Publications

2021

Verhagen, Johan et al. Human CD4+ T cells specific for dominant epitopes of SARS-CoV-2 Spike and Nucleocapsid proteins with therapeutic potential. Clinical and experimental immunology, 1 Jun. 2021, https://doi.org/10.1111/cei.13627

Yan, Q. et al. Germline IGHV3-53-encoded RBD-targeting neutralizing antibodies are commonly present in the antibody repertoires of COVID-19 patients. Emerging Microbes & Infections, 2021 https://doi.org/10.1080/22221751.2021.1925594 

Khabouri, S. A. et al. TCRβ Sequencing Reveals Spatial and Temporal Evolution of Clonal CD4 T Cell Responses in a Breach of Tolerance Model of Inflammatory. Arthritis. Front. Immunol., 27 April 2021 https://doi.org/10.3389/fimmu.2021.669856 

Chen, Z. et al. Decreased Treg Cell and TCR Expansion Are Involved in Long-Lasting Graves’ Disease. Front. Endocrinol. 2021; 12: 632492 https://doi.org/10.3389/fendo.2021.632492 

Coelho, C. H. et al. A human monoclonal antibody blocks malaria transmission and defines a highly conserved neutralizing epitope on gametes. Nat Commun 12, 1750 (2021). https://doi.org/10.1038/s41467-021-21955-1

Maoz, A. et al. Elevated T cell repertoire diversity is associated with progression of lung squamous cell premalignant lesions. medRxiv 2021.02.25.21252467. https://doi.org/10.1101/2021.02.25.21252467 

Yang, Y., Li, X., Ma, Z. et al. CTLA-4 expression by B-1a B cells is essential for immune tolerance. Nat Commun, 12, Article number: 525 (2021) https://doi.org/10.1038/s41467-020-20874-x 

Akiyoshi, T. et al. T-cell complexity and density are associated with sensitivity to neoadjuvant chemoradiotherapy in patients with rectal cancer. Cancer Immunology, Immunotherapy volume (2021) 70:509–518 https://doi.org/10.1007/s00262-020-02705-6 

2020

Hoof, I. et al. Allergen-specific IgG+ memory B cells are temporally linked to IgE memory responses. Journal of Allergy and Clinical Immunology 146, 1, 7 2020, 180-191. https://doi.org/10.1016/j.jaci.2019.11.046 

Ekeke, C. N. et al. Intrapleural interleukin-2–expressing oncolytic virotherapy enhances acute antitumor effects and T-cell receptor diversity in malignant pleural disease. JTCVS 2020 11.160 https://doi.org/10.1016/j.jtcvs.2020.11.160  

Mitchell, A. M. et al. T cell receptor sequencing in autoimmunity. J Life Sci. 2020 Dec; 2(4): 38–58. https://doi.org/fmcz 

Tang, Y. et al. TruNeo: an integrated pipeline improves personalized true tumor neoantigen identification. BMC Bioinformatics 21, 532 (2020). https://doi.org/10.1186/s12859-020-03869-9 

Poran, A. et al. Combined TCR Repertoire Profiles and Blood Cell Phenotypes Predict Melanoma Patient Response to Personalized Neoantigen Therapy plus Anti-PD-1. CR Med 1, (2020). https://doi.org/10.1016/j.xcrm.2020.100141

Wang, D. et al. Identification of Potential Immunogenic Molecules During the Allogeneic Transplantation of Human Adipose-derived Mesenchymal Stem Cells. Research Square, 2020. https://doi.org/10.21203/rs.3.rs-105760/v1 

Coelho, C. H. et al. Antimalarial antibody repertoire defined by plasma IG proteomics and single B cell IG sequencing. JCI Insight (2020). https://doi.org/10.1172/jci.insight.143471

Soloff, A. C. et al. HMGB1 Promotes Myeloid Egress and Limits Lymphatic Clearance of Malignant Pleural Effusions. Frontiers in Immunology 11, (2020). https://doi.org/10.3389/fimmu.2020.02027

