Citation Information :
Vats A, Yadav R, Bhatia A, Kumar Y. Using Ribonucleic Acid Sequencing to Gain Single-cell Understanding. J Postgrad Med Edu Res 2024; 58 (4):183-196.
Single-cell analysis has emerged as a powerful tool in molecular biology, offering unprecedented resolution into the complexities and heterogeneity of biological systems at the cellular level. This technique surpasses traditional bulk analysis methods, which often obscure cellular diversity by analyzing populations of cells as a homogeneous entity. Single-cell analysis is revolutionizing our understanding of various biological processes and disease mechanisms by providing insights previously unattainable. As technological and computational methods continue to evolve, single-cell analysis is expected to experience a further expansion in its capabilities and applications, leading to breakthroughs in precision medicine and a deeper understanding of biological processes. The goal of this review is to provide a brief overview of how this technique has evolved, tracing its development from rudimentary genetic analytical tools to its current state as a highly sophisticated methodology. It includes a thorough summary of the methods and instruments used in single-cell analysis, particularly via ribonucleic acid (RNA) sequencing, the complexities of data analysis, benefits and drawbacks, and finally its clinical applications. The review will assist researchers in choosing and putting into practice the best methodologies for their research requirements.
Bhattachan P, Jeschke MG. Single-cell transcriptome analysis in health and disease. Shock 2024;61(1):19–27. DOI: 10.1097/SHK.0000000000002274
Al-Hajj M, Wicha MS, Benito-Hernandez A, et al. Prospective identification of tumorigenic breast cancer cells. Proc Natl Acad Sci 2003;100(7):3983–3988. DOI: 10.1073/pnas.0530291100
Prince ME, Sivanandan R, Kaczorowski A, et al. Identification of a subpopulation of cells with cancer stem cell properties in head and neck squamous cell carcinoma. Proc Natl Acad Sci 2007;104(3):973–978. DOI: 10.1073/pnas.0610117104
Stuart T, Butler A, Hoffman P, et al. Comprehensive integration of single-cell data. Cell 2019;177(7):1888–1902. DOI: 10.1016/j.cell.2019.05.031
Macaulay IC, Ponting CP, Voet T. Single-cell multiomics: multiple measurements from single cells. Trends Genet 2017;33(2):155–168. DOI: 10.1016/j.tig.2016.12.003
Mullis KB, Faloona FA. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. In: Ehrlich HA (Ed). Methods in Enzymology. Vol. 155. San Diego: Academic Press; 1987. pp. 335–350.
Wang Y, Navin NE. Advances and applications of single-cell sequencing technologies. Mol Cell 2015;58(4):598–609. DOI: 10.1016/j.molcel.2015.05.005
Lee J, Hyeon DY, Hwang D. Single-cell multiomics: technologies and data analysis methods. Exp Mol Med 2020;52(9):1428–1442. DOI: 10.1038/s12276-020-0420-2
Flynn E, Almonte-Loya A, Fragiadakis GK. Single-cell multiomics. Annu Rev Biomed Data Sci 2023;6(1):313–337. DOI: 10.1146/annurev-biodatasci-020422-050645
Stuart T, Satija R. Integrative single-cell analysis. Nat Rev Genet 2019;20(5):257–272. DOI: 10.1038/s41576-019-0093-7
Kalisky T, Oriel S, Bar-Lev TH, et al. A brief review of single-cell transcriptomic technologies. Brief Funct Genomics 2018;17(1):64–76. DOI: 10.1093/bfgp/elx019
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009;10(1):57–63. DOI: 10.1038/nrg2484
Marinov GK, Williams BA, McCue K, et al. From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. Genome Res 2014;24(3):496–510. DOI: 10.1101/gr.161034.113
Trapnell C, Cacchiarelli D, Grimsby J, et al. Pseudo-temporal ordering of individual cells reveals dynamics and regulators of cell fate decisions. Nat Biotechnol 2014;32(4):381. DOI: 10.1038/nbt.2859
Yu Y, Tsang JC, Wang C, et al. Single-cell RNA-seq identifies a PD-1hi ILC progenitor and defines its development pathway. Nature 2016;539(7627):102–106. DOI: 10.1038/nature20105
Nguyen A, Khoo WH, Moran I, et al. Single-cell RNA sequencing of rare immune cell populations. Front Immunol 2018;9:1553. DOI: 10.3389/fimmu.2018.01553
Chen H, Albergante L, Hsu JY, et al. Single-cell trajectories reconstruction, exploration, and mapping of omics data with STREAM. Nat Commun 2019;10(1):1903. DOI: 10.1038/s41467-019-09670-4
Cheng S, Pei Y, He L, et al. Single-cell RNA-seq reveals cellular heterogeneity of pluripotency transition and X chromosome dynamics during early mouse development. Cell Rep 2019;26(10):2593–2607. DOI: 10.1016/j.celrep.2019.02.031
Bendall SC, Davis KL, Amir E ad D, et al. Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell 2014;157(3):714–725. DOI: 10.1016/j.cell.2014.04.005
Heumos L, Schaar AC, Lance C, et al. Best practices for single-cell analysis across modalities. Nat Rev Genet 2023;24(8):550–572. DOI: 10.1038/s41576-023-00586-w
Hu P, Zhang W, Xin H, et al. Single-cell isolation and analysis. Front Cell Dev Biol 2016;4:116. DOI: 10.3389/fcell.2016.00116
Pensold D, Zimmer-Bensch G. Methods for single-cell isolation and preparation. In: Yu B, Zhang J, Zeng Y, Li L, Wang X (Eds). Single-cell sequencing and methylation. Vol. 1255. Advances in Experimental Medicine and Biology. Singapore: Springer; 2020. pp. 7–27.
