生物技术通报 ›› 2022, Vol. 38 ›› Issue (3): 226-233.doi: 10.13560/j.cnki.biotech.bull.1985.2021-0523
熊和丽(), 沙茜, 刘韶娜, 相德才, 张斌, 赵智勇()
收稿日期:
2021-04-20
出版日期:
2022-03-26
发布日期:
2022-04-06
作者简介:
熊和丽,女,博士,助理研究员,研究方向:动物遗传育种;E-mail: 基金资助:
XIONG He-li(), SHA Qian, LIU Shao-na, XIANG De-cai, ZHANG Bin, ZHAO Zhi-yong()
Received:
2021-04-20
Published:
2022-03-26
Online:
2022-04-06
摘要:
细胞是机体最基本的结构组成及功能单位,细胞类型和功能由其整个转录表达谱决定,通过单细胞转录组测序可以获得单个细胞转录表达谱,由此以高精度分辨率鉴定细胞类型、细胞状态以及稀有类型细胞,从而可以在单细胞水平分析细胞动态变化及细胞间的关系,深入解析驱动细胞变化及细胞异常背后的分子细胞机制。随着单细胞测序技术稳定性和测序通量的提高,以及测序成本的降低,其在发育生物学、肿瘤、免疫及疾病等领域被广泛应用,研究对象主要涉及人及模式生物,在动物上的应用研究相对较少。本文主要介绍单细胞转录组测序技术及其生物学应用并综述目前其在动物上的一些开创性研究,以期为今后更好的在动物上应用单细胞转录组测序提供方法参考。
熊和丽, 沙茜, 刘韶娜, 相德才, 张斌, 赵智勇. 单细胞转录组测序技术在动物上的应用研究[J]. 生物技术通报, 2022, 38(3): 226-233.
XIONG He-li, SHA Qian, LIU Shao-na, XIANG De-cai, ZHANG Bin, ZHAO Zhi-yong. Application of Single-cell Transcriptome Sequencing in Animals[J]. Biotechnology Bulletin, 2022, 38(3): 226-233.
[1] |
Tang F, Barbacioru C, Nordman E, et al. RNA-Seq analysis to capture the transcriptome landscape of a single cell[J]. Nat Protoc, 2010, 5(3):516-535.
doi: 10.1038/nprot.2009.236 URL |
[2] | 周子茗, 郭国骥. 细胞图谱:解码人体基本单元的奥秘[J]. 科学, 2020, 72(4):30-32, 4. |
Zhou ZM, Guo GJ. Cell atlas:decoding the basic unit of the human body[J]. Science, 2020, 72(4):30-32, 4.
doi: 10.1126/science.72.1854.30.b URL |
|
[3] | Tang F, Barbacioru C, Wang Y, et al. mRNA-Seq whole-transcriptome analysis of a single cell[J]. Nat Methods, 2009, 6(5):377-382. |
[4] |
Kolodziejczyk AA, Kim JK, Svensson V, et al. The technology and biology of single-cell RNA sequencing[J]. Mol Cell, 2015, 58(4):610-620.
doi: 10.1016/j.molcel.2015.04.005 pmid: 26000846 |
[5] | Olsen TK, Baryawno N. Introduction to single-cell RNA sequencing[J]. Curr Protoc Mol Biol, 2018, 122(1):e57. |
[6] |
Hedlund E, Deng Q. Single-cell RNA sequencing:Technical advancements and biological applications[J]. Mol Aspects Med, 2018, 59:36-46.
doi: S0098-2997(17)30053-5 pmid: 28754496 |
[7] | Shum EY, Walczak EM, Chang C, et al. Quantitation of mRNA transcripts and proteins using the BD rhapsodyTM single-cell analysis system[J]. Adv Exp Med Biol, 2019, 1129:63-79. |
[8] | 王权, 王铸, 张振, 等. 单细胞测序的技术概述[J]. 中国医药导刊, 2020, 22(7):433-439. |
Wang Q, Wang Z, Zhang Z, et al. Overview of the technology of single cell sequencing[J]. Chin J Med Guide, 2020, 22(7):433-439. | |
[9] | 文路, 汤富酬. 单细胞转录组分析研究进展[J]. 生命科学, 2014, 26(3):228-233. |
Wen L, Tang FC. Recent progresses in single-cell transcriptome analysis[J]. Chin Bull Life Sci, 2014, 26(3):228-233. | |
[10] | Ziegenhain C, Vieth B, Parekh S, et al. Comparative analysis of single-cell RNA sequencing methods[J]. Mol Cell, 2017,65(4):631- 643.e4. |
[11] |
Ding J, Adiconis X, Simmons SK, et al. Systematic comparison of single-cell and single-nucleus RNA-sequencing methods[J]. Nat Biotechnol, 2020, 38(6):737-746.
