Resolving the single-cell and spatial transcriptomic architecture of inflammatory tertiary lymphoid structures to decode gastric cancer immunotherapy prognosis

Abstract The tertiary lymphoid structure (TLS) served as prognostic and immunotherapeutic indicator in cancer, influenced by its spatial distribution and density. Herein, we implemented TCR, single-cell, and spatial sequencing to elucidate the tumor microenvironment (TME) complexity in 25 gastric cancer (GC) samples with varying TLS distributions. We observed significant accumulation of CXCL13 + CD103 + T lymphocyte cell (TLC), CXCR5 + germinal center B lymphocyte cell (BLC), LAMP3 + dendritic cell (DC), SELP + high endothelial venule (HEV), CXCL12 + matrix cancer associated fibroblast (mCAF) and CXCL16 + tumor cell in intratumor TLS (iTLS) GC compared to peritumor TLS (pTLS) and desert TLS (dTLS). Intercellular crosstalk unveiled CXCL16 + tumor cells, CXCL12 + mCAFs, and SELP + HEVs mediate the recruitment of CXCL13 + TLCs through the CXCL16-CXCR6 and CXCL12-CXCR4 pathways, generating CXCR5 + BLCs recruitment via the CXCL13-CXCR5 pathway, indicative of GC TLS formation mechanism. Lastly, we proposed inflammatory TLS (iTLS) signature with cellular features within iTLS-GC TME, predicting GC immunotherapy prognosis.