Although patient-derived tumor organoids are widely applied for evaluating anti-tumor drugs, the lack of a physiologically relevant environment limits drug assessment. Intestinal absorption and liver metabolism are critical for drug efficacy but cannot be recapitulated in single-organoid models. Here, we establish an intestine-liver-tumor multi-organoid system to simulate in vivo absorption and metabolism, which allows for more physiologically relevant evaluations of drug efficacy and toxicity. Under fluidic conditions, the system maintains the viability of intestinal cells and liver organoids, which exhibit superior cellular diversity and close transcriptional resemblance to native tissues, with enhanced differentiation and metabolism. The system reveals the decreased effectiveness of the liver-deactivated drugs docetaxel and 5-FU, and the increased efficacy of the liver-activated drugs capecitabine and ifosfamide, on tumor organoids, which cannot be revealed by tumor organoid models alone. With gravity-driven flow and multi-organ interactions, this system recapitulates drug absorption and metabolism, thus providing a platform for accurate evaluations of metabolism-dependent drugs and advancing precision medicine.
Protein/RNA condensates participate in many cellular processes, but their functional roles often remain unclear. We recently found that condensates of the RNA-binding protein ATXN2 oscillate with the circadian cycle, recruit translation machinery and circadian mRNAs such as Per2, and promote translation. Using mathematical modeling, we show that dynamic condensate assembly enhances the robustness and phase coherence of oscillations in a transcription-translation feedback loop (TTFL). This effect cannot be reproduced by simply increasing repressive-protein translation through static condensates. Condensates that oscillate with the core TTFL at an appropriate phase shift can increase protein translation without depleting the corresponding mRNA. Two circuit designs can generate this timing: TTFL-regulated condensate transcription or a hybrid architecture in which an intrinsically oscillatory condensate loop is coupled to the core loop. Knockdown of Per2, Bmal1, and Clock showed residual 24-h ATXN2 condensate oscillations, supporting the hybrid model.A record of this paper’s transparent peer review process is included in the supplemental information.
Many molecular signals are known to be organized in subcellular regions termed microdomains. One example entails Rho GTPases, which control a range of cell behaviors through their functional patterning in spatiotemporal units. While fluorescent biosensors have allowed precise measurement of Rho GTPase activity in living cells, computational tools to delineate and track signaling microdomains in time-lapse image sequences of such biosensors do not exist. Here, we introduce a method that centers on the notion of activation time series coordination to identify signaling microdomains in space and time. After validating the algorithm with simulated microdomains, we show that our method identifies domains that support current hypotheses on the signaling architecture governing Rho GTPase organization and also respond to perturbation with optogenetics. A record of this paper's transparent peer review process is included in the supplemental information.
