References
- Wahren-Herlenius M, Dorner T. Immunopathogenic mechanisms of systemic autoimmune disease. Lancet. 2013;382(9894):819–831. doi:10.1016/S0140-6736(13)60954-X.
- Anderson MS, Mackay F. Editorial overview: autoimmunity. Curr Opin Immunol. 2015;37:v–7. doi:10.1016/j.coi.2015.10.004.
- Goodnow CC, Sprent J, Fazekas de St Groth B, et al. Cellular and genetic mechanisms of self tolerance and autoimmunity. Nature. 2005;435(7042):590–597. doi:10.1038/nature03724.
- Feng Y, van der Veeken J, Shugay M, et al. A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance. Nature. 2015;528(7580):132–136. doi:10.1038/nature16141.
- De Palma R, Del Galdo F, Lupoli S, et al. Peripheral T lymphocytes from patients with early systemic sclerosis co-cultured with autologous fibroblasts undergo an oligoclonal expansion similar to that occurring in the skin. Clin Exp Immunol. 2006;144(1):169–176. doi:10.1111/j.1365-2249.2006.03041.x.
- Spreafico R, Rossetti M, van Loosdregt J, et al. A circulating reservoir of pathogenic-like CD4+ T cells shares a genetic and phenotypic signature with the inflamed synovial micro-environment. Ann Rheum Dis. 2016;75(2):459–465. doi:10.1136/annrheumdis-2014-206226.
- Farge D, Arruda LC, Brigant F, et al. Long-term immune reconstitution and T cell repertoire analysis after autologous hematopoietic stem cell transplantation in systemic sclerosis patients. J Hematol Oncol. 2017;10(1):21–24. doi:10.1186/s13045-016-0388-5.
- Henriksen EK, Jorgensen KK, Kaveh F, et al. Gut and liver T-cells of common clonal origin in primary sclerosing cholangitis-inflammatory bowel disease. J Hepatol. 2017;66(1):116–122. doi:10.1016/j.jhep.2016.09.002.
- Michels AW, Landry LG, McDaniel KA, et al. Islet-derived CD4 T cells targeting proinsulin in human autoimmune diabetes. Diabetes. 2017;66(3):722–734. doi:10.2337/db16-1025.
- Lu J, Van Laethem F, Bhattacharya A, et al. Molecular constraints on CDR3 for thymic selection of MHC-restricted TCRs from a random pre-selection repertoire. Nat Commun. 2019;10(1):1019. doi:10.1038/s41467-019-08906-7.
- Miqueu P, Guillet M, Degauque N, et al. Statistical analysis of CDR3 length distributions for the assessment of T and B cell repertoire biases. Mol Immunol. 2007;44(6):1057–1064. doi:10.1016/j.molimm.2006.06.026.
- Vanderlugt CL, Miller SD. Epitope spreading in immune-mediated diseases: implications for immunotherapy. Nat Rev Immunol. 2002;2(2):85–95. doi:10.1038/nri724.
- Wu J, Pendegraft AH, Byrne-Steele M, et al. Expanded TCRβ CDR3 clonotypes distinguish Crohn’s disease and ulcerative colitis patients. Mucosal Immunol. 2018;11(5):1487–1495. doi:10.1038/s41385-018-0046-z.
- Vaitaitis GM, Wagner DH.Jr. CD40 interacts directly with RAG1 and RAG2 in autoaggressive T cells and Fas prevents CD40-induced RAG expression. Cell Mol Immunol. 2013;10(6):483–489. doi:10.1038/cmi.2013.24.
- Wagner DH.Jr. Overlooked mechanisms in Type 1 diabetes etiology: how unique costimulatory molecules contribute to diabetogenesis. Front Endocrinol (Lausanne). 2017;8:208. doi:10.3389/fendo.2017.00208.
- Long SA, Khalili J, Ashe J, et al. Standardized analysis for the quantification of Vbeta CDR3 T-cell receptor diversity. J Immunol Methods. 2006;317(1–2):100–113. doi:10.1016/j.jim.2006.09.015.
- Oettinger MA, Schatz DG, Gorka C, et al. RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science. 1990;248(4962):1517–1523. doi:10.1126/science.2360047.
- Schatz DG, Ji Y. Recombination centres and the orchestration of V(D)J recombination. Nat Rev Immunol. 2011;11(4):251–263. doi:10.1038/nri2941.
- Starr TK, Jameson SC, Hogquist KA. Positive and negative selection of T cells. Annu Rev Immunol. 2003;21:139–176. doi:10.1146/annurev.immunol.21.120601.141107.
- Zarnitsyna VI, Evavold BD, Schoettle LN, et al. Estimating the diversity, completeness, and cross-reactivity of the T cell repertoire. Front Immunol. 2013;4:485–489. doi:10.3389/fimmu.2013.00485.
- Liuzzi AR, McLaren JE, Price DA, et al. Early innate responses to pathogens: pattern recognition by unconventional human T-cells. Curr Opin Immunol. 2015;36:31–37. doi:10.1016/j.coi.2015.06.002.
- Wong GK, Heather JM, Barmettler S, et al. Immune dysregulation in immunodeficiency disorders: the role of T-cell receptor sequencing. J Autoimmun. 2017;80:1–9. doi:10.1016/j.jaut.2017.04.002.
