SPP1 and hepatocellular carcinoma: CellChat analysis of our RNA-seq data confirmed that SPP1+ macrophage interactions with pTRT cells also occurred in HCC (Figure S9A).44 The CODEX imaging identified cell types at a single-cell resolution using our previously published thresholds to define the positive population for each marker (Figure 5A).44 This high-dimensional, integrated multi-omic analysis of protein (CODEX) and mRNA expression (scRNA-seq) connects intercellular signaling on a spatial and transcript level in the context of a single pathology.