山东大学耳鼻喉眼学报 ›› 2025, Vol. 39 ›› Issue (1): 162-170.doi: 10.6040/j.issn.1673-3770.0.2023.222

• 综述 • 上一篇    

单细胞RNA测序技术在视网膜中的研究进展

杨淞月,张美霞   

  1. 四川大学华西医院 眼科, 四川 成都 610041
  • 发布日期:2025-01-17
  • 通讯作者: 张美霞. E-mail:zhangmeixia@scu.edu.cn

Advances in single-cell RNA sequencing in the retina

YANG Songyue, ZHANG Meixia   

  1. Department of Ophthalmology, West China Hospital, Sichuan University, Sichuan 610041, Chengdu, China
  • Published:2025-01-17

摘要: 视网膜是充满异质性的组织,其结构复杂,由多种细胞构成,且每个细胞都拥有其独特的转录组信息。以往传统的RNA测序技术实现了对视网膜细胞整体的转录组测序研究。近年来,单细胞RNA测序(single-cell RNA sequencing, scRNA-seq)技术的出现,使我们能够从单个细胞水平出发,对不同视网膜细胞的转录组进行测序和分析,更精准地进行细胞分类,探索其生理功能及发育特点。目前,scRNA-seq主要集中于各种视网膜疾病的机制研究。本文首先对scRNA-seq原理进行简要介绍,随后对scRNA-seq技术在视网膜中的应用研究展开综述,包括视网膜细胞亚型及特异性标志物的发现,视网膜疾病的发病机制,视网膜生长发育的特点,不同部位的视网膜组织以及不同物种视网膜的差异性比较等方面,最后对其未来发展方向进行展望。

关键词: 单细胞RNA测序, 转录组, 异质性, 视网膜, 视网膜病变

Abstract: The retina is a heterogeneous tissue. This intricate structure is composed of various types of cells with distinct transcriptomes. The traditional bulk RNA sequencing has quantified the global transcriptome of retinal cells. In recent years, single-cell RNA sequencing(scRNA-seq)methods have enabled profiling the transcriptome of retinal cells at a single-cell resolution, improving our understanding of cell classification, physiology, and developmental patterns of the retina. Currently, scRNA-seq is mainly focused on exploring the mechanism of retinal diseases. This review provides a comprehensive overview of the utilization of scRNA-seq in retinal research. It encompasses the delineation of cell subtypes, identification of specific markers, insights into retinal disease pathogenesis, developmental patterns, interspecies and interregional retinal tissue comparisons, as well as a concise introduction to scRNA-seq methodologies and prospective advancements in the field.

Key words: Single-cell RNA sequencing, Transcriptome, Heterogeneity, Retina, Retinopathy

中图分类号: 