- Aris M, Bravo AI, Pampena MB, et al. Changes in the TCRβ repertoire and tumor immune signature from a cutaneous melanoma patient immunized with the CSF-470 vaccine: a case report. Front Immunol. 2018;9:955–959. doi:10.3389/fimmu.2018.00955.
- Poiret T, Axelsson-Robertson R, Remberger M, et al. Cytomegalovirus-specific CD8+ T-cells with different T-cell receptor affinities segregate T-cell phenotypes and correlate with chronic graft-versus-host disease in patients post-hematopoietic stem cell transplantation. Front Immunol. 2018;9:760–765. doi:10.3389/fimmu.2018.00760.
- Blish CA, Gallay BJ, Turk GL, et al. Chronic modulation of the TCR repertoire in the lymphoid periphery. J Immunol. 1999;162(6):3131–3140.
- Scherer MT, Ignatowicz L, Pullen A, et al. The use of mammary tumor virus (Mtv)-negative and single-Mtv mice to evaluate the effects of endogenous viral superantigens on the T cell repertoire. J Exp Med. 1995;182(5):1493–1504. doi:10.1084/jem.182.5.1493.
- Higdon LE, Deets KA, Friesen TJ, et al. Receptor revision in CD4 T cells is influenced by follicular helper T cell formation and germinal-center interactions. Proc Natl Acad Sci U S A. 2014;111(15):5652–5657. doi:10.1073/pnas.1321803111.
- Fink PJ, Fang CA, Turk GL. The induction of peripheral tolerance by the chronic activation and deletion of CD4 + V beta 5+ cells. J Immunol. 1994;152(9):4270–4281.
- Ali M, Weinreich M, Balcaitis S, et al. Differential regulation of peripheral CD4+ T cell tolerance induced by deletion and TCR revision. J Immunol. 2003;171(11):6290–6296. doi:10.4049/jimmunol.171.11.6290.
- Vaitaitis GM, Poulin M, Sanderson RJ, et al. Jr. Cutting edge: CD40-induced expression of recombination activating gene (RAG) 1 and RAG2: a mechanism for the generation of autoaggressive T cells in the periphery. J Immunol. 2003;170(7):3455–3459. doi:10.4049/jimmunol.170.7.3455.
- Schlissel M, Constantinescu A, Morrow T, et al. Double-strand signal sequence breaks in V(D)J recombination are blunt, 5’-phosphorylated, RAG-dependent, and cell cycle regulated. Genes Dev. 1993;7(12B):2520–2532. doi:10.1101/gad.7.12b.2520.
- Lewis SM. The mechanism of V(D)J joining: lessons from molecular, immunological, and comparative analyses. Adv Immunol. 1994;56:27–150.
- McMahan CJ, Fink PJ. RAG reexpression and DNA recombination at T cell receptor loci in peripheral CD4+ T cells. Immunity. 1998;9(5):637–647. doi:10.1016/S1074-7613(00)80661-5.
- Hale JS, Nelson LT, Simmons KB, et al. Bcl-2-interacting mediator of cell death influences autoantigen-driven deletion and TCR revision. J Immunol. 2011;186(2):799–806. doi:10.4049/jimmunol.1002933.
- Schneider-Hohendorf T, Görlich D, Savola P, et al. Sex bias in MHC I-associated shaping of the adaptive immune system. Proc Natl Acad Sci U S A. 2018;115(9):2168–2173. doi:10.1073/pnas.1716146115.
- Di Sante G, Tolusso B, Fedele AL, et al. Collagen specific T-cell repertoire and HLA-DR alleles: biomarkers of active refractory rheumatoid arthritis. EBioMedicine. 2015;2(12):2037–2045. doi:10.1016/j.ebiom.2015.11.019.
- Hale JS, Ames KT, Boursalian TE, et al. Cutting Edge: rag deletion in peripheral T cells blocks TCR revision. J Immunol. 2010;184(11):5964–5968. doi:10.4049/jimmunol.1000876.
- McGuire HM, Watkins TS, Field M, et al. TCR deep sequencing of transgenic RAG-1-deficient mice reveals endogenous TCR recombination: a cause for caution. Immunol Cell Biol. 2018;96(6):642–644. doi:10.1111/imcb.12033.
- Serra P, Amrani A, Han B, et al. RAG-dependent peripheral T cell receptor diversification in CD8+ T lymphocytes. Proc Natl Acad Sci U S A. 2002;99(24):15566–15571. doi:10.1073/pnas.242321099.
- Bynoe MS, Viret C, Flavell RA, et al. T cells from epicutaneously immunized mice are prone to T cell receptor revision. Proc Natl Acad Sci U S A. 2005;102(8):2898–2903. doi:10.1073/pnas.0409880102.
- Lantelme E, Palermo B, Granziero L, et al. Cutting edge: recombinase-activating gene expression and V(D)J recombination in CD4 + CD3low mature T lymphocytes. J Immunol. 2000;164(7):3455–3459. doi:10.4049/jimmunol.164.7.3455.
