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For: Oakes T, Heather JM, Best K, Byng-Maddick R, Husovsky C, Ismail M, Joshi K, Maxwell G, Noursadeghi M, Riddell N, Ruehl T, Turner CT, Uddin I, Chain B. Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile. Front Immunol 2017;8:1267. [PMID: 29075258 PMCID: PMC5643411 DOI: 10.3389/fimmu.2017.01267] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/22/2017] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Lindeboom RGH, Worlock KB, Dratva LM, Yoshida M, Scobie D, Wagstaffe HR, Richardson L, Wilbrey-Clark A, Barnes JL, Kretschmer L, Polanski K, Allen-Hyttinen J, Mehta P, Sumanaweera D, Boccacino JM, Sungnak W, Elmentaite R, Huang N, Mamanova L, Kapuge R, Bolt L, Prigmore E, Killingley B, Kalinova M, Mayer M, Boyers A, Mann A, Swadling L, Woodall MNJ, Ellis S, Smith CM, Teixeira VH, Janes SM, Chambers RC, Haniffa M, Catchpole A, Heyderman R, Noursadeghi M, Chain B, Mayer A, Meyer KB, Chiu C, Nikolić MZ, Teichmann SA. Human SARS-CoV-2 challenge uncovers local and systemic response dynamics. Nature 2024;631:189-198. [PMID: 38898278 PMCID: PMC11222146 DOI: 10.1038/s41586-024-07575-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/16/2024] [Indexed: 06/21/2024]
2
Baker AM, Nageswaran G, Nenclares P, Ronel T, Smith K, Kimberley C, Laclé MM, Bhide S, Harrington KJ, Melcher A, Rodriguez-Justo M, Chain B, Graham TA. FUME-TCRseq Enables Sensitive and Accurate Sequencing of the T-cell Receptor from Limited Input of Degraded RNA. Cancer Res 2024;84:1560-1569. [PMID: 38479434 PMCID: PMC11094417 DOI: 10.1158/0008-5472.can-23-3340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/19/2024] [Accepted: 02/27/2024] [Indexed: 05/16/2024]
3
Chen PL, Hung SI, Chung WH, Chen CB, Kuo CN, Lin YK, Chiu CY. T-cell receptor diversity and allergen sensitivity in childhood asthma and atopic dermatitis. Pediatr Allergy Immunol 2024;35:e14143. [PMID: 38745384 DOI: 10.1111/pai.14143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
4
Mhanna V, Barennes P, Vantomme H, Fourcade G, Coatnoan N, Six A, Klatzmann D, Mariotti-Ferrandiz E. Enhancing comparative T cell receptor repertoire analysis in small biological samples through pooling homologous cell samples from multiple mice. CELL REPORTS METHODS 2024;4:100753. [PMID: 38614088 PMCID: PMC11045977 DOI: 10.1016/j.crmeth.2024.100753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/28/2024] [Accepted: 03/19/2024] [Indexed: 04/15/2024]
5
Hung SI, Chu MT, Hou MM, Lee YS, Yang CK, Chu SY, Liu FY, Hsu HC, Pao SC, Teng YC, Chen CB, Chao A, Chung WH, Chang JWC, Lai CH. Personalized neoantigen-based T cell therapy triggers cytotoxic lymphocytes expressing polyclonal TCR against metastatic ovarian cancer. Biomed Pharmacother 2023;169:115928. [PMID: 38011788 DOI: 10.1016/j.biopha.2023.115928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 11/29/2023]  Open
6
Lehikoinen J, Valori M, Jääskeläinen AJ, Laakso SM, Arstila TP, Tienari PJ. High Epstein-Barr virus capsid antigen IgG level associates with the carriership of CD8+ T cell somatic mutations in the STAT3 SH2 domain. Clin Immunol 2023;255:109733. [PMID: 37572949 DOI: 10.1016/j.clim.2023.109733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/14/2023]
7
Wu Z, Gao S, Gao Q, Patel BA, Groarke EM, Feng X, Manley AL, Li H, Ospina Cardona D, Kajigaya S, Alemu L, Quinones Raffo D, Ombrello AK, Ferrada MA, Grayson PC, Calvo KR, Kastner DL, Beck DB, Young NS. Early activation of inflammatory pathways in UBA1-mutated hematopoietic stem and progenitor cells in VEXAS. Cell Rep Med 2023;4:101160. [PMID: 37586319 PMCID: PMC10439277 DOI: 10.1016/j.xcrm.2023.101160] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 04/18/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023]