  • R774.1
[1] Hangauer MJ, Vaughn IW, McManus MT. Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs[J]. PLoS Genet, 2013, 9(6): 1003569. doi:10.1371/journal.pgen.1003569
[2] Cech T, Steitz J. The noncoding RNA revolution—trashing old rules to forge new ones[J]. Cell, 2014, 157(1): 77-94. doi:10.1016/j.cell.2014.03.008
[3] Farkas MH, Grant GR, White JA, et al. Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes[J]. BMC Genomics, 2013, 14: 486. doi:10.1186/1471-2164-14-486
[4] Tang FC, Barbacioru C, Wang YZ, et al. mRNA-Seq whole-transcriptome analysis of a single cell[J]. Nat Methods, 2009, 6(5): 377-382. doi:10.1038/nmeth.1315
[5] Macosko E, 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. doi:10.1016/j.cell.2015.05.002
[6] Haque A, Engel J, Teichmann SA, et al. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications[J].Genome Med, 2017, 9(1): 1-12. doi:10.1186/s13073-017-0467-4
[7] Jin SQ, Guerrero-Juarez CF, Zhang LH, et al. Inference and analysis of cell-cell communication using CellChat[J]. Nat Commun, 2021, 12(1): 1088. doi:10.1038/s41467-021-21246-9
[8] Lukowski SW, Lo CY, Sharov AA, et al. A single-cell transcriptome atlas of the adult human retina[J]. EMBO J, 2019, 38(18): e100811. doi:10.15252/embj.2018100811
[9] Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles[J]. Proc Natl Acad Sci USA, 2005, 102(43): 15545-15550. doi:10.1073/pnas.0506580102
[10] Menon M, Mohammadi S, Davila-Velderrain J, et al. Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration[J]. Nat Commun, 2019, 10(1): 4902. doi:10.1038/s41467-019-12780-8
[11] Collin J, Queen R, Zerti D, et al. Deconstructing retinal organoids: single cell RNA-seq reveals the cellular components of human pluripotent stem cell-derived retina[J]. Stem Cells, 2019, 37(5): 593-598. doi:10.1002/stem.2963
[12] Pandey RS, Krebs MP, Bolisetty MT, et al. Single-cell RNA sequencing reveals molecular features of heterogeneity in the murine retinal pigment epithelium[J]. Int J Mol Sci, 2022, 23(18): 10419. doi:10.3390/ijms231810419
[13] Li QY, Barres BA. Microglia and macrophages in brain homeostasis and disease[J]. Nat Rev Immunol, 2018, 18(4): 225-242. doi:10.1038/nri.2017.125
[14] Ronning KE, Karlen SJ, Miller EB, et al. Molecular profiling of resident and infiltrating mononuclear phagocytes during rapid adult retinal degeneration using single-cell RNA sequencing[J]. Sci Rep, 2019, 9(1): 4858. doi:10.1038/s41598-019-41141-0
[15] Wieghofer P, Hagemeyer N, Sankowski R, et al. Mapping the origin and fate of myeloid cells in distinct compartments of the eye by single-cell profiling[J]. EMBO J, 2021, 40(6): 105123. doi:10.15252/embj.2020105123
[16] Shekhar K, Lapan SW, Whitney IE, et al. Comprehensive classification of retinal bipolar neurons by single-cell transcriptomics[J]. Cell, 2016, 166(5): 1308-1323.e30. doi:10.1016/j.cell.2016.07.054
[17] Jeon CJ, Strettoi E, Masland RH. The major cell populations of the mouse retina[J]. J Neurosci, 1998, 18(21): 8936-8946. doi:10.1523/jneurosci.18-21-08936.1998
[18] Rheaume BA, Jereen A, Bolisetty M, et al. Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes[J]. Nat Commun, 2018, 9(1): 2759. doi:10.1038/s41467-018-05134-3
[19] Peng YR, Shekhar K, Yan WJ, et al. Molecular classification and comparative taxonomics of foveal and peripheral cells in primate retina[J]. Cell, 2019, 176(5): 1222-1237,22. doi:10.1016/j.cell.2019.01.004
[20] Theune WC, Frost MP, Trakhtenberg EF. Transcriptomic profiling of retinal cells reveals a subpopulation of microglia/macrophages expressing Rbpms marker of retinal ganglion cells(RGCs)that confound identification of RGCs[J]. Brain Res, 2023, 1811: 148377. doi:10.1016/j.brainres.2023.148377
[21] Welby E, Lakowski J, Di Foggia V, et al. Isolation and comparative transcriptome analysis of human fetal and iPSC-derived cone photoreceptor cells[J]. Stem Cell Rep, 2017, 9(6): 1898-1915. doi:10.1016/j.stemcr.2017.10.018
[22] Fritsche LG, Igl W, Cooke Bailey JN, et al. A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants[J]. Nat Genet, 2016, 48(2): 134-143. doi:10.1038/ng.3448
[23] Gamazon ER, Wheeler HE, Shah KP, et al. A gene-based association method for mapping traits using reference transcriptome data[J]. Nat Genet, 2015, 47(9): 1091-1098. doi:10.1038/ng.3367