Niu, X. et al. Longitudinal Analysis of T and B Cell Receptor Repertoire Transcripts Reveal Dynamic Immune Response in COVID-19 Patients. Front. Immunol. 11, (2020). https://doi.org/10.3389/fimmu.2020.582010

Chen, H. et al. Profiling the pattern of the human T-cell receptor γδ complementary determinant region 3 repertoire in patients with lung carcinoma via high-throughput sequencing analysis. Cell Mol Immunol 16, 250–259 (2019). https://doi.org/10.1038/cmi.2017.157

Stankovic, S. et al. Cytomegalovirus replication is associated with enrichment of distinct γδ T cell subsets following lung transplantation: A novel therapeutic approach? Journal of Heart and Lung Transplantation 39.11, 1300-1312 (2020). https://doi.org/10.1016/j.healun.2020.08.014 

Ye, X. et al. High-Throughput Sequencing-Based Analysis of T Cell Repertoire in Lupus Nephritis. Front. Immunol., 06 August 2020. https://doi.org/10.3389/fimmu.2020.01618 

Boi, S. K. et al. Obesity diminishes response to PD-1-based immunotherapies in renal cancer. Journal for immunotherapy of cancer, 8(2), 2020. https://doi.org/10.1136/jitc-2020-000725 

Choi, D. W. et al. Co‑transplantation of tonsil‑derived mesenchymal stromal cells in bone marrow transplantation promotes thymus regeneration and T cell diversity following cytotoxic conditioning. International Journal of Molecular Medicine 46.3 (2020): 1166-1174. https://doi.org/10.3892/ijmm.2020.4657 

Prokop, J. W. et al. Virus-induced genetics revealed by multidimensional precision medicine transcriptional workflow applicable to COVID-19. Physiological Genomics 52, 255–268 (2020). https://doi.org/10.1152/physiolgenomics.00045.2020

Tune, C. et al. Effects of sleep on the splenic milieu in mice and the T cell receptor repertoire recruited into a T cell dependent B cell response. Brain, Behavior, & Immunity – Health 5, 2020. https://doi.org/10.1016/j.bbih.2020.100082 

Zhang, L. et al. Comprehensive investigation of T and B cell receptor repertoires in an MC38 tumor model following murine anti‑PD‑1 administration. Molecular Medicine Reports, 22, 975-985. https://doi.org/10.3892/mmr.2020.11169 

Yeh, T. W. et al. APRIL-dependent lifelong plasmacyte maintenance and immunoglobulin production in humans. Journal of Allergy and Clinical Immunology, 146. 5, (2020) 1013-1015. https://doi.org/10.1016/j.jaci.2020.03.025 

Amoriello, R. et al. The TCR Repertoire Reconstitution in Multiple Sclerosis: Comparing One-Shot and Continuous Immunosuppressive Therapies. Front. Immunol., 4 2020. https://doi.org/10.3389/fimmu.2020.00559 

Quayle, S. N. et al. CUE-101, a Novel E7-pHLA-IL2-Fc Fusion Protein, Enhances Tumor Antigen-Specific T-Cell Activation for the Treatment of HPV16-Driven Malignancies. Clinical Cancer Research 26, 1953–1964 (2020). https://doi.org/10.1158/1078-0432.CCR-19-3354

Yang, H, G. et al. Transforming growth factor-β promotes the function of HIV-specific CXCR5+CD8 T cells https://doi.org/10.1111/1348-0421.12789 

Djaoud, Z. et al. Dimorphism in the TCRγ-chain repertoire defines 2 types of human immunity to Epstein-Barr virus. Blood Adv (2020) 4 (7): 1198–1205. https://doi.org/10.1182/bloodadvances.2019001179 

Liao, Y. W. et al. Enterovirus 71 Infection Shapes Host T Cell Receptor Repertoire and Presumably Expands VP1-Specific TCRβ CDR3 Cluster. Pathogens 2020, 9(2), 121; https://doi.org/10.3390/pathogens9020121 

2019

Zhang, J. et al. Analysis of TCR β CDR3 sequencing data for tracking anti-tumor immunity. Methods in enzymology, 2019. https://doi.org/10.1016/bs.mie.2019.08.006 

