Algorithm maps gene expression within tissues

A new algorithm can map three-dimensional patterns of gene expression.

Scientists in Switzerland, have developed a new technique that can reveal the spatial pattern of gene expression inside the body without the need for imaging equipment. Named 'Tomographer', it may enable better understanding of how gene expression patterns vary across different cell types and locations within organs and tissues.

'The Tomographer algorithm opens a promising and robust path to "spatialise" different genomics measurement techniques,' said Dr Gioele La Manno from the Brain Mind Institute at the École Polytechnique Fédérale de Lausanne, Switzerland.

Existing approaches to mapping gene expression (such as fluorescence in situ hybridisation) involve attaching fluorescent tags to a target gene, which 'light up' when the gene is active and can be detected by a specialist microscope. However, this limits the number of genes that can be visualised at once.

With Tomographer, tissue samples are cut into strips at different angles and the messenger RNA (mRNA) from each strip is extracted and sequenced – so the whole transcriptome can be read at once. mRNA is produced when a gene is being expressed, so this information, paired with the known pattern of how the strips were cut is used by the Tomographer algorithm to reconstruct spatial gene expression patterns across the tissue.

The new approach may have lower resolution compared to microscopy-based methods, but the authors hope it can capture broader, tissue-level patterns of expression.

To demonstrate their technique, the team used the algorithm to spatially map the molecular anatomy of the brain of the Australian bearded dragon, which is not commonly used in research.

'So far, we have focused on applications in neurodevelopmental biology, but in the future, we can certainly imagine molecular tomography becoming a constituent in personalised medicine' said co-lead author Christian Schneider.

The study is published in Nature Biotechnology.