{"id":12885,"date":"2018-03-22T12:26:22","date_gmt":"2018-03-22T11:26:22","guid":{"rendered":"https:\/\/news.embl.de\/?p=12885"},"modified":"2024-03-23T22:02:56","modified_gmt":"2024-03-23T21:02:56","slug":"gene-expression-cell-location","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/gene-expression-cell-location\/","title":{"rendered":"New method probes gene expression by cell location"},"content":{"rendered":"\n

Scientists at the European Bioinformatics Institute (EMBL-EBI)<\/a> and the Wellcome Sanger Institute<\/a> have developed a new computational method that improves the interpretation of data from the most recent single-cell technologies. SpatialDE is the first method to analyse gene expression variation while taking into account the cell\u2019s precise location in tissues. Published in Nature Methods<\/em><\/a>, the new approach will help scientists understand where and when genes are active or inactive within the same tissue. Having a clearer view of which genes are expressed most in a tissue has transformative potential for biomedical research.<\/p>\n\n\n\n

Cell geography matters<\/h2>\n\n\n\n

\u201cWe used to define cells by looking at them and observing what they do, but we did not know exactly where in a tissue each cell originated from. Now, sequencing and imaging technologies allow us to have a much closer look, and to study the properties of a tissue cell by cell,\u201d explains Oliver Stegle, Research Group Leader at EMBL-EBI<\/a>.<\/p>\n\n\n\n

Existing methods for analysing single-cell data cannot use this information, however, and do not take into account where it is located within a tissue \u2013 for example, the right or left side of the heart.<\/p>\n\n\n\n

\u201cSpatialDE lets us see which genes turn off and on in different parts of a tissue, by leveraging the location of cells in a tissue,\u201d adds Stegle. \u201cIt is a new computational approach that helps us understand how gene expression changes according to where a cell is, and who its neighbours are. This information lets us make sense of what\u2019s going on in different parts of a tissue.\u201d<\/p>\n\n\n\n

\u201cOur method is a first step to bring information from time and space to the analysis of gene expression. SpatialDE can be applied to a wide range of single-cell technologies and is also fast, which means that researchers can use it to interpret their data on their laptop,\u201d adds Valentine Svensson, PhD student at Sanger and EMBL-EBI who lead the work. \u201cUsing SpatialDE, researchers can start to investigate how genes are used to define the components of tissues.\u201d<\/p>\n\n\n\n

What this means for biomedical research<\/h2>\n\n\n\n

SpatialDE can address fundamental questions such as:<\/p>\n\n\n\n