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Lazarski CA, Hanley PJ. Review of flow cytometry as a tool for cell and gene therapy. Cytotherapy 2024; 26:103-112. [PMID: 37943204 PMCID: PMC10872958 DOI: 10.1016/j.jcyt.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023]
Abstract
Quality control testing and analytics are critical for the development and manufacture of cell and gene therapies, and flow cytometry is a key quality control and analytical assay that is used extensively. However, the technical scope of characterization assays and safety assays must keep apace as the breadth of cell therapy products continues to expand beyond hematopoietic stem cell products into producing novel adoptive immune therapies and gene therapy products. Flow cytometry services are uniquely positioned to support the evolving needs of cell therapy facilities, as access to flow cytometers, new antibody clones and improved fluorochrome reagents becomes more egalitarian. This report will outline the features, logistics, limitations and the current state of flow cytometry within the context of cellular therapy.
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Affiliation(s)
- Christopher A Lazarski
- Program for Cell Enhancement and Technology for Immunotherapy, Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA; The George Washington University, Washington, DC, USA.
| | - Patrick J Hanley
- Program for Cell Enhancement and Technology for Immunotherapy, Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA; The George Washington University, Washington, DC, USA.
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CD49d promotes disease progression in chronic lymphocytic leukemia: new insights from CD49d bimodal expression. Blood 2020; 135:1244-1254. [PMID: 32006000 DOI: 10.1182/blood.2019003179] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/22/2020] [Indexed: 12/22/2022] Open
Abstract
CD49d is a remarkable prognostic biomarker of chronic lymphocytic leukemia (CLL). The cutoff value for the extensively validated 30% of positive CLL cells is able to separate CLL patients into 2 subgroups with different prognoses, but it does not consider the pattern of CD49d expression. In the present study, we analyzed a cohort of 1630 CLL samples and identified the presence of ∼20% of CLL cases (n = 313) characterized by a bimodal expression of CD49d, that is, concomitant presence of a CD49d+ subpopulation and a CD49d- subpopulation. At variance with the highly stable CD49d expression observed in CLL patients with a homogeneous pattern of CD49d expression, CD49d bimodal CLL showed a higher level of variability in sequential samples, and an increase in the CD49d+ subpopulation over time after therapy. The CD49d+ subpopulation from CD49d bimodal CLL displayed higher levels of proliferation compared with the CD49d- cells; and was more highly represented in the bone marrow compared with peripheral blood (PB), and in PB CLL subsets expressing the CXCR4dim/CD5bright phenotype, known to be enriched in proliferative cells. From a clinical standpoint, CLL patients with CD49d bimodal expression, regardless of whether the CD49d+ subpopulation exceeded the 30% cutoff or not, experienced clinical behavior similar to CD49d+ CLL, both in chemoimmunotherapy (n = 1522) and in ibrutinib (n = 158) settings. Altogether, these results suggest that CD49d can drive disease progression in CLL, and that the pattern of CD49d expression should also be considered to improve the prognostic impact of this biomarker in CLL.
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Byrd TA, Erez A, Vogel RM, Peterson C, Vennettilli M, Altan-Bonnet G, Mugler A. Critical slowing down in biochemical networks with feedback. Phys Rev E 2019; 100:022415. [PMID: 31574667 PMCID: PMC8499154 DOI: 10.1103/physreve.100.022415] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Indexed: 06/10/2023]
Abstract
Near a bifurcation point, the response time of a system is expected to diverge due to the phenomenon of critical slowing down. We investigate critical slowing down in well-mixed stochastic models of biochemical feedback by exploiting a mapping to the mean-field Ising universality class. We analyze the responses to a sudden quench and to continuous driving in the model parameters. In the latter case, we demonstrate that our class of models exhibits the Kibble-Zurek collapse, which predicts the scaling of hysteresis in cellular responses to gradual perturbations. We discuss the implications of our results in terms of the tradeoff between a precise and a fast response. Finally, we use our mapping to quantify critical slowing down in T cells, where the addition of a drug is equivalent to a sudden quench in parameter space.