8
Myronov A, Mazzocco G, Król P, Plewczynski D. BERTrand-peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing. Bioinformatics 2023;39:btad468. [PMID: 37535685 PMCID: PMC10444968 DOI: 10.1093/bioinformatics/btad468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/28/2023] [Accepted: 08/01/2023] [Indexed: 08/05/2023]  Open
9
Milighetti M, Peng Y, Tan C, Mark M, Nageswaran G, Byrne S, Ronel T, Peacock T, Mayer A, Chandran A, Rosenheim J, Whelan M, Yao X, Liu G, Felce SL, Dong T, Mentzer AJ, Knight JC, Balloux F, Greenstein E, Reich-Zeliger S, Pade C, Gibbons JM, Semper A, Brooks T, Otter A, Altmann DM, Boyton RJ, Maini MK, McKnight A, Manisty C, Treibel TA, Moon JC, Noursadeghi M, Chain B. Large clones of pre-existing T cells drive early immunity against SARS-COV-2 and LCMV infection. iScience 2023;26:106937. [PMID: 37275518 PMCID: PMC10201888 DOI: 10.1016/j.isci.2023.106937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/14/2023] [Accepted: 05/17/2023] [Indexed: 06/07/2023]  Open
10
Mark M, Reich-Zeliger S, Greenstein E, Biram A, Chain B, Friedman N, Madi A. Viral infection reveals hidden sharing of TCR CDR3 sequences between individuals. Front Immunol 2023;14:1199064. [PMID: 37325645 PMCID: PMC10266217 DOI: 10.3389/fimmu.2023.1199064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/16/2023] [Indexed: 06/17/2023]  Open
11
Luo J, Wang X, Zou Y, Chen L, Liu W, Zhang W, Li SC. Quantitative annotations of T-Cell repertoire specificity. Brief Bioinform 2023;24:bbad175. [PMID: 37150761 DOI: 10.1093/bib/bbad175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/03/2023] [Accepted: 04/17/2023] [Indexed: 05/09/2023]  Open
12
Sidlik Muskatel R, Nathansohn-Levi B, Reich-Zeliger S, Mark M, Stoler-Barak L, Rosen C, Milman-Krentsis I, Bachar Lustig E, Pete Gale R, Friedman N, Reisner Y. Correction of T-Cell Repertoire and Autoimmune Diabetes in NOD Mice by Non-myeloablative T-Cell Depleted Allogeneic HSCT. Stem Cells Transl Med 2023;12:281-292. [PMID: 37184893 PMCID: PMC10184699 DOI: 10.1093/stcltm/szad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 03/03/2023] [Indexed: 05/16/2023]  Open
13
Sharma S, Woods M, Mehta NU, Sauer T, Parikh KS, Schmuck-Henneresse M, Zhang H, Mehta B, Brenner MK, Heslop HE, Rooney CM. Naive T cells inhibit the outgrowth of intractable antigen-activated memory T cells: implications for T-cell immunotherapy. J Immunother Cancer 2023;11:e006267. [PMID: 37072346 PMCID: PMC10124261 DOI: 10.1136/jitc-2022-006267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2023] [Indexed: 04/20/2023]  Open
14
Smirnova AO, Miroshnichenkova AM, Olshanskaya YV, Maschan MA, Lebedev YB, Chudakov DM, Mamedov IZ, Komkov A. The use of non-functional clonotypes as a natural calibrator for quantitative bias correction in adaptive immune receptor repertoire profiling. eLife 2023;12:69157. [PMID: 36692004 PMCID: PMC9901932 DOI: 10.7554/elife.69157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 01/22/2023] [Indexed: 01/25/2023]  Open
15
Camaglia F, Ryvkin A, Greenstein E, Reich-Zeliger S, Chain B, Mora T, Walczak AM, Friedman N. Quantifying changes in the T cell receptor repertoire during thymic development. eLife 2023;12:81622. [PMID: 36661220 PMCID: PMC9934861 DOI: 10.7554/elife.81622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/18/2023] [Indexed: 01/21/2023]  Open
16
Zhi Y, Li M, Lv G. Into the multi-omics era: Progress of T cells profiling in the context of solid organ transplantation. Front Immunol 2023;14:1058296. [PMID: 36798139 PMCID: PMC9927650 DOI: 10.3389/fimmu.2023.1058296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023]  Open
