Dual TCR-a Expression on Mucosal-Associated Invariant T Cells as a Potential Confounder of TCR Interpretation

Sara Suliman; Lars Kjer-Nielsen; Sarah K Iwany; Kattya Lopez Tamara; Liyen Loh; Ludivine Grzelak; Katherine Kedzierska; Tonatiuh A Ocampo; Alexandra J Corbett; James McCluskey; Jamie Rossjohn; Segundo R León; Roger Calderon; Leonid Lecca-Garcia; Megan B Murray; D Branch Moody; Ildiko Van Rhijn

doi:10.4049/jimmunol.2100275

Dual TCR-a Expression on Mucosal-Associated Invariant T Cells as a Potential Confounder of TCR Interpretation

Sara Suliman, Lars Kjer-Nielsen, Sarah K Iwany, Kattya Lopez Tamara, Liyen Loh, Ludivine Grzelak, Katherine Kedzierska, Tonatiuh A Ocampo, Alexandra J Corbett, James McCluskey, Jamie Rossjohn, Segundo R León, Roger Calderon, Leonid Lecca-Garcia, Megan B Murray, D Branch Moody, Ildiko Van Rhijn

Immunology

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

Mucosal-associated invariant T (MAIT) cells are innate-like T cells that are highly abundant in human blood and tissues. Most MAIT cells have an invariant TCRa-chain that uses T cell receptor a-variable 1-2 (TRAV1-2) joined to TRAJ33/20/12 and recognizes metabolites from bacterial riboflavin synthesis bound to the Ag-presenting molecule MHC class I related (MR1). Our attempts to identify alternative MR1-presented Ags led to the discovery of rare MR1-restricted T cells with non-TRAV1-2 TCRs. Because altered Ag specificity likely alters affinity for the most potent known Ag, 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil (5-OP-RU), we performed bulk TCRa- and TCRb-chain sequencing and single-cell-based paired TCR sequencing on T cells that bound the MR1-5-OP-RU tetramer with differing intensities. Bulk sequencing showed that use of V genes other than TRAV1-2 was enriched among MR1-5-OP-RU tetramer^low cells. Although we initially interpreted these as diverse MR1-restricted TCRs, single-cell TCR sequencing revealed that cells expressing atypical TCRa-chains also coexpressed an invariant MAIT TCRa-chain. Transfection of each non-TRAV1-2 TCRa-chain with the TCRb-chain from the same cell demonstrated that the non-TRAV1-2 TCR did not bind the MR1-5-OP-RU tetramer. Thus, dual TCRa-chain expression in human T cells and competition for the endogenous b-chain explains the existence of some MR1-5-OP-RU tetramer^low T cells. The discovery of simultaneous expression of canonical and noncanonical TCRs on the same T cell means that claims of roles for non-TRAV1-2 TCR in MR1 response must be validated by TCR transfer-based confirmation of Ag specificity. The Journal of Immunology, 2022, 208: 1-7.

Original language	English
Pages (from-to)	1389-1395
Number of pages	7
Journal	Journal of Immunology
Volume	208
Issue number	6
DOIs	https://doi.org/10.4049/jimmunol.2100275
Publication status	Published - 15 Mar 2022

Bibliographical note

Funding Information:
the National Institutes of Health, Grant R01 AI 148407-01 A1. S.S. received the Justice, Equity, Diversity and Inclusion award, which provided free language editorial service for the manuscript. A.J.C. is supported by a future fellowship (FT160100083) from the Australian Research Council, an investigator grant from the National Health and Medical Research Council (1193745), and a Dame Kate Campbell Fellowship from the University of Melbourne. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. K.K. was supported by National Health and Medical Research Council Leadership Investigator Grant 1173871.

Funding Information:
This work was supported by National Institutes of Health TB Research Unit Network Grants U19 AI111224 and R01AI049313. J.R. and J.M. are supported by a grant from

Publisher Copyright:
Copyright © 2022 by The American Association of Immunologists, Inc. 0022-1767/22/$37.50

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10.4049/jimmunol.2100275

1389.fullFinal published version, 2.06 MBLicence: Taverne

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Suliman, S., Kjer-Nielsen, L., Iwany, S. K., Lopez Tamara, K., Loh, L., Grzelak, L., Kedzierska, K., Ocampo, T. A., Corbett, A. J., McCluskey, J., Rossjohn, J., León, S. R., Calderon, R., Lecca-Garcia, L., Murray, M. B., Moody, D. B., & Van Rhijn, I. (2022). Dual TCR-a Expression on Mucosal-Associated Invariant T Cells as a Potential Confounder of TCR Interpretation. Journal of Immunology, 208(6), 1389-1395. https://doi.org/10.4049/jimmunol.2100275

