Computational Models of the Human Cell Cycle to Reveal Disease Mechanism and Inform Treatment

项目摘要/摘要 这个项目的总体目标是开发预测人类细胞周期如何变化的计算模型 对临床相关干扰的反应，如放射治疗、靶向治疗、致癌突变和 定向分化。这些模型将填补我们对机制理解的一个重大空白。 涉及细胞异常增殖的疾病的发生、发展和治疗的基础。我们的 方法是使用定量单细胞成像来测量增殖细胞的分子状态，并 将这些数据集成到预测性建模框架中。我们已经组建了一个跨机构的团队 由一名计算生物学家、两名细胞生物学家和一名擅长于 放射肿瘤学。该团队拥有强大而富有成效的合作历史，与六家联合出版物合作，以 约会。目的1研究视网膜上皮细胞对辐射诱导的DNA反应的机制 S期间破损执行G2抓捕。延时成像和确定性建模将预测：如何 对脱氧核糖核酸损伤的反应延迟到S/G2的过渡；脱氧核糖核酸的小分子抑制物如何 修复--目前正在进行临床试验--增强了止血反应；以及肿瘤如何消失 抑制子P53使细胞对联合治疗难以抵抗。AIM 2问胰腺上皮细胞如何与 KRAS的突变逃脱了永久性的细胞周期停滞。我们将使用高内容成像来分析多个 表达致癌KRAS的单细胞中的信号活性。这些数据将被用来构建流形 跨越致癌KRAS介导的两周时间进程的细胞周期进程的表示 转型。对流形几何的计算分析将确定分子分支点 控制胰腺细胞增殖/停滞决策的G1，我们将验证这些预测 通过小分子和基因操作。Aim 3测试了人类胚胎干细胞的假设 细胞继承细胞周期特异性基因产物(具体地说，G1调节器)，从前一个G2期到 促进子代细胞的多能性。我们将结合有丝分裂特异的染色质图谱和卷积 基于神经网络的图像分析识别干细胞维持快速增殖的机制 以及多个细胞周期世代的多能性。每个目标都产生了基础知识和应用知识， 提供对扰动下细胞周期进程的基本见解，并产生特定的、 分子预测为新的治疗方案提供信息。着眼于未来，预测模型 人类细胞周期将使患者能够针对由异常细胞驱动的疾病进行治疗 扩散。

PROJECT SUMMARY / ABSTRACT The overall goal of this project is to develop computational models that predict how the human cell cycle responds to clinically-relevant perturbations such as radiotherapy, targeted therapy, oncogenic mutation, and directed differentiation. These models will fill a significant void in our understanding of the mechanisms underlying the initiation, progression, and treatment of diseases that involve abnormal cell proliferation. Our approach is to use quantitative single-cell imaging to measure the molecular states of proliferating cells and to integrate these data into predictive modeling frameworks. We have assembled a cross-institutional team comprising a computational biologist, two cell biologists, and a physician scientist with specialization in radiation oncology. The team has a strong and productive history of collaboration with six joint publications to date. Aim 1 investigates the mechanism by which retinal epithelial cells respond to radiation-induced DNA damage during S phase to execute G2 arrest. Time-lapse imaging and deterministic modeling will predict: how the response to DNA damage is delayed until the S/G2 transition; how a small-molecule inhibitor of DNA repair—currently involved in clinical trial—intensifies the arrest response; and how loss of the tumor suppressor p53 renders cells refractory to combination therapy. Aim 2 asks how pancreatic epithelial cells with mutations in KRAS escape permanent cell cycle arrest. We will use high-content imaging to profile multiple signaling activities in single cells expressing oncogenic KRAS. These data will be used to construct a manifold representation of cell cycle progression that spans a two-week time course of oncogenic KRAS-mediated transformation. Computational analysis of the manifold’s geometry will identify molecular branching points in G1 that govern the proliferation/arrest decision in pancreatic cells, and we will validate these predictions through small molecules and genetic manipulation. Aim 3 tests the hypothesis that human embryonic stem cells inherit cell-cycle-specific gene products (specifically, G1 regulators) from the previous G2 phase to promote pluripotency in daughter cells. We will combine mitosis-specific chromatin profiling with convolutional neural network-based image analysis to identify the mechanisms by which stem cells sustain rapid proliferation and pluripotency over multiple cell-cycle generations. Each aim yields both basic and applied knowledge, providing fundamental insights into cell cycle progression under perturbation and generating specific, molecular predictions to inform new treatment schemes. With an eye toward the future, predictive models of the human cell cycle will enable patient-specific treatments for diseases that are driven by abnormal cell proliferation.