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Rho, Y.

Publications and source records attributed to Rho, Y..

2 recordsLinked to original sources

Signal Associa: hot tumors elicit field-spanning NK cell coordination linked to their recruitment

Cells coordinate through coupled dynamics, yet whether observed correlations reflect genuine coupling is rarely tested. Signal Associa is an open-source framework uniting six coupling methods with automated stationarization and surrogate testing. Benchmarking against six ground truth systems reveals a trichotomy of coupling regimes, each with a different best method: correlation for coupling carried by shared trends and cycles, Granger causality for linear stochastic coupling, and convergent cross-mapping for nonlinear coupling; agreement across methods identifies the regime from data. In 13 movies of natural killer (NK) cells across three colorectal tumor microenvironments, NK cells formed field-spanning coupling networks at a conserved rate; at matched exposure to tumor signal, NK cells around hot tumors were more globally integrated, and hot tumors with a more integrated NK network tended to attract more NK cells. In focal adhesions, stiffness strengthened vinculin-FAK coupling, most at protruding edges. Surrogates cut lagged-correlation false positives from 23-92% to about 5%.

systems biology↗

Proteomic Sensors for Quantitative, Multiplexed and Spatial Monitoring of Kinase Signaling

Understanding kinase action requires precise quantitative measurements of their activity in vivo. In addition, the ability to capture spatial information of kinase activity is crucial to deconvolute complex signaling networks, interrogate multifaceted kinase actions, and assess drug effects or genetic perturbations. Here we developed a proteomic kinase activity sensor platform (ProKAS) for the analysis of kinase signaling using mass spectrometry. ProKAS is based on a tandem array of peptide sensors with amino acid barcodes that allow multiplexed analysis for spatial, kinetic, and screening applications. We engineered a ProKAS module to simultaneously monitor the activities of the DNA damage response kinases ATR, ATM, and CHK1 in response to genotoxic drugs, while also uncovering differences between these signaling responses in the nucleus, cytosol, and replication factories. Furthermore, we developed an in silico approach for the rational design of specific substrate peptides expandable to other kinases. Overall, ProKAS is a novel versatile system for systematically and spatially probing kinase action in cells.

molecular biology↗