Sette, A. & Crotty, S. Immunological reminiscence to SARS‐CoV‐2 an infection and COVID‐19 vaccines. Immunol. Rev. 310, 27–46 (2022).
Allie, S. R. & Randall, T. D. Resident reminiscence B cells. Viral Immunol. 33, 282–293 (2020).
Topol, E. J. & Iwasaki, A. Operation nasal vaccine-lightning velocity to counter COVID-19. Sci. Immunol. 7, eadd9947 (2022).
Zheng, M. Z. M. & Wakim, L. M. Tissue resident reminiscence T cells within the respiratory tract. Mucosal Immunol. 15, 379–388 (2022).
Poon, M. M. L. et al. Tissue adaptation and clonal segregation of human reminiscence T cells in barrier websites. Nat. Immunol. 24, 309–319 (2023).
Domínguez Conde, C. et al. Cross-tissue immune cell evaluation reveals tissue-specific options in people. Science 376, eabl5197 (2022).
Clark, R. A. Resident reminiscence T cells in human well being and illness. Sci. Transl. Med. 7, 269rv1 (2015).
Lange, J., Rivera-Ballesteros, O. & Buggert, M. Human mucosal tissue-resident reminiscence T cells in well being and illness. Mucosal Immunol. 15, 389–397 (2022).
Thome, J. J. C. et al. Spatial map of human T cell compartmentalization and upkeep over many years of life. Cell 159, 814–828 (2014).
Grey, J. I. & Farber, D. L. Tissue-resident immune cells in people. Annu. Rev. Immunol. 40, 195–220 (2022).
Masopust, D. & Soerens, A. G. Tissue-resident T cells and different resident leukocytes. Annu. Rev. Immunol. 37, 521–546 (2019).
Snyder, M. E. et al. Technology and persistence of human tissue-resident reminiscence T cells in lung transplantation. Sci. Immunol. 4, eaav5581 (2019).
Weisel, N. M. et al. Complete analyses of B-cell compartments throughout the human physique reveal novel subsets and a gut-resident reminiscence phenotype. Blood 136, 2774–2785 (2020).
Havenar-Daughton, C., Lee, J. H. & Crotty, S. Tfh cells and HIV bnAbs, an immunodominance mannequin of the HIV neutralizing antibody era drawback. Immunol. Rev. 275, 49–61 (2017).
Havenar-Daughton, C. et al. Regular human lymph node T follicular helper cells and germinal heart B cells accessed by way of high-quality needle aspirations. J. Immunol. Strategies 479, 112746 (2020).
Alsoussi, W. B. et al. SARS-CoV-2 Omicron boosting induces de novo B cell response in people. Nature 617, 592–598 (2023).
Leggat, D. J. et al. Vaccination induces HIV broadly neutralizing antibody precursors in people. Science 378, eadd6502 (2022).
Victora, G. D. & Nussenzweig, M. C. Germinal Facilities. Annu. Rev. Immunol. 40, 413–442 (2022).
Xu, Q. et al. Adaptive immune responses to SARS-CoV-2 persist within the pharyngeal lymphoid tissue of youngsters. Nat. Immunol. 24, 186–199 (2023).
Kumar, B. V. et al. Human tissue-resident reminiscence T cells are outlined by core transcriptional and practical signatures in lymphoid and mucosal websites. Cell Rep. 20, 2921–2934 (2017).
Kusnadi, A. et al. Severely ailing COVID-19 sufferers show impaired exhaustion options in SARS-CoV-2-reactive CD8+ T cells. Sci. Immunol. 6, eabe4782 (2021).
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).
Schmiedel, B. J. et al. Single-cell eQTL evaluation of activated T cell subsets reveals activation and cell type-dependent results of disease-risk variants. Sci. Immunol. 7, eabm2508 (2022).
FitzPatrick, M. E. B. et al. Human intestinal tissue-resident reminiscence T cells comprise transcriptionally and functionally distinct subsets. Cell Experiences 34, 108661 (2021).
Crotty, S. T follicular helper cell biology: a decade of discovery and ailments. Immunity 50, 1132–1148 (2019).
