1
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Stankiewicz LN, Rossi FMV, Zandstra PW. Rebuilding and rebooting immunity with stem cells. Cell Stem Cell 2024; 31:597-616. [PMID: 38593798 DOI: 10.1016/j.stem.2024.03.012] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/08/2024] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
Advances in modern medicine have enabled a rapid increase in lifespan and, consequently, have highlighted the immune system as a key driver of age-related disease. Immune regeneration therapies present exciting strategies to address age-related diseases by rebooting the host's primary lymphoid tissues or rebuilding the immune system directly via biomaterials or artificial tissue. Here, we identify important, unanswered questions regarding the safety and feasibility of these therapies. Further, we identify key design parameters that should be primary considerations guiding technology design, including timing of application, interaction with the host immune system, and functional characterization of the target patient population.
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Affiliation(s)
- Laura N Stankiewicz
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Fabio M V Rossi
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Peter W Zandstra
- 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.
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2
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Heydari T, Zandstra PW. Inferring Gene Regulatory Networks and Predicting the Effect of Gene Perturbations via IQCELL. Methods Mol Biol 2024; 2767:251-262. [PMID: 36790623 DOI: 10.1007/7651_2022_465] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
IQCELL is a platform that infers Boolean gene regulatory networks from single-cell RNA sequencing data. Boolean networks can be simulated under normal and perturbed conditions. In this chapter, we provide a detailed guideline for implementing IQCELL from a raw dataset. The steps include processing data, inferring informative genes, inferring gene regulatory network, and simulating the resulted network under normal and perturbed conditions.
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Affiliation(s)
- Tiam Heydari
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Peter W Zandstra
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
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3
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Kirouac DC, Zmurchok C, Deyati A, Sicherman J, Bond C, Zandstra PW. Author Correction: Deconvolution of clinical variance in CAR-T cell pharmacology and response. Nat Biotechnol 2023; 41:1655. [PMID: 37188917 PMCID: PMC10635823 DOI: 10.1038/s41587-023-01816-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Affiliation(s)
| | | | | | | | - Chris Bond
- Notch Therapeutics, Vancouver, BC, Canada
| | - Peter W Zandstra
- Notch Therapeutics, Vancouver, BC, Canada
- School of Biomedical Engineering and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
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4
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Kirouac DC, Zmurchok C, Deyati A, Sicherman J, Bond C, Zandstra PW. Deconvolution of clinical variance in CAR-T cell pharmacology and response. Nat Biotechnol 2023; 41:1606-1617. [PMID: 36849828 PMCID: PMC10635825 DOI: 10.1038/s41587-023-01687-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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] [Received: 03/14/2022] [Accepted: 01/20/2023] [Indexed: 03/01/2023]
Abstract
Chimeric antigen receptor T cell (CAR-T) expansion and persistence vary widely among patients and predict both efficacy and toxicity. However, the mechanisms underlying clinical outcomes and patient variability are poorly defined. In this study, we developed a mathematical description of T cell responses wherein transitions among memory, effector and exhausted T cell states are coordinately regulated by tumor antigen engagement. The model is trained using clinical data from CAR-T products in different hematological malignancies and identifies cell-intrinsic differences in the turnover rate of memory cells and cytotoxic potency of effectors as the primary determinants of clinical response. Using a machine learning workflow, we demonstrate that product-intrinsic differences can accurately predict patient outcomes based on pre-infusion transcriptomes, and additional pharmacological variance arises from cellular interactions with patient tumors. We found that transcriptional signatures outperform T cell immunophenotyping as predictive of clinical response for two CD19-targeted CAR-T products in three indications, enabling a new phase of predictive CAR-T product development.
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Affiliation(s)
| | | | | | | | - Chris Bond
- Notch Therapeutics, Vancouver, BC, Canada
| | - Peter W Zandstra
- Notch Therapeutics, Vancouver, BC, Canada
- School of Biomedical Engineering and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
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5
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Stankiewicz LN, Salim K, Flaschner EA, Wang YX, Edgar JM, Lin BZB, Bingham GC, Major MC, Jones RD, Blau HM, Rideout EJ, Levings MK, Zandstra PW, Rossi FMV. Sex biased human thymic architecture guides T cell development through spatially defined niches. bioRxiv 2023:2023.04.13.536804. [PMID: 37090676 PMCID: PMC10120731 DOI: 10.1101/2023.04.13.536804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Within the thymus, regulation of the cellular cross-talk directing T cell development is dependent on spatial interactions within specialized niches. To create a holistic, spatially defined map of tissue niches guiding postnatal T cell development we employed the multidimensional imaging platform CO-detection by indEXing (CODEX), as well as CITE-seq and ATAC-seq. We generated age-matched 4-5-month-old postnatal thymus datasets for male and female donors, and identify significant sex differences in both T cell and thymus biology. We demonstrate a crucial role for JAG ligands in directing thymic-like dendritic cell development, reveal important functions of a novel population of ECM- fibroblasts, and characterize the medullary niches surrounding Hassall's corpuscles. Together, these data represent a unique age-matched spatial multiomic resource to investigate how sex-based differences in thymus regulation and T cell development arise, and provide an essential resource to understand the mechanisms underlying immune function and dysfunction in males and females.
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Affiliation(s)
| | - Kevin Salim
- Department of Surgery, University of British Columbia, Canada
- BC Children’s Hospital Research Institute, Canada
| | - Emily A Flaschner
- School of Biomedical Engineering, University of British Columbia, Canada
| | - Yu Xin Wang
- Center for Genetic Disorders and Aging, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - John M Edgar
- School of Biomedical Engineering, University of British Columbia, Canada
| | - Bruce ZB Lin
- School of Biomedical Engineering, University of British Columbia, Canada
| | - Grace C Bingham
- Department of Biomedical Engineering, University of Virginia, USA
| | - Matthew C Major
- School of Biomedical Engineering, University of British Columbia, Canada
| | - Ross D Jones
- School of Biomedical Engineering, University of British Columbia, Canada
| | - Helen M Blau
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, USA
| | | | - Megan K Levings
- School of Biomedical Engineering, University of British Columbia, Canada
- Department of Surgery, University of British Columbia, Canada
- BC Children’s Hospital Research Institute, Canada
| | - Peter W Zandstra
- School of Biomedical Engineering, University of British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Canada
- These authors contributed equally
- Lead contact
| | - Fabio MV Rossi
- School of Biomedical Engineering, University of British Columbia, Canada
- These authors contributed equally
- Lead contact
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6
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Michaels YS, Durland LJ, Zandstra PW. Engineering T Cell Development for the Next Generation of Stem Cell-Derived Immunotherapies. GEN Biotechnol 2023; 2:106-119. [PMID: 37928777 PMCID: PMC10624212 DOI: 10.1089/genbio.2023.0008] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/31/2023] [Indexed: 11/07/2023]
Abstract
Engineered T cells are at the leading edge of clinical cell therapy. T cell therapies have had a remarkable impact on patient care for a subset of hematological malignancies. This foundation has motivated the development of off-the-shelf engineered cell therapies for a broad range of devastating indications. Achieving this vision will require cost-effective manufacturing of precision cell products capable of addressing multiple process and clinical-design challenges. Pluripotent stem cell (PSC)-derived engineered T cells are emerging as a solution of choice. To unleash the full potential of PSC-derived T cell therapies, the field will require technologies capable of robustly orchestrating the complex series of time- and dose-dependent signaling events needed to recreate functional T cell development in the laboratory. In this article, we review the current state of allogenic T cell therapies, focusing on strategies to generate engineered lymphoid cells from PSCs. We highlight exciting recent progress in this field and outline timely opportunities for advancement with an emphasis on niche engineering and synthetic biology.
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Affiliation(s)
- Yale S. Michaels
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada; University of British Columbia, Vancouver, Canada
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada; University of British Columbia, Vancouver, Canada
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, Canada; and University of British Columbia, Vancouver, Canada
| | - Lauren J. Durland
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada; University of British Columbia, Vancouver, Canada
| | - Peter W. Zandstra
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada; University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
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7
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Prochazka L, Michaels YS, Lau C, Jones RD, Siu M, Yin T, Wu D, Jang E, Vázquez‐Cantú M, Gilbert PM, Kaul H, Benenson Y, Zandstra PW. Synthetic gene circuits for cell state detection and protein tuning in human pluripotent stem cells. Mol Syst Biol 2022; 18:e10886. [PMID: 36366891 PMCID: PMC9650275 DOI: 10.15252/msb.202110886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 12/21/2021] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
During development, cell state transitions are coordinated through changes in the identity of molecular regulators in a cell type‐ and dose‐specific manner. The ability to rationally engineer such transitions in human pluripotent stem cells (hPSC) will enable numerous applications in regenerative medicine. Herein, we report the generation of synthetic gene circuits that can detect a desired cell state using AND‐like logic integration of endogenous miRNAs (classifiers) and, upon detection, produce fine‐tuned levels of output proteins using an miRNA‐mediated output fine‐tuning technology (miSFITs). Specifically, we created an “hPSC ON” circuit using a model‐guided miRNA selection and circuit optimization approach. The circuit demonstrates robust PSC‐specific detection and graded output protein production. Next, we used an empirical approach to create an “hPSC‐Off” circuit. This circuit was applied to regulate the secretion of endogenous BMP4 in a state‐specific and fine‐tuned manner to control the composition of differentiating hPSCs. Our work provides a platform for customized cell state‐specific control of desired physiological factors in hPSC, laying the foundation for programming cell compositions in hPSC‐derived tissues and beyond.
