Validation of an in vitro model of progressive fibrosis that mimics Idiopathic Pulmonary Fibrosis

摘要 我们开发了一种3D生物工程人诱导多能干细胞(IPSC)来源的IPF模型，该模型 表现为进行性纤维化，与IPF密切相关的几个特征。这个型号是 我们的2D进行性纤维化模型的扩展(Vijayaraj等人，Cell Reports-in Press)。为了让我们的 针对IPF的进行性纤维化模型，我们已将其发展为利用肺3D的模型系统 架构和特定的单元类型。我们的3D模型显示了IPF的其他特征，如呼吸道上皮 细胞(AEC)凋亡、上皮-间充质转化(EMT)和肺泡结构改变。 我们的建议旨在改进和验证这一3D模型，使其能够适应高通量药物 发现平台以患者特有的方式进行精准医疗。我们的项目旨在利用我们独特的 建立IPF的干细胞/祖细胞模型，以增加我们对疾病的了解和药物发现。 具体目的1.改进和验证三维生物工程人IPSC来源的IPF模型 A.通过与人类相比对模型进行广泛的表征来验证IPF的3D模型 IPF肺组织。 B.描述不同患者间IPF的异质性。 C.通过已知的遗传危险因素来表征3D IPF模型。 特定目标2-使用我们的3D生物工程IPSC衍生模型来研究IPF的细胞可塑性 在我们的IPF三维模型中分析AECs的细胞可塑性，并与使用单细胞的人IPF组织进行比较 RNA测序。 具体目标3-开发和标准化高通量药物筛选(HTS)平台，以识别 使用IPF三维模型的新的抗纤维化治疗 A.使用IPF的3D模型开发HTS。 B.开发采用高级深度学习组合的健壮的图像分析管道 技术和传统的图像处理方法，以生成组织健康的定量测量。 C.开发和运行试点HTS，以确定将执行以下一项或多项任务的小分子) 抑制血管内皮细胞的凋亡；b)促进间充质细胞的凋亡；c)减少-SMA的表达。 我们的团队包括研究肺生物学(Gomperts，UCLA)、纤维化生物学(Vijayaraj， 加州大学洛杉矶分校)，IPF临床医生和研究员(Belperio，UCLA)，肺部病理学家(华莱士，南加州大学)，IPSC呼吸道 上皮细胞分化(密歇根州斯宾塞)、单细胞RNA序列和分析(普拉斯，加州大学洛杉矶分校)和高 吞吐量药物发现(Damoiseaux，UCLA)和用于分析的机器学习算法(Shattuck，UCLA)。 我们是一个高度协作的团队，正在使用创新的、与患者相关的研究进行合作 解决建立IPF模型以确定新疗法的挑战的方法。

Abstract We have developed a 3D bioengineered human induced pluripotent stem cell (iPSC) derived model of IPF that displays progressive fibrosis and closely phenocopies several characteristics associated with IPF. This model is an extension of our 2D model of progressive fibrosis (Vijayaraj et al., Cell Reports – in press). To make our progressive fibrosis model specific to IPF, we have developed it into a model system that utilizes the lung 3D architecture and specific cell types. Our 3D model displays additional features of IPF such as airway epithelial cell (AEC) apoptosis, epithelial-mesenchymal transition (EMT) and replacement of alveolar architecture. Our proposal aims to improve and validate this 3D model such that it will be amenable to a high throughput drug discovery platform in a patient specific manner for precision medicine. Our project aims to use our unique stem/progenitor cell models of IPF to increase our understanding of the disease and for drug discovery. Specific Aim 1. To improve and validate the 3D bioengineered human iPSC derived model of IPF A. To validate the 3D model of IPF by performing extensive characterization of the model compared to human IPF lung tissue. B. To characterize the heterogeneity of IPF seen across different patients. C. To characterize the 3D IPF model by known genetic risk factors. Specific Aim 2 – To use our 3D bioengineered iPSC-derived model to study cellular plasticity in IPF To profile cellular plasticity of AECs in our 3D model of IPF and compare it to human IPF tissue using single cell RNA sequencing. Specific Aim 3 – To develop and standardize a high throughput drug screening (HTS) platform to identify new anti-fibrotic therapies using the 3D model of IPF A. To develop a HTS using the 3D model of IPF. B. To develop robust, image analysis pipelines that employ a combination of advanced deep learning techniques and traditional image processing methods to generate quantitative measures of tissue health. C. To develop and run a pilot HTS to identify small molecules that will perform one or more of the following a) prevent apoptosis of AEC; b) enhance apoptosis of mesenchymal cells; c) decrease expression of -SMA. Our team includes international experts who study lung biology (Gomperts, UCLA), biology of fibrosis (Vijayaraj, UCLA), an IPF clinician and researcher (Belperio, UCLA), lung pathologist (Wallace, USC), iPSC airway epithelial cell differentiation (Spence, Michigan), single cell RNA seq and analysis (Plath, UCLA), and high throughput drug discovery (Damoiseaux, UCLA) with machine learning algorithms for analysis (Shattuck, UCLA). We are a highly collaborative team that is working together using innovative, patient relevant research approaches to tackle the challenges of modeling IPF to identify new therapies.