Nature

Immunological memory diversity in the human upper airway

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  • Sette, A. & Crotty, S. Immunological memory to SARS‐CoV‐2 infection and COVID‐19 vaccines. Immunol. Rev. 310, 27–46 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Allie, S. R. & Randall, T. D. Resident memory B cells. Viral Immunol. 33, 282–293 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Topol, E. J. & Iwasaki, A. Operation nasal vaccine-lightning speed to counter COVID-19. Sci. Immunol. 7, eadd9947 (2022).

    Article 
    PubMed 

    Google Scholar
     

  • Zheng, M. Z. M. & Wakim, L. M. Tissue resident memory T cells in the respiratory tract. Mucosal Immunol. 15, 379–388 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Poon, M. M. L. et al. Tissue adaptation and clonal segregation of human memory T cells in barrier sites. Nat. Immunol. 24, 309–319 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Domínguez Conde, C. et al. Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science 376, eabl5197 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Clark, R. A. Resident memory T cells in human health and disease. Sci. Transl. Med. 7, 269rv1 (2015).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lange, J., Rivera-Ballesteros, O. & Buggert, M. Human mucosal tissue-resident memory T cells in health and disease. Mucosal Immunol. 15, 389–397 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Thome, J. J. C. et al. Spatial map of human T cell compartmentalization and maintenance over decades of life. Cell 159, 814–828 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gray, J. I. & Farber, D. L. Tissue-resident immune cells in humans. Annu. Rev. Immunol. 40, 195–220 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Masopust, D. & Soerens, A. G. Tissue-resident T cells and other resident leukocytes. Annu. Rev. Immunol. 37, 521–546 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Snyder, M. E. et al. Generation and persistence of human tissue-resident memory T cells in lung transplantation. Sci. Immunol. 4, eaav5581 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Weisel, N. M. et al. Comprehensive analyses of B-cell compartments across the human body reveal novel subsets and a gut-resident memory phenotype. Blood 136, 2774–2785 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Havenar-Daughton, C., Lee, J. H. & Crotty, S. Tfh cells and HIV bnAbs, an immunodominance model of the HIV neutralizing antibody generation problem. Immunol. Rev. 275, 49–61 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Havenar-Daughton, C. et al. Normal human lymph node T follicular helper cells and germinal center B cells accessed via fine needle aspirations. J. Immunol. Methods 479, 112746 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Alsoussi, W. B. et al. SARS-CoV-2 Omicron boosting induces de novo B cell response in humans. Nature 617, 592–598 (2023).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Leggat, D. J. et al. Vaccination induces HIV broadly neutralizing antibody precursors in humans. Science 378, eadd6502 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Victora, G. D. & Nussenzweig, M. C. Germinal Centers. Annu. Rev. Immunol. 40, 413–442 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Xu, Q. et al. Adaptive immune responses to SARS-CoV-2 persist in the pharyngeal lymphoid tissue of children. Nat. Immunol. 24, 186–199 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kumar, B. V. et al. Human tissue-resident memory T cells are defined by core transcriptional and functional signatures in lymphoid and mucosal sites. Cell Rep. 20, 2921–2934 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kusnadi, A. et al. Severely ill COVID-19 patients display impaired exhaustion features in SARS-CoV-2-reactive CD8+ T cells. Sci. Immunol. 6, eabe4782 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Meckiff, B. J. et al. Imbalance of regulatory and cytotoxic SARS-CoV-2-reactive CD4+ T cells in COVID-19. Cell 183, 1340–1353.e16 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schmiedel, B. J. et al. Single-cell eQTL analysis of activated T cell subsets reveals activation and cell type-dependent effects of disease-risk variants. Sci. Immunol. 7, eabm2508 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • FitzPatrick, M. E. B. et al. Human intestinal tissue-resident memory T cells comprise transcriptionally and functionally distinct subsets. Cell Reports 34, 108661 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Crotty, S. T follicular helper cell biology: a decade of discovery and diseases. Immunity 50, 1132–1148 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mudd, P. A. et al. SARS-CoV-2 mRNA vaccination elicits a robust and persistent T follicular helper cell response in humans. Cell 185, 603–613.e15 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Nolan, S. et al. A large-scale database of T-cell receptor beta (TCRb) sequences and binding associations from natural and synthetic exposure to SARS-CoV-2. Preprint at Research Square https://doi.org/10.21203/rs.3.rs-51964/v1 (2020).

