|
|
|
| Single-cell Transcriptome Sequencing Technology and Its Application in the Field of Animal Science |
| LOU Ji-Ying1, GUO Qi-Xin1, BI Yu-Lin1, JIANG Yong1, WANG Zhi-Xiu1, CHEN Guo-Hong1,2, BAI Hao2*, CHANG Guo-Bin1,2* |
1 College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China;
2 Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China |
|
|
|
|
Abstract Single-cell sequencing is a new research area, which mainly includes transcriptome sequencing, whole genome sequencing, and epigenomic sequencing. Single-cell RNA-sequencing (scRNA-seq) refers to a new technique for high-throughput sequencing and analysis of RNA at the single cell level. Recently, single- cell related experimental technology has developed rapidly and has been widely used in the field of biology and medicine, mainly for the study of biological evolution process, tissue and organ development, tumor disease occurrence and precision medical diagnosis. However, few studies were reported in the field of animal science research and its application, currently, most of them focus on the field of animal physiology and evolutionary development. This article summarized the technical methods of single-cell transcriptome sequencing and its application in the field of animal science. This review provides a theoretical basis for the development of single-cell transcriptome sequencing technology and its application in the field of animal science.
|
|
Received: 29 March 2022
|
|
|
|
Corresponding Authors:
*bhowen1027@yzu.edu.cn; gbchang@yzu.edu.cn
|
|
|
|
[1] 崔治中. 2009. 我国鸡群中禽白血病流行现状和对策[J]. 中国家禽, 31(13): 1-3.
(Cui Z Z. 2009. Epidemic status and countermeasures of avian leukemia in chickens in China[J]. China Poultry, 31(13): 1-3.)
[2] 李京徽. 2020. 利用单细胞 RNA 测序技术鉴别鸡胸肌组织细胞亚群和特异性表达基因[D]. 硕士学位论文, 中国农业科学院, 导师: 刘冉冉, pp. 54-57.
(Li J H. 2020. Identification of cell diversity and specific expressed genes in chicken breast muscle using single-cell RNA sequencing. [D]. Thesis for M. S., Chinese Academy of Agricultural Sciences, Supervisor: Liu R R, pp. 54-57.)
[3] 陶正博. 2021. 基于单细胞转录组测序技术对人骨髓间充质干细胞的亚群分析及骨质疏松症的发病机制研究[D]. 硕士学位论文, 中国医科大学, 导师: 朱悦, pp. 9-10.
(Tao Z B. 2021. Analysis of human bone marrow mesenchymal stem cell subgroups based on single-cell transcriptome sequencing technology and research on the pathogenesis of osteoporosis[D]. Thesis for M. S., China Medical University, Supervisor: Zhu Y, pp. 9-10.)
[4] 周彦, 王超杰, 朱纯超,等. 2017. 组织单腺体内单细胞的基因变异分析方法[J]. 遗传, 39(08): 753-762.
(Zhou Y, Wang C J, Zhu C C, et al., 2017. Single-cell gene variation analysis method for single gland[J]. Hereditas, 39(08): 753-762.)
[5] 周子茗, 郭国骥. 2020. 细胞图谱: 解码人体基本单元的奥秘[J]. 科学, 72(04): 30-32.
(Zhou Z M, Guo G J. 2020. Cell Atlas: Decoding the basic unit of the human body[J]. Science, 72(04): 30-32.)
[6] Alles J, Karaiskos N, Praktiknjo S D, et al. 2017. Cell fixation and preservation for droplet-based single-cell transcriptomics[J]. BMC Biology, 15(1): 44.
[7] Avital G, Avraham R, Fan A, et al. 2017. scDual-Seq: Mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing.[J]. Genome Biology, 18(1): 200.
[8] Baron C S, Barve A, Muraro M J, et al. 2019. Cell type purification by single-cell transcriptome-trained sorting[J]. Cell, 179(2): 527-542.
[9] Bengtsson M, Hemberg M, Rorsman P, et al. 2008. Quantification of mRNA in single cells and modelling of RT-qPCR induced noise[J]. BMC Molecular Biology, 9: 63.
[10] Blue B L, Rizi A, Gwendolyn E K, et al. 2016. Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain[J]. Science, 352(6293): 1586-1590.
[11] Chavkin N W, Hirschi K K. 2020. Single cell analysis in vascular biology[J]. Frontiers in Cardiovascular Medicine, 7: 42.
[12] Cloonan N, Forrest A R R, Kolle G, et al. 2008. Stem cell transcriptome profiling via massive-scale mRNA sequencing[J]. Nature Methods, 5(7): 613-619.
