The chemical reprogramming of unipotent adult germ cells towards authentic pluripotency and de novo establishment of imprinting
Yuhan Chen, Jiansen Lu, Yanwen Xu, Yaping Huang, Dazhuang Wang, Peiling Liang, Shaofang Ren, Xuesong Hu, Yewen Qin, Wei Ke, Ralf Jauch, Andrew Paul Hutchins, Mei Wang, Fuchou Tang, Xiao-Yang Zhao
The chemical reprogramming of unipotent adult germ cells towards authentic pluripotency and de novo establishment of imprinting
Although somatic cells can be reprogrammed to pluripotent stem cells (PSCs) with pure chemicals, authentic pluripotency of chemically induced pluripotent stem cells (CiPSCs) has never been achieved through tetraploid complementation assay. Spontaneous reprogramming of spermatogonial stem cells (SSCs) was another non-transgenic way to obtain PSCs, but this process lacks mechanistic explanation. Here, we reconstructed the trajectory of mouse SSC reprogramming and developed a five-chemical combination, boosting the reprogramming efficiency by nearly 80- to 100-folds. More importantly, chemical induced germline-derived PSCs (5C-gPSCs), but not gPSCs and chemical induced pluripotent stem cells, had authentic pluripotency, as determined by tetraploid complementation. Mechanistically, SSCs traversed through an inverted pathway of in vivo germ cell development, exhibiting the expression signatures and DNA methylation dynamics from spermatogonia to primordial germ cells and further to epiblasts. Besides, SSC-specific imprinting control regions switched from biallelic methylated states to monoallelic methylated states by imprinting demethylation and then re-methylation on one of the two alleles in 5C-gPSCs, which was apparently distinct with the imprinting reprogramming in vivo as DNA methylation simultaneously occurred on both alleles. Our work sheds light on the unique regulatory network underpinning SSC reprogramming, providing insights to understand generic mechanisms for cell-fate decision and epigenetic-related disorders in regenerative medicine.
reprogramming / spermatogonial stem cell / tetraploid complementation / imprinting
[1] |
Aibar S, Gonzalez-Blas CB, Moerman T et al. SCENIC: single-cell regulatory network inference and clustering. Nat Methods 2017;14:1083–+.
CrossRef
Google scholar
|
[2] |
Alquicira-Hernandez J, Sathe A, Ji HP et al. scPred: accurate super-vised method for cell-type classification from single-cell RNA-seq data. Genome Biol 2019;20:264.
CrossRef
Google scholar
|
[3] |
An J, Zheng Y, Dann CT. Mesenchymal to epithelial transition mediated by CDH1 promotes spontaneous reprogramming of male germline stem cells to pluripotency. Stem Cell Rep 2017;8:446–459.
CrossRef
Google scholar
|
[4] |
Bian S, Hou Y, Zhou X et al. Single-cell multiomics sequencing and analyses of human colorectal cancer. Science 2018;362:1060–1063.
CrossRef
Google scholar
|
[5] |
Butler A, Hoffman P, Smibert P et al. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol 2018;36:411–+.
CrossRef
Google scholar
|
[6] |
Byrne JA, Pedersen DA, Clepper LL et al. Producing primate embryonic stem cells by somatic cell nuclear transfer. Nature 2007;450:497–502.
CrossRef
Google scholar
|
[7] |
Cao S, Yu S, Li D et al. Chromatin accessibility dynamics during chemical induction of pluripotency. Cell Stem Cell 2018;22:529–542.e525.
CrossRef
Google scholar
|
[8] |
Choi J, Huebner AJ, Clement K et al. Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells. Nature 2017;548:219–223.
CrossRef
Google scholar
|
[9] |
Costoya JA, Hobbs RM, Barna M et al. Essential role of Plzf in maintenance of spermatogonial stem cells. Nat Genet 2004;36:653–659.
CrossRef
Google scholar
|
[10] |
Dobin A, Davis CA, Schlesinger F et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013;29:15–21.
CrossRef
Google scholar
|
[11] |
Dong J, Hu Y, Fan X et al. Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis. Genome Biol 2018;19:31.
