Multiomics identifies tumor-intrinsic SREBP1 driving immune exclusion in hepatocellular carcinoma

Abstract

Immune checkpoint inhibitors (ICI) have improved patient outcomes in hepatocellular carcinoma (HCC); however, most patients do not experience durable benefit. The non-T cell-inflamed tumor microenvironment, characterized by limited CD8+ T-cell infiltration, reduced dendritic cell function, and low interferon-γ-associated gene expression, is associated with a lower likelihood of response to ICI. To nominate new therapeutic targets for overcoming ICI resistance in HCC, we conducted a large-scale multiomic analysis on 900+human specimens (RNA sequencing (RNA-seq), proteomics) and 31 tumor single-cell (sc) RNA-seq samples, with tissue validation through imaging mass cytometry (IMC) and spatial lipidomics by matrix-assisted laser desorption/ionization (MALDI), with experimental investigation by in vitro CD8+ T-cell recruitment and macrophage polarization functional assays using three-dimensional (3D) co-culture models. We discovered 32 oncogenic pathways associated with immune exclusion, with sterol regulatory element binding protein 1 (SREBP1, encoded by SREBF1) as a hub regulator. scRNA-seq analysis showed that SREBP1 signaling is associated with enriched lipid biogenesis pathways in tumor cells, elevated immunosuppressive markers in macrophages, and diminished CD8+ T-cell infiltration. Integration of IMC and MALDI images revealed distinct lipid species differentially abundant in tumor regions with low versus high CD8+ T cell infiltration. Functional studies in a 3D in vitro tumor-immune co-culture system demonstrated that CRISPR-mediated SREBF1 knockout (KO) in HepG2 cells reduced monocyte recruitment, decreased expression of the protumorigenic CD206 marker in macrophages, and enhanced CD8+ T-cell migration compared with wild-type (WT) (p<0.0001). RNA-seq of SREBF1 KO versus WT tumor cells confirmed suppression of lipid biosynthesis genes.Our findings nominate an atlas of tumor-intrinsic drivers of immune exclusion, particularly SREBP1 via pro-tumorigenic macrophage (M2-like) reprogramming. These pathways may represent novel therapeutic targets to enhance antitumor immunity and deserve further study as targeted therapy candidates to enhance ICI in HCC.