endogenous Nodal expression, with up-regulation of Nodal correlated with expression of a gastrulation-associated gene profile, and Nodal down-regulation correlated with a preneurulation-associated gene profile expression. We harness this knowledge to establish a platform of preneurulation-like fate patterning in geometrically confined hPSC colonies in which fates arise because of a BMPs signalling gradient conveying positional information. Our work identifies a Nodal signalling-dependent switch in peri-gastrulation versus preneurulation-associated fate patterning in hPSC cells, provides a technology to robustly assay hPSC differentiation outcomes, and suggests conserved mechanisms of organized fate specification in differentiating epiblast and ectodermal tissues. This study describes a method to generate a robust high-throughput micropatterning platform, and uses it to reveal the role played by Nodal signalling in the self-organization of BMP signalling and the consequent fates that arise in micropatterned human embryonic stem cell colonies.
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Affiliation(s)
- Mukul Tewary
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Collaborative Program in Developmental Biology, University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Centre for Stem Cells & Regenerative Medicine, King's College London, London, United Kingdom
| | - Dominika Dziedzicka
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Joel Ostblom
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Laura Prochazka
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Nika Shakiba
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Tiam Heydari
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel Aguilar-Hidalgo
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Curtis Woodford
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Elia Piccinini
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - David Becerra-Alonso
- Department of Quantitative Methods, Universidad Loyola Andalucia, Sevilla, Spain
| | - Alice Vickers
- Centre for Stem Cells & Regenerative Medicine, King's College London, London, United Kingdom
| | - Blaise Louis
- Centre for Stem Cells & Regenerative Medicine, King's College London, London, United Kingdom
| | - Nafees Rahman
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Davide Danovi
- Centre for Stem Cells & Regenerative Medicine, King's College London, London, United Kingdom
| | - Mieke Geens
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Fiona M. Watt
- Centre for Stem Cells & Regenerative Medicine, King's College London, London, United Kingdom
| | - Peter W. Zandstra
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Collaborative Program in Developmental Biology, University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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14
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Zhang S, Scott EY, Singh J, Chen Y, Zhang Y, Elsayed M, Chamberlain MD, Shakiba N, Adams K, Yu S, Morshead CM, Zandstra PW, Wheeler AR. The optoelectronic microrobot: A versatile toolbox for micromanipulation. Proc Natl Acad Sci U S A 2019; 116:14823-14828. [PMID: 31289234 PMCID: PMC6660717 DOI: 10.1073/pnas.1903406116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Microrobotics extends the reach of human-controlled machines to submillimeter dimensions. We introduce a microrobot that relies on optoelectronic tweezers (OET) that is straightforward to manufacture, can take nearly any desirable shape or form, and can be programmed to carry out sophisticated, multiaxis operations. One particularly useful program is a serial combination of "load," "transport," and "deliver," which can be applied to manipulate a wide range of micrometer-dimension payloads. Importantly, microrobots programmed in this manner are much gentler on fragile mammalian cells than conventional OET techniques. The microrobotic system described here was demonstrated to be useful for single-cell isolation, clonal expansion, RNA sequencing, manipulation within enclosed systems, controlling cell-cell interactions, and isolating precious microtissues from heterogeneous mixtures. We propose that the optoelectronic microrobotic system, which can be implemented using a microscope and consumer-grade optical projector, will be useful for a wide range of applications in the life sciences and beyond.
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Affiliation(s)
- Shuailong Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Erica Y Scott
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Jastaranpreet Singh
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Yujie Chen
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics and Information Technology, Sun Yat-sen University, 510275 Guangzhou, China
| | - Yanfeng Zhang
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics and Information Technology, Sun Yat-sen University, 510275 Guangzhou, China
| | - Mohamed Elsayed
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - M Dean Chamberlain
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Nika Shakiba
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Kelsey Adams
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Siyuan Yu
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics and Information Technology, Sun Yat-sen University, 510275 Guangzhou, China
- Photonics Group, Merchant Venturers School of Engineering, University of Bristol, BS8 1UB Bristol, United Kingdom
| | - Cindi M Morshead
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Surgery, University of Toronto, Toronto, ON M5T 1P5, Canada
| | - Peter W Zandstra
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- The Biomedical Research Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Aaron R Wheeler
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada;
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
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15
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Abstract
New fundamental discoveries in stem cell biology have yielded potentially transformative regenerative therapeutics. However, widespread implementation of stem-cell-derived therapeutics remains sporadic. Barriers that impede the development of these therapeutics can be linked to our incomplete understanding of how the regulatory networks that encode stem cell fate govern the development of the complex tissues and organs that are ultimately required for restorative function. Bioengineering tools, strategies and design principles represent core components of the stem cell bioengineering toolbox. Applied to the different layers of complexity present in stem-cell-derived systems - from gene regulatory networks in single stem cells to the systemic interactions of stem-cell-derived organs and tissues - stem cell bioengineering can address existing challenges and advance regenerative medicine and cellular therapies.