Cunningham RE. Tissue disaggregation. In: Oliver C, Jamur MC (Eds). Immunocytochemical Methods and Protocols. Vol. 588. Methods in Molecular Biology. Totowa: Humana Press; 2010. pp. 327–330.
Aliaghaei M, Haun JB. Optimization of mechanical tissue dissociation using an integrated microfluidic device for improved generation of single cells following digestion. Front Bioeng Biotechnol 2022;10:841046. DOI: 10.3389/fbioe.2022.841046
Telford WG. Flow cytometry and cell sorting. Front Med 2023;10:1287884. DOI: 10.3389/fmed.2023.1287884
Mazutis L, Gilbert J, Ung WL, et al. Single-cell analysis and sorting using droplet-based microfluidics. Nat Protoc 2013;8(5):870–891. DOI: 10.1038/nprot.2013.046
Kumari S, Saha U, Bose M, et al. Microfluidic platforms for single cell analysis: applications in cellular manipulation and optical biosensing. Chemosensors 2023;11(2):107. DOI: 10.3390/chemosensors11020107
Rodríguez CF, Guzmán-Sastoque P, Gantiva-Diaz M, et al. Low-cost inertial microfluidic device for microparticle separation: a laser-Ablated PMMA lab-on-a-chip approach without a cleanroom. HardwareX 2023;16:e00493. DOI: 10.1016/j.ohx.2023.e00493
Dahl JB, Lin JMG, Muller SJ, et al. Microfluidic strategies for understanding the mechanics of cells and cell-mimetic systems. Annu Rev Chem Biomol Eng 2015;6(1):293–317. DOI: 10.1146/annurev-chembioeng-061114-123407
Datta S, Malhotra L, Dickerson R, et al. Laser capture microdissection: big data from small samples. Histol Histopathol 2015;30(11):1255. DOI: 10.14670/HH-11-622
Ellis P, Moore L, Sanders MA, et al. Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing. Nat Protoc 2021;16(2):841–871. DOI: 10.1038/s41596-020-00437-6
Eberwine J, Yeh H, Miyashiro K, et al. Analysis of gene expression in single live neurons. Proc Natl Acad Sci 1992;89(7):3010–3014. DOI: 10.1073/pnas.89.7.3010
Citri A, Pang ZP, Südhof TC, et al. Comprehensive qPCR profiling of gene expression in single neuronal cells. Nat Protoc 2012;7(1):118–127. DOI: 10.1038/nprot.2011.430
Fuss IJ, Kanof ME, Smith PD, et al. Isolation of whole mononuclear cells from peripheral blood and cord blood. Curr Protoc Immunol 2009;85(1). DOI: 10.1002/0471142735.im0701s85
Sutermaster BA, Darling EM. Considerations for high-yield, high-throughput cell enrichment: fluorescence versus magnetic sorting. Sci Rep 2019;9(1):227. DOI: 10.1038/s41598-018-36698-1
Frenea-Robin M, Marchalot J. Basic principles and recent advances in magnetic cell separation. Magnetochemistry 2022;8:11. DOI: 10.3390/magnetochemistry8010011
Gross A, Schoendube J, Zimmermann S, et al. Technologies for single-cell isolation. Int J Mol Sci 2015;16(8):16897–16919. DOI: 10.3390/ijms160816897
Trombetta JJ, Gennert D, Lu D, et al. Preparation of single-cell RNA-Seq libraries for next generation sequencing. Curr Protoc Mol Biol 2014;107(1). DOI: 10.1002/0471142727.mb0422s107
Haque A, Engel J, Teichmann SA, et al. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. Genome Med 2017;9(1):75. DOI: 10.1186/s13073-017-0467-4
Tomlinson MJ, Tomlinson S, Yang XB, et al. Cell separation: terminology and practical considerations. J Tissue Eng 2013;4:204173141247269. DOI: 10.1177/2041731412472690
