Analys av lokala cellgenom i vävnad med hjälp av streckkodsmärkning

Tidsperiod: 2015-07-01 till 2017-10-01

Projektledare: Marco Mignardi

Finansiär: Vetenskapsrådet

Bidragstyp: Bidrag för anställning eller stipendier

Budget: 3 150 000 SEK

Next-generation sequencing (NGS) technologies are the methods of choice to study molecular heterogeneity at single-cell level. However, when it comes to tissue analysis these methods are limited in spatial resolution which is relevant information to describe many biological processes or in cancer diagnostics. My research activity will focus on the development of a method that enables spatially-resolved high-throughput genomics analysis of tissue sections with single-cell resolution. The method consists of a novel molecular barcoding approach to uniquely label and identify the cells composing a tissue. The cellular tagging can be achieved by several means and the barcodes are read by fluorescence imaging. The tissue section is then dissociated in single cells that are tested with single cell genomics techniques (high-throughput sequencing or multiplex qPCR) for gene expression or mutational analysis. By reading the molecular barcodes each cell can be identified and its molecular information can be located to the original position on the tissue.In principle this novel strategy will be compatible with most single-cell genomic techniques enabling analysis of different molecular features. Of immediate interest is the analysis of gene expression in heterogeneous tumor samples where this method will be able to precisely characterize the cellular components of a tumor tissue as well as the surrounding healthy tissue and their spatial relation. The clonal evolution of a tumor will be visualized instead by mutational analysis of the single tumor cells at genomic level. When new NGS technologies will further reduce the costs of single-cell sequencing, their combination with this method will enable the so called “digital pathology”, the representation of tissue morphological and molecular information at cellular and spatial resolution and its analysis in automated fashion.The completion of this project requires different areas of expertise. I gained knowledge of tissue molecular analysis and in situ techniques during my PhD in Professor Nilsson lab. I aim to transfer this knowledge to Professor Quake’s lab, a pioneer and worldwide leading laboratory in single-cell genomics and microfluidics. The goal is to expand single-cell genomic analysis to the dimension of tissue analysis for tumor biology and molecular diagnostics applications. Image analysis is a fundamental part of the method that I aim to develop and a crucial step to transform the molecular information into biological interpretation. The Wählby group focuses on the development of tools for the analysis of microscopy images and more particularly on analysis of data acquired from high throughput imaging systems. This represents a unique expertise in Sweden, and a necessary one to successfully complete the proposed research project.