- Li TT, Han S, Cubbage M, Zheng B. Continued expression of recombination-activating genes and TCR gene recombination in human peripheral T cells. Eur J Immunol. 2002;32(10):2792–2799. doi:10.1002/1521-4141(2002010)32:10 < 2792::AID-IMMU2792 > 3.0.CO;2-I.
- Lantelme E, Orlando L, Porcedda P, et al. An in vitro model of T cell receptor revision in mature human CD8+ T cells. Mol Immunol. 2008;45(2):328–337. doi:10.1016/j.molimm.2007.06.153.
- Cooper CJ, Turk GL, Sun M, et al. Cutting edge: TCR revision occurs in germinal centers. J Immunol. 2004;173(11):6532–6536. doi:10.4049/jimmunol.173.11.6532.
- Hale JS, Fink PJ. T-cell receptor revision: friend or foe?Immunology. 2010;129(4):467–473. doi:10.1111/j.1365-2567.2010.03250.x.
- Kim SJ, Schatzle S, Ahmed SS, et al. Increased cathepsin S in Prdm1-/- dendritic cells alters the TFH cell repertoire and contributes to lupus. Nat Immunol. 2017;18(9):1016–1024. doi:10.1038/ni.3793.
- De Libero G, Rocci MP, Casorati G, et al. T cell receptor heterogeneity in gamma delta T cell clones from intestinal biopsies of patients with celiac disease. Eur J Immunol. 1993;23(2):499–504. doi:10.1002/eji.1830230230.
- Ciupe SM, Devlin BH, Markert ML, et al. Quantification of total T-cell receptor diversity by flow cytometry and spectratyping. BMC Immunol. 2013;14:35–39. doi:10.1186/1471-2172-14-35.
- Cook L, Munier CML, Seddiki N, et al. Circulating gluten-specific, but not CMV-specific, CD39+ regulatory T cells have an oligoclonal TCR repertoire. Clin Transl Immunol. 2020;9(1):e1096. doi:10.1002/cti2.1096.
- Barennes P, Quiniou V, Shugay M, et al. Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases. Nat Biotechnol. 2021;39(2):236–245. doi:10.1038/s41587-020-0656-3.
- Okino ST, Kong M, Sarras H, et al. Evaluation of bias associated with high-multiplex, target-specific pre-amplification. Biomol Detect Quantif. 2016;6:13–21. doi:10.1016/j.bdq.2015.12.001.
- Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol. 2008;26(10):1135–1145. doi:10.1038/nbt1486.
- Freeman JD, Warren RL, Webb JR, et al. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res. 2009;19(10):1817–1824. doi:10.1101/gr.092924.109.
- Ye B, Smerin D, Gao Q, et al. High-throughput sequencing of the immune repertoire in oncology: applications for clinical diagnosis, monitoring, and immunotherapies. Cancer Lett. 2018;416:42–56. doi:10.1016/j.canlet.2017.12.017.
- Heather JM, Ismail M, Oakes T, et al. High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities. Brief Bioinform. 2017;1:1–12. doi:10.1093/bib/bbw138.
- Kitaura K, Shini T, Matsutani T, et al. A new high-throughput sequencing method for determining diversity and similarity of T cell receptor (TCR) α and β repertoires and identifying potential new invariant TCR α chains. BMC Immunol. 2016;17(1):38–44. doi:10.1186/s12865-016-0177-5.
- Schirmer M, Ijaz UZ, D’Amore R, et al. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Res. 2015;43(6):1–6. doi:10.1093/nar/gku1341.
- Matos TR, de Rie MA, Teunissen MBM. Research techniques made simple: high-throughput sequencing of the T-cell receptor. J Invest Dermatol. 2017;137(6):131–138. doi:10.1016/j.jid.2017.04.001.
- Howie B, Sherwood AM, Berkebile AD, et al. High-throughput pairing of T cell receptor alpha and beta sequences. Sci Transl Med. 2015;7(301):121–131. doi:10.1126/scitranslmed.aac5624.
- Eltahla AA, Rizzetto S, Pirozyan MR, et al. Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells. Immunol Cell Biol. 2016;94(6):604–611. doi:10.1038/icb.2016.16.
- Hanson WM, Chen Z, Jackson LK, et al. Reversible oligonucleotide chain blocking enables bead capture and amplification of T-cell receptor α and β chain mRNAs. J Am Chem Soc. 2016;138(35):11073–11076. doi:10.1021/jacs.6b04465.
- McDaniel JR, DeKosky BJ, Tanno H, et al. Ultra-high-throughput sequencing of the immune receptor repertoire from millions of lymphocytes. Nat Protoc. 2016;11(3):429–442. doi:10.1038/nprot.2016.024.
- Redmond D, Poran A, Elemento O. Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq. Genome Med. 2016;8(1):80–87. doi:10.1186/s13073-016-0335-7.
- Lee ES, Thomas PG, Mold JE, et al. Identifying T cell receptors from high-throughput sequencing: dealing with promiscuity in TCRalpha and TCRbeta pairing. PLoS Comput Biol. 2017;13(1):e1005313–109. doi:10.1371/journal.pcbi.1005313.
