166P - Unravelling HR-positive, HER2-negative breast cancer and its tumor microenvironment heterogeneity using spatial transcriptomics

Background

Hormone receptor-positive (HR+)/HER2-negative (HER2-) breast cancer (BC) is the most prevalent type of breast cancer. Here we aim to describe HR+/HER2- tumor microenvironment (TME) heterogeneity and investigate its association with prognosis.

Methods

Spatial transcriptomics (ST, Visium 10X) was performed on 86 HR+/HER2- of no special type of frozen tumor samples. Gene modules describing highly correlated genes and gene co-expression networks were generated from pseudobulks via weighted gene co-expression network analysis (WGCNA). Gene signatures of modules were computed at the spatial level to assess their spatial distribution and correlation with cell types (from single cell deconvolution of ST spots) and morphological annotation. Cox proportional hazard models assessed associations between gene modules and survival, in the 86 ST samples pseudobulks and the METABRIC microarray dataset (n=1041) separately.

Results

We identified 40 modules of co-expressed genes out of which 5 were associated with disease outcome in our dataset. Modules enriched in metabolism, proliferation, and innate immunity-related processes were associated to worse prognosis for relapse free survival (RFS) in our dataset. This association was validated in METABRIC by means of overall survival (OS). In METABRIC, the innate immunity-related module was associated with a higher presence of macrophages (from xCell deconvolution). When computing the same module gene signature at the spot level in our ST cohort, its expression correlated with the presence of myeloid cells (in particular CXCL-10 macrophages). Of note, higher levels of gene signature describing CXCL-10 macrophages (from single cell) was associated to worse prognosis in both ST cohort (HR = 1.6, p = 0.026 for RFS) and METABRIC (HR = 1.1, p = 0.027 for OS).

Conclusions

WGCNA revealed genes modules that are associated to different cell types. Interestingly, the innate immunity-related module was associated to worse disease outcome and correlated with the presence of subpopulations of macrophages. These results pave the way to a better understanding of the immune landscape in HR+/HER2- BC and its role in disease progression. Further validation is needed.

Editorial acknowledgement

Clinical trial identification

Legal entity responsible for the study

The authors.

Funding

FNRS, Télévie, Association Jules Bordet, BCRF.

Disclosure

F.P. Duhoux: Financial Interests, Institutional, Advisory Board: Roche, Pfizer, AstraZeneca, Lilly, Novartis, Amgen, Daiichi Sankyo, Pierre Fabre, Gilead, Seagen, MSD; Financial Interests, Institutional, Invited Speaker: Novartis, Pfizer, MSD, Roche, MSD, Boehringer Ingelheim, Pfizer, Novartis, Lilly, AbbVie, Seagen, Gilead, AstraZeneca, Menarini, Immutep; Financial Interests, Institutional, Expert Testimony: Seagen, Novartis, MSD. C. Sotiriou: Financial Interests, Institutional, Advisory Board: Astellas, Seattle Genetics, Amgen, Merck & Co; Financial Interests, Personal, Advisory Board: Cepheid; Financial Interests, Institutional, Other, Travel: Roche; Financial Interests, Personal, Other, Travel: Pfizer; Financial Interests, Institutional, Invited Speaker: Exact Sciences; Financial Interests, Personal, Invited Speaker: Prime oncology; Financial Interests, Personal, Advisory Board, Stock options: Signatur Biosciences; Financial Interests, Personal, Stocks/Shares, Stock: Signatur Biosciences. All other authors have declared no conflicts of interest.