单细胞RNA测序技术在病毒研究中的应用

doi:10.16288/j.yczz.19-223

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Hereditas(Beijing) ›› 2020, Vol. 42 ›› Issue (3): 269-277.doi: 10.16288/j.yczz.19-223

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Applications of single-cell RNA sequencing in virology

Liang Qu, Su Li, Huaji Qiu()

State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China

Received:2019-10-31 Revised:2020-01-10 Online:2020-03-20 Published:2020-01-17
Contact: Qiu Huaji E-mail:qiuhuaji@caas.cn
Supported by:
Supported by the National Natural Science Foundation of China Nos(31630080);Supported by the National Natural Science Foundation of China Nos(31672537)

Abstract

Abstract:

Single-cell RNA sequencing (scRNA-seq) is now emerging as a powerful tool to characterize the roles of cell heterogeneity in many fields, including virus infection. Transcriptional profiling at the single-cell level has enabled a greater appreciation of the dynamic changes of virus infection and the complex interactions between viruses and host cells. In this review, we briefly introduce the scRNA-seq technology, and the researches progress of scRNA-seq applied to virus infection. Moreover, we summarize the effects of cell heterogeneity, such as cell cycle, gene expression, and cell state, and virus mutations on the virus infection. We also analyze the unique advantages of scRNA-seq in researches of the dynamic changes of virus-host interaction, and the profound prospects of this technology used in virology for future studies. This review aims to provide a useful reference for the application of scRNA-seq in the understanding of the viral infection and pathogenicity mechanisms which may lead to the development of potential antiviral targets.

Key words: single cell RNA sequencing, heterogeneity, virus infection

Liang Qu, Su Li, Huaji Qiu. Applications of single-cell RNA sequencing in virology[J]. Hereditas(Beijing), 2020, 42(3): 269-277.

