1
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Zhang Y, Liu G, Zeng Q, Wu W, Lei K, Zhang C, Tang M, Zhang Y, Xiang X, Tan L, Cui R, Qin S, Song X, Yin C, Chen Z, Kuang M. CCL19-producing fibroblasts promote tertiary lymphoid structure formation enhancing anti-tumor IgG response in colorectal cancer liver metastasis. Cancer Cell 2024; 42:1370-1385.e9. [PMID: 39137726 DOI: 10.1016/j.ccell.2024.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 05/05/2024] [Accepted: 07/17/2024] [Indexed: 08/15/2024]
Abstract
Tertiary lymphoid structures (TLSs) are associated with enhanced immunity in tumors. However, their formation and functions in colorectal cancer liver metastasis (CRLM) remain unclear. Here, we reveal that intra- and peri-tumor mature TLSs (TLS+) are associated with improved clinical outcomes than TLS- tumors. Using single-cell-RNA-sequencing and spatial-enhanced-resolution-omics-sequencing (Stereo-seq), we reveal that TLS+ tumors are enriched with IgG+ plasma cells (PCs), while TLS- tumors are characterized with IgA+ PCs. By generating TLS-associated PC-derived monoclonal antibodies in vitro, we show that TLS-PCs secrete tumor-targeting antibodies. As the proof-of-concept, we demonstrate the anti-tumor activities of TLS-PC-mAb6 antibody in humanized mouse model of colorectal cancer. We identify a fibroblast lineage secreting CCL19 that facilitates lymphocyte trafficking to TLSs. CCL19 treatment promotes TLS neogenesis and prevents tumor growth in mice. Our data uncover the central role of CCL19+ fibroblasts in TLS formation, which in turn generates therapeutic antibodies to restrict CRLM.
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Affiliation(s)
- Yifan Zhang
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Guangjian Liu
- Department of Medical Ultrasonics, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Qianwen Zeng
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Wenrui Wu
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Kai Lei
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Chuankai Zhang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Oncology, Cancer Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Miaoling Tang
- Department of Oncology, Cancer Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Yuting Zhang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiao Xiang
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Li Tan
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Rui Cui
- Department of Medical Ultrasonics, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Si Qin
- Department of Medical Ultrasonics, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Xinming Song
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Changjun Yin
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, 80336 Munich, Germany.
| | - Zhihang Chen
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| | - Ming Kuang
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Sun Yat-sen University Zhongshan School of Medicine, Guangzhou 510080, China.
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2
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Priest DG, Ebihara T, Tulyeu J, Søndergaard JN, Sakakibara S, Sugihara F, Nakao S, Togami Y, Yoshimura J, Ito H, Onishi S, Muratsu A, Mitsuyama Y, Ogura H, Oda J, Okusaki D, Matsumoto H, Wing JB. Atypical and non-classical CD45RB lo memory B cells are the majority of circulating SARS-CoV-2 specific B cells following mRNA vaccination or COVID-19. Nat Commun 2024; 15:6811. [PMID: 39122676 PMCID: PMC11315995 DOI: 10.1038/s41467-024-50997-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Resting memory B cells can be divided into classical or atypical groups, but the heterogenous marker expression on activated memory B cells makes similar classification difficult. Here, by longitudinal analysis of mass cytometry and CITE-seq data from cohorts with COVID-19, bacterial sepsis, or BNT162b2 mRNA vaccine, we observe that resting B cell memory consist of classical CD45RB+ memory and CD45RBlo memory, of which the latter contains of two distinct groups of CD11c+ atypical and CD23+ non-classical memory cells. CD45RB levels remain stable in these cells after activation, thereby enabling the tracking of activated B cells and plasmablasts derived from either CD45RB+ or CD45RBlo memory B cells. Moreover, in both COVID-19 patients and mRNA vaccination, CD45RBlo B cells formed the majority of SARS-CoV2 specific memory B cells and correlated with serum antibodies, while CD45RB+ memory are activated by bacterial sepsis. Our results thus identify that stably expressed CD45RB levels can be exploited to trace resting memory B cells and their activated progeny, and suggest that atypical and non-classical CD45RBlo memory B cells contribute to SARS-CoV-2 infection and vaccination.
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Affiliation(s)
- David G Priest
- Laboratory of Human Single Cell Immunology, World Premier International Research Center Initiative Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Osaka, 563-0793, Japan
| | - Takeshi Ebihara
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Janyerkye Tulyeu
- Human Single Cell Immunology Team, Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Jonas N Søndergaard
- Human Single Cell Immunology Team, Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Shuhei Sakakibara
- Laboratory of Immune Regulation, IFReC, Osaka University, Suita, Osaka, 563-0793, Japan
- Graduate School of Medical Safety Management, Jikei University of Health Care Sciences, Osaka, 532-0003, Japan
| | - Fuminori Sugihara
- Core Instrumentation Facility, Immunology Frontier Research Center and Research Institute for Microbial Disease, Osaka University, Suita, Osaka, 563-0793, Japan
- Research Institute for Microbial Disease, Osaka University, Suita, Osaka, 563-0793, Japan
| | - Shunichiro Nakao
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Yuki Togami
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Jumpei Yoshimura
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Hiroshi Ito
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Shinya Onishi
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Arisa Muratsu
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Yumi Mitsuyama
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
- Division of Trauma and Surgical Critical Care, Osaka General Medical Center, Osaka, 558-8558, Japan
| | - Hiroshi Ogura
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Jun Oda
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Daisuke Okusaki
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
- Laboratory of Human Immunology (Single Cell Genomics), WPI-IFReC, Osaka University, Suita, 565-0871, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, 565-0871, Japan
| | - Hisatake Matsumoto
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan.
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan.
| | - James B Wing
- Laboratory of Human Single Cell Immunology, World Premier International Research Center Initiative Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Osaka, 563-0793, Japan.
- Human Single Cell Immunology Team, Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan.
- Center for Advanced Modalities and DDS (CAMaD), Osaka University, Osaka, Japan.
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3
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Raeber ME, Caspar DP, Zurbuchen Y, Guo N, Schmid J, Michler J, Martin AC, Steiner UC, Moor AE, Koning F, Boyman O. Interleukin-2 immunotherapy reveals human regulatory T cell subsets with distinct functional and tissue-homing characteristics. Immunity 2024:S1074-7613(24)00365-0. [PMID: 39137779 DOI: 10.1016/j.immuni.2024.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 05/24/2024] [Accepted: 07/18/2024] [Indexed: 08/15/2024]
Abstract
Due to its stimulatory potential for immunomodulatory CD4+ regulatory T (Treg) cells, low-dose interleukin-2 (IL-2) immunotherapy has gained considerable attention for the treatment of autoimmune diseases. In this investigator-initiated single-arm non-placebo-controlled phase-2 clinical trial of low-dose IL-2 immunotherapy in systemic lupus erythematosus (SLE) patients, we generated a comprehensive atlas of in vivo human immune responses to low-dose IL-2. We performed an in-depth study of circulating and cutaneous immune cells by imaging mass cytometry, high-parameter flow cytometry, transcriptomics, and targeted serum proteomics. Low-dose IL-2 stimulated various circulating immune cells, including Treg cells with a skin-homing phenotype that appeared in the skin of SLE patients in close interaction with endothelial cells. Analysis of surface proteins and transcriptomes revealed different IL-2-driven Treg cell activation programs, including gut-homing CD38+, skin-homing HLA-DR+, and highly proliferative inflammation-homing CD38+ HLA-DR+ Treg cells. Collectively, these data define the distinct human Treg cell subsets that are responsive to IL-2 immunotherapy.
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Affiliation(s)
- Miro E Raeber
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland; Faculty of Medicine, University of Zurich, 8032 Zurich, Switzerland; Center of Human Immunology, University of Zurich, 8006 Zurich, Switzerland
| | - Dominic P Caspar
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Yves Zurbuchen
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Nannan Guo
- Department of Immunology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Jonas Schmid
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Jan Michler
- Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
| | - Alina C Martin
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Urs C Steiner
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
| | - Frits Koning
- Department of Immunology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland; Faculty of Medicine, University of Zurich, 8032 Zurich, Switzerland; Center of Human Immunology, University of Zurich, 8006 Zurich, Switzerland; Faculty of Science, University of Zurich, 8057 Zurich, Switzerland.
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4
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McIntire KM, Meng H, Lin TH, Kim W, Moore NE, Han J, McMahon M, Wang M, Malladi SK, Mohammed BM, Zhou JQ, Schmitz AJ, Hoehn KB, Carreño JM, Yellin T, Suessen T, Middleton WD, Teefey SA, Presti RM, Krammer F, Turner JS, Ward AB, Wilson IA, Kleinstein SH, Ellebedy AH. Maturation of germinal center B cells after influenza virus vaccination in humans. J Exp Med 2024; 221:e20240668. [PMID: 38935072 PMCID: PMC11211068 DOI: 10.1084/jem.20240668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Germinal centers (GC) are microanatomical lymphoid structures where affinity-matured memory B cells and long-lived bone marrow plasma cells are primarily generated. It is unclear how the maturation of B cells within the GC impacts the breadth and durability of B cell responses to influenza vaccination in humans. We used fine needle aspiration of draining lymph nodes to longitudinally track antigen-specific GC B cell responses to seasonal influenza vaccination. Antigen-specific GC B cells persisted for at least 13 wk after vaccination in two out of seven individuals. Monoclonal antibodies (mAbs) derived from persisting GC B cell clones exhibit enhanced binding affinity and breadth to influenza hemagglutinin (HA) antigens compared with related GC clonotypes isolated earlier in the response. Structural studies of early and late GC-derived mAbs from one clonal lineage in complex with H1 and H5 HAs revealed an altered binding footprint. Our study shows that inducing sustained GC reactions after influenza vaccination in humans supports the maturation of responding B cells.
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Affiliation(s)
- Katherine M. McIntire
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Hailong Meng
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Ting-Hui Lin
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Wooseob Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Microbiology, Korea University College of Medicine, Seoul, Korea
| | - Nina E. Moore
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Meagan McMahon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Meng Wang
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Sameer Kumar Malladi
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Bassem M. Mohammed
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Julian Q. Zhou
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Aaron J. Schmitz
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Kenneth B. Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Temima Yellin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Teresa Suessen
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - William D. Middleton
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - Sharlene A. Teefey
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - Rachel M. Presti
- Department of Internal Medicine-Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jackson S. Turner
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Steven H. Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Ali H. Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
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5
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Lanahan SM, Yang L, Jones KM, Qi Z, Cabrera EC, Cominsky LY, Ramaswamy A, Barmada A, Gabernet G, Uthaya Kumar DB, Xu L, Shan P, Wymann MP, Kleinstein SH, Rao VK, Mustillo P, Romberg N, Abraham RS, Lucas CL. PI3Kγ in B cells promotes antibody responses and generation of antibody-secreting cells. Nat Immunol 2024; 25:1422-1431. [PMID: 38961274 DOI: 10.1038/s41590-024-01890-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 06/07/2024] [Indexed: 07/05/2024]
Abstract
The differentiation of naive and memory B cells into antibody-secreting cells (ASCs) is a key feature of adaptive immunity. The requirement for phosphoinositide 3-kinase-delta (PI3Kδ) to support B cell biology has been investigated intensively; however, specific functions of the related phosphoinositide 3-kinase-gamma (PI3Kγ) complex in B lineage cells have not. In the present study, we report that PI3Kγ promotes robust antibody responses induced by T cell-dependent antigens. The inborn error of immunity caused by human deficiency in PI3Kγ results in broad humoral defects, prompting our investigation of roles for this kinase in antibody responses. Using mouse immunization models, we found that PI3Kγ functions cell intrinsically within activated B cells in a kinase activity-dependent manner to transduce signals required for the transcriptional program supporting differentiation of ASCs. Furthermore, ASC fate choice coincides with upregulation of PIK3CG expression and is impaired in the context of PI3Kγ disruption in naive B cells on in vitro CD40-/cytokine-driven activation, in memory B cells on toll-like receptor activation, or in human tonsillar organoids. Taken together, our study uncovers a fundamental role for PI3Kγ in supporting humoral immunity by integrating signals instructing commitment to the ASC fate.