McCaw, T.R. et al. The expression of MHC class II molecules on murine breast tumors delays T-cell exhaustion, expands the T-cell repertoire, and slows tumor growth. Cancer Immunol Immunother68, 175–188 (2019). https://doi.org/10.1007/s00262-018-2262-5

Guo, C. et al. Deep targeted sequencing reveals the diversity of TRB-CDR3 repertoire in patients with preeclampsia. Hum Immunol. 2019 Oct;80(10):848-854. https://doi.org/10.1016/j.humimm.2019.04.003 

Kuo, H. C. et al. Global Investigation of Immune Repertoire Suggests Kawasaki Disease Has Infectious Cause Circulation journal: official journal of the Japanese Circulation Society, 83(10), 2070–2078. https://doi.org/10.1253/circj.CJ-19-0206 

Li, Y. et al. Identification of the Ligands of TCRγδ by Screening the Immune Repertoire of γδT Cells From Patients With Tuberculosis. Front. Immunol., 24 September 2019. https://doi.org/10.3389/fimmu.2019.02282 

Chang, C. M. et al. Characterization of T-Cell Receptor Repertoire in Patients with Rheumatoid Arthritis Receiving Biologic Therapies. Disease Markers, 2019. https://doi.org/10.1155/2019/2364943 

Strauli, N. et al. The genetic interaction between HIV and the antibody repertoire. bioRxiv 646968 (2019). https://doi.org/10.1101/646968

Konishi, H. et al. Capturing the differences between humoral immunity in the normal and tumor environments from repertoire-seq of B-cell receptors using supervised machine learning. BMC Bioinformatics 20, 267 (2019). https://doi.org/10.1186/s12859-019-2853-y

Fuchs, T. et al. Immediate Neutrophil-Variable-T Cell Receptor Host Response in Bacterial Meningitis. Front. Neurol., 02 April 2019. https://doi.org/10.3389/fneur.2019.00307 

Lee, M. et al. Preferential Infiltration of Unique Vγ9Jγ2-Vδ2 T Cells Into Glioblastoma Multiforme. Front. Immunol., 22 March 2019. https://doi.org/10.3389/fimmu.2019.00555 

Geng, Z. H. et al. Human colorectal cancer cells frequently express IgG and display unique Ig repertoire. World journal of gastrointestinal oncology, 2019 11(3), 195–207. https://doi.org/10.4251/wjgo.v11.i3.195 

Yamashita, M. et al. A synonymous splice site mutation in IL2RG gene causes late-onset combined immunodeficiency Int J Hematol 109, 603–611 (2019). https://doi.org/10.1007/s12185-019-02619-9 

Wu, S. G. et al. High throughput sequencing of T-cell receptor repertoire using dry blood spots J Transl Med 17, 47 (2019). https://doi.org/10.1186/s12967-019-1796-4 

Chen, H. et al. Profiling the pattern of the human T-cell receptor γδ complementary determinant region 3 repertoire in patients with lung carcinoma via high-throughput sequencing analysis. Cell Mol Immunol 16, 250–259 (2019). https://doi.org/10.1038/cmi.2017.157 

Rettig, T. A. et al. A comparison of unamplified and massively multiplexed PCR amplification for murine antibody repertoire sequencing. FASEB bioAdvances vol. 1,1 (2019): 6-17. https://doi.org/10.1096/fba.1017 

2018

Huang, W. et al. Belimumab promotes negative selection of activated autoreactive B cells in systemic lupus erythematosus patients. JCI Insight 3, (2018). https://doi.org/10.1172/jci.insight.122525.

