D23-15 Spatial Transcriptomics of Fibrotic Niches in IPF Reveals Compartment-specific Programs Linked to Survival

Abstract Rationale Patients with idiopathic pulmonary fibrosis (IPF) experience heterogeneous clinical trajectories. We posited that differential immunologic response to lung injury in IPF would influence fibrotic niches and inform clinical heterogeneity. We surveyed molecular programs in the immune (CD45+) vs stromal/myofibroblast (ACTA2+) niches in IPF lung tissue to identify gene and pathway signatures within fibrotic regions that differentiate survival in IPF. Methods Digital spatial transcriptomics profiling using NanoString GeoMx was performed on surgical lung biopsy tissue from 10 IPF patients undergoing research protocol surgical lung biopsy. Regions of dense fibrosis were segmented by CD45 (immune-enriched) and ACTA2 (myofibroblast-enriched). Differential expression compared long survival and short survival within each compartment (|log2FC| 0.5, p 0.05, nominal). Pathway enrichment was identified using Reactome. Results The long-survival (n = 5) and short-survival (n = 5) groups were matched for age (62 vs. 63 years, p = 0.72) and baseline FVC (60 vs. 51 % predicted, p = 0.28) yet differed significantly in survival duration (1348 vs. 143 days, p = 0.04).In CD45+ immune niches, nine transcripts were upregulated in long survival (|log2FC| 0.5, p 0.05), including MMP3, ETS1, HDAC5, MRPS10, EVA1B, TPSAB1, DOCK6, PACRG, and RASL10A. These genes mapped to pathways related to extracellular matrix remodeling and tissue repair (MMP3), mast-cell signaling (TPSAB1), cytoskeletal and vesicular dynamics (DOCK6, RASL10A), and immune transcriptional regulation (ETS1, HDAC5), consistent with an effectively regulated reparative immune milieu.In ACTA2+ myofibroblast niches, the long survival group demonstrated down-regulation of multiple stromal, epigenetic, and biosynthetic transcripts, including TIMP1, CHRDL2, ADAMTS4, GALNT2, CREB3, ATP6V0B, PRRG3, SOX9, and SBSN. Reactome enrichment analysis highlighted suppression of chromatin and ribosomal programs, notably RUNX1-regulated megakaryocyte/platelet gene expression (NES = 2.66; adj. p ≈ 0.03), SIRT1-mediated repression of rRNA synthesis (NES = 2.58; adj. p ≈ 0.03), condensation of prophase chromosomes (NES = 2.56; adj. p ≈ 0.03), defective pyroptosis (NES = 2.47; adj. p ≈ 0.03), and DNA methylation and RNA polymerase I promoter opening (both NES ≈ 2.46; adj. p ≈ 0.03). Conclusions Survival in IPF is associated with immune remodeling and stromal restraint within fibrotic niches. Long survival lungs express genes associated with (i) active regulation of controlled repair/ECM programs in immune compartment, and (ii) suppression of chromatin/rRNA biogenesis and matrix-stabilizing signals in myofibroblast compartment. This is consistent with a transcriptionally quiescent, less biosynthetically active fibroblast state. Spatially resolved profiling may delineate compartment-specific endotypes in IPF. This abstract is funded by: RO1HL176772