Spatial transcriptomic sequencing identifies lipid metabolism and mitochondrial respiration as central features of T...

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.