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Affiliation(s)
- Laura Prochazka
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
| | - Yale S Michaels
- Michael Smith Laboratories University of British Columbia Vancouver BC Canada
- School of Biomedical Engineering University of British Columbia Vancouver BC Canada
| | - Charles Lau
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
- Michael Smith Laboratories University of British Columbia Vancouver BC Canada
- School of Biomedical Engineering University of British Columbia Vancouver BC Canada
| | - Ross D Jones
- Michael Smith Laboratories University of British Columbia Vancouver BC Canada
- School of Biomedical Engineering University of British Columbia Vancouver BC Canada
| | - Mona Siu
- Michael Smith Laboratories University of British Columbia Vancouver BC Canada
- School of Biomedical Engineering University of British Columbia Vancouver BC Canada
| | - Ting Yin
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
| | - Diana Wu
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
| | - Esther Jang
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
| | - Mercedes Vázquez‐Cantú
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
- Swiss Federal Institute of Technology (ETH) Zürich, Department of Biosystems Science and Engineering (D‐BSSE) Basel Switzerland
| | - Penney M Gilbert
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
- Department of Cell and Systems Biology University of Toronto Toronto ON Canada
| | - Himanshu Kaul
- School of Engineering University of Leicester Leicester UK
- Department of Respiratory Sciences University of Leicester Leicester UK
| | - Yaakov Benenson
- Swiss Federal Institute of Technology (ETH) Zürich, Department of Biosystems Science and Engineering (D‐BSSE) Basel Switzerland
| | - Peter W Zandstra
- Michael Smith Laboratories University of British Columbia Vancouver BC Canada
- School of Biomedical Engineering University of British Columbia Vancouver BC Canada
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8
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Michaels YS, Edgar JM, Major MC, Castle EL, Zimmerman C, Yin T, Hagner A, Lau C, Hsu HH, Ibañez-Rios MI, Durland LJ, Knapp DJHF, Zandstra PW. DLL4 and VCAM1 enhance the emergence of T cell-competent hematopoietic progenitors from human pluripotent stem cells. Sci Adv 2022; 8:eabn5522. [PMID: 36001668 PMCID: PMC9401626 DOI: 10.1126/sciadv.abn5522] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 07/12/2022] [Indexed: 05/13/2023]
Abstract
T cells show tremendous efficacy as cellular therapeutics. However, obtaining primary T cells from human donors is expensive and variable. Pluripotent stem cells (PSCs) have the potential to provide a renewable source of T cells, but differentiating PSCs into hematopoietic progenitors with T cell potential remains an important challenge. Here, we report an efficient serum- and feeder-free system for differentiating human PSCs into hematopoietic progenitors and T cells. This fully defined approach allowed us to study the impact of individual proteins on blood emergence and differentiation. Providing DLL4 and VCAM1 during the endothelial-to-hematopoietic transition enhanced downstream progenitor T cell output by ~80-fold. These two proteins synergized to activate notch signaling in nascent hematopoietic stem and progenitor cells, and VCAM1 additionally promoted an inflammatory transcriptional program. We also established optimized medium formulations that enabled efficient and chemically defined maturation of functional CD8αβ+, CD4-, CD3+, TCRαβ+ T cells with a diverse TCR repertoire.
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Affiliation(s)
- Yale S. Michaels
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - John M. Edgar
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Matthew C. Major
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Elizabeth L. Castle
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Carla Zimmerman
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Ting Yin
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Andrew Hagner
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Charles Lau
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Han Hsuan Hsu
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - M. Iliana Ibañez-Rios
- Institut de recherche en immunologie et en cancérologie and Département de pathologie et biologie cellulaire, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Lauren J. Durland
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - David J. H. F. Knapp
- Institut de recherche en immunologie et en cancérologie and Département de pathologie et biologie cellulaire, Université de Montréal, Montreal, QC H3T 1J4, Canada
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Peter W. Zandstra
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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9
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Heydari T, A. Langley M, Fisher CL, Aguilar-Hidalgo D, Shukla S, Yachie-Kinoshita A, Hughes M, M. McNagny K, Zandstra PW. IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data. PLoS Comput Biol 2022; 18:e1009907. [PMID: 35213533 PMCID: PMC8906617 DOI: 10.1371/journal.pcbi.1009907] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 08/20/2021] [Revised: 03/09/2022] [Accepted: 02/08/2022] [Indexed: 01/03/2023] Open
Abstract
The increasing availability of single-cell RNA-sequencing (scRNA-seq) data from various developmental systems provides the opportunity to infer gene regulatory networks (GRNs) directly from data. Herein we describe IQCELL, a platform to infer, simulate, and study executable logical GRNs directly from scRNA-seq data. Such executable GRNs allow simulation of fundamental hypotheses governing developmental programs and help accelerate the design of strategies to control stem cell fate. We first describe the architecture of IQCELL. Next, we apply IQCELL to scRNA-seq datasets from early mouse T-cell and red blood cell development, and show that the platform can infer overall over 74% of causal gene interactions previously reported from decades of research. We will also show that dynamic simulations of the generated GRN qualitatively recapitulate the effects of known gene perturbations. Finally, we implement an IQCELL gene selection pipeline that allows us to identify candidate genes, without prior knowledge. We demonstrate that GRN simulations based on the inferred set yield results similar to the original curated lists. In summary, the IQCELL platform offers a versatile tool to infer, simulate, and study executable GRNs in dynamic biological systems. Executable GRNs provide an important strategy to model complex intracellular dynamics in development and disease. Here we introduce IQCELL, a platform to infer, simulate, and study executable logical GRNs directly from single cell sequencing data. IQCELL is an integrative platform that includes modules for gene selection, building logical GRNs, and simulating developmental trajectories under normal and perturbed conditions. We demonstrate the utility of IQCELL by reconstructing GRNs for early mouse T-cell and red blood cell development. We show that IQCELL can “automatically” infer the vast majority of gene interactions previously reported from decades of experimental research. IQCELL also provides users with a platform to simulate the developmental trajectories of cells. We show that dynamic simulations of the inferred GRNs resemble experimentally observed gene expression dynamics and capture the effects of genetic perturbation studies. IQCELL offers a versatile tool to infer and simulate GRNs in dynamic biological systems.
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Affiliation(s)
- Tiam Heydari
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew A. Langley
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Cynthia L. Fisher
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel Aguilar-Hidalgo
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shreya Shukla
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
- Notch Therapeutics, Vancouver, British Columbia, Canada
| | - Ayako Yachie-Kinoshita
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Michael Hughes
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Kelly M. McNagny
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Peter W. Zandstra
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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10
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Ma J, Tran G, Wan AMD, Young EWK, Kumacheva E, Iscove NN, Zandstra PW. Microdroplet-based one-step RT-PCR for ultrahigh throughput single-cell multiplex gene expression analysis and rare cell detection. Sci Rep 2021; 11:6777. [PMID: 33762663 PMCID: PMC7990930 DOI: 10.1038/s41598-021-86087-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/10/2021] [Indexed: 01/31/2023] Open
Abstract
Gene expression analysis of individual cells enables characterization of heterogeneous and rare cell populations, yet widespread implementation of existing single-cell gene analysis techniques has been hindered due to limitations in scale, ease, and cost. Here, we present a novel microdroplet-based, one-step reverse-transcriptase polymerase chain reaction (RT-PCR) platform and demonstrate the detection of three targets simultaneously in over 100,000 single cells in a single experiment with a rapid read-out. Our customized reagent cocktail incorporates the bacteriophage T7 gene 2.5 protein to overcome cell lysate-mediated inhibition and allows for one-step RT-PCR of single cells encapsulated in nanoliter droplets. Fluorescent signals indicative of gene expressions are analyzed using a probabilistic deconvolution method to account for ambient RNA and cell doublets and produce single-cell gene signature profiles, as well as predict cell frequencies within heterogeneous samples. We also developed a simulation model to guide experimental design and optimize the accuracy and precision of the assay. Using mixtures of in vitro transcripts and murine cell lines, we demonstrated the detection of single RNA molecules and rare cell populations at a frequency of 0.1%. This low cost, sensitive, and adaptable technique will provide an accessible platform for high throughput single-cell analysis and enable a wide range of research and clinical applications.
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Affiliation(s)
- Jennifer Ma
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
| | - Gary Tran
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Alwin M D Wan
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON, M5S 3G8, Canada
| | - Edmond W K Young
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON, M5S 3G8, Canada
| | - Eugenia Kumacheva
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON, M5S 3G8, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
| | - Norman N Iscove
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Peter W Zandstra
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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11
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Dziedzicka D, Tewary M, Keller A, Tilleman L, Prochazka L, Östblom J, Couvreu De Deckersberg E, Markouli C, Franck S, Van Nieuwerburgh F, Spits C, Zandstra PW, Sermon K, Geens M. Endogenous suppression of WNT signalling in human embryonic stem cells leads to low differentiation propensity towards definitive endoderm. Sci Rep 2021; 11:6137. [PMID: 33731744 PMCID: PMC7969605 DOI: 10.1038/s41598-021-85447-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 10/09/2020] [Accepted: 02/23/2021] [Indexed: 02/06/2023] Open
Abstract
Low differentiation propensity towards a targeted lineage can significantly hamper the utility of individual human pluripotent stem cell (hPSC) lines in biomedical applications. Here, we use monolayer and micropatterned cell cultures, as well as transcriptomic profiling, to investigate how variability in signalling pathway activity between human embryonic stem cell lines affects their differentiation efficiency towards definitive endoderm (DE). We show that endogenous suppression of WNT signalling in hPSCs at the onset of differentiation prevents the switch from self-renewal to DE specification. Gene expression profiling reveals that this inefficient switch is reflected in NANOG expression dynamics. Importantly, we demonstrate that higher WNT stimulation or inhibition of the PI3K/AKT signalling can overcome the DE commitment blockage. Our findings highlight that redirection of the activity of Activin/NODAL pathway by WNT signalling towards mediating DE fate specification is a vulnerable spot, as disruption of this process can result in poor hPSC specification towards DE.