Kimmerling RJ, Lee Szeto G, Li JW, et al. A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages. Nat Commun 2016;7(1):10220. DOI: 10.1038/ncomms10220
Wang Y, Zhou X, Yang Z, et al. An integrated and multi-functional droplet-based microfluidic platform for digital DNA amplification. Biosens Bioelectron 2024;246:115831. DOI: 10.1016/j.bios.2023.115831
Lee CS. Grand challenges in microfluidics: a call for biological and engineering action. Front Sens 2020;1:583035. DOI: 10.3389/fsens.2020.583035
Picelli S, Faridani OR, Björklund ÅK, et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 2014;9(1):171–181. DOI: 10.1038/nprot.2014.006
Hagemann-Jensen M, Ziegenhain C, Sandberg R. Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress. Nat Biotechnol 2022;40(10):1452–1457. DOI: 10.1038/s41587-022-01311-4
Hwang B, Lee DS, Tamaki W, et al. SCITO-seq: single-cell combinatorial indexed cytometry sequencing. Nat Methods 2021;18(8):903–911. DOI: 10.1038/s41592-021-01222-3
Martin BK, Qiu C, Nichols E, et al. Optimized single-nucleus transcriptional profiling by combinatorial indexing. Nat Protoc 2023;18(1):188–207. DOI: 10.1038/s41596-022-00752-0
Vandereyken K, Sifrim A, Thienpont B, et al. Methods and applications for single-cell and spatial multi-omics. Nat Rev Genet 2023;24(8):494–515. DOI: 10.1038/s41576-023-00580-2
Williams CG, Lee HJ, Asatsuma T, et al. An introduction to spatial transcriptomics for biomedical research. Genome Med 2022;14(1):68. DOI: 10.1186/s13073-022-01075-1
Jain S, Eadon MT. Spatial transcriptomics in health and disease. Nat Rev Nephrol 2024:1–13. DOI: 10.1038/s41581-024-00841-1
Lee MY, Li M. Integration of multi-modal single-cell data. Nat Biotechnol 2024;42(2):190–191. DOI: 10.1038/s41587-023-01826-4
Zhu C, Preissl S, Ren B. Single-cell multimodal omics: the power of many. Nat Methods 2020;17(1):11–14. DOI: 10.1038/s41592-019-0691-5
Dalton L, Ballarin V, Brun M. Clustering algorithms: on learning, validation, performance, and applications to genomics. Curr Genomics 2009;10(6):430–445. DOI: 10.2174/138920209789177601
Evans C, Hardin J, Stoebel DM. Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions. Brief Bioinform 2018;19(5):776–792. DOI: 10.1093/bib/bbx008
Bullard JH, Purdom E, Hansen KD, et al. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 2010;11(1):94. DOI: 10.1186/1471-2105-11-94
Li X, Cooper NGF, O'Toole TE, et al. Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies. BMC Genomics 2020;21(1):75. DOI: 10.1186/s12864-020-6502-7
Kolodziejczyk AA, Kim JK, Svensson V, et al. The technology and biology of single-cell RNA sequencing. Mol Cell 2015;58(4):610–620. DOI: 10.1016/j.molcel.2015.04.005
Jia W, Sun M, Lian J, et al. Feature dimensionality reduction: a review. Complex Intell Syst 2022;8(3):2663–2693. DOI: 10.1007/s40747-021-00637-x
Jolliffe IT, Cadima J. Principal component analysis: a review and recent developments. Philos Trans R Soc Math Phys Eng Sci 2016;374(2065):20150202. DOI: 10.1098/rsta.2015.0202
Zhou Y, Sharpee TO. Using Global t-SNE to preserve intercluster data structure. Neural Comput 2022;34(8):1637–1651. DOI: 10.1162/neco_a_01504
Van der Maaten L, Hinton G. Visualizing data using t-SNE. J Mach Learn Res 2008;9(11).
