INVESTIGATING THE TUMOUR MICROENVIRONMENT FOR BRAIN METASTASES USING SPATIAL TRANSCRIPTOMICS AND SURGICALLY GUIDED SAMPLING

Abstract AIMS Brain metastases (BM) represent a significant unmet clinical need with poor survival and limited drug thera- pies. Recent evidence suggests a subset of BM have a more locally invasive phenotype. We sought to determine whether the tumour leading edge and tumour microenvironment (TME) differed between BM of different phe- notypes using spatial transcriptomics. METHODS Image guided surgical sampling of the tumour margin in operated BM cases using a previously described method (“Geo-Tagging”). Tumour microarray from FFPE blocks assembled using 2mm dots in triplicate. Spatial transcriptomics analysis using Nanostring GeoMX platform and immune-oncology panel (86 markers). Mart1 (melanoma BM) or CK7 (breast and lung adenocarcinoma BM) was used to delineate the tumour, GFAP for per- itumoral brain (TME) and CD45 for immune compartment. Annotation of tissue with clinical data for overall survival, local recurrence, primary cancer and assessment of BM leading edge using established criteria – dif- fuse or border. RESULTS 22 cases were analyzed in triplicate, 5 breast cancer, 8 metastatic melanoma and 9 lung adenocarcinoma. Data was analysed using established bioinformatics pipelines in R. As expected there were significant differences in gene expression between all BM of different primary cancers but not in the portion of T cells, macrophages and NK cells. PDL1 was upregulated in the tumour compartment and HLA-E downregulated in the TME com- partment of BM without a clear border. Locally recurrent BM significantly overexpressed a number of genes previously established as important in BM, including for adhesion (ICAM1, EPCAM), microglia-tumour interac- tion (STAT3) and local invasion (CCND1, VEGFA). CONCLUSION BM have different phenotypes that are dependent on both tumour and local microenvironmental factors with the future potential for therapeutic targeting to modify tumour behaviour and reduce local invasion and recur- rence.