PhD positions Horizon Europe MSCA Doctoral Network SPACE-MEL

Host institution

Erasmus University Medical Centre Rotterdam (EMC-a), Department of Molecular Genetics, Rotterdam, Netherlands

Dr. Miao-Ping Chien

• Prof. Thierry Voet, Katholieke Universiteit Leuven, Department of Human Genetics, Belgium (Academic)
• Dr. Domenico Bellomo, Skyline Dx B.V., Netherlands (Industry)

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 Skyline Dx 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.