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Affiliation(s)
- Dominika Dziedzicka
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Mukul Tewary
- grid.17063.330000 0001 2157 2938Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1 Canada ,grid.13097.3c0000 0001 2322 6764Centre for Stem Cells and Regenerative Medicine, King’s College London, Guy’s Hospital, London, SE1 9RT UK
| | - Alexander Keller
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Laurentijn Tilleman
- grid.5342.00000 0001 2069 7798Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Laura Prochazka
- grid.17063.330000 0001 2157 2938Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1 Canada
| | - Joel Östblom
- grid.17063.330000 0001 2157 2938Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1 Canada
| | - Edouard Couvreu De Deckersberg
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Christina Markouli
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Silvie Franck
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Filip Van Nieuwerburgh
- grid.5342.00000 0001 2069 7798Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Claudia Spits
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Peter W. Zandstra
- grid.17063.330000 0001 2157 2938Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1 Canada ,grid.17091.3e0000 0001 2288 9830Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4 Canada ,grid.17091.3e0000 0001 2288 9830School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Karen Sermon
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Mieke Geens
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
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12
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Afshar ME, Abraha HY, Bakooshli MA, Davoudi S, Thavandiran N, Tung K, Ahn H, Ginsberg HJ, Zandstra PW, Gilbert PM. A 96-well culture platform enables longitudinal analyses of engineered human skeletal muscle microtissue strength. Sci Rep 2020; 10:6918. [PMID: 32332853 PMCID: PMC7181829 DOI: 10.1038/s41598-020-62837-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [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: 07/25/2019] [Accepted: 03/20/2020] [Indexed: 12/11/2022] Open
Abstract
Three-dimensional (3D) in vitro models of human skeletal muscle mimic aspects of native tissue structure and function, thereby providing a promising system for disease modeling, drug discovery or pre-clinical validation, and toxicity testing. Widespread adoption of this research approach is hindered by the lack of easy-to-use platforms that are simple to fabricate and that yield arrays of human skeletal muscle micro-tissues (hMMTs) in culture with reproducible physiological responses that can be assayed non-invasively. Here, we describe a design and methods to generate a reusable mold to fabricate a 96-well platform, referred to as MyoTACTIC, that enables bulk production of 3D hMMTs. All 96-wells and all well features are cast in a single step from the reusable mold. Non-invasive calcium transient and contractile force measurements are performed on hMMTs directly in MyoTACTIC, and unbiased force analysis occurs by a custom automated algorithm, allowing for longitudinal studies of function. Characterizations of MyoTACTIC and resulting hMMTs confirms the capability of the device to support formation of hMMTs that recapitulate biological responses. We show that hMMT contractile force mirrors expected responses to compounds shown by others to decrease (dexamethasone, cerivastatin) or increase (IGF-1) skeletal muscle strength. Since MyoTACTIC supports hMMT long-term culture, we evaluated direct influences of pancreatic cancer chemotherapeutics agents on contraction competent human skeletal muscle myotubes. A single application of a clinically relevant dose of Irinotecan decreased hMMT contractile force generation, while clear effects on myotube atrophy were observed histologically only at a higher dose. This suggests an off-target effect that may contribute to cancer associated muscle wasting, and highlights the value of the MyoTACTIC platform to non-invasively predict modulators of human skeletal muscle function.
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Affiliation(s)
- Mohammad E Afshar
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Toronto, Canada
| | - Haben Y Abraha
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Toronto, Canada
| | - Mohsen A Bakooshli
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Toronto, Canada
| | - Sadegh Davoudi
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Toronto, Canada
| | - Nimalan Thavandiran
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Toronto, Canada
| | - Kayee Tung
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
| | - Henry Ahn
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada.,Department of Surgery, University of Toronto, Toronto, Canada
| | - Howard J Ginsberg
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada.,Department of Surgery, University of Toronto, Toronto, Canada
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Toronto, Canada.,Michael Smith Laboratories and the School of Biomedical Engineering, University of British Columbia, Vancouver, Canada
| | - Penney M Gilbert
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada. .,Donnelly Centre for Cellular and Biomolecular Research, Toronto, Canada. .,Department of Biochemistry, University of Toronto, Toronto, Canada. .,Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.
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13
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Thavandiran N, Hale C, Blit P, Sandberg ML, McElvain ME, Gagliardi M, Sun B, Witty A, Graham G, Do VTH, Bakooshli MA, Le H, Ostblom J, McEwen S, Chau E, Prowse A, Fernandes I, Norman A, Gilbert PM, Keller G, Tagari P, Xu H, Radisic M, Zandstra PW. Functional arrays of human pluripotent stem cell-derived cardiac microtissues. Sci Rep 2020; 10:6919. [PMID: 32332814 PMCID: PMC7181791 DOI: 10.1038/s41598-020-62955-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 08/01/2019] [Accepted: 03/18/2020] [Indexed: 11/09/2022] Open
Abstract
To accelerate the cardiac drug discovery pipeline, we set out to develop a platform that would be capable of quantifying tissue-level functions such as contractile force and be amenable to standard multiwell-plate manipulations. We report a 96-well-based array of 3D human pluripotent stem cell (hPSC)-derived cardiac microtissues - termed Cardiac MicroRings (CaMiRi) - in custom 3D-print-molded multiwell plates capable of contractile force measurement. Within each well, two elastomeric microcantilevers are situated above a circumferential ramp. The wells are seeded with cell-laden collagen, which, in response to the gradual slope of the circumferential ramp, self-organizes around tip-gated microcantilevers to form contracting CaMiRi. The contractile force exerted by the CaMiRi is measured and calculated using the deflection of the cantilevers. Platform responses were robust and comparable across wells, and we used it to determine an optimal tissue formulation. We validated the contractile force response of CaMiRi using selected cardiotropic compounds with known effects. Additionally, we developed automated protocols for CaMiRi seeding, image acquisition, and analysis to enable the measurement of contractile force with increased throughput. The unique tissue fabrication properties of the platform, and the consequent effects on tissue function, were demonstrated upon adding hPSC-derived epicardial cells to the system. This platform represents an open-source contractile force screening system useful for drug screening and tissue engineering applications.
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Affiliation(s)
- Nimalan Thavandiran
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Christopher Hale
- Amgen Discovery Research, Amgen Inc., South San Francisco, CA, USA
| | | | | | | | - Mark Gagliardi
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, Ontario, Canada
| | - Bo Sun
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, Ontario, Canada
| | - Alec Witty
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, Ontario, Canada
| | | | | | - Mohsen Afshar Bakooshli
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Hon Le
- Amgen Discovery Research, Amgen Inc., South San Francisco, CA, USA
| | - Joel Ostblom
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Samuel McEwen
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Erik Chau
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, Canada
| | | | - Ian Fernandes
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, Ontario, Canada
| | | | - Penney M Gilbert
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Gordon Keller
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, Ontario, Canada
| | - Philip Tagari
- Amgen Discovery Research, Amgen Inc., South San Francisco, CA, USA
| | - Han Xu
- A2 Biotherapeutics Inc., Agoura Hills, CA, USA.
| | - Milica Radisic
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada. .,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada. .,Heart and Stroke/Richard Lewar Centre of Excellence, University of Toronto, Toronto, Ontario, Canada.
| | - Peter W Zandstra
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada. .,CCRM, Toronto, Ontario, Canada. .,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada. .,Michael Smith Laboratories, School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
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14
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Cohen S, Roy J, Lachance S, Delisle JS, Marinier A, Busque L, Roy DC, Barabé F, Ahmad I, Bambace N, Bernard L, Kiss T, Bouchard P, Caudrelier P, Landais S, Larochelle F, Chagraoui J, Lehnertz B, Corneau S, Tomellini E, van Kampen JJA, Cornelissen JJ, Dumont-Lagacé M, Tanguay M, Li Q, Lemieux S, Zandstra PW, Sauvageau G. Hematopoietic stem cell transplantation using single UM171-expanded cord blood: a single-arm, phase 1-2 safety and feasibility study. Lancet Haematol 2019; 7:e134-e145. [PMID: 31704264 DOI: 10.1016/s2352-3026(19)30202-9] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/27/2019] [Accepted: 08/30/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND Benefits of cord blood transplantation include low rates of relapse and chronic graft-versus-host disease (GVHD). However, the use of cord blood is rapidly declining because of the high incidence of infections, severe acute GVHD, and transplant-related mortality. UM171, a haematopoietic stem cell self-renewal agonist, has been shown to expand cord blood stem cells and enhance multilineage blood cell reconstitution in mice. We aimed to investigate the safety and feasibility of single UM171-expanded cord blood transplantation in patients with haematological malignancies who do not have a suitable HLA-matched donor. METHODS This single-arm, open-label, phase 1-2 safety and feasibility study was done at two hospitals in Canada. The study had two parts. In part 1, patients received two cord blood units (one expanded with UM171 and one unmanipulated cord blood) until UM171-expanded cord blood demonstrated engraftment. Once engraftment was documented we initiated part 2, reported here, in which patients received a single UM171-expanded cord blood unit with a dose de-escalation design to determine the minimal cord blood unit cell dose that achieved prompt engraftment. Eligible patients were aged 3-64 years, weighed 12 kg or more, had a haematological malignancy with an indication for allogeneic hematopoietic stem cell transplant and did not have a suitable HLA-matched donor, and a had a Karnofsky performance status score of 70% or more. Five clinical sites were planned to participate in the study; however, only two study sites opened, both of which only treated adult patients, thus no paediatric patients (aged <18 years) were recruited. Patients aged younger than 50 years without comorbidities received a myeloablative conditioning regimen (cyclophosphamide 120 mg/kg, fludarabine 75 mg/m2, and 12 Gy total body irradiation) and patients aged older than 50 years and those with comorbidities received a less myeloablative conditioning regimen (cyclophosphamide 50 mg/kg, thiotepa 10 mg/kg, fludarabine 150 mg/m2, and 4 Gy total body irradiation). Patients were infused with the 7-day UM171-expanded CD34-positive cells and the lymphocyte-containing CD34-negative fraction. The primary endpoints were feasibility of UM171 expansion, safety of the transplant, kinetics of hematopoietic reconstitution (time to neutrophil and platelet engraftment) of UM171-expanded cord blood, and minimal pre-expansion cord blood unit cell dose that achieved prompt engraftment. We analysed feasibility in all enrolled patients and all other primary outcomes were analysed per protocol, in all patients who received single UM171-expanded cord blood transplantation. This trial has been completed and was registered with ClinicalTrials.gov, NCT02668315. FINDINGS Between Feb 17, 2016, and Nov 11, 2018, we enrolled 27 patients, four of whom received two cord blood units for safety purposes in part 1 of the study. 23 patients were subsequently enrolled in part 2 to receive a single UM171-expanded cord blood transplant and 22 patients received a single UM171-expanded cord blood transplantation. At data cutoff (Dec 31, 2018), median follow-up was 18 months (IQR 12-22). The minimal cord blood unit cell dose at thaw that achieved prompt engraftment as a single cord transplant after UM171 expansion was 0·52 × 105 CD34-positive cells. We successfully expanded 26 (96%) of 27 cord blood units with UM171. Among the 22 patients who received single UM171-expanded cord blood transplantation, median time to engraftment of 100 neutrophils per μL was 9·5 days (IQR 8-12), median time to engraftment of 500 neutrophils per μL was 18 days (12·5-20·0), and no graft failure occurred. Median time to platelet recovery was 42 days (IQR 35-47). The most common non-haematological adverse events were grade 3 febrile neutropenia (16 [73%] of 22 patients) and bacteraemia (nine [41%]). No unexpected adverse events were observed. One (5%) of 22 patients died due to treatment-related diffuse alveolar haemorrhage. INTERPRETATION Our preliminary findings suggest that UM171 cord blood stem cell expansion is feasible, safe, and allows for the use of small single cords without compromising engraftment. UM171-expanded cord blood might have the potential to overcome the disadvantages of other cord blood transplants while maintaining the benefits of low risk of chronic GVHD and relapse, and warrants further investigation in randomised trials. FUNDING Canadian Institutes of Health Research, Canadian Cancer Society and Stem Cell Network.