Figures/Tables 1

References 57

[1]	Kalisky T, Blainey P, Quake SR . Genomic analysis at the single-cell level. Annu Rev Genet, 2011,45:431-445.
[2]	Di Palma S, Bodenmiller B . Unraveling cell populations in tumors by single-cell mass cytometry. Curr Opin Biotechnol, 2015,31:122-129.
[3]	Yuan JD, Hegde PS, Clynes R, Foukas PG, Harari A, Kleen TO, Kvistborg P, Maccalli C, Maecker HT, Page DB, Robins H, Song WR, Stack EC, Wang EN, Whiteside TL, Zhao YD, Zwierzina H, Butterfield LH, Fox BA . Novel technologies and emerging biomarkers for personalized cancer immunotherapy. J Immunother Cancer, 2016,4(1):3.
[4]	Winter DR, Ledergor G, Amit I . From mass cytometry to cancer prognosis. Nat Biotechnol, 2015,33(9):931-932.
[5]	Tang FC, Barbacioru C, Wang YZ, Nordman E, Lee C, Xu NL, Wang XH, Bodeau J, Tuch BB, Siddiqui A, Lao KQ, Surani MA. mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods, 2009,6(5):377-382.
[6]	Razooky BS, Gutierrez E, Terry VH, Spina CA, Groisman A, Weinberger LS . Microwell devices with finger-like channels for long-term imaging of HIV-1 expression kinetics in primary human lymphocytes. Lab Chip, 2012,12(21):4305-4312.
[7]	Hu P, Zhang WH, Xin HB, Deng G . Single cell isolation and analysis. Front Cell Dev Biol, 2016,4:116.
[8]	Prakadan SM, Shalek AK, Weitz DA . Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices. Nat Rev Genet, 2017,18(6):345-361.
[9]	Yao YX, La YF, Di R, Liu QY, Hu WP, Wang XY, Chu MX . Comparison of different single cell whole genome amplification methods and MALBAC applications in assisted reproduction. Hereditas(Beijing), 2018,40(8):620-631.
	姚雅馨, 喇永富, 狄冉, 刘秋月, 胡文萍, 王翔宇, 储明星 . 不同单细胞全基因组扩增方法的比较及MALBAC在辅助生殖中的应用. 遗传, 2018,40(8):620-631.
[10]	Stoeger T, Battich N, Pelkmans L . Passive noise filtering by cellular compartmentalization. Cell, 2016,164(6):1151-1161.
[11]	Wang Y, Navin NE . Advances and applications of single- cell sequencing technologies. Mol Cell, 2015,58(4):598-609.
[12]	Puram SV, Tirosh I, Parikh AS, Patel AP, Yizhak K, Gillespie S, Rodman C, Luo CL, Mroz EA, Emerick KS, Deschler DG, Varvares MA, Mylvaganam R, Rozenblatt- Rosen O, Rocco JW, Faquin WC, Lin DT, Regev A, Bernstein BE . Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer. Cell, 2017,171(7):1611-1624.
[13]	Patil VS, Madrigal A, Schmiedel BJ, Clarke J, O'rourke P, De Silva AD, Harris E, Peters B, Seumois G, Weiskopf D, Sette A, Vijayanand P. Precursors of human CD4 + cytotoxic T lymphocytes identified by single-cell transcriptome analysis. Sci Immunol, 2018,3(19): eaan8664.
[14]	Jaitin DA, Kenigsberg E, Keren-Shaul H, Elefant N, Paul F, Zaretsky I, Mildner A, Cohen N, Jung S, Tanay A, Amit I . Massively parallel single-cell rna-seq for marker-free decomposition of tissues into cell types. Science, 2014,343(6172):776-779.
[15]	Drayman N, Patel P, Vistain L, Tay S . HSV-1 single-cell analysis reveals the activation of anti-viral and developmental programs in distinct sub-populations. eLife, 2019,8:e46339.
[16]	Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL . The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol, 2014,32(4):381-386.
[17]	Yan LY, Yang MY, Guo HS, Yang L, Wu J, Li R, Liu P, Lian Y, Zheng XY, Yan J, Huang J, Li M, Wu XL, Wen L, Lao KQ, Li RQ, Qiao J, Tang FC . Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol, 2013,20(9):1131-1139.
[18]	Saliba AE, Li L, Westermann AJ, Appenzeller S, Stapels DA, Schulte LN, Helaine S, Vogel J . Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella. Nat Microbiol, 2016,2:1-8.
[19]	Lake BB, Ai R, Kaeser GE, Salathia NS, Yung YC, Liu R, Wildberg A, Gao D, Fung HL, Chen S, Vijayaraghavan R, Wong J, Chen A, Sheng X, Kaper F, Shen R, Ronaghi M, Fan JB, Wang W, Chun J, Zhang K . Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. Science, 2016,352(6293):1586-1590.
[20]	Habib N, Li YQ, Heidenreich M, Swiech L, Avraham- Davidi I, Trombetta JJ, Hession C, Zhang F, Regev A . Div-Seq: single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons. Science, 2016,353(6302):925-928.