- Liu Z, Cort L, Eberwine R, et al. Prevention of type 1 diabetes in the rat with an allele-specific anti-T-cell receptor antibody: Vβ13 as a therapeutic target and biomarker. Diabetes. 2012;61(5):1160–1168. doi:10.2337/db11-0867.
- Marrero I, Hamm DE, Davies JD. High-throughput sequencing of islet-infiltrating memory CD4+ T cells reveals a similar pattern of TCR Vbeta usage in prediabetic and diabetic NOD mice. PLoS One. 2013;8(10):e76546–85. doi:10.1371/journal.pone.0076546.
- Liaskou E, Klemsdal Henriksen EK, Holm K, et al. High-throughput T-cell receptor sequencing across chronic liver diseases reveals distinct disease-associated repertoires. Hepatology. 2016;63(5):1608–1619. doi:10.1002/hep.28116.
- Winchester R, Wiesendanger M, Zhang HZ, et al. Immunologic characteristics of intrarenal T cells: trafficking of expanded CD8+ T cell β-chain clonotypes in progressive lupus nephritis. Arthritis Rheum. 2012;64(5):1589–1600. doi:10.1002/art.33488.
- Alexander T, Sattler A, Templin L, et al. Foxp3+ Helios + regulatory T cells are expanded in active systemic lupus erythematosus. Ann Rheum Dis. 2013;72(9):1549–1558. doi:10.1136/annrheumdis-2012-202216.
- Costa N, Pires AE, Gabriel AM, et al. Broadened T-cell repertoire diversity in ivIg-treated SLE patients is also related to the individual status of regulatory T-cells. J Clin Immunol. 2013;33(2):349–360. doi:10.1007/s10875-012-9816-7.
- Li Z, Long M, ChunMei L, et al. Composition and variation analysis of TCR β-chain CDR3 repertoire in the thymus and spleen of MRL/lpr mouse at different ages. Immunogenetics. 2015;67(1):25–37. doi:10.1007/s00251-014-0809-y.
- Thapa DR, Tonikian R, Sun C, et al. Longitudinal analysis of peripheral blood T cell receptor diversity in patients with systemic lupus erythematosus by next-generation sequencing. Arthritis Res Ther. 2015;17(1):132–145. doi:10.1186/s13075-015-0655-9.
- Yu J, Shi B, Ma L, et al. Case report for recurrent and new-onset SLE patients treated by high-dose glucocorticoid therapy: characteristics of peripheral TCR beta chain CDR3 repertoires. Medicine (Baltimore). 2017;96(49):e9022–102. doi:10.1097/MD.0000000000009022.
- Ye X, Wang Z, Ye Q, et al. High-throughput sequencing-based analysis of T cell repertoire in Lupus Nephritis. Front Immunol. 2020;11:1618. doi:10.3389/fimmu.2020.01618.
- Liu X, Zhang W, Zhao M, et al. T cell receptor β repertoires as novel diagnostic markers for systemic lupus erythematosus and rheumatoid arthritis. Ann Rheum Dis. 2019;78(8):1070–1078. doi:10.1136/annrheumdis-2019-215442.
- Jakez-Ocampo J, Paulin-Vera CM, Rivadeneyra-Espinoza L, et al. Vβ T cell receptor (TCR) genes in circulating cells of patients with systemic lupus erythematosus and their healthy relatives. Gac Med Mex. 2018;154(1):74–79. doi:10.24875/GMM.17002697.
- Luo W, Ma L, Wen Q, et al. Analysis of the interindividual conservation of T cell receptor alpha- and beta-chain variable regions gene in the peripheral blood of patients with systemic lupus erythematosus. Clin Exp Immunol. 2008;154(3):316–324. doi:10.1111/j.1365-2249.2008.03770.x.
- Tzifi F, Kanariou M, Tzanoudaki M, et al. Flow cytometric analysis of the CD4+ TCR Vbeta repertoire in the peripheral blood of children with type 1 diabetes mellitus, systemic lupus erythematosus and age-matched healthy controls. BMC Immunol. 2013;14(1):33–42. doi:10.1186/1471-2172-14-33.
- Sui W, Hou X, Zou G, et al. Composition and variation analysis of the TCR β-chain CDR3 repertoire in systemic lupus erythematosus using high-throughput sequencing. Mol Immunol. 2015;67(2 Pt B):455–464. doi:10.1016/j.molimm.2015.07.012.
- Harris ED, Jr. Rheumatoid arthritis. Pathophysiology and implications for therapy. N Engl J Med. 1990;322(18):1277–1289. doi:10.1056/NEJM199005033221805.
- Jiang X, Wang S, Zhou C, et al. Comprehensive TCR repertoire analysis of CD4+ T-cell subsets in rheumatoid arthritis. J Autoimmun. 2020;109:102432. doi:10.1016/j.jaut.2020.102432.
- Sakurai K, Ishigaki K, Shoda H, et al. HLA-DRB1 shared epitope alleles and disease activity are correlated with reduced T cell receptor repertoire diversity in CD4+ T cells in rheumatoid arthritis. J Rheumatol. 2018;45(7):905–914. doi:10.3899/jrheum.170909.
- Zhou J, Kong C, Yu J, et al. Skewness of TCR Vβ of peripheral blood and synovial fluid of patients with rheumatoid arthritis. J Immunoassay Immunochem. 2014;35(2):207–219. doi:10.1080/15321819.2013.841192.
