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Current Genomics

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ISSN (Print): 1389-2029
ISSN (Online): 1875-5488

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Review Article

Single-cell Sequencing in the Field of Stem Cells

Author(s): Tian Chen, Jiawei Li, Yichen Jia, Jiyan Wang, Ruirui Sang, Yi Zhang* and Ruiming Rong*

Volume 21, Issue 8, 2020

Page: [576 - 584] Pages: 9

DOI: 10.2174/1389202921999200624154445

Price: $65

Abstract

Variation and heterogeneity between cells are the basic characteristics of stem cells. Traditional sequencing analysis methods often cover up this difference. Single-cell sequencing technology refers to the technology of high-throughput sequencing analysis of genomes at the single-cell level. It can effectively analyze cell heterogeneity and identify a small number of cell populations. With the continuous progress of cell sorting, nucleic acid extraction and other technologies, single-cell sequencing technology has also made great progress. Encouraging new discoveries have been made in stem cell research, including pluripotent stem cells, tissue-specific stem cells and cancer stem cells. In this review, we discuss the latest progress and future prospects of single-cell sequencing technology in the field of stem cells.

Keywords: Single-cell sequencing, pluripotent stem cell, tissue-specific stem cell, cancer stem cell, RNA sequencing, heterogeneity.

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Graphical Abstract

[1]
Navin, N.; Hicks, J. Future medical applications of single-cell sequencing in cancer. Genome Med., 2011, 3(5), 31.
[http://dx.doi.org/10.1186/gm247] [PMID: 21631906]
[2]
Junker, J.P.; van Oudenaarden, A. Every cell is special: genome-wide studies add a new dimension to single-cell biology. Cell, 2014, 157(1), 8-11.
[http://dx.doi.org/10.1016/j.cell.2014.02.010] [PMID: 24679522]
[3]
Wang, Z.; Gerstein, M.; Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 2009, 10(1), 57-63.
[http://dx.doi.org/10.1038/nrg2484] [PMID: 19015660]
[4]
Picelli, S.; Faridani, O.R.; Björklund, Å.K.; Winberg, G.; Sagasser, S.; Sandberg, R. Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc., 2014, 9(1), 171-181.
[http://dx.doi.org/10.1038/nprot.2014.006] [PMID: 24385147]
[5]
Buettner, F.; Natarajan, K.N.; Casale, F.P.; Proserpio, V.; Scialdone, A.; Theis, F.J.; Teichmann, S.A.; Marioni, J.C.; Stegle, O. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat. Biotechnol., 2015, 33(2), 155-160.
[http://dx.doi.org/10.1038/nbt.3102] [PMID: 25599176]
[6]
Spiro, A.; Shapiro, E. Accuracy of answers to cell lineage questions depends on single-cell genomics data quality and quantity. PLOS Comput. Biol., 2016, 12(6)e1004983
[http://dx.doi.org/10.1371/journal.pcbi.1004983] [PMID: 27295404]
[7]
Haque, A.; Engel, J.; Teichmann, S.A.; Lönnberg, T. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. Genome Med., 2017, 9(1), 75.
[http://dx.doi.org/10.1186/s13073-017-0467-4] [PMID: 28821273]
[8]
Tang, F.; Barbacioru, C.; Wang, Y.; Nordman, E.; Lee, C.; Xu, N.; Wang, X.; Bodeau, J.; Tuch, B.B.; Siddiqui, A.; Lao, K.; Surani, M.A. mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods, 2009, 6(5), 377-382.
[http://dx.doi.org/10.1038/nmeth.1315] [PMID: 19349980]
[9]