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Affiliation(s)
- Stephen M Lanahan
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Lucas Yang
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Kate M Jones
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Zhihong Qi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Emylette Cruz Cabrera
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lauren Y Cominsky
- Immunology Graduate Group, Perelman School of Medicine, Philadelphia, PA, USA
| | - Anjali Ramaswamy
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Anis Barmada
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Gisela Gabernet
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Lan Xu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Peiying Shan
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Steven H Kleinstein
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - V Koneti Rao
- Primary Immunodeficiency Clinic, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Peter Mustillo
- Division of Allergy and Immunology, Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH, USA
| | - Neil Romberg
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA, USA
| | - Roshini S Abraham
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Carrie L Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
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6
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Ramirez SI, Faraji F, Hills LB, Lopez PG, Goodwin B, Stacey HD, Sutton HJ, Hastie KM, Saphire EO, Kim HJ, Mashoof S, Yan CH, DeConde AS, Levi G, Crotty S. Immunological memory diversity in the human upper airway. Nature 2024; 632:630-636. [PMID: 39085605 DOI: 10.1038/s41586-024-07748-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 06/24/2024] [Indexed: 08/02/2024]
Abstract
The upper airway is an important site of infection, but immune memory in the human upper airway is poorly understood, with implications for COVID-19 and many other human diseases1-4. Here we demonstrate that nasal and nasopharyngeal swabs can be used to obtain insights into these challenging problems, and define distinct immune cell populations, including antigen-specific memory B cells and T cells, in two adjacent anatomical sites in the upper airway. Upper airway immune cell populations seemed stable over time in healthy adults undergoing monthly swabs for more than 1 year, and prominent tissue resident memory T (TRM) cell and B (BRM) cell populations were defined. Unexpectedly, germinal centre cells were identified consistently in many nasopharyngeal swabs. In subjects with SARS-CoV-2 breakthrough infections, local virus-specific BRM cells, plasma cells and germinal centre B cells were identified, with evidence of local priming and an enrichment of IgA+ memory B cells in upper airway compartments compared with blood. Local plasma cell populations were identified with transcriptional profiles of longevity. Local virus-specific memory CD4+ TRM cells and CD8+ TRM cells were identified, with diverse additional virus-specific T cells. Age-dependent upper airway immunological shifts were observed. These findings provide new understanding of immune memory at a principal mucosal barrier tissue in humans.
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Affiliation(s)
- Sydney I Ramirez
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Farhoud Faraji
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, CA, USA
| | - L Benjamin Hills
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Paul G Lopez
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Benjamin Goodwin
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Hannah D Stacey
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Henry J Sutton
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kathryn M Hastie
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Erica Ollmann Saphire
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Hyun Jik Kim
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Otorhinolaryngology, College of Medicine, Seoul National University, Seoul, Korea
| | - Sara Mashoof
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Carol H Yan
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, CA, USA
| | - Adam S DeConde
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, CA, USA
| | - Gina Levi
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Shane Crotty
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA, USA.
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7
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García-Vega M, Llamas-Covarrubias MA, Loza M, Reséndiz-Sandoval M, Hinojosa-Trujillo D, Melgoza-González E, Valenzuela O, Mata-Haro V, Hernández-Oñate M, Soto-Gaxiola A, Chávez-Rueda K, Nakai K, Hernández J. Single-cell transcriptomic analysis of B cells reveals new insights into atypical memory B cells in COVID-19. J Med Virol 2024; 96:e29851. [PMID: 39132689 DOI: 10.1002/jmv.29851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/10/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024]
Abstract
Here, we performed single-cell RNA sequencing of S1 and receptor binding domain protein-specific B cells from convalescent COVID-19 patients with different clinical manifestations. This study aimed to evaluate the role and developmental pathway of atypical memory B cells (MBCs) in response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The results revealed a proinflammatory signature across B cell subsets associated with disease severity, as evidenced by the upregulation of genes such as GADD45B, MAP3K8, and NFKBIA in critical and severe individuals. Furthermore, the analysis of atypical MBCs suggested a developmental pathway similar to that of conventional MBCs through germinal centers, as indicated by the expression of several genes involved in germinal center processes, including CXCR4, CXCR5, BCL2, and MYC. Additionally, the upregulation of genes characteristic of the immune response in COVID-19, such as ZFP36 and DUSP1, suggested that the differentiation and activation of atypical MBCs may be influenced by exposure to SARS-CoV-2 and that these genes may contribute to the immune response for COVID-19 recovery. Our study contributes to a better understanding of atypical MBCs in COVID-19 and the role of other B cell subsets across different clinical manifestations.
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Affiliation(s)
- Melissa García-Vega
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| | | | - Martin Loza
- The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Mónica Reséndiz-Sandoval
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| | - Diana Hinojosa-Trujillo
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| | - Edgar Melgoza-González
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| | - Olivia Valenzuela
- Departamento de Ciencias Químico Biológicas, División de Ciencias Biológicas y de la Salud, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Verónica Mata-Haro
- Laboratorio de Microbiología e Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| | - Miguel Hernández-Oñate
- CONAHCYT-Laboratorio de Fisiología y Biología Molecular de Plantas, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
| | - Alan Soto-Gaxiola
- Hospital General del Estado de Sonora "Dr. Ernesto Ramos Bours", Secretaria de Salud del Estado de Sonora, Hermosillo, Sonora, Mexico
| | - Karina Chávez-Rueda
- Unidad de Investigación Médica en Inmunología, UMAE, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Kenta Nakai
- The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Jesús Hernández
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C, Hermosillo, Sonora, Mexico
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8
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Wang LT, Cooper AJR, Farrell B, Miura K, Diouf A, Müller-Sienerth N, Crosnier C, Purser L, Kirtley PJ, Maciuszek M, Barrett JR, McHugh K, Ogwang R, Tucker C, Li S, Doumbo S, Doumtabe D, Pyo CW, Skinner J, Nielsen CM, Silk SE, Kayentao K, Ongoiba A, Zhao M, Nguyen DC, Lee FEH, Minassian AM, Geraghty DE, Traore B, Seder RA, Wilder BK, Crompton PD, Wright GJ, Long CA, Draper SJ, Higgins MK, Tan J. Natural malaria infection elicits rare but potent neutralizing antibodies to the blood-stage antigen RH5. Cell 2024:S0092-8674(24)00711-6. [PMID: 39059381 DOI: 10.1016/j.cell.2024.06.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 04/15/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024]
Abstract
Plasmodium falciparum reticulocyte-binding protein homolog 5 (RH5) is the most advanced blood-stage malaria vaccine candidate and is being evaluated for efficacy in endemic regions, emphasizing the need to study the underlying antibody response to RH5 during natural infection, which could augment or counteract responses to vaccination. Here, we found that RH5-reactive B cells were rare, and circulating immunoglobulin G (IgG) responses to RH5 were short-lived in malaria-exposed Malian individuals, despite repeated infections over multiple years. RH5-specific monoclonal antibodies isolated from eight malaria-exposed individuals mostly targeted non-neutralizing epitopes, in contrast to antibodies isolated from five RH5-vaccinated, malaria-naive UK individuals. However, MAD8-151 and MAD8-502, isolated from two malaria-exposed Malian individuals, were among the most potent neutralizers out of 186 antibodies from both cohorts and targeted the same epitopes as the most potent vaccine-induced antibodies. These results suggest that natural malaria infection may boost RH5-vaccine-induced responses and provide a clear strategy for the development of next-generation RH5 vaccines.
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Affiliation(s)
- Lawrence T Wang
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; Medical Scientist Training Program, University of California, San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Andrew J R Cooper
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Brendan Farrell
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Ababacar Diouf
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | | | - Cécile Crosnier
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
| | - Lauren Purser
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Payton J Kirtley
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Portland, OR 97006, USA
| | - Maciej Maciuszek
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jordan R Barrett
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | - Kirsty McHugh
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | - Rodney Ogwang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Courtney Tucker
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Shanping Li
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Safiatou Doumbo
- Mali International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Point G, BP 1805 Bamako, Mali
| | - Didier Doumtabe
- Mali International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Point G, BP 1805 Bamako, Mali
| | - Chul-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jeff Skinner
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Carolyn M Nielsen
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | - Sarah E Silk
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | - Kassoum Kayentao
- Mali International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Point G, BP 1805 Bamako, Mali
| | - Aissata Ongoiba
- Mali International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Point G, BP 1805 Bamako, Mali
| | - Ming Zhao
- Protein Chemistry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Doan C Nguyen
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Emory University, Atlanta, GA 30322, USA
| | - F Eun-Hyung Lee
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Emory University, Atlanta, GA 30322, USA
| | - Angela M Minassian
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Boubacar Traore
- Mali International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Point G, BP 1805 Bamako, Mali
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brandon K Wilder
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Portland, OR 97006, USA
| | - Peter D Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Gavin J Wright
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
| | - Carole A Long
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Simon J Draper
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK
| | - Matthew K Higgins
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | - Joshua Tan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA.
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9
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Fantin RF, Clark JJ, Cohn H, Jaiswal D, Bozarth B, Civljak A, Rao V, Lobo I, Nardulli JR, Srivastava K, Yong J, Andreata-Santos R, Bushfield K, Lee ES, Singh G, Kleinstein SH, Krammer F, Simon V, Bajic G, Coelho CH. Dissecting human monoclonal antibody responses from mRNA- and protein-based XBB.1.5 COVID-19 monovalent vaccines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.15.602781. [PMID: 39071292 PMCID: PMC11275766 DOI: 10.1101/2024.07.15.602781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The emergence of highly contagious and immune-evasive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has required reformulation of coronavirus disease 2019 (COVID-19) vaccines to target those new variants specifically. While previous infections and booster vaccinations can enhance variant neutralization, it is unclear whether the monovalent version, administered using either mRNA or protein-based vaccine platforms, can elicit de novo B-cell responses specific for Omicron XBB.1.5 variants. Here, we dissected the genetic antibody repertoire of 603 individual plasmablasts derived from five individuals who received a monovalent XBB.1.5 vaccination either with mRNA (Moderna or Pfizer/BioNtech) or adjuvanted protein (Novavax). From these sequences, we expressed 100 human monoclonal antibodies and determined binding, affinity and protective potential against several SARS-CoV-2 variants, including JN.1. We then select two vaccine-induced XBB.1.5 mAbs, M2 and M39. M2 mAb was a de novo, antibody, i.e., specific for XBB.1.5 but not ancestral SARS-CoV-2. M39 bound and neutralized both XBB.1.5 and JN.1 strains. Our high-resolution cryo-electron microscopy (EM) structures of M2 and M39 in complex with the XBB.1.5 spike glycoprotein defined the epitopes engaged and revealed the molecular determinants for the mAbs' specificity. These data show, at the molecular level, that monovalent, variant-specific vaccines can elicit functional antibodies, and shed light on potential functional and genetic differences of mAbs induced by vaccinations with different vaccine platforms.\.
