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

ABSTRACT 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.