Carolina Wahlby: "Exploring spatial (transcript)omics - from cell function to tissue architecture."

Carolina Wählby (Uppsala University)
Abstract: Optical microscopy combined with specific staining techniques has been crucial for much of the understanding we have today of both developmental processes, and disease, such as cancer. Via single cell transcriptomics, we have learnt that mRNA sequencing is an efficient way to identify different cell types and their function. By doing the sequencing directly in the tissue, via in situ sequencing, we can now map function to subcellular tissue architecture, and not only know which cells and functions are present, but also where, and in what context, they are present. This information can further be combined with detection of specific interactions between e.g., a drug and drug target. On top of this, we can apply learning-based methods describing tissue morphology. Visual assessment of the data becomes limiting as dataset size and complexity grows. At the same time, data is very rich and diverse, and one cannot under-estimate the value of incorporating human expert knowledge in the analysis. We, therefore, created TissUUmaps (tissuumaps.github.io/), a free and open-source on-line tool for interactive viewing, exploring, and sharing of data. I will present some of our data exploration tools, as well as some recent results.