Date of Award

Spring 5-13-2016

Level of Access

Campus-Only Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Functional Genomics/Interdisciplinary

Advisor

Carol J Bult

Second Committee Member

Viravuth P. Yin

Third Committee Member

Lenny D. Shultz

Additional Committee Members

Leif Oxburgh

Renee J. LeClair

Abstract

Despite advances in environmental safety and neonatal care, lung disease remains a significant cause of mortality worldwide. To understand the genetic mechanisms that may be disrupted during pathogenesis, a comprehensive understanding of normal lung development is necessary. Animal models provide a robust tool for investigating the role of individual genes and proteins on lung development and physiological similarities between the murine and human respiratory system make the mouse an ideal model for studying mammalian lung organogenesis.

My thesis work had three specific objectives: 1) to identify novel transcriptomic patterns associated with lung development, 2) to compare the developing lung characteristic subtranscriptomes between mouse and human, and 3) to compare strain-dependent differences in gene expression between three common strains of laboratory mice exhibiting differences in adult lung physiology and disease susceptibility. To characterize temporal patterns of transcriptional activity during lung development, I analyzed genome wide gene expression data for 26 pre- and post-natal time points during normal lung development in three common inbred strains of laboratory mice (C57BL/6J, A/J, C3H/HeJ). Principal components analysis (PCA) identified major sources of sample variation within the data that are associated with global gene expression patterns, which vary as a function of time and/or strain. This approach was used to define a murine Developing Lung Characteristic Subtranscriptome (mDLCS) comprised of 4683 genes that are central to lung developmental processes in mice regardless of strain. Regression modeling of the Principal Components was used to build a novel nine-stage model of lung development in the mouse and bioontological annotation analysis was then used to summarize the functional enrichment of resulting patterns of gene expression.

The resulting model supports the canonical stages of embryonic lung development defined by morphology and histology (embryonic, pseudoglandular, canalicular, saccular, alveolar) while also providing a dense molecular characterization of the transcriptomic changes occurring across these stages. Postnatally, the developmental gene expression data are consistent with two distinct phases of postnatal alveolarization that are marked by transcriptional activity of genes related to pulmonary vascularization. Comparing mouse and human lung transcriptomic data sets revealed 771 conserved genes associated with cell cycle, axon guidance, immune function, and metabolism as well as differences between species in ECM organization. Finally, strain specific genes were enriched for annotations related to neurogenesis, extracellular matrix organization, and Wnt signaling, suggesting there are substantial differences in the lung microenvironment among inbred mouse strains. These findings reveal genes that are expressed in a strain-dependent manner that have significant value to understanding the genetic basis of lung disease.

AppendixA_FilteredDataset.txt (13555 kB)
Variance Filtered Transcriptional Dataset

AppendixB_PCA-GeneLoadings.txt (12351 kB)
PCA Results - Gene Loadings

AppendixC_PCA-SampleScores.txt (57 kB)
PCA Results - Sample Scores

AppendixD_DifferentialGeneExpressionAcrossStages_SAM.xlsx (537 kB)
Differential Gene Expression Across Stages (SAM)

AppendixE_README.docx (104 kB)
Enrichment Results from mDLCS_README

AppendixE_VLAD-Enrichment_mDLCS.xls (13778 kB)
Enrichment Results from mDLCS

AppendixF_PreviousLungDevelopmentGeneLists.xlsx (267 kB)
Lung Development Genes (Previous Transcriptional Studies)

AppendixG_AnnotatedMouseLungGenes.xlsx (738 kB)
Lung Development/Disease Genes (GO/MP Annotation)

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