1711P Spatial transcriptomics reveals substantial heterogeneity in TNBC tumor and stroma compartments with potential clinical implications

Abstract

Triple negative breast cancer (TNBC) is a heterogeneous disease characterized by at least five molecular subtypes, namely basal like (BL), immunomodulatory (IM), luminal AR (LAR), mesenchymal (M) and mesenchymal stem like (MSL), associated with distinct gene expression, genomic and tumor microenvironment (TME) profiles. Recent technological advances allow to investigate intratumor geographic heterogeneity ignored by bulk tumor analyses. Here, we deployed spatial transcriptomics (ST) to interrogate tumor and stroma compartments heterogeneity and assess its association with clinical outcome. Spatial transcriptomics was performed on a series of 94 case-control TNBC samples matched for known clinic-pathological parameters. Detailed morphological annotations spanning 11 histomorphological categories were performed by a breast dedicated pathologist assisted by the automated QuPath digital pathology software. Bioinformatics analyses were performed using in house pipelines. Morphologically, LAR, M and MSL tumors were more diffused and surrounded by more stroma, as compared to BL and IM TNBCs displaying large tumor patches with higher immune infiltration. Indeed, overall, LAR and MSL tumors were more enriched in stroma, fat tissue and vessels. Spatial gene expression analysis identified 418 individual clusters, which were grouped to define 11 ecotypes (i.e. cluster combinations) associated with specific molecular and cellular features, including EMT, angiogenesis, DNA repair and immune profiles. In particular, we identified 2 ecotypes (6 and 8) within the IM subtype with distinct clinical outcomes, with the ecotype 6 associated with EMT and mesenchymal stroma having worse prognosis (p = 0,021). To our knowledge, this is the largest study demonstrating at an unprecedented level the substantial intra- and inter-patient heterogeneity characterizing TNBC, with regards to morphology, as well as molecular and cellular features. Our results hightlight the need to consider TNBC heterogeneity for future clinical development and patients’ care.