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Affiliation(s)
- Sandra Cohen
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada; Department of Medicine, Montreal, QC, Canada.
| | - Jean Roy
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada; Department of Medicine, Montreal, QC, Canada
| | - Silvy Lachance
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada; Department of Medicine, Montreal, QC, Canada
| | - Jean-Sébastien Delisle
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada; Department of Medicine, Montreal, QC, Canada
| | - Anne Marinier
- Drug Discovery Unit, Montreal, QC, Canada; ExCellThera, Montreal, QC, Canada
| | - Lambert Busque
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada; Department of Medicine, Montreal, QC, Canada
| | - Denis-Claude Roy
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada; Department of Medicine, Montreal, QC, Canada
| | - Frédéric Barabé
- Division of Hematology, CHU de Québec-Université Laval (Hôpital de l'Enfant-Jésus), Quebec, QC, Canada; Department of Medicine, Université Laval, Quebec, QC, Canada
| | - Imran Ahmad
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada; Department of Medicine, Montreal, QC, Canada
| | - Nadia Bambace
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada; Department of Medicine, Montreal, QC, Canada
| | - Léa Bernard
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada; Department of Medicine, Montreal, QC, Canada
| | - Thomas Kiss
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada; Department of Medicine, Montreal, QC, Canada
| | - Philippe Bouchard
- Department of Pharmacy, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada
| | | | - Sévérine Landais
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada
| | - Fannie Larochelle
- Center of Excellence for Cellular Therapy, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada
| | - Jalila Chagraoui
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | - Bernhard Lehnertz
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | - Sophie Corneau
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | - Elisa Tomellini
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | - Jeroen J A van Kampen
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Jan J Cornelissen
- Department of Hematology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | | | - Mégane Tanguay
- Department of Medicine, Montreal, QC, Canada; Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada
| | - Qi Li
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada; Department of Medicine, Montreal, QC, Canada
| | - Sébastien Lemieux
- Molecular Genetics of Stem Cells Laboratory, and Department of Biochemistry and Molecular Medicine, Montreal, QC, Canada
| | - Peter W Zandstra
- ExCellThera, Montreal, QC, Canada; School of Biomedical Engineering and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Guy Sauvageau
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada; Department of Medicine, Montreal, QC, Canada; Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, Canada; ExCellThera, Montreal, QC, Canada
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15
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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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16
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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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17
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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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18
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Romagnuolo R, Masoudpour H, Porta-Sánchez A, Qiang B, Barry J, Laskary A, Qi X, Massé S, Magtibay K, Kawajiri H, Wu J, Valdman Sadikov T, Rothberg J, Panchalingam KM, Titus E, Li RK, Zandstra PW, Wright GA, Nanthakumar K, Ghugre NR, Keller G, Laflamme MA. Human Embryonic Stem Cell-Derived Cardiomyocytes Regenerate the Infarcted Pig Heart but Induce Ventricular Tachyarrhythmias. Stem Cell Reports 2019; 12:967-981. [PMID: 31056479 PMCID: PMC6524945 DOI: 10.1016/j.stemcr.2019.04.005] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [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: 06/11/2018] [Revised: 04/04/2019] [Accepted: 04/05/2019] [Indexed: 12/25/2022] Open
Abstract
Human embryonic stem cell-derived cardiomyocytes (hESC-CMs) show considerable promise for regenerating injured hearts, and we therefore tested their capacity to stably engraft in a translationally relevant preclinical model, the infarcted pig heart. Transplantation of immature hESC-CMs resulted in substantial myocardial implants within the infarct scar that matured over time, formed vascular networks with the host, and evoked minimal cellular rejection. While arrhythmias were rare in infarcted pigs receiving vehicle alone, hESC-CM recipients experienced frequent monomorphic ventricular tachycardia before reverting back to normal sinus rhythm by 4 weeks post transplantation. Electroanatomical mapping and pacing studies implicated focal mechanisms, rather than macro-reentry, for these graft-related tachyarrhythmias as evidenced by an abnormal centrifugal pattern with earliest electrical activation in histologically confirmed graft tissue. These findings demonstrate the suitability of the pig model for the preclinical development of a hESC-based cardiac therapy and provide new insights into the mechanistic basis of electrical instability following hESC-CM transplantation. hESC-CM transplantation partially remuscularizes the infarcted pig heart hESC-CM recipients show frequent tachyarrhythmias at early time points Graft-related arrhythmias arise from focal mechanisms rather than macro-reentry
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Affiliation(s)
- Rocco Romagnuolo
- McEwen Stem Cell Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Hassan Masoudpour
- McEwen Stem Cell Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Andreu Porta-Sánchez
- Peter Munk Cardiac Centre, University Health Network, Toronto, ON M5G 2N2, Canada
| | - Beiping Qiang
- McEwen Stem Cell Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Jennifer Barry
- Schulich Heart Research Program, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - Andrew Laskary
- McEwen Stem Cell Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Xiuling Qi
- Schulich Heart Research Program, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - Stéphane Massé
- Peter Munk Cardiac Centre, University Health Network, Toronto, ON M5G 2N2, Canada
| | - Karl Magtibay
- Peter Munk Cardiac Centre, University Health Network, Toronto, ON M5G 2N2, Canada
| | - Hiroyuki Kawajiri
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Jun Wu
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | | | - Janet Rothberg
- Centre for Commercialization of Regenerative Medicine, Toronto, ON M5G 1M1, Canada
| | | | - Emily Titus
- Centre for Commercialization of Regenerative Medicine, Toronto, ON M5G 1M1, Canada
| | - Ren-Ke Li
- Peter Munk Cardiac Centre, University Health Network, Toronto, ON M5G 2N2, Canada; Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 1L7, Canada; University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Peter W Zandstra
- Centre for Commercialization of Regenerative Medicine, Toronto, ON M5G 1M1, Canada; University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Graham A Wright
- Schulich Heart Research Program, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Kumaraswamy Nanthakumar
- Peter Munk Cardiac Centre, University Health Network, Toronto, ON M5G 2N2, Canada; University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Nilesh R Ghugre
- Schulich Heart Research Program, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Gordon Keller
- McEwen Stem Cell Institute, University Health Network, Toronto, ON M5G 1L7, Canada; University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Michael A Laflamme
- McEwen Stem Cell Institute, University Health Network, Toronto, ON M5G 1L7, Canada; Peter Munk Cardiac Centre, University Health Network, Toronto, ON M5G 2N2, Canada; University of Toronto, Toronto, ON M5G 1L7, Canada.
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19
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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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20
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Vigilante A, Laddach A, Moens N, Meleckyte R, Leha A, Ghahramani A, Culley OJ, Kathuria A, Hurling C, Vickers A, Wiseman E, Tewary M, Zandstra PW, Durbin R, Fraternali F, Stegle O, Birney E, Luscombe NM, Danovi D, Watt FM. Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors. Cell Rep 2019; 26:2078-2087.e3. [PMID: 30784590 PMCID: PMC6381787 DOI: 10.1016/j.celrep.2019.01.094] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 12/11/2018] [Accepted: 01/24/2019] [Indexed: 01/08/2023] Open
Abstract
Large cohorts of human induced pluripotent stem cells (iPSCs) from healthy donors are a potentially powerful tool for investigating the relationship between genetic variants and cellular behavior. Here, we integrate high content imaging of cell shape, proliferation, and other phenotypes with gene expression and DNA sequence datasets from over 100 human iPSC lines. By applying a dimensionality reduction approach, Probabilistic Estimation of Expression Residuals (PEER), we extracted factors that captured the effects of intrinsic (genetic concordance between different cell lines from the same donor) and extrinsic (cell responses to different fibronectin concentrations) conditions. We identify genes that correlate in expression with intrinsic and extrinsic PEER factors and associate outlier cell behavior with genes containing rare deleterious non-synonymous SNVs. Our study, thus, establishes a strategy for examining the genetic basis of inter-individual variability in cell behavior.
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Affiliation(s)
- Alessandra Vigilante
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Anna Laddach
- Randall Division, King's College London, New Hunts House, Great Maze Pond, London SE1 9RT, UK
| | - Nathalie Moens
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Ruta Meleckyte
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Andreas Leha
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Arsham Ghahramani
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Oliver J Culley
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Annie Kathuria
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Chloe Hurling
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Alice Vickers
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Erika Wiseman
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Mukul Tewary
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK; School of Biomedical Engineering, The University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Michael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Peter W Zandstra
- School of Biomedical Engineering, The University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada; Michael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Richard Durbin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Franca Fraternali
- Randall Division, King's College London, New Hunts House, Great Maze Pond, London SE1 9RT, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Davide Danovi
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK.
| | - Fiona M Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, Floor 28, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK.