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Affiliation(s)
- Raianna F. Fantin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jordan J. Clark
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hallie Cohn
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Deepika Jaiswal
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bailey Bozarth
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alesandro Civljak
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vishal Rao
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Igor Lobo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica R. Nardulli
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Komal Srivastava
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremy Yong
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Andreata-Santos
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Retrovirology Laboratory, Department of Microbiology, Immunology and Parasitology, Paulista School of Medicine, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Kaitlyn Bushfield
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edward S. Lee
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - PVI Study Group
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven H. Kleinstein
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
- Program in Computational Biology and Biomedical Informatics, Yale University, New Haven, CT 06520, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ignaz Semmelweis Institute, Interuniversity Institute for Infection Research, Medical University of Vienna, Vienna, Austria
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Goran Bajic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Camila H. Coelho
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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10
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Yang Y, Chen X, Pan J, Ning H, Zhang Y, Bo Y, Ren X, Li J, Qin S, Wang D, Chen MM, Zhang Z. Pan-cancer single-cell dissection reveals phenotypically distinct B cell subtypes. Cell 2024:S0092-8674(24)00712-8. [PMID: 39047727 DOI: 10.1016/j.cell.2024.06.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 04/25/2024] [Accepted: 06/26/2024] [Indexed: 07/27/2024]
Abstract
Characterizing the compositional and phenotypic characteristics of tumor-infiltrating B cells (TIBs) is important for advancing our understanding of their role in cancer development. Here, we establish a comprehensive resource of human B cells by integrating single-cell RNA sequencing data of B cells from 649 patients across 19 major cancer types. We demonstrate substantial heterogeneity in their total abundance and subtype composition and observe immunoglobulin G (IgG)-skewness of antibody-secreting cell isotypes. Moreover, we identify stress-response memory B cells and tumor-associated atypical B cells (TAABs), two tumor-enriched subpopulations with prognostic potential, shared in a pan-cancer manner. In particular, TAABs, characterized by a high clonal expansion level and proliferative capacity as well as by close interactions with activated CD4 T cells in tumors, are predictive of immunotherapy response. Our integrative resource depicts distinct clinically relevant TIB subsets, laying a foundation for further exploration of functional commonality and diversity of B cells in cancer.
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Affiliation(s)
- Yu Yang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xueyan Chen
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jieying Pan
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Huiheng Ning
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yaojun Zhang
- State Key Laboratory of Oncology in South China, Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yufei Bo
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xianwen Ren
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jiesheng Li
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Shishang Qin
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Dongfang Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China.
| | - Min-Min Chen
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Zemin Zhang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China.
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11
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Farjami T, Sharma A, Hagen L, Jensen IJ, Falch E. Comparative study on composition and functional properties of brewer's spent grain proteins precipitated by citric acid and hydrochloric acid. Food Chem 2024; 446:138863. [PMID: 38428084 DOI: 10.1016/j.foodchem.2024.138863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/21/2024] [Accepted: 02/25/2024] [Indexed: 03/03/2024]
Abstract
Brewer's spent grain (BSG) is an abundant agro-industrial residue and a sustainable low-cost source for extracting proteins. The composition and functionality of BSG protein concentrates are affected by extraction conditions. This study examined the use of citric acid (CA) and HCl to precipitate BSG proteins. The resultant protein concentrates were compared in terms of their composition and functional properties. The BSG protein concentrate precipitated by CA had 10% lower protein content, 5.8% higher carbohydrate, and 5.4% higher lipid content than the sample precipitated by HCl. Hydrophilic/hydrophobic protein and saturated/unsaturated fatty acid ratios increased by 16.9% and 26.5% respectively, in the sample precipitated by CA. The formation of CA-cross-linkages was verified using shotgun proteomics and Fourier transform infrared spectroscopy. Precipitation by CA adversely affected protein solubility and emulsifying properties, while improving foaming properties. This study provides insights into the role of precipitants in modulating the properties of protein concentrates.
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Affiliation(s)
- Toktam Farjami
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway.
| | - Animesh Sharma
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway; Proteomics and Modomics Experimental Core (PROMEC), NTNU and the Central Norway Regional Health Authority, N-7491 Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway; Proteomics and Modomics Experimental Core (PROMEC), NTNU and the Central Norway Regional Health Authority, N-7491 Trondheim, Norway
| | - Ida-Johanne Jensen
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Eva Falch
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
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12
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Tuong ZK, van der Merwe R, Canete PF, Roco JA. Computational estimation of clonal diversity in autoimmunity. Immunol Cell Biol 2024. [PMID: 39010261 DOI: 10.1111/imcb.12801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/17/2024]
Abstract
Diversity is the cornerstone of the adaptive immune system, crucial for its effectiveness against constantly evolving pathogens that pose threats to higher vertebrates. Accurately measuring and interpreting this diversity presents challenges for immunologists, as changes in diversity and clonotype composition can tip the balance between protective immunity and autoimmunity. In this review, we present the current methods commonly used to measure diversity from single-cell T-cell receptor and B-cell receptor sequencing. We also discuss two case studies where single-cell sequencing and diversity estimations have led to breakthroughs in autoimmune disease discovery and therapeutic innovation, and reflect upon the necessity and importance of accurately defining and measuring lymphocyte diversity in these contexts.
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Affiliation(s)
- Zewen Kelvin Tuong
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Rohan van der Merwe
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Pablo F Canete
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Jonathan A Roco
- Biological Data Science Institute, College of Science, The Australian National University, Canberra, ACT, Australia
- Clinical Hub for Interventional Research, College of Health & Medicine, The Australian National University, Canberra, ACT, Australia
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13
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Richardson E, Bibi S, McLean F, Schimanski L, Rijal P, Ghraichy M, von Niederhäusern V, Trück J, Clutterbuck EA, O’Connor D, Luhn K, Townsend A, Peters B, Pollard AJ, Deane CM, Kelly DF. Computational mining of B cell receptor repertoires reveals antigen-specific and convergent responses to Ebola vaccination. Front Immunol 2024; 15:1383753. [PMID: 39040106 PMCID: PMC11260629 DOI: 10.3389/fimmu.2024.1383753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/11/2024] [Indexed: 07/24/2024] Open
Abstract
Outbreaks of Ebolaviruses, such as Sudanvirus (SUDV) in Uganda in 2022, demonstrate that species other than the Zaire ebolavirus (EBOV), which is currently the sole virus represented in current licensed vaccines, remain a major threat to global health. There is a pressing need to develop effective pan-species vaccines and novel monoclonal antibody-based therapeutics for Ebolavirus disease. In response to recent outbreaks, the two dose, heterologous Ad26.ZEBOV/MVA-BN-Filo vaccine regimen was developed and was tested in a large phase II clinical trial (EBL2001) as part of the EBOVAC2 consortium. Here, we perform bulk sequencing of the variable heavy chain (VH) of B cell receptors (BCR) in forty participants from the EBL2001 trial in order to characterize the BCR repertoire in response to vaccination with Ad26.ZEBOV/MVA-BN-Filo. We develop a comprehensive database, EBOV-AbDab, of publicly available Ebolavirus-specific antibody sequences. We then use our database to predict the antigen-specific component of the vaccinee repertoires. Our results show striking convergence in VH germline gene usage across participants following the MVA-BN-Filo dose, and provide further evidence of the role of IGHV3-15 and IGHV3-13 antibodies in the B cell response to Ebolavirus glycoprotein. Furthermore, we found that previously described Ebola-specific mAb sequences present in EBOV-AbDab were sufficient to describe at least one of the ten most expanded BCR clonotypes in more than two thirds of our cohort of vaccinees following the boost, providing proof of principle for the utility of computational mining of immune repertoires.
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Affiliation(s)
- Eve Richardson
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford, United Kingdom
- La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Sagida Bibi
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford, United Kingdom
| | - Florence McLean
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford, United Kingdom
| | - Lisa Schimanski
- Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Pramila Rijal
- Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Marie Ghraichy
- Divisions of Allergy and Immunology, University Children’s Hospital and Children’s Research Center, University of Zurich (UZH), Zurich, Switzerland
| | - Valentin von Niederhäusern
- Divisions of Allergy and Immunology, University Children’s Hospital and Children’s Research Center, University of Zurich (UZH), Zurich, Switzerland
| | - Johannes Trück
- Divisions of Allergy and Immunology, University Children’s Hospital and Children’s Research Center, University of Zurich (UZH), Zurich, Switzerland
| | | | - Daniel O’Connor
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford, United Kingdom
| | - Kerstin Luhn
- Janssen Vaccines and Prevention, Leiden, Netherlands
| | - Alain Townsend
- Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford, United Kingdom
| | | | - Dominic F. Kelly
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
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14
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Gabernet G, Marquez S, Bjornson R, Peltzer A, Meng H, Aron E, Lee NY, Jensen CG, Ladd D, Polster M, Hanssen F, Heumos S, Yaari G, Kowarik MC, Nahnsen S, Kleinstein SH. nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework. PLoS Comput Biol 2024; 20:e1012265. [PMID: 39058741 PMCID: PMC11305553 DOI: 10.1371/journal.pcbi.1012265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 08/07/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data with sequencing errors and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls, including a mixture of bulk and single-cell sequencing datasets. Using this dataset, we extended the convergence findings to 20 additional subjects, highlighting the applicability of nf-core/airrflow to validate findings in small in-house cohorts with reanalysis of large publicly available AIRR datasets.
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Affiliation(s)
- Gisela Gabernet
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Susanna Marquez
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Robert Bjornson
- Yale Center for Research Computing, New Haven, Connecticut, United States of America
| | | | - Hailong Meng
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Edel Aron
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Noah Y. Lee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Cole G. Jensen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - David Ladd
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Mark Polster
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, Tübingen, Germany
- M3 Research Center, University Hospital, Tübingen, Germany
| | - Friederike Hanssen
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, Tübingen, Germany
- M3 Research Center, University Hospital, Tübingen, Germany
| | - Simon Heumos
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, Tübingen, Germany
- M3 Research Center, University Hospital, Tübingen, Germany
| | | | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Markus C. Kowarik
- Department of Neurology and Stroke, Center for Neurology, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Hertie Institute for Clinical Brain Research, Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, Tübingen, Germany
- M3 Research Center, University Hospital, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Steven H. Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
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15
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Wang Z, Zhao Y, Wo Y, Peng Y, Hu W, Wu Z, Liu P, Shang Y, Liu C, Chen X, Huang K, Chen Y, Hong H, Li F, Sun Y. The single cell immunogenomic landscape after neoadjuvant immunotherapy combined chemotherapy in esophageal squamous cell carcinoma. Cancer Lett 2024; 593:216951. [PMID: 38734159 DOI: 10.1016/j.canlet.2024.216951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 04/19/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Neoadjuvant immunotherapy represents promising strategy in the treatment of esophageal squamous cell carcinoma (ESCC). However, the mechanisms underlying its impact on treatment sensitivity or resistance remain a subject of controversy. In this study, we conducted single-cell RNA and T/B cell receptor (scTCR/scBCR) sequencing of CD45+ immune cells on samples from 10 patients who received neoadjuvant immunotherapy and chemotherapy. We also validated our findings using multiplexed immunofluorescence and analyzed bulk RNA-seq from other cohorts in public database. By integrating analysis of 87357 CD45+ cells, we found GZMK + effector memory T cells (Tem) were relatively enriched and CXCL13+ exhausted T cells (Tex) and regulator T cells (Treg) decreased among responders, indicating a persistent anti-tumor memory process. Additionally, the enhanced presence of BCR expansion and somatic hypermutation process within TNFRSF13B + memory B cells (Bmem) suggested their roles in antigen presentation. This was further corroborated by the evidence of the T-B co-stimulation pattern and CXCL13-CXCR5 axis. The complexity of myeloid cell heterogeneity was also particularly pronounced. The elevated expression of S100A7 in ESCC, as detected by bulk RNA-seq, was associated with an exhausted and immunosuppressive tumor microenvironment. In summary, this study has unveiled a potential regulatory network among immune cells and the clonal dynamics of their functions, and the mechanisms of exhaustion and memory conversion between GZMK + Tem and TNFRSF13B + Bmem from antigen presentation and co-stimulation perspectives during neoadjuvant PD-1 blockade treatment in ESCC.
