The landscape of tertiary lymphoid structures in endometrial cancer revealed through harmonized multi-level transcriptomics

Summary Tertiary lymphoid structures (TLSs) are ectopic lymphoid tissues that form within tumors. TLSs are associated with improved prognosis and better responses to immune checkpoint inhibitors (ICI) in cancer. However, the contribution of genetic, immune, and (micro)environmental factors to TLS formation and function remain incompletely understood. Using harmonized bulk and single-cell RNA-sequencing coupled with spatial transcriptomics, we present a comprehensive characterization of tumor-associated TLSs in endometrial cancer (EC). Our integrated datasets reveal the cellular architecture of TLSs, their organizing principles—including chemokine-receptor gradients—and TLS activity compared to paired tumor-draining lymph nodes, as well as spatial preferences in IgA/IgG plasma cell and T cell distribution. We identified a consensus set of transcriptional components that independently predict the presence of TLS in EC. Furthermore, we demonstrate that clinical neoadjuvant ICI in EC patients shifts the cellular balance in favor of immunogenic CXCL13 + PDCD1 + T cells, providing a mechanistic insight into ICI-induced TLSs formation. Our data offers a systems-level understanding of TLSs and a roadmap for their therapeutic exploitation.