NSF CMaT ERC Researchers Evolve Imaging Algorithms to Assess and Predict Potency during iPSC Differentiation
Outcome/Accomplishment
Researchers at the National Science Foundation (NSF)-funded Engineering Research Center (ERC) for Cell Manufacturing Technologies (NSF CMaT) have developed new imaging processing algorithms to quantify mitochondrial morphology as a label-free methodology for evaluating induced pluripotent stem cells (iPSC)-cardiomyocytes (CM). They discovered that binucleation correlates with chromatin reorganization and is indicative of cardiac progenitor cell maturation. The work allows the establishment of early quality markers (CQAs) to monitor lineage progression and predict terminal differentiation outcomes in human pluripotent stem cells (hPSC)-CM production.
Impact/Benefits
Cell therapies, especially stem cell and immune cell therapies, are revolutionizing the way we treat devastating, incurable, and chronic diseases, such as heart disease. Human induced iPSCs hold great promise for reducing the mortality of cardiovascular disease by cellular replacement of infarcted cardiomyocytes—the cells responsible for generating contractile force in the intact heart. NSF CMaT’s work on iPSC-derived cardiac cells will impact how manufacturing develops in early-stage clinical implementation of these cells and other cell types that require differentiation. Specifically, NSF CMaT research enhances the scalability of manufacturing iPSC-derived cardiac cells and microtissues and improves the quality and maturity of the resulting cells for in vitro diagnostic and in vivo therapeutic applications.
Explanation/Background
NSF CMaT ERC’s research team’s goal is to inform the development of a small number of critical quality attributes (CQAs) that can be used for biochemical assays in in-line or label-free methods derived from imaging-based techniques. To achieve these goals, imaging techniques to assess morphological CQAs and various cell penetrating peptides (CPPs), such as cell density or timing of application of differentiation factors in response to these measures were used.
Two primary modes of potency prediction were developed. First, Optical Metabolic Imaging (OMI) of iPSC-CMs during differentiation was applied to quantify mitochondrial morphology. Second, the team found that epigenetic changes in H3K56ac promoter binding occur concomitantly with changes in chromatin accessibility at key genomic loci involved in pluripotency and cardiomyocyte differentiation. The results indicated that there is a major change in mesoscale chromatin organization during the process of cardiomyocyte binucleation. Cardiomyocyte binucleation is associated with the formation of mature cardiomyocytes. Importantly, binucleate cardiomyocytes exhibit a significantly greater number of heterochromatin domains or chromocenters compared with mononucleated cardiomyocytes.
The work has been featured in eight publications and three conference presentations.
Publications:
Baumann C, Zhang X, De La Fuente R. Acute irradiation induces a senescence-like chromatin structure in mammalian oocytes. Commun Biol. 2023 Dec 12; 6(1): 1258
Baumann C, Zhang X, Viveiros MM, De La Fuente R. Pericentric major satellite transcription is essential for meiotic chromosome stability and spindle pole organization. Open Biol. 2023 Nov; 13(11): 230133
Desa, D.E., Amitrano, M.J., Murphy, W.L., Skala, M.C. (2024). Optical redox imaging to screen synthetic hydrogels for stem cell-derived cardiomyocyte differentiation and maturation. Biophotonics Discovery. 2024 Apr 1;1(1):015002.
Feeney, A.K., Simmons, A.D., Palecek, S.P. (2024). “Reseeding and cryopreservation of cardiomyocyte progenitors during human pluripotent stem cell differentiation increases cardiomyocyte purity. (submitted).
Luna-Alvear A, Suárez-Gómez D, Sanchez-Castro AA, Rentas-Echeverria AC, Cabrera-Ríos M., Isaza CE, Assessment of the Degree of Coincidence between Differentially Expressed Genes in Pancreatic Cancer with and without CAR T Cell treatment, bioRxiv 2024.04.15.589636; doi: https://doi.org/10.1101/2024.04.15.589636.
Samimi K, Pasachhe O, Guzman EC, Riendeau J, Gillette AA, Pham DL, Wiech KJ, Moore DL, Skala MC. (2024). Autofluorescence lifetime flow cytometry with time-correlated single photon counting. Cytometry A. https://doi.org/10.1002/cyto.a.24883.
Simmons AD, Baumann C, Zhang X, Kamp TJ, De La Fuente R, Palecek SP (2024). “Integrated multi-omics analysis identifies features that predict human pluripotent stem cell-derived progenitor differentiation to cardiomyocytes.” J Mol Cell Cardiol. 2024 Nov;196:52-70. doi: 10.1016/j.yjmcc.2024.08.007.
Zhang X, Baumann C and De La Fuente R (2024) A deep learning pipeline for the non-invasive prediction of chromatin structure and developmental potential in mouse oocytes. Communications Biology (Accepted).
Conference Presentations:
Feeney, A.K., Simmons, A.D., Palecek, S.P. “Reseeding during early phases of small molecule-based human pluripotent stem cell cardiomyocyte differentiation increases cardiomyocyte purity and enables cryopreservation.” Wisconsin Stem Cell Symposium, April 2024, Madison, Wisconsin.
Palecek, S.P. “Predicting outcomes of iPSC differentiation to cardiomyocytes to reduce batch failures.” SBE 8th Bioengineering and Translational Medicine Conference. October, 2024. San Diego, CA.
Palecek, S.P. “Biomanufacturing cardiomyocytes from human pluripotent stem cells.” Cardiology Grand Rounds, SUNY Stony Brook. November, 2024. Stony Brook, NY.