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Affiliation(s)
- Mukul Tewary
- Institute of Biomaterials and Biomedical Engineering (IBBME) and The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada.,Collaborative Program in Developmental Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nika Shakiba
- Institute of Biomaterials and Biomedical Engineering (IBBME) and The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering (IBBME) and The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada. .,Collaborative Program in Developmental Biology, University of Toronto, Toronto, Ontario, Canada. .,Michael Smith Laboratories and School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
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16
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Shakiba N, Fahmy A, Jayakumaran G, McGibbon S, David L, Trcka D, Elbaz J, Puri MC, Nagy A, van der Kooy D, Goyal S, Wrana JL, Zandstra PW. Cell competition during reprogramming gives rise to dominant clones. Science 2019; 364:science.aan0925. [DOI: 10.1126/science.aan0925] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 08/02/2018] [Accepted: 02/25/2019] [Indexed: 12/25/2022]
Abstract
The ability to generate induced pluripotent stem cells from differentiated cell types has enabled researchers to engineer cell states. Although studies have identified molecular networks that reprogram cells to pluripotency, the cellular dynamics of these processes remain poorly understood. Here, by combining cellular barcoding, mathematical modeling, and lineage tracing approaches, we demonstrate that reprogramming dynamics in heterogeneous populations are driven by dominant “elite” clones. Clones arise a priori from a population of poised mouse embryonic fibroblasts derived from Wnt1-expressing cells that may represent a neural crest–derived population. This work highlights the importance of cellular dynamics in fate programming outcomes and uncovers cell competition as a mechanism by which cells with eliteness emerge to occupy and dominate the reprogramming niche.
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17
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Zhang S, Shakiba N, Chen Y, Zhang Y, Tian P, Singh J, Chamberlain MD, Satkauskas M, Flood AG, Kherani NP, Yu S, Zandstra PW, Wheeler AR. Patterned Optoelectronic Tweezers: A New Scheme for Selecting, Moving, and Storing Dielectric Particles and Cells. Small 2018; 14:e1803342. [PMID: 30307718 DOI: 10.1002/smll.201803342] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Indexed: 06/08/2023]
Abstract
Optical micromanipulation has become popular for a wide range of applications. In this work, a new type of optical micromanipulation platform, patterned optoelectronic tweezers (p-OET), is introduced. In p-OET devices, the photoconductive layer (that is continuous in a conventional OET device) is patterned, forming regions in which the electrode layer is locally exposed. It is demonstrated that micropatterns in the photoconductive layer are useful for repelling unwanted particles/cells, and also for keeping selected particles/cells in place after turning off the light source, minimizing light-induced heating. To clarify the physical mechanism behind these effects, systematic simulations are carried out, which indicate the existence of strong nonuniform electric fields at the boundary of micropatterns. The simulations are consistent with experimental observations, which are explored for a wide variety of geometries and conditions. It is proposed that the new technique may be useful for myriad applications in the rapidly growing area of optical micromanipulation.
