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Mamaeva A, Krasnova O, Khvorova I, Kozlov K, Gursky V, Samsonova M, Tikhonova O, Neganova I. Quality Control of Human Pluripotent Stem Cell Colonies by Computational Image Analysis Using Convolutional Neural Networks. Int J Mol Sci 2022; 24:ijms24010140. [PMID: 36613583 PMCID: PMC9820636 DOI: 10.3390/ijms24010140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/08/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Human pluripotent stem cells are promising for a wide range of research and therapeutic purposes. Their maintenance in culture requires the deep control of their pluripotent and clonal status. A non-invasive method for such control involves day-to-day observation of the morphological changes, along with imaging colonies, with the subsequent automatic assessment of colony phenotype using image analysis by machine learning methods. We developed a classifier using a convolutional neural network and applied it to discriminate between images of human embryonic stem cell (hESC) colonies with "good" and "bad" morphological phenotypes associated with a high and low potential for pluripotency and clonality maintenance, respectively. The training dataset included the phase-contrast images of hESC line H9, in which the morphological phenotype of each colony was assessed through visual analysis. The classifier showed a high level of accuracy (89%) in phenotype prediction. By training the classifier on cropped images of various sizes, we showed that the spatial scale of ~144 μm was the most informative in terms of classification quality, which was an intermediate size between the characteristic diameters of a single cell (~15 μm) and the entire colony (~540 μm). We additionally performed a proteomic analysis of several H9 cell samples used in the computational analysis and showed that cells of different phenotypes differentiated at the molecular level. Our results indicated that the proposed approach could be used as an effective method of non-invasive automated analysis to identify undesirable developmental anomalies during the propagation of pluripotent stem cells.
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Affiliation(s)
- Anastasiya Mamaeva
- Mathematical Biology and Bioinformatics Lab, Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
| | - Olga Krasnova
- Institute of Cytology, 194064 Saint Petersburg, Russia
| | - Irina Khvorova
- Faculty of Biology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia
| | - Konstantin Kozlov
- Mathematical Biology and Bioinformatics Lab, Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
| | | | - Maria Samsonova
- Mathematical Biology and Bioinformatics Lab, Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
| | - Olga Tikhonova
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Irina Neganova
- Institute of Cytology, 194064 Saint Petersburg, Russia
- Correspondence:
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Kusena JWT, Shariatzadeh M, Studd AJ, James JR, Thomas RJ, Wilson SL. The importance of cell culture parameter standardization: an assessment of the robustness of the 2102Ep reference cell line. Bioengineered 2021; 12:341-357. [PMID: 33380247 PMCID: PMC8806261 DOI: 10.1080/21655979.2020.1870074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 11/24/2022] Open
Abstract
Work undertaken using the embryonic carcinoma 2102Ep line, highlighted the requirement for robust, well-characterized and standardized protocols. A systematic approach utilizing 'quick hit' experiments demonstrated variability introduced into culture systems resulting from slight changes to culture conditions (route A). This formed the basis for longitudinal experiments investigating long-term effects of culture parameters including seeding density and feeding regime (route B).Results demonstrated that specific growth rates (SGR) of passage 59 (P59) cells seeded at 20,000 cells/cm2 and subjected to medium exchange after 48h prior to reseeding at 72h (route B2) on average was marginally higher than, P55 cells cultured under equivalent conditions (route A1); whereby SGR values were (0.021±0.004) and (0.019±0.004). Viability was higher in route B2 over 10 passages with average viability reported as (86.3%±8.1) compared to route A1 (83.3±8.8). The metabolite data demonstrated both culture route B1 (P57 cells seeded at 66,667 cells/cm2) and B2 had consistent-specific metabolite rates (SMR) for glucose, but SMR values of route B1 was consistently lower than route B2 (0.00001 mmol, cell-1.d-1 and 0.000025).Results revealed interactions between phenotype, SMR and feeding regime that may not be accurately reflected by growth rate or observed morphology. This implies that current schemes of protocol control do not adequately account for variability, since key cell characteristics, including phenotype and SMR, change regardless of standardized seeding densities. This highlights the need to control culture parameters through defined protocols, for processes that involve culture for therapeutic use, biologics production, and reference lines.