- Klarenbeek PL, de Hair MJ, Doorenspleet ME, et al. Inflamed target tissue provides a specific niche for highly expanded T-cell clones in early human autoimmune disease. Ann Rheum Dis. 2012;71(6):1088–1093. doi:10.1136/annrheumdis-2011-200612.
- Chini L, Bardare M, Cancrini C, et al. Evidence of clonotypic pattern of T-cell repertoire in synovial fluid of children with juvenile rheumatoid arthritis at the onset of the disease. Scand J Immunol. 2002;56(5):512–517. doi:10.1046/j.1365-3083.2002.01153.x.
- Sun W, Nie H, Li N, et al. Skewed T-cell receptor BV14 and BV16 expression and shared CDR3 sequence and common sequence motifs in synovial T cells of rheumatoid arthritis. Genes Immun. 2005;6(3):248–261. doi:10.1038/sj.gene.6364166.
- Li DS, Warnock GL, Tu HJ, et al. Do immunotherapy and beta cell replacement play a synergistic role in the treatment of type 1 diabetes?Life Sci. 2009a;85(15-16):549–556. doi:10.1016/j.lfs.2009.08.016.
- Fischer DC, Opalka B, Hoffmann A, et al. Limited heterogeneity of rearranged T cell receptor V alpha and V beta transcripts in synovial fluid T cells in early stages of rheumatoid arthritis. Arthritis Rheum. 1996;39(3):454–462. doi:10.1002/art.1780390313.
- Elewaut D, De Keyser F, Van den Bosch F, et al. Broadening of the T cell receptor spectrum among rheumatoid arthritis synovial cell-lines in relation to disease duration. Clin Exp Rheumatol. 2000;18(2):201–207.
- Sakkas LI, Xu B, Artlett CM, et al. Oligoclonal T cell expansion in the skin of patients with systemic sclerosis. J Immunol. 2002;168(7):3649–3659. doi:10.4049/jimmunol.168.7.3649.
- Tang B, Kim S, Hammond S, et al. Characterization of T cell phenotype and function in a double transgenic (collagen-specific TCR/HLA-DR1) humanized model of arthritis. Arthritis Res Ther. 2014;16(1):R7–20. doi:10.1186/ar4433.
- Chemin K, Pollastro S, James E, et al. A novel HLA-DRB1*10:01-restricted T cell epitope from citrullinated type II collagen relevant to rheumatoid arthritis. Arthritis Rheumatol. 2016;68(5):1124–1135. doi:10.1002/art.39553.
- Ito Y, Hashimoto M, Hirota K, et al. Detection of T cell responses to a ubiquitous cellular protein in autoimmune disease. Science. 2014;346(6207):363–368. doi:10.1126/science.1259077.
- Hirota K, Hashimoto M, Yoshitomi H, et al. T cell self-reactivity forms a cytokine milieu for spontaneous development of IL-17+ Th cells that cause autoimmune arthritis. J Exp Med. 2007;204(1):41–47. doi:10.1084/jem.20062259.
- Atkinson MA, Eisenbarth GS, Michels AW. Type 1 diabetes. Lancet. 2014;383(9911):69–82. doi:10.1016/S0140-6736(13)60591-7.
- Roep BO, Peakman M. Diabetogenic T lymphocytes in human Type 1 diabetes. Curr Opin Immunol. 2011;23(6):746–753. doi:10.1016/j.coi.2011.10.001.
- Gomez-Tourino I, Kamra Y, Baptista R, et al. T cell receptor β-chains display abnormal shortening and repertoire sharing in type 1 diabetes. Nat Commun. 2017;8(1):1792. doi:10.1038/s41467-017-01925-2.
- Cerosaletti K, Barahmand-Pour-Whitman F, Yang J, et al. Single-cell RNA sequencing reveals expanded clones of islet antigen-reactive CD4+ T cells in peripheral blood of subjects with Type 1 diabetes. J Immunol. 2017;199(1):323–335. doi:10.4049/jimmunol.1700172.
- Seay HR, Yusko E, Rothweiler SJ, et al. Tissue distribution and clonal diversity of the T and B cell repertoire in type 1 diabetes. JCI Insight. 2016;1(20):88–94. doi:10.1172/jci.insight.88242.
- Marrero I, Aguilera C, Hamm DE, et al. High-throughput sequencing reveals restricted TCR Vβ usage and public TCRβ clonotypes among pancreatic lymph node memory CD4(+) T cells and their involvement in autoimmune diabetes. Mol Immunol. 2016;74:82–95. doi:10.1016/j.molimm.2016.04.013.
- Tong Y, Li Z, Zhang H, et al. T cell repertoire diversity is decreased in Type 1 diabetes patients. Genom Proteom Bioinform. 2016;14(6):338–348. doi:10.1016/j.gpb.2016.10.003.
- Eugster A, Lindner A, Catani M, et al. High diversity in the TCR repertoire of GAD65 autoantigen-specific human CD4+ T cells. JI. 2015;194(6):2531–2538. doi:10.4049/jimmunol.1403031.
