Single-cell Sequencing: A Cutting Edge Tool in Molecular Medical Research

Overview

Journal Med J Armed Forces India

Specialty General Medicine

Date 2022 Sep 23

PMID 36147383

Authors

Pratibha Misra

Amruta R Jadhav

Sharmila A Bapat

Affiliations

Soon will be listed here.

Abstract

The rapid development of advanced high throughput technologies and introduction of high resolution "omics" data through analysis of biological molecules has revamped medical research. Single-cell sequencing in recent years, is in fact revolutionising the field by providing a deeper, spatio-temporal analyses of individual cells within tissues and their relevance to disease. Like conventional sequencing, the single-cell approach deciphers the sequence of nucleotides in a given Deoxyribose Nucleic Acid (DNA), Ribose Nucleic Acid (RNA), Micro Ribose Nucleic Acid (miRNA), epigenetically modified DNA or chromatin DNA; however, the unit of analyses is changed to single cells rather than the entire tissue. Further, a large number of single cells analysed from a single tissue generate a unique holistic perception capturing all kinds of perturbations across different cells in the tissue that increases the precision of data. Inherently, execution of the technique generates a large amount of data, which is required to be processed in a specific manner followed by customised bioinformatic analysis to produce meaningful results. The most crucial role of single-cell sequencing technique is in elucidating the inter-cell genetic, epigenetic, transcriptomic and proteomic heterogeneity in health and disease. The current review presents a brief overview of this cutting-edge technology and its applications in medical research.

Citing Articles

Single-Cell Sequencing: Genomic and Transcriptomic Approaches in Cancer Cell Biology.

Ortega-Batista A, Jaen-Alvarado Y, Moreno-Labrador D, Gomez N, Garcia G, Guerrero E Int J Mol Sci. 2025; 26(5).

PMID: 40076700 PMC: 11901077. DOI: 10.3390/ijms26052074.

Comprehensive SHAP Values and Single-Cell Sequencing Technology Reveal Key Cell Clusters in Bovine Skeletal Muscle.

Guo Y, Ma F, Li P, Guo L, Liu Z, Huo C Int J Mol Sci. 2025; 26(5).

PMID: 40076676 PMC: 11900076. DOI: 10.3390/ijms26052054.

Perspective from single-cell sequencing: Is inflammation in acute ischemic stroke beneficial or detrimental?.

Deng X, Hu Z, Zhou S, Wu Y, Fu M, Zhou C CNS Neurosci Ther. 2023; 30(1):e14510.

PMID: 37905592 PMC: 10805403. DOI: 10.1111/cns.14510.

References

Stein C, Weiskirchen R, Damm F, Strzelecka P . Single-cell omics: Overview, analysis, and application in biomedical science. J Cell Biochem. 2021; 122(11):1571-1578. DOI: 10.1002/jcb.30134. View

Hashimshony T, Wagner F, Sher N, Yanai I . CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep. 2012; 2(3):666-73. DOI: 10.1016/j.celrep.2012.08.003. View

Liu X, Yan Z, Wu C, Yang Y, Li X, Zhang G . FastProNGS: fast preprocessing of next-generation sequencing reads. BMC Bioinformatics. 2019; 20(1):345. PMC: 6580563. DOI: 10.1186/s12859-019-2936-9. View

Townes F, Hicks S, Aryee M, Irizarry R . Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model. Genome Biol. 2019; 20(1):295. PMC: 6927135. DOI: 10.1186/s13059-019-1861-6. View

Buettner F, Natarajan K, Casale F, Proserpio V, Scialdone A, Theis F . Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat Biotechnol. 2015; 33(2):155-60. DOI: 10.1038/nbt.3102. View

Vistain L, Tay S . Single-Cell Proteomics. Trends Biochem Sci. 2021; 46(8):661-672. PMC: 11697639. DOI: 10.1016/j.tibs.2021.01.013. View

Wang N, Zheng J, Chen Z, Liu Y, Dura B, Kwak M . Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation. Nat Commun. 2019; 10(1):95. PMC: 6327095. DOI: 10.1038/s41467-018-07981-6. View

Slatko B, Gardner A, Ausubel F . Overview of Next-Generation Sequencing Technologies. Curr Protoc Mol Biol. 2018; 122(1):e59. PMC: 6020069. DOI: 10.1002/cpmb.59. View

Macaulay I, Voet T . Single cell genomics: advances and future perspectives. PLoS Genet. 2014; 10(1):e1004126. PMC: 3907301. DOI: 10.1371/journal.pgen.1004126. View

10.

Ahn J, Heo S, Lee J, Bang D . Introduction to Single-Cell DNA Methylation Profiling Methods. Biomolecules. 2021; 11(7). PMC: 8301785. DOI: 10.3390/biom11071013. View

11.

Li Y, Ma L, Wu D, Chen G . Advances in bulk and single-cell multi-omics approaches for systems biology and precision medicine. Brief Bioinform. 2021; 22(5). DOI: 10.1093/bib/bbab024. View

12.

Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N . mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods. 2009; 6(5):377-82. DOI: 10.1038/nmeth.1315. View

13.

Grun D, van Oudenaarden A . Design and Analysis of Single-Cell Sequencing Experiments. Cell. 2015; 163(4):799-810. DOI: 10.1016/j.cell.2015.10.039. View

14.

Frumkin D, Wasserstrom A, Itzkovitz S, Harmelin A, Rechavi G, Shapiro E . Amplification of multiple genomic loci from single cells isolated by laser micro-dissection of tissues. BMC Biotechnol. 2008; 8:17. PMC: 2266725. DOI: 10.1186/1472-6750-8-17. View

15.

Lee H, Deignan J, Dorrani N, Strom S, Kantarci S, Quintero-Rivera F . Clinical exome sequencing for genetic identification of rare Mendelian disorders. JAMA. 2014; 312(18):1880-7. PMC: 4278636. DOI: 10.1001/jama.2014.14604. View

16.

Li Y, Luo P, Lu Y, Wu F . Identifying cell types from single-cell data based on similarities and dissimilarities between cells. BMC Bioinformatics. 2021; 22(Suppl 3):255. PMC: 8132444. DOI: 10.1186/s12859-020-03873-z. View

17.

Wang Y, Navin N . Advances and applications of single-cell sequencing technologies. Mol Cell. 2015; 58(4):598-609. PMC: 4441954. DOI: 10.1016/j.molcel.2015.05.005. View

18.

Ilicic T, Kim J, Kolodziejczyk A, Bagger F, McCarthy D, Marioni J . Classification of low quality cells from single-cell RNA-seq data. Genome Biol. 2016; 17:29. PMC: 4758103. DOI: 10.1186/s13059-016-0888-1. View

19.

Lei Y, Tang R, Xu J, Wang W, Zhang B, Liu J . Applications of single-cell sequencing in cancer research: progress and perspectives. J Hematol Oncol. 2021; 14(1):91. PMC: 8190846. DOI: 10.1186/s13045-021-01105-2. View

20.

Adusumalli S, Omar M, Soong R, Benoukraf T . Methodological aspects of whole-genome bisulfite sequencing analysis. Brief Bioinform. 2014; 16(3):369-79. DOI: 10.1093/bib/bbu016. View