Research Progress of Single-cell Sequencing in Tuberculosis

Overview

Journal Front Immunol

Specialty Allergy & Immunology

Date 2023 Oct 30

PMID 37901241

Authors

Jiahui Pan

Zecheng Chang

Xinyue Zhang

Qinzhou Dong

He Zhao

Jingwei Shi

Guoqing Wang

Affiliations

Soon will be listed here.

Abstract

Tuberculosis is a major infectious disease caused by infection. The pathogenesis and immune mechanism of tuberculosis are not clear, and it is urgent to find new drugs, diagnosis, and treatment targets. A useful tool in the quest to reveal the enigmas related to infection and disease is the single-cell sequencing technique. By clarifying cell heterogeneity, identifying pathogenic cell groups, and finding key gene targets, the map at the single cell level enables people to better understand the cell diversity of complex organisms and the immune state of hosts during infection. Here, we briefly reviewed the development of single-cell sequencing, and emphasized the different applications and limitations of various technologies. Single-cell sequencing has been widely used in the study of the pathogenesis and immune response of tuberculosis. We review these works summarizing the most influential findings. Combined with the multi-molecular level and multi-dimensional analysis, we aim to deeply understand the blank and potential future development of the research on infection using single-cell sequencing technology.

Citing Articles

Single-cell sequencing: Current applications in various tuberculosis specimen types.

Zeng Y, Ma Q, Chen J, Kong X, Chen Z, Liu H Cell Prolif. 2024; 57(11):e13698.

PMID: 38956399 PMC: 11533074. DOI: 10.1111/cpr.13698.

References

Zumla A, Nahid P, Cole S . Advances in the development of new tuberculosis drugs and treatment regimens. Nat Rev Drug Discov. 2013; 12(5):388-404. DOI: 10.1038/nrd4001. View

Buenrostro J, Giresi P, Zaba L, Chang H, Greenleaf W . Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods. 2013; 10(12):1213-8. PMC: 3959825. DOI: 10.1038/nmeth.2688. View

Wang L, Wu J, Li J, Yang H, Tang T, Liang H . Host-mediated ubiquitination of a mycobacterial protein suppresses immunity. Nature. 2020; 577(7792):682-688. DOI: 10.1038/s41586-019-1915-7. View

Yang X, Yan J, Xue Y, Sun Q, Zhang Y, Guo R . Single-cell profiling reveals distinct immune response landscapes in tuberculous pleural effusion and non-TPE. Front Immunol. 2023; 14:1191357. PMC: 10331301. DOI: 10.3389/fimmu.2023.1191357. View

Khan N, Vidyarthi A, Amir M, Mushtaq K, Agrewala J . T-cell exhaustion in tuberculosis: pitfalls and prospects. Crit Rev Microbiol. 2016; 43(2):133-141. DOI: 10.1080/1040841X.2016.1185603. View

Ho D, Tsui Y, Chan L, Sze K, Zhang X, Cheu J . Single-cell RNA sequencing shows the immunosuppressive landscape and tumor heterogeneity of HBV-associated hepatocellular carcinoma. Nat Commun. 2021; 12(1):3684. PMC: 8211687. DOI: 10.1038/s41467-021-24010-1. View

Lebrun L, Espinasse F, Poveda J . Evaluation of nonradioactive DNA probes for identification of mycobacteria. J Clin Microbiol. 1992; 30(9):2476-8. PMC: 265528. DOI: 10.1128/jcm.30.9.2476-2478.1992. View

Bossel Ben-Moshe N, Hen-Avivi S, Levitin N, Yehezkel D, Oosting M, Joosten L . Predicting bacterial infection outcomes using single cell RNA-sequencing analysis of human immune cells. Nat Commun. 2019; 10(1):3266. PMC: 6646406. DOI: 10.1038/s41467-019-11257-y. View

Ramachandran P, Matchett K, Dobie R, Wilson-Kanamori J, Henderson N . Single-cell technologies in hepatology: new insights into liver biology and disease pathogenesis. Nat Rev Gastroenterol Hepatol. 2020; 17(8):457-472. DOI: 10.1038/s41575-020-0304-x. View

10.

Zong C, Lu S, Chapman A, Xie X . Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science. 2012; 338(6114):1622-6. PMC: 3600412. DOI: 10.1126/science.1229164. View

11.

Stahl P, Salmen F, Vickovic S, Lundmark A, Fernandez Navarro J, Magnusson J . Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science. 2016; 353(6294):78-82. DOI: 10.1126/science.aaf2403. View

12.

Pisu D, Huang L, Narang V, Theriault M, Le-Bury G, Lee B . Single cell analysis of M. tuberculosis phenotype and macrophage lineages in the infected lung. J Exp Med. 2021; 218(9). PMC: 8302446. DOI: 10.1084/jem.20210615. View

13.

Pederson T . The spatial organization of the genome in mammalian cells. Curr Opin Genet Dev. 2004; 14(2):203-9. DOI: 10.1016/j.gde.2004.02.008. View

14.

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

15.

Islam S, Kjallquist U, Moliner A, Zajac P, Fan J, Lonnerberg P . Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res. 2011; 21(7):1160-7. PMC: 3129258. DOI: 10.1101/gr.110882.110. View

16.

Chen K, Boettiger A, Moffitt J, Wang S, Zhuang X . RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science. 2015; 348(6233):aaa6090. PMC: 4662681. DOI: 10.1126/science.aaa6090. View

17.

Li X, Chen W, Chen Y, Zhang X, Gu J, Zhang M . Network embedding-based representation learning for single cell RNA-seq data. Nucleic Acids Res. 2017; 45(19):e166. PMC: 5737094. DOI: 10.1093/nar/gkx750. View

18.

Hameed H, Islam M, Chhotaray C, Wang C, Liu Y, Tan Y . Molecular Targets Related Drug Resistance Mechanisms in MDR-, XDR-, and TDR- Strains. Front Cell Infect Microbiol. 2018; 8:114. PMC: 5932416. DOI: 10.3389/fcimb.2018.00114. View

19.

Femino A, Fay F, Fogarty K, Singer R . Visualization of single RNA transcripts in situ. Science. 1998; 280(5363):585-90. DOI: 10.1126/science.280.5363.585. View

20.

Cai Y, Wang Y, Shi C, Dai Y, Li F, Xu Y . Single-cell immune profiling reveals functional diversity of T cells in tuberculous pleural effusion. J Exp Med. 2022; 219(3). PMC: 8789099. DOI: 10.1084/jem.20211777. View