Mudd, P. A. et al. SARS-CoV-2 mRNA vaccination elicits a sturdy and chronic T follicular helper cell response in people. Cell 185, 603–613.e15 (2022).
Nolan, S. et al. A big-scale database of T-cell receptor beta (TCRb) sequences and binding associations from pure and artificial publicity to SARS-CoV-2. Preprint at Analysis Sq. https://doi.org/10.21203/rs.3.rs-51964/v1 (2020).
Goncharov, M. et al. VDJdb within the pandemic period: a compendium of T cell receptors particular for SARS-CoV-2. Nat. Strategies 19, 1017–1019 (2022).
Rowntree, L. C. et al. SARS-CoV-2-specific T cell reminiscence with widespread TCRαβ motifs is established in unvaccinated youngsters who seroconvert after an infection. Immunity 55, 1299–1315.e4 (2022).
Pogorelyy, M. V. et al. Resolving SARS-CoV-2 CD4+ T cell specificity by way of reverse epitope discovery. Cell Rep. Med. 3, 100697 (2022).
Tan, H.-X. et al. Lung-resident reminiscence B cells established after pulmonary influenza an infection show distinct transcriptional and phenotypic profiles. Sci. Immunol. 7, eabf5314 (2022).
Barker, Okay. A. et al. Lung-resident reminiscence B cells defend towards bacterial pneumonia. J. Clin. Make investments. 131, e141810 (2021).
Gregoire, C. et al. Viral an infection engenders bona fide and bystander subsets of lung-resident reminiscence B cells by means of a permissive mechanism. Immunity 55, 1216–1233.e9 (2022).
Allie, S. R. et al. The institution of resident reminiscence B cells within the lung requires native antigen encounter. Nat. Immunol. 20, 97–108 (2019).
Ehrhardt, G. R. A. et al. Expression of the immunoregulatory molecule FcRH4 defines a particular tissue-based inhabitants of reminiscence B cells. J. Exp. Med. 202, 783–791 (2005).
Ehrhardt, G. R. A. et al. Discriminating gene expression profiles of reminiscence B cell subpopulations. J. Exp. Med. 205, 1807–1817 (2008).
King, H. W. et al. Single-cell evaluation of human B cell maturation predicts how antibody class switching shapes choice dynamics. Sci. Immunol. 6, eabe6291 (2021).
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).
Knox, J. J. et al. T-bet+ B cells are induced by human viral infections and dominate the HIV gp140 response. JCI Perception 2, e92943 (2017).
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).
Lim, J. M. E. et al. SARS-CoV-2 breakthrough an infection in vaccinees induces virus-specific nasal-resident CD8+ and CD4+ T cells of broad specificity. J. Exp. Med. 219, e20220780 (2022).
Dan, J. M. et al. Immunological reminiscence to SARS-CoV-2 assessed for as much as 8 months after an infection. Science 371, eabf4063 (2021).
Grifoni, A. et al. Targets of T cell responses to SARS-CoV-2 coronavirus in people with COVID-19 illness and unexposed people. Cell 181, 1489–1501.e15 (2020).
Dan, J. M. et al. Recurrent group A Streptococcus tonsillitis is an immunosusceptibility illness involving antibody deficiency and aberrant T FH cells. Sci. Transl. Med. 11, eaau3776 (2019).
Ramirez, S. I. et al. Bamlanivimab remedy for acute COVID-19 doesn’t blunt SARS-CoV-2–particular reminiscence T cell responses. JCI Perception 7, e163471 (2022).
Yu, E. D. et al. Growth of a T cell-based immunodiagnostic system to successfully distinguish SARS-CoV-2 an infection and COVID-19 vaccination standing. Cell Host Microbe 30, 388–399.e3 (2022).
Grifoni, A. et al. SARS-CoV-2 human T cell epitopes: adaptive immune response towards COVID-19. Cell Host Microbe 29, 1076–1092 (2021).
Hao, Y. et al. Built-in evaluation of multimodal single-cell knowledge. Cell 184, 3573–3587.e29 (2021).