17
Tettamanti Boshier FA, Reeves DB, Duke ER, Swan DA, Prlic M, Cardozo-Ojeda EF, Schiffer JT. Substantial uneven proliferation of CD4+ T cells during recovery from acute HIV infection is sufficient to explain the observed expanded clones in the HIV reservoir. J Virus Erad 2022;8:100091. [PMID: 36582473 PMCID: PMC9792356 DOI: 10.1016/j.jve.2022.100091] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 09/08/2022] [Accepted: 10/10/2022] [Indexed: 12/03/2022]  Open
18
Phenomenology and dynamics of competitive ecosystems beyond the niche-neutral regimes. Proc Natl Acad Sci U S A 2022;119:e2204394119. [PMID: 36251996 PMCID: PMC9618050 DOI: 10.1073/pnas.2204394119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
19
Liu S, Iorgulescu JB, Li S, Borji M, Barrera-Lopez IA, Shanmugam V, Lyu H, Morriss JW, Garcia ZN, Murray E, Reardon DA, Yoon CH, Braun DA, Livak KJ, Wu CJ, Chen F. Spatial maps of T cell receptors and transcriptomes reveal distinct immune niches and interactions in the adaptive immune response. Immunity 2022;55:1940-1952.e5. [PMID: 36223726 PMCID: PMC9745674 DOI: 10.1016/j.immuni.2022.09.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 06/21/2022] [Accepted: 08/31/2022] [Indexed: 12/15/2022]
20
Mark M, Reich-Zeliger S, Greenstein E, Reshef D, Madi A, Chain B, Friedman N. A hierarchy of selection pressures determines the organization of the T cell receptor repertoire. Front Immunol 2022;13:939394. [PMID: 35967295 PMCID: PMC9372880 DOI: 10.3389/fimmu.2022.939394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022]  Open
21
Sun X, Nguyen T, Achour A, Ko A, Cifello J, Ling C, Sharma J, Hiroi T, Zhang Y, Chia CW, Wood Iii W, Wu WW, Zukley L, Phue JN, Becker KG, Shen RF, Ferrucci L, Weng NP. Longitudinal analysis reveals age-related changes in the T cell receptor repertoire of human T cell subsets. J Clin Invest 2022;132:158122. [PMID: 35708913 PMCID: PMC9433102 DOI: 10.1172/jci158122] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/14/2022] [Indexed: 11/17/2022]  Open
22
Dessalles R, Pan Y, Xia M, Maestrini D, D'Orsogna MR, Chou T. How Naive T-Cell Clone Counts Are Shaped By Heterogeneous Thymic Output and Homeostatic Proliferation. Front Immunol 2022;12:735135. [PMID: 35250963 PMCID: PMC8891377 DOI: 10.3389/fimmu.2021.735135] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022]  Open
23
Chandran A, Rosenheim J, Nageswaran G, Swadling L, Pollara G, Gupta RK, Burton AR, Guerra-Assunção JA, Woolston A, Ronel T, Pade C, Gibbons JM, Sanz-Magallon Duque De Estrada B, Robert de Massy M, Whelan M, Semper A, Brooks T, Altmann DM, Boyton RJ, McKnight Á, Captur G, Manisty C, Treibel TA, Moon JC, Tomlinson GS, Maini MK, Chain BM, Noursadeghi M. Rapid synchronous type 1 IFN and virus-specific T cell responses characterize first wave non-severe SARS-CoV-2 infections. Cell Rep Med 2022;3:100557. [PMID: 35474751 PMCID: PMC8895494 DOI: 10.1016/j.xcrm.2022.100557] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 11/22/2021] [Accepted: 02/09/2022] [Indexed: 12/15/2022]
24
Dahal-Koirala S, Balaban G, Neumann RS, Scheffer L, Lundin KEA, Greiff V, Sollid LM, Qiao SW, Sandve GK. TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences. Brief Bioinform 2022;23:bbab566. [PMID: 35062022 PMCID: PMC8921636 DOI: 10.1093/bib/bbab566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/02/2021] [Accepted: 12/11/2021] [Indexed: 01/19/2023]  Open
25
