Single cell transcriptomics in a treatment-segregated cohort exposes a STAT3-regulated therapeutic gap in idiopathic pulmonary fibrosis

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Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic pulmonary disease of unknown etiology. Since approved IPF drugs only slow disease progression, novel therapeutics are required that improve clinical outcomes. Here we report a single cell RNA-Seq and gene regulatory network analysis of the largest IPF cohort assembled to date. Segregating this cohort based on status of treatment with approved antifibrotics (untreated, nintedanib- and pirfenidone-treated), we describe for the first time the transcriptional landscape of untreated IPF across 40 lung cell types, and the elements of this program that are impacted by approved antifibrotics. On average, nearly 60% of the untreated IPF-dysregulated transcriptome is refractory to treatment with these drugs, a transcriptional deficit we refer to as the IPF therapeutic gap. Gene regulatory network analysis indicated a dominant functional footprint for the transcription factor STAT3 in both untreated IPF and the IPF therapeutic gap. Validating our analysis in a translational precision cut lung slice platform that recapitulates IPF explants, pharmacological inhibition of STAT3 reduced the IPF therapeutic gap in numerous lung cell types. Finally, we implicated STAT3 as a master transcription factor that regulates a network comprising numerous profibrotic transcription factors in IPF alveolar fibroblasts, a critical fibrotic lineage. Our study represents a comprehensive resource for translational lung fibrosis research and establishes a novel strategy for drug discovery in human disease more broadly. One Sentence Summary: Segregation of a clinical IPF cohort by treatment status identifies STAT3 as a prominent and targetable driver of IPF transcriptional programs that are refractory to approved antifibrotics.

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