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Scaling of joint mass and metabolism fluctuations in in silico cell-laden spheroids. Proc Natl Acad Sci U S A 2021; 118:2025211118. [PMID: 34526399 PMCID: PMC8463845 DOI: 10.1073/pnas.2025211118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2021] [Indexed: 11/24/2022] Open
Abstract
Allometric scaling has many applications, from the prediction of pharmacokinetics in animals and humans to the probing of ecosystem dynamics. Most studies have neglected to account for variations and fluctuations, although they are intrinsic features of all biological systems. To understand how metabolic scaling emerges in the presence of variations, we developed computer-generated models of cell-laden spheroids to define the experimental size range of cell cultures with quantifiable similitudes in terms of fluctuations and metabolic scaling with living organisms. We show that the estimates of scaling exponents may change with increasing variability in both mass and metabolic rate. The computational pipeline described underpins the sound design of statistically meaningful cell-based models, with impacts in both biomedical science and ecology. Variations and fluctuations are characteristic features of biological systems and are also manifested in cell cultures. Here, we describe a computational pipeline for identifying the range of three-dimensional (3D) cell-aggregate sizes in which nonisometric scaling emerges in the presence of joint mass and metabolic rate fluctuations. The 3D cell-laden spheroids with size and single-cell metabolic rates described by probability density functions were randomly generated in silico. The distributions of the resulting metabolic rates of the spheroids were computed by modeling oxygen diffusion and reaction. Then, a method for estimating scaling exponents of correlated variables through statistically significant data collapse of joint probability distributions was developed. The method was used to identify a physiologically relevant range of spheroid sizes, where both nonisometric scaling and a minimum oxygen concentration (0.04 mol⋅m−3) is maintained. The in silico pipeline described enables the prediction of the number of experiments needed for an acceptable collapse and, thus, a consistent estimate of scaling parameters. Using the pipeline, we also show that scaling exponents may be significantly different in the presence of joint mass and metabolic-rate variations typically found in cells. Our study highlights the importance of incorporating fluctuations and variability in size and metabolic rates when estimating scaling exponents. It also suggests the need for taking into account their covariations for better understanding and interpreting experimental observations both in vitro and in vivo and brings insights for the design of more predictive and physiologically relevant in vitro models.
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Kamm RD, Bashir R, Arora N, Dar RD, Gillette MU, Griffith LG, Kemp ML, Kinlaw K, Levin M, Martin AC, McDevitt TC, Nerem RM, Powers MJ, Saif TA, Sharpe J, Takayama S, Takeuchi S, Weiss R, Ye K, Yevick HG, Zaman MH. Perspective: The promise of multi-cellular engineered living systems. APL Bioeng 2018; 2:040901. [PMID: 31069321 PMCID: PMC6481725 DOI: 10.1063/1.5038337] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/18/2018] [Indexed: 12/31/2022] Open
Abstract
Recent technological breakthroughs in our ability to derive and differentiate induced pluripotent stem cells, organoid biology, organ-on-chip assays, and 3-D bioprinting have all contributed to a heightened interest in the design, assembly, and manufacture of living systems with a broad range of potential uses. This white paper summarizes the state of the emerging field of "multi-cellular engineered living systems," which are composed of interacting cell populations. Recent accomplishments are described, focusing on current and potential applications, as well as barriers to future advances, and the outlook for longer term benefits and potential ethical issues that need to be considered.
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Affiliation(s)
- Roger D. Kamm
- Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
| | - Rashid Bashir
- University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, USA
| | - Natasha Arora
- Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
| | - Roy D. Dar
- University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, USA
| | | | - Linda G. Griffith
- Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
| | - Melissa L. Kemp
- Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | | | | | - Adam C. Martin
- Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
| | | | - Robert M. Nerem
- Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Mark J. Powers
- Thermo Fisher Scientific, Frederick, Maryland 21704, USA
| | - Taher A. Saif
- University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, USA
| | - James Sharpe
- EMBL Barcelona, European Molecular Biology Laboratory, Barcelona 08003, Spain
| | | | | | - Ron Weiss
- Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
| | - Kaiming Ye
- Binghamton University, Binghamton, New York 13902, USA
| | - Hannah G. Yevick
- Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
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Yesil-Celiktas O, Hassan S, Miri AK, Maharjan S, Al-kharboosh R, Quiñones-Hinojosa A, Zhang YS. Mimicking Human Pathophysiology in Organ-on-Chip Devices. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201800109] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ozlem Yesil-Celiktas
- Division of Engineering in Medicine; Department of Medicine; Brigham and Women's Hospital; Harvard Medical School; Cambridge MA 02139 USA
