Clonal expansion of intra‐epithelial T cells in breast cancer revealed by spatial transcriptomics

Abstract

The spatial distribution of tumor‐infiltrating lymphocytes (TIL) predicts breast cancer outcome and response to systemic therapy, highlighting the importance of an intact tissue structure for characterizing tumors. Here, we present ST‐FFPE, a spatial transcriptomics method for the analysis of formalin‐fixed paraffin‐embedded samples, which opens the possibility of interrogating archival tissue. The method involves extraction, exome capture and sequencing of RNA from different tumor compartments microdissected by laser‐capture, and can be used to study the cellular composition of tumor microenvironment. Focusing on triple‐negative breast cancer (TNBC), we characterized T cells, B cells, dendritic cells, fibroblasts and endothelial cells in both stromal and intra‐epithelial compartments. We found a highly variable spatial distribution of immune cell subsets among tumors. This analysis revealed that the immune repertoires of intra‐epithelial T and B cells were consistently less diverse and more clonal than those of stromal T and B cells. T‐cell receptor (TCR) sequencing confirmed a reduced diversity and higher clonality of intra‐epithelial T cells relative to the corresponding stromal T cells. Analysis of the top 10 dominant clonotypes in the two compartments showed a majority of shared but also some unique clonotypes both in stromal and intra‐epithelial T cells. Hyperexpanded clonotypes were more abundant among intra‐epithelial than stromal T cells. These findings validate the ST‐FFPE method and suggest an accumulation of antigen‐specific T cells within tumor core. Because ST‐FFPE is applicable for analysis of previously collected tissue samples, it could be useful for rapid assessment of intratumoral cellular heterogeneity in multiple disease and treatment settings.

Spatial transcriptomics in cancer research and potential clinical impact: a narrative review

“…Found immune repertoires of intra-epithelial T and B cells were consistently less diverse and more clonal than those in stroma. (Romanens et al 2023a ) Breast cancer ‘Spatial transcriptomics’ 1 sample Original 2016 publication in Science , demonstrated ST method with arrayed oligonucleotides with positional barcordes. ST applied to mouse brain and human breast cancer tissue containing DCIS and invasive components.…”

“…They showed that axillary lymph nodes transform into a tumor-like state with T-cell exhaustion, as well as a decrease in B cells and neutrophils (Mao et al 2023 ). Additionally, based on a laser capture microdissection approach, the immune repertoires of intraepithelial T and B cells have been shown to be consistently less diverse and more clonal than those of stromal T and B cells (Romanens et al 2023b ). A comparative analysis of samples from African American women and Caucasian women revealed race-associated differences in regions with immune-rich infiltrates (Bassiouni et al 2023 ).…”