Deciphering cell signaling networks with massively multiplexed biosensor barcoding

Abstract

Highlights d Large numbers of fluorescent biosensors can be concurrently tracked in barcoded cells d Biosensor activities are synchronized in mixed populations of barcoded cells d Deep learning models facilitate image analysis for biosensor barcoding d Simultaneous biosensor tracking reveals signaling network structures and interactions

Biomarkers of Cancer Stem Cells for Experimental Research and Clinical Application

“…The identification of cellular plasticity and biomarkers are useful approaches for the study of cancer stemness and new oncogenic pathway. Recently, Yang et al [ 107 ] developed a specific genetically encoded biosensor with 72 barcodes (or 128 biosensors) expressed in each cell. In combination with the use of fluorescence, it is now possible to precisely identify the nature of cellular plasticity and discover new cellular pathways, connections, and mechanisms.…”

Imaging and analysis for simultaneous tracking of fluorescent biosensors in barcoded cells

“…To address this limitation, we recently developed a method for massively multiplexed imaging of biosensors ( Yang et al., 2021 ). In this “biosensor barcoding” method, cells expressing different biosensors are separately labeled with barcodes composed of a pair of barcoding proteins, which are blue or red FPs targeted to different subcellular locations ( Figure 1 A).…”

“…First, cells in the same mixture and concurrently imaged show more synchronized responses to perturbations than if they are separately imaged, thus facilitating the kinetic comparison of different biosensors. Second, the ability to label different cell populations in the same mix allows for the delineation of cell-autonomous and non-autonomous effects ( Yang et al., 2021 ).…”

“…We describe the steps involved in cell barcoding, image acquisition, and analysis by deep learning models. For complete details on the use and execution of this protocol, please refer to Yang et al. (2021) .…”

“…For complete details on the use and execution of this protocol, please refer to Yang et al. (2021) .…”