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Affiliation(s)
- Shuailong Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
| | - Nika Shakiba
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
| | - Yujie Chen
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yanfeng Zhang
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Pengfei Tian
- Institute for Electric Light Sources, Fudan University, Shanghai, 200433, China
| | - Jastaranpreet Singh
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
| | - M Dean Chamberlain
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
| | - Monika Satkauskas
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
| | - Andrew G Flood
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON, M5S 3G4, Canada
| | - Nazir P Kherani
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON, M5S 3G4, Canada
- Department of Materials Science and Engineering, University of Toronto, Toronto, ON, M5S 3E4, Canada
| | - Siyuan Yu
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, 510275, China
- Photonics Group, Merchant Venturers School of Engineering, University of Bristol, Bristol, BS81UB, UK
| | - Peter W Zandstra
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
- Medicine by Design, University of Toronto, Toronto, ON, M5S 3G9, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Aaron R Wheeler
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
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18
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Tewary M, Ostblom J, Prochazka L, Zulueta-Coarasa T, Shakiba N, Fernandez-Gonzalez R, Zandstra PW. A stepwise model of reaction-diffusion and positional information governs self-organized human peri-gastrulation-like patterning. Development 2017; 144:4298-4312. [PMID: 28870989 PMCID: PMC5769627 DOI: 10.1242/dev.149658] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 08/23/2017] [Indexed: 12/15/2022]
Abstract
How position-dependent cell fate acquisition occurs during embryogenesis is a central question in developmental biology. To study this process, we developed a defined, high-throughput assay to induce peri-gastrulation-associated patterning in geometrically confined human pluripotent stem cell (hPSC) colonies. We observed that, upon BMP4 treatment, phosphorylated SMAD1 (pSMAD1) activity in the colonies organized into a radial gradient. We developed a reaction-diffusion (RD)-based computational model and observed that the self-organization of pSMAD1 signaling was consistent with the RD principle. Consequent fate acquisition occurred as a function of both pSMAD1 signaling strength and duration of induction, consistent with the positional-information (PI) paradigm. We propose that the self-organized peri-gastrulation-like fate patterning in BMP4-treated geometrically confined hPSC colonies arises via a stepwise model of RD followed by PI. This two-step model predicted experimental responses to perturbations of key parameters such as colony size and BMP4 dose. Furthermore, it also predicted experimental conditions that resulted in RD-like periodic patterning in large hPSC colonies, and rescued peri-gastrulation-like patterning in colony sizes previously thought to be reticent to this behavior.
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Affiliation(s)
- Mukul Tewary
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, M5S 3E1, Canada
- Collaborative Program in Developmental Biology, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
| | - Joel Ostblom
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, M5S 3E1, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
| | - Laura Prochazka
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, M5S 3E1, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
| | - Teresa Zulueta-Coarasa
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, M5S 3E1, Canada
- Ted Rogers Centre for Heart Research, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Nika Shakiba
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, M5S 3E1, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
| | - Rodrigo Fernandez-Gonzalez
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, M5S 3E1, Canada
- Collaborative Program in Developmental Biology, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
- Ted Rogers Centre for Heart Research, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, M5S 3G5, Canada
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, M5S 3E1, Canada
- Collaborative Program in Developmental Biology, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3ES, Canada
- Medicine by Design: A Canada First Research Excellence Fund Program, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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19
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Abstract
Cell competition results in the loss of weaker cells and the dominance of stronger cells. So-called 'loser' cells are either removed by active elimination or by limiting their access to survival factors. Recently, competition has been shown to serve as a surveillance mechanism against emerging aberrant cells in both the developing and adult organism, contributing to overall organism fitness and survival. Here, we explore the origins and implications of cell competition in development, tissue homeostasis, and in vitro culture. We also provide a forward look on the use of cell competition to interpret multicellular dynamics while offering a perspective on harnessing competition to engineer cells with optimized and controllable fitness characteristics for regenerative medicine applications.
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Affiliation(s)
- Nika Shakiba
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario M5S 3E1, Canada; The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario M5S 3E1, Canada; Medicine by Design, University of Toronto, Toronto, Ontario M5S 3G9, Canada.
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20
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Hussein SMI, Puri MC, Tonge PD, Benevento M, Corso AJ, Clancy JL, Mosbergen R, Li M, Lee DS, Cloonan N, Wood DLA, Munoz J, Middleton R, Korn O, Patel HR, White CA, Shin JY, Gauthier ME, Cao KAL, Kim JI, Mar JC, Shakiba N, Ritchie W, Rasko JEJ, Grimmond SM, Zandstra PW, Wells CA, Preiss T, Seo JS, Heck AJR, Rogers IM, Nagy A. Corrigendum: Genome-wide characterization of the routes to pluripotency. Nature 2015; 523:626. [PMID: 26083747 DOI: 10.1038/nature14606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Shakiba N, White CA, Lipsitz YY, Yachie-Kinoshita A, Tonge PD, Hussein SMI, Puri MC, Elbaz J, Morrissey-Scoot J, Li M, Munoz J, Benevento M, Rogers IM, Hanna JH, Heck AJR, Wollscheid B, Nagy A, Zandstra PW. CD24 tracks divergent pluripotent states in mouse and human cells. Nat Commun 2015; 6:7329. [PMID: 26076835 PMCID: PMC4490408 DOI: 10.1038/ncomms8329] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 04/27/2015] [Indexed: 12/12/2022] Open
Abstract
Reprogramming is a dynamic process that can result in multiple pluripotent cell types emerging from divergent paths. Cell surface protein expression is a particularly desirable tool to categorize reprogramming and pluripotency as it enables robust quantification and enrichment of live cells. Here we use cell surface proteomics to interrogate mouse cell reprogramming dynamics and discover CD24 as a marker that tracks the emergence of reprogramming-responsive cells, while enabling the analysis and enrichment of transgene-dependent (F-class) and -independent (traditional) induced pluripotent stem cells (iPSCs) at later stages. Furthermore, CD24 can be used to delineate epiblast stem cells (EpiSCs) from embryonic stem cells (ESCs) in mouse pluripotent culture. Importantly, regulated CD24 expression is conserved in human pluripotent stem cells (PSCs), tracking the conversion of human ESCs to more naive-like PSC states. Thus, CD24 is a conserved marker for tracking divergent states in both reprogramming and standard pluripotent culture. Characterizing the cellular stages that lead to induced reprogramming is of much interest and cell surface markers could offer unique advantages for this. Here the authors use surface proteomics and discover CD24 as a marker that tracks reprogramming-responsive cells and enables the analysis and enrichment of transgene-dependent and -independent induced pluriopotent stem cells.