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MESH Headings
- Humans
- Neoadjuvant Therapy/methods
- Esophageal Squamous Cell Carcinoma/immunology
- Esophageal Squamous Cell Carcinoma/genetics
- Esophageal Squamous Cell Carcinoma/therapy
- Esophageal Squamous Cell Carcinoma/drug therapy
- Esophageal Squamous Cell Carcinoma/pathology
- Esophageal Neoplasms/immunology
- Esophageal Neoplasms/genetics
- Esophageal Neoplasms/therapy
- Esophageal Neoplasms/drug therapy
- Esophageal Neoplasms/pathology
- Immunotherapy/methods
- Single-Cell Analysis/methods
- Female
- Male
- Tumor Microenvironment/immunology
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Chemokine CXCL13/genetics
- Chemokine CXCL13/metabolism
- Middle Aged
- Aged
- Memory T Cells/immunology
- Memory T Cells/metabolism
- Leukocyte Common Antigens/metabolism
- Leukocyte Common Antigens/genetics
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/drug effects
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/metabolism
- Receptors, Antigen, B-Cell/immunology
- Receptors, CXCR5/metabolism
- Receptors, CXCR5/genetics
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Affiliation(s)
- Zheyi Wang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yue Zhao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yang Wo
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yizhou Peng
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Weilei Hu
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China; State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Zhigang Wu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Pengcheng Liu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yan Shang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chunnan Liu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kan Huang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuting Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hui Hong
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fei Li
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Yihua Sun
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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16
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Bruhn M, Obara M, Salam A, Costa B, Ziegler A, Waltl I, Pavlou A, Hoffmann M, Graalmann T, Pöhlmann S, Schambach A, Kalinke U. Diversification of the VH3-53 immunoglobulin gene segment by somatic hypermutation results in neutralization of SARS-CoV-2 virus variants. Eur J Immunol 2024; 54:e2451056. [PMID: 38593351 DOI: 10.1002/eji.202451056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
COVID-19 induces re-circulating long-lived memory B cells (MBC) that, upon re-encounter with the pathogen, are induced to mount immunoglobulin responses. During convalescence, antibodies are subjected to affinity maturation, which enhances the antibody binding strength and generates new specificities that neutralize virus variants. Here, we performed a single-cell RNA sequencing analysis of spike-specific B cells from a SARS-CoV-2 convalescent subject. After COVID-19 vaccination, matured infection-induced MBC underwent recall and differentiated into plasmablasts. Furthermore, the transcriptomic profiles of newly activated B cells transiently shifted toward the ones of atypical and CXCR3+ B cells and several B-cell clonotypes massively expanded. We expressed monoclonal antibodies (mAbs) from all B-cell clones from the largest clonotype that used the VH3-53 gene segment. The in vitro analysis revealed that some somatic hypermutations enhanced the neutralization breadth of mAbs in a putatively stochastic manner. Thus, somatic hypermutation of B-cell clonotypes generates an anticipatory memory that can neutralize new virus variants.
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Affiliation(s)
- Matthias Bruhn
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Maureen Obara
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Abdus Salam
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Bibiana Costa
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Annett Ziegler
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Inken Waltl
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Andreas Pavlou
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology, Georg-August-University Göttingen, Göttingen, Germany
| | - Theresa Graalmann
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
- Junior Research Group for Translational Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
- Biomedical Research in End-Stage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany
- Faculty of Biology, Georg-August-University Göttingen, Göttingen, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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17
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Nguyen A, Zhao H, Myagmarsuren D, Srinivasan S, Wu D, Chen J, Piszczek G, Schuck P. Modulation of biophysical properties of nucleocapsid protein in the mutant spectrum of SARS-CoV-2. eLife 2024; 13:RP94836. [PMID: 38941236 PMCID: PMC11213569 DOI: 10.7554/elife.94836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024] Open
Abstract
Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage of the uniquely large genomic database of SARS-CoV-2, we examine the impact of mutations across the spectrum of viable amino acid sequences on the biophysical phenotypes of the highly expressed and multifunctional nucleocapsid protein. We find variation in the physicochemical parameters of its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also observe functional constraints that similarly occur in related coronaviruses. In biophysical experiments with several N-protein species carrying mutations associated with major variants, we find that point mutations in the IDRs can have nonlocal impact and modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, and liquid-liquid phase separation. In the Omicron variant, distant mutations in different IDRs have compensatory effects in shifting a delicate balance of interactions controlling protein assembly properties, and include the creation of a new protein-protein interaction interface in the N-terminal IDR through the defining P13L mutation. A picture emerges where genetic diversity is accompanied by significant variation in biophysical characteristics of functional N-protein species, in particular in the IDRs.
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Affiliation(s)
- Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Dulguun Myagmarsuren
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Sanjana Srinivasan
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
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18
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Nicholas CA, Tensun FA, Evans SA, Toole KP, Broncucia H, Hesselberth JR, Gottlieb PA, Wells KL, Smith MJ. Islet-antigen reactive B cells display a unique phenotype and BCR repertoire in autoantibody positive and recent-onset type 1 diabetes patients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599914. [PMID: 38979376 PMCID: PMC11230262 DOI: 10.1101/2024.06.20.599914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Autoreactive B cells play an important but ill-defined role in autoimmune type 1 diabetes (T1D). To better understand their contribution, we performed single cell gene and BCR-seq analysis on pancreatic islet antigen-reactive (IAR) B cells from the peripheral blood of nondiabetic (ND), autoantibody positive prediabetic (AAB), and recent-onset T1D individuals. We found that the frequency of IAR B cells was increased in AAB and T1D. IAR B cells from these donors had altered expression of B cell signaling, pro-inflammatory, infection, and antigen processing and presentation genes. Both AAB and T1D donors demonstrated a significant increase in certain heavy and light chain V genes, and these V genes were enriched in islet-reactivity. Public clones of IAR B cells were restricted almost entirely to AAB and T1D donors. IAR B cells were clonally expanded in the autoimmune donors, particularly the AAB group. Notably, a substantial fraction of IAR B cells in AAB and T1D donors appeared to be polyreactive, which was corroborated by analysis of recombinant monoclonal antibodies. These results expand our understanding of autoreactive B cell activation during T1D and identify unique BCR repertoire changes that may serve as biomarkers for increased disease risk.
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Affiliation(s)
- Catherine A. Nicholas
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Molecular Biology Graduate Program, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Fatima A. Tensun
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Spencer A. Evans
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kevin P. Toole
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Hali Broncucia
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jay R Hesselberth
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Molecular Biology Graduate Program, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Peter A. Gottlieb
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kristen L. Wells
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Mia J. Smith
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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19
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Wang K, Cai L, Wang H, Shan S, Hu X, Zhang J. Protocol for fast clonal family inference and analysis from large-scale B cell receptor repertoire sequencing data. STAR Protoc 2024; 5:102969. [PMID: 38502687 PMCID: PMC10963638 DOI: 10.1016/j.xpro.2024.102969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/26/2024] [Accepted: 03/03/2024] [Indexed: 03/21/2024] Open
Abstract
The expeditious identification and comprehensive analysis of clonal families from extensive B cell receptor (BCR) repertoire sequencing data are imperative for elucidating the intricacies of B cell immune responses. Here, we introduce a computational pipeline designed to swiftly deduce clonal families from bulk BCR heavy-chain sequencing data, accompanied by a suite of functional modules tailored to streamline post-clustering analysis. The outlined methodology encompasses guidelines for software installation, meticulous data preparation, and the systematic inference and analysis of clonal families. For complete details on the use and execution of this protocol, please refer to Wang et al.1.
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Affiliation(s)
- Kaixuan Wang
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Linru Cai
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Hao Wang
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China; Georgia Tech Shenzhen Institute (GTSI), Tianjin University, Shenzhen, Guangdong, China
| | - Shiwen Shan
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Xihao Hu
- GV20 Therapeutics, Cambridge, MA, USA
| | - Jian Zhang
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China.
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20
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Verma S, Dufort MJ, Olsen TM, Kimmel S, Labuda JC, Scharffenberger S, McGuire AT, Harrison OJ. Antigen-level resolution of commensal-specific B cell responses can be enabled by phage display screening coupled with B cell tetramers. Immunity 2024; 57:1428-1441.e8. [PMID: 38723638 PMCID: PMC11168869 DOI: 10.1016/j.immuni.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/07/2024] [Accepted: 04/16/2024] [Indexed: 06/14/2024]
Abstract
Induction of commensal-specific immunity contributes to tissue homeostasis, yet the mechanisms underlying induction of commensal-specific B cells remain poorly understood in part due to a lack of tools to identify these cells. Using phage display, we identified segmented filamentous bacteria (SFB) antigens targeted by serum and intestinal antibodies and generated B cell tetramers to track SFB-specific B cells in gut-associated lymphoid tissues. We revealed a compartmentalized response in SFB-specific B cell activation, with a gradient of immunoglobulin A (IgA), IgG1, and IgG2b isotype production along Peyer's patches contrasted by selective production of IgG2b within mesenteric lymph nodes. V(D)J sequencing and monoclonal antibody generation identified somatic hypermutation driven affinity maturation to SFB antigens under homeostatic conditions. Combining phage display and B cell tetramers will enable investigation of the ontogeny and function of commensal-specific B cell responses in tissue immunity, inflammation, and repair.
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Affiliation(s)
- Sheenam Verma
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Matthew J Dufort
- Center for Systems Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Tayla M Olsen
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Samantha Kimmel
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Jasmine C Labuda
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Sam Scharffenberger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Andrew T McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Oliver J Harrison
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA; Department of Immunology, University of Washington, Seattle, WA, USA.
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21
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Dunlap G, Wagner A, Meednu N, Wang R, Zhang F, Ekabe JC, Jonsson AH, Wei K, Sakaue S, Nathan A, Bykerk VP, Donlin LT, Goodman SM, Firestein GS, Boyle DL, Holers VM, Moreland LW, Tabechian D, Pitzalis C, Filer A, Raychaudhuri S, Brenner MB, Thakar J, McDavid A, Rao DA, Anolik JH. Clonal associations between lymphocyte subsets and functional states in rheumatoid arthritis synovium. Nat Commun 2024; 15:4991. [PMID: 38862501 PMCID: PMC11167034 DOI: 10.1038/s41467-024-49186-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 05/20/2024] [Indexed: 06/13/2024] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease involving antigen-specific T and B cells. Here, we perform single-cell RNA and repertoire sequencing on paired synovial tissue and blood samples from 12 seropositive RA patients. We identify clonally expanded CD4 + T cells, including CCL5+ cells and T peripheral helper (Tph) cells, which show a prominent transcriptomic signature of recent activation and effector function. CD8 + T cells show higher oligoclonality than CD4 + T cells, with the largest synovial clones enriched in GZMK+ cells. CD8 + T cells with possibly virus-reactive TCRs are distributed across transcriptomic clusters. In the B cell compartment, NR4A1+ activated B cells, and plasma cells are enriched in the synovium and demonstrate substantial clonal expansion. We identify synovial plasma cells that share BCRs with synovial ABC, memory, and activated B cells. Receptor-ligand analysis predicted IFNG and TNFRSF members as mediators of synovial Tph-B cell interactions. Together, these results reveal clonal relationships between functionally distinct lymphocyte populations that infiltrate the synovium of patients with RA.
