(663b) Increasing the Dimensionality of Single Cell Transcriptomics: Proteins, Imaging, and More

Systems biology is concerned with the complex interactions within and between cells that animate biology and create organisms that are more than the sum of their parts. This is currently exemplified in the field of single cell transcriptomics, where thousands of cells are analyzed with thousands of degrees of freedom, revealing novel cell types and interactions in heterogeneous tissues and diseases like cancer. One caveat however, is that single cell transcriptomics addresses a single class of molecules, poly-A-tailed mRNA, while systems biology has proven that proteins, lipids, metabolites, and more all play important roles. Here we demonstrate new methods to extend the functionality and dimensionality of single cell transcriptomics methods to address the concurrent biology of single cells beyond transcriptomics. This addresses the critical question of how different classes of molecules interact in single cells, and how this multi-modal heterogeneity manifests in biology. Current methods of multi-modal single cell analysis require interconversions of measurements, resulting in inevitable signal losses. Here we show that a microfluidic chip can integrate proteomic and transcriptomic measurements by embedding location information within transcriptomic measurements. The transcriptome is sequenced, while proteins are measured by fluorescent immunoassays. This is done with a location encoding strategy and microfluidic flow patterning, linking single cell transcriptomics captured by Dropseq-style bead based methods to single cell protein measurements made using DNA-Encoded Antibody Libraries. With this method, we measure full transcriptomes as well as proteins localized to the cytosol, mitochondria, and nucleus within the same single cells. We then show how this generalized strategy can be extended to augment single cell transcriptomics with completely orthogonal measurements, such as fluorescent measurements of glucose uptake and imaging analyses, to extend the reach of multi-modal single cell measurements in new directions.