CrossRef
Google scholar
|
[12] |
Gu C, Liu S, Wu Q et al. Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes. Cell Res 2019;29:110–123.
CrossRef
Google scholar
|
[13] |
Guan K, Nayernia K, Maier LS et al. Pluripotency of spermatogonial stem cells from adult mouse testis. Nature 2006;440:1199–1203.
CrossRef
Google scholar
|
[14] |
Gurdon JB, Byrne JA. Classic Perspective: The first half-century of nuclear transplantation. Proc Natl Acad Sci USA 2003;100:8048–8052.
CrossRef
Google scholar
|
[15] |
Hou P, Li Y, Zhang X et al. Pluripotent stem cells induced from mouse somatic cells by small-molecule compounds. Science 2013;341:651–654.
CrossRef
Google scholar
|
[16] |
Jeong HS, Bhin J, Joon Kim H et al. Transcriptional regulatory net-works underlying the reprogramming of spermatogonial stem cells to multipotent stem cells. Exp Mol Med 2017;49:e315.
CrossRef
Google scholar
|
[17] |
Kanatsu-Shinohara M, Inoue K, Lee J et al. Generation of pluripotent stem cells from neonatal mouse testis. Cell 2004;119:1001–1012.
CrossRef
Google scholar
|
[18] |
Kanatsu-Shinohara M, Ogonuki N, Inoue K et al. Long-term proliferation in culture and germline transmission of mouse male germline stem cells. Biol Reprod 2003;69:612–616.
CrossRef
Google scholar
|
[19] |
Kanatsu-Shinohara M, Tanaka T, Ogonuki N et al. Myc/Mycn-mediated glycolysis enhances mouse spermatogonial stem cell self-renewal. Genes Dev 2016;30:2637–2648.
CrossRef
Google scholar
|
[20] |
Kiselev VY, Yiu A, Hemberg M. scmap: projection of single-cell RNA-seq data across data sets. Nat Methods 2018;15:359–362.
CrossRef
Google scholar
|
[21] |
Ko K, Tapia N, Wu G et al. Induction of pluripotency in adult unipotent germline stem cells. Cell stem cell 2009;5:87–96.
CrossRef
Google scholar
|
[22] |
Konermann S, Lotfy P, Brideau NJ et al. Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors. Cell 2018;173:665–+.
CrossRef
Google scholar
|
[23] |
Korsunsky I, Millard N, Fan J et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat Methods 2019;16:1289–1296.
CrossRef
Google scholar
|
[24] |
Krueger F, Andrews SR. SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes. F1000Res 2016;5:1479.
CrossRef
Google scholar
|
[25] |
La Manno G, Soldatov R, Zeisel A et al. RNA velocity of single cells. Nature 2018;560:494–+.
CrossRef
Google scholar
|
[26] |
Li R, Liang J, Ni S et al. A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts. Cell Stem Cell 2010;7:51–63.
CrossRef
Google scholar
|
[27] |
Li TD, Feng GH, Li YF et al. Rat embryonic stem cells produce fertile offspring through tetraploid complementation. Proc Natl Acad Sci USA 2017;114:11974–11979.
CrossRef
Google scholar
|
[28] |
Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 2014;30:923–930.
CrossRef
Google scholar
|
[29] |
Liu L, Luo GZ, Yang W et al. Activation of the imprinted Dlk1-Dio3 region correlates with pluripotency levels of mouse stem cells. J Biol Chem 2010;285:19483–19490.
CrossRef
Google scholar
|
[30] |
Ly CH, Lynch GS, Ryall JG. A metabolic roadmap for somatic stem cell fate. Cell Metab 2020;31:1052–1067.
CrossRef
Google scholar
|
[31] |
Matoba S, Wang H, Jiang L et al. Loss of H3K27me3 imprinting in somatic cell nuclear transfer embryos disrupts post-implantation development. Cell stem cell 2018;23:343–354.e345.
CrossRef
Google scholar
|
[32] |
Moore L, Cagan A, Coorens THH et al. The mutational landscape of human somatic and germline cells. Nature 2021;597:381–386.