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Grants
- UH2 AR067685 NIAMS NIH HHS
- UM2 AR067678 NIAMS NIH HHS
- K08 AR081412 NIAMS NIH HHS
- UH2 AR067681 NIAMS NIH HHS
- UH2 AR067688 NIAMS NIH HHS
- UH2 AR067689 NIAMS NIH HHS
- UH2 AR067690 NIAMS NIH HHS
- UH2 AR067677 NIAMS NIH HHS
- UH2 AR067694 NIAMS NIH HHS
- UH2 AR067679 NIAMS NIH HHS
- UH2 AR067676 NIAMS NIH HHS
- UH2 AR067691 NIAMS NIH HHS
- Funding for AMP RA/SLE work was provided through grants from the National Institutes of Health (UH2-AR067676, UH2-AR067677, UH2-AR067679, UH2-AR067681, UH2-AR067685, UH2-AR067688, UH2-AR067689, UH2-AR067690, UH2-AR067691, UH2-AR067694, and UM2-AR067678).
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Affiliation(s)
- Garrett Dunlap
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Aaron Wagner
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Nida Meednu
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA
| | - Ruoqiao Wang
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Fan Zhang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology and the Center for Health Artificial Intelligence, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jabea Cyril Ekabe
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA
| | - Anna Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Saori Sakaue
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vivian P Bykerk
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Laura T Donlin
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Susan M Goodman
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Gary S Firestein
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego;, La Jolla, CA, USA
| | - David L Boyle
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego;, La Jolla, CA, USA
| | - V Michael Holers
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Larry W Moreland
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Darren Tabechian
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA
| | - Costantino Pitzalis
- Centre for Experimental Medicine & Rheumatology, EULAR Centre of Excellence, William Harvey Research Institute, Queen Mary University of London, London, UK
- Barts Health NHS Trust, Barts Biomedical Research Centre (BRC), National Institute for Health and Care Research (NIHR), London, UK
- Department of Biomedical Sciences, Humanitas University and Humanitas Research Hospital, Milan, Italy
| | - Andrew Filer
- Rheumatology Research Group, Institute for Inflammation and Ageing, University of Birmingham, NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
- Birmingham Tissue Analytics, Institute of Translational Medicine, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Juilee Thakar
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Andrew McDavid
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Jennifer H Anolik
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA.
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
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22
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Johnson MB, Ogishi M, Domingo-Vila C, De Franco E, Wakeling MN, Imane Z, Resnick B, Williams E, Galão RP, Caswell R, Russ-Silsby J, Seeleuthner Y, Rinchai D, Fagniez I, Benson B, Dufort MJ, Speake C, Smithmyer ME, Hudson M, Dobbs R, Quandt Z, Hattersley AT, Zhang P, Boisson-Dupuis S, Anderson MS, Casanova JL, Tree TI, Oram RA. Human inherited PD-L1 deficiency is clinically and immunologically less severe than PD-1 deficiency. J Exp Med 2024; 221:e20231704. [PMID: 38634869 PMCID: PMC11032109 DOI: 10.1084/jem.20231704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/16/2024] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
We previously reported two siblings with inherited PD-1 deficiency who died from autoimmune pneumonitis at 3 and 11 years of age after developing other autoimmune manifestations, including type 1 diabetes (T1D). We report here two siblings, aged 10 and 11 years, with neonatal-onset T1D (diagnosed at the ages of 1 day and 7 wk), who are homozygous for a splice-site variant of CD274 (encoding PD-L1). This variant results in the exclusive expression of an alternative, loss-of-function PD-L1 protein isoform in overexpression experiments and in the patients' primary leukocytes. Surprisingly, cytometric immunophenotyping and single-cell RNA sequencing analysis on blood leukocytes showed largely normal development and transcriptional profiles across lymphoid and myeloid subsets in the PD-L1-deficient siblings, contrasting with the extensive dysregulation of both lymphoid and myeloid leukocyte compartments in PD-1 deficiency. Our findings suggest that PD-1 and PD-L1 are essential for preventing early-onset T1D but that, unlike PD-1 deficiency, PD-L1 deficiency does not lead to fatal autoimmunity with extensive leukocytic dysregulation.
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Affiliation(s)
- Matthew B. Johnson
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Clara Domingo-Vila
- Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK
| | - Elisa De Franco
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Matthew N. Wakeling
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Zineb Imane
- Faculty of Medicine and Pharmacy, Mohammed 5 University of Rabat, Rabat, Morocco
| | - Brittany Resnick
- National Institute for Health and Care Research Exeter Clinical Research Facility, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Evangelia Williams
- Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK
| | - Rui Pedro Galão
- Department of Infectious Diseases, School of Immunobiology and Microbial Sciences, Kings College London, London, UK
| | - Richard Caswell
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - James Russ-Silsby
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Imagine Institute, Paris Cité University, Paris, France
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Iris Fagniez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Basilin Benson
- Center for Systems Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Matthew J. Dufort
- Center for Systems Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Cate Speake
- Center for Interventional Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Megan E. Smithmyer
- Center for Interventional Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Michelle Hudson
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
- National Institute for Health and Care Research Exeter Clinical Research Facility, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Rebecca Dobbs
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
- National Institute for Health and Care Research Exeter Clinical Research Facility, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Zoe Quandt
- Endocrine Division, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Andrew T. Hattersley
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Stephanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Imagine Institute, Paris Cité University, Paris, France
| | - Mark S. Anderson
- Endocrine Division, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Imagine Institute, Paris Cité University, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Timothy I. Tree
- Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK
| | - Richard A. Oram
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
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23
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Voss K, Kaur KM, Banerjee R, Breden F, Pennell M. Evaluating methods for B-cell clonal family assignment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596491. [PMID: 38853833 PMCID: PMC11160721 DOI: 10.1101/2024.05.29.596491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The adaptive immune response relies on a diverse repertoire of B-cell receptors, each of which is characterized by a distinct sequence resulting from VDJ-recombination. Upon binding to an antigen, B-cells undergo clonal expansion and in a process unique to B-cells the overall binding affinity of the repertoire is further enhanced by somatic hypermutations in the receptor sequence. For B-cell repertoires it is therefore particularly important to analyze the dynamics of clonal expansion and patterns of somatic hypermutations and thus it is necessary to group the sequences into distinct clones to determine the number and identity of expanding clonal families responding to an antigen. Multiple methods are currently used to identify clones from sequences, employing distinct approaches to the problem. Until now there has not been an extensive comparison of how well these methods perform under the same conditions. Furthermore, since this is fundamentally a phylogenetics problem, we speculated that the mPTP method, which delimits species based on an analysis of changes in the underlying process of diversification, might perform as well as or better than existing methods. Here we conducted extensive simulations of B-cell repertoires under a diverse set of conditions and studied errors in clonal assignment and in downstream ancestral state reconstruction. We demonstrated that SCOPer-H consistently yielded superior results across parameters. However, this approach relies on a good reference assembly for the germline immunoglobulin genes which is lacking for many species. Using mPTP had lower error rates than tailor-made immunogenetic methods and should therefore be considered by researchers studying antibody evolution in non-model organisms without a reference genome.
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Affiliation(s)
- Katalin Voss
- Department of Quantitative and Computational Biology, University of Southern California, USA
| | - Katrina M. Kaur
- Department of Zoology, University of British Columbia, Canada
| | - Rituparna Banerjee
- Bioinformatics Graduate Program, Faculty of Science, University of British Columbia, Canada
| | - Felix Breden
- Department of Biological Sciences, Simon Fraser University, Canada
| | - Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, USA
- Department of Biological Sciences, University of Southern California, USA
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24
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Schiffner T, Phung I, Ray R, Irimia A, Tian M, Swanson O, Lee JH, Lee CCD, Marina-Zárate E, Cho SY, Huang J, Ozorowski G, Skog PD, Serra AM, Rantalainen K, Allen JD, Baboo S, Rodriguez OL, Himansu S, Zhou J, Hurtado J, Flynn CT, McKenney K, Havenar-Daughton C, Saha S, Shields K, Schultze S, Smith ML, Liang CH, Toy L, Pecetta S, Lin YC, Willis JR, Sesterhenn F, Kulp DW, Hu X, Cottrell CA, Zhou X, Ruiz J, Wang X, Nair U, Kirsch KH, Cheng HL, Davis J, Kalyuzhniy O, Liguori A, Diedrich JK, Ngo JT, Lewis V, Phelps N, Tingle RD, Spencer S, Georgeson E, Adachi Y, Kubitz M, Eskandarzadeh S, Elsliger MA, Amara RR, Landais E, Briney B, Burton DR, Carnathan DG, Silvestri G, Watson CT, Yates JR, Paulson JC, Crispin M, Grigoryan G, Ward AB, Sok D, Alt FW, Wilson IA, Batista FD, Crotty S, Schief WR. Vaccination induces broadly neutralizing antibody precursors to HIV gp41. Nat Immunol 2024; 25:1073-1082. [PMID: 38816615 PMCID: PMC11147780 DOI: 10.1038/s41590-024-01833-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 04/04/2024] [Indexed: 06/01/2024]
Abstract
A key barrier to the development of vaccines that induce broadly neutralizing antibodies (bnAbs) against human immunodeficiency virus (HIV) and other viruses of high antigenic diversity is the design of priming immunogens that induce rare bnAb-precursor B cells. The high neutralization breadth of the HIV bnAb 10E8 makes elicitation of 10E8-class bnAbs desirable; however, the recessed epitope within gp41 makes envelope trimers poor priming immunogens and requires that 10E8-class bnAbs possess a long heavy chain complementarity determining region 3 (HCDR3) with a specific binding motif. We developed germline-targeting epitope scaffolds with affinity for 10E8-class precursors and engineered nanoparticles for multivalent display. Scaffolds exhibited epitope structural mimicry and bound bnAb-precursor human naive B cells in ex vivo screens, protein nanoparticles induced bnAb-precursor responses in stringent mouse models and rhesus macaques, and mRNA-encoded nanoparticles triggered similar responses in mice. Thus, germline-targeting epitope scaffold nanoparticles can elicit rare bnAb-precursor B cells with predefined binding specificities and HCDR3 features.
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Affiliation(s)
- Torben Schiffner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Institute for Drug Discovery, Leipzig University Medical Faculty, Leipzig, Germany
| | - Ivy Phung
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Rashmi Ray
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Adriana Irimia
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ming Tian
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Olivia Swanson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Jeong Hyun Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Chang-Chun D Lee
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ester Marina-Zárate
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - So Yeon Cho
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jiachen Huang
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gabriel Ozorowski
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Patrick D Skog
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Andreia M Serra
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Kimmo Rantalainen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | | | - Jianfu Zhou
- Department of Computer Science, Dartmouth College, Hanover, NH, USA
| | - Jonathan Hurtado
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Claudia T Flynn
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Katherine McKenney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Colin Havenar-Daughton
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Swati Saha
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Kaitlyn Shields
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Steven Schultze
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Melissa L Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Chi-Hui Liang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Toy
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Simone Pecetta
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Ying-Cing Lin
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Jordan R Willis
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Fabian Sesterhenn
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel W Kulp
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Xiaozhen Hu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Christopher A Cottrell
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Xiaoya Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Jennifer Ruiz
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Xuesong Wang
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Usha Nair
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Kathrin H Kirsch
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Hwei-Ling Cheng
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jillian Davis
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Alessia Liguori
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Julia T Ngo
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Vanessa Lewis
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Nicole Phelps
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Ryan D Tingle
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Skye Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Erik Georgeson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Yumiko Adachi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Michael Kubitz
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Saman Eskandarzadeh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Marc A Elsliger
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rama R Amara
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Atlanta, GA, USA
| | - Elise Landais
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Multi-omics Vaccine Evaluation Consortium, The Scripps Research Institute, La Jolla, CA, USA
- San Diego Center for AIDS Research, The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Diane G Carnathan
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Guido Silvestri
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - James C Paulson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Gevorg Grigoryan
- Department of Computer Science, Dartmouth College, Hanover, NH, USA
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
- Generate Biomedicines, Inc., Somerville, MA, USA
| | - Andrew B Ward
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ian A Wilson
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Facundo D Batista
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Shane Crotty
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - William R Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA.
