PROJECT SUMMARY Lymphangioleiomyomatosis (LAM), a lung neoplasm affecting reproductive age women, is caused by loss-of- function mutations in tuberous sclerosis 1 (TSC1) or TSC2 genes. Hyperactivation of the mechanistic target of rapamycin 1 leads to cystic lung remodeling and progressive respiratory failure. Sirolimus therapy stabilizes lung function and improves symptoms in LAM patients, but the long-term benefit and toxicity are unknown, and some patients do not respond to therapy. LAM cells are metastatic but the primary tissue of origin is unknown. Unknown mechanisms underlying lung-specific metastasis, primary pathogenesis and female prevalence of LAM are obstacles to the development of new curative therapies. Our preliminary data from LAM lung single cell RNA sequencing (scRNAseq) analysis identified a unique population of cells (LAMCORE) expressing uterine- specific homeobox (HOX) transcription factors (TFs) that are not detected in normal lung; TF profiling of LAM patient-derived cells identified activation of Pre-B-cell leukemia homeobox 1 (PBX1), a cofactor of HOXs; comparative analysis of LAM lung scRNAseq and breast cancer cell PBX1-ChIPseq revealed overly represented LAMCORE signature genes with positive PBX1 binding peaks. Collectively, this strongly suggests a uterine origin of LAM cells and a central role of HOX/PBX1 signaling in LAM pathogenesis. The objective of this proposal is to identify mechanisms by which HOXs-associated gene networks regulate LAM pathogenesis and progression. Our central hypothesis is that HOX/PBX1 orchestrates a cell-specific gene network downstream of female hormones that regulates the survival and lung metastasis of LAMCORE cells. Three specific aims are proposed to delineate the molecular mechanisms through which HOX/PBX1 gene network contributes to LAM lesion metastasis, formation and progression. Aim 1: Determine pulmonary LAM-specific genomic and epigenomic responses and mechanisms underlying HOX/PBX1-mediated LAM pathogenesis. Aim 2: Determine the functional impacts of HOX/PBX1 network genes on metastatic potentials of LAM-derived cells in vitro and in vivo. Aim 3: Determine the effect of the HOX/PBX1 antagonist, HXR9, singly or in combination with Sirolimus, on estrogen-promoted lung metastasis potentials and lung remodeling in vivo. The completion of this proposal will provide for the first time: 1) a high-resolution integrative genomic/epigenomic blueprint of the LAMCORE cells, 2) a LAMCORE cell-specific HOX/PBX1 gene network with predicted key regulatory factors and targets within the network for follow-up perturbation and clinical diagnostic tests, 3) novel mechanistic insights into HOX/PBX1 regulatory circuits and their functional impact on LAM pathogenesis, and 4) preclinical proof-of-principle evidence for targeting HOX/PBX1-regulated female hormone-mediated LAM progression as a novel remission-inducing therapeutic strategy for LAM patients. Our work has major biomedical relevance for understanding LAM pathogenesis, developing new approaches for LAM diagnosis and designing alternative remission-inducing therapeutic strategies to maximize the benefit/toxicity ratio LAM treatment.

Public Health Relevance/Narrative The objective of this application is to determine the potential role of a newly discovered HOX/PBX1 gene regulatory network in causing the initial formation and subsequent progression of a rare but life-threatening lung disease, lymphangioleiomyomatosis (LAM), which affects women in their reproductive age. This project will not only increase our understanding of how female hormones predispose to LAM but also provide insights into the design of new treatments that may lead to a cure for LAM patients.