[21]	Wesolowska-Andersen A, Everman JL, Davidson R, Rios C, Herrin R, Eng C, Janssen WJ, Liu AH, Oh SS, Kumar R, Fingerlin TE, Rodriguez-Santana J, Burchard EG, Seibold MA . Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome. Genome Biol, 2017,18(1):12.
[22]	Krzywkowski T, Ciftci S, Assadian F, Nilsson M, Punga T . Simultaneous single-cell in situ analysis of human adenovirus type 5 dna and mrna expression patterns in lytic and persistent infection. J Virol, 2017,91(11):e00166-17.
[23]	Hoeve MA, Nash AA, Jackson D, Randall RE, Dransfield I . Influenza virus A infection of human monocyte and macrophage subpopulations reveals increased susceptibility associated with cell differentiation. PLoS One, 2012,7(1):e29443.
[24]	Mussil B, Suspène R, Caval V, Durandy A, Wain-Hobson S, Vartanian JP . Genotoxic stress increases cytoplasmic mitochondrial DNA editing by human APOBEC3 mutator enzymes at a single cell level. Sci Rep, 2019,9(1):3109.
[25]	Lodge R, Gilmore JC, Ferreira Barbosa JA, Lombard- Vadnais F, Cohen ÉA . Regulation of CD4 receptor and HIV-1 entry by microRNAs-221 and -222 during differentiation of THP-1 cells. Viruses, 2017,10(1):13.
[26]	Afik S, Yates KB, Bi K, Darko S, Godec J, Gerdemann U, Swadling L, Douek DC, Klenerman P, Barnes EJ, Sharpe AH, Haining WN, Yosef N . Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state. Nucleic Acids Res, 2017,45(16):e148.
[27]	Wu L, Zhang XL, Zhao ZK, Wang L, Li B, Li GB, Dean M, Yu QC, Wang YH, Lin XX, Rao WJ, Mei ZL, Li Y, Jiang RZ, Yang H, Li FQ, Xie GY, Xu LQ, Wu K, Zhang J, Chen JH, Wang T, Kristiansen K, Zhang XQ, Li YR, Yang HM, Wang J, Hou Y, Xu X . Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells. Gigascience, 2015,4(1):51.
[28]	Tsioris K, Gupta NT, Ogunniyi AO, Zimnisky RM, Qian F, Yao Y, Wang X, Stern JN, Chari R, Briggs AW, Clouser CR, Vigneault F, Church GM, Garcia MN, Murray KO, Montgomery RR, Kleinstein SH, Love JC . Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing. Integr Biol (Camb), 2015,7(12):1587-1597.
[29]	Gorman MJ, Caine EA, Zaitsev K, Begley MC, Weger- Lucarelli J, Uccellini MB, Tripathi S, Morrison J, Yount BL, Dinnon KH 3rd, Rückert C, Young MC, Zhu Z, Robertson SJ, Mcnally KL, Ye J, Cao B, Mysorekar IU, Ebel GD, Baric RS, Best SM, Artyomov MN, Garcia- Sastre A, Diamond MS . An immunocompetent mouse model of zika virus infection. Cell Host Microbe, 2018,23(5):672-685.
[30]	Johnson TS, Abrams ZB, Mo XK, Zhang Y, Huang K . Lack of human cytomegalovirus expression in single cells from glioblastoma tumors and cell lines. J Neurovirol, 2017,23(5):671-678.
[31]	Golumbeanu M, Cristinelli S, Rato S, Munoz M, Cavassini M, Beerenwinkel N, Ciuffi A . Single-Cell RNA-Seq Reveals transcriptional heterogeneity in latent and reactivated hiv-infected cells. Cell Rep, 2018,23(4):942-950.
[32]	Zanini F, Robinson ML, Croote D, Sahoo MK, Sanz AM, Ortiz-Lasso E, Albornoz LL, Rosso F, Montoya JG, Goo L, Pinsky BA, Quake SR, Einav S . Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue. Proc Natl Acad Sci USA, 2018,115(52):E12363-E21369.
[33]	Kannan RP, Hensley LL, Evers LE, Lemon SM, Mcgivern DR . Hepatitis C virus infection causes cell cycle arrest at the level of initiation of mitosis. J Virol, 2011,85(16):7989-8001.
[34]	Timm A, Yin J . Kinetics of virus production from single cells. Virology, 2012,424(1):11-17.
[35]	Xin X, Wang HL, Han LL, Wang MZ, Fang H, Hao Y, Li JD, Zhang H, Zheng CY, Shen C . Single-cell analysis of the impact of host cell heterogeneity on infection with foot-and-mouth disease virus. J Virol, 2018,92(9):e00179-18.
[36]	Schulte MB, Andino R . Single-cell analysis uncovers extensive biological noise in poliovirus replication. J Virol, 2014,88(11):6205-6212.
[37]	Heldt FS, Kupke SY, Dorl S, Reichl U, Frensing T . Single-cell analysis and stochastic modelling unveil large cell-to-cell variability in influenza A virus infection. Nat Commun, 2015,6:8938.
[38]	Zhu Y, Yongky A, Yin J . Growth of an RNA virus in single cells reveals a broad fitness distribution. Virology, 2009,385(1):39-46.
