单细胞转录组测序技术进展及其在间充质干细胞研究中的应用#br#

doi:10.3969/j.issn.1005-4979.2019.03.010

摘要/Abstract

摘要： 单细胞转录组测序技术可在单个细胞水平上定量分析细胞间的基因表达差异。随着该技术的迅速发展，高通量单细胞转录组测序的出现可实现数千个细胞的同时测序，使群体细胞的异质性分析更加高效。间充质干细胞是具有异质性的干细胞群体，这种异质性使干细胞治疗的临床应用变得复杂。此篇综述讨论了单细胞转录组测序的技术发展及其在间充质干细胞研究中的应用现状。

关键词: 单细胞转录组测序； , 间充质干细胞； , 干细胞异质性

Abstract: Department of Implantology, School and Hospital of Stomatology, Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai 200072,China

Key words: single cell RNA-Seq, mesenchymal stem cells, stem cell heterogeneous

中图分类号:

R782.4

孙睿男，王佐林. 单细胞转录组测序技术进展及其在间充质干细胞研究中的应用#br#[J]. 《口腔颌面外科杂志》, doi: 10.3969/j.issn.1005-4979.2019.03.010.

SUN Rui nan, WANG Zuo lin. Recent Advances in Single Cell RNA-Seq and its Application in the Studies of Mesenchymal Stem Cell Research[J]. 《Journal of Oral and Maxillofacial Surgery》, doi: 10.3969/j.issn.1005-4979.2019.03.010.