Hou, X. et al. Identification of paired heavy and light chains from single B-cells from immunized Malian adults with rapid functional confirmation using iPair-BCRTM, NGS, and iScreenTM. J. Immunol. 200, 174.36 (2018). https://www.jimmunol.org/content/200/1_Supplement/174.36

Wu, J. et al. Expanded TCRβ CDR3 clonotypes distinguish Crohn’s disease and ulcerative colitis patients. Mucosal Immunol 11, 1487–1495 (2018). https://doi.org/10.1038/s41385-018-0046-z

Cheng, C. et al. Next generation sequencing reveals changes of the γδ T cell receptor repertoires in patients with pulmonary tuberculosis. Sci Rep 8, 1–13 (2018). https://doi.org/10.1038/s41598-018-22061-x

Hunter, S. et al. Human liver infiltrating γδ T cells are composed of clonally expanded circulating and tissue-resident populations. Journal of Hepatology 69, 654–665 (2018). https://doi.org/10.1016/j.jhep.2018.05.007

Jiang, Q. et al. Patient-shared TCRβ-CDR3 clonotypes correlate with favorable prognosis in chronic hepatitis B. European Journal of Immunology 48, 1539–1549 (2018). https://doi.org/10.1002/eji.201747327

Dickinson, G. S. et al. IL-7 Enables Antibody Responses to Bacterial Polysaccharides by Promoting B Cell Receptor Diversity. The Journal of Immunology 201, 1229–1240 (2018). https://doi.org/10.4049/jimmunol.1800162

Jiang, Q. et al. Analysis of T cell receptor repertoire in monozygotic twins concordant and discordant for chronic hepatitis B infection. Biochemical and Biophysical Research Communications 497, 153–159 (2018). https://doi.org/10.1016/j.bbrc.2018.02.043

Textor, J. et al. Deep Sequencing Reveals Transient Segregation of T Cell Repertoires in Splenic T Cell Zones during an Immune Response. The Journal of Immunology 201, 350–358 (2018). https://doi.org/10.4049/jimmunol.1800091

Fähnrich, A. et al. CD154 Costimulation Shifts the Local T-Cell Receptor Repertoire Not Only During Thymic Selection but Also During Peripheral T-Dependent Humoral Immune Responses. Front. Immunol. 9, (2018). https://dx.doi.org/10.3389%2Ffimmu.2018.01019

Tedesco, D. et al. Alterations in Intestinal Microbiota Lead to Production of Interleukin 17 by Intrahepatic γδ T-Cell Receptor–Positive Cells and Pathogenesis of Cholestatic Liver Disease. Gastroenterology 154, 2178–2193 (2018). https://doi.org/10.1053/j.gastro.2018.02.019

Davey, M. S. et al. The human Vδ2 + T-cell compartment comprises distinct innate-like Vγ9 + and adaptive Vγ9 – subsets. Nat Commun 9, 1–14 (2018). https://doi.org/10.1038/s41467-018-04076-0

Shukla, G. S. et al. Immunization with tumor neoantigens displayed on T7 phage nanoparticles elicits plasma antibody and vaccine-draining lymph node B cell responses. Journal of Immunological Methods 460, 51–62 (2018). https://doi.org/10.1016/j.jim.2018.06.009

Fahl, S. P. et al. Role of a selecting ligand in shaping the murine γδ-TCR repertoire. Proc Natl Acad Sci USA 115, 1889 (2018). https://doi.org/10.1073/pnas.1718328115

Davey, M. S. et al. Recasting Human Vδ1 Lymphocytes in an Adaptive Role. Trends in Immunology 39, 446–459 (2018). https://doi.org/10.1016/j.it.2018.03.003

Zhang, C. et al. Impact of a 3-Months Vegetarian Diet on the Gut Microbiota and Immune Repertoire. Front. Immunol. 9, (2018). https://doi.org/10.3389/fimmu.2018.00908

McCaw, T. R. et al. The expression of class II major histocompatibility molecules on breast tumors delays T cell exhaustion, expands the T cell repertoire and slows tumor growth. bioRxiv 294124 (2018). https://doi.org/10.1101/294124

Spence, A. et al. Revealing the specificity of regulatory T cells in murine autoimmune diabetes. PNAS 115, 5265–5270 (2018). https://doi.org/10.1073/pnas.1715590115

2017

Mitchell, A. M. et al. CD4+ T cell receptor repertoire in sarcoidosis patients. The Journal of Immunology 198, 55.36-55.36 (2017). https://www.jimmunol.org/content/198/1_Supplement/55.36