Macosko, E.Z.; Basu, A.; Satija, R.; Nemesh, J.; Shekhar, K.; Goldman, M.; Tirosh, I.; Bialas, A.R.; Kamitaki, N.; Martersteck, E.M.; Trombetta, J.J.; Weitz, D.A.; Sanes, J.R.; Shalek, A.K.; Regev, A.; McCarroll, S.A. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell, 2015, 161(5), 1202-1214.
[http://dx.doi.org/10.1016/j.cell.2015.05.002] [PMID: 26000488]
[10]
Soumillon, M.; Cacchiarelli, D.; Semrau, S.; van Oudenaarden, A.; Mikkelsen, T.S. Characterization of directed differentiation by high-throughput single-cell RNA-Seq. bioRxiv, 2014.003236
[11]
Ramsköld, D.; Luo, S.; Wang, Y-C.; Li, R.; Deng, Q.; Faridani, O.R.; Daniels, G.A.; Khrebtukova, I.; Loring, J.F.; Laurent, L.C.; Schroth, G.P.; Sandberg, R. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat. Biotechnol., 2012, 30(8), 777-782.
[http://dx.doi.org/10.1038/nbt.2282] [PMID: 22820318]
[12]
Picelli, S.; Björklund, Å.K.; Faridani, O.R.; Sagasser, S.; Winberg, G.; Sandberg, R. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat. Methods, 2013, 10(11), 1096-1098.
[http://dx.doi.org/10.1038/nmeth.2639] [PMID: 24056875]
[13]
Hashimshony, T.; Wagner, F.; Sher, N.; Yanai, I. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep., 2012, 2(3), 666-673.
[http://dx.doi.org/10.1016/j.celrep.2012.08.003] [PMID: 22939981]
[14]
Ziegenhain, C.; Vieth, B.; Parekh, S.; Reinius, B.; Guillaumet-Adkins, A.; Smets, M.; Leonhardt, H.; Heyn, H.; Hellmann, I.; Enard, W. Comparative analysis of single-cell RNA sequencing methods. Mol. Cell, 2017, 65(4), 631-643.
[http://dx.doi.org/10.1016/j.molcel.2017.01.023]
[15]
Tang, F.; Barbacioru, C.; Nordman, E.; Bao, S.; Lee, C.; Wang, X.; Tuch, B.B.; Heard, E.; Lao, K.; Surani, M.A. Deterministic and stochastic allele specific gene expression in single mouse blastomeres. PLoS One, 2011, 6(6)e21208
[http://dx.doi.org/10.1371/journal.pone.0021208] [PMID: 21731673]
[16]
Yan, L.; Yang, M.; Guo, H.; Yang, L.; Wu, J.; Li, R.; Liu, P.; Lian, Y.; Zheng, X.; Yan, J.; Huang, J.; Li, M.; Wu, X.; Wen, L.; Lao, K.; Li, R.; Qiao, J.; Tang, F. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat. Struct. Mol. Biol., 2013, 20(9), 1131-1139.
[http://dx.doi.org/10.1038/nsmb.2660] [PMID: 23934149]
[17]
Xue, Z.; Huang, K.; Cai, C.; Cai, L.; Jiang, C.Y.; Feng, Y.; Liu, Z.; Zeng, Q.; Cheng, L.; Sun, Y.E.; Liu, J.Y.; Horvath, S.; Fan, G. Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature, 2013, 500(7464), 593-597.
[http://dx.doi.org/10.1038/nature12364] [PMID: 23892778]
[18]
Biase, F.H.; Cao, X.; Zhong, S. Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing. Genome Res., 2014, 24(11), 1787-1796.
[http://dx.doi.org/10.1101/gr.177725.114] [PMID: 25096407]
[19]
Huang, W.; Cao, X.; Biase, F.H.; Yu, P.; Zhong, S. Time-variant clustering model for understanding cell fate decisions. Proc. Natl. Acad. Sci. USA, 2014, 111(44), E4797-E4806.
[http://dx.doi.org/10.1073/pnas.1407388111] [PMID: 25339442]
[20]
Tang, F.; Barbacioru, C.; Bao, S.; Lee, C.; Nordman, E.; Wang, X.; Lao, K.; Surani, M.A. Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. Cell Stem Cell, 2010, 6(5), 468-478.
[http://dx.doi.org/10.1016/j.stem.2010.03.015] [PMID: 20452321]
[21]
van den Hurk, M.; Erwin, J.A.; Yeo, G.W.; Gage, F.H.; Bardy, C. Corrigendum: Patch-Seq protocol to analyze the electrophysiology, morphology and transcriptome of whole single neurons derived from human pluripotent stem cells. Front. Mol. Neurosci., 2019, 12, 150.
[http://dx.doi.org/10.3389/fnmol.2019.00150] [PMID: 31244603]
[22]