Sandgaard KS, Gkouleli T, Attenborough T, Adams S, Gibbons D, Holm M, Eisen S, Baxendale H, De Rossi A, Pahwa S, Chain B, Gkazi AS, Klein N. The importance of taking ART appropriately in children and adolescents with HIV-1 to reach the highest capacity of immune function later in life. Front Immunol 2022;13:860316. [PMID: 35967315 PMCID: PMC9364750 DOI: 10.3389/fimmu.2022.860316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/28/2022] [Indexed: 11/26/2022]  Open
26
Heather JM, Spindler MJ, Alonso M, Shui Y, Millar DG, Johnson D, Cobbold M, Hata A. OUP accepted manuscript. Nucleic Acids Res 2022;50:e68. [PMID: 35325179 PMCID: PMC9262623 DOI: 10.1093/nar/gkac190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/18/2022] [Accepted: 03/09/2022] [Indexed: 11/17/2022]  Open
27
Nageswaran G, Byrne S, Veeriah S, Chain B. The Intra-Tumoral T Cell Receptor Repertoire: Steps Towards a Useful Clinical Biomarker. Methods Mol Biol 2022;2574:135-158. [PMID: 36087200 DOI: 10.1007/978-1-0716-2712-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
28
Valori M, Jansson L, Tienari PJ. CD8+ cell somatic mutations in multiple sclerosis patients and controls-Enrichment of mutations in STAT3 and other genes implicated in hematological malignancies. PLoS One 2021;16:e0261002. [PMID: 34874980 PMCID: PMC8651110 DOI: 10.1371/journal.pone.0261002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/23/2021] [Indexed: 01/14/2023]  Open
29
Moretti FA, Giardino G, Attenborough TCH, Gkazi AS, Margetts BK, la Marca G, Fairbanks L, Crompton T, Gaspar HB. Metabolite and thymocyte development defects in ADA-SCID mice receiving enzyme replacement therapy. Sci Rep 2021;11:23221. [PMID: 34853379 PMCID: PMC8636570 DOI: 10.1038/s41598-021-02572-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/15/2021] [Indexed: 11/22/2022]  Open
30
Au L, Hatipoglu E, Robert de Massy M, Litchfield K, Beattie G, Rowan A, Schnidrig D, Thompson R, Byrne F, Horswell S, Fotiadis N, Hazell S, Nicol D, Shepherd STC, Fendler A, Mason R, Del Rosario L, Edmonds K, Lingard K, Sarker S, Mangwende M, Carlyle E, Attig J, Joshi K, Uddin I, Becker PD, Sunderland MW, Akarca A, Puccio I, Yang WW, Lund T, Dhillon K, Vasquez MD, Ghorani E, Xu H, Spencer C, López JI, Green A, Mahadeva U, Borg E, Mitchison M, Moore DA, Proctor I, Falzon M, Pickering L, Furness AJS, Reading JL, Salgado R, Marafioti T, Jamal-Hanjani M, Kassiotis G, Chain B, Larkin J, Swanton C, Quezada SA, Turajlic S. Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma. Cancer Cell 2021;39:1497-1518.e11. [PMID: 34715028 PMCID: PMC8599450 DOI: 10.1016/j.ccell.2021.10.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/19/2021] [Accepted: 10/06/2021] [Indexed: 02/08/2023]
31
Fu J, Khosravi-Maharlooei M, Sykes M. High Throughput Human T Cell Receptor Sequencing: A New Window Into Repertoire Establishment and Alloreactivity. Front Immunol 2021;12:777756. [PMID: 34804070 PMCID: PMC8604183 DOI: 10.3389/fimmu.2021.777756] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/20/2021] [Indexed: 12/25/2022]  Open
32
Postpartum breast cancer has a distinct molecular profile that predicts poor outcomes. Nat Commun 2021;12:6341. [PMID: 34732713 PMCID: PMC8566602 DOI: 10.1038/s41467-021-26505-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 10/06/2021] [Indexed: 12/21/2022]  Open
33
Wang S, Wang L, Liu Y, Zhu Y, Liu Y. Characteristics of T-cell receptor repertoire of stem cell-like memory CD4+ T cells. PeerJ 2021;9:e11987. [PMID: 34527440 PMCID: PMC8401816 DOI: 10.7717/peerj.11987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/26/2021] [Indexed: 11/20/2022]  Open
34
