March 11, 2020 |

Publications and patents

Publications

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

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

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

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

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

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

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

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

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

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

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

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

Patents

Han, Jian. Method for Evaluating and Comparing Immunorepertoires. Jian Han, assignee. Patent 9012148. 21 Apr. 2015. Print.

Han, Jian. Amplicon Rescue Multiplex Polymerase Chain Reaction for Amplification of Multiple Targets. HudsonAlpha Institute for Biotechnology, assignee. Patent 7999092. 16 Aug. 2011. Print.