Okano, T. et al. Maternal T and B cell engraftment in two cases of X-linked severe combined immunodeficiency with IgG1 gammopathy. Clinical Immunology 183, 112–120 (2017). https://doi.org/10.1016/j.clim.2017.08.003

Davey, M. S. et al. Clonal selection in the human Vδ1 T cell repertoire indicates γδ TCR-dependent adaptive immune surveillance. Nat Commun 8, 1–15 (2017). https://doi.org/10.1038/ncomms14760

Barisa, M. et al. E. coli promotes human Vγ9Vδ2 T cell transition from cytokine-producing bactericidal effectors to professional phagocytic killers in a TCR-dependent manner. Sci Rep 7, 1–12 (2017). https://doi.org/10.1038/s41598-017-02886-8

Mitchell, A. M. et al. Shared αβ TCR Usage in Lungs of Sarcoidosis Patients with Löfgren’s Syndrome. The Journal of Immunology 199, 2279–2290 (2017). https://doi.org/10.4049/jimmunol.1700570

Probst, P. et al. Sarcoma eradication by doxorubicin and targeted TNF relies upon CD8+ T cell recognition of a retroviral antigen. Cancer Res canres.2946.2016 (2017). https://cancerres.aacrjournals.org/content/early/2017/05/06/0008-5472.CAN-16-2946

Chen, H. et al. Characterization of the diversity of T cell receptor γδ complementary determinant region 3 in human peripheral blood by Immune Repertoire Sequencing. Journal of Immunological Methods 443, 9–17 (2017). https://doi.org/10.1016/j.jim.2017.01.009

Katoh, H. et al. Immunogenetic Profiling for Gastric Cancers Identifies Sulfated Glycosaminoglycans as Major and Functional B Cell Antigens in Human Malignancies. Cell Reports 20, 1073–1087 (2017). https://doi.org/10.1016/j.celrep.2017.07.016

Wong, H.S. et al. V-J combinations of T-cell receptor predict responses to erythropoietin in end-stage renal disease patients. J Biomed Sci 24, 43 (2017). https://doi.org/10.1186/s12929-017-0349-5

Ritvo, P.-G. et al. High-resolution repertoire analysis of Tfr and Tfh cells reveals unexpectedly high diversities indicating a bystander activation of follicular T cells. bioRxiv 231977 (2017). https://doi.org/10.1101/231977

2016

Hou, D. et al. Immune Repertoire Diversity Correlated with Mortality in Avian Influenza A (H7N9) Virus Infected Patients. Sci Rep 6, 1–11 (2016). https://doi.org/10.1038/srep33843

Al-Hussaini, M. et al. Targeting CD123 in acute myeloid leukemia using a T-cell–directed dual-affinity retargeting platform. Blood 127, 122–131 (2016). https://doi.org/10.1182/blood-2014-05-575704

Lee, Y. N. et al. Characterization of T and B cell repertoire diversity in patients with RAG deficiency. Science Immunology 1, (2016). https://immunology.sciencemag.org/content/1/6/eaah6109

Sims, J. S. et al. Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire. PNAS 113, E3529–E3537 (2016). https://doi.org/10.1073/pnas.1601012113

2015

Riser, et al. A Comprehensive Analysis of Relapse in Multiple Sclerosis. CMSC Actrims (2015). https://cmsc.confex.com/cmsc/2015/webprogram/Paper3660.html

Byrne-Steele, M. et al. iRock 2.0 and the iR-Processor: an automated immune repertoire library preparation platform for NGS (TECH2P.919). The Journal of Immunology 194, 206.29-206.29 (2015). https://www.jimmunol.org/content/194/1_Supplement/206.29

Yang, Y. et al. Distinct mechanisms define murine B cell lineage immunoglobulin heavy chain (IgH) repertoires. eLife 4, e09083 (2015). https://doi.org/10.7554/eLife.09083

Zhao, T. et al. Humanized Mice Reveal Differential Immunogenicity of Cells Derived from Autologous Induced Pluripotent Stem Cells. Cell Stem Cell 17, 353–359 (2015). https://doi.org/10.1016/j.stem.2015.07.021