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title = "Dual TCR-a Expression on Mucosal-Associated Invariant T Cells as a Potential Confounder of TCR Interpretation",

abstract = "Mucosal-associated invariant T (MAIT) cells are innate-like T cells that are highly abundant in human blood and tissues. Most MAIT cells have an invariant TCRa-chain that uses T cell receptor a-variable 1-2 (TRAV1-2) joined to TRAJ33/20/12 and recognizes metabolites from bacterial riboflavin synthesis bound to the Ag-presenting molecule MHC class I related (MR1). Our attempts to identify alternative MR1-presented Ags led to the discovery of rare MR1-restricted T cells with non-TRAV1-2 TCRs. Because altered Ag specificity likely alters affinity for the most potent known Ag, 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil (5-OP-RU), we performed bulk TCRa- and TCRb-chain sequencing and single-cell-based paired TCR sequencing on T cells that bound the MR1-5-OP-RU tetramer with differing intensities. Bulk sequencing showed that use of V genes other than TRAV1-2 was enriched among MR1-5-OP-RU tetramerlow cells. Although we initially interpreted these as diverse MR1-restricted TCRs, single-cell TCR sequencing revealed that cells expressing atypical TCRa-chains also coexpressed an invariant MAIT TCRa-chain. Transfection of each non-TRAV1-2 TCRa-chain with the TCRb-chain from the same cell demonstrated that the non-TRAV1-2 TCR did not bind the MR1-5-OP-RU tetramer. Thus, dual TCRa-chain expression in human T cells and competition for the endogenous b-chain explains the existence of some MR1-5-OP-RU tetramerlow T cells. The discovery of simultaneous expression of canonical and noncanonical TCRs on the same T cell means that claims of roles for non-TRAV1-2 TCR in MR1 response must be validated by TCR transfer-based confirmation of Ag specificity. The Journal of Immunology, 2022, 208: 1-7.",

author = "Sara Suliman and Lars Kjer-Nielsen and Iwany, {Sarah K} and {Lopez Tamara}, Kattya and Liyen Loh and Ludivine Grzelak and Katherine Kedzierska and Ocampo, {Tonatiuh A} and Corbett, {Alexandra J} and James McCluskey and Jamie Rossjohn and Le{\'o}n, {Segundo R} and Roger Calderon and Leonid Lecca-Garcia and Murray, {Megan B} and Moody, {D Branch} and {Van Rhijn}, Ildiko",

note = "Funding Information: the National Institutes of Health, Grant R01 AI 148407-01 A1. S.S. received the Justice, Equity, Diversity and Inclusion award, which provided free language editorial service for the manuscript. A.J.C. is supported by a future fellowship (FT160100083) from the Australian Research Council, an investigator grant from the National Health and Medical Research Council (1193745), and a Dame Kate Campbell Fellowship from the University of Melbourne. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. K.K. was supported by National Health and Medical Research Council Leadership Investigator Grant 1173871. Funding Information: This work was supported by National Institutes of Health TB Research Unit Network Grants U19 AI111224 and R01AI049313. J.R. and J.M. are supported by a grant from Publisher Copyright: Copyright {\textcopyright} 2022 by The American Association of Immunologists, Inc. 0022-1767/22/$37.50",

year = "2022",

month = mar,

day = "15",

doi = "10.4049/jimmunol.2100275",

language = "English",

volume = "208",

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Suliman, S, Kjer-Nielsen, L, Iwany, SK, Lopez Tamara, K, Loh, L, Grzelak, L, Kedzierska, K, Ocampo, TA, Corbett, AJ, McCluskey, J, Rossjohn, J, León, SR, Calderon, R, Lecca-Garcia, L, Murray, MB, Moody, DB & Van Rhijn, I 2022, 'Dual TCR-a Expression on Mucosal-Associated Invariant T Cells as a Potential Confounder of TCR Interpretation', Journal of Immunology, vol. 208, no. 6, pp. 1389-1395. https://doi.org/10.4049/jimmunol.2100275

TY - JOUR

T1 - Dual TCR-a Expression on Mucosal-Associated Invariant T Cells as a Potential Confounder of TCR Interpretation

