@article{d32a734f2a824f7199807f6842cddd11,
title = "Deciphering cell signaling networks with massively multiplexed biosensor barcoding",
abstract = "Genetically encoded fluorescent biosensors are powerful tools for monitoring biochemical activities in live cells, but their multiplexing capacity is limited by the available spectral space. We overcome this problem by developing a set of barcoding proteins that can generate over 100 barcodes and are spectrally separable from commonly used biosensors. Mixtures of barcoded cells expressing different biosensors are simultaneously imaged and analyzed by deep learning models to achieve massively multiplexed tracking of signaling events. Importantly, different biosensors in cell mixtures show highly coordinated activities, thus facilitating the delineation of their temporal relationship. Simultaneous tracking of multiple biosensors in the receptor tyrosine kinase signaling network reveals distinct mechanisms of effector adaptation, cell autonomous and non-autonomous effects of KRAS mutations, as well as complex interactions in the network. Biosensor barcoding presents a scalable method to expand multiplexing capabilities for deciphering the complexity of signaling networks and their interactions between cells.",
keywords = "KRAS, adaptation, barcode, cell non-autonomous effect, fluorescent biosensor, live cell imaging, machine learning, multiplexing, receptor tyrosine kinase, signaling network",
author = "Yang, {Jr Ming} and Chi, {Wei Yu} and Jessica Liang and Saki Takayanagi and Iglesias, {Pablo A.} and Huang, {Chuan Hsiang}",
note = "Funding Information: We would like to thank Hoku West-Foyle and Takanari Inoue for helpful discussions, as well as Michiyuki Matsuda for plasmids of PicchuEV, Prin-BRAF, Prin-CRAF, EV-RSK, EV-ROCK, and EV-S6K. Zeiss LSM 780 and 880 confocal microscopes were purchased with NIH grants S10OD016374 and S10OD023548, respectively. This work was supported by NIH (K22CA212060 and R01GM136711 to C.-H.H.), Cervical Cancer SPORE P50CA098252 (Career Development Award to J.-M.Y. Pilot Project Award to C.-H.H.), the W.W. Smith Charitable Trust (C1901 to C.-H.H.), and the Sol Goldman Pancreatic Cancer Research Center (to C.-H.H.). J.-M.Y. and C.-H.H. conceived the project and designed the experiments. J.-M.Y. W.-Y.C. and S.T. conducted the experiments. J.-M.Y. W.-Y.C. J.L. and C.-H.H. analyzed the data. W.-Y.C. developed deep learning models. P.A.I. carried out computational model fitting and simulations. J.-M.Y. and C.-H.H. wrote the manuscript with inputs from W.-Y.C. J.L. S.T. and P.A.I. C.-H.H. and J.-M.Y. supervised the study. The authors declare no competing interests. Funding Information: We would like to thank Hoku West-Foyle and Takanari Inoue for helpful discussions, as well as Michiyuki Matsuda for plasmids of PicchuEV, Prin-BRAF, Prin-CRAF, EV-RSK, EV-ROCK, and EV-S6K. Zeiss LSM 780 and 880 confocal microscopes were purchased with NIH grants S10OD016374 and S10OD023548 , respectively. This work was supported by NIH ( K22CA212060 and R01GM136711 to C.-H.H.), Cervical Cancer SPORE P50CA098252 (Career Development Award to J.-M.Y., Pilot Project Award to C.-H.H.), the W.W. Smith Charitable Trust ( C1901 to C.-H.H.), and the Sol Goldman Pancreatic Cancer Research Center (to C.-H.H.). Publisher Copyright: {\textcopyright} 2021 The Author(s)",
year = "2021",
month = dec,
day = "9",
doi = "10.1016/j.cell.2021.11.005",
language = "English (US)",
volume = "184",
pages = "6193--6206.e14",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "25",
}