Dynamic network biomarker factors orchestrate cell-fate determination at tipping points during hESC differentiation

The Innovation - Tập 4 - Trang 100364 - 2023
Lin Li1, Yilin Xu1, Lili Yan1, Xiao Li1, Fei Li1, Zhuang Liu1, Chuanchao Zhang2, Yuan Lou3, Dong Gao1, Xin Cheng1, Luonan Chen1,2,4
1Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
2Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
3School of Mathematical Sciences, CMA-Shanghai and MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
4West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China

Tài liệu tham khảo

Lewis, 2006, Definitive endoderm of the mouse embryo: formation, cell fates, and morphogenetic function, Dev. Dyn., 235, 2315, 10.1002/dvdy.20846 Wang, 2016, Signaling control of differentiation of embryonic stem cells toward mesendoderm, J. Mol. Biol., 428, 1409, 10.1016/j.jmb.2015.06.013 Sumi, 2008, Defining early lineage specification of human embryonic stem cells by the orchestrated balance of canonical Wnt/beta-catenin, Activin/Nodal and BMP signaling, Development, 135, 2969, 10.1242/dev.021121 Chen, 2012, Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers, Sci. Rep., 2, 342, 10.1038/srep00342 Yang, 2018, Dynamic network biomarker indicates pulmonary metastasis at the tipping point of hepatocellular carcinoma, Nat. Commun., 9, 678, 10.1038/s41467-018-03024-2 Cliff, 2017, MYC controls human pluripotent stem cell fate decisions through regulation of metabolic flux, Cell Stem Cell, 21, 502, 10.1016/j.stem.2017.08.018 Loh, 2014, Efficient endoderm induction from human pluripotent stem cells by logically directing signals controlling lineage bifurcations, Cell Stem Cell, 14, 237, 10.1016/j.stem.2013.12.007 Tosic, 2019, Eomes and Brachyury control pluripotency exit and germ-layer segregation by changing the chromatin state, Nat. Cell Biol., 21, 1518, 10.1038/s41556-019-0423-1 Wang, 2017, The p53 family coordinates Wnt and Nodal inputs in mesendodermal differentiation of embryonic stem cells, Cell Stem Cell, 20, 70, 10.1016/j.stem.2016.10.002 Zhang, 2016, MycN is critical for the maintenance of human rmbryonic stem cell-derived neural crest stem cells, PLoS One, 11, e0148062, 10.1371/journal.pone.0148062 Knoepfler, 2002, N-myc is essential during neurogenesis for the rapid expansion of progenitor cell populations and the inhibition of neuronal differentiation, Genes Dev., 16, 2699, 10.1101/gad.1021202 Varlakhanova, 2010, Myc maintains embryonic stem cell pluripotency and self-renewal, Differntiation, 80, 9, 10.1016/j.diff.2010.05.001 Nelson, 2014, Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression, BMC Biol., 12, 81, 10.1186/s12915-014-0081-5 D'Amour, 2005, Efficient differentiation of human embryonic stem cells to definitive endoderm, Nat. Biotechnol., 23, 1534, 10.1038/nbt1163 Zorn, 2009, Vertebrate endoderm development and organ formation, Annu. Rev. Cell Dev. Biol., 25, 221, 10.1146/annurev.cellbio.042308.113344 Richard, 2016, Single-cell-based analysis highlights a surge in cell-to-cell molecular variability preceding irreversible commitment in a differentiation process, PLoS Biol., 14, e1002585, 10.1371/journal.pbio.1002585 Liu, 2015, Identifying early-warning signals of critical transitions with strong noise by dynamical network markers, Sci. Rep., 5, 17501, 10.1038/srep17501 Grün, 2015, Single-cell messenger RNA sequencing reveals rare intestinal cell types, Nature, 525, 251, 10.1038/nature14966 Jaitin, 2014, Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types, Science, 343, 776, 10.1126/science.1247651 Wen, 2022, Single-cell technologies: from research to application, Innovation, 3, 100342 Dai, 2019, Cell-specific network constructed by single-cell RNA sequencing data, Nucleic Acids Res., 47, e62, 10.1093/nar/gkz172 Li, 2021, c-CSN: single-cell RNA sequencing data analysis by conditional cell-specific network, Genom. Proteom. Bioinform., 19, 319, 10.1016/j.gpb.2020.05.005 Chu, 2016, Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm, Genome Biol., 17, 173, 10.1186/s13059-016-1033-x Leng, 2016, SCPattern: a statistical approach to identify and classify expression changes in single cell RNA-seq experiments with ordered conditions, bioRxiv Fong, 2013, Skeletal muscle programming and re-programming, Curr. Opin. Genet. Dev., 23, 568, 10.1016/j.gde.2013.05.002 Takahashi, 2016, A decade of transcription factor-mediated reprogramming to pluripotency, Nat. Rev. Mol. Cell Biol., 17, 183, 10.1038/nrm.2016.8 Lambert, 2018, The human transcription factors, Cell, 172, 650, 10.1016/j.cell.2018.01.029 Scognamiglio, 2016, Myc depletion induces a pluripotent dormant state mimicking diapause, Cell, 164, 668, 10.1016/j.cell.2015.12.033 Smith, 2010, Myc represses primitive endoderm differentiation in pluripotent stem cells, Cell Stem Cell, 7, 343, 10.1016/j.stem.2010.06.023 Shi, 2018, Quantifying Waddington's epigenetic landscape: a comparison of single-cell potency measures, Brief. Bioinform., 21, 248 Yu, 2015, ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization, Bioinformatics, 31, 2382, 10.1093/bioinformatics/btv145 Liu, 2019, Hunt for the tipping point during endocrine resistance process in breast cancer by dynamic network biomarkers, J. Mol. Cell Biol., 11, 649, 10.1093/jmcb/mjy059