Preserving chromatin nano-structure to enhance chondrocyte therapeutic potential for cartilage repair

保留染色质纳米结构以增强软骨细胞修复软骨的治疗潜力

基本信息

批准号：
10706966
负责人：
Su Chin Heo
金额：
$ 41.66万
依托单位：
UNIVERSITY OF PENNSYLVANIA
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-09-20 至 2027-07-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10706966
关键词：
3-Dimensional Amino Acids Animal Model Architecture Biochemical Biocompatible Materials Biological Assay Biology Biophysics Cartilage Cartilage injury Cell Differentiation process Cell Therapy Cells Chemicals Chondrocytes Chromatin Clinical Cues Data Defect Disease Epigenetic Process Exhibits Fluorescent in Situ Hybridization Future Gene Expression Gene Expression Profile Genes Genetic Transcription Genome Goals Heterogeneity Histologic Histone Deacetylase Inhibitor Human Hydrogels Hypoxia Image Implant In Vitro Knowledge Label Machine Learning Measures Mechanics Mesenchymal Stem Cells Metabolic Mission Modeling Modification Musculoskeletal Nanostructures Natural regeneration Outcome Output Phenotype Population Production Property Proteins Proxy Public Health RNA Research Research Personnel Site Technology Testing Therapeutic Tissue Engineering Tissues Transforming Growth Factor beta Translations Treatment Efficacy United States National Institutes of Health Work articular cartilage cartilage repair clinical application clinical practice design differential expression genome-wide genomic locus improved in vivo evaluation induced pluripotent stem cell inhibitor innovation joint destruction machine learning model nano nanoscale novel preservation prevent repaired single molecule single-cell RNA sequencing stem superresolution imaging superresolution microscopy tissue regeneration transcriptome ultra high resolution

项目摘要

Summary There is a gap in the knowledge about how chondrocytes lose their phenotype and matrix production capacity during in vitro expansion. This gap in knowledge stems from the paucity of studies that directly interrogate chondrocyte genome architecture and transcriptional profiles in single cells to capture the inherent heterogeneity of cell differentiation. To fill this unmet gap, we will use state-of-the-art super-resolution imaging, single cell RNA Sequencing (RNA-Seq), high-throughput RNA-FISH (MERFISH) and metabolic labeling (FUNCAT) technologies to relate, on a cell-by-cell level, the chromatin nano-structure, transcriptional output, epigenetic modifications and matrix production capacity of single chondrocytes expanded in culture under different epigenetic and chemo-physical cues. We will further develop machine learning models to predict chondrocyte phenotype using super-resolution images of chondrocyte chromatin nano-structure. Our central hypothesis is that there are distinct chromatin nano-structural arrangements and transcriptional signatures associated with chondrocytes that have high matrix production capacity, and that chromatin nano-structure can be manipulated in a predictive manner via the combination of epigenetic and chemo-physical cues to improve chondrocyte therapeutic potential. The basis for this hypothesis is our preliminary super-resolution data of chromatin nano-structure in in vitro expanded chondrocytes and mesenchymal stem cells grown on substrates of varying stiffness and subjected to various chemical cues. The proposed work is significant as it will generate new knowledge about how chromatin nano-structure and epigenetic landscape regulates matrix production capacity of chondrocytes and how this capacity can be enhanced through manipulation of chromatin and epigenetic states. Our Aims are: matrix whether chromatin nano-structure and transcription are predictive of chondrocyte production capacity Aim 1: Determine Aim 2: Determine how chemo-physical and epigenetic cues impact transitions in chromatin nano- structure and matrix production in chondrocytes Aim 3: Determine whether predicted cues improve chondrocyte therapeutic efficacy In summary, we expect to contribute to the identification of new in vitro expansion conditions that maintain naïve chondrocyte phenotype and enhance their therapeutic potential. The proposed research is innovative as it represents a drastic departure from the status quo by applying multi-faceted, single-cell based imaging and sequencing technologies to determine the relationship between chondrocyte chromatin and epigenetic state, transcriptional activities, and matrix production. If successful, this work may change clinical practice by providing improved cell populations for cartilage repair.

概括关于软骨细胞如何失去表型和基质产生的知识存在差距体外扩张期间的容量。从缺乏的研究中，知识步骤的差距直接询问单个细胞中的软骨细胞基因组结构和转录谱以捕获继承细胞分化的异质性。为了填补这个未满足的空白，我们将使用最先进的超分辨率成像，单细胞RNA测序（RNA-SEQ），高通量RNA-FISH（Merfish）和代谢标记（funcat）在细胞级别上与染色质纳米结构，转录输出相关联的技术，单个软骨细胞的表观遗传修饰和基质生产能在培养中扩展不同的表观遗传和化学形态提示。我们将进一步开发机器学习模型以预测使用软骨细胞染色质纳米结构的超分辨率图像使用软骨细胞表型。我们的中心假设是有不同的染色质纳米结构布置和转录特征与具有高基质生产能力的软骨细胞相关，并且染色质纳米结构可以通过表观遗传学和化学意识的组合以预测的方式进行操纵以改善软骨细胞治疗潜力。该假设的基础是我们的初步超分辨率数据染色质纳米结构在体外膨胀的软骨细胞和间充质干细胞生长在底物上刚度变化，并受到各种化学提示。拟议的工作很重要，因为它将产生关于染色质纳米结构和表观遗传景观如何调节基质生产的新知识软骨细胞的能力以及如何通过操纵染色质和表观遗传状态。我们的目标是：矩阵染色质纳米结构和转录是否可以预测软骨细胞生产能力目标1：确定目标2：确定化学物理和表观遗传提示如何影响染色质纳米的转变软骨细胞的结构和基质产生目标3：确定预测的提示是否改善软骨细胞治疗总而言之，我们希望有助于确定维持的新体外扩张条件拟议的研究是创新的它通过应用多方面的，基于单细胞的成像和测序技术以确定软骨细胞染色质和表观遗传状态之间的关系，转录活动和矩阵生产。如果成功，这项工作可能会通过提供来改变临床实践改善了软骨修复的细胞群体。