12
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      Long-primed germinal centres with enduring affinity maturation and clonal migration

      research-article
      1 , 2 , 3 , 1 , 2 , 2 , 3 , 4 , 1 , 2 , 5 , 2 , 3 , 6 , 6 , 4 , 1 , 2 , 7 , 6 , 6 , 6 , 2 , 3 , 4 , 2 , 3 , 4 , 2 , 3 , 4 , 2 , 3 , 4 , 2 , 3 , 4 , 1 , 2 , 8 , 8 , 8 , 8 , 8 , 8 , 8 , 2 , 3 , 4 , 2 , 3 , 4 , 2 , 9 , 2 , 9 , 10 , 10 , 8 , 2 , 3 , 6 , 2 , 4 , 2 , 3 , 4 , 11 , 2 , 7 , 11 , 12 , 13 , 14 , 2 , 3 , 4 , 11 , 1 , 2 , 5 ,
      Nature
      Nature Publishing Group UK
      Germinal centres, Protein vaccines, Antibodies

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Germinal centres are the engines of antibody evolution. Here, using human immunodeficiency virus (HIV) Env protein immunogen priming in rhesus monkeys followed by a long period without further immunization, we demonstrate germinal centre B (B GC) cells that last for at least 6 months. A 186-fold increase in B GC cells was present by week 10 compared with conventional immunization. Single-cell transcriptional profiling showed that both light- and dark-zone germinal centre states were sustained. Antibody somatic hypermutation of B GC cells continued to accumulate throughout the 29-week priming period, with evidence of selective pressure. Env-binding B GC cells were still 49-fold above baseline at 29 weeks, which suggests that they could remain active for even longer periods of time. High titres of HIV-neutralizing antibodies were generated after a single booster immunization. Fully glycosylated HIV trimer protein is a complex antigen, posing considerable immunodominance challenges for B cells 1, 2 . Memory B cells generated under these long priming conditions had higher levels of antibody somatic hypermutation, and both memory B cells and antibodies were more likely to recognize non-immunodominant epitopes. Numerous B GC cell lineage phylogenies spanning more than the 6-month germinal centre period were identified, demonstrating continuous germinal centre activity and selection for at least 191 days with no further antigen exposure. A long-prime, slow-delivery (12 days) immunization approach holds promise for difficult vaccine targets and suggests that patience can have great value for tuning of germinal centres to maximize antibody responses.

          Abstract

          Using HIV Env protein immunogen priming in rhesus monkeys followed by a long period without further immunization, we demonstrate germinal centre B cells lasting at least 6 months, showing promise in regard to difficult vaccine targets.

          Related collections

          Most cited references44

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          Integrated analysis of multimodal single-cell data

          Summary The simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal data. Here, we introduce “weighted-nearest neighbor” analysis, an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities. We apply our procedure to a CITE-seq dataset of 211,000 human peripheral blood mononuclear cells (PBMCs) with panels extending to 228 antibodies to construct a multimodal reference atlas of the circulating immune system. Multimodal analysis substantially improves our ability to resolve cell states, allowing us to identify and validate previously unreported lymphoid subpopulations. Moreover, we demonstrate how to leverage this reference to rapidly map new datasets and to interpret immune responses to vaccination and coronavirus disease 2019 (COVID-19). Our approach represents a broadly applicable strategy to analyze single-cell multimodal datasets and to look beyond the transcriptome toward a unified and multimodal definition of cellular identity.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            New tools for automated high-resolution cryo-EM structure determination in RELION-3

            Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, de novo model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides higher resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resolution for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2–0.7 Å compared to previous RELION versions.
              Bookmark
              • Record: found
              • Abstract: not found
              • Article: not found

              iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)