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21
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Ostblom J, Nazareth EJP, Tewary M, Zandstra PW. Context-explorer: Analysis of spatially organized protein expression in high-throughput screens. PLoS Comput Biol 2019; 15:e1006384. [PMID: 30601802 PMCID: PMC6331134 DOI: 10.1371/journal.pcbi.1006384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 01/14/2019] [Accepted: 11/08/2018] [Indexed: 11/18/2022] Open
Abstract
A growing body of evidence highlights the importance of the cellular microenvironment as a regulator of phenotypic and functional cellular responses to perturbations. We have previously developed cell patterning techniques to control population context parameters, and here we demonstrate context-explorer (CE), a software tool to improve investigation cell fate acquisitions through community level analyses. We demonstrate the capabilities of CE in the analysis of human and mouse pluripotent stem cells (hPSCs, mPSCs) patterned in colonies of defined geometries in multi-well plates. CE employs a density-based clustering algorithm to identify cell colonies. Using this automatic colony classification methodology, we reach accuracies comparable to manual colony counts in a fraction of the time, both in micropatterned and unpatterned wells. Classifying cells according to their relative position within a colony enables statistical analysis of spatial organization in protein expression within colonies. When applied to colonies of hPSCs, our analysis reveals a radial gradient in the expression of the transcription factors SOX2 and OCT4. We extend these analyses to colonies of different sizes and shapes and demonstrate how the metrics derived by CE can be used to asses the patterning fidelity of micropatterned plates. We have incorporated a number of features to enhance the usability and utility of CE. To appeal to a broad scientific community, all of the software’s functionality is accessible from a graphical user interface, and convenience functions for several common data operations are included. CE is compatible with existing image analysis programs such as CellProfiler and extends the analytical capabilities already provided by these tools. Taken together, CE facilitates investigation of spatially heterogeneous cell populations for fundamental research and drug development validation programs. Cell behavior is influenced by cues that cells receive from their surrounding environment such as signals secreted from other cells and cell-to-cell contact. These factors are spatially heterogeneous and cells at different positions within a colony will experience varying degrees of influence from such environmental cues. In vitro assays often do not allow control over environmental variables and there is a lack of easy to use software to investigate the effect of spatial variation in these factors. We have developed a software package to address this gap and facilitate the quantification of spatially heterogeneous cell responses. Our software accurately identifies colonies of cells within a well and individual cells can be grouped according to their position within these colonies, which enables quantification of cell response as a function of cellular location. To support broad scientific accessibility, the full functionality of the software is available through a graphical user interface. Using this software to analyze data from a screening-optimized micropatterning platform, we show that human pluripotent stem cell-derived colonies grown either under pluripotency maintenance or differentiation-inducing conditions exhibit cell responses that are dependent on spatial organization. This technology should enable more accurate and predictive context-dependent drug screening and cell-fate investigation.
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Affiliation(s)
- Joel Ostblom
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Emanuel J. P. Nazareth
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Mukul Tewary
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Peter W. Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Medicine by Design, A Canada First Research Excellence Program at the University of Toronto, Toronto, ON, 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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22
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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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23
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Wang W, Fujii H, Kim HJ, Hermans K, Usenko T, Xie S, Luo ZJ, Ma J, Celso CL, Dick JE, Schroeder T, Krueger J, Wall D, Egeler RM, Zandstra PW. Enhanced human hematopoietic stem and progenitor cell engraftment by blocking donor T cell-mediated TNFα signaling. Sci Transl Med 2018; 9:9/421/eaag3214. [PMID: 29263228 DOI: 10.1126/scitranslmed.aag3214] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/21/2017] [Accepted: 10/17/2017] [Indexed: 12/13/2022]
Abstract
Allogeneic hematopoietic stem cell transplantation (HSCT) is a curative therapy, but the large number of HSCs required limits its widespread use. Host conditioning and donor cell composition are known to affect HSCT outcomes. However, the specific role that the posttransplantation signaling environment plays in donor HSC fate is poorly understood. To mimic clinical HSCT, we injected human umbilical cord blood (UCB) cells at different doses and compositions into immunodeficient NOD/SCID/IL-2Rgc-null (NSG) mice. Surprisingly, higher UCB cell doses inversely correlated with stem and progenitor cell engraftment. This observation was attributable to increased donor cell-derived inflammatory signals. Donor T cell-derived tumor necrosis factor-α (TNFα) was specifically found to directly impair the survival and division of transplanted HSCs and progenitor cells. Neutralizing donor T cell-derived TNFα in vivo increased short-term stem and progenitor cell engraftment, accelerated hematopoietic recovery, and altered donor immune cell compositions. This direct effect of TNFα on transplanted cells could be decoupled from the indirect effect of alleviating graft-versus-host disease (GVHD) by interleukin-6 (IL-6) blockade. Our study demonstrates that donor immune cell-derived inflammatory signals directly influence HSC fate, and provides new clinically relevant strategies to improve engraftment efficiency during HSCT.
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Affiliation(s)
- Weijia Wang
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Basel 4058, Switzerland
| | - Hisaki Fujii
- Division of Haematology and Oncology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Hye Jin Kim
- Division of Haematology and Oncology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Karin Hermans
- Division of Haematology and Oncology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Tatiana Usenko
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Stephanie Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Zhi-Juan Luo
- Division of Haematology and Oncology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Jennifer Ma
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Cristina Lo Celso
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Basel 4058, Switzerland
| | - Joerg Krueger
- Division of Haematology and Oncology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Donna Wall
- Division of Haematology and Oncology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - R Maarten Egeler
- Division of Haematology and Oncology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E1, Canada. .,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada.,Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Medicine by Design-A Canada First Research Excellence Fund program, Toronto, Ontario M5G 1M1, Canada
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24
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Affiliation(s)
- Mukul Tewary
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
- School of Biomedical Engineering, and the Michael Smith Laboratories at the University of British Columbia, Vancouver, British Columbia, Canada.
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25
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Bahr C, von Paleske L, Uslu VV, Remeseiro S, Takayama N, Ng SW, Murison A, Langenfeld K, Petretich M, Scognamiglio R, Zeisberger P, Benk AS, Amit I, Zandstra PW, Lupien M, Dick JE, Trumpp A, Spitz F. Author Correction: A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies. Nature 2018; 558:E4. [PMID: 29769714 DOI: 10.1038/s41586-018-0113-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the originally published version of this Letter, ref. 43 was erroneously provided twice. In the 'Estimation of relative cell-type-specific composition of AML samples' section in the Methods, the citation to ref. 43 after the GEO dataset GSE24759 is correct. However, in the 'Mice' section of the Methods, the citation to ref. 43 after 'TAMERE' should have been associated with a new reference1. The original Letter has been corrected online (with the new reference included as ref. 49).
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Affiliation(s)
- Carsten Bahr
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Lisa von Paleske
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Veli V Uslu
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Silvia Remeseiro
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Naoya Takayama
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Stanley W Ng
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Katja Langenfeld
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Massimo Petretich
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Roberta Scognamiglio
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Petra Zeisberger
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Amelie S Benk
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.,Michael Smith Laboratories, School of Biomedical Engineering, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany. .,Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany. .,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany. .,Nationales Zentrum für Tumorerkrankungen (NCT), Heidelberg, Germany.
| | - François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,CNRS, UMR3738, 25 Rue du Dr Roux, Paris, France.,(Epi)genomics of Animal Development Unit, Developmental and Stem Cell Biology Department, Institut Pasteur, Paris, France
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26
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Lipsitz YY, Tonge PD, Zandstra PW. Chemically controlled aggregation of pluripotent stem cells. Biotechnol Bioeng 2018; 115:2061-2066. [PMID: 29679475 PMCID: PMC6055717 DOI: 10.1002/bit.26719] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/28/2018] [Accepted: 04/17/2018] [Indexed: 01/18/2023]
Abstract
Heterogeneity in pluripotent stem cell (PSC) aggregation leads to variability in mass transfer and signaling gradients between aggregates, which results in heterogeneous differentiation and therefore variability in product quality and yield. We have characterized a chemical‐based method to control aggregate size within a specific, tunable range with low heterogeneity, thereby reducing process variability in PSC expansion. This method enables controlled, scalable, stirred suspension‐based manufacturing of PSC cultures that are critical for the translation of regenerative medicine strategies to clinical products.
