Spatial Transcriptional Dynamics of CD74⁺ B Cells in Tertiary Lymphoid Structures Drive Immune Evolution in Penile Squamous Cell Carcinoma

Abstract Penile squamous cell carcinoma (PSCC) is a malignancy characterized by a poor prognosis and lack of reliable biomarkers, presenting considerable therapeutic challenges. Tertiary lymphoid structures (TLSs) are critical modulators of antitumor immunity; however, the immunological dynamics, particularly the roles of B cells and their interactions with naive T cells in PSCC tissues, remain inadequately understood. This study integrates transcriptomic approaches, including spatial transcriptomics, single‐cell sequencing (scRNA‐seq), and bulk RNA sequencing (bulk RNA‐seq), and immunohistochemistry to elucidate the immune architecture of and functional mechanisms within TLSs. The results reveal a positive correlation between TLS density and patient survival, with CD74⁺ B cells tending to be enriched during early TLS formation. These cells exhibit strong immune activation and a propensity to differentiate into plasma cells. By engaging with naive T cells through HLA‐DRA via ligand–receptor interactions, CD74⁺ B cells activate transcription factors, including NFKB1 , NFKB2 , NFATC1 , NFATC2 , FOS , and RUNX1 , in naive T cells, thereby enhancing the immune response. Consequently, CD74⁺ B cells represent a compelling biomarker for and therapeutic target of PSCC, offering profound insights into the immunological mechanisms that drive PSCC progression and response to immunotherapy.