doi: 10.1038/s41587-020-0465-8 URL |
[12] |
Chen X, Love JC, Navin NE, et al. Single-cell analysis at the threshold[J]. Nat Biotechnol, 2016, 34(11):1111-1118.
doi: 10.1038/nbt.3721 pmid: 27824834 |
[13] |
Pollen AA, Nowakowski TJ, Shuga J, et al. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex[J]. Nat Biotechnol, 2014, 32(10):1053-1058.
doi: 10.1038/nbt.2967 pmid: 25086649 |
[14] | Trombetta JJ, Gennert D, Lu D, et al. Preparation of single-cell RNA-seq libraries for next generation sequencing[J]. Curr Protoc Mol Biol, 2014,107: 4. 22. 1- 4. 2217. |
[15] |
Rozenblatt-Rosen O, Stubbington MJT, Regev A, et al. The Human Cell Atlas:from vision to reality[J]. Nature, 2017, 550(7677):451-453.
doi: 10.1038/550451a URL |
[16] | Poulin JF, Tasic B, Hjerling-Leffler J, et al. Disentangling neural cell diversity using single-cell transcriptomics[J]. Nat Neurosci, 2016, 19(9):1131-1141. |
[17] |
Han X, Zhou Z, Fei L, et al. Construction of a human cell landscape at single-cell level[J]. Nature, 2020, 581(7808):303-309.
doi: 10.1038/s41586-020-2157-4 URL |
[18] |
Gawad C, Koh W, Quake SR. Single-cell genome sequencing:current state of the science[J]. Nat Rev Genet, 2016, 17(3):175-188.
doi: 10.1038/nrg.2015.16 URL |
[19] | Guo JT, Nie XC, Giebler M, et al. The dynamic transcriptional cell atlas of testis development during human puberty[J]. Cell Stem Cell, 2020,26(2):262- 276.e4. |
[20] | Carter RA, Bihannic L, Rosencrance C, et al. A single-cell transcriptional atlas of the developing murine cerebellum[J]. Curr Biol, 2018,28(18):2910- 2920. e2. |
[21] |
Park JE, Botting RA, Conde CD, et al. A cell atlas of human thymic development defines T cell repertoire formation[J]. bioRxiv, 2020, DOI: 10.1101/2020.01.28.911115.
doi: 10.1101/2020.01.28.911115 |
[22] | Hernandez PP, Strzelecka PM, Athanasiadis EI, et al. Single-cell transcriptional analysis reveals ILC-like cells in zebrafish[J]. Sci Immunol, 2018, 3(29):u5265. |
[23] | Azizi E, Carr AJ, Plitas G, et al. Single-cell map of diverse immune phenotypes in the breast tumor microenvironment[J]. Cell, 2018,174(5):1293-1308. e36. |
[24] | Han X, Wang R, Zhou Y, et al. Mapping the mouse cell atlas by microwell-seq[J]. Cell, 2018,172(5):1091- 1107. e17. |
[25] |
Qiu X, Mao Q, Tang Y, et al. Reversed graph embedding resolves complex single-cell trajectories[J]. Nat Methods, 2017, 14(10):979-982.
doi: 10.1038/NMETH.4402 |
[26] | Sharon N, Chawla R, Mueller J, et al. A peninsular structure coordinates asynchronous differentiation with morphogenesis to generate pancreatic islets[J]. Cell, 2019, 176(4):790-804.e13. |
[27] |
Pijuan-Sala B, Griffiths JA, Guibentif C, et al. A single-cell molecular map of mouse gastrulation and early organogenesis[J]. Nature, 2019, 566(7745):490-495.
doi: 10.1038/s41586-019-0933-9 URL |
[28] |
Cao J, Spielmann M, Qiu X, et al. The single-cell transcriptional landscape of mammalian organogenesis[J]. Nature, 2019, 566(7745):496-502.
doi: 10.1038/s41586-019-0969-x URL |
[29] |
Armingol E, Officer A, Harismendy O, et al. Deciphering cell-cell interactions and communication from gene expression[J]. Nat Rev Genet, 2021, 22(2):71-88.
doi: 10.1038/s41576-020-00292-x pmid: 33168968 |
[30] |
Vento-Tormo R, Efremova M, Botting RA, et al. Single-cell reconstruction of the early maternal-fetal interface in humans[J]. Nature, 2018, 563(7731):347-353.
doi: 10.1038/s41586-018-0698-6 URL |
[31] |
Davidson S, Efremova M, Riedel A, et al. Single-cell RNA sequencing reveals a dynamic stromal niche that supports tumor growth[J]. Cell Rep, 2020, 31(7):107628.