[13] DeLaughter D M, Bick A G, Wakimoto H, et al. 2016. Single- cell resolution of temporal gene expression during heart development[J]. Developmental Cell, 39(4): 480-490.
[14] Diego A J, Ephraim K, Hadas K, et al. 2014. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types[J]. Science, 343(6172): 776-779.
[15] Dominic G, Mauro J M, Jean-Charles B, et al. 2016. De Novo prediction of stem cell identity using single-cell transcriptome data[J]. Cell Stem Cell, 19(2): 266-277.
[16] Dries R, Chen J, Del R N, et al. 2021. Advances in spatial transcriptomic data analysis[J]. Genome Research, 31(10): 1706-1718.
[17] Eberwine J, Yeh H, Miyashiro K, et al. 1992. Analysis of gene expression in single live neurons[J]. Proceedings of the National Academy of Sciences of the USA, 89(7): 3010-3014.
[18] Emont M P, Jacobs C, Essene A L, et al. 2022. A single-cell atlas of human and mouse white adipose tissue[J]. Nature, 603(7903): 926-933.
[19] Fan H C, Fu G K, Fodor S P A. 2015. Combinatorial labeling of single cells for gene expression cytometry[J]. Science, 347(6222): 1258367.
[20] Faridani O R, Abdullayev I, Hagemann-Jensen M, et al. 2016. Single-cell sequencing of the small-RNA transcriptome[J]. Nature Biotechnology, 34(12): 1264-1266.
[21] Fu G K, Hu J, Wang P, et al. 2011. Counting individual DNA molecules by the stochastic attachment of diverse labels[J]. Proceedings of the National Academy of Sciences of the USA, 108(22): 9026-9031.
[22] Gao C, Lei C, Zhang M N. 2020. The Comparison of two single-cell sequencing platforms: BD rhapsody and 10x genomics chromium[J]. Current Genomics, 21(8): 602-609.
[23] Graf A, Krebs S, Zakhartchenko V, et al. 2014. Fine mapping of genome activation in bovine embryos by RNA sequencing[J]. Proceedings of the National Academy of Sciences of The USA, 111(11): 4139-4144.
[24] Grimmer A, Haselmayr W, Wille R. 2020. Automatic droplet sequence generation for microfluidic networks with passive droplet routing[J]. IEEE Transactions on Computer- Aided Design of Integrated Circuits and Systems, 39(2): 387.
[25] Grün D, Kester L, van Oudenaarden A. 2014. Validation of noise models for single-cell transcriptomics[J]. Nature Methods, 11(6): 637-640.
[26] Guillaumet-Adkins A, Rodriguez-Esteban G, Mereu E, et al. 2017. Single-cell transcriptome conservation in cryopreserved cells and tissues[J]. Genome Biology, 18(1): 45.
[27] Habib N, Avraham-Davidi I, Basu A, et al. 2017. Massively parallel single-nucleus RNA-seq with DroNc-seq[J]. Nature Methods, 14(10): 955-958.
[28] Hedlund E, Deng Q. 2018. Single-cell RNA sequencing: Technical advancements and biological applications[J]. Molecular Aspects of Medicine, 59: 36-46.
[29] Han X P, Wang Y C, Zhou Y C, et al. 2018. Mapping the mouse cell atlas by microwell-seq[J]. Cell, 172(5): 1091-1107.
[30] Hayrabedyan S, Kostova P, Zlatkov V, et al. 2021. Single-cell transcriptomics in the context of long-read nanopore sequencing[J]. Biotechnology and Biotechnological Equipment, 35(1):1439-1451.
[31] Herrera-Uribe J, Wiarda J E, Sivasankaran S K, et al. 2021. Reference transcriptomes of porcine peripheral immune cells created through bulk and single-cell RNA sequencing[J]. Frontiers in Genetics, 12: 689406.
[32] Herring C A, Banerjee A, McKinley E T, et al. 2018. Unsupervised trajectory analysis of single-cell RNA-seq and imaging data reveals alternative tuft cell origins in the gut[J]. Cell Systems, 6(1): 37-51.
[33] Hochgerner H, Lönnerberg P, Hodge R, et al. 2017. STRT-seq-2i: Dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array[J]. Scientific Reports, 7(1): 16327.
[34] Ibarra-Soria X, Jawaid W, Pijuan-Sala B, et al. 2018. Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation[J]. Nature Cell Biology, 20(2): 127-134.
[35] Islam S, Zeisel A, Joost S, et al. 2014. Quantitative single-cell RNA-seq with unique molecular identifiers[J]. Nature Methods, 11(2):163-166.
