Single-cell multi-omics analysis reveals two molecular subtypes of human male breast cancer with distinct neuroendocrine and immune characteristics

• There are two major subtypes of MBC with distinct neuroendocrine and immune states. MBC with high neuroendocrine score tends to have more aggressive clinical performance. • DLX2 is a key transcription factor which potentially regulated the neuroendocrine characteristics of MBC cells. • The cell–cell communication between NPY + and NPY1R + cells may also play an important role in promoting the neuroendocrine features of MBC. • MBC with strong neuroendocrine features showed “cold tumor” state, BCL2 may serve as a potential therapeutic target for MBC with high NE score. • CD45+/KRT18+ cells were present in MBC, which were associate to the neuroendocrine state of tumor cells. Male breast cancer (MBC) is a rare and malignant disease with limited molecular understanding. There is still no specific therapeutic strategy for patients with MBC in the clinic, the current treatment options for MBC still mainly refer to those of female breast cancer (FBC). This study aims to report a comprehensive dissection of MBC at the single-cell resolution is urgently required to elucidate the underlying mechanisms of MBC, providing a basis and novel insights into molecular subtypes and developing innovative treatment options for patients with MBC. In this study, we accumulated and analyzed large-scale multi-omics datasets from MBC patients to elucidate the molecular landscape of tumor development at different levels of multi-omics layers. Using single-cell RNA sequencing, bulk RNA sequencing, and imaging mass cytometry analysis, we identified two major molecular subtypes of MBC with distinct neuroendocrine (NE) and immune states, and CD45 + /KRT18 + cells were present in human MBC. MBC with a high NE score tends to exhibit more aggressive clinical performance, including lymph node metastasis and vascular invasion. Furthermore, we identified a key transcription factor, DLX2, which potentially regulates the NE features of MBC. Cell-cell communication between NPY + and NPY1R + cells may also promote NE features. Moreover, we identified that MBC with high NE features was a “cold tumor” and may not be suitable for immunotherapy. Instead, BCL2 may be a potential therapeutic target for MBC with NE features. Our study enhances the understanding of MBC and provides valuable insights into clinical diagnosis and therapy.