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.
The molecules and regulatory processes involved in development of the alveoli in the lung are highly complex and we do not have a comprehensive understanding of this process. By identifying changes in genes and proteins that contribute to alveolar septation, followed by development of computational models, we will determine the mechanisms by which alveoli develop in the human lung.
| Yu, Guoying; Ibarra, Gabriel H; Kaminski, Naftali (2018) Fibrosis: Lessons from OMICS analyses of the human lung. Matrix Biol 68-69:422-434 |
| Lutful Kabir, Farruk; Ambalavanan, Namasivayam; Liu, Gang et al. (2018) MicroRNA-145 Antagonism Reverses TGF-? Inhibition of F508del CFTR Correction in Airway Epithelia. Am J Respir Crit Care Med 197:632-643 |
| Duong, Thu Elizabeth; Hagood, James S (2018) Epigenetic Regulation of Myofibroblast Phenotypes in Fibrosis. Curr Pathobiol Rep 6:79-96 |
| Ding, Jun; Hagood, James S; Ambalavanan, Namasivayam et al. (2018) iDREM: Interactive visualization of dynamic regulatory networks. PLoS Comput Biol 14:e1006019 |
| Zhou, Yong; Horowitz, Jeffrey C; Naba, Alexandra et al. (2018) Extracellular matrix in lung development, homeostasis and disease. Matrix Biol 73:77-104 |
| Olave, Nelida; Lal, Charitharth Vivek; Halloran, Brian et al. (2018) Iloprost attenuates hyperoxia-mediated impairment of lung development in newborn mice. Am J Physiol Lung Cell Mol Physiol 315:L535-L544 |
| Ding, Jun; Aronow, Bruce J; Kaminski, Naftali et al. (2018) Reconstructing differentiation networks and their regulation from time series single-cell expression data. Genome Res : |
| Sucre, Jennifer M S; Deutsch, Gail H; Jetter, Christopher S et al. (2018) A Shared Pattern of ?-Catenin Activation in Bronchopulmonary Dysplasia and Idiopathic Pulmonary Fibrosis. Am J Pathol 188:853-862 |
| Ryu, Changwan; Sun, Huanxing; Gulati, Mridu et al. (2017) Extracellular Mitochondrial DNA Is Generated by Fibroblasts and Predicts Death in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 196:1571-1581 |
| Saadoon, Ammar; Ambalavanan, Namasivayam; Zinn, Kurt et al. (2017) Effect of Prenatal versus Postnatal Vitamin D Deficiency on Pulmonary Structure and Function in Mice. Am J Respir Cell Mol Biol 56:383-392 |
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