Shevyrev D, Tereshchenko V, Kozlov V. Immune Equilibrium Depends on the Interaction Between Recognition and Presentation Landscapes. Front Immunol 2021;12:706136. [PMID: 34394106 PMCID: PMC8362327 DOI: 10.3389/fimmu.2021.706136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/12/2021] [Indexed: 12/15/2022]  Open
35
Sandgaard KS, Margetts B, Attenborough T, Gkouleli T, Adams S, Holm M, Gibb D, Gibbons D, Giaquinto C, De Rossi A, Bamford A, Palma P, Chain B, Gkazi AS, Klein N. Plasticity of the Immune System in Children Following Treatment Interruption in HIV-1 Infection. Front Immunol 2021;12:643189. [PMID: 34475868 PMCID: PMC8406805 DOI: 10.3389/fimmu.2021.643189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 07/16/2021] [Indexed: 11/13/2022]  Open
36
Dvorkin S, Levi R, Louzoun Y. Autoencoder based local T cell repertoire density can be used to classify samples and T cell receptors. PLoS Comput Biol 2021;17:e1009225. [PMID: 34310600 PMCID: PMC8341707 DOI: 10.1371/journal.pcbi.1009225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 08/05/2021] [Accepted: 06/28/2021] [Indexed: 11/18/2022]  Open
37
Conforti F, Pala L, Pagan E, Bagnardi V, De Pas T, Queirolo P, Pennacchioli E, Catania C, Cocorocchio E, Ferrucci PF, Saponara M, Orsolini G, Zagami P, Nicoló E, De Marinis F, Tortora G, Bria E, Minucci S, Joffe H, Veronesi P, Wargo J, Rosenthal R, Swanton C, Mantovani A, Gelber RD, Viale G, Goldhirsch A, Giaccone G. Sex-Based Dimorphism of Anticancer Immune Response and Molecular Mechanisms of Immune Evasion. Clin Cancer Res 2021;27:4311-4324. [PMID: 34016641 PMCID: PMC7611463 DOI: 10.1158/1078-0432.ccr-21-0136] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/01/2021] [Accepted: 05/13/2021] [Indexed: 12/14/2022]
38
Peacock T, Heather JM, Ronel T, Chain B. Decombinator V4: an improved AIRR compliant-software package for T-cell receptor sequence annotation? Bioinformatics 2021;37:876-878. [PMID: 32853330 PMCID: PMC8098023 DOI: 10.1093/bioinformatics/btaa758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/15/2020] [Accepted: 08/20/2020] [Indexed: 11/14/2022]  Open
39
Chiou SH, Tseng D, Reuben A, Mallajosyula V, Molina IS, Conley S, Wilhelmy J, McSween AM, Yang X, Nishimiya D, Sinha R, Nabet BY, Wang C, Shrager JB, Berry MF, Backhus L, Lui NS, Wakelee HA, Neal JW, Padda SK, Berry GJ, Delaidelli A, Sorensen PH, Sotillo E, Tran P, Benson JA, Richards R, Labanieh L, Klysz DD, Louis DM, Feldman SA, Diehn M, Weissman IL, Zhang J, Wistuba II, Futreal PA, Heymach JV, Garcia KC, Mackall CL, Davis MM. Global analysis of shared T cell specificities in human non-small cell lung cancer enables HLA inference and antigen discovery. Immunity 2021;54:586-602.e8. [PMID: 33691136 PMCID: PMC7960510 DOI: 10.1016/j.immuni.2021.02.014] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/08/2020] [Accepted: 02/11/2021] [Indexed: 12/12/2022]
40
Turner CT, Brown J, Shaw E, Uddin I, Tsaliki E, Roe JK, Pollara G, Sun Y, Heather JM, Lipman M, Chain B, Noursadeghi M. Persistent T Cell Repertoire Perturbation and T Cell Activation in HIV After Long Term Treatment. Front Immunol 2021;12:634489. [PMID: 33732256 PMCID: PMC7959740 DOI: 10.3389/fimmu.2021.634489] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/11/2021] [Indexed: 12/11/2022]  Open
41
Barennes P, Quiniou V, Shugay M, Egorov ES, Davydov AN, Chudakov DM, Uddin I, Ismail M, Oakes T, Chain B, Eugster A, Kashofer K, Rainer PP, Darko S, Ransier A, Douek DC, Klatzmann D, Mariotti-Ferrandiz E. Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases. Nat Biotechnol 2021;39:236-245. [PMID: 32895550 DOI: 10.1038/s41587-020-0656-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/28/2020] [Indexed: 12/13/2022]
42
