About the project
Objective
This project will provide novel methodology to reconstruct the evolutionary history of cancer cells in their spatial context from widely used data. We will integrate single-cell and spatial transcriptomics data to reconstruct the evolutionary history of cancer cells and describe their spatial structure. These results will reveal how different cancer cell states arise and organize in space during tumor evolution, and how different states may be shaped by their interactions with the tumor microenvironment.
Background
Single-cell sequencing data has enabled highly detailed descriptions of intra-tumor heterogeneity in terms of the genotypes and phenotypes of cancer cells, as well as maps of the non-cancer cell types present within the tumor microenvironment. While standard single-cell sequencing techniques such as scRNA-seq provide detailed information on the cell states that make up a tumor, they do not capture the spatial distribution of the cells that it captures, which is lost in the process. In contrast, spatial transcriptomics technologies maintain the spatial structure of 2D tumor slices intact while still obtaining transcriptome-wide measurements of the cells therein. Integrating both data types may reveal novel therapeutic targets.
About the Digital Futures Postdoc Fellow
Pedro F. Ferreira holds a PhD in Computational Biology from ETH Zürich in Switzerland and a MSc in Electrical and Computer Engineering from IST in Portugal. He is interested in using single-cell sequencing data to reconstruct cell lineages and trajectories in order to identify key processes involved in tumor progression. To this end, Pedro has developed computational tools to characterize the populations of cells that constitute a tumor. These include learning the evolutionary history of cancer cells and identifying the gene expression patterns of malignant and normal cells. Pedro enjoys collaborating with biologists, bioinformaticians and machine learning experts in order to design powerful computational methods able to describe the heterogeneous populations of cells that constitute tumors.
Main supervisor
Jens Lagergren, KTH
Co-supervisor
Joakim Lundeberg, KTH.
