2 PhD positions in the Horizon Europe MSCA Doctoral Network SPACE-MEL

PhD positions in the Horizon Europe MSCA Doctoral Network SPACE-MEL

DC2: 3D spatial FUN-G&T-seq and/or scNMT-seq

Functie inhoud

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

Supervisor: Dr. Miao-Ping Chien

Co-supervisors: Prof. Thierry Voet, Katholieke Universiteit Leuven, Department of Human Genetics, Belgium (Academic); Dr. Domenico Bellomo, SkylineDx B.V., Netherlands (Industry)

Project description:

At Erasmus University Medical Centre Rotterdam (EMC-a), Department of Molecular Genetics, Rotterdam, Netherlands, under the supervision of Dr. Miao-Ping Chien and co-supervision of Prof. Thierry Voet, Katholieke Universiteit Leuven, Department of Human Genetics, Belgium (Academic), and Dr. Domenico Bellomo, SkylineDx B.V., Netherlands (Industry), the candidate 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:

1. Establish a methodology for 3D spatial FUN-G&T-seq and/or spatial scNMT-seq.
2. 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.