doi: 10.1016/j.celrep.2020.107628 URL |
[32] | Kalucka J, de Rooij LPMH, Goveia J, et al. Single-cell transcriptome atlas of murine endothelial cells[J]. Cell, 2020,180(4):764-779. e20. |
[33] | Davie K, Janssens J, Koldere D, et al. A single-cell transcriptome atlas of the aging Drosophila brain[J]. Cell, 2018,174(4):982-998. e20. |
[34] | Ma S, Sun S, Geng L, et al. Caloric restriction reprograms the single-cell transcriptional landscape of Rattus norvegicus aging[J]. Cell, 2020,180(5):984- 1001. e22. |
[35] |
Ma S, Sun SH, Li JM, et al. Single-cell transcriptomic atlas of primate cardiopulmonary aging[J]. Cell Res, 2021, 31(4):415-432.
doi: 10.1038/s41422-020-00412-6 URL |
[36] | Wang S, Zheng Y, Li J, et al. Single-cell transcriptomic atlas of primate ovarian aging[J]. Cell, 2020,180(3):585-600. e19. |
[37] |
Tabula Muris Consortium. A single-cell transcriptomic atlas characterizes ageing tissues in the mouse[J]. Nature, 2020, 583(7817):590-595.
doi: 10.1038/s41586-020-2496-1 URL |
[38] | Li Z, Zheng M, Mo J, et al. Single-cell RNA sequencing of preadipocytes reveals the cell fate heterogeneity induced by melatonin[J]. J Pineal Res, 2021, 70(3):e12725. |
[39] | Cosacak MI, Bhattarai P, Reinhardt S, et al. Single-cell transcriptomics analyses of neural stem cell heterogeneity and contextual plasticity in a zebrafish brain model of amyloid toxicity[J]. Cell Rep, 2019,27(4):1307-1318. e3. |
[40] |
Zarei K, Stroik MR, Gansemer ND, et al. Early pathogenesis of cystic fibrosis gallbladder disease in a porcine model[J]. Lab Invest, 2020, 100(11):1388-1399.
doi: 10.1038/s41374-020-0474-8 URL |
[41] |
Estermann MA, Williams S, Hirst CE, et al. Insights into gonadal sex differentiation provided by single-cell transcriptomics in the chicken embryo[J]. Cell Rep, 2020, 31(1):107491.
doi: 10.1016/j.celrep.2020.03.055 URL |
[42] |
Feregrino C, Sacher F, Parnas O, et al. A single-cell transcriptomic atlas of the developing chicken limb[J]. BMC Genomics, 2019, 20(1):401.
doi: 10.1186/s12864-019-5802-2 URL |
[43] |
Qiu K, Xu DD, Wang LQ, et al. Association analysis of single-cell RNA sequencing and proteomics reveals a vital role of Ca2+ signaling in the determination of skeletal muscle development potential[J]. Cells, 2020, 9(4):1045.
doi: 10.3390/cells9041045 URL |
[44] | 张恒. L1-siRNAs在猪早期胚胎中的功能研究及猪早期胚胎单细胞转录组分析[D]. 哈尔滨:东北农业大学, 2018. |
Zhang H. Functional study of L1-siRNAs and single cell transcriptome analysis in porcine preimplantation embryos[D]. Harbin:Northeast Agricultural University, 2018. | |
[45] |
Goodpaster BH, Sparks LM. Metabolic flexibility in health and disease[J]. Cell Metab, 2017, 25(5):1027-1036.
doi: S1550-4131(17)30220-6 pmid: 28467922 |
[46] | Yang H, Ma JY, Wan Z, et al. Characterization of sheep spermatogenesis through single-cell RNA sequencing[J]. FASEB J, 2021, 35(2):e21187. |
[47] | 葛伟. 单细胞分辨率解析绒山羊及小鼠毛囊发生的转录调控机制[D]. 杨凌:西北农林科技大学, 2019. |
Ge W. Dissecting the transcriptional regulatory mechanism underlying cashmere goat and murine hair follicle morphogenesis at single-cell resolution[D]. Yangling:Northwest A & F University, 2019. | |
[48] |
Li Y, Haug S, Schlosser P, et al. Integration of GWAS summary statistics and gene expression reveals target cell types underlying kidney function traits[J]. J Am Soc Nephrol, 2020, 31(10):2326-2340.
doi: 10.1681/ASN.2020010051 URL |
[49] |
Farmer A, Thibivilliers S, Ryu KH, et al. Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level[J]. Mol Plant, 2021, 14(3):372-383.
doi: 10.1016/j.molp.2021.01.001 URL |
[50] | Ranzoni AM, Tangherloni A, Berest I, et al. Integrative single-cell RNA-seq and ATAC-seq analysis of human developmental hematopoiesis[J]. Cell Stem Cell, 2021, 28(3):472-487. e7. |
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