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Affiliation(s)
- Nika Shakiba
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Carl A White
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada M5S 3E1.,The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Yonatan Y Lipsitz
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Ayako Yachie-Kinoshita
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada M5S 3E1.,The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Peter D Tonge
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Samer M I Hussein
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Mira C Puri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5T 3H7
| | - Judith Elbaz
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - James Morrissey-Scoot
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Mira Li
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
| | - Javier Munoz
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht University for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Marco Benevento
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht University for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ian M Rogers
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5.,Department of Physiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8.,Department of Obstetrics and Gynecology, University of Toronto, Toronto, Ontario, Canada M5G 1E2
| | - Jacob H Hanna
- The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel 76100
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht University for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Bernd Wollscheid
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, Wolfgang-Pauli Strasse 16, 8093 Zürich, Switzerland.,NCCR Neuro Center for Proteomics, University and Swiss Federal Institute of Technology (ETH) Zürich, Wolfgang-Pauli Strasse 16, 8093 Zurich, Switzerland.,Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zürich, Universitätstrasse 2, 8092 Zurich, Switzerland
| | - Andras Nagy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5.,Department of Obstetrics and Gynecology, University of Toronto, Toronto, Ontario, Canada M5G 1E2.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada M5T 3H7
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada M5S 3E1.,The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada M5S 3E1
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22
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Hussein SMI, Puri MC, Tonge PD, Benevento M, Corso AJ, Clancy JL, Mosbergen R, Li M, Lee DS, Cloonan N, Wood DLA, Munoz J, Middleton R, Korn O, Patel HR, White CA, Shin JY, Gauthier ME, Cao KAL, Kim JI, Mar JC, Shakiba N, Ritchie W, Rasko JEJ, Grimmond SM, Zandstra PW, Wells CA, Preiss T, Seo JS, Heck AJR, Rogers IM, Nagy A. Genome-wide characterization of the routes to pluripotency. Nature 2014; 516:198-206. [DOI: 10.1038/nature14046] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 11/10/2014] [Indexed: 12/24/2022]
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23
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Fluri DA, Tonge PD, Song H, Baptista RP, Shakiba N, Shukla S, Clarke G, Nagy A, Zandstra PW. Derivation, expansion and differentiation of induced pluripotent stem cells in continuous suspension cultures. Nat Methods 2012; 9:509-16. [PMID: 22447133 PMCID: PMC4954777 DOI: 10.1038/nmeth.1939] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 01/24/2012] [Indexed: 12/21/2022]
Abstract
We describe derivation of induced pluripotent stem cells (iPSCs) from terminally differentiated mouse cells in serum- and feeder-free stirred suspension cultures. Temporal analysis of global gene expression revealed high correlations between cells reprogrammed in suspension and cells reprogrammed in adhesion-dependent conditions. Suspension culture-reprogrammed iPSCs (SiPSCs) could be differentiated into all three germ layers in vitro and contributed to chimeric embryos in vivo. SiPSC generation allowed for efficient selection of reprogramming factor-expressing cells based on their differential survival and proliferation in suspension culture. Seamless integration of SiPSC reprogramming and directed differentiation enabled scalable production of beating cardiac cells in a continuous single cell- and small aggregate-based process. This method is an important step toward the development of robust PSC generation, expansion and differentiation technology.
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Affiliation(s)
- David A Fluri
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
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