High-throughput and Single-cell T Cell Receptor Sequencing Technologies

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2021 Jul 20

PMID 34282327

Citations 126

Authors

Joy A Pai

Ansuman T Satpathy

Affiliations

Soon will be listed here.

Abstract

T cells express T cell receptors (TCRs) composed of somatically recombined TCRα and TCRβ chains, which mediate recognition of major histocompatibility complex (MHC)-antigen complexes and drive the antigen-specific adaptive immune response to pathogens and cancer. The TCR repertoire in each individual is highly diverse, which allows for recognition of a wide array of foreign antigens, but also presents a challenge in analyzing this response using conventional methods. Recent studies have developed high-throughput sequencing technologies to identify TCR sequences, analyze their antigen specificities using experimental and computational tools, and pair TCRs with transcriptional and epigenetic cell state phenotypes in single cells. In this Review, we highlight these technological advances and describe how they have been applied to discover fundamental insights into T cell-mediated immunity.

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References

Seitz S, Schneider C, Malotka J, Nong X, Engel A, Wekerle H . Reconstitution of paired T cell receptor alpha- and beta-chains from microdissected single cells of human inflammatory tissues. Proc Natl Acad Sci U S A. 2006; 103(32):12057-62. PMC: 1567696. DOI: 10.1073/pnas.0604247103. View

Dash P, Wang G, Thomas P . Single-Cell Analysis of T-Cell Receptor αβ Repertoire. Methods Mol Biol. 2015; 1343:181-97. DOI: 10.1007/978-1-4939-2963-4_15. View

Klinger M, Pepin F, Wilkins J, Asbury T, Wittkop T, Zheng J . Multiplex Identification of Antigen-Specific T Cell Receptors Using a Combination of Immune Assays and Immune Receptor Sequencing. PLoS One. 2015; 10(10):e0141561. PMC: 4624875. DOI: 10.1371/journal.pone.0141561. View

Kivioja T, Vaharautio A, Karlsson K, Bonke M, Enge M, Linnarsson S . Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods. 2011; 9(1):72-4. DOI: 10.1038/nmeth.1778. View

Bradley P, Thomas P . Using T Cell Receptor Repertoires to Understand the Principles of Adaptive Immune Recognition. Annu Rev Immunol. 2019; 37:547-570. DOI: 10.1146/annurev-immunol-042718-041757. View

Durruthy-Durruthy R, Ray M . Using Fluidigm C1 to Generate Single-Cell Full-Length cDNA Libraries for mRNA Sequencing. Methods Mol Biol. 2018; 1706:199-221. DOI: 10.1007/978-1-4939-7471-9_11. View

Benichou J, Ben-Hamo R, Louzoun Y, Efroni S . Rep-Seq: uncovering the immunological repertoire through next-generation sequencing. Immunology. 2011; 135(3):183-91. PMC: 3311040. DOI: 10.1111/j.1365-2567.2011.03527.x. View

Picelli S, Faridani O, Bjorklund A, Winberg G, Sagasser S, Sandberg R . Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc. 2014; 9(1):171-81. DOI: 10.1038/nprot.2014.006. View

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

10.

Afik S, Yates K, Bi K, Darko S, Godec J, Gerdemann U . 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. PMC: 5766189. DOI: 10.1093/nar/gkx615. View

11.

Davis M, Bjorkman P . T-cell antigen receptor genes and T-cell recognition. Nature. 1988; 334(6181):395-402. DOI: 10.1038/334395a0. View

12.

Riaz N, Havel J, Makarov V, Desrichard A, Urba W, Sims J . Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab. Cell. 2017; 171(4):934-949.e16. PMC: 5685550. DOI: 10.1016/j.cell.2017.09.028. View

13.

Bolotin D, Poslavsky S, Davydov A, Frenkel F, Fanchi L, Zolotareva O . Antigen receptor repertoire profiling from RNA-seq data. Nat Biotechnol. 2017; 35(10):908-911. PMC: 6169298. DOI: 10.1038/nbt.3979. View

14.

Fozza C, Barraqueddu F, Corda G, Contini S, Virdis P, Dore F . Study of the T-cell receptor repertoire by CDR3 spectratyping. J Immunol Methods. 2016; 440:1-11. DOI: 10.1016/j.jim.2016.11.001. View

15.

Eltahla A, Rizzetto S, Pirozyan M, Betz-Stablein B, Venturi V, Kedzierska K . Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells. Immunol Cell Biol. 2016; 94(6):604-11. DOI: 10.1038/icb.2016.16. View

16.

De Neuter N, Bittremieux W, Beirnaert C, Cuypers B, Mrzic A, Moris P . On the feasibility of mining CD8+ T cell receptor patterns underlying immunogenic peptide recognition. Immunogenetics. 2017; 70(3):159-168. DOI: 10.1007/s00251-017-1023-5. View

17.

Rodriques S, Stickels R, Goeva A, Martin C, Murray E, Vanderburg C . Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science. 2019; 363(6434):1463-1467. PMC: 6927209. DOI: 10.1126/science.aaw1219. View

18.

Macosko E, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M . Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell. 2015; 161(5):1202-1214. PMC: 4481139. DOI: 10.1016/j.cell.2015.05.002. View

19.

Yost K, Satpathy A, Wells D, Qi Y, Wang C, Kageyama R . Clonal replacement of tumor-specific T cells following PD-1 blockade. Nat Med. 2019; 25(8):1251-1259. PMC: 6689255. DOI: 10.1038/s41591-019-0522-3. View

20.

Lanzavecchia A, Sallusto F . Progressive differentiation and selection of the fittest in the immune response. Nat Rev Immunol. 2002; 2(12):982-7. DOI: 10.1038/nri959. View