DC2 will develop a 3D spatial FUN-G&T-seq and/or scNMT-seq workflow for multimodal profiling of melanoma models and tissue samples. The project will translate the protocol developed by DC3 into 3D melanoma organoid and immune cell co-cultures, fresh 200-400 μm tissue sections or explant samples. It pursues two integrated objectives: i) establish a methodology for 3D spatial FUN-G&T-seq and/or spatial scNMT-seq; ii) apply this workflow to profile tumour and immune cells in melanoma organoid co-cultures and live tissue slices.
At Erasmus MC, the candidate will work to combine spatial FUNseq with single-cell genome and transcriptome sequencing and/or single-cell nucleosome, methylation and transcriptome sequencing. The workflow will be adapted to 3D light-sheet microscopy and thick melanoma samples, addressing challenges linked to image quality, cell selection, tissue depth and multimodal data integration. During a secondment with Dr. Chien’s group, the candidate will receive training in spatial FUNseq and image-guided single-cell isolation. A second secondment at SkylineDx will explore the possible translation of emerging signatures towards a clinically oriented assay. Expected outcomes include an established 3D spatial FUN-G&T-seq and/or scNMT-seq methodology and multimodal maps of tumour and immune cell states in 3D melanoma models.