                Bookmark

                Author and article information

                Contributors
                shane@lji.org
                Journal
                Nature
                Nature
                Nature
                Nature Publishing Group UK (London )
                0028-0836
                1476-4687
                21 September 2022
                : 1-7
                Affiliations
                [1 ]GRID grid.185006.a, ISNI 0000 0004 0461 3162, Center for Infectious Disease and Vaccine Research, , La Jolla Institute for Immunology, ; La Jolla, CA USA
                [2 ]GRID grid.214007.0, ISNI 0000000122199231, Consortium for HIV/AIDS Vaccine Development, , The Scripps Research Institute, ; La Jolla, CA USA
                [3 ]GRID grid.214007.0, ISNI 0000000122199231, IAVI Neutralizing Antibody Center, , The Scripps Research Institute, ; La Jolla, CA USA
                [4 ]GRID grid.214007.0, ISNI 0000000122199231, Department of Immunology and Microbiology, , The Scripps Research Institute, ; La Jolla, CA USA
                [5 ]GRID grid.266100.3, ISNI 0000 0001 2107 4242, Department of Medicine, Division of Infectious Diseases and Global Public Health, , University of California, San Diego, ; La Jolla, CA USA
                [6 ]GRID grid.214007.0, ISNI 0000000122199231, Department of Integrative Structural and Computational Biology, , The Scripps Research Institute, ; La Jolla, CA USA
                [7 ]GRID grid.116068.8, ISNI 0000 0001 2341 2786, Koch Institute for Integrative Cancer Research, , Massachusetts Institute of Technology, ; Cambridge, MA USA
                [8 ]GRID grid.265219.b, ISNI 0000 0001 2217 8588, Tulane National Primate Research Center, , Tulane School of Medicine, ; Covington, LA USA
                [9 ]GRID grid.189967.8, ISNI 0000 0001 0941 6502, Emory National Primate Research Center and Emory Vaccine Center, , Emory University School of Medicine, ; Atlanta, GA USA
                [10 ]GRID grid.26009.3d, ISNI 0000 0004 1936 7961, Department of Surgery, Laboratory for AIDS Vaccine Research & Development, , Duke University Medical Center, Duke University, ; Durham, NC USA
                [11 ]GRID grid.32224.35, ISNI 0000 0004 0386 9924, Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, ; Cambridge, MA USA
                [12 ]GRID grid.116068.8, ISNI 0000 0001 2341 2786, Department of Biological Engineering, , Massachusetts Institute of Technology, ; Cambridge, MA USA
                [13 ]GRID grid.116068.8, ISNI 0000 0001 2341 2786, Department of Materials Science and Engineering, , Massachusetts Institute of Technology, ; Cambridge, MA USA
                [14 ]GRID grid.413575.1, ISNI 0000 0001 2167 1581, Howard Hughes Medical Institute, ; Chevy Chase, MD USA
                Author information
                http://orcid.org/0000-0002-6472-7116
                http://orcid.org/0000-0002-3364-3083
                http://orcid.org/0000-0001-7283-4766
                http://orcid.org/0000-0002-9695-8138
                http://orcid.org/0000-0003-0137-8497
                http://orcid.org/0000-0001-9445-6671
                http://orcid.org/0000-0001-5137-4625
                http://orcid.org/0000-0002-2597-7147
                http://orcid.org/0000-0002-4764-3965
                http://orcid.org/0000-0002-5273-1951
                http://orcid.org/0000-0002-6298-2391
                http://orcid.org/0000-0001-7153-3769
                http://orcid.org/0000-0002-3165-2058
                http://orcid.org/0000-0001-6711-9864
                http://orcid.org/0000-0002-8637-1405
                http://orcid.org/0000-0002-1120-0150
                http://orcid.org/0000-0002-6484-6262
                Article
                5216
                10.1038/s41586-022-05216-9
                9491273
                36131022
                61f2f497-b693-49b5-84dd-21cc6376d479
                © The Author(s), under exclusive licence to Springer Nature Limited 2022, Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

                This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.

                History
                : 13 December 2021
                : 9 August 2022
                Categories
                Article

                Uncategorized
                germinal centres,protein vaccines,antibodies
                Uncategorized
                germinal centres, protein vaccines, antibodies

                Comments

                Comment on this article