LSD1 Promotes Immune Exclusion and Suppresses IFN-γ-Associated Transcriptional Programs in Triple-Negative Breast Cancer.

Background

Triple-negative breast cancer (TNBC) exhibits aggressive biology and heterogeneous immune infiltration. Lysine-specific demethylase 1 (LSD1/KDM1A) is an epigenetic regulator implicated in oncogenic transcriptional programs, but its role in immune exclusion remains incompletely defined.

Methods

LSD1 expression was evaluated by immunohistochemistry in TNBC specimens and correlated with survival. Functional effects of LSD1 depletion or pharmacological inhibition were assessed in TNBC cell lines and patient-derived xenograft organoids (PDXOs). Transcriptomic, ChIP-seq, multiplex immunofluorescence, and GeoMX digital spatial profiling analyses were integrated to characterize LSD1-associated transcriptional, chromatin, and immune programs. PBMC-PDXO co-cultures evaluated the effects of LSD1 inhibition on tumor growth and immune cell infiltration.

Results

High LSD1 expression was associated with inferior overall survival, hypoxia-associated programs and suppressed immune pathways. LSD1-high tumors exhibited reduced infiltration of T cells, B cells, NKT-like cells, and macrophages. Spatial profiling revealed suppressed innate immune responses and type I interferon signaling within B-cell and T-cell compartments, respectively. ChIP-seq demonstrated preferential LSD1 occupancy at AP-1 motif-enriched regions, while co-immunoprecipitation supported association with AP-1 complexes. Integration of LSD1 chromatin occupancy sites with transcriptomics data identified SPPL2A and NCOA3 as candidate LSD1-regulated genes associated with interferon-γ response pathways. LSD1 depletion increased SPPL2A, NCOA3, MHC-I and PD-L1 expression. LSD1 inhibition reduced PDXO growth and increased immune cell infiltration.

Conclusions

LSD1 is associated with a poor clinical outcome and immune exclusion in TNBC. These findings support a role for LSD1 in AP-1-associated chromatin regulation and interferon-γ-related transcriptional response; they warrant further investigation into LSD1 inhibition as a therapeutic strategy for immune-cold TNBCs.