Spatial transcriptomic sequencing identifies lipid metabolism and mitochondrial respiration as central features of T cell excluded esophageal adenocarcinomas

The tumour immune microenvironment influences neoadjuvant chemoradiotherapy success in esophageal adenocarcinoma (EAC). Complete responders show higher treatment-naïve intratumoral CD8+ T cell levels before treatment than non-complete responders. Understanding mechanisms driving CD8+ T cells exclusion from the TIME is essential to improving outcomes. We performed spatial transcriptomics on treatment-naive CD8-low and high EACs ( N = 12). Regions of interest (ROIs) were selected based on tumour annotation by a pathologist. Cancer (CK+) cells and immune (CD45+) cells were analysed within the same ROI. Findings were validated using bulk transcriptome data (TCGA) and metabolic profiling (SCENITH) of fresh tumour specimen ( n = 5). Whole transcriptomic profiling showed cancer cell clustering based on T cell infiltration. Cancer cell transcriptomes of CD8-low tumours exhibited reduced antigen presentation and upregulated lipid and mitochondrial metabolism, while CD8-high tumours showed increased cytokine signalling and apoptotic pathways. In CD45+ compartments, CD8-low tumours were enriched for the PGC-1α pathway, linked to mitochondrial biogenesis and immunosuppressive myeloid populations. These findings were supported by TCGA data. SCENITH confirmed mitochondrial dependence of macrophages in CD8-low tumours. Our results suggest that mitochondrial metabolism and impaired antigen presentation contribute to T cell exclusion in EAC. These findings raise the hypothesis that targeting mitochondrial metabolism in these cancers can modulate the anti-tumour immune response and thereby improve the response to chemoradiotherapy.