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Affiliation(s)
- Yonatan Y. Lipsitz
- Institute of Biomaterials and Biomedical EngineeringUniversity of TorontoTorontoOntarioCanada
| | - Peter D. Tonge
- Institute of Biomaterials and Biomedical EngineeringUniversity of TorontoTorontoOntarioCanada
- Centre for Commercialization of Regenerative MedicineTorontoOntarioCanada
| | - Peter W. Zandstra
- Institute of Biomaterials and Biomedical EngineeringUniversity of TorontoTorontoOntarioCanada
- Centre for Commercialization of Regenerative MedicineTorontoOntarioCanada
- The Donnelly Centre for Cellular and Biomolecular ResearchUniversity of TorontoTorontoOntarioCanada
- Medicine by Design: A Canada First Research Excellence Fund ProgramUniversity of TorontoTorontoOntarioCanada
- School of Biomedical EngineeringUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Michael Smith LaboratoriesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
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27
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Tedesco S, De Majo F, Kim J, Trenti A, Trevisi L, Fadini GP, Bolego C, Zandstra PW, Cignarella A, Vitiello L. Convenience versus Biological Significance: Are PMA-Differentiated THP-1 Cells a Reliable Substitute for Blood-Derived Macrophages When Studying in Vitro Polarization? Front Pharmacol 2018. [PMID: 29520230 PMCID: PMC5826964 DOI: 10.3389/fphar.2018.00071] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [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] [Indexed: 12/31/2022] Open
Abstract
Human peripheral-blood monocytes are used as an established in vitro system for generating macrophages. For several reasons, monocytic cell lines such as THP-1 have been considered as a possible alternative. In view of their distinct developmental origins and phenotypic attributes, we set out to assess the extent to which human monocyte-derived macrophages (MDMs) and phorbol-12-myristate-13-acetate (PMA)-differentiated THP-1 cells were overlapping across a variety of responses to activating stimuli. Resting (M0) macrophages were polarized toward M1 or M2 phenotypes by 48-h incubation with LPS (1 μg/ml) and IFN-γ (10 ng/ml) or with IL-4 (20 ng/ml) and IL-13 (5 ng/ml), respectively. At the end of stimulation, MDMs displayed more pronounced changes in marker gene expression than THP-1. Upon assaying an array of 41 cytokines, chemokines and growth factors in conditioned media (CM) using the Luminex technology, secretion of 29 out of the 41 proteins was affected by polarized activation. While in 12 of them THP-1 and MDM showed comparable trends, for the remaining 17 proteins their responses to activating stimuli did markedly differ. Quantitative comparison for selected analytes confirmed this pattern. In terms of phenotypic activation markers, measured by flow cytometry, M1 response was similar but the established MDM M2 marker CD163 was undetectable in THP-1 cells. In a beads-based assay, MDM activation did not induce significant changes, whereas M2 activation of THP-1 decreased phagocytic activity compared to M0 and M1. In further biological activity tests, both MDM and THP-1 CM failed to affect proliferation of mouse myogenic progenitors, whereas they both reduced adipogenic differentiation of mouse fibro-adipogenic progenitor cells (M2 to a lesser extent than M1 and M0). Finally, migration of human umbilical vein endothelial cells was enhanced by CM irrespective of cell type and activation state except for M0 CM from MDMs. In summary, PMA-differentiated THP-1 macrophages did not entirely reproduce the response spectrum of primary MDMs to activating stimuli. We suggest that THP-1 be regarded as a simplified model of human macrophages when investigating relatively straightforward biological processes, such as polarization and its functional implications, but not as an alternative source in more comprehensive immunopharmacology and drug screening programs.
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Affiliation(s)
| | | | - Jieun Kim
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Annalisa Trenti
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Lucia Trevisi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Gian Paolo Fadini
- Venetian Institute of Molecular Medicine, Padova, Italy.,Department of Medicine, University of Padova, Padova, Italy
| | - Chiara Bolego
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada.,The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Medicine by Design, University of Toronto, Toronto, ON, Canada
| | | | - Libero Vitiello
- Department of Biology, University of Padova, Padova, Italy.,Interuniversity Institute of Myology (IIM), Italy
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28
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Yachie-Kinoshita A, Onishi K, Ostblom J, Langley MA, Posfai E, Rossant J, Zandstra PW. Modeling signaling-dependent pluripotency with Boolean logic to predict cell fate transitions. Mol Syst Biol 2018; 14:e7952. [PMID: 29378814 PMCID: PMC5787708 DOI: 10.15252/msb.20177952] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [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] [Indexed: 12/18/2022] Open
Abstract
Pluripotent stem cells (PSCs) exist in multiple stable states, each with specific cellular properties and molecular signatures. The mechanisms that maintain pluripotency, or that cause its destabilization to initiate development, are complex and incompletely understood. We have developed a model to predict stabilized PSC gene regulatory network (GRN) states in response to input signals. Our strategy used random asynchronous Boolean simulations (R-ABS) to simulate single-cell fate transitions and strongly connected components (SCCs) strategy to represent population heterogeneity. This framework was applied to a reverse-engineered and curated core GRN for mouse embryonic stem cells (mESCs) and used to simulate cellular responses to combinations of five signaling pathways. Our simulations predicted experimentally verified cell population compositions and input signal combinations controlling specific cell fate transitions. Extending the model to PSC differentiation, we predicted a combination of signaling activators and inhibitors that efficiently and robustly generated a Cdx2+Oct4- cells from naïve mESCs. Overall, this platform provides new strategies to simulate cell fate transitions and the heterogeneity that typically occurs during development and differentiation.
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Affiliation(s)
- Ayako Yachie-Kinoshita
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada.,The Systems Biology Institute, Minato, Tokyo, Japan
| | - Kento Onishi
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Joel Ostblom
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Matthew A Langley
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Eszter Posfai
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Janet Rossant
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada .,The Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada.,Medicine by Design, A Canada First Research Excellence Program at the University of Toronto, Toronto, ON, Canada
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29
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Yoon C, Song H, Yin T, Bausch-Fluck D, Frei AP, Kattman S, Dubois N, Witty AD, Hewel JA, Guo H, Emili A, Wollscheid B, Keller G, Zandstra PW. FZD4 Marks Lateral Plate Mesoderm and Signals with NORRIN to Increase Cardiomyocyte Induction from Pluripotent Stem Cell-Derived Cardiac Progenitors. Stem Cell Reports 2017; 10:87-100. [PMID: 29249665 PMCID: PMC5768897 DOI: 10.1016/j.stemcr.2017.11.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 04/25/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 01/14/2023] Open
Abstract
The identification of cell surface proteins on stem cells or stem cell derivatives is a key strategy for the functional characterization, isolation, and understanding of stem cell population dynamics. Here, using an integrated mass spectrometry- and microarray-based approach, we analyzed the surface proteome and transcriptome of cardiac progenitor cells (CPCs) generated from the stage-specific differentiation of mouse and human pluripotent stem cells. Through bioinformatics analysis, we have identified and characterized FZD4 as a marker for lateral plate mesoderm. Additionally, we utilized FZD4, in conjunction with FLK1 and PDGFRA, to further purify CPCs and increase cardiomyocyte (CM) enrichment in both mouse and human systems. Moreover, we have shown that NORRIN presented to FZD4 further increases CM output via proliferation through the canonical WNT pathway. Taken together, these findings demonstrate a role for FZD4 in mammalian cardiac development. Identified and characterized FZD4 as a new marker for lateral plate mesoderm FZD4, in conjunction with FLK1 and PDGFRA, increases cardiomyocyte enrichment FZD4 is expressed in the human system and shows enrichment in cardiomyocytes NORRIN addition shows increase in cardiomyocyte output from FZD4 progenitor cells
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Affiliation(s)
- Charles Yoon
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Hannah Song
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Ting Yin
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Damaris Bausch-Fluck
- Institute of Molecular Systems Biology at the Department of Health Sciences and Technology, Zurich 8092, Switzerland
| | - Andreas P Frei
- Institute of Molecular Systems Biology at the Department of Health Sciences and Technology, Zurich 8092, Switzerland
| | - Steven Kattman
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
| | - Nicole Dubois
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
| | - Alec D Witty
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
| | - Johannes A Hewel
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Hongbo Guo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Andrew Emili
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Bernd Wollscheid
- Institute of Molecular Systems Biology at the Department of Health Sciences and Technology, Zurich 8092, Switzerland
| | - Gordon Keller
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Centre for Commercialization of Regenerative Medicine, Toronto, ON M5G 1M1, Canada; Medicine by Design: A Canada First Research Excellence Fund Program, University of Toronto, Toronto, ON M5G 1M1, Canada.
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30
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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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31
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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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32
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Rahman N, Brauer PM, Ho L, Usenko T, Tewary M, Zúñiga-Pflücker JC, Zandstra PW. Engineering the haemogenic niche mitigates endogenous inhibitory signals and controls pluripotent stem cell-derived blood emergence. Nat Commun 2017; 8:15380. [PMID: 28541275 PMCID: PMC5477512 DOI: 10.1038/ncomms15380] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 03/22/2017] [Indexed: 12/13/2022] Open
Abstract
Efforts to recapitulate haematopoiesis, a process guided by spatial and temporal inductive signals, to generate haematopoietic progenitors from human pluripotent stem cells (hPSCs) have focused primarily on exogenous signalling pathway activation or inhibition. Here we show haemogenic niches can be engineered using microfabrication strategies by micropatterning hPSC-derived haemogenic endothelial (HE) cells into spatially-organized, size-controlled colonies. CD34+VECAD+ HE cells were generated with multi-lineage potential in serum-free conditions and cultured as size-specific haemogenic niches that displayed enhanced blood cell induction over non-micropatterned cultures. Intra-colony analysis revealed radial organization of CD34 and VECAD expression levels, with CD45+ blood cells emerging primarily from the colony centroid area. We identify the induced interferon gamma protein (IP-10)/p-38 MAPK signalling pathway as the mechanism for haematopoietic inhibition in our culture system. Our results highlight the role of spatial organization in hPSC-derived blood generation, and provide a quantitative platform for interrogating molecular pathways that regulate human haematopoiesis.
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Affiliation(s)
- Nafees Rahman
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3ES
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada M5S 3G9
| | - Patrick M. Brauer
- Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada M4N 3M5
| | - Lilian Ho
- Life Sciences (Biochemistry), University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Tatiana Usenko
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada M5S 3G9
| | - Mukul Tewary
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada M5S 3G9
- Collaborative Program in Developmental Biology, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Juan Carlos Zúñiga-Pflücker
- Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada M4N 3M5
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada M5S 1A8
- Medicine by Design, a Canada First Research Excellence Program at the University of Toronto, Toronto, Ontario, Canada M5S 3G9
| | - Peter W. Zandstra
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3ES
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada M5S 3G9
- Medicine by Design, a Canada First Research Excellence Program at the University of Toronto, Toronto, Ontario, Canada M5S 3G9
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
- Collaborative Program in Developmental Biology, University of Toronto, Toronto, Ontario, Canada M5S 3E1
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33
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Abstract
The ex vivo expansion of hematopoietic stem cells is significantly inhibited by secreted proteins that induce negative feedback loops. The ability to effectively monitor these factors is critical for their real-time regulation and control and, by extension, enhancing stem cell expansion. Here, we describe a novel monitoring strategy for the detection of soluble signaling factors in stem cell cultures using a DNA-based sensing mechanism on a chip-based nanostructured microelectrode platform. We combine DNA hybridization engineering with antibody-capturing chemistry in an amplified steric hindrance hybridization assay. This method enables the quantification of important secreted proteins, showcased by the detection of 10 pg·mL-1 level concentrations of three proteins in stem cell culture samples. This approach is the first universal nonsandwich technique that permits pg·mL-1 level quantification of small proteins in stem cell culture media without signal loss.