[24] Cookson W, Liang LM, Abecasis G, et al. Mapping complex disease traits with global gene expression[J]. Nat Rev Genet, 2009, 10(3): 184-194. doi:10.1038/nrg2537
[25] Orozco LD, Chen HH, Cox C, et al. Integration of eQTL and a single-cell atlas in the human eye identifies causal genes for age-related macular degeneration[J]. Cell Rep, 2020, 30(4): 1246-1259.e6. doi:10.1016/j.celrep.2019.12.082
[26] Mullins RF, Schoo DP, Sohn EH, et al. The membrane attack complex in aging human choriocapillaris: relationship to macular degeneration and choroidal thinning[J]. Am J Pathol, 2014, 184(11): 3142-3153. doi:10.1016/j.ajpath.2014.07.017
[27] Voigt AP, Mulfaul K, Mullin NK, et al. Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration[J]. Proc Natl Acad Sci USA, 2019, 116(48): 24100-24107. doi:10.1073/pnas.1914143116
[28] An Xiaojin, Jin Yi, Guo Hongnian, et al. Response gene to complement 32, a novel hypoxia-regulated angiogenic inhibitor[J]. Circulation, 2009, 120(7):617-627. doi: 10.1161/CIRCULATIONAHA.108.841502
[29] Voigt AP, Whitmore SS, Mulfaul K, et al. Bulk and single-cell gene expression analyses reveal aging human choriocapillaris has pro-inflammatory phenotype[J]. Microvasc Res, 2020, 131: 104031. doi:10.1016/j.mvr.2020.104031
[30] McLeod DS, Lefer DJ, Merges C, et al. Enhanced expression of intracellular adhesion molecule-1 and P-selectin in the diabetic human retina and choroid[J]. Am J Pathol, 1995, 147(3): 642-653.
[31] Steen R, Egeland T. CD34 molecule epitope distribution on cells of haematopoietic origin[J]. Leuk Lymphoma, 1998, 30(1/2): 23-30. doi:10.3109/10428199809050926
[32] Rohlenova K, Goveia J, García-Caballero M, et al. Single-cell RNA sequencing maps endothelial metabolic plasticity in pathological angiogenesis[J]. Cell Metab, 2020, 31(4): 862-877, 14. doi:10.1016/j.cmet.2020.03.009
[33] Jampol LM. Antioxidants and zinc to prevent progression of age-related macular degeneration[J]. JAMA, 2001, 286(19): 2466. doi:10.1001/jama.286.19.2466
[34] Emri E, Cappa O, Kelly C, et al. Zinc supplementation induced transcriptional changes in primary human retinal pigment epithelium: a single-cell RNA sequencing study to understand age-related macular degeneration[J]. Cells, 2023, 12(5): 773. doi:10.3390/cells12050773
[35] Cao JY, Spielmann M, Qiu XJ, et al. The single-cell transcriptional landscape of mammalian organogenesis[J]. Nature, 2019, 566(7745): 496-502. doi:10.1038/s41586-019-0969-x
[36] 王娇娇, 李苗. 糖尿病视网膜病变的机制和细胞模型研究进展[J]. 山东大学耳鼻喉眼学报, 2022, 36(5): 93-99. doi: 10.6040/j.issn.1673-3770.0.2021.203 WANG Jiaojiao, LI Miao. Progress in diabetic retinopathy mechanisms and cellular models[J]. Journal of Otolaryngology and Ophthalmology of Shandong University, 2022, 36(5): 93-99. doi: 10.6040/j.issn.1673-3770.0.2021.203
[37] Van Hove I, De Groef L, Boeckx B, et al. Single-cell transcriptome analysis of the Akimba mouse retina reveals cell-type-specific insights into the pathobiology of diabetic retinopathy[J]. Diabetologia, 2020, 63(10): 2235-2248. doi:10.1007/s00125-020-05218-0
[38] Sun LC, Wang RN, Hu GY, et al. Single cell RNA sequencing(scRNA-Seq)deciphering pathological alterations in streptozotocin-induced diabetic retinas[J]. Exp Eye Res, 2021, 210: 108718. doi:10.1016/j.exer.2021.108718
[39] Niu T, Fang JW, Shi X, et al. Pathogenesis study based on high-throughput single-cell sequencing analysis reveals novel transcriptional landscape and heterogeneity of retinal cells in type 2 diabetic mice[J]. Diabetes, 2021, 70(5): 1185-1197. doi:10.2337/db20-0839
[40] de Carvalho JRL Jr, Kim HJ, Ueda K, et al. Effects of deficiency in the RLBP1-encoded visual cycle protein CRALBP on visual dysfunction in humans and mice[J]. J Biol Chem, 2020, 295(19): 6767-6780. doi:10.1074/jbc.RA120.012695
[41] Chen K, Wang YH, Huang YY, et al. Cross-species scRNA-seq reveals the cellular landscape of retina and early alterations in type 2 diabetes mice[J]. Genomics, 2023, 115(4): 110644. doi:10.1016/j.ygeno.2023.110644
[42] Buckley MT, Sun ED, George BM, et al. Cell-type-specific aging clocks to quantify aging and rejuvenation in neurogenic regions of the brain[J]. Nat Aging, 2023, 3(1): 121-137. doi:10.1038/s43587-022-00335-4
[43] Becker K, Klein H, Simon E, et al. In-depth transcriptomic analysis of human retina reveals molecular mechanisms underlying diabetic retinopathy[J]. Sci Rep, 2021, 11(1): 10494. doi:10.1038/s41598-021-88698-3