2014

Byrne-Steele, M. et al. Automation of immune repertoire amplification on the iC-Processor (TECH1P.851). The Journal of Immunology 192, 69.19-69.19 (2014). https://www.jimmunol.org/content/192/1_Supplement/69.19

Alleyne, J. et al. Biomarker: long term study of breast cancer specific CDR3s in peripheral blood (TUM2P.894). J. Immunol. 192, 71.18 (2014). https://www.jimmunol.org/content/192/1_Supplement/71.18

O’Connell, A. E. et al. Next Generation Sequencing Reveals Skewing of the T and B Cell Receptor Repertoires in Patients with Wiskott–Aldrich Syndrome. Front. Immunol. 5, (2014). https://doi.org/10.3389/fimmu.2014.00340

Lee, Y. N. et al. A systematic analysis of recombination activity and genotype-phenotype correlation in human recombination-activating gene 1 deficiency. Journal of Allergy and Clinical Immunology 133, 1099-1108.e12 (2014). https://doi.org/10.1016/j.jaci.2013.10.007

Sims, J. et al. IT-32 Divergence of Intratumoral and Systemic T Cell Repertoires Reflects Local Monocyte Profiles During Glioma Progression. Neuro Oncol 16, v116–v117 (2014). https://doi.org/10.1093/neuonc/nou258.30

Sims, J. et al. TCR repertoire divergence reflects micro-environmental immune phenotypes in glioma. J Immunother Cancer 2, O19 (2014). http://dx.doi.org/10.1186/2051-1426-2-S3-O19

Wang, C. et al. Breast cancer diagnosis by high throughput sequencing of T cell receptors from peripheral blood samples (TUM2P.905). The Journal of Immunology 192, 71.29-71.29 (2014). https://www.jimmunol.org/content/192/1_Supplement/71.29

2013

Sims, J. S. et al. Tumor-associated T cell receptor repertoires in low- and high-grade gliomas. J Immunother Cancer 1, P143 (2013). http://dx.doi.org/10.1186/2051-1426-1-S1-P143

Han, J. et al. R10K update: NGS of immune repertoire for biomarker discoveries (P3241). J. Immunol. 190, 192.6 (2013). https://www.jimmunol.org/content/190/1_Supplement/192.6

2012

Peaudecerf, L. et al. Thymocytes may persist and differentiate without any input from bone marrow progenitors. J Exp Med 209, 1401–1408 (2012). https://doi.org/10.1084/jem.20120845

Han, J. et al. Identification and temporal monitoring of breast cancer-associated T cell receptors with high throughput sequencing (46.23). The Journal of Immunology 188, 46.23-46.23 (2012). https://www.jimmunol.org/content/188/1_Supplement/46.23

Wang, C. et al. Evaluation of three next generation sequencing platforms for immune repertoire sequencing (58.10). The Journal of Immunology 188, 58.10-58.10 (2012). https://www.jimmunol.org/content/188/1_Supplement/58.10

Han, J. et al. R10K: an international collaborative project for biomarker discovery (58.7). The Journal of Immunology 188, 58.7-58.7 (2012). https://www.jimmunol.org/content/188/1_Supplement/58.7

2011

Byrne-Steele, M. et al. Development of an alternative method for the identification and production of antigen-specific monoclonal antibodies (65.16). The Journal of Immunology 186, 65.16-65.16 (2011). https://www.jimmunol.org/content/186/1_Supplement/65.16

Han, J. et al. Profiling the pattern of human immunoglobulin SHM and CSR in B memory cells via high-throughput sequencing (62.11). The Journal of Immunology 186, 62.11-62.11 (2011). https://www.jimmunol.org/content/186/1_Supplement/62.11

Wang, C. et al. Immune repertoire high-throughput sequence analysis (IRAS) web service (65.20). J. Immunol. 186, 65.20 (2011). https://www.jimmunol.org/content/186/1_Supplement/65.20

2010

Wang, C. et al. High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets. PNAS 107, 1518–1523 (2010). https://doi.org/10.1073/pnas.0913939107