Korotkevich, G. et al. Quick gene set enrichment evaluation. Preprint at bioRXiv https://doi.org/10.1101/060012 (2016).
Lee, J. H. et al. Lengthy-primed germinal centres with enduring affinity maturation and clonal migration. Nature 609, 998–1004 (2022).
Holla, P. et al. Shared transcriptional profiles of atypical B cells counsel widespread drivers of enlargement and performance in malaria, HIV, and autoimmunity. Sci. Adv. 7, eabg8384 (2021).
Lopes De Assis, F. et al. Monitoring B cell responses to the SARS-CoV-2 mRNA-1273 vaccine. Cell Rep. 42, 112780 (2023).
Yermanos, A. et al. Platypus: an open-access software program for integrating lymphocyte single-cell immune repertoires with transcriptomes. NAR Genom. Bioinform. 3, lqab023 (2021).
Gupta, N. T. et al. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing knowledge. Bioinformatics 31, 3356–3358 (2015).
Vander Heiden, J. A. et al. pRESTO: a toolkit for processing high-throughput sequencing uncooked reads of lymphocyte receptor repertoires. Bioinformatics 30, 1930–1932 (2014).
Gupta, N. T. et al. Hierarchical clustering can establish B cell clones with excessive confidence in Ig repertoire sequencing knowledge. J. Immunol. 198, 2489–2499 (2017).
Nouri, N. & Kleinstein, S. H. Somatic hypermutation evaluation for improved identification of B cell clonal households from next-generation sequencing knowledge. PLoS Comput. Biol. 16, e1007977 (2020).
Ye, J., Ma, N., Madden, T. L. & Ostell, J. M. IgBLAST: an immunoglobulin variable area sequence evaluation software. Nucleic Acids Res. 41, W34–W40 (2013).
Giudicelli, V., Chaume, D. & Lefranc, M.-P. IMGT/GENE-DB: a complete database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res. 33, D256–D261 (2005).
Hoehn, Okay. B. et al. Repertoire-wide phylogenetic fashions of B cell molecular evolution reveal evolutionary signatures of ageing and vaccination. Proc. Natl Acad. Sci. USA 116, 22664–22672 (2019).
Hoehn, Okay. B. et al. Human B cell lineages related to germinal facilities following influenza vaccination are measurably evolving. eLife 10, e70873 (2021).
Hoehn, Okay. B., Pybus, O. G. & Kleinstein, S. H. Phylogenetic evaluation of migration, differentiation, and sophistication switching in B cells. PLoS Comput. Biol. 18, e1009885 (2022).
Raybould, M. I. J., Kovaltsuk, A., Marks, C. & Deane, C. M. CoV-AbDab: the coronavirus antibody database. Bioinformatics 37, 734–735 (2021).
Kaku, C. I. et al. Evolution of antibody immunity following Omicron BA.1 breakthrough an infection. Nat. Commun. 14, 2751 (2023).
Chen, E. C. et al. Convergent antibody responses to the SARS-CoV-2 spike protein in convalescent and vaccinated people. Cell Rep. 36, 109604 (2021).
Barnes, C. O. et al. Buildings of human antibodies sure to SARS-CoV-2 spike reveal widespread epitopes and recurrent options of antibodies. Cell 182, 828–842.e16 (2020).
Tarke, A. et al. SARS-CoV-2 vaccination induces immunological T cell reminiscence in a position to cross-recognize variants from Alpha to Omicron. Cell 185, 847–859.e11 (2022).
Hastie, Okay. M. et al. Potent Omicron-neutralizing antibodies remoted from a affected person vaccinated 6 months earlier than Omicron emergence. Cell Rep. 42, 112421 (2023).
Lee, J. H. et al. A broadly neutralizing antibody targets the dynamic HIV envelope trimer apex by way of an extended, rigidified, and anionic β-hairpin construction. Immunity 46, 690–702 (2017).
Zhang, Z. et al. Humoral and mobile immune reminiscence to 4 COVID-19 vaccines. Cell 185, 2434–2451.e17 (2022).