Lund University

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Spatially-guided transcriptional profiling and bioinformatics

Principle Investigator Sara Ek

Are you interested in developing novel bioinformatic strategies to combine clinical data with spatially resolved omics data? This recent technology will enable a leap for advancing cancer therapeutics and improve outcome for patients, through identifying novel target molecules on tumor cells and infiltrating immune cells.


Improved understanding of the complex interplay between immune and tumor cells and the resulting molecular profiles of those cells is fundamental for further progress in developing and selecting immune-oncology drugs in a patient-specific manner. Technological breakthroughs within spatial omics have recently allowed researchers to pose detailed questions on cellular, molecular and spatial interplay, and the relation to patient outcome. In the proposed research area, we will use the newly established GeoMx™ digital imaging platform from Nanostring™ for cellular resolution, multiplexed in-situ quantification of up to 96 proteins  or 18000 RNA targets in formalin-fixed paraffin embedded (FFPE) tissue. FFPE is the main material routinely collected at hospitals and during clinical trials, and the possibility to use such material for high-resolution analysis opens novel possibilities to perform large collaborative, multicenter translational research projects that provide a detailed molecular characterization of the tumor.

More precise biomarkers for guiding treatment decision and predicting therapy outcome are highly warranted, as novel targeted cancer therapies are emerging. Within immuno-oncology, biomarker signatures should optimally include information on both the tumor and the composition of the tumor microenvironment to achieve high accuracy. The proposed project will include identification of spatially resolved tumor and immune integrated signatures, which will enable characterization of cellular crosstalk and regulatory networks as well as tentative novel targets within specific patient groups. In particular, the project will involve identifying complex patterns in spatially resolved high plex data modeled on clinical parameters.The work will be conducted in close liasion with clinicians, pathologist and the SpatialOmics@LU core facility at the Department of Immunotechnolgy. The specific focus of the position will be set in dialogue with the applicant based on previous knowledge and experience but will be in relation to already initiated projects focused on B and T-cell lymphomas, lung cancer or ovarian cancer. A creative mindset and deep interest in data mining and visualization is a must.


Key requirements: PhD in bioinformatics, immunology, cancer biology or similar; experience in bioinformatics including R and/or Python; experience in tissue-based image analysis

Advantageous skills: experience in omics-related technologies or handling large cancer-related data sets combining clinical and molecular data

Group website: Sara Ek

Partners: Clinical oncologists and pathologists at Skåne University Hospital and the Nordic lymphoma group.