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The Department of Biomedicine

CCBIO seminar: Inge Jonassen

Towards characterizing tumour microenvironments – experimental and computational approaches

Inge Jonassen
Centre for Cancer Biomarkers (CCBIO) and Computational Biology Unit, Department of Informatics, University of Bergen

The development of a tumour and how it responds to treatment depends on its microenvironment. The environment can be assessed for example by mapping out which cell types are present. When genomic measurements are taken from a complex sample, including both tumour and other cells from its environment, the resulting data reflect both the tumour cells and the other cell types present in the sample. Computational approaches exist to break down such data into components corresponding to the different cell types present; some of these are aimed at subtracting data resulting from non-tumour cells. Such approaches can be applied to for example expression data. Many methods require pre-defined expression profiles for each cell type suspected to be present in the samples. An alternative approach is to perform measurements on individual cells, for example through sequencing their transcriptomes. Single-cell expression profiling can provide information about different cell types present in a sample, and also their regulatory state and how much the expression of individual genes differs from cell to cell. Of relevance is also single cell genomic sequencing that can reveal information about tumour clonality and evolution. In this presentation I will review some recent methods for both single cell sequencing and for computational de-convolution of complex expression profiles, and briefly discuss methods aimed at understanding tumour evolution. The aim of the seminar is to present some recent experimental and computational approaches towards understanding tumours and their environments, that may be of relevance for the Centre for Cancer Biomarkers.

Chairperson: Lars A. Akslen <lars.akslen@k1.uib.no>, CCBIO