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Affiliation(s)
- Wendi Zhou
- Electrical
and Computer Engineering, University of Toronto, Toronto M5S 1A4 Canada
| | - Sahar S. Mahshid
- Leslie
Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2 Canada
| | - Weijia Wang
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, Toronto M5S 3G9 Canada
| | | | - Peter W. Zandstra
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, Toronto M5S 3G9 Canada
| | - Edward H. Sargent
- Electrical
and Computer Engineering, University of Toronto, Toronto M5S 1A4 Canada
| | - Shana O. Kelley
- Leslie
Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2 Canada
- Institute
of Biomaterials and Biomedical Engineering, University of Toronto, Toronto M5S 3G9 Canada
- Department
of Biochemistry, University of Toronto, Toronto M5S 1A8 Canada
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34
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Martine LC, Holzapfel BM, McGovern JA, Wagner F, Quent VM, Hesami P, Wunner FM, Vaquette C, De-Juan-Pardo EM, Brown TD, Nowlan B, Wu DJ, Hutmacher CO, Moi D, Oussenko T, Piccinini E, Zandstra PW, Mazzieri R, Lévesque JP, Dalton PD, Taubenberger AV, Hutmacher DW. Engineering a humanized bone organ model in mice to study bone metastases. Nat Protoc 2017; 12:639-663. [PMID: 28253234 DOI: 10.1038/nprot.2017.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Current in vivo models for investigating human primary bone tumors and cancer metastasis to the bone rely on the injection of human cancer cells into the mouse skeleton. This approach does not mimic species-specific mechanisms occurring in human diseases and may preclude successful clinical translation. We have developed a protocol to engineer humanized bone within immunodeficient hosts, which can be adapted to study the interactions between human cancer cells and a humanized bone microenvironment in vivo. A researcher trained in the principles of tissue engineering will be able to execute the protocol and yield study results within 4-6 months. Additive biomanufactured scaffolds seeded and cultured with human bone-forming cells are implanted ectopically in combination with osteogenic factors into mice to generate a physiological bone 'organ', which is partially humanized. The model comprises human bone cells and secreted extracellular matrix (ECM); however, other components of the engineered tissue, such as the vasculature, are of murine origin. The model can be further humanized through the engraftment of human hematopoietic stem cells (HSCs) that can lead to human hematopoiesis within the murine host. The humanized organ bone model has been well characterized and validated and allows dissection of some of the mechanisms of the bone metastatic processes in prostate and breast cancer.
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Affiliation(s)
- Laure C Martine
- Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Boris M Holzapfel
- Queensland University of Technology (QUT), Brisbane, Queensland, Australia.,Orthopedic Center for Musculoskeletal Research, University of Wuerzburg, Wuerzburg, Germany
| | - Jacqui A McGovern
- Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Ferdinand Wagner
- Queensland University of Technology (QUT), Brisbane, Queensland, Australia.,Department of Orthopedics for the University of Regensburg, Asklepios Klinikum Bad Abbach, Bad Abbach, Germany.,Department of Pediatric Surgery, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Verena M Quent
- Queensland University of Technology (QUT), Brisbane, Queensland, Australia.,Department of Obstetrics and Gynecology, Martin-Luther-Krankenhaus, Academic Teaching Hospital of the Charité Berlin, Berlin, Germany
| | - Parisa Hesami
- Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Felix M Wunner
- Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Cedryck Vaquette
- Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | | | - Toby D Brown
- Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Bianca Nowlan
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Dan Jing Wu
- Queensland University of Technology (QUT), Brisbane, Queensland, Australia.,Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | | | - Davide Moi
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Tatiana Oussenko
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Elia Piccinini
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Roberta Mazzieri
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Jean-Pierre Lévesque
- Stem Cell Biology Group - Blood and Bone Diseases Program, Mater Research Institute - The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia.,Faculty of Medicine and Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Paul D Dalton
- Queensland University of Technology (QUT), Brisbane, Queensland, Australia.,Department of Functional Materials in Medicine and Dentistry, and Bavarian Polymer Institute, University of Wuerzburg, Wuerzburg, Germany
| | - Anna V Taubenberger
- Queensland University of Technology (QUT), Brisbane, Queensland, Australia.,Biotec TU Dresden, Dresden, Germany
| | - Dietmar W Hutmacher
- Queensland University of Technology (QUT), Brisbane, Queensland, Australia.,George W Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA.,Institute for Advanced Study, Technical University Munich, Garching, Germany
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35
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Yuzwa SA, Yang G, Borrett MJ, Clarke G, Cancino GI, Zahr SK, Zandstra PW, Kaplan DR, Miller FD. Proneurogenic Ligands Defined by Modeling Developing Cortex Growth Factor Communication Networks. Neuron 2016; 91:988-1004. [PMID: 27545711 DOI: 10.1016/j.neuron.2016.07.037] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/29/2016] [Accepted: 07/21/2016] [Indexed: 12/19/2022]
Abstract
The neural stem cell decision to self-renew or differentiate is tightly regulated by its microenvironment. Here, we have asked about this microenvironment, focusing on growth factors in the embryonic cortex at a time when it is largely comprised of neural precursor cells (NPCs) and newborn neurons. We show that cortical NPCs secrete factors that promote their maintenance, while cortical neurons secrete factors that promote differentiation. To define factors important for these activities, we used transcriptome profiling to identify ligands produced by NPCs and neurons, cell-surface mass spectrometry to identify receptors on these cells, and computational modeling to integrate these data. The resultant model predicts a complex growth factor environment with multiple autocrine and paracrine interactions. We tested this communication model, focusing on neurogenesis, and identified IFNγ, Neurturin (Nrtn), and glial-derived neurotrophic factor (GDNF) as ligands with unexpected roles in promoting neurogenic differentiation of NPCs in vivo.
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Affiliation(s)
- Scott A Yuzwa
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Guang Yang
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Michael J Borrett
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Geoff Clarke
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5G 1A8, Canada
| | - Gonzalo I Cancino
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Siraj K Zahr
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; Institute of Medical Sciences, University of Toronto, Toronto, ON M5G 1A8, Canada
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5G 1A8, Canada; The Donnelly Centre, University of Toronto, Toronto, ON M5G 1A8, Canada; McEwen Centre for Regenerative Medicine, University of Toronto, Toronto, ON M5G 1A8, Canada; Departments of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5G 1A8, Canada
| | - David R Kaplan
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; Institute of Medical Sciences, University of Toronto, Toronto, ON M5G 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1A8, Canada.
| | - Freda D Miller
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; Institute of Medical Sciences, University of Toronto, Toronto, ON M5G 1A8, Canada; McEwen Centre for Regenerative Medicine, University of Toronto, Toronto, ON M5G 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1A8, Canada; Department of Physiology, University of Toronto, Toronto, ON M5G 1A8, Canada.
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36
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Lechman ER, Gentner B, Ng SW, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, Nilsson B, Hermans KG, Eppert K, Marke R, Isserlin R, Voisin V, Bader GD, Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JC, Naldini L, Dick JE. miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells. Cancer Cell 2016; 29:602-606. [PMID: 27070706 PMCID: PMC5628169 DOI: 10.1016/j.ccell.2016.03.015] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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37
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Lipsitz YY, Timmins NE, Zandstra PW. Quality cell therapy manufacturing by design. Nat Biotechnol 2016; 34:393-400. [DOI: 10.1038/nbt.3525] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 01/14/2016] [Indexed: 11/09/2022]
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38
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Lechman ER, Gentner B, Ng SWK, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, Nilsson B, Hermans KG, Eppert K, Marke R, Isserlin R, Voisin V, Bader GD, Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JCY, Naldini L, Dick JE. miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells. Cancer Cell 2016; 29:214-28. [PMID: 26832662 PMCID: PMC4749543 DOI: 10.1016/j.ccell.2015.12.011] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/13/2015] [Accepted: 12/21/2015] [Indexed: 12/16/2022]
Abstract
To investigate miRNA function in human acute myeloid leukemia (AML) stem cells (LSC), we generated a prognostic LSC-associated miRNA signature derived from functionally validated subpopulations of AML samples. For one signature miRNA, miR-126, high bioactivity aggregated all in vivo patient sample LSC activity into a single sorted population, tightly coupling miR-126 expression to LSC function. Through functional studies, miR-126 was found to restrain cell cycle progression, prevent differentiation, and increase self-renewal of primary LSC in vivo. Compared with prior results showing miR-126 regulation of normal hematopoietic stem cell (HSC) cycling, these functional stem effects are opposite between LSC and HSC. Combined transcriptome and proteome analysis demonstrates that miR-126 targets the PI3K/AKT/MTOR signaling pathway, preserving LSC quiescence and promoting chemotherapy resistance.
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Affiliation(s)
- Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Bernhard Gentner
- San Raffaele Telethon Institute for Gene Therapy, San Raffaele Hospital, Milan 20132, Italy; Vita Salute San Raffaele University, San Raffaele Scientific Institute, San Raffaele Hospital, Milan 20132, Italy; Hematology and Bone Marrow Transplantation Unit, San Raffaele Hospital, Milan 20132, Italy
| | - Stanley W K Ng
- Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5G 2M9, Canada; The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Erwin M Schoof
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Peter van Galen
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - James A Kennedy
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Medicine, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Silvia Nucera
- San Raffaele Telethon Institute for Gene Therapy, San Raffaele Hospital, Milan 20132, Italy; Vita Salute San Raffaele University, San Raffaele Scientific Institute, San Raffaele Hospital, Milan 20132, Italy
| | - Fabio Ciceri
- Vita Salute San Raffaele University, San Raffaele Scientific Institute, San Raffaele Hospital, Milan 20132, Italy; Hematology and Bone Marrow Transplantation Unit, San Raffaele Hospital, Milan 20132, Italy
| | - Kerstin B Kaufmann
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Naoya Takayama
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Stephanie M Dobson
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Aaron Trotman-Grant
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Gabriela Krivdova
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Janneke Elzinga
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Amanda Mitchell
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Björn Nilsson
- Department of Hematology and Transfusion Medicine, Lund University Hospital, Lund 221 84, Sweden
| | - Karin G Hermans
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Kolja Eppert
- Department of Pediatrics, McGill University and The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Rene Marke
- Laboratory of Pediatric Oncology, Radboud University Medical Center, Nijmegen, 6500 HB, Netherlands
| | - Ruth Isserlin
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Veronique Voisin
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Peter W Zandstra
- Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5G 2M9, Canada; The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Todd R Golub
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
| | - Benjamin L Ebert
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Lu
- Yale Stem Cell Center, Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mark Minden
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Medicine, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Jean C Y Wang
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Medicine, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy, San Raffaele Hospital, Milan 20132, Italy; Vita Salute San Raffaele University, San Raffaele Scientific Institute, San Raffaele Hospital, Milan 20132, Italy
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Research Tower, Room 8-301, 101 College Street, Toronto M5G 1L7, Canada.