AU - Suliman, Sara

AU - Kjer-Nielsen, Lars

AU - Iwany, Sarah K

AU - Lopez Tamara, Kattya

AU - Loh, Liyen

AU - Grzelak, Ludivine

AU - Kedzierska, Katherine

AU - Ocampo, Tonatiuh A

AU - Corbett, Alexandra J

AU - McCluskey, James

AU - Rossjohn, Jamie

AU - León, Segundo R

AU - Calderon, Roger

AU - Lecca-Garcia, Leonid

AU - Murray, Megan B

AU - Moody, D Branch

AU - Van Rhijn, Ildiko

N1 - Funding Information: the National Institutes of Health, Grant R01 AI 148407-01 A1. S.S. received the Justice, Equity, Diversity and Inclusion award, which provided free language editorial service for the manuscript. A.J.C. is supported by a future fellowship (FT160100083) from the Australian Research Council, an investigator grant from the National Health and Medical Research Council (1193745), and a Dame Kate Campbell Fellowship from the University of Melbourne. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. K.K. was supported by National Health and Medical Research Council Leadership Investigator Grant 1173871. Funding Information: This work was supported by National Institutes of Health TB Research Unit Network Grants U19 AI111224 and R01AI049313. J.R. and J.M. are supported by a grant from Publisher Copyright: Copyright © 2022 by The American Association of Immunologists, Inc. 0022-1767/22/$37.50

PY - 2022/3/15

Y1 - 2022/3/15

N2 - Mucosal-associated invariant T (MAIT) cells are innate-like T cells that are highly abundant in human blood and tissues. Most MAIT cells have an invariant TCRa-chain that uses T cell receptor a-variable 1-2 (TRAV1-2) joined to TRAJ33/20/12 and recognizes metabolites from bacterial riboflavin synthesis bound to the Ag-presenting molecule MHC class I related (MR1). Our attempts to identify alternative MR1-presented Ags led to the discovery of rare MR1-restricted T cells with non-TRAV1-2 TCRs. Because altered Ag specificity likely alters affinity for the most potent known Ag, 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil (5-OP-RU), we performed bulk TCRa- and TCRb-chain sequencing and single-cell-based paired TCR sequencing on T cells that bound the MR1-5-OP-RU tetramer with differing intensities. Bulk sequencing showed that use of V genes other than TRAV1-2 was enriched among MR1-5-OP-RU tetramerlow cells. Although we initially interpreted these as diverse MR1-restricted TCRs, single-cell TCR sequencing revealed that cells expressing atypical TCRa-chains also coexpressed an invariant MAIT TCRa-chain. Transfection of each non-TRAV1-2 TCRa-chain with the TCRb-chain from the same cell demonstrated that the non-TRAV1-2 TCR did not bind the MR1-5-OP-RU tetramer. Thus, dual TCRa-chain expression in human T cells and competition for the endogenous b-chain explains the existence of some MR1-5-OP-RU tetramerlow T cells. The discovery of simultaneous expression of canonical and noncanonical TCRs on the same T cell means that claims of roles for non-TRAV1-2 TCR in MR1 response must be validated by TCR transfer-based confirmation of Ag specificity. The Journal of Immunology, 2022, 208: 1-7.

AB - Mucosal-associated invariant T (MAIT) cells are innate-like T cells that are highly abundant in human blood and tissues. Most MAIT cells have an invariant TCRa-chain that uses T cell receptor a-variable 1-2 (TRAV1-2) joined to TRAJ33/20/12 and recognizes metabolites from bacterial riboflavin synthesis bound to the Ag-presenting molecule MHC class I related (MR1). Our attempts to identify alternative MR1-presented Ags led to the discovery of rare MR1-restricted T cells with non-TRAV1-2 TCRs. Because altered Ag specificity likely alters affinity for the most potent known Ag, 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil (5-OP-RU), we performed bulk TCRa- and TCRb-chain sequencing and single-cell-based paired TCR sequencing on T cells that bound the MR1-5-OP-RU tetramer with differing intensities. Bulk sequencing showed that use of V genes other than TRAV1-2 was enriched among MR1-5-OP-RU tetramerlow cells. Although we initially interpreted these as diverse MR1-restricted TCRs, single-cell TCR sequencing revealed that cells expressing atypical TCRa-chains also coexpressed an invariant MAIT TCRa-chain. Transfection of each non-TRAV1-2 TCRa-chain with the TCRb-chain from the same cell demonstrated that the non-TRAV1-2 TCR did not bind the MR1-5-OP-RU tetramer. Thus, dual TCRa-chain expression in human T cells and competition for the endogenous b-chain explains the existence of some MR1-5-OP-RU tetramerlow T cells. The discovery of simultaneous expression of canonical and noncanonical TCRs on the same T cell means that claims of roles for non-TRAV1-2 TCR in MR1 response must be validated by TCR transfer-based confirmation of Ag specificity. The Journal of Immunology, 2022, 208: 1-7.

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JO - Journal of Immunology

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Dual TCR-a Expression on Mucosal-Associated Invariant T Cells as a Potential Confounder of TCR Interpretation

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