- Moderna, Inc., Cambridge, MA, USA.
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25
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Skinner OP, Asad S, Haque A. Advances and challenges in investigating B-cells via single-cell transcriptomics. Curr Opin Immunol 2024; 88:102443. [PMID: 38968762 DOI: 10.1016/j.coi.2024.102443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/07/2024]
Abstract
Single-cell RNA sequencing (scRNAseq) and Variable, Diversity, Joining (VDJ) profiling have improved our understanding of B-cells. Recent scRNAseq-based approaches have led to the discovery of intermediate B-cell states, including preplasma cells and pregerminal centre B-cells, as well as unveiling protective roles for B-cells within tertiary lymphoid structures in respiratory infections and cancers. These studies have improved our understanding of transcriptional and epigenetic control of B-cell development and of atypical and memory B-cell differentiation. Advancements in temporal profiling in parallel with transcriptomic and VDJ sequencing have consolidated our understanding of the trajectory of B-cell clones over the course of infection and vaccination. Challenges remain in studying B-cell states across tissues in humans, in relating spatial location with B-cell phenotype and function, in examining antibody isotype switching events, and in unequivocal determination of clonal relationships. Nevertheless, ongoing multiomic assessments and studies of cellular interactions within tissues promise new avenues for improving humoral immunity and combatting autoimmune conditions.
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Affiliation(s)
- Oliver P Skinner
- Department of Microbiology & Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Parkville, Melbourne, VIC 3000, Australia.
| | - Saba Asad
- Department of Microbiology & Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Parkville, Melbourne, VIC 3000, Australia
| | - Ashraful Haque
- Department of Microbiology & Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Parkville, Melbourne, VIC 3000, Australia.
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26
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Leighton PA, Ching K, Reynolds K, Vuong CN, Zeng B, Zhang Y, Gupta A, Morales J, Rivera GS, Srivastava DB, Cotter R, Pedersen D, Collarini E, Izquierdo S, van de Lavoir MC, Harriman W. Chickens with a Truncated Light Chain Transgene Express Single-Domain H Chain-Only Antibodies. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1744-1753. [PMID: 38629917 PMCID: PMC11102025 DOI: 10.4049/jimmunol.2300617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 03/22/2024] [Indexed: 05/20/2024]
Abstract
H chain-only Igs are naturally produced in camelids and sharks. Because these Abs lack the L chain, the Ag-binding domain is half the size of a traditional Ab, allowing this type of Ig to bind to targets in novel ways. Consequently, the H chain-only single-domain Ab (sdAb) structure has the potential to increase the repertoire and functional range of an active humoral immune system. The majority of vertebrates use the standard heterodimeric (both H and L chains) structure and do not produce sdAb format Igs. To investigate if other animals are able to support sdAb development and function, transgenic chickens (Gallus gallus) were designed to produce H chain-only Abs by omitting the L chain V region and maintaining only the LC region to serve as a chaperone for Ab secretion from the cell. These birds produced 30-50% normal B cell populations within PBMCs and readily expressed chicken sequence sdAbs. Interestingly, the H chains contained a spontaneous CH1 deletion. Although no isotype switching to IgY or IgA occurred, the IgM repertoire was diverse, and immunization with a variety of protein immunogens rapidly produced high and specific serum titers. mAbs of high affinity were efficiently recovered by single B cell screening. In in vitro functional assays, the sdAbs produced by birds immunized against SARS-CoV-2 were also able to strongly neutralize and prevent viral replication. These data suggest that the truncated L chain design successfully supported sdAb development and expression in chickens.
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27
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Tambe A, MacCarthy T, Pavri R. Interpretable deep learning reveals the role of an E-box motif in suppressing somatic hypermutation of AGCT motifs within human immunoglobulin variable regions. Front Immunol 2024; 15:1407470. [PMID: 38863710 PMCID: PMC11165027 DOI: 10.3389/fimmu.2024.1407470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/08/2024] [Indexed: 06/13/2024] Open
Abstract
Introduction Somatic hypermutation (SHM) of immunoglobulin variable (V) regions by activation induced deaminase (AID) is essential for robust, long-term humoral immunity against pathogen and vaccine antigens. AID mutates cytosines preferentially within WRCH motifs (where W=A or T, R=A or G and H=A, C or T). However, it has been consistently observed that the mutability of WRCH motifs varies substantially, with large variations in mutation frequency even between multiple occurrences of the same motif within a single V region. This has led to the notion that the immediate sequence context of WRCH motifs contributes to mutability. Recent studies have highlighted the potential role of local DNA sequence features in promoting mutagenesis of AGCT, a commonly mutated WRCH motif. Intriguingly, AGCT motifs closer to 5' ends of V regions, within the framework 1 (FW1) sub-region1, mutate less frequently, suggesting an SHM-suppressing sequence context. Methods Here, we systematically examined the basis of AGCT positional biases in human SHM datasets with DeepSHM, a machine-learning model designed to predict SHM patterns. This was combined with integrated gradients, an interpretability method, to interrogate the basis of DeepSHM predictions. Results DeepSHM predicted the observed positional differences in mutation frequencies at AGCT motifs with high accuracy. For the conserved, lowly mutating AGCT motifs in FW1, integrated gradients predicted a large negative contribution of 5'C and 3'G flanking residues, suggesting that a CAGCTG context in this location was suppressive for SHM. CAGCTG is the recognition motif for E-box transcription factors, including E2A, which has been implicated in SHM. Indeed, we found a strong, inverse relationship between E-box motif fidelity and mutation frequency. Moreover, E2A was found to associate with the V region locale in two human B cell lines. Finally, analysis of human SHM datasets revealed that naturally occurring mutations in the 3'G flanking residues, which effectively ablate the E-box motif, were associated with a significantly increased rate of AGCT mutation. Discussion Our results suggest an antagonistic relationship between mutation frequency and the binding of E-box factors like E2A at specific AGCT motif contexts and, therefore, highlight a new, suppressive mechanism regulating local SHM patterns in human V regions.
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Affiliation(s)
- Abhik Tambe
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, United States
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
| | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King’s College London, London, United Kingdom
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28
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Steichen JM, Phung I, Salcedo E, Ozorowski G, Willis JR, Baboo S, Liguori A, Cottrell CA, Torres JL, Madden PJ, Ma KM, Sutton HJ, Lee JH, Kalyuzhniy O, Allen JD, Rodriguez OL, Adachi Y, Mullen TM, Georgeson E, Kubitz M, Burns A, Barman S, Mopuri R, Metz A, Altheide TK, Diedrich JK, Saha S, Shields K, Schultze SE, Smith ML, Schiffner T, Burton DR, Watson CT, Bosinger SE, Crispin M, Yates JR, Paulson JC, Ward AB, Sok D, Crotty S, Schief WR. Vaccine priming of rare HIV broadly neutralizing antibody precursors in nonhuman primates. Science 2024; 384:eadj8321. [PMID: 38753769 PMCID: PMC11309785 DOI: 10.1126/science.adj8321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 04/05/2024] [Indexed: 05/18/2024]
Abstract
Germline-targeting immunogens hold promise for initiating the induction of broadly neutralizing antibodies (bnAbs) to HIV and other pathogens. However, antibody-antigen recognition is typically dominated by heavy chain complementarity determining region 3 (HCDR3) interactions, and vaccine priming of HCDR3-dominant bnAbs by germline-targeting immunogens has not been demonstrated in humans or outbred animals. In this work, immunization with N332-GT5, an HIV envelope trimer designed to target precursors of the HCDR3-dominant bnAb BG18, primed bnAb-precursor B cells in eight of eight rhesus macaques to substantial frequencies and with diverse lineages in germinal center and memory B cells. We confirmed bnAb-mimicking, HCDR3-dominant, trimer-binding interactions with cryo-electron microscopy. Our results demonstrate proof of principle for HCDR3-dominant bnAb-precursor priming in outbred animals and suggest that N332-GT5 holds promise for the induction of similar responses in humans.
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Affiliation(s)
- Jon M Steichen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Ivy Phung
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for Vaccine Innovation, La Jolla Institute for Immunology; La Jolla, CA 92037, USA
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego; La Jolla, CA 92037, USA
| | - Eugenia Salcedo
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Gabriel Ozorowski
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Jordan R. Willis
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Sabyasachi Baboo
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alessia Liguori
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Christopher A. Cottrell
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Jonathan L. Torres
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Patrick J. Madden
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for Vaccine Innovation, La Jolla Institute for Immunology; La Jolla, CA 92037, USA
| | - Krystal M. Ma
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Henry J. Sutton
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for Vaccine Innovation, La Jolla Institute for Immunology; La Jolla, CA 92037, USA
| | - Jeong Hyun Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Joel D. Allen
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Oscar L. Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Yumiko Adachi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Tina-Marie Mullen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Erik Georgeson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Michael Kubitz
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Alison Burns
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Shawn Barman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Rohini Mopuri
- Division of Microbiology and Immunology, Emory National Primate Research Center; Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Amanda Metz
- Division of Microbiology and Immunology, Emory National Primate Research Center; Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Tasha K. Altheide
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for Vaccine Innovation, La Jolla Institute for Immunology; La Jolla, CA 92037, USA
| | - Jolene K. Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Swati Saha
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Kaitlyn Shields
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Steven E. Schultze
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Melissa L. Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Torben Schiffner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
- Ragon Institute of MGH, MIT & Harvard, Cambridge, MA 02139, USA
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Steven E. Bosinger
- Division of Microbiology and Immunology, Emory National Primate Research Center; Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Max Crispin
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - John R. Yates
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James C. Paulson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B. Ward
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Shane Crotty
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for Vaccine Innovation, La Jolla Institute for Immunology; La Jolla, CA 92037, USA
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego; La Jolla, CA 92037, USA
| | - William R. Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla; CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute; La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute; La Jolla, CA 92037, USA
- Ragon Institute of MGH, MIT & Harvard, Cambridge, MA 02139, USA
- Moderna, Inc., Cambridge, MA 02139, USA
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29
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Jensen CG, Sumner JA, Kleinstein SH, Hoehn KB. Inferring B Cell Phylogenies from Paired H and L Chain BCR Sequences with Dowser. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1579-1588. [PMID: 38557795 PMCID: PMC11073909 DOI: 10.4049/jimmunol.2300851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Abstract
Abs are vital to human immune responses and are composed of genetically variable H and L chains. These structures are initially expressed as BCRs. BCR diversity is shaped through somatic hypermutation and selection during immune responses. This evolutionary process produces B cell clones, cells that descend from a common ancestor but differ by mutations. Phylogenetic trees inferred from BCR sequences can reconstruct the history of mutations within a clone. Until recently, BCR sequencing technologies separated H and L chains, but advancements in single-cell sequencing now pair H and L chains from individual cells. However, it is unclear how these separate genes should be combined to infer B cell phylogenies. In this study, we investigated strategies for using paired H and L chain sequences to build phylogenetic trees. We found that incorporating L chains significantly improved tree accuracy and reproducibility across all methods tested. This improvement was greater than the difference between tree-building methods and persisted even when mixing bulk and single-cell sequencing data. However, we also found that many phylogenetic methods estimated significantly biased branch lengths when some L chains were missing, such as when mixing single-cell and bulk BCR data. This bias was eliminated using maximum likelihood methods with separate branch lengths for H and L chain gene partitions. Thus, we recommend using maximum likelihood methods with separate H and L chain partitions, especially when mixing data types. We implemented these methods in the R package Dowser: https://dowser.readthedocs.io.