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39
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Wang Y, Li Y, Thérien-Aubin H, Ma J, Zandstra PW, Kumacheva E. Two-dimensional arrays of cell-laden polymer hydrogel modules. Biomicrofluidics 2016; 10:014110. [PMID: 26858822 PMCID: PMC4723409 DOI: 10.1063/1.4940430] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/07/2016] [Indexed: 05/05/2023]
Abstract
Microscale technologies offer the capability to generate in vitro artificial cellular microenvironments that recapitulate the spatial, biochemical, and biophysical characteristics of the native extracellular matrices and enable systematic, quantitative, and high-throughput studies of cell fate in their respective environments. We developed a microfluidic platform for the generation of two-dimensional arrays of micrometer-size cell-laden hydrogel modules (HMs) for cell encapsulation and culture. Fibroblast cells (NIH 3T3) and non-adherent T cells (EL4) encapsulated in HMs showed high viability and proliferation. The platform was used for real-time studies of the effect of spatial constraints and structural and mechanical properties of HMs on cell growth, both on the level of individual cells. Due to the large number of cell-laden HMs and stochastic cell distribution, cell studies were conducted in a time- and labor efficient manner. The platform has a broad range of applications in the exploration of the role of chemical and biophysical cues on individual cells, studies of in vitro cell migration, and the examination of cell-extracellular matrix and cell-cell interactions.
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Affiliation(s)
- Yihe Wang
- Department of Chemistry, University of Toronto , Toronto, Ontario M5S 3H6, Canada
| | - Yunfeng Li
- Department of Chemistry, University of Toronto , Toronto, Ontario M5S 3H6, Canada
| | | | - Jennifer Ma
- Institute of Biomaterials & Biomedical Engineering, University of Toronto , 164 College Street, Toronto, Ontario M5S 3G9, Canada
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41
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Abstract
Leukemia inhibitory factor (LIF) is a member of the interleukin-6 (IL-6) cytokine family. All members of this family activate signal transducer and activator of transcription 3 (STAT3), a transcription factor that influences stem and progenitor cell identity, proliferation and cytoprotection. The role of LIF in development was first identified when LIF was demonstrated to support the propagation of mouse embryonic stem cells. Subsequent studies of mice deficient for components of the LIF pathway have revealed important roles for LIF signaling during development and homeostasis. Here and in the accompanying poster, we provide a broad overview of JAK-STAT signaling during development, with a specific focus on LIF-mediated JAK-STAT3 activation.
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Affiliation(s)
- Kento Onishi
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada M5S 3G9
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada M5S 3G9 Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3E5 The Donnelly Centre, University of Toronto, 160 College St., Toronto, Ontario, Canada M5S 3E1 McEwen Centre for Regenerative Medicine, University Health Network, 101 College St., Toronto, Ontario, Canada M5G 1L7
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42
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Caldwell J, Wang W, Zandstra PW. Proportional-Integral-Derivative (PID) Control of Secreted Factors for Blood Stem Cell Culture. PLoS One 2015; 10:e0137392. [PMID: 26348930 PMCID: PMC4562642 DOI: 10.1371/journal.pone.0137392] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/17/2015] [Indexed: 12/20/2022] Open
Abstract
Clinical use of umbilical cord blood has typically been limited by the need to expand hematopoietic stem and progenitor cells (HSPC) ex vivo. This expansion is challenging due to the accumulation of secreted signaling factors in the culture that have a negative regulatory effect on HSPC output. Strategies for global regulation of these factors through dilution have been developed, but do not accommodate the dynamic nature or inherent variability of hematopoietic cell culture. We have developed a mathematical model to simulate the impact of feedback control on in vitro hematopoiesis, and used it to design a proportional-integral-derivative (PID) control algorithm. This algorithm was implemented with a fed-batch bioreactor to regulate the concentrations of secreted factors. Controlling the concentration of a key target factor, TGF-β1, through dilution limited the negative effect it had on HSPCs, and allowed global control of other similarly-produced inhibitory endogenous factors. The PID control algorithm effectively maintained the target soluble factor at the target concentration. We show that feedback controlled dilution is predicted to be a more cost effective dilution strategy compared to other open-loop strategies, and can enhance HSPC expansion in short term culture. This study demonstrates the utility of secreted factor process control strategies to optimize stem cell culture systems, and motivates the development of multi-analyte protein sensors to automate the manufacturing of cell therapies.
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Affiliation(s)
- Julia Caldwell
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Weijia Wang
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Peter W. Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- McEwen Centre for Regenerative Medicine, University of Health Network, Toronto, Ontario, Canada
- * E-mail:
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43
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Kana K, Song H, Laschinger C, Zandstra PW, Radisic M. PI3K Phosphorylation Is Linked to Improved Electrical Excitability in an In Vitro Engineered Heart Tissue Disease Model System. Tissue Eng Part A 2015; 21:2379-89. [PMID: 26120935 DOI: 10.1089/ten.tea.2014.0412] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Myocardial infarction, a prevalent cardiovascular disease, is associated with cardiomyocyte cell death, and eventually heart failure. Cardiac tissue engineering has provided hopes for alternative treatment options, and high-fidelity tissue models for drug discovery. The signal transduction mechanisms relayed in response to mechanoelectrical (physical) stimulation or biochemical stimulation (hormones, cytokines, or drugs) in engineered heart tissues (EHTs) are poorly understood. In this study, an EHT model was used to elucidate the signaling mechanisms involved when insulin was applied in the presence of electrical stimulation, a stimulus that mimics functional heart tissue environment in vitro. EHTs were insulin treated, electrically stimulated, or applied in combination (insulin and electrical stimulation). Electrical excitability parameters (excitation threshold and maximum capture rate) were measured. Protein kinase B (AKT) and phosphatidylinositol-3-kinase (PI3K) phosphorylation revealed that insulin and electrical stimulation relayed electrical excitability through two separate signaling cascades, while there was a negative crosstalk between sustained activation of AKT and PI3K.
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Affiliation(s)
- Kujaany Kana
- 1 Institute of Biomaterials and Biomedical Engineering , Toronto, Canada
| | - Hannah Song
- 1 Institute of Biomaterials and Biomedical Engineering , Toronto, Canada
| | - Carol Laschinger
- 2 Department of Chemical Engineering and Applied Chemistry, University of Toronto , Canada
| | - Peter W Zandstra
- 1 Institute of Biomaterials and Biomedical Engineering , Toronto, Canada .,3 Heart & Stroke/Richard Lewar Centre of Excellence , Toronto, Canada .,4 McEwen Centre for Regenerative Medicine, University of Health Network , Toronto, Canada
| | - Milica Radisic
- 1 Institute of Biomaterials and Biomedical Engineering , Toronto, Canada .,2 Department of Chemical Engineering and Applied Chemistry, University of Toronto , Canada .,3 Heart & Stroke/Richard Lewar Centre of Excellence , Toronto, Canada
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44
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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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45
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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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Kim H, Baptista RP, Trampler F, Zandstra PW, Timmins N. Process development towards efficient large-scale manufacturing of an allogenic natural killer cell therapy. Cytotherapy 2015. [DOI: 10.1016/j.jcyt.2015.03.323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Affiliation(s)
- Sidhartha Goyal
- Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, and at the Donnelly Centre for Cellular and Biomolecular Research, University of Toronto
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48
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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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49
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DeVeale B, Bausch-Fluck D, Seaberg R, Runciman S, Akbarian V, Karpowicz P, Yoon C, Song H, Leeder R, Zandstra PW, Wollscheid B, van der Kooy D. Surfaceome profiling reveals regulators of neural stem cell function. Stem Cells 2014; 32:258-68. [PMID: 24023036 DOI: 10.1002/stem.1550] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 05/03/2013] [Accepted: 07/24/2013] [Indexed: 11/11/2022]
Abstract
The composition of cell-surface proteins changes during lineage specification, altering cellular responses to their milieu. The changes that characterize maturation of early neural stem cells (NSCs) remain poorly understood. Here we use mass spectrometry-based cell surface capture technology to profile the cell surface of early NSCs and demonstrate functional requirements for several enriched molecules. Primitive NSCs arise from embryonic stem cells upon removal of Transforming growth factor-β signaling, while definitive NSCs arise from primitive NSCs upon Lif removal and FGF addition. In vivo aggregation assays revealed that N-cadherin upregulation is sufficient for the initial exclusion of definitive NSCs from pluripotent ectoderm, while c-kit signaling limits progeny of primitive NSCs. Furthermore, we implicate EphA4 in primitive NSC survival signaling and Erbb2 as being required for NSC proliferation. This work elucidates several key mediators of NSC function whose relevance is confirmed on forebrain-derived populations and identifies a host of other candidates that may regulate NSCs.
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Affiliation(s)
- Brian DeVeale
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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50
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Prowse AB, Timmins NE, Yau TM, Li RK, Weisel RD, Keller G, Zandstra PW. Transforming the Promise of Pluripotent Stem Cell-Derived Cardiomyocytes to a Therapy: Challenges and Solutions for Clinical Trials. Can J Cardiol 2014; 30:1335-49. [DOI: 10.1016/j.cjca.2014.08.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 08/06/2014] [Accepted: 08/11/2014] [Indexed: 01/08/2023] Open
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