Single-Cell Analysis Identifies LYPD6B as a Tumor-Intrinsic Candidate Associated With Immunotherapy Nonresponse in Breast Cancer

Immune checkpoint blockade (ICB) induces durable responses in a subset of breast cancer patients, yet many show limited benefit from anti-PD-1/PD-L1 therapy. Understanding differences in the tumor microenvironment (TME) and tumor-intrinsic immune evasion between responders (R) and nonresponders (NR) is key to improving outcomes. We integrated three public scRNA-seq datasets from PD-(L)1-treated breast cancer (51 patients; 327022 cells) and analyzed paired pre-/posttreatment samples. Compared to NR, R patients exhibited increased CD8⁺ T cell infiltration, enhanced interferon-response activity, and myeloid/B-cell remodeling. Pseudotime analysis showed T cells in R progressed from activation to cytotoxic differentiation and ultimately exhaustion, consistent with effective ICB response patterns. Through tumor-intrinsic screening, we identified LYPD6B-a membrane gene upregulated in NR cancer cells that suppresses antigen processing/presentation and IFNα/β signaling. Functional assays confirmed that LYPD6B ablation impairs proliferation, clonogenic growth, and induces apoptosis. Drug-repurposing analyses revealed venetoclax binds LYPD6B and recapitulates its antiproliferative effects. Immunohistochemistry (IHC) and pan-cancer analyses verified LYPD6B's tumor-cell localization, association with immune infiltration, and checkpoint expression. Collectively, LYPD6B emerges as a tumor-intrinsic mediator of immune evasion and PD-(L)1 resistance, representing a promising target for combination immunotherapy in breast cancer.