CrossRef
Google scholar
|
[33] |
Neri F, Krepelova A, Incarnato D et al. Dnmt3L antagonizes DNA methylation at bivalent promoters and favors DNA methylation at gene bodies in ESCs. Cell 2013;155:121–134.
CrossRef
Google scholar
|
[34] |
Reik W, Dean W, Walter J. Epigenetic reprogramming in mammalian development. Science 2001;293:1089–1093.
CrossRef
Google scholar
|
[35] |
Romanienko PJ, Camerini-Otero RD. The mouse Spo11 gene is required for meiotic chromosome synapsis. Mol Cell 2000;6:975–987.
CrossRef
Google scholar
|
[36] |
Samavarchi-Tehrani P, Golipour A, David L et al. Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming. Cell stem cell 2010;7:64–77.
CrossRef
Google scholar
|
[37] |
Schiebinger G, Shu J, Tabaka M et al. Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming. Cell 2019;176:928–943.e922.
CrossRef
Google scholar
|
[38] |
Schmeier S, Alam T, Essack M et al. TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions. Nucleic Acids Res 2017;45:D145–D150.
CrossRef
Google scholar
|
[39] |
Schrans-Stassen BH, Saunders PT, Cooke HJ et al. Nature of the sper-matogenic arrest in Dazl -/- mice. Biol Reprod 2001;65:771–776.
CrossRef
Google scholar
|
[40] |
Seisenberger S, Andrews S, Krueger F et al. The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol Cell 2012;48:849–862.
CrossRef
Google scholar
|
[41] |
Shannon P, Markiel A, Ozier O et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003;13:2498–2504.
CrossRef
Google scholar
|
[42] |
Smallwood SA, Lee HJ, Angermueller C et al. Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nat Methods 2014;11:817–820.
CrossRef
Google scholar
|
[43] |
Smith T, Heger A, Sudbery I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome Res 2017;27:491–499.
CrossRef
Google scholar
|
[44] |
Stadtfeld M, Apostolou E, Akutsu H et al. Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells. Nature 2010;465:175–181.
CrossRef
Google scholar
|
[45] |
Stuart T, Butler A, Hoffman P et al. Comprehensive integration of single-cell data. Cell 2019;177:1888–1902.e1821.
CrossRef
Google scholar
|
[46] |
Szabó PE, Hübner K, Schöler H et al. Allele-specific expression of imprinted genes in mouse migratory primordial germ cells. Mech Dev 2002;115:157–160.
CrossRef
Google scholar
|
[47] |
Takahashi K, Tanabe K, Ohnuki M et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 2007;131:861–872.
CrossRef
Google scholar
|
[48] |
Takahashi K, Tanabe K, Ohnuki M et al. Induction of pluripotency in human somatic cells via a transient state resembling primitive streak- like mesendoderm. Nat Commun 2014;5:3678.
CrossRef
Google scholar
|
[49] |
Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 2006;126:663–676.
CrossRef
Google scholar
|
[50] |
Takashima S, Hirose M, Ogonuki N et al. Regulation of pluripotency in male germline stem cells by Dmrt1. Genes Dev 2013;27:1949–1958.
CrossRef
Google scholar
|
[51] |
Takikawa S, Ray C, Wang X et al. Genomic imprinting is variably lost during reprogramming of mouse iPS cells. Stem Cell Res 2013;11:861–873.
CrossRef
Google scholar
|
[52] |
Tarazona OA, Pourquie O. Exploring the influence of cell metabolism on cell fate through protein post-translational modifications. Dev Cell 2020;54:282–292.
CrossRef
Google scholar
|
[53] |
Trapnell C, Cacchiarelli D, Grimsby J et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol 2014;32:381–386.
CrossRef
Google scholar
|
[54] |
Tucci V, Isles AR, Kelsey G et al; Erice Imprinting Group. Genomic imprinting and physiological processes in mammals. Cell 2019;176:952–965.
CrossRef
Google scholar
|
[55] |
Van de Sande B, Flerin C, Davie K et al. A scalable SCENIC workflow for single-cell gene regulatory network analysis. Nat Protocols 2020;15:2247–2276.
