Alveolar DevMAP

描述(由申请人提供)：“肺泡DevMAP”的总体目标我们对RFA-HL-14-008肺发育研究中心(RC)分子图谱(U01)的回应是生成在肺泡间隔期间发生的表观遗传标记、microRNA、mRNA和蛋白质的动态和区域性变化的概要，并使用该概要生成正常肺泡间隔的动态时间调节模型。为了实现这一目标，我们组建了一个多学科的专家小组，研究领域包括肺发育、基因组学、表观基因组学、定量成像、系统和计算生物学以及生物统计学。该建议小组的PI先前已确定异常肺泡化(Ambalavanan)、肺细胞表观遗传学改变(Hagood)及肺纤维化(Kaminski)中发育编码及非编码RNA表达谱改变(Kaminski)的机制，最近(与Bar-Joseph博士)应用mirDREM，一种重建动态调控网络的概率建模方法，以解释在肺泡间隔形成过程中，时间基因表达如何受到miRNAs和转录因子的联合调控，并应用新的方法对组织基因的表达进行定位和定量。我们将通过以下特定目标来实现该中心的目标：特定目标1-确定肺泡间隔期间编码和非编码RNA的变化特定目标2-确定肺泡间隔期间全球DNA甲基化的变化特定目标3-确定在肺泡间隔期间转录因子和蛋白质组特征的变化特定目标4-使用、扩展和验证我们的分析工具来模拟在肺发育中被激活的动态信号和调节网络，这些将与联盟的其他成员共享在所有目标中我们将使用从激光捕获显微切割(LCM)获得的样本来发展分散的肺泡细胞或荧光激活细胞分类(FACS)，每隔一小段时间收集 允许进行详细的分析。定量免疫组织化学和原位转录的确认将包括以及一些实验验证。在这个项目中，来自人类组织核心(HTC)的样本将被提供给UAB。Ambalavanan博士(联系Pi，UAB)将负责UAB的LCM和FACS。样本将分发给卡明斯基博士(耶鲁大学)进行miRNA和mRNA分析，哈古德博士(UCSD)进行DNA甲基化，莫布利博士(UAB)进行蛋白质组学分析。数据集成和计算模型开发将由CMU的Bar-Joseph博士完成。通过这些研究开发的肺泡DevMAP和计算模型将确定肺泡发育的调节“控制点”。至少，这些研究将使用系统生物学的方法来确定肺发育中关键的miRNA、mRNA和DNA甲基化控制点，以评估多个分子、途径和细胞之间的相互作用网络，因为它们聚集在一起确定肺泡间隔的形成。(摘要结束)

DESCRIPTION (provided by applicant): The overall objective of "Alveolar DevMAP" our response to RFA-HL-14-008 Molecular Atlas of Lung Development - Research Center (RC) (U01) is to generate a compendium of the dynamic and regional changes in epigenetic marks, microRNA, mRNA and proteins that happen during alveolar septation, and use this compendium to generate a dynamic temporal regulatory model of normal alveolar septation. To address this objective we have assembled a multidisciplinary group of experts in lung development, genomics, epigenomics, quantitative imaging, systems and computational biology, and biostatistics. The PIs on this proposal group have previously identified mechanisms underlying abnormal alveolarization (Ambalavanan), epigenetic alterations in lung cell phenotype programming (Hagood), and altered developmental coding and non-coding RNA expression profiles in lung fibrosis (Kaminski) and more recently (together with Dr. Bar- Joseph) applied mirDREM, a probabilistic modeling method to reconstruct dynamic regulatory networks to explain how temporal gene expression is jointly regulated by miRNAs and transcription factors in the mouse lung during alveolar septation as well as applied novel approaches for localization and quantitation of tissue gene expression. We will address the objectives of this center by the following Specific Aims: Specific Aim 1 - to identify changes in coding and non-coding RNAs during alveolar septation Specific Aim 2 - to determine changes in global DNA methylation during alveolar septation Specific Aim 3 - To identify the shifts in transcription factor and proteomic profile during alveolar septation Specific Aim 4 - To use, extend and validate our analytical tools to model dynamic signaling and regulatory networks activated in lung development that will be shared with other members of the consortium In all aims we will we will use samples acquired from laser capture microdissection )LCM) of developing alveoli or fluorescence activated cell sorting (FACS) of dispersed lung cells, collected at tight intervals to allow detailed analysis. Confirmation by quantitative immunohistochemistry and in-situ for transcripts will be included as well as some experimental validations. For this project, samples from the Human Tissue Core (HTC) will be supplied to UAB. Dr. Ambalavanan (Contact PI, UAB) will oversee LCM and FACS at UAB. Samples will be distributed to Dr. Kaminski (Yale) for miRNA and mRNA analysis, Dr. Hagood (UCSD) for DNA methylation, and Dr. Mobley (UAB) for proteomics. Data integration and computational model development will be done by Dr. Bar-Joseph at CMU. The Alveolar DevMAP and computational models developed through these studies will identify regulatory "control points" in alveolar development. At a minimum, these studies will determine key miRNA, mRNA and DNA methylation control points in lung development using a systems biology approach to evaluate the network of interactions between multiple molecules, pathways, and cells as they converge to determine formation of the alveolar septum. (End of Abstract)