[44] Xiao YH, Hu X, Fan SX, et al. Single-cell transcriptome profiling reveals the suppressive role of retinal neurons in microglia activation under diabetes mellitus[J]. Front Cell Dev Biol, 2021, 9: 680947. doi:10.3389/fcell.2021.680947
[45] Liu ZP, Shi HD, Xu JA, et al. Single-cell transcriptome analyses reveal microglia types associated with proliferative retinopathy[J]. JCI Insight, 2022, 7(23): 160940. doi:10.1172/jci.insight.160940
[46] Bell OH, Copland DA, Ward A, et al. Single eye mRNA-seq reveals normalisation of the retinal microglial transcriptome following acute inflammation[J]. Front Immunol, 2020, 10: 3033. doi:10.3389/fimmu.2019.03033
[47] Shi Yunhong, Liu Yidan, Wu Caiqing, et al. N, N-Dimethyl-3β-hydroxycholenamide attenuates neuronal death and retinal inflammation in retinal ischemia/reperfusion injury by inhibiting Ninjurin 1[J]. J Neuroinflammation, 2023, 20(1):91. doi: 10.1186/s12974-023-02754-5
[48] Schneider N, Sundaresan Y, Gopalakrishnan P, et al. Inherited retinal diseases: linking genes, disease-causing variants, and relevant therapeutic modalities[J]. Prog Retin Eye Res, 2022, 89: 101029. doi:10.1016/j.preteyeres.2021.101029
[49] Chang B, Hawes NL, Hurd RE, et al. Retinal degeneration mutants in the mouse[J]. Vis Res, 2002, 42(4): 517-525. doi:10.1016/S0042-6989(01)00146-8
[50] Chen YY, Dong YJ, Yan J, et al. Single-cell transcriptomic profiling in inherited retinal degeneration reveals distinct metabolic pathways in rod and cone photoreceptors[J]. Int J Mol Sci, 2022, 23(20): 12170. doi:10.3390/ijms232012170
[51] Dong YJ, Xu WR, Li Y, et al. Inhibition of the MAPK/c-Jun-EGR1 pathway decreases photoreceptor cell death in the rd1 mouse model for inherited retinal degeneration[J]. Int J Mol Sci, 2022, 23(23): 14600. doi:10.3390/ijms232314600
[52] Kumari A, Ayala-Ramirez R, Zenteno JC, et al. Single cell RNA sequencing confirms retinal microglia activation associated with early onset retinal degeneration[J]. Sci Rep, 2022, 12(1): 15273. doi:10.1038/s41598-022-19351-w
[53] Clark BS, Stein-O’Brien GL, Shiau F, et al. Single-cell RNA-seq analysis of retinal development identifies NFI factors as regulating mitotic exit and late-born cell specification[J]. Neuron, 2019, 102(6): 1111-1126.e5. doi:10.1016/j.neuron.2019.04.010
[54] Lyu P, Hoang T, Santiago CP, et al. Gene regulatory networks controlling temporal patterning, neurogenesis, and cell-fate specification in mammalian retina[J]. Cell Rep, 2021, 37(7): 109994. doi:10.1016/j.celrep.2021.109994
[55] Hu YQ, Wang XY, Hu BQ, et al. Dissecting the transcriptome landscape of the human fetal neural retina and retinal pigment epithelium by single-cell RNA-seq analysis[J]. PLoS Biol, 2019, 17(7): 3000365. doi:10.1371/journal.pbio.3000365
[56] Norrie JL, Lupo MS, Xu BS, et al. Nucleome dynamics during retinal development[J]. Neuron, 2019, 104(3): 512-528, 11. doi:10.1016/j.neuron.2019.08.002
[57] Voigt AP, Whitmore SS, Flamme-Wiese MJ, et al. Molecular characterization of foveal versus peripheral human retina by single-cell RNA sequencing[J]. Exp Eye Res, 2019, 184: 234-242. doi:10.1016/j.exer.2019.05.001
[58] Voigt AP, Mullin NK, Whitmore SS, et al. Human photoreceptor cells from different macular subregions have distinct transcriptional profiles[J]. Hum Mol Genet, 2021, 30(16): 1543-1558. doi:10.1093/hmg/ddab140
[59] Sridhar A, Hoshino A, Finkbeiner CR, et al. Single-cell transcriptomic comparison of human fetal retina, hPSC-derived retinal organoids, and long-term retinal cultures[J]. Cell Rep, 2020, 30(5): 1644-1659.e4. doi:10.1016/j.celrep.2020.01.007
[60] Liang QN, Dharmat R, Owen L, et al. Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling[J]. Nat Commun, 2019, 10(1): 5743. doi:10.1038/s41467-019-12917-9
[61] Yan WJ, Peng YR, van Zyl T, et al. Cell atlas of the human fovea and peripheral retina[J]. Sci Rep, 2020, 10(1): 9802. doi:10.1038/s41598-020-66092-9
[62] Gautam P, Hamashima K, Chen Y, et al. Multi-species single-cell transcriptomic analysis of ocular compartment regulons[J]. Nat Commun, 2021, 12(1): 5675. doi:10.1038/s41467-021-25968-8
[63] Grindberg RV, Yee-Greenbaum JL, McConnell MJ, et al. RNA-sequencing from single nuclei[J]. Proc Natl Acad Sci USA, 2013, 110(49): 19802-19807. doi:10.1073/pnas.1319700110
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