Kobak D, Berens P. The art of using t-SNE for single-cell transcriptomics. Nat Commun 2019;10(1):5416. DOI: 10.1038/s41467-019-13056-x
Stolarek I, Samelak-Czajka A, Figlerowicz M, et al. Dimensionality reduction by UMAP for visualizing and aiding in classification of imaging flow cytometry data. iScience 2022;25(10):105142. DOI: 10.1016/j.isci.2022.105142
Yang Y, Sun H, Zhang Y, et al. Dimensionality reduction by UMAP reinforces sample heterogeneity analysis in bulk transcriptomic data. Cell Rep 2021;36(4):109442. DOI: 10.1016/j.celrep.2021.109442
Sompairac N, Nazarov PV, Czerwinska U, et al. Independent component analysis for unraveling the complexity of cancer omics datasets. Int J Mol Sci 2019;20(18):4414. DOI: 10.3390/ijms20184414
Hyvärinen A. Independent component analysis: recent advances. Philos Trans R Soc Math Phys Eng Sci 2013;371(1984):20110534. DOI: 10.1098/rsta.2011.0534
Koldovsky Z, Tichavsky P, Oja E. Efficient variant of algorithm FastICA for independent component analysis attaining the Cramér-Rao lower bound. IEEE Trans Neural Netw 2006;17(5):1265–1277. DOI: 10.1109/TNN.2006.875991
Haghverdi L, Buettner F, Theis FJ. Diffusion maps for high-dimensional single-cell analysis of differentiation data. Bioinformatics 2015;31(18):2989–2998. DOI: 10.1093/bioinformatics/btv325
Moon KR, Van Dijk D, Wang Z, et al. Visualizing structure and transitions in high-dimensional biological data. Nat Biotechnol 2019;37(12):1482–1492. DOI: 10.1038/s41587-019-0336-3
Zhang S, Li X, Lin J, et al. Review of single-cell RNA-seq data clustering for cell-type identification and characterization. RNA 2023;29(5):517–530. DOI: 10.1261/rna.078965.121
Ikotun AM, Ezugwu AE. Boosting k-means clustering with symbiotic organisms search for automatic clustering problems. PLoS One 2022;17(8):e0272861. DOI: 10.1371/journal.pone.0272861
Žurauskienė J, Yau C. pcaReduce: hierarchical clustering of single-cell transcriptional profiles. BMC Bioinformatics 2016;17(1):140. DOI: 10.1186/s12859-016-0984-y
Blondel VD, Guillaume JL, Lambiotte R, et al. Fast unfolding of communities in large networks. J Stat Mech Theory Exp 2008;2008(10):P10008. DOI: 10.1088/1742-5468/2008/10/P10008
Chen L, Chu C, Lu J, et al. Gene ontology and KEGG pathway enrichment analysis of a drug target-based classification system. PloS One 2015;10(5):e0126492. DOI: 10.1371/journal.pone.0126492
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Stat Methodol 1995;57(1):289–300. DOI: 10.1111/j.2517-6161.1995.tb02031.x
Butler A, Hoffman P, Smibert P, et al. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol 2018;36(5):411–420. DOI: 10.1038/nbt.4096
Patel RK, Jaszczak RG, Im K, et al. Cyclone: an accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data. Front Immunol 2023;14:1167241. DOI: 10.3389/fimmu.2023.1167241
Zhang Y, Parmigiani G, Johnson WE. ComBat-seq: batch effect adjustment for RNA-seq count data. NAR Genomics Bioinforma 2020;2(3):lqaa078. DOI: 10.1093/nargab/lqaa078
Colpitts SJ, Budd MA, Monajemi M, et al. Strategies for optimizing CITE-seq for human islets and other tissues. Front Immunol 2023;14:1107582. DOI: 10.3389/fimmu.2023.1107582
Akhtyamov P, Shaheen L, Raevskiy M, et al. scATAC-seq preprocessing and imputation evaluation system for visualization, clustering and digital footprinting. Brief Bioinform 2024;25(1):bbad447. DOI: 10.1093/bib/bbad447
Brennecke P, Anders S, Kim JK, et al. Accounting for technical noise in single-cell RNA-seq experiments. Nat Methods 2013;10(11):1093–1095. DOI: 10.1038/nmeth.2645
Su M, Pan T, Chen QZ, et al. Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications. Mil Med Res 2022;9(1):68. DOI: 10.1186/s40779-022-00434-8
