Supplementary file 1_Continuous spatially informed microenvironment programs show cross-cohort concordance and context-dependent spatial organization in diffuse large B-cell lymphoma.xlsx

Background<p>Spatial transcriptomics resolves tissue organization in diffuse large B-cell lymphoma (DLBCL), whereas most clinically annotated cohorts remain bulk transcriptomic datasets.</p>Methods<p>We evaluated six literature-informed curated composite programs across bulk, single-cell and spatial datasets without assuming a discrete ecosystem taxonomy. The programs comprised Macrophage-rich, T cell-inflamed, Antigen-presentation, Stromal/fibrotic, Immune-cold/exclusion and Proliferative/cycling, with 22 memberships per program (132 memberships, 121 unique genes and 11 shared memberships).</p>Results<p>In 498 GSE31312 tumors, principal components 1 and 2 (PC1 and PC2) explained 48.6% and 20.8% of score variance.

No candidate discrete taxonomy demonstrated sufficient stability for retention; k=2 met silhouette and size criteria but failed both bootstrap-stability thresholds. Historical 15-edge concordance was high for GSE10846 (rho=0.936) and GSE181063 (rho=0.982), whereas the most restrictive GSE10846 edge-exclusion sensitivity, removing both shared-gene and proliferation-associated edges, reduced rho to 0.690. Single-cell analysis of 14,368 DLBCL cells from four patients and eight samples provided descriptive lineage context.