Decoding the bridges and barriers to cellular reprogramming and lineage identity

解码细胞重编程和谱系身份的桥梁和障碍

• 批准号: 10020996
• 负责人: Rajan Jain
• 金额: $ 112.82万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-19 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10020996
• 关键词: Adopted; Automobile Driving; Back; Bar Codes; Biological; Biology; CRISPR/Cas technology; Cardiac; Cardiac Myocytes; Cell Fate Control; Cells; Computer Analysis; DNA; Development; Developmental Biology; Elements; Exposure to; Frequencies; Gene Delivery; Gene Expression; Genes; Genetic; Genetic Screening; Genetic Transcription; Genomics; Goals; Human body; Image; Individual; Knowledge; Maps; Measures; Methodology; Methods; Molecular; Molecular Profiling; Nature; Pathway interactions; Pharmaceutical Preparations; Phenotype; Population; RNA; Regenerative Medicine; Research; Rest; Series; Sorting - Cell Movement; Source; Techniques; Technology; Thinking; Time; Viral; Work; base; cell transformation; cell type; clinical application; experimental study; innovation; interest; new technology; response; screening; small molecule; tool; transdifferentiation; translational approach

Project Summary The human body is composed of a large number of cell types. These types are generally quite stable in the sense that cells of one type, once established, typically do not switch to other cell types. A major goal for regenerative medicine and our understanding of cell type in general is to discover if and how we can force cells to switch from one type to another. Recent results over roughly the last decade have shown that it is in principle possible to convert cells from one type by forcing them to turn on small sets of genes. However, in the vast majority of cases, we have no idea what these sets of genes are out of the many thousands of potential ones, and so our understanding has largely been dictated by picking candidates based on prior knowledge. Furthermore, even when these sets of genes are identified, the efficiency of interconversion of cell type is very low, with only a small percentage of source cells converting to the target type. Our proposed research tackles both of these challenges using a combination of new concepts of cell identity and new technology for tracing individual cells back in time. For cell identity, the approach most common in the field is to use profiles of which genes are on or off in any particular cell type to determine lineage-specific factors. However, while these genes are lineage-specific, they may not be lineage-determining in the sense that they may not drive a cell to a particular type per se. We have developed a methodology we call PerturbID that uses a series of systematic perturbations to identify specific genes that turn on and off in response, which we have shown have the capacity to interconvert cells. We propose to use PerturbID to identify and validate candidates for cell type transformation across a range of cell types, ultimately arriving at a set of general principles for cellular reprogramming. This will have applications for regenerative medicine as well as across biology as a whole. The other major problem, of efficiency, has remained mysterious because nobody currently knows why some cells are capable of reprogramming while the vast majority are not. The challenge is the lack of tools for retrospective profiling of cells: how do we rewind time to profile the cells that will ultimately adopt a different fate? We have developed tools for performing this retrospective profiling. We will apply this “time machine” methodology to the problem of inefficient reprogramming to determine the unique signature of cells primed for cell type conversion, and will perform genetic screens to isolate pathways capable of manipulating this frequency. Together, our work will transform our concepts of cell type and will have enormous practical implications for its application in regenerative medicine.

项目摘要 人体由大量细胞类型组成。这些类型通常在 感觉到一种类型的单元格一旦建立，通常不会切换到其他单元格。一个主要目标 再生医学及我们对细胞类型的理解通常是发现以及如何迫使细胞 从一种类型切换到另一种类型。在过去的十年中，最近的结果表明它在 可以通过迫使它们打开小型基因来转换细胞的原理。但是，在 绝大多数情况下，我们不知道这些基因集中有什么潜力 那些，因此我们的理解在很大程度上是通过基于先验知识来挑选候选人来决定的。 此外，即使确定了这些基因集，细胞类型的相互转换的效率也非常 低，只有一小部分源单元转换为目标类型。 我们拟议的研究通过新的细胞身份概念结合了这两个挑战 和新技术，以及时追溯各个单元。对于细胞身份，该方法最常见 字段是使用哪些基因在任何特定细胞类型中打开或关闭的曲线来确定特定于谱系的谱系 因素。但是，尽管这些基因是谱系特异性的，但在意义上可能并不是谱系决定的 他们可能不会将单元格驱动到特定类型本身。我们已经开发了一种称为derturbid的方法论 这使用一系列系统的扰动来识别响应中打开和关闭的特定基因 我们已经显示，具有互连细胞的能力。我们建议使用derturbid来识别和验证 跨各种细胞类型的细胞类型转换的候选者，最终到达一组一般 细胞重编程的原理。这将适用于再生医学以及跨越 整个生物学。效率的另一个主要问题仍然是神秘的，因为目前没有人 知道为什么某些细胞能够重新编程，而绝大多数细胞却没有。挑战是缺乏 用于回顾性分析的工具：我们如何倒带时间来介绍最终将采用的单元格 不同的命运？我们已经开发了执行此回顾性分析的工具。我们将应用这个“时间 机器”方法论，用于确定细胞独特签名的效率低下的问题问题 用于细胞类型转化的启动，并将执行遗传筛选以分离能够操纵的途径 这个频率。一起，我们的工作将改变我们的细胞类型概念，并具有巨大的实用性 对其在再生医学中的应用的影响。