CrossRef
Google scholar
|
[56] |
Wang L, Zhang J, Duan J et al. Programming and inheritance of parental DNA methylomes in mammals. Cell 2014;157:979–991.
CrossRef
Google scholar
|
[57] |
Wang M, Xu YW, Zhang YC et al. Deciphering the autophagy regulatory network via single-cell transcriptome analysis reveals a requirement for autophagy homeostasis in spermatogenesis. Theranostics 2021;11:5010–5027.
CrossRef
Google scholar
|
[58] |
Wessels HH, Mendez-Mancilla A, Guo XY et al. Massively parallel Cas13 screens reveal principles for guide RNA design. Nat Biotechnol 2020;38:722–+.
CrossRef
Google scholar
|
[59] |
Wolf FA, Angerer P, Theis FJ. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol 2018;19:15.
CrossRef
Google scholar
|
[60] |
Wolf FA, Hamey FK, Plass M et al. PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biol 2019;20:59.
CrossRef
Google scholar
|
[61] |
Xie Y, Khan R, Wahab F et al. The testis-specifically expressed Dpep3 is not essential for male fertility in mice. Gene 2019;711:143925.
CrossRef
Google scholar
|
[62] |
Yagi M, Kabata M, Ukai T et al. De Novo DNA methylation at imprinted loci during reprogramming into naive and primed pluripotency. Stem Cell Rep 2019;12:1113–1128.
CrossRef
Google scholar
|
[63] |
Yagi M, Kishigami S, Tanaka A et al. Derivation of ground-state female ES cells maintaining gamete-derived DNA methylation. Nature 2017;548:224–227.
CrossRef
Google scholar
|
[64] |
Yang XX, Breuss MW, Xu X et al. Developmental and temporal characteristics of clonal sperm mosaicism. Cell 2021;184:4772–+.
CrossRef
Google scholar
|
[65] |
Ying QL, Wray J, Nichols J et al. The ground state of embryonic stem cell self-renewal. Nature 2008;453:519–523.
CrossRef
Google scholar
|
[66] |
Zhang J, Zhang M, Acampora D et al. OTX2 restricts entry to the mouse germline. Nature 2018;562:595–599.
CrossRef
Google scholar
|
[67] |
Zhang T, Oatley J, Bardwell VJ et al. DMRT1 is required for mouse spermatogonial stem cell maintenance and replenishment. PLoS Genet 2016;12:e1006293.
CrossRef
Google scholar
|
[68] |
Zhao J, Lu P, Wan C et al. Cell-fate transition and determination analysis of mouse male germ cells throughout development. Nat Commun 2021;12:6839.
CrossRef
Google scholar
|
[69] |
Zhao T, Fu Y, Zhu J et al. Single-cell RNA-Seq reveals dynamic early embryonic-like programs during chemical reprogramming. Cell stem cell 2018;23:31–45.e37.
CrossRef
Google scholar
|
[70] |
Zhao XY, Li W, Lv Z et al. iPS cells produce viable mice through tetraploid complementation. Nature 2009;461:86–90.
CrossRef
Google scholar
|
[71] |
Zhao Y, Zhao T, Guan J et al. A XEN-like state bridges somatic cells to pluripotency during chemical reprogramming. Cell 2015;163:1678–1691.
CrossRef
Google scholar
|
[72] |
Zhou Q, Jouneau A, Brochard V et al. Developmental potential of mouse embryos reconstructed from metaphase embryonic stem cell nuclei. Biol Reprod 2001;65:412–419.
CrossRef
Google scholar
|
[73] |
Zhou Q, Wang M, Yuan Y et al. Complete meiosis from embryonic stem cell-derived germ cells in vitro. Cell Stem Cell 2016;18:330–340.
CrossRef
Google scholar
|
[74] |
Zhou Y, Zhou B, Pache L et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 2019;10:1523.
CrossRef
Google scholar
|
[75] |
Zhuang Q, Li WJ, Benda C et al. NCoR/SMRT co-repressors cooperate with c-MYC to create an epigenetic barrier to somatic cell reprogramming (vol 20, pg 400, 2018). Nat Cell Biol 2018;20:1227–1227.
CrossRef
Google scholar
|
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