Location
Atlanta, GeorgiaStart Year
Advanced Manufacturing
Advanced Manufacturing
Lead Institution
Core Partners
Fact Sheet
Outcome/Accomplishment
Researchers at the National Science Foundation (NSF)-funded Engineering Research Center (ERC) for Cell Manufacturing Technologies (NSF CMaT) have developed new imaging processing algorithms to quantify mitochondrial morphology as a label-free methodology for evaluating induced pluripotent stem cells (iPSC)-cardiomyocytes (CM). They discovered that binucleation correlates with chromatin reorganization and is indicative of cardiac progenitor cell maturation. The work allows the establishment of early quality markers (CQAs) to monitor lineage progression and predict terminal differentiation outcomes in human pluripotent stem cells (hPSC)-CM production.
Location
Atlanta, GeorgiaStart Year
Advanced Manufacturing
Advanced Manufacturing
Lead Institution
Core Partners
Fact Sheet
Impact/benefits
Cell therapies, especially stem cell and immune cell therapies, are revolutionizing the way we treat devastating, incurable, and chronic diseases, such as heart disease. Human induced iPSCs hold great promise for reducing the mortality of cardiovascular disease by cellular replacement of infarcted cardiomyocytes—the cells responsible for generating contractile force in the intact heart. NSF CMaT’s work on iPSC-derived cardiac cells will impact how manufacturing develops in early-stage clinical implementation of these cells and other cell types that require differentiation. Specifically, NSF CMaT research enhances the scalability of manufacturing iPSC-derived cardiac cells and microtissues and improves the quality and maturity of the resulting cells for in vitro diagnostic and in vivo therapeutic applications.
Explanation/Background
NSF CMaT ERC’s research team’s goal is to inform the development of a small number of critical quality attributes (CQAs) that can be used for biochemical assays in in-line or label-free methods derived from imaging-based techniques. To achieve these goals, imaging techniques to assess morphological CQAs and various cell penetrating peptides (CPPs), such as cell density or timing of application of differentiation factors in response to these measures were used.
Two primary modes of potency prediction were developed. First, Optical Metabolic Imaging (OMI) of iPSC-CMs during differentiation was applied to quantify mitochondrial morphology. Second, the team found that epigenetic changes in H3K56ac promoter binding occur concomitantly with changes in chromatin accessibility at key genomic loci involved in pluripotency and cardiomyocyte differentiation. The results indicated that there is a major change in mesoscale chromatin organization during the process of cardiomyocyte binucleation. Cardiomyocyte binucleation is associated with the formation of mature cardiomyocytes. Importantly, binucleate cardiomyocytes exhibit a significantly greater number of heterochromatin domains or chromocenters compared with mononucleated cardiomyocytes.
The work has been featured in eight publications and three conference presentations.
Publications:
Baumann C, Zhang X, De La Fuente R. Acute irradiation induces a senescence-like chromatin structure in mammalian oocytes. Commun Biol. 2023 Dec 12; 6(1): 1258
Baumann C, Zhang X, Viveiros MM, De La Fuente R. Pericentric major satellite transcription is essential for meiotic chromosome stability and spindle pole organization. Open Biol. 2023 Nov; 13(11): 230133
Desa, D.E., Amitrano, M.J., Murphy, W.L., Skala, M.C. (2024). Optical redox imaging to screen synthetic hydrogels for stem cell-derived cardiomyocyte differentiation and maturation. Biophotonics Discovery. 2024 Apr 1;1(1):015002.
Feeney, A.K., Simmons, A.D., Palecek, S.P. (2024). “Reseeding and cryopreservation of cardiomyocyte progenitors during human pluripotent stem cell differentiation increases cardiomyocyte purity. (submitted).
Luna-Alvear A, Suárez-Gómez D, Sanchez-Castro AA, Rentas-Echeverria AC, Cabrera-Ríos M., Isaza CE, Assessment of the Degree of Coincidence between Differentially Expressed Genes in Pancreatic Cancer with and without CAR T Cell treatment, bioRxiv 2024.04.15.589636; doi: https://doi.org/10.1101/2024.04.15.589636.
Samimi K, Pasachhe O, Guzman EC, Riendeau J, Gillette AA, Pham DL, Wiech KJ, Moore DL, Skala MC. (2024). Autofluorescence lifetime flow cytometry with time-correlated single photon counting. Cytometry A. https://doi.org/10.1002/cyto.a.24883.
Simmons AD, Baumann C, Zhang X, Kamp TJ, De La Fuente R, Palecek SP (2024). “Integrated multi-omics analysis identifies features that predict human pluripotent stem cell-derived progenitor differentiation to cardiomyocytes.” J Mol Cell Cardiol. 2024 Nov;196:52-70. doi: 10.1016/j.yjmcc.2024.08.007.
Zhang X, Baumann C and De La Fuente R (2024) A deep learning pipeline for the non-invasive prediction of chromatin structure and developmental potential in mouse oocytes. Communications Biology (Accepted).
Conference Presentations:
Feeney, A.K., Simmons, A.D., Palecek, S.P. “Reseeding during early phases of small molecule-based human pluripotent stem cell cardiomyocyte differentiation increases cardiomyocyte purity and enables cryopreservation.” Wisconsin Stem Cell Symposium, April 2024, Madison, Wisconsin.
Palecek, S.P. “Predicting outcomes of iPSC differentiation to cardiomyocytes to reduce batch failures.” SBE 8th Bioengineering and Translational Medicine Conference. October, 2024. San Diego, CA.
Palecek, S.P. “Biomanufacturing cardiomyocytes from human pluripotent stem cells.” Cardiology Grand Rounds, SUNY Stony Brook. November, 2024. Stony Brook, NY.