- Department of Bioengineering; Faculty of Engineering; Ege University; Bornova-Izmir 35100 Turkey
| | - Shabir Hassan
- Division of Engineering in Medicine; Department of Medicine; Brigham and Women's Hospital; Harvard Medical School; Cambridge MA 02139 USA
| | - Amir K. Miri
- Division of Engineering in Medicine; Department of Medicine; Brigham and Women's Hospital; Harvard Medical School; Cambridge MA 02139 USA
- Department of Mechanical Engineering Rowan University; 401 North Campus Drive Glassboro NJ 08028 USA
| | - Sushila Maharjan
- Division of Engineering in Medicine; Department of Medicine; Brigham and Women's Hospital; Harvard Medical School; Cambridge MA 02139 USA
- Research Institute for Bioscience and Biotechnology; Nakkhu-4 Lalitpur 44600 Nepal
| | - Rawan Al-kharboosh
- Mayo Clinic College of Medicine; Mayo Clinic Graduate School; Neuroscience, NBD Track Rochester MN 55905 USA
- Department of Neurosurgery, Oncology, Neuroscience; Mayo Clinic; Jacksonville FL 32224 USA
| | | | - Yu Shrike Zhang
- Division of Engineering in Medicine; Department of Medicine; Brigham and Women's Hospital; Harvard Medical School; Cambridge MA 02139 USA
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Mertz DR, Ahmed T, Takayama S. Engineering cell heterogeneity into organs-on-a-chip. LAB ON A CHIP 2018; 18:2378-2395. [PMID: 30040104 PMCID: PMC6081245 DOI: 10.1039/c8lc00413g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Organ-on-a-chip development is an application that will benefit from advances in cell heterogeneity characterization because these culture models are intended to mimic in vivo microenvironments, which are complex and dynamic. Due in no small part to advances in microfluidic single cell analysis methods, cell-to-cell variability is an increasingly understood feature of physiological tissues, with cell types from as common as 1 out of every 2 cells to as rare as 1 out of every 100 000 cells having important roles in the biochemical and biological makeup of tissues and organs. Variability between neighboring cells can be transient or maintained, and ordered or stochastic. This review covers three areas of well-studied cell heterogeneity that are informative for organ-on-a-chip development efforts: tumors, the lung, and the intestine. Then we look at how recent single cell analysis strategies have enabled better understanding of heterogeneity within in vitro and in vivo tissues. Finally, we provide a few work-arounds for adapting current on-chip culture methods to better mimic physiological cell heterogeneity including accounting for crucial rare cell types and events.
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Affiliation(s)
- David R Mertz
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, USA.
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Kim GA, Ginga NJ, Takayama S. Integration of Sensors in Gastrointestinal Organoid Culture for Biological Analysis. Cell Mol Gastroenterol Hepatol 2018; 6:123-131.e1. [PMID: 29928682 PMCID: PMC6007820 DOI: 10.1016/j.jcmgh.2018.03.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 03/19/2018] [Indexed: 12/11/2022]
Abstract
The gastrointestinal (GI) tract regulates physiologic responses in complex ways beyond facilitating nutrient entry into the circulatory system. Because of the anatomic location of the GI tract, studying in vivo physiology of the human gut, including host cell interaction with the microbiota, is limited. GI organoids derived from human stem cells are gaining interest as they recapitulate in vivo cellular phenotypes and functions. An underdeveloped capability that would further enhance the utility of these miniature models of the GI tract is to use sensors to quantitatively characterize the organoid systems with high spatiotemporal resolution. In this review, we first discuss tools to capture changes in the fluid milieu of organoid cultures both in the organoid exterior as well as the luminal side of the organoids. The subsequent section describes approaches to characterize barrier functions across the epithelial layer of the GI organoids directly or after transferring the epithelial cells to a 2-dimensional culture format in Transwells or compartmentalized microchannel devices. The final section introduces recently developed bioengineered bacterial sensors that sense intestinal inflammation-related small molecules in the lumen using lambda cI/Cro genetic elements or fluorescence as readouts. Considering the small size and cystic shape of GI organoids, sensors used in conventional macroscopic intestinal models are often not suitable, particularly for time-lapse monitoring. Unmet needs for GI organoid analysis provides many opportunities for the development of noninvasive and miniaturized biosensors.
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Key Words
- 2D, 2-dimensional
- 3D, 3-dimensional
- Bioengineered Sensor
- FITC, fluorescein isothiocyanate
- FITC-Dex, fluorescein isothiocyanate-dextran
- GI Organoids
- GI, gastrointestinal
- HIO, human intestinal organoid
- NO, nitric oxide
- Organoid Microenvironment
- RT-PCR, reverse-transcription polymerase chain reaction
- SNARF, seminaphtharhodafluor
- TCRS, 2-component regulatory system
- TEER, transepithelial/transendothelial electric resistance
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Affiliation(s)
- Ge-Ah Kim
- Department of Materials Science and Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, Georgia
| | - Nicholas J. Ginga
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, Georgia
| | - Shuichi Takayama
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, Georgia
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
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