Bardy, C.; van den Hurk, M.; Kakaradov, B.; Erwin, J.A.; Jaeger, B.N.; Hernandez, R.V.; Eames, T.; Paucar, A.A.; Gorris, M.; Marchand, C.; Jappelli, R.; Barron, J.; Bryant, A.K.; Kellogg, M.; Lasken, R.S.; Rutten, B.P.; Steinbusch, H.W.; Yeo, G.W.; Gage, F.H. Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology. Mol. Psychiatry, 2016, 21(11), 1573-1588.
[http://dx.doi.org/10.1038/mp.2016.158] [PMID: 27698428]
[23]
Cadwell, C.R.; Palasantza, A.; Jiang, X.; Berens, P.; Deng, Q.; Yilmaz, M.; Reimer, J.; Shen, S.; Bethge, M.; Tolias, K.F.; Sandberg, R.; Tolias, A.S. Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq. Nat. Biotechnol., 2016, 34(2), 199-203.
[http://dx.doi.org/10.1038/nbt.3445] [PMID: 26689543]
[24]
Fuzik, J.; Zeisel, A.; Máté, Z.; Calvigioni, D.; Yanagawa, Y.; Szabó, G.; Linnarsson, S.; Harkany, T. Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes. Nat. Biotechnol., 2016, 34(2), 175-183.
[http://dx.doi.org/10.1038/nbt.3443] [PMID: 26689544]
[25]
Camp, J.G.; Badsha, F.; Florio, M.; Kanton, S.; Gerber, T.; Wilsch-Bräuninger, M.; Lewitus, E.; Sykes, A.; Hevers, W.; Lancaster, M.; Knoblich, J.A.; Lachmann, R.; Pääbo, S.; Huttner, W.B.; Treutlein, B. Human cerebral organoids recapitulate gene expression programs of fetal neocortex development. Proc. Natl. Acad. Sci. USA, 2015, 112(51), 15672-15677.
[http://dx.doi.org/10.1073/pnas.1520760112] [PMID: 26644564]
[26]
Renner, M.; Lancaster, M.A.; Bian, S.; Choi, H.; Ku, T.; Peer, A.; Chung, K.; Knoblich, J.A. Self-organized developmental patterning and differentiation in cerebral organoids. EMBO J., 2017, 36(10), 1316-1329.
[http://dx.doi.org/10.15252/embj.201694700] [PMID: 28283582]
[27]
Quadrato, G.; Nguyen, T.; Macosko, E.Z.; Sherwood, J.L.; Min Yang, S.; Berger, D.R.; Maria, N.; Scholvin, J.; Goldman, M.; Kinney, J.P.; Boyden, E.S.; Lichtman, J.W.; Williams, Z.M.; McCarroll, S.A.; Arlotta, P. Cell diversity and network dynamics in photosensitive human brain organoids. Nature, 2017, 545(7652), 48-53.
[http://dx.doi.org/10.1038/nature22047] [PMID: 28445462]
[28]
Daniszewski, M.; Senabouth, A.; Nguyen, Q.H.; Crombie, D.E.; Lukowski, S.W.; Kulkarni, T.; Sluch, V.M.; Jabbari, J.S.; Chamling, X.; Zack, D.J.; Pébay, A.; Powell, J.E.; Hewitt, A.W. Single cell RNA sequencing of stem cell-derived retinal ganglion cells. Sci. Data, 2018, 5180013
[http://dx.doi.org/10.1038/sdata.2018.13] [PMID: 29437159]
[29]
Langer, K.B.; Ohlemacher, S.K.; Phillips, M.J.; Fligor, C.M.; Jiang, P.; Gamm, D.M.; Meyer, J.S. Retinal ganglion cell diversity and subtype specification from human pluripotent stem cells. Stem Cell Reports, 2018, 10(4), 1282-1293.
[http://dx.doi.org/10.1016/j.stemcr.2018.02.010] [PMID: 29576537]
[30]
Conrad, S.; Azizi, H.; Skutella, T. Single-cell expression profiling and proteomics of primordial germ cells, spermatogonial stem cells, adult germ stem cells, and oocytes.Stem Cells: Biology and Engineering; Springer, 2017, pp. 77-87.
[http://dx.doi.org/10.1007/5584_2017_117]
[31]
Li, L.; Dong, J.; Yan, L.; Yong, J.; Liu, X.; Hu, Y.; Fan, X.; Wu, X.; Guo, H.; Wang, X. Single-cell RNA-seq analysis maps development of human germline cells and gonadal niche interactions. Cell Stem Cell, 2017, 20(6), 858-873.
[32]
Wen, L.; Tang, F. Single-cell sequencing in stem cell biology. Genome Biol., 2016, 17(1), 71.
[http://dx.doi.org/10.1186/s13059-016-0941-0] [PMID: 27083874]
[33]