Byrne A, Cole C, Volden R, et al. Realizing the potential of full-length transcriptome sequencing. Philos Trans R Soc B Biol Sci 2019;374(1786):20190097. DOI: 10.1098/rstb.2019.0097
Olbrecht S, Busschaert P, Qian J, et al. High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification. Genome Med 2021;13(1):111. DOI: 10.1186/s13073-021-00922-x
Cheng Z, Li S, Yang S, et al. Endoplasmic reticulum stress promotes hepatocellular carcinoma by modulating immunity: a study based on artificial neural networks and single-cell sequencing. J Transl Med 2024;22(1):658. DOI: 10.1186/s12967-024-05460-9
Li Q, Fang J, Liu K, et al. Multi-omic validation of the cuproptosis-sphingolipid metabolism network: modulating the immune landscape in osteosarcoma. Front Immunol 2024;15:1424806. DOI: 10.3389/fimmu.2024.1424806
Tran MA, Youssef D, Shroff S, et al. Urine scRNAseq reveals new insights into the bladder tumor immune microenvironment. J Exp Med 2024;221(8):e20240045. DOI: 10.1084/jem.20240045
Chen R, Zou L. Combined analysis of single-cell sequencing and bulk transcriptome sequencing reveals new mechanisms for non-healing diabetic foot ulcers. Plos One 2024;19(7):e0306248. DOI: 10.1371/journal.pone.0306248
Leenders F, de Koning EJ, Carlotti F. Pancreatic β-cell identity change through the lens of single-cell omics research. Int J Mol Sci 2024;25(9):4720. DOI: 10.3390/ijms25094720
Quan M, Zhang H, Han X, et al. Single-cell RNA sequencing reveals transcriptional landscape of neutrophils and highlights the role of TREM-1 in EAE. Neurol Neuroimmunol Neuroinflamm 2024;11(5):e200278. DOI: 10.1212/NXI.0000000000200278
Fournier AP, Tastet O, Charabati M, et al. Single-cell transcriptomics identifies brain endothelium inflammatory networks in experimental autoimmune encephalomyelitis. Neurol Neuroimmunol Neuroinflamm 2023;10(1):e200046. DOI: 10.1212/NXI.0000000000200046
Mittnenzweig M, Mayshar Y, Cheng S, et al. A single-embryo, single-cell time-resolved model for mouse gastrulation. Cell 2021;184(11):2825–2842. DOI: 10.1016/j.cell.2021.04.004
Chu LF, Leng N, Zhang J, et al. Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm. Genome Biol. 2016;17(1):173. DOI: 10.1186/s13059-016-1033-x
Antolović V, Chubb JR. Single cell transcriptome analysis during development in Dictyostelium. In: Kimmel AR (Ed). Dictyostelium discoideum. Vol. 2814. Methods in Molecular Biology. New York: Springer; 2024. pp. 223–245.
Ayyaz A, Kumar S, Sangiorgi B, et al. Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell. Nature 2019;569(7754):121–125. DOI: 10.1038/s41586-019-1154-y
Huang K, Xu Y, Feng T, et al. The advancement and application of the single-cell transcriptome in biological and medical research. Biology 2024;13(6):451. DOI: 10.3390/biology13060451
Curion F, Theis FJ. Machine learning integrative approaches to advance computational immunology. Genome Med 2024;16:80. DOI: 10.1186/s13073-024-01350-3
Rhoads A, Au KF. PacBio sequencing and its applications. Genomics Proteomics Bioinformatics 2015;13(5):278–289. DOI: 10.1016/j.gpb.2015.08.002
Wang Y, Zhao Y, Bollas A, et al. Nanopore sequencing technology, bioinformatics, and applications. Nat Biotechnol 2021;39(11):1348–1365. DOI: 10.1038/s41587-021-01108-x
Huo Y, Guo Y, Wang J, et al. Integrating multi-modal information to detect spatial domains of spatial transcriptomics by graph attention network. J Genet Genomics 2023;50(9):720–733. DOI: 10.1016/j.jgg.2023.06.005
Vicari M, Mirzazadeh R, Nilsson A, et al. Spatial multimodal analysis of transcriptomes and metabolomes in tissues. Nat Biotechnol 2023;42(7):1046–1050. DOI: 10.1038/s41587-023-01937-y