The landscape of melanoma progression and immune surveillance at single cell resolution

To build a pre-cancer atlas for melanoma that reveals early events in disease initiation and immune response, we performed RNA sequencing of 222 histologically distinct micro-regions (~5-20 cells per region) extracted from 3 formalin-fixed paraffin-embedded tissue sections collected from a melanoma patient. These sections capture multiple phases of disease progression from melanoma in situ to metastatic invasive melanoma and areas of effective immune surveillance. Micro-region transcript data is complemented by sub-cellular resolution imaging using tissue-based cyclic immunofluorescence and will be released via the Human Tumor Atlas data portal. mRNA from 40μm regions of interest were extracted from 3 FFPE melanoma tissue sections (F8, F9, F12) containing multiple histological sites (melanoma in situ, invasive melanoma, invasive melanoma boundary, exophytic melanoma, inflammatory regression and brisk TIL region). The micro-regions were sequenced and their gene expression profiles were analyzed.