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Affiliation(s)
- Cole G. Jensen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Jacob A. Sumner
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, 06520, USA
| | - Steven H. Kleinstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Kenneth B. Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Current address: Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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30
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Pacheco GA, Rao V, Yoo DK, Saghaei S, Tong P, Kumar S, Marini-Rapoport O, Allahyari Z, Moghaddam AS, Esbati R, Alirezaee A, Parnes A, Patil SU, Wesemann DR. Origins and diversity of pan-isotype human bone marrow plasma cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.592267. [PMID: 38766053 PMCID: PMC11100731 DOI: 10.1101/2024.05.08.592267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Bone marrow plasma cells (BMPCs) produce durable, protective IgM, IgG, and IgA antibodies, and in some cases, pro-allergic IgE antibodies, but their properties and sources are unclear. We charted single BMPC transcriptional and clonal heterogeneity in food-allergic and non-allergic individuals across CD19 protein expression given its inverse correlation to BMPC longevity. Transcriptional and clonal diversity revealed distinct functional profiles. Additionally, distribution of somatic hypermutation and intraclonal antibody sequence variance suggest that CD19low and CD19high BMPCs arise from recalled memory and germinal center B cells, respectively. Most IgE BMPCs were from peanut-allergic individuals; two out of 32 from independent donors bound peanut antigens in vitro and in vivo. These findings shed light on BMPC origins and highlight the bone marrow as a source of pathogenic IgE in peanut allergy.
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Affiliation(s)
- Gaspar A. Pacheco
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital; Boston, MA 02115, USA
- Harvard Medical School; Boston, MA 02115, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02124, USA
- The Ragon Institute of MGH, MIT and Harvard; Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness; Boston, MA 02115, USA
| | - Vishal Rao
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital; Boston, MA 02115, USA
- Harvard Medical School; Boston, MA 02115, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02124, USA
- The Ragon Institute of MGH, MIT and Harvard; Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness; Boston, MA 02115, USA
| | - Duck Kyun Yoo
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital; Boston, MA 02115, USA
- Harvard Medical School; Boston, MA 02115, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02124, USA
- The Ragon Institute of MGH, MIT and Harvard; Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness; Boston, MA 02115, USA
| | - Shahab Saghaei
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital; Boston, MA 02115, USA
- Harvard Medical School; Boston, MA 02115, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02124, USA
- The Ragon Institute of MGH, MIT and Harvard; Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness; Boston, MA 02115, USA
| | - Pei Tong
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital; Boston, MA 02115, USA
- Harvard Medical School; Boston, MA 02115, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02124, USA
- The Ragon Institute of MGH, MIT and Harvard; Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness; Boston, MA 02115, USA
| | - Sachin Kumar
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital; Boston, MA 02115, USA
- Harvard Medical School; Boston, MA 02115, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02124, USA
- The Ragon Institute of MGH, MIT and Harvard; Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness; Boston, MA 02115, USA
| | - Orlee Marini-Rapoport
- Food Allergy Center and Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital; Boston, MA 02115, USA
| | - Zahra Allahyari
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital; Boston, MA 02115, USA
- Harvard Medical School; Boston, MA 02115, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02124, USA
- The Ragon Institute of MGH, MIT and Harvard; Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness; Boston, MA 02115, USA
| | - Ali S. Moghaddam
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital; Boston, MA 02115, USA
- Harvard Medical School; Boston, MA 02115, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02124, USA
- The Ragon Institute of MGH, MIT and Harvard; Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness; Boston, MA 02115, USA
| | - Romina Esbati
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital; Boston, MA 02115, USA
- Harvard Medical School; Boston, MA 02115, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02124, USA
- The Ragon Institute of MGH, MIT and Harvard; Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness; Boston, MA 02115, USA
| | - Aida Alirezaee
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital; Boston, MA 02115, USA
- Harvard Medical School; Boston, MA 02115, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02124, USA
- The Ragon Institute of MGH, MIT and Harvard; Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness; Boston, MA 02115, USA
| | - Aric Parnes
- Department of Medicine, Division of Hematology, Brigham and Women’s Hospital; Boston, MA 02115, USA
| | - Sarita U. Patil
- Food Allergy Center and Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital; Boston, MA 02115, USA
| | - Duane R. Wesemann
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital; Boston, MA 02115, USA
- Harvard Medical School; Boston, MA 02115, USA
- The Broad Institute of MIT and Harvard; Cambridge, MA 02124, USA
- The Ragon Institute of MGH, MIT and Harvard; Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness; Boston, MA 02115, USA
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31
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Hahn WO, Parks KR, Shen M, Ozorowski G, Janes H, Ballweber-Fleming L, Woodward Davis AS, Duplessis C, Tomai M, Dey AK, Sagawa ZK, De Rosa SC, Seese A, Siddaramaiah LK, Stamatatos L, Lee WH, Sewall LM, Karlinsey D, Turner HL, Rubin V, Furth S, MacPhee K, Duff M, Corey L, Keefer MC, Edupuganti S, Frank I, Maenza J, Baden LR, Hyrien O, Sanders RW, Moore JP, Ward AB, Tomaras GD, Montefiori DC, Rouphael N, McElrath MJ. HIV BG505 SOSIP.664 trimer with 3M-052-AF/alum induces human autologous tier-2 neutralizing antibodies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.08.24306957. [PMID: 38766048 PMCID: PMC11100857 DOI: 10.1101/2024.05.08.24306957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Stabilized trimers preserving the native-like HIV envelope structure may be key components of a preventive HIV vaccine regimen to induce broadly neutralizing antibodies (bnAbs). We evaluated trimeric BG505 SOSIP.664 gp140, formulated with a novel TLR7/8 signaling adjuvant, 3M-052-AF/Alum, for safety, adjuvant dose-finding and immunogenicity in a first-in-healthy adult (n=17), randomized, placebo-controlled trial (HVTN 137A). The vaccine regimen appeared safe. Robust, trimer-specific antibody, B-cell and CD4+ T-cell responses emerged post-vaccination. Five vaccinees developed serum autologous tier-2 nAbs (ID50 titer, 1:28-1:8647) after 2-3 doses targeting C3/V5 and/or V1/V2/V3 Env regions by electron microscopy and mutated pseudovirus-based neutralization analyses. Trimer-specific, B-cell-derived monoclonal antibody activities confirmed these results and showed weak heterologous neutralization in the strongest responder. Our findings demonstrate the clinical utility of the 3M-052-AF/alum adjuvant and support further improvements of trimer-based Env immunogens to focus responses on multiple broad nAb epitopes. KEY TAKEAWAY/TAKE-HOME MESSAGES HIV BG505 SOSIP.664 trimer with novel 3M-052-AF/alum adjuvant in humans appears safe and induces serum neutralizing antibodies to matched clade A, tier 2 virus, that map to diverse Env epitopes with relatively high titers. The novel adjuvant may be an important mediator of vaccine response.
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32
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Ma J, Wu Y, Ma L, Yang X, Zhang T, Song G, Li T, Gao K, Shen X, Lin J, Chen Y, Liu X, Fu Y, Gu X, Chen Z, Jiang S, Rao D, Pan J, Zhang S, Zhou J, Huang C, Shi S, Fan J, Guo G, Zhang X, Gao Q. A blueprint for tumor-infiltrating B cells across human cancers. Science 2024; 384:eadj4857. [PMID: 38696569 DOI: 10.1126/science.adj4857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 03/06/2024] [Indexed: 05/04/2024]
Abstract
B lymphocytes are essential mediators of humoral immunity and play multiple roles in human cancer. To decode the functions of tumor-infiltrating B cells, we generated a B cell blueprint encompassing single-cell transcriptome, B cell-receptor repertoire, and chromatin accessibility data across 20 different cancer types (477 samples, 269 patients). B cells harbored extraordinary heterogeneity and comprised 15 subsets, which could be grouped into two independent developmental paths (extrafollicular versus germinal center). Tumor types grouped into the extrafollicular pathway were linked with worse clinical outcomes and resistance to immunotherapy. The dysfunctional extrafollicular program was associated with glutamine-derived metabolites through epigenetic-metabolic cross-talk, which promoted a T cell-driven immunosuppressive program. These data suggest an intratumor B cell balance between extrafollicular and germinal-center responses and suggest that humoral immunity could possibly be harnessed for B cell-targeting immunotherapy.
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Affiliation(s)
- Jiaqiang Ma
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yingcheng Wu
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Lifeng Ma
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, and Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Xupeng Yang
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Tiancheng Zhang
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Guohe Song
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Teng Li
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ke Gao
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xia Shen
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jian Lin
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yamin Chen
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaoshan Liu
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuting Fu
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, and Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Xixi Gu
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zechuan Chen
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shan Jiang
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Dongning Rao
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jiaomeng Pan
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Shu Zhang
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Chen Huang
- Department of Gastrointestinal Surgery, Shanghai General Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200080, China
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Jia Fan
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, and Stem Cell Institute, Zhejiang University, Hangzhou 310058, China
| | - Xiaoming Zhang
- The Center for Microbes, Development and Health, Key Laboratory of Immune Response and Immunotherapy, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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33
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Thomas MF, Slowikowski K, Manakongtreecheep K, Sen P, Samanta N, Tantivit J, Nasrallah M, Zubiri L, Smith NP, Tirard A, Ramesh S, Arnold BY, Nieman LT, Chen JH, Eisenhaure T, Pelka K, Song Y, Xu KH, Jorgji V, Pinto CJ, Sharova T, Glasser R, Chan P, Sullivan RJ, Khalili H, Juric D, Boland GM, Dougan M, Hacohen N, Li B, Reynolds KL, Villani AC. Single-cell transcriptomic analyses reveal distinct immune cell contributions to epithelial barrier dysfunction in checkpoint inhibitor colitis. Nat Med 2024; 30:1349-1362. [PMID: 38724705 DOI: 10.1038/s41591-024-02895-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 03/01/2024] [Indexed: 05/23/2024]
Abstract
Immune checkpoint inhibitor (ICI) therapy has revolutionized oncology, but treatments are limited by immune-related adverse events, including checkpoint inhibitor colitis (irColitis). Little is understood about the pathogenic mechanisms driving irColitis, which does not readily occur in model organisms, such as mice. To define molecular drivers of irColitis, we used single-cell multi-omics to profile approximately 300,000 cells from the colon mucosa and blood of 13 patients with cancer who developed irColitis (nine on anti-PD-1 or anti-CTLA-4 monotherapy and four on dual ICI therapy; most patients had skin or lung cancer), eight controls on ICI therapy and eight healthy controls. Patients with irColitis showed expanded mucosal Tregs, ITGAEHi CD8 tissue-resident memory T cells expressing CXCL13 and Th17 gene programs and recirculating ITGB2Hi CD8 T cells. Cytotoxic GNLYHi CD4 T cells, recirculating ITGB2Hi CD8 T cells and endothelial cells expressing hypoxia gene programs were further expanded in colitis associated with anti-PD-1/CTLA-4 therapy compared to anti-PD-1 therapy. Luminal epithelial cells in patients with irColitis expressed PCSK9, PD-L1 and interferon-induced signatures associated with apoptosis, increased cell turnover and malabsorption. Together, these data suggest roles for circulating T cells and epithelial-immune crosstalk critical to PD-1/CTLA-4-dependent tolerance and barrier function and identify potential therapeutic targets for irColitis.
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Affiliation(s)
- Molly Fisher Thomas
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA.
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Division of Gastroenterology, Department of Medicine, Oregon Health and Sciences University, Portland, OR, USA.