https://journal06.magtech.org.cn/Jweb_joms/CN/Y2019/V29/I3/174

参考文献

[1] Kumar RM, Cahan P, Shalek AK, et al. Deconstructing transcriptional heterogeneity in pluripotent stem cells[J]. Nature, 2014, 516(7529):56.
[2] Hwang B, Lee JH, Bang D. Single-cell RNA sequencing technologies and bioinformatics pipelines[J]. Exp Mol Med, 2018, 50:96.
[3] Wu XJ, Yang B, Udo-Inyang I, et al. Research techniques made simple: single-cell RNA sequencing and its applications in dermatology[J]. J Invest Dermatol, 2018, 138(5):1004-1009.
[4] Tang FC, Barbacioru C, Wang YZ, et al. mRNA-Seq whole-transcriptome analysis of a single cell[J]. Nat Methods, 2009, 6(5):377.
[5] Ramskold D, Luo S, Wang YC, et al. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells[J]. Nat Biotechnol, 2012, 30(8):777-782.
[6] Picelli S, Bjorklund AK, Faridani OR, et al. Smart-seq2 for sensitive full-length transcriptome profiling in single cells[J]. Nat Methods, 2013, 10(11):1096-8.
[7] Hashimshony T, Wagner F, Sher N, et al. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification[J]. Cell Rep, 2012, 2(3):666-73.
[8] Hashimshony T, Senderovich N, Avital G, et al. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq[J]. Genome Biol, 2016, 17(1):77.
[9] Islam S, Kjallquist U, Moliner A, et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq[J]. Genome Res, 2011, 21(7):1160-7.
[10] Islam S, Zeisel A, Joost S, et al. Quantitative single-cellRNA-seq with unique molecular identifiers[J]. Nat Methods, 2014, 11(2):163-6.
[11] Jaitin DA, Kenigsberg E, Keren-Shaul H, et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types[J]. Science, 2014, 343(6172):776-9.
[12] Klein AM, Mazutis L, Akartuna I, et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells[J]. Cell, 2015, 161(5):1187-1201.
[13] Macosko EZ, Basu A, Satija R, et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets[J]. Cell, 2015, 161(5):1202-1214.
[14] Vitak SA, Torkenczy KA, Rosenkrantz JL, et al. Sequencing thousands of single-cell genomes with combinatorial indexing[J]. Nat Methods, 2017, 14(3):302-308.
[15] Chen J, Suo SB, Tam PPL, et al. Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq[J]. Nat Protoc, 2017, 12(3):566-580.
[16] Datlinger P, Rendeiro AF, Schmidl C, et al. Pooled CRISPR screening with single-cell transcriptome readout[J]. Nat Methods, 2017, 14(3):297-301.
[17] Zheng GXY, Terry JM, Belgrader P, et al. Massively parallel digital transcriptional profiling of single cells[J]. Nat Commun, 2017, 8:14049.
[18] Birey F, Andersen J, Makinson CD, et al. Assembly of functionally integrated human forebrain spheroids[J]. Nature, 2017, 545(7652):54.
[19] Hedlund E,Deng QL. Single-cell RNA sequencing: Technical advancements and biological applications[J]. Mol Aspects Med, 2018, 59:36-46.
[20] Liu TT, Wu HJ, Wu SX, et al. Single-cell sequencing technologies for cardiac stem cell studies[J]. Stem Cells Dev, 2017, 26(21):1540-1551.
[21] Murphy TW, Zhang Q, Naler LB, et al. Recent advances in the use of microfluidic technologies for single cell analysis[J]. Analyst, 2018, 143(1):60-80.
[22] Espina V, Wulfkuhle JD, Calvert VS, et al. Laser-capture microdissection[J]. Nat Protoc, 2006, 1(2):586-603.
[23] Dalerba P, Kalisky T, Sahoo D, et al. Single-cell dissection of transcriptional heterogeneity in human colon tumors[J]. Nat Biotechnol, 2011, 29(12):1120-1127.
[24] Boon WC, Petkovic-Duran K, Zhu YG, et al. Increasing cDNA yields from single-cell quantities of mRNA in standard laboratory reverse transcriptase reactions using acoustic microstreaming[J]. J Vis Exp, 2011(53):3144.
[25] Svensson V, Vento-Tormo R,Teichmann SA. Exponential scaling of single-cell RNA-seq in the past decade[J]. Nat Protoc, 2018, 13(4):599-604.
[26] Kivioja T, Vaharautio A, Karlsson K, et al. Counting absolute numbers of molecules using unique molecular identifiers[J]. Nat Methods, 2012, 9(1):72.
[27] Potter SS. Single-cell RNA sequencing for the study of development, physiology and disease[J]. Nat Rev Nephrol, 2018, 14(8):479-492.
[28] Buettner F, Natarajan KN, Casale FP, et al. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells[J]. Nat Biotechnol, 2015, 33(2):155-160.
[29] Brennecke P, Anders S, Kim JK, et al. Accounting for technical noise in single-cell RNA-seq experiments[J]. Nat Methods, 2013, 10(11):1093-1095.
[30] Kester L,van Oudenaarden A. Single-cell transcriptomics meets lineage tracing[J]. Cell Stem Cell, 2018, 23(2):166-179.
[31] Barry FP,Murphy JM. Mesenchymal stem cells: clinical applications and biological characterization[J]. Int J Biochem Cell Biol, 2004, 36(4):568-584.
[32] Woodbury D, Schwarz EJ, Prockop DJ, et al. Adult rat and human bone marrow stromal cells differentiate into neurons[J]. J Neurosci Res, 2000, 61(4):364-370.
[33] Ghannam S, Bouffi C, Djouad F, et al. Immunosuppression by mesenchymal stem cells: mechanisms and clinical applications[J]. Stem Cell Res Ther, 2010, 1(1): 2.
[34] Wang J, Liao LM,Tan JM. Mesenchymal-stem-cell-based experimental and clinical trials: current status and open questions[J]. Expert Opin Biol Ther, 2011, 11(7):893-909.
[35] McLeod CM,Mauck RL. On the origin and impact of mesenchymal stem cell heterogeneity: new insights and emerging tools for single cell analysis[J]. Eur Cells Mater, 2017, 34:217-231.
[36] Mindaye ST, Ra M, Lo Surdo JL, et al. Global proteomic signature of undifferentiated human bone marrow stromal cells: Evidence for donor-to-donor proteome heterogeneity[J]. Stem Cell Res, 2013, 11(2):793-805.
[37] Melief SM, Zwaginga JJ, Fibbe WE, et al. Adipose tissue-derived multipotent stromal cells have a higher immunomodulatory capacity than their bone marrow-derived counterparts[J]. Stem Cell Transl Med, 2013, 2(6):455-463.
[38] Vogel W, Grunebach F, Messam CA, et al. Heterogeneity among human bone marrow-derived mesenchymal stem cells and neural progenitor cells[J]. Haematologica, 2003, 88(2):126-133.
[39] Wagner W, Feldmann RE, Seckinger A, et al. The heterogeneity of human mesenchymal stem cell preparations - Evidence from simultaneous analysis of proteomes and transcriptomes[J]. Exp Hematol, 2006, 34(4):536-548.
[40] Wislet-Gendebien S, Poulet C, Neirinckx V, et al. In Vivo tumorigenesis was observed after injection of In Vitro expanded neural crest stem cells isolated from adult bone marrow[J]. PLoS One, 2012, 7(10):e46425.
[41] Li ZJ, Zhang C, Weiner LP, et al. Molecular characterization of heterogeneous mesenchymal stem cells with single-cell transcriptomes[J]. Biotechnol Adv, 2013, 31(2):312-317.
[42] Lei JX, Hui DY, Huang WJ, et al. Heterogeneity of the biological properties and gene expression profiles of murine bone marrow stromal cells[J]. Int J Biochem Cell B, 2013, 45(11):2431-2443.
[43] Rennerfeldt DA,Van Vliet KJ. Concise review: when colonies are not clones: evidence and implications of intracolony heterogeneity in mesenchymal stem cells[J]. Stem Cells, 2016, 34(5):1135-1141.
[44] Cote AJ, McLeod CM, Farrell MJ, et al. Single-cell differences in matrix gene expression do not predict matrix deposition[J]. Nat Commun, 2016, 7: 10865.
[45] Freeman BT, Jung JP,Ogle BM. Single-cell RNA-Seq of bone marrow-derived mesenchymal stem cells reveals unique profiles of lineage priming[J]. PLoS One, 2015, 10(9):e0136199.
[46] Li H, Zhu L, Chen H, et al. Generation of Functional hepatocytes from human adipose-derived MYC(+) KLF4(+) GMNN(+) stem cells analyzed by single-Cell RNA-Seq Profiling[J]. Stem Cells Transl Med, 2018,7(11):792-805.
[47] Spitzer MH, Nolan GP. Mass cytometry: single cells, Many features[J]. Cell, 2016, 165(4):780-791.
[48] Bongiorno T, Kazlow J, Mezencev R, et al. Mechanical stiffness as an improved single-cell indicator of osteoblastic human mesenchymal stem cell differentiation[J]. J Biomech, 2014, 47(9):2197-2204.
[49] Li BJ, Menzel U, Loebel C, et al. Monitoring live human mesenchymal stromal cell differentiation and subsequent selection using fluorescent RNA-based probes[J]. Sci Rep, 2016, 6:26014.

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