  • Goncharov, M. et al. VDJdb in the pandemic era: a compendium of T cell receptors specific for SARS-CoV-2. Nat. Methods 19, 1017–1019 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rowntree, L. C. et al. SARS-CoV-2-specific T cell memory with common TCRαβ motifs is established in unvaccinated children who seroconvert after infection. Immunity 55, 1299–1315.e4 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pogorelyy, M. V. et al. Resolving SARS-CoV-2 CD4+ T cell specificity via reverse epitope discovery. Cell Rep. Med. 3, 100697 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tan, H.-X. et al. Lung-resident memory B cells established after pulmonary influenza infection display distinct transcriptional and phenotypic profiles. Sci. Immunol. 7, eabf5314 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Barker, K. A. et al. Lung-resident memory B cells protect against bacterial pneumonia. J. Clin. Invest. 131, e141810 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gregoire, C. et al. Viral infection engenders bona fide and bystander subsets of lung-resident memory B cells through a permissive mechanism. Immunity 55, 1216–1233.e9 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Allie, S. R. et al. The establishment of resident memory B cells in the lung requires local antigen encounter. Nat. Immunol. 20, 97–108 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ehrhardt, G. R. A. et al. Expression of the immunoregulatory molecule FcRH4 defines a distinctive tissue-based population of memory B cells. J. Exp. Med. 202, 783–791 (2005).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ehrhardt, G. R. A. et al. Discriminating gene expression profiles of memory B cell subpopulations. J. Exp. Med. 205, 1807–1817 (2008).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • King, H. W. et al. Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics. Sci. Immunol. 6, eabe6291 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zumaquero, E. et al. IFNγ induces epigenetic programming of human T-bethi B cells and promotes TLR7/8 and IL-21 induced differentiation. eLife 8, e41641 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Knox, J. J. et al. T-bet+ B cells are induced by human viral infections and dominate the HIV gp140 response. JCI Insight 2, e92943 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Duan, M. et al. Understanding heterogeneity of human bone marrow plasma cell maturation and survival pathways by single-cell analyses. Cell Rep. 42, 112682 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lim, J. M. E. et al. SARS-CoV-2 breakthrough infection in vaccinees induces virus-specific nasal-resident CD8+ and CD4+ T cells of broad specificity. J. Exp. Med. 219, e20220780 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dan, J. M. et al. Immunological memory to SARS-CoV-2 assessed for up to 8 months after infection. Science 371, eabf4063 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Grifoni, A. et al. Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals. Cell 181, 1489–1501.e15 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dan, J. M. et al. Recurrent group A Streptococcus tonsillitis is an immunosusceptibility disease involving antibody deficiency and aberrant T FH cells. Sci. Transl. Med. 11, eaau3776 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ramirez, S. I. et al. Bamlanivimab therapy for acute COVID-19 does not blunt SARS-CoV-2–specific memory T cell responses. JCI Insight 7, e163471 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yu, E. D. et al. Development of a T cell-based immunodiagnostic system to effectively distinguish SARS-CoV-2 infection and COVID-19 vaccination status. Cell Host Microbe 30, 388–399.e3 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Grifoni, A. et al. SARS-CoV-2 human T cell epitopes: adaptive immune response against COVID-19. Cell Host Microbe 29, 1076–1092 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e29 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Korotkevich, G. et al. Fast gene set enrichment analysis. Preprint at bioRXiv https://doi.org/10.1101/060012 (2016).

  • Lee, J. H. et al. Long-primed germinal centres with enduring affinity maturation and clonal migration. Nature 609, 998–1004 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Holla, P. et al. Shared transcriptional profiles of atypical B cells suggest common drivers of expansion and function in malaria, HIV, and autoimmunity. Sci. Adv. 7, eabg8384 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lopes De Assis, F. et al. Tracking B cell responses to the SARS-CoV-2 mRNA-1273 vaccine. Cell Rep. 42, 112780 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yermanos, A. et al. Platypus: an open-access software for integrating lymphocyte single-cell immune repertoires with transcriptomes. NAR Genom. Bioinform. 3, lqab023 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gupta, N. T. et al. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinformatics 31, 3356–3358 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vander Heiden, J. A. et al. pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics 30, 1930–1932 (2014).

    Article 

    Google Scholar
     

  • Gupta, N. T. et al. Hierarchical clustering can identify B cell clones with high confidence in Ig repertoire sequencing data. J. Immunol. 198, 2489–2499 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Nouri, N. & Kleinstein, S. H. Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data. PLoS Comput. Biol. 16, e1007977 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ye, J., Ma, N., Madden, T. L. & Ostell, J. M. IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res. 41, W34–W40 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Giudicelli, V., Chaume, D. & Lefranc, M.-P. IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res. 33, D256–D261 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hoehn, K. B. et al. Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination. Proc. Natl Acad. Sci. USA 116, 22664–22672 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hoehn, K. B. et al. Human B cell lineages associated with germinal centers following influenza vaccination are measurably evolving. eLife 10, e70873 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hoehn, K. B., Pybus, O. G. & Kleinstein, S. H. Phylogenetic analysis of migration, differentiation, and class switching in B cells. PLoS Comput. Biol. 18, e1009885 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Raybould, M. I. J., Kovaltsuk, A., Marks, C. & Deane, C. M. CoV-AbDab: the coronavirus antibody database. Bioinformatics 37, 734–735 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kaku, C. I. et al. Evolution of antibody immunity following Omicron BA.1 breakthrough infection. Nat. Commun. 14, 2751 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen, E. C. et al. Convergent antibody responses to the SARS-CoV-2 spike protein in convalescent and vaccinated individuals. Cell Rep. 36, 109604 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Barnes, C. O. et al. Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies. Cell 182, 828–842.e16 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tarke, A. et al. SARS-CoV-2 vaccination induces immunological T cell memory able to cross-recognize variants from Alpha to Omicron. Cell 185, 847–859.e11 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hastie, K. M. et al. Potent Omicron-neutralizing antibodies isolated from a patient vaccinated 6 months before Omicron emergence. Cell Rep. 42, 112421 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lee, J. H. et al. A broadly neutralizing antibody targets the dynamic HIV envelope trimer apex via a long, rigidified, and anionic β-hairpin structure. Immunity 46, 690–702 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, Z. et al. Humoral and cellular immune memory to four COVID-19 vaccines. Cell 185, 2434–2451.e17 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     



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