Transcriptomic differences between human 8-cell-like cells reprogrammed with different methods

Elsevier BV - Tập 18 - Trang 1621-1628 - 2023
Masahito Yoshihara1,2,3, Juha Kere1,4,5
1Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
2Institute for Advanced Academic Research, Chiba University, Chiba, Japan
3Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
4Folkhälsan Research Center, Helsinki, Finland
5Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland

Tài liệu tham khảo

Aran, 2019, Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage, Nat. Immunol., 20, 163, 10.1038/s41590-018-0276-y Bosnakovski, 2008, An isogenetic myoblast expression screen identifies DUX4-mediated FSHD-associated molecular pathologies, EMBO J., 27, 2766, 10.1038/emboj.2008.201 Dobin, 2013, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, 29, 15, 10.1093/bioinformatics/bts635 Genet, 2020, The molecular and cellular features of 2-cell-like cells: a reference guide, Development, 147, 10.1242/dev.189688 Guo, 2021, Human naive epiblast cells possess unrestricted lineage potential, Cell Stem Cell, 28, 1040, 10.1016/j.stem.2021.02.025 Guo, 2017, Epigenetic resetting of human pluripotency, Development, 144, 2748, 10.1242/dev.146811 Haghverdi, 2018, Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors, Nat. Biotechnol., 36, 421, 10.1038/nbt.4091 Hendrickson, 2017, Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons, Nat. Genet., 49, 925, 10.1038/ng.3844 Kagawa, 2022, Human blastoids model blastocyst development and implantation, Nature, 601, 600, 10.1038/s41586-021-04267-8 Li, 2011, RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome, BMC Bioinf., 12, 323, 10.1186/1471-2105-12-323 Liu, 2020, Reprogramming roadmap reveals route to human induced trophoblast stem cells, Nature, 586, 101, 10.1038/s41586-020-2734-6 Macfarlan, 2012, Embryonic stem cell potency fluctuates with endogenous retrovirus activity, Nature, 487, 57, 10.1038/nature11244 Mazid, 2022, Rolling back human pluripotent stem cells to an eight-cell embryo-like stage, Nature, 605, 315, 10.1038/s41586-022-04625-0 Messmer, 2019, Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution, Cell Rep., 26, 815, 10.1016/j.celrep.2018.12.099 Moya-Jódar, 2023, Revealing cell populations catching the early stages of human embryo development in naive pluripotent stem cell cultures, Stem Cell Rep., 18, 64, 10.1016/j.stemcr.2022.11.015 Ouyang, 2021, ShinyCell: simple and sharable visualization of single-cell gene expression data, Bioinformatics, 37, 3374, 10.1093/bioinformatics/btab209 Petropoulos, 2016, Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos, Cell, 165, 1012, 10.1016/j.cell.2016.03.023 Rodriguez-Terrones, 2018, A molecular roadmap for the emergence of early-embryonic-like cells in culture, Nat. Genet., 50, 106, 10.1038/s41588-017-0016-5 Stirparo, 2018, Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human pre-implantation epiblast, Development, 145, 10.1242/dev.169672 Taubenschmid-Stowers, 2022, 8C-like cells capture the human zygotic genome activation program in vitro, Cell Stem Cell, 29, 449, 10.1016/j.stem.2022.01.014 Theunissen, 2014, Systematic identification of culture conditions for induction and maintenance of naive human pluripotency, Cell Stem Cell, 15, 524, 10.1016/j.stem.2014.09.003 Töhönen, 2015, Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development, Nat. Commun., 6, 8207, 10.1038/ncomms9207 Vuoristo, 2022, DUX4 is a multifunctional factor priming human embryonic genome activation, iScience, 25, 10.1016/j.isci.2022.104137 Yan, 2013, Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells, Nat. Struct. Mol. Biol., 20, 1131, 10.1038/nsmb.2660 Yanagida, 2021, Naive stem cell blastocyst model captures human embryo lineage segregation, Cell Stem Cell, 28, 1016, 10.1016/j.stem.2021.04.031 Yoshihara, 2022, Transient DUX4 expression in human embryonic stem cells induces blastomere-like expression program that is marked by SLC34A2, Stem Cell Rep., 17, 1743, 10.1016/j.stemcr.2022.06.002 Yu, 2021, Blastocyst-like structures generated from human pluripotent stem cells, Nature, 591, 620, 10.1038/s41586-021-03356-y Yu, 2022, Recapitulating early human development with 8C-like cells, Cell Rep., 39, 10.1016/j.celrep.2022.110994 Zhao, 2021, Reprogrammed blastoids contain amnion-like cells but not trophectoderm, bioRxiv