- Department of Cell, Developmental, and Cancer Biology, Oregon Health and Sciences University, Portland, OR, USA.
| | - Kamil Slowikowski
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA.
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Kasidet Manakongtreecheep
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Pritha Sen
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Transplant, Oncology, and Immunocompromised Host Group, Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nandini Samanta
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Jessica Tantivit
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Mazen Nasrallah
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Department of Medicine, North Shore Physicians Group, Mass General Brigham Healthcare Center, Lynn, MA, USA
| | - Leyre Zubiri
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Neal P Smith
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Alice Tirard
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Swetha Ramesh
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Benjamin Y Arnold
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Linda T Nieman
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jonathan H Chen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Thomas Eisenhaure
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Karin Pelka
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Yuhui Song
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Katherine H Xu
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Vjola Jorgji
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Tatyana Sharova
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Rachel Glasser
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - PuiYee Chan
- Harvard Medical School, Boston, MA, USA
- Clinical Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Ryan J Sullivan
- Harvard Medical School, Boston, MA, USA
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Hamed Khalili
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Dejan Juric
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Genevieve M Boland
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Dougan
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nir Hacohen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Bo Li
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Kerry L Reynolds
- Harvard Medical School, Boston, MA, USA
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alexandra-Chloé Villani
- Department of Medicine, Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA.
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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34
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Irac SE, Soon MSF, Borcherding N, Tuong ZK. Single-cell immune repertoire analysis. Nat Methods 2024; 21:777-792. [PMID: 38637691 DOI: 10.1038/s41592-024-02243-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/12/2024] [Indexed: 04/20/2024]
Abstract
Single-cell T cell and B cell antigen receptor-sequencing data analysis can potentially perform in-depth assessments of adaptive immune cells that inform on understanding immune cell development to tracking clonal expansion in disease and therapy. However, it has been extremely challenging to analyze and interpret T cells and B cells and their adaptive immune receptor repertoires at the single-cell level due to not only the complexity of the data but also the underlying biology. In this Review, we delve into the computational breakthroughs that have transformed the analysis of single-cell T cell and B cell antigen receptor-sequencing data.
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Affiliation(s)
- Sergio E Irac
- Cancer Immunoregulation and Immunotherapy, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Megan Sioe Fei Soon
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicholas Borcherding
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Omniscope, Palo Alto, CA, USA
| | - Zewen Kelvin Tuong
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
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Lindeman I, Høydahl LS, Christophersen A, Risnes LF, Jahnsen J, Lundin KEA, Sollid LM, Iversen R. Generation of circulating autoreactive pre-plasma cells fueled by naive B cells in celiac disease. Cell Rep 2024; 43:114045. [PMID: 38578826 DOI: 10.1016/j.celrep.2024.114045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/22/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
Autoantibodies against the enzyme transglutaminase 2 (TG2) are characteristic of celiac disease (CeD), and TG2-specific immunoglobulin (Ig) A plasma cells are abundant in gut biopsies of patients. Here, we describe the corresponding population of autoreactive B cells in blood. Circulating TG2-specific IgA cells are present in untreated patients on a gluten-containing diet but not in controls. They are clonally related to TG2-specific small intestinal plasma cells, and they express gut-homing molecules, indicating that they are plasma cell precursors. Unlike other IgA-switched cells, the TG2-specific cells are negative for CD27, placing them in the double-negative (IgD-CD27-) category. They have a plasmablast or activated memory B cell phenotype, and they harbor fewer variable region mutations than other IgA cells. Based on their similarity to naive B cells, we propose that autoreactive IgA cells in CeD are generated mainly through chronic recruitment of naive B cells via an extrafollicular response involving gluten-specific CD4+ T cells.
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Affiliation(s)
- Ida Lindeman
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital - Rikshospitalet, Oslo, Norway
| | - Lene S Høydahl
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital - Rikshospitalet, Oslo, Norway
| | - Asbjørn Christophersen
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital - Rikshospitalet, Oslo, Norway
| | - Louise F Risnes
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital - Rikshospitalet, Oslo, Norway
| | - Jørgen Jahnsen
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - Knut E A Lundin
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Gastroenterology, Oslo University Hospital - Rikshospitalet, Oslo, Norway
| | - Ludvig M Sollid
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital - Rikshospitalet, Oslo, Norway
| | - Rasmus Iversen
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital - Rikshospitalet, Oslo, Norway.
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36
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Shehata L, Thouvenel CD, Hondowicz BD, Pew LA, Pritchard GH, Rawlings DJ, Choi J, Pepper M. Interleukin-4 downregulates transcription factor BCL6 to promote memory B cell selection in germinal centers. Immunity 2024; 57:843-858.e5. [PMID: 38513666 PMCID: PMC11104266 DOI: 10.1016/j.immuni.2024.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 08/04/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
Germinal center (GC)-derived memory B cells (MBCs) are critical for humoral immunity as they differentiate into protective antibody-secreting cells during re-infection. GC formation and cellular interactions within the GC have been studied in detail, yet the exact signals that allow for the selection and exit of MBCs are not understood. Here, we showed that IL-4 cytokine signaling in GC B cells directly downregulated the transcription factor BCL6 via negative autoregulation to release cells from the GC program and to promote MBC formation. This selection event required additional survival cues and could therefore result in either GC exit or death. We demonstrate that both increasing IL-4 bioavailability or limiting IL-4 signaling disrupted MBC selection stringency. In this way, IL-4 control of BCL6 expression serves as a tunable switch within the GC to tightly regulate MBC selection and affinity maturation.
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Affiliation(s)
- Laila Shehata
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Christopher D Thouvenel
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Brian D Hondowicz
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Lucia A Pew
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | | | - David J Rawlings
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA; Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Jinyong Choi
- Department of Microbiology, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, South Korea
| | - Marion Pepper
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA.
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37
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Grigoryan L, Feng Y, Bellusci L, Lai L, Wali B, Ellis M, Yuan M, Arunachalam PS, Hu M, Kowli S, Gupta S, Maysel-Auslender S, Maecker HT, Samaha H, Rouphael N, Wilson IA, Moreno AC, Suthar MS, Khurana S, Pillet S, Charland N, Ward BJ, Pulendran B. AS03 adjuvant enhances the magnitude, persistence, and clonal breadth of memory B cell responses to a plant-based COVID-19 vaccine in humans. Sci Immunol 2024; 9:eadi8039. [PMID: 38579013 DOI: 10.1126/sciimmunol.adi8039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 03/11/2024] [Indexed: 04/07/2024]
Abstract
Vaccine adjuvants increase the breadth of serum antibody responses, but whether this is due to the generation of antigen-specific B cell clones with distinct specificities or the maturation of memory B cell clones that produce broadly cross-reactive antibodies is unknown. Here, we longitudinally analyzed immune responses in healthy adults after two-dose vaccination with either a virus-like particle COVID-19 vaccine (CoVLP), CoVLP adjuvanted with AS03 (CoVLP+AS03), or a messenger RNA vaccination (mRNA-1273). CoVLP+AS03 enhanced the magnitude and durability of circulating antibodies and antigen-specific CD4+ T cell and memory B cell responses. Antigen-specific CD4+ T cells in the CoVLP+AS03 group at day 42 correlated with antigen-specific memory B cells at 6 months. CoVLP+AS03 induced memory B cell responses, which accumulated somatic hypermutations over 6 months, resulting in enhanced neutralization breadth of monoclonal antibodies. Furthermore, the fraction of broadly neutralizing antibodies encoded by memory B cells increased between day 42 and 6 months. These results indicate that AS03 enhances the antigenic breadth of B cell memory at the clonal level and induces progressive maturation of the B cell response.
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Affiliation(s)
- Lilit Grigoryan
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Yupeng Feng
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | | | - Lilin Lai
- Department of Pediatrics and Department of Microbiology and Immunology, Emory Vaccine Center, Emory National Primate Research Center, Emory School of Medicine, Atlanta, GA 30329, USA
| | - Bushra Wali
- Department of Pediatrics and Department of Microbiology and Immunology, Emory Vaccine Center, Emory National Primate Research Center, Emory School of Medicine, Atlanta, GA 30329, USA
| | - Madison Ellis
- Department of Pediatrics and Department of Microbiology and Immunology, Emory Vaccine Center, Emory National Primate Research Center, Emory School of Medicine, Atlanta, GA 30329, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mengyun Hu
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sangeeta Kowli
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sheena Gupta
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Sofia Maysel-Auslender
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Holden T Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Hady Samaha
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nadine Rouphael
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
- Hope Clinic of Emory Vaccine Center, Emory University, Decatur, GA 30030, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alberto C Moreno
- Department of Medicine, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Mehul S Suthar
- Department of Pediatrics and Department of Microbiology and Immunology, Emory Vaccine Center, Emory National Primate Research Center, Emory School of Medicine, Atlanta, GA 30329, USA
| | | | - Stéphane Pillet
- Medicago Inc., Québec, QC G1V 3V9, Canada
- Research Institute of the McGill University Health Center, 1001 Decarie St., Montréal, QC H4A 3J1, Canada
| | | | - Brian J Ward
- Medicago Inc., Québec, QC G1V 3V9, Canada
- Research Institute of the McGill University Health Center, 1001 Decarie St., Montréal, QC H4A 3J1, Canada
| | - Bali Pulendran
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
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38
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Fitzpatrick Z, Ghabdan Zanluqui N, Rosenblum JS, Tuong ZK, Lee CYC, Chandrashekhar V, Negro-Demontel ML, Stewart AP, Posner DA, Buckley M, Allinson KSJ, Mastorakos P, Chittiboina P, Maric D, Donahue D, Helmy A, Tajsic T, Ferdinand JR, Portet A, Peñalver A, Gillman E, Zhuang Z, Clatworthy MR, McGavern DB. Venous-plexus-associated lymphoid hubs support meningeal humoral immunity. Nature 2024; 628:612-619. [PMID: 38509366 DOI: 10.1038/s41586-024-07202-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 02/16/2024] [Indexed: 03/22/2024]
Abstract
There is increasing interest in how immune cells in the meninges-the membranes that surround the brain and spinal cord-contribute to homeostasis and disease in the central nervous system1,2. The outer layer of the meninges, the dura mater, has recently been described to contain both innate and adaptive immune cells, and functions as a site for B cell development3-6. Here we identify organized lymphoid structures that protect fenestrated vasculature in the dura mater. The most elaborate of these dural-associated lymphoid tissues (DALT) surrounded the rostral-rhinal confluence of the sinuses and included lymphatic vessels. We termed this structure, which interfaces with the skull bone marrow and a comparable venous plexus at the skull base, the rostral-rhinal venolymphatic hub. Immune aggregates were present in DALT during homeostasis and expanded with age or after challenge with systemic or nasal antigens. DALT contain germinal centre B cells and support the generation of somatically mutated, antibody-producing cells in response to a nasal pathogen challenge. Inhibition of lymphocyte entry into the rostral-rhinal hub at the time of nasal viral challenge abrogated the generation of germinal centre B cells and class-switched plasma cells, as did perturbation of B-T cell interactions. These data demonstrate a lymphoid structure around vasculature in the dura mater that can sample antigens and rapidly support humoral immune responses after local pathogen challenge.
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Affiliation(s)
- Zachary Fitzpatrick
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institute of Health (NIH), Bethesda, MD, USA
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nagela Ghabdan Zanluqui
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institute of Health (NIH), Bethesda, MD, USA
| | | | - Zewen Kelvin Tuong
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Colin Y C Lee
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | | | - Maria Luciana Negro-Demontel
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institute of Health (NIH), Bethesda, MD, USA
| | - Andrew P Stewart
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - David A Posner
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Monica Buckley
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institute of Health (NIH), Bethