Single Cell Fluorescent Labelling in 3-Dimensional Environments

Abstract

The ability to conduct image-based, non-invasive cell tagging is key to cell biology applications. This allows studying cells without prior knowledge of cell surface chemistry or genetic manipulation. We previously introduced Cell Labeling via Photobleaching (CLaP) (Binan L. et al., Nat Comm, 11636, May 2016) a method that enables instant, specific tagging of individual cells based on a wide array of visible criteria such as shape, behavior or positional information. CLaP uses laser illumination to crosslink biotin onto the plasma membrane. Streptavidin conjugates are then used to label individual cells for sequencing, cell-tracking, flow cytometry or ultra-microscopy applications. We have shown that the mark incorporated on the cell membrane is stable, resistant to usual cell culture protocols, non-toxic, retained for several days, and transferred by cell division but not to adjacent cells in culture and can be used in combination with microfluidics-based single-cell capture followed by transcriptome-wide next-generation sequencing. Here we report the next step of CLaP to 3-dimensional environments for ex vivo and in vivo studies. Changing continuous laser illumination for ultrashort laser pulses as a way to spatially confine photobleaching by two-photon absorption, we are able to tag single cells in their natural environment. Cells are cultured in collagen hydrogels, labeled using CLaP and recovered after tissue digestion, as a step toward in vivo tagging of individual cells.