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Communications Biology

Communications Biology

IF: 5.2
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PC3T: a signature-driven predictor of chemical compounds for cellular transition

Published:27 September 2023 DOI: 10.1038/s42003-023-05225-y PMID: 37758874
Lu Han, Bin Song, Peilin Zhang, Zhi Zhong, Yongxiang Zhang, Xiaochen Bo, Hongyang Wang, Yong Zhang, Xiuliang Cui, Wenxia Zhou

Abstract

Cellular transitions hold great promise in translational medicine research. However, therapeutic applications are limited by the low efficiency and safety concerns of using transcription factors. Small molecules provide a temporal and highly tunable approach to overcome these issues. Here, we present PC3T, a computational framework to enrich molecules that induce desired cellular transitions, and PC3T was able to consistently enrich small molecules that had been experimentally validated in both bulk and single-cell datasets. We then predicted small molecule reprogramming of fibroblasts into hepatic progenitor-like cells (HPLCs). The converted cells exhibited epithelial cell-like morphology and HPLC-like gene expression pattern. Hepatic functions were also observed, such as glycogen storage and lipid accumulation. Finally, we collected and manually curated a cell state transition resource containing 224 time-course gene expression datasets and 153 cell types. Our framework, together with the data resource, is freely available at http://pc3t.idrug.net.cn/ . We believe that PC3T is a powerful tool to promote chemical-induced cell state transitions. PC3T is an in silico chemical screening pipeline to identify small-molecule treatments that induce cell state transitions for any given initial and terminal state or any intermediate state in the cell transition trajectory.

Substances (34)

Materials
Procduct Name CAS Molecular Formula Supplier Price
2-Propylpentanoic acid 99-66-1 C8H16O2 630 suppliers $5.00-$2153.25
2-Propylpentanoic acid 99-66-1 C8H16O2 630 suppliers $5.00-$2153.25
2-Propylpentanoic acid 99-66-1 C8H16O2 630 suppliers $5.00-$2153.25
2-Propylpentanoic acid 99-66-1 C8H16O2 630 suppliers $5.00-$2153.25
Forskolin 66575-29-9 C22H34O7 538 suppliers $12.00-$3200.00
Forskolin 66575-29-9 C22H34O7 538 suppliers $12.00-$3200.00
Forskolin 66575-29-9 C22H34O7 538 suppliers $12.00-$3200.00
Forskolin 66575-29-9 C22H34O7 538 suppliers $12.00-$3200.00
CHIR-99021 252917-06-9 C22H18Cl2N8 343 suppliers $28.00-$4401.00
CHIR-99021 252917-06-9 C22H18Cl2N8 343 suppliers $28.00-$4401.00

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