Dissecting the role of lung macrophages in sarcoidosis using genomic approaches

Despite the prevalence of sarcoidosis, the underlying cause is not well understood. In particular, the driver behind the granulomas that are distinct to sarcoidosis compared to other immune-driven diseases is unclear. There is evidence to suggest that macrophage plays a key role in the development of sarcoidosis. Thus, we propose to examine lung macrophages in order to understand how they are altered in disease. We have previously shown that the epigenomic landscape of tissue-resident macrophages, such as alveolar macrophages in the lung, are shaped by the local environment. Signals in the environment trigger tissue-specific transcription factors that work in combination with lineage factors to specify the gene regulatory networks (GRN) of macrophages – in other words, the interactions between genes and cis-regulatory elements that regulate gene expression. The plastic nature of macrophage GRN allows them to adopt distinct functions depending on the tissue in which they reside. Moreover, studies in in vitro macrophages have shown that their response to stimuli, such as LPS, is largely determined by their pre-existing epigenomic landscape. A similar process is likely to be at work in the disease environment. In other diseases, different macrophage populations are thought to have differing functions in pathogenesis. For example, in inflammation, it is the macrophages that differentiate from infiltrating monocytes that exhibit a pro-inflammatory phenotype rather than the resident macrophages. In order to understand the pathogenesis of sarcoidosis, it is critical to determine which populations are driving the disease phenotype and by what mechanism they are altered. We hypothesize that lung macrophages in sarcoidosis patients will exhibit a unique genomic signature in response to the disease environment. To test this hypothesis, we propose to use state-of the-art genomic technology to map the GRN of macrophages isolated from bronchoalveolar lavage (BAL) of sarcoidosis patients and healthy controls. We will use two complementary approaches to define subpopulations within the lung macrophages and assay their epigenomic landscape. In Aim1, we will perform single-cell RNA-seq on myeloid cells from the BAL fluid. Using a clustering approach, we will group macrophages and related based on sharing a similar transcriptional profile. We expect to identify sub-populations of cells that are unique to sarcoidosis patients. In Aim 2, we will perform will perform genomic assays, including RNA-seq for gene expression, ATAC-seq for chromatin accessibility, and ChIP-seq for histone modification on lung macrophage populations from BAL fluid. By integrating these diverse assays, we will be able to identify the regulatory modules that comprise macrophage GRN in sarcoidosis. Using our novel computational framework, we will implicate key factors in regulating macrophage response. We expect that macrophages in sarcoidosis will exhibit a distinctive signature of disease. Together, these results will further our understanding of the role of macrophage in the pathogenesis of sarcoidosis and will provide a valuable resource for future studies. Importantly, this approach can be used to study other cell types and tissues affected by sarcoidosis as well. As a computational immunologist, I bring a fresh perspective and rare skill set, particularly with respect to complex analysis required. With the support of my collaborators, who bring additional expertise in sarcoidosis and lung injury, and the resources at Northwestern, I am uniquely position