Computational and experimental modeling of cell function in response to 3D oxygen transport in vitro.

细胞功能响应体外 3D 氧运输的计算和实验模型。

基本信息

批准号：
9895842
负责人：
Ian S Kinstlinger
金额：
$ 2.9万
依托单位：
RICE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-04-16 至 2020-11-15
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9895842
关键词：
3-Dimensional Animal Model Architecture Area Behavior Biochemical Biocompatible Materials Biological Assay Biology Blood Blood Vessels Cardiac Output Cell Culture Techniques Cell Death Cell Density Cell Proliferation Cell Survival Cell model Cell physiology Cells Cellular Morphology Characteristics Computer Models Consumption Convection Coupled Cues Diffusion Engineering Environment Equation Evaluation Experimental Models Exposure to Gel Gene Expression Gene Expression Profile Goals HepG2 Hepatic Hepatocyte Heterogeneity Hydrogels Hypoxia Image Impairment In Vitro Incubated Jordan Knowledge Length Link Liver Maps Measurement Measures Metabolic Metabolism Modeling Organ Oxygen Pattern Perfusion Phenotype Physiological Play Population Positioning Attribute Protocols documentation Radial Regenerative Medicine Reproducibility Research Resources Role Structure Supporting Cell Techniques Therapeutic Time Tissue Engineering Tissue Model Tissues To specify Training Validation Variant Vision base biofabrication cell behavior cell type density design design and construction experimental study human tissue imaging Segmentation in vivo insight novel oxygen transport predictive modeling response spatiotemporal three dimensional cell culture three-dimensional modeling transcriptome sequencing

项目摘要

Abstract To advance regenerative medicine towards recapitulating the structures and functions of human tissues at physi- ologic length scales and with relevant cell densities, strategies must be developed to meet their unrelenting metabolic demands. In order to effectively and efﬁciently oxygenate functional engineered tissues, we must understand how changes in oxygen tension modulate cell viability, proliferation, and phenotype. Decades of studying cell cultures incubated under low oxygen levels have unveiled some aspects of the hypoxic response and many key in- sights into its mechanism. Separately, an astonishing array of biomaterials have been developed which can support cells in 3D environments and can recapitulate native cell morphologies and functions to a much greater extent than 2D culture. However, as emerging areas such as regenerative medicine have sought to incorporate cells within these materials, new questions have emerged regarding the roles played by oxygen transport and hypoxia in directing the density and function of the cell populations. Currently, we lack a comprehensive framework to describe and pre- dict how cell populations will alter their densities and functions over time in the presence of spatiotemporally heterogeneous oxygen gradients. We need to extend our knowledge of cellular responses to hypoxia into 3D and we need to proﬁle how tissue-speciﬁc cell functions are impacted by local oxygen cues. In this proposal, I and a sup- porting team of experts in biomaterials, computational modeling, and liver biology will unify computational models of hypoxic response with engineered model tissues to link oxygen transport with tissue function in 3D. Our ﬁndings will be incorporated into an experimentally validated model capable of predicting how cell popula- tions change in density and function in response to speciﬁed oxygen gradients. Cellular responses to hypoxia will be parameterized by cell-speciﬁc response functions and integrated with oxygen transport equations in an agent-based computational model. We will ﬁt parameters using advanced volumetric imaging and image segmentation along with biochemical assays to map cellular markers of viability, proliferation, hypoxia, and phenotype within 3D hydrogels containing HepG2 liver cells, a well-deﬁned model cell type from a highly metabolic tissue. I hypothesize that our closed-loop computational and experimental workﬂow will yield a scalable model of cell behavior at the tissue level which captures previously unstudied functional responses to hypoxia. Finally, to broadly proﬁle the phe- notypic landscape of cells growing in the presence of oxygen gradients, we will use RNA sequencing to map spatial zonation of cell phenotypes along axial and radial oxygen gradients in perfused hydrogels. Controlled encapsulation of cells within hydrogels of reproducible architecture will enable us to evaluate these spatial patterns in gene expres- sion with a degree of experimental control and reproducibility beyond the capabilities of in vivo approaches. Taken together, these studies will provide fundamental insights into how cells respond to local oxygen gradients in 3D environments. Analysis of the spatial heterogeneity introduced by oxygen gradients is also expected to inspire new paradigms for engineering zones of cell function within tissues.

抽象的促进再生医学以概括人体组织的结构和功能植物长度尺度和相关的细胞密度，必须制定策略以满足其不懈的代谢需求。为了有效，有效地氧合功能性的组织，我们必须理解氧张力的变化如何调节细胞活力，增殖和表型。研究细胞数十年低氧水平下孵育的培养物已经揭示了低氧反应的某些方面看到其机制。另外，已经开发了一个惊人的生物材料，可以支持在3D环境中的细胞，可以比以前概括天然细胞的形态和功能 2d文化。但是，随着新兴地区（例如再生医学）试图将细胞纳入其中材料，关于氧气运输和缺氧在指导氧气发挥的作用的新问题细胞群的密度和功能。目前，我们缺乏描述和预先描述和预先的全面框架在空间存在的情况下，指定细胞种群如何随着时间的流逝而改变其密度和功能异质氧梯度。我们需要将细胞对低氧反应的了解扩展到3D，然后我们需要提出组织特异性细胞功能如何受到局部氧气提示的影响。在此提案中，我和一个sup- 生物材料，计算建模和肝生物学专家的移植团队将统一计算使用工程模型组织的低氧反应模型将氧气传输与组织功能联系起来 3D。我们的发现将被整合到经过实验验证的模型中，能够预测细胞popula- 响应于指定的氧梯度而变化和功能变化。细胞对缺氧的反应将是通过细胞特异性响应函数进行参数化，并与基于代理的氧气传输方程集成计算模型。我们将使用高级容积成像和图像分割以及生化分析以绘制3D水凝胶中生存力，增殖，缺氧和表型的细胞标记含有HEPG2肝细胞，一种来自高度代谢组织的良好模型细胞类型。我假设我们的闭环计算和实验工作流量将在组织中产生可扩展的细胞行为模型水平捕获了先前未研究的对缺氧的功能反应。最后，要广泛说明在存在氧梯度的情况下生长的细胞的不形式景观，我们将使用RNA测序来绘制空间在灌注水凝胶中沿轴向和径向氧梯度的细胞表型进行分区。受控封装可再现结构水凝胶中的细胞将使我们能够评估基因表达中的这些空间模式 - 具有一定程度的实验控制和可重复性的sion超出了体内方法的能力。拍摄这些研究将共同提供有关细胞如何对局部氧梯度反应的基本见解 3D环境。对氧梯度引入的空间异质性的分析也有望激发用于组织内部细胞功能的工程区域的新范例。