Alveolar DevMAP

描述（由申请人提供）：“肺泡DevMAP”的总体目标是我们对RFA-HL-14-008肺发育分子图谱-研究中心（RC） （U01）的响应是生成肺泡分隔过程中表观遗传标记、microRNA、mRNA和蛋白质的动态和区域变化的纲要，并使用该纲要生成正常肺泡分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专家小组，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。该提案组的pi先前已经确定了异常肺泡化（Ambalavanan），肺细胞表型编程的表观遗传改变（Hagood）以及肺纤维化中发育编码和非编码RNA表达谱的改变（Kaminski）的机制，最近（与Bar- Joseph博士一起）应用了mirDREM。一种概率建模方法来重建动态调控网络，以解释小鼠肺泡分隔过程中mirna和转录因子如何共同调控时间基因表达，以及应用新的方法来定位和定量组织基因表达。我们将通过以下具体目标来实现本中心的目标：特异性目的1 -确定肺泡分隔过程中编码和非编码rna的变化特异性目的2 -确定肺泡分隔过程中全局DNA甲基化的变化特异性目的3 -确定肺泡分隔过程中转录因子和蛋白质组学谱的变化特异性目的4 -使用扩展和验证我们的分析工具，以模拟在肺发育中激活的动态信号和调控网络，这将与联盟的其他成员共享。在所有目标中，我们将使用从正在发育的肺泡的激光捕获显微解剖（LCM）或分散的肺细胞的荧光激活细胞分选（FACS）中获得的样本，以紧密的间隔收集，以便进行详细的分析。将包括定量免疫组织化学和原位转录本的确认以及一些实验验证。在这个项目中，人体组织核心（HTC）的样品将提供给UAB。Ambalavanan博士（联络PI， UAB）将负责UAB的LCM和FACS。样品将分发给卡明斯基博士（耶鲁大学）进行miRNA和mRNA分析，Hagood博士（加州大学圣地亚哥分校）进行DNA甲基化分析，Mobley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方法确定肺发育中的关键miRNA， mRNA和DNA甲基化控制点，以评估多分子，途径和细胞之间的相互作用网络，因为它们聚集在一起决定肺泡隔的形成。

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.