[39]	Kempe H, Schwabe A, Crémazy F, Verschure PJ, Bruggeman FJ . The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise. Mol Biol Cell, 2015,26(4):797-804.
[40]	He Y, Xu K, Keiner B, Zhou JF, Czudai V, Li TX, Chen Z, Liu JH, Klenk HD, Shu YL, Sun B . Influenza A virus replication induces cell cycle arrest in G₀/G₁ phase. J Virol, 2010,84(24):12832-12840.
[41]	Bradley T, Ferrari G, Haynes BF, Margolis DM, Browne EP . Single-cell analysis of quiescent HIV infection reveals host transcriptional profiles that regulate proviral latency. Cell Rep, 2018,25(1):107-117.
[42]	Golumbeanu M, Cristinelli S, Rato S, Munoz M, Cavassini M, Beerenwinkel N, Ciuffi A . Single-cell RNA-seq reveals transcriptional heterogeneity in latent and reactivated HIV-infected cells. Cell Rep, 2018,23(4):942-950.
[43]	Ma JZ, Russell TA, Spelman T, Carbone FR, Tscharke DC . Lytic gene expression is frequent in HSV-1 latent infection and correlates with the engagement of a cell-intrinsic transcriptional response. Plos Pathog, 2014,10(7):e1004237.
[44]	Zanini F, Pu SY, Bekerman E, Einav S, Quake SR . Single-cell transcriptional dynamics of flavivirus infection. eLife, 2018,7:e32942.
[45]	Medigeshi GR, Lancaster AM, Hirsch AJ, Briese T, Lipkin WI, Defilippis V, Früh K, Mason PW, Nikolich-Zugich J, Nelson JA . West Nile virus infection activates the unfolded protein response, leading to CHOP induction and apoptosis. J Virol, 2007,81(20):10849-10860.
[46]	Marceau CD, Puschnik AS, Majzoub K, Ooi YS, Brewer SM, Fuchs G, Swaminathan K, Mata MA, Elias JE, Sarnow P, Carette JE . Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens. Nature, 2016,535(7610):159-163.
[47]	Metz P, Chiramel A, Chatel-Chaix L, Alvisi G, Bankhead P, Mora-Rodriguez R, Long G, Hamacher-Brady A, Brady NR, Bartenschlager R . Dengue virus inhibition of autophagic flux and dependency of viral replication on proteasomal degradation of the autophagy receptor p62. J Virol, 2015,89(15):8026-8041.
[48]	Killip MJ, Jackson D, Pérez-Cidoncha M, Fodor E, Randall RE . Single-cell studies of IFN-β promoter activation by wild-type and NS1-defective influenza A viruses. J Gen Virol, 2017,98(3):357-363.
[49]	Jackson D, Killip MJ, Galloway CS, Russell RJ, Randall RE . Loss of function of the influenza A virus NS1 protein promotes apoptosis but this is not due to a failure to activate phosphatidylinositol 3-kinase (PI3K). Virology, 2010,396(1):94-105.
[50]	O'neal JT, Upadhyay AA, Wolabaugh A, Patel NB, Bosinger SE, Suthar MS . West Nile virus-inclusive single-cell RNA sequencing reveals heterogeneity in the type i interferon response within single cells. J Virol, 2019,93(6):e01778-18.
[51]	Quicke KM, Suthar MS . The innate immune playbook for restricting West Nile virus infection. Viruses, 2013,5(11):2643-2658.
[52]	Wimmers F, Subedi N, Van Buuringen N, Heister D, Vivie J, Beeren-Reinieren I, Woestenenk R, Dolstra H, Piruska A, Jacobs JFM, Van Oudenaarden A, Figdor CG, Huck WTS, De Vries IJM, Tel J . Single-cell analysis reveals that stochasticity and paracrine signaling control interferon- alpha production by plasmacytoid dendritic cells. Nat Commun, 2018,9(1):3317.
[53]	Bhushal S, Wolfsmüller M, Selvakumar TA, Kemper L, Wirth D, Hornef MW, Hauser H, Köster M . Cell polarization and epigenetic status shape the heterogeneous response to type III interferons in intestinal epithelial cells. Front Immunol, 2017,8:671.
[54]	Lauring AS, Frydman J, Andino R . The role of mutational robustness in RNA virus evolution. Nat Rev Microbiol, 2013,11(5):327-336.
[55]	Combe M, Garijo R, Geller R, Cuevas JM, Sanjuán R . Single-cell analysis of RNA virus infection identifies multiple genetically diverse viral genomes within single infectious units. Cell Host Microbe, 2015,18(4):424-432.
[56]	Russell AB, Elshina E, Kowalsky JR, Te Velthuis AJW, Bloom JD . Single-cell virus sequencing of influenza infections that trigger innate immunity. J Virol, 2019,93(14):e00500-19.
[57]	Hale BG, Randall RE, Ortín J, Jackson D . The multifunctional NS1 protein of influenza A viruses. J Gen Virol, 2008,89:2359-2376.

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