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

模拟特发性肺纤维化的进行性纤维化体外模型的验证

• 批准号: 10350549
• 负责人: JOHN A BELPERIO
• 金额: $ 63.04万
• 依托单位: UNIVERSITY OF CALIFORNIA LOS ANGELES
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-02-15 至 2025-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10350549
• 关键词: 3-Dimensional; Affect; Age; Algorithmic Analysis; Alveolar; Animal Model; Apoptosis; Architecture; Biological Assay; Biological Models; Biological Process; Biology; Biomedical Engineering; CASP3 gene; Cell Aging; Cell Differentiation process; Cell Line; Cell model; Cell physiology; Cells; Characteristics; Chronic; Collection; Data; Disease; Disease model; Drug Modelings; Drug Screening; Epithelial; Epithelial Cells; Ethnic Origin; Etiology; Extracellular Matrix; Fibroblasts; Fibrosis; Gender; Goals; Health; Heterogeneity; Host Defense; Human; Image; Image Analysis; Inflammatory; International; Interstitial Lung Diseases; Lung; Lung diseases; MUC5B gene; Measures; Mesenchymal; Methods; Michigan; Modeling; Molecular; Pathogenesis; Pathologist; Patients; Phenocopy; Phenotype; RNA analysis; Race; Reporter; Reporting; Research; Research Personnel; Running; Signal Transduction; Standardization; Structure of parenchyma of lung; System; Techniques; Tissues; Validation; airway epithelium; analysis pipeline; antifibrotic treatment; base; cell type; chemokine; clinically relevant; curative treatments; cytokine; deep learning; drug discovery; drug use screening; efficacy study; fibrotic lung; genetic risk factor; genetic variant; high-throughput drug screening; human model; idiopathic pulmonary fibrosis; image processing; improved; in vitro Model; induced pluripotent stem cell; innovation; machine learning algorithm; novel therapeutics; precision medicine; prevent; senescence; single-cell RNA sequencing; small molecule; stem; stem cell model; stem cells; success; three-dimensional modeling

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.

摘要 我们已经开发了3D生物工程化的人诱导多能干细胞（iPSC）衍生的IPF模型， 表现出进行性纤维化，并密切模仿与IPF相关的几种特征。该模型 我们的进行性纤维化的2D模型的扩展（Vijayaraj等人，Cell Reports - in press）。使我们的 IPF特异性进行性纤维化模型，我们已将其开发为利用肺3D 结构和特定的细胞类型。我们的3D模型显示了IPF的其他特征，如气道上皮细胞 细胞（AEC）凋亡、上皮-间质转化（EMT）和肺泡结构的替代。 我们的建议旨在改进和验证这种3D模型，使其能够用于高通量药物 以患者特定的方式为精准医疗提供发现平台。我们的项目旨在利用我们独特的 IPF的干/祖细胞模型，以增加我们对疾病的理解和药物发现。 具体目标1。改进和验证IPF的3D生物工程人iPSC衍生模型 A.通过对IPF的3D模型进行广泛表征，与人类模型进行比较，验证IPF的3D模型 IPF肺组织。 B。描述不同患者间观察到的IPF异质性。 C.通过已知遗传风险因素表征3D IPF模型。 具体目标2 -使用我们的3D生物工程iPSC衍生模型研究IPF中的细胞可塑性 在我们的IPF 3D模型中描绘AEC的细胞可塑性，并使用单细胞技术将其与人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， 使用IPF 3D模型的新型抗纤维化疗法 A.使用IPF的3D模型开发HTS。 B。开发强大的图像分析管道，结合高级深度学习 技术和传统的图像处理方法来生成组织健康的定量测量。 C.开发和运行一个试点HTS，以确定将执行以下一项或多项的小分子a） 抑制AEC凋亡; B）促进间充质细胞凋亡; c）降低β-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， UCLA）、IPF临床医生和研究人员（Belperio，UCLA）、肺部病理学家（Wallace，USC）、iPSC气道 上皮细胞分化（Spence，Michigan），单细胞RNA测序和分析（普拉斯，UCLA），以及高 利用机器学习算法进行分析（Shattuck，UCLA）。 我们是一个高度协作的团队，共同使用创新的，与患者相关的研究 解决IPF建模挑战的方法，以确定新的治疗方法。