[36] Jensen B, Tobias W, Vincent M C, et al. 2013. Evolution and development of the building plan of the vertebrate heart[J]. Biochimica et Biophysica Acta, 1833(4): 783-794.
[37] Jaitin D A, Kenigsberg E, Keren-Shaul H, et al. 2014. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types[J]. Science, 343(6172): 776-779.
[38] Jang S H, Woo Y S, Lee S, et al. 2020. The Brain-Gut-Microbiome Axis in Psychiatry[J]. International Journal of Molecular Sciences, 21(19): 7122.
[39] Joost S, Zeisel A, Jacob T, et al. 2016. Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity[J]. Cell Systems, 3(3): 221-237.
[40] Kamme F, Salunga R, Yu J, et al. 2003. Single-cell microarray analysis in hippocampus CA1: demonstration and validation of cellular heterogeneity[J]. The Journal of Neuroscience the Official Journal of the Society for Neuroscience, 23(9): 3607-3615.
[41] Kim D H, Marinov G K, Pepke S, et al. 2015. Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming[J]. Cell Stem Cell, 16(1): 88-101.
[42] Kurimoto K, Yabuta Y, Ohinata Y, et al. 2007. Global single- cell cDNA amplification to provide a template for representative high-density oligonucleotide microarray analysis[J]. Nature Protocols, 2(3): 739-752.
[43] Lake B B, Codeluppi S, Yung Y C, et al. 2017. A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA[J]. Scientific Reports, 7(1): 6031.
[44] Lambolez B, Audinat E, Bochet P, et al. 1992. AMPA receptor subunits expressed by single Purkinje cells[J]. Neuron, 9(2): 247-258.
[45] Lavagi I, Krebs S, Simmet K, et al. 2018. Single-cell RNA sequencing reveals developmental heterogeneity of blastomeres during major genome activation in bovine embryos[J]. Scientific Reports, 8(1): 4071.
[46] Lafzi A, Moutinho C, Picelli S. 2018. Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies[J]. Nature Protocols, 13(12): 2742-2757.
[47] Li C Y, Liu Q L, Welborn M, et al. 2021. PSIV-6 differential gene expression of fibro/adipogenic progenitors between Wagyu and Brahman cattle: A possible contribution to their different meat quality[J]. Journal of Animal Science, 993: 301.
[48] Li F, Li D, Zhang M, et al. 2019. miRNA-223 targets the GPAM gene and regulates the differentiation of intramuscular adipocytes[J]. Gene, 685, 106-113.
[49] Liang J, Cai W, Sun Z. 2014. Single-cell sequencing technologies: Current and future[J]. Journal of Genetics and Genomics, 41(10): 513-528.
[50] Liu X M, Wang Y K, Liu Y H, et al. 2018. Single-cell transcriptome sequencing reveals that cell division cycle 5- like protein is essential for porcine oocyte maturation[J]. The Journal of Biological Chemistry, 293(5): 1767-1780.
[51] Ma S, Sun S H, Geng L L, et al. 2020. Caloric restriction reprograms the single-cell transcriptional landscape of rattus norvegicus aging[J]. Cell, 180(5): 984-1001.
[52] Merrick D, Sakers A, Lrgebay Z, et al. 2019. Identification of a mesenchymal progenitor cell hierarchy in adipose tissue[J]. Science, 364(6438): eaav2501.
[53] Mustachio L M, Roszik J. 2022. Single-cell sequencing: Current applications in precision onco-genomics and cancer therapeutics[J]. Cancers, 14(3): 657.
[54] Olsen T K, Baryawno N. 2018. Introduction to single-cell RNA sequencing[J]. Current Protocols in Molecular Biology, 122(1): e57.
[55] Peixoto A, Monteiro M, Rocha B, et al. 2004. Quantification of multiple gene expression in individual cells[J]. Genome Research, 14(10A): 1938-1947.
[56] Pietu G, Alibert O, Guichard V, et al. 1996. Novel gene transcripts preferentially expressed in human muscles revealed by quantitative hybridization of a high density cDNA array[J]. Genome Research, 6(6): 492-503.
[57] Pijuan-Sala B, Griffiths J A, Guibentif C, et al. 2019. A single- cell molecular map of mouse gastrulation and early organogenesis[J]. Nature, 566(7745): 490-495.
[58] Pockwinse S M, Wilming L G, Conlon D M, et al. 1992. Expression of cell growth and bone specific genes at single cell resolution during development of bone tissue-like organization in primary osteoblast cultures[J]. Journal of Cellular Biochemistry, 49(3): 310-323.