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Affiliation(s)
- James Willard Tonderai Kusena
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Loughborough, Leicestershire, UK
| | - Maryam Shariatzadeh
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Loughborough, Leicestershire, UK
| | - Adam James Studd
- Stem Cell Glycobiology Group, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Queen’s Medical Centre, Nottingham, UK
| | - Jenna Rebekah James
- Stem Cell Glycobiology Group, Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Queen’s Medical Centre, Nottingham, UK
| | - Robert James Thomas
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Loughborough, Leicestershire, UK
| | - Samantha Loiuse Wilson
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Loughborough, Leicestershire, UK
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Kusena JWT, Shariatzadeh M, Thomas RJ, Wilson SL. Understanding cell culture dynamics: a tool for defining protocol parameters for improved processes and efficient manufacturing using human embryonic stem cells. Bioengineered 2021; 12:979-996. [PMID: 33757391 PMCID: PMC8806349 DOI: 10.1080/21655979.2021.1902696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 12/16/2022] Open
Abstract
Standardization is crucial when culturing cells including human embryonic stem cells (hESCs) which are valuable for therapy development and disease modeling. Inherent issues regarding reproducibility of protocols are problematic as they hinder translation to good manufacturing practice (GMP), thus reducing clinical efficacy and uptake. Pluripotent cultures require standardization to ensure that input material is consistent prior to differentiation, as inconsistency of input cells creates end-product variation. To improve protocols, developers first must understand the cells they are working with and their related culture dynamics. This innovative work highlights key conditions required for optimized and cost-effective bioprocesses compared to generic protocols typically implemented. This entailed investigating conditions affecting growth, metabolism, and phenotype dynamics to ensure cell quality is appropriate for use. Results revealed critical process parameters (CPPs) including feeding regime and seeding density impact critical quality attributes (CQAs) including specific metabolic rate (SMR) and specific growth rate (SGR). This implied that process understanding, and control is essential to maintain key cell characteristics, reduce process variation and retain CQAs. Examination of cell dynamics and CPPs permitted the formation of a defined protocol for culturing H9 hESCs. The authors recommend that H9 seeding densities of 20,000 cells/cm2, four-day cultures or three-day cultures following a recovery passage from cryopreservation and 100% medium exchange after 48 hours are optimal. These parameters gave ~SGR of 0.018 hour-1 ± 1.5x10-3 over three days and cell viabilities ≥95%±0.4, while producing cells which highly expressed pluripotent and proliferation markers, Oct3/4 (>99% positive) and Ki-67 (>99% positive).
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Affiliation(s)
- J W T Kusena
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Epinal Way, Loughborough University, Loughborough, Leicestershire, UK
| | - M Shariatzadeh
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Epinal Way, Loughborough University, Loughborough, Leicestershire, UK
| | - R J Thomas
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Epinal Way, Loughborough University, Loughborough, Leicestershire, UK
| | - S L Wilson
- Centre for Biological Engineering, Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Epinal Way, Loughborough University, Loughborough, Leicestershire, UK
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Uçkan-Çetinkaya D, Haider KH. Induced Pluripotent Stem Cells in Pediatric Research and Clinical Translation. Stem Cells 2021. [DOI: 10.1007/978-3-030-77052-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Raman S, Srinivasan G, Brookhouser N, Nguyen T, Henson T, Morgan D, Cutts J, Brafman DA. A Defined and Scalable Peptide-Based Platform for the Generation of Human Pluripotent Stem Cell-Derived Astrocytes. ACS Biomater Sci Eng 2020; 6:3477-3490. [PMID: 32550261 PMCID: PMC7284803 DOI: 10.1021/acsbiomaterials.0c00067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/06/2020] [Indexed: 01/07/2023]
Abstract
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Astrocytes
comprise the most abundant cell type in the central
nervous system (CNS) and play critical roles in maintaining neural
tissue homeostasis. In addition, astrocyte dysfunction and death has
been implicated in numerous neurological disorders such as multiple
sclerosis, Alzheimer’s disease, amyotrophic lateral sclerosis
(ALS), and Parkinson’s disease (PD). As such, there is much
interest in using human pluripotent stem cell (hPSC)-derived astrocytes
for drug screening, disease modeling, and regenerative medicine applications.
However, current protocols for generation of astrocytes from hPSCs
are limited by the use of undefined xenogeneic components and two-dimensional
(2D) culture surfaces, which limits their downstream applications
where large-quantities of cells generated under defined conditions
are required. Here, we report the use of a completely synthetic, peptide-based
substrate that allows for the differentiation of highly pure populations
of astrocytes from several independent hPSC lines, including those
derived from patients with neurodegenerative disease. This substrate,
which we demonstrate is compatible with both conventional 2D culture
formats and scalable microcarrier (MC)-based technologies, leads to
the generation of cells that express high levels of canonical astrocytic
markers as well as display properties characteristic of functionally
mature cells including production of apolipoprotein E (ApoE), responsiveness
to inflammatory stimuli, ability to take up amyloid-β (Aβ),
and appearance of robust calcium transients. Finally, we show that
these astrocytes can be cryopreserved without any loss of functionality.
In the future, we anticipate that these methods will enable the development
of bioprocesses for the production of hPSC-derived astrocytes needed
for biomedical research and clinical applications.
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Affiliation(s)
- Sreedevi Raman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Gayathri Srinivasan
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Nicholas Brookhouser
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States.,Graduate Program in Clinical Translational Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona 85004, United States
| | - Toan Nguyen
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Tanner Henson
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Daylin Morgan
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Joshua Cutts
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - David A Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
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