- Diz R, Garland A, Vincent BG, et al. Autoreactive effector/memory CD4+ and CD8+ T cells infiltrating grafted and endogenous islets in diabetic NOD mice exhibit similar T cell receptor usage. PLoS One. 2012;7(12):e52054–64. doi:10.1371/journal.pone.0052054.
- Li L, He Q, Garland A, et al. beta cell-specific CD4+ T cell clonotypes in peripheral blood and the pancreatic islets are distinct. J Immunol. 2009b;183(11):7585–7591. doi:10.4049/jimmunol.0901587.
- Velthuis JH, Unger WW, van der Slik AR, et al. Accumulation of autoreactive effector T cells and allo-specific regulatory T cells in the pancreas allograft of a type 1 diabetic recipient. Diabetologia. 2009;52(3):494–503. doi:10.1007/s00125-008-1237-z.
- Velthuis JH, Unger WW, Abreu JR, et al. Simultaneous detection of circulating autoreactive CD8+ T-cells specific for different islet cell-associated epitopes using combinatorial MHC multimers. Diabetes. 2010;59(7):1721–1730. doi:10.2337/db09-1486.
- Root-Bernstein R. Autoreactive T-cell receptor (Vbeta/D/Jbeta) sequences in diabetes are homologous to insulin, glucagon, the insulin receptor, and the glucagon receptor. J Mol Recognit. 2009;22(3):177–187. doi:10.1002/jmr.930.
- Atkinson MA, Kaufman DL, Campbell L, et al. Response of peripheral-blood mononuclear cells to glutamate decarboxylase in insulin-dependent diabetes. Lancet. 1992;339(8791):458–459. doi:10.1016/0140-6736(92)91061-c.
- Yang J, Danke NA, Berger D, et al. Islet-specific glucose-6-phosphatase catalytic subunit-related protein-reactive CD4+ T cells in human subjects. J Immunol. 2006;176(5):2781–2789. doi:10.4049/jimmunol.176.5.2781.
- Abreu JR, Martina S, Verrijn Stuart AA, et al. CD8 T cell autoreactivity to preproinsulin epitopes with very low human leucocyte antigen class I binding affinity. Clin Exp Immunol. 2012;170(1):57–65. doi:10.1111/j.1365-2249.2012.04635.x.
- Kronenberg D, Knight RR, Estorninho M, et al. Circulating preproinsulin signal peptide-specific CD8 T cells restricted by the susceptibility molecule HLA-A24 are expanded at onset of type 1 diabetes and kill β-cells. Diabetes. 2012;61(7):1752–1759. doi:10.2337/db11-1520.
- Pathiraja V, Kuehlich JP, Campbell PD, et al. Proinsulin-specific, HLA-DQ8, and HLA-DQ8-transdimer-restricted CD4+ T cells infiltrate islets in type 1 diabetes. Diabetes. 2015;64(1):172–182. doi:10.2337/db14-0858.
- Torres J, Mehandru S, Colombel JF, et al. Crohn’s disease. Lancet. 2017;389(10080):1741–1755. doi:10.1016/S0140-6736(16)31711-1.
- Ungaro R, Mehandru S, Allen PB, et al. Ulcerative colitis. Lancet. 2017;389(10080):1756–1770. doi:10.1016/S0140-6736(16)32126-2.
- Sturm A, de Souza HS, Fiocchi C. Mucosal T cell proliferation and apoptosis in inflammatory bowel disease. Curr Drug Targets. 2008;9(5):381–387. doi:10.2174/138945008784221198.
- Root-Bernstein R. Autoimmunity and the microbiome: T-cell receptor mimicry of "self" and microbial antigens mediates self tolerance in holobionts: the concepts of "holoimmunity" (TcR-mediated tolerance for the holobiont) and "holoautoimmunity" (loss of tolerance for the holobiont) are introduced. Bioessays. 2016;38(11):1068–1083. doi:10.1002/bies.201600083.
- Kakuta Y, Nakano T, Naito T, et al. Repertoire analysis of memory T-cell receptors in Japanese patients with inflammatory bowel disease. JGH Open. 2020;4(4):624–631. doi:10.1002/jgh3.12305.
- Allez M, Auzolle C, Ngollo M, REMIND Study Group, et al. T cell clonal expansions in ileal Crohn’s disease are associated with smoking behaviour and postoperative recurrence. Gut. 2019;68(11):1961–1970. doi:10.1136/gutjnl-2018-317878.
- Werner L, Nunberg MY, Rechavi E, et al. Altered T cell receptor beta repertoire patterns in pediatric ulcerative colitis. Clin Exp Immunol. 2019;196(1):1–11. doi:10.1111/cei.13247.
- Gunaltay S, Repsilber D, Helenius G, et al. Oligoclonal T-cell receptor repertoire in colonic biopsies of patients with microscopic colitis and ulcerative colitis. Inflamm Bowel Dis. 2017;23(6):932–945. doi:10.1097/MIB.0000000000001127.
- Lord J, Chen J, Thirlby RC, et al. T-cell receptor sequencing reveals the clonal diversity and overlap of colonic effector and FOXP3+ T cells in ulcerative colitis. Inflamm Bowel Dis. 2015;21(1):19–30. doi:10.1097/MIB.0000000000000242.