Ronel T, Harries M, Wicks K, Oakes T, Singleton H, Dearman R, Maxwell G, Chain B. The clonal structure and dynamics of the human T cell response to an organic chemical hapten. eLife 2021;10:54747. [PMID: 33432924 PMCID: PMC7880692 DOI: 10.7554/elife.54747] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 01/12/2021] [Indexed: 12/27/2022]  Open
43
Dupic T, Bensouda Koraichi M, Minervina AA, Pogorelyy MV, Mora T, Walczak AM. Immune fingerprinting through repertoire similarity. PLoS Genet 2021;17:e1009301. [PMID: 33395405 PMCID: PMC7808657 DOI: 10.1371/journal.pgen.1009301] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 01/14/2021] [Accepted: 12/07/2020] [Indexed: 11/18/2022]  Open
44
Gaimann MU, Nguyen M, Desponds J, Mayer A. Early life imprints the hierarchy of T cell clone sizes. eLife 2020;9:e61639. [PMID: 33345776 PMCID: PMC7870140 DOI: 10.7554/elife.61639] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/20/2020] [Indexed: 12/30/2022]  Open
45
Preece R, Pavesi A, Gkazi SA, Stegmann KA, Georgiadis C, Tan ZM, Aw JYJ, Maini MK, Bertoletti A, Qasim W. CRISPR-Mediated Base Conversion Allows Discriminatory Depletion of Endogenous T Cell Receptors for Enhanced Synthetic Immunity. Mol Ther Methods Clin Dev 2020;19:149-161. [PMID: 33102612 PMCID: PMC7549055 DOI: 10.1016/j.omtm.2020.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/04/2020] [Indexed: 12/26/2022]
46
Poran A, Scherer J, Bushway ME, Besada R, Balogh KN, Wanamaker A, Williams RG, Prabhakara J, Ott PA, Hu-Lieskovan S, Khondker ZS, Gaynor RB, Rooney MS, Srinivasan L. Combined TCR Repertoire Profiles and Blood Cell Phenotypes Predict Melanoma Patient Response to Personalized Neoantigen Therapy plus Anti-PD-1. CELL REPORTS MEDICINE 2020;1:100141. [PMID: 33294862 PMCID: PMC7691446 DOI: 10.1016/j.xcrm.2020.100141] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 09/02/2020] [Accepted: 10/22/2020] [Indexed: 01/15/2023]
47
Hughes TK, Wadsworth MH, Gierahn TM, Do T, Weiss D, Andrade PR, Ma F, de Andrade Silva BJ, Shao S, Tsoi LC, Ordovas-Montanes J, Gudjonsson JE, Modlin RL, Love JC, Shalek AK. Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies. Immunity 2020;53:878-894.e7. [PMID: 33053333 PMCID: PMC7562821 DOI: 10.1016/j.immuni.2020.09.015] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 05/21/2020] [Accepted: 09/18/2020] [Indexed: 01/10/2023]
48
Ultra-efficient sequencing of T Cell receptor repertoires reveals shared responses in muscle from patients with Myositis. EBioMedicine 2020;59:102972. [PMID: 32891935 PMCID: PMC7484536 DOI: 10.1016/j.ebiom.2020.102972] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/10/2020] [Accepted: 08/10/2020] [Indexed: 12/24/2022]  Open
49
Amoriello R, Greiff V, Aldinucci A, Bonechi E, Carnasciali A, Peruzzi B, Repice AM, Mariottini A, Saccardi R, Mazzanti B, Massacesi L, Ballerini C. The TCR Repertoire Reconstitution in Multiple Sclerosis: Comparing One-Shot and Continuous Immunosuppressive Therapies. Front Immunol 2020;11:559. [PMID: 32328061 PMCID: PMC7160336 DOI: 10.3389/fimmu.2020.00559] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/11/2020] [Indexed: 11/13/2022]  Open
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Aversa I, Malanga D, Fiume G, Palmieri C. Molecular T-Cell Repertoire Analysis as Source of Prognostic and Predictive Biomarkers for Checkpoint Blockade Immunotherapy. Int J Mol Sci 2020;21:ijms21072378. [PMID: 32235561 PMCID: PMC7177412 DOI: 10.3390/ijms21072378] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/22/2020] [Accepted: 03/28/2020] [Indexed: 02/08/2023]  Open
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