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Lineage-based inference of cell state transition dynamics in development and disease

基于谱系的发育和疾病中细胞状态转变动力学的推断

基本信息

批准号：
9089662
负责人：
Sahand Hormoz
金额：
$ 9万
依托单位：
CALIFORNIA INSTITUTE OF TECHNOLOGY
依托单位国家：
美国
项目类别：
财政年份：
2016
资助国家：
美国
起止时间：
2016-07-15 至 2017-05-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9089662
关键词：
Affect Area Award Back Beta Cell Biology Cell Cycle Cell Lineage Cells Cellular biology Clustered Regularly Interspaced Short Palindromic Repeats Complex DNA Dependence Development Developmental Biology Disease Embryo Engineering Ensure Epiblast Event Exhibits Faculty Fibroblasts Gene Expression Gene Expression Profile Generations Genes Genome Health Human Biology Image In Situ Individual Interdisciplinary Study Lead Learning Length Life Maintenance Malignant Neoplasms Mammalian Cell Measurement Measures Mediating Mentors Methodology Methods Microscopy Molecular Molecular Profiling Mus Mutagenesis Mutation Natural regeneration Neurodevelopmental Disorder Neurons Non-Insulin-Dependent Diabetes Mellitus Pathology Patients Phase Positioning Attribute Predisposition Process Protocols documentation RNA Reading Recording of previous events Research Signal Transduction Site Somatic Cell Stem cells System Techniques Time Tissues Totipotent Training Trees Validation Williams Syndrome Work base cancer cell cell motility computer framework developmental disease embryonic stem cell in vivo induced pluripotent stem cell laboratory experience neoplastic cell neurodevelopment neurogenesis novel novel strategies pluripotency progenitor programs public health relevance relating to nervous system research study single molecule synthetic biology theories time use tumor

项目摘要

DESCRIPTION (provided by applicant): Living cells transition among many physiologically distinct states during development, for tissue maintenance, and in disease. Dysregulation of transition rates between cell states can lead to pathologies, such as developmental disorders and cancer. In these systems and others, we would like to know which transitions can occur between the cellular states, in what sequence, and at what rates. Single-cell methods have expanded the ability to identify distinct cellular states in many systems. State of the art single-cell techniques can measure the expression levels of thousands of genes, but destroy cells in the process, and provide only static snapshots. No existing method can be used to infer the complex dynamics of state transitions in situ and without perturbations. To overcome this problem, we recently showed that combining the lineage history of a group of related cells with single-cell measurements of their gene expression profiles can be used to infer the dynamic transition rates between the cellular states. Here, I propose a comprehensive interdisciplinary research program to: 1) Use this approach to infer the rates of stochastic and reversible cell state transitions between the distinct pluripotent states in mouse embryonic (ES) cells, and identify the sequence of transitions involved in reprogramming of somatic cells into stem cells. 2) Extend the framework to in vivo systems by developing a synthetic platform for individual cells to autonomously record their lineage history within their DNA. 3) Apply the inference framework and the lineage-recording platform to study the dynamics of neural differentiation and neurodevelopmental diseases. My extensive background in theoretical/computational quantitative biology and training in experimental cell biology puts me in a unique position to accomplish the objectives of this proposal, which requires a seamless integration between computational and experimental approaches. I will use the mentoring phase of the K99 to facilitate my transition from theory to experimental biology and complete my laboratory training in mammalian cell biology and synthetic biology. In addition, I will work closely with collaborator to learn emerging techniques in multiplexed single-molecule imaging, the protocols for reprogramming, and methodology for induced neurogenesis. Together, the research program proposed here and the training during the mentored phase of the award will ensure that I will be well equipped to start an independent research lab and bring a novel approach to fundamental questions in diverse areas of developmental biology.