- Doorenspleet ME, Westera L, Peters CP, et al. Profoundly expanded T-cell clones in the inflamed and uninflamed intestine of patients with Crohn’s disease. J Crohns Colitis. 2017;11(7):831–839. doi:10.1093/ecco-jcc/jjx012.
- Chapman CG, Yamaguchi R, Tamura K, et al. Characterization of T-cell receptor repertoire in inflamed tissues of patients with Crohn’s disease through deep sequencing. Inflamm Bowel Dis. 2016;22(6):1275–1285. doi:10.1097/MIB.0000000000000752.
- de Paula Alves Sousa A, Johnson KR, Nicholas R, et al. Intrathecal T-cell clonal expansions in patients with multiple sclerosis. Ann Clin Transl Neurol. 2016;3(6):422–433. doi:10.1002/acn3.310.
- Salou M, Garcia A, Michel L, et al. Expanded CD8 T-cell sharing between periphery and CNS in multiple sclerosis. Ann Clin Transl Neurol. 2015;2(6):609–622. doi:10.1002/acn3.199.
- Lossius A, Johansen JN, Vartdal F, et al. High-throughput sequencing of TCR repertoires in multiple sclerosis reveals intrathecal enrichment of EBV-reactive CD8+ T cells. Eur J Immunol. 2014;44(11):3439–3452. doi:10.1002/eji.201444662.
- Muraro PA, Robins H, Malhotra S, et al. T cell repertoire following autologous stem cell transplantation for multiple sclerosis. J Clin Invest. 2014;124(3):1168–1172. doi:10.1172/JCI71691.
- Bao J, Xu Q, Zou Y, et al. Deep sequencing of the T cell receptor Vb CDR3 repertoire of peripheral CD4 + T cells in primary biliary cirrhosis. Zhonghua Gan Zang Bing Za Zhi. 2015;23(8):580–585. doi:10.3760/cma.j.issn.1007-3418.2015.08.005.
- Gross G, Waks T, Eshhar Z. Expression of immunoglobulin-T-cell receptor chimeric molecules as functional receptors with antibody-type specificity. Proc Natl Acad Sci U S A. 1989;86(24):10024–10028. doi:10.1073/pnas.86.24.10024.
- Adair PR, Kim YC, Zhang AH, et al. Human Tregs made antigen specific by gene modification: the power to treat autoimmunity and antidrug antibodies with precision. Front Immunol. 2017;8:1117–1129. doi:10.3389/fimmu.2017.01117.
- Chitnis T. The role of CD4 T cells in the pathogenesis of multiple sclerosis. Int Rev Neurobiol. 2007;79:43–72. doi:10.1016/S0074-7742(07)79003-7.
- Wright GP, Notley CA, Xue SA, et al. Adoptive therapy with redirected primary regulatory T cells results in antigen-specific suppression of arthritis. Proc Natl Acad Sci U S A. 2009;106(45):19078–19083. doi:10.1073/pnas.0907396106.
- Brusko TM, Koya RC, Zhu S, et al. Human antigen-specific regulatory T cells generated by T cell receptor gene transfer. PLoS One. 2010;5(7):e11726–126. doi:10.1371/journal.pone.0011726.
- Hull CM, Nickolay LE, Estorninho M, et al. Generation of human islet-specific regulatory T cells by TCR gene transfer. J Autoimmun. 2017;79:63–73. doi:10.1016/j.jaut.2017.01.001.
- Eyquem J, Mansilla-Soto J, Giavridis T, et al. Targeting a CAR to the TRAC locus with CRISPR/Cas9 enhances tumour rejection. Nature. 2017;543(7643):113–117. doi:10.1038/nature21405.
- Sicard A, Levings MK, Scott DW. Engineering therapeutic T cells to suppress alloimmune responses using TCRs, CARs, or BARs. Am J Transplant. 2018;18(6):1305–1311. doi:10.1111/ajt.14747.
- Cai B, Guo M, Wang Y, et al. Co-infusion of haplo-identical CD19-chimeric antigen receptor T cells and stem cells achieved full donor engraftment in refractory acute lymphoblastic leukemia. J Hematol Oncol. 2016;9(1):131–142. doi:10.1186/s13045-016-0357-z.
- Hu Y, Sun J, Wu Z, et al. Predominant cerebral cytokine release syndrome in CD19-directed chimeric antigen receptor-modified T cell therapy. J Hematol Oncol. 2016;9(1):70–81. doi:10.1186/s13045-016-0299-5.
- Hu Y, Wu Z, Luo Y, et al. Potent anti-leukemia activities of chimeric antigen receptor-modified T cells against CD19 in Chinese patients with relapsed/refractory acute lymphocytic leukemia. Clin Cancer Res. 2017;23(13):3297–3306. doi:10.1158/1078-0432.CCR-16-1799.
- Dawson NAJ, Vent-Schmidt J, Levings MK. Engineered tolerance: tailoring development, function, and antigen-specificity of regulatory T cells. Front Immunol. 2017;8:1460–1471. doi:10.3389/fimmu.2017.01460.
- McGovern JL, Wright GP, Stauss HJ. Engineering specificity and function of therapeutic regulatory T cells. Front Immunol. 2017;8:1517–1529. doi:10.3389/fimmu.2017.01517.