Treutlein, B.; Brownfield, D.G.; Wu, A.R.; Neff, N.F.; Mantalas, G.L.; Espinoza, F.H.; Desai, T.J.; Krasnow, M.A.; Quake, S.R. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature, 2014, 509(7500), 371-375.
[http://dx.doi.org/10.1038/nature13173] [PMID: 24739965]
[34]
Desai, T.J.; Brownfield, D.G.; Krasnow, M.A. Alveolar progenitor and stem cells in lung development, renewal and cancer. Nature, 2014, 507(7491), 190-194.
[http://dx.doi.org/10.1038/nature12930] [PMID: 24499815]
[35]
Brunskill, E.W.; Park, J-S.; Chung, E.; Chen, F.; Magella, B.; Potter, S.S. Single cell dissection of early kidney development: multilineage priming. Development, 2014, 141(15), 3093-3101.
[http://dx.doi.org/10.1242/dev.110601] [PMID: 25053437]
[36]
Hanchate, N.K.; Kondoh, K.; Lu, Z.; Kuang, D.; Ye, X.; Qiu, X.; Pachter, L.; Trapnell, C.; Buck, L.B. Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis. Science, 2015, 350(6265), 1251-1255.
[http://dx.doi.org/10.1126/science.aad2456] [PMID: 26541607]
[37]
Kumar, P.; Tan, Y.; Cahan, P. Understanding development and stem cells using single cell-based analyses of gene expression. Development, 2017, 144(1), 17-32.
[http://dx.doi.org/10.1242/dev.133058] [PMID: 28049689]
[38]
Patel, A.P.; Tirosh, I.; Trombetta, J.J.; Shalek, A.K.; Gillespie, S.M.; Wakimoto, H.; Cahill, D.P.; Nahed, B.V.; Curry, W.T.; Martuza, R.L.; Louis, D.N.; Rozenblatt-Rosen, O.; Suvà, M.L.; Regev, A.; Bernstein, B.E. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science, 2014, 344(6190), 1396-1401.
[http://dx.doi.org/10.1126/science.1254257] [PMID: 24925914]
[39]
Yang, Z.; Li, C.; Fan, Z.; Liu, H.; Zhang, X.; Cai, Z.; Xu, L.; Luo, J.; Huang, Y.; He, L.; Liu, C.; Wu, S. Single-cell sequencing reveals variants in ARID1A, GPRC5A and MLL2 driving self-renewal of human bladder cancer stem cells. Eur. Urol., 2017, 71(1), 8-12.
[http://dx.doi.org/10.1016/j.eururo.2016.06.025] [PMID: 27387124]
[40]
Liu, J.; Adhav, R.; Xu, X. Current progresses of single cell DNA sequencing in breast cancer research. Int. J. Biol. Sci., 2017, 13(8), 949-960.
[http://dx.doi.org/10.7150/ijbs.19627] [PMID: 28924377]
[41]
Navin, N.; Kendall, J.; Troge, J.; Andrews, P.; Rodgers, L.; McIndoo, J.; Cook, K.; Stepansky, A.; Levy, D.; Esposito, D.; Muthuswamy, L.; Krasnitz, A.; McCombie, W.R.; Hicks, J.; Wigler, M. Tumour evolution inferred by single-cell sequencing. Nature, 2011, 472(7341), 90-94.
[http://dx.doi.org/10.1038/nature09807] [PMID: 21399628]
[42]
Wang, Y.; Waters, J.; Leung, M.L.; Unruh, A.; Roh, W.; Shi, X.; Chen, K.; Scheet, P.; Vattathil, S.; Liang, H.; Multani, A.; Zhang, H.; Zhao, R.; Michor, F.; Meric-Bernstam, F.; Navin, N.E. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature, 2014, 512(7513), 155-160.
[http://dx.doi.org/10.1038/nature13600] [PMID: 25079324]
[43]
Gao, R.; Davis, A.; McDonald, T.O.; Sei, E.; Shi, X.; Wang, Y.; Tsai, P-C.; Casasent, A.; Waters, J.; Zhang, H.; Meric-Bernstam, F.; Michor, F.; Navin, N.E. Punctuated copy number evolution and clonal stasis in triple-negative breast cancer. Nat. Genet., 2016, 48(10), 1119-1130.
[http://dx.doi.org/10.1038/ng.3641] [PMID: 27526321]
[44]
Karaayvaz, M.; Cristea, S.; Gillespie, S.M.; Patel, A.P.; Mylvaganam, R.; Luo, C.C.; Specht, M.C.; Bernstein, B.E.; Michor, F.; Ellisen, L.W. Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq. Nat. Commun., 2018, 9(1), 3588.
[http://dx.doi.org/10.1038/s41467-018-06052-0] [PMID: 30181541]

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