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Affiliation(s)
- Tommy A. Byrd
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Amir Erez
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Robert M. Vogel
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA
| | - Curtis Peterson
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Physics and School of Mathematical and Statistical Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Michael Vennettilli
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Grégoire Altan-Bonnet
- Immunodynamics Group, Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Andrew Mugler
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, USA
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Erez A, Mukherjee R, Altan-Bonnet G. Quantifying the Dynamics of Hematopoiesis by In Vivo IdU Pulse-Chase, Mass Cytometry, and Mathematical Modeling. Cytometry A 2019; 95:1075-1084. [PMID: 31150166 DOI: 10.1002/cyto.a.23799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 05/06/2019] [Accepted: 05/09/2019] [Indexed: 11/09/2022]
Abstract
We present a new method to directly quantify the dynamics of differentiation of multiple cellular subsets in unperturbed mice. We combine a pulse-chase protocol of 5-iodo-2'-deoxyuridine (IdU) injections with subsequent analysis by mass cytometry (CyTOF) and mathematical modeling of the IdU dynamics. Measurements by CyTOF allow for a wide range of cells to be analyzed at once, due to the availability of a large staining panel without the complication of fluorescence spillover. These are also compatible with direct detection of integrated iodine signal, with minimal impact on immunophenotyping based on the surface markers. Mathematical modeling beyond a binary classification of surface marker abundance allows for a continuum of cellular states as the cells transition from one state to another. Thus, we present a complete and robust method for directly quantifying differentiation at the systemic level, allowing for system-wide comparisons between different mouse strains and/or experimental conditions. Published 2019. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Amir Erez
- Immunodynamics Group, Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ratnadeep Mukherjee
- Immunodynamics Group, Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Grégoire Altan-Bonnet
- Immunodynamics Group, Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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Erez A, Byrd TA, Vogel RM, Altan-Bonnet G, Mugler A. Universality of biochemical feedback and its application to immune cells. Phys Rev E 2019; 99:022422. [PMID: 30934371 DOI: 10.1103/physreve.99.022422] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Indexed: 11/06/2022]
Abstract
We map a class of well-mixed stochastic models of biochemical feedback in steady state to the mean-field Ising model near the critical point. The mapping provides an effective temperature, magnetic field, order parameter, and heat capacity that can be extracted from biological data without fitting or knowledge of the underlying molecular details. We demonstrate this procedure on fluorescence data from mouse T cells, which reveals distinctions between how the cells respond to different drugs. We also show that the heat capacity allows inference of the absolute molecule number from fluorescence intensity. We explain this result in terms of the underlying fluctuations, and we demonstrate the generality of our work.
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Affiliation(s)
- Amir Erez
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Tommy A Byrd
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Robert M Vogel
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA
| | - Grégoire Altan-Bonnet
- Immunodynamics Group, Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Andrew Mugler
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, USA
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Nussinov R, Tsai CJ, Shehu A, Jang H. Computational Structural Biology: Successes, Future Directions, and Challenges. Molecules 2019; 24:molecules24030637. [PMID: 30759724 PMCID: PMC6384756 DOI: 10.3390/molecules24030637] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/05/2019] [Accepted: 02/10/2019] [Indexed: 02/06/2023] Open
Abstract
Computational biology has made powerful advances. Among these, trends in human health have been uncovered through heterogeneous 'big data' integration, and disease-associated genes were identified and classified. Along a different front, the dynamic organization of chromatin is being elucidated to gain insight into the fundamental question of genome regulation. Powerful conformational sampling methods have also been developed to yield a detailed molecular view of cellular processes. when combining these methods with the advancements in the modeling of supramolecular assemblies, including those at the membrane, we are finally able to get a glimpse into how cells' actions are regulated. Perhaps most intriguingly, a major thrust is on to decipher the mystery of how the brain is coded. Here, we aim to provide a broad, yet concise, sketch of modern aspects of computational biology, with a special focus on computational structural biology. We attempt to forecast the areas that computational structural biology will embrace in the future and the challenges that it may face. We skirt details, highlight successes, note failures, and map directions.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
| | - Amarda Shehu
- Departments of Computer Science, Department of Bioengineering, and School of Systems Biology, George Mason University, Fairfax, VA 22030, USA.
| | - Hyunbum Jang
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
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