- Scott DW. From IgG fusion proteins to engineered-specific human regulatory T cells: a life of tolerance. Front Immunol. 2017;8:1576–1583. doi:10.3389/fimmu.2017.01576.
- Tao JH, Cheng M, Tang JP, et al. Foxp3, regulatory T cell, and autoimmune diseases. Inflammation. 2017;40(1):328–339. doi:10.1007/s10753-016-0470-8.
- Marek-Trzonkowska N, Mysliwiec M, Dobyszuk A, et al. Administration of CD4 + CD25highCD127-regulatory T cells preserves beta-cell function in type 1 diabetes in children. Diabetes Care. 2012;35(9):1817–1820. doi:10.2337/dc12-0038.
- Marek-Trzonkowska N, Mysliwiec M, Dobyszuk A, et al. Therapy of type 1 diabetes with CD4(+)CD25(high)CD127-regulatory T cells prolongs survival of pancreatic islets - results of one year follow-up. Clin Immunol. 2014;153(1):23–30. doi:10.1016/j.clim.2014.03.016.
- Bluestone JA, Buckner JH, Fitch M, et al. Type 1 diabetes immunotherapy using polyclonal regulatory T cells. Sci Transl Med. 2015;7(315):315–330. doi:10.1126/scitranslmed.aad4134.
- Canavan JB, Scotta C, Vossenkamper A, et al. Developing in vitro expanded CD45RA + regulatory T cells as an adoptive cell therapy for Crohn’s disease. Gut. 2016;65(4):584–594. doi:10.1136/gutjnl-2014-306919.
- Lin M, Stoica-Nazarov C, Surls J, et al. Reversal of type 1 diabetes by a new MHC II-peptide chimera: "Single-epitope-mediated suppression" to stabilize a polyclonal autoimmune T-cell process. Eur J Immunol. 2010;40(8):2277–2288. doi:10.1002/eji.200940094.
- Tarbell KV, Petit L, Zuo X, et al. Dendritic cell-expanded, islet-specific CD4+ CD25+ CD62L + regulatory T cells restore normoglycemia in diabetic NOD mice. J Exp Med. 2007;204(1):191–201. doi:10.1084/jem.20061631.
- Voss RH, Willemsen RA, Kuball J, et al. Molecular design of the Calphabeta interface favors specific pairing of introduced TCRalphabeta in human T cells. J Immunol. 2008;180(1):391–401. doi:10.4049/jimmunol.180.1.391.
- Stone JD, Harris DT, Soto CM, et al. A novel T cell receptor single-chain signaling complex mediates antigen-specific T cell activity and tumor control. Cancer Immunol Immunother. 2014;63(11):1163–1176. doi:10.1007/s00262-014-1586-z.
- Elinav E, Waks T, Eshhar Z. Redirection of regulatory T cells with predetermined specificity for the treatment of experimental colitis in mice. Gastroenterology. 2008;134(7):2014–2024. doi:10.1053/j.gastro.2008.02.060.
- Elinav E, Adam N, Waks T, et al. Amelioration of colitis by genetically engineered murine regulatory T cells redirected by antigen-specific chimeric receptor. Gastroenterology. 2009;136(5):1721–1731. doi:10.1053/j.gastro.2009.01.049.
- Fransson M, Piras E, Burman J, et al. CAR/FoxP3-engineered T regulatory cells target the CNS and suppress EAE upon intranasal delivery. J Neuroinflammation. 2012;9:112–121. doi:10.1186/1742-2094-9-112.
- Blat D, Zigmond E, Alteber Z, et al. Suppression of murine colitis and its associated cancer by carcinoembryonic antigen-specific regulatory T cells. Mol Ther. 2014;22(5):1018–1028. doi:10.1038/mt.2014.41.
- Jansen MA, van Herwijnen MJ, van Kooten PJ, et al. Generation of the first TCR transgenic mouse with CD4(+) T cells recognizing an anti-inflammatory regulatory T cell-inducing Hsp70 peptide. Front Immunol. 2016;7:90–101. doi:10.3389/fimmu.2016.00090.
- Schloss J, Ali R, Racine JJ, et al. HLA-B*39:06 efficiently mediates type 1 diabetes in a mouse model incorporating reduced thymic insulin expression. J Immunol. 2018;200(10):3353–3363. doi:10.4049/jimmunol.1701652.
- Gioia L, Holt M, Costanzo A, et al. Position β57 of I-A g7 controls early anti-insulin responses in NOD mice, linking an MHC susceptibility allele to type 1 diabetes onset. Sci Immunol. 2019;4(38):eaaw6329. doi:10.1126/sciimmunol.aaw6329.
- Fernández-Quintero ML, Pomarici ND, Loeffler JR, et al. T-cell receptor CDR3 loop conformations in solution shift the relative Vα-Vβ domain distributions. Front Immunol. 2020;11:1440. doi:10.3389/fimmu.2020.01440.
- Klein L, Kyewski B, Allen PM, et al. Positive and negative selection of the T cell repertoire: what thymocytes see (and don’t see). Nat Rev Immunol. 2014;14(6):377–391. doi:10.1038/nri3667.