[59] Pollen A A, Nowakowski T J, Shuga J, et al. 2014. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex[J]. Nature Biotechnology, 32(10): 1053-1058.
[60] Qu X Y, Li X B, Li Z W, et al. 2022. Chicken peripheral blood mononuclear cells response to Avian leukosis virus subgroup J infection assessed by single-cell RNA sequencing[J]. Frontiers in Microbiology, 13: 800618.
[61] Regev A, Teichmann S A, Lander E S, et al. 2017. The Human Cell Atlas[J]. eLife, 6: e27041.
[62] Schwalie P C, Dong H, Zachara M, et al. 2018. A stromal cell population that inhibits adipogenesis in mammalian fat depots[J]. Nature, 559(7712): 103-108.
[63] Scott A Y, Michael J B, Brendan T I, et al. 2017. Developmental emergence of adult neural stem cells as revealed by single-cell transcriptional profiling[J]. Cell Reports, 21(13): 3970-3986.
[64] Shum E Y, Walczak E M, Chang C, et al. 2019. Quantitation of mRNA transcripts and proteins using the BD rhapsody single-cell analysis system[J]. Advances in Experimental Medicine and Biology, 1129: 63-79.
[65] Su X B, Shi Y, Zou X, et al. 2017. Single-cell RNA-Seq analysis reveals dynamic trajectories during mouse liver development[J]. BMC Genomics, 18(1): 946.
[66] Svensson V, Vento-Tormo R. 2018. Exponential scaling of single-cell RNA-seq in the past decade[J]. Nature Protocols, 13(4): 599-604.
[67] Sun D, Liu Z, Li T, et al. 2022. STRIDE: Accurately decomposing and integrating spatial transcriptomics using single-cell RNA sequencing[J]. Nucleic Acids Research, 50(7): e42.
[68] Tang F, Barbacioru C, Wang Y, et al. 2009. mRNA-Seq whole- transcriptome analysis of a single cell[J]. Nature Methods, 6(5): 377-382.
[69] Tietjen I, Rihel J M, Cao Y, et al. 2003. Single-cell transcriptional analysis of neuronal progenitors[J]. Neuron, 38(2): 161-175.
[70] Treutlein B, Brownfield D G, Wu A R, et al. 2014. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq[J]. Nature, 509(7500): 371-375.
[71] Villageliu D N, Lyte M. 2017. Microbial endocrinology: Why the intersection of microbiology and neurobiology matters to poultry health[J]. Poultry Science, 96(8): 2501-2508.
[72] Villani A, Satija R, Reynolds G, et al. 2017. Single-cell RNA- seq reveals new types of human blood dendritic cells, monocytes, and progenitors[J]. Science, 356(6335): eaah4573.
[73] Wang S H, Wu T Y, Sun J Y, et al. 2021a. Single-cell transcriptomics reveals the molecular anatomy of sheep hair follicle heterogeneity and wool curvature[J]. Frontiers in Cell and Developmental Biology, 9: 800157.
[74] Wang W, Penland L, Gokce O, et al. 2018. High fidelity hypothermic preservation of primary tissues in organ transplant preservative for single cell transcriptome analysis[J]. BMC Genomics, 19(1): 140.
[75] Wang X, Ning Y, Zhang P, et al. 2021b. Comparison of the major cell populations among osteoarthritis, Kashin- Beck disease and healthy chondrocytes by single-cell RNA-seq analysis[J]. Cell Death Disease, 12(6): 551.
[76] Wollny D, Zhao S, Everlien I, et al. 2016. Single-cell analysis uncovers clonal acinar cell heterogeneity in the adult pancreas[J]. Development Cell, 39(3): 289-301.
[77] Yu Z, Liao J, Chen Y, et al. 2019. Single-cell transcriptomic map of the human and mouse bladders[J]. Journal of the American Society of Nephrology, 30(11): 2159-2176.
[78] Yang Y, Sun H, Zhang Y Zhang T, et al. 2021. Dimensionality reduction by UMAP reinforces sample heterogeneity analysis in bulk transcriptomic data[J]. Cell Reports, 36(4): 109442.
[79] Zeisel A, Munoz-Manchado A B, Codeluppi S, et al. 2015. Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq[J]. Science, 347(6226): 1138-1142.
[80] Zhang J, Lv C, Mo C, et al. 2021. Single-cell RNA sequencing analysis of chicken anterior pituitary: A bird's-eye view on vertebrate pituitary[J]. Frontiers in Physiology, 12: 562817.
[81] Zhu Y, Huang Y H, Tan Y, et al. 2020. Single-cell RNA sequencing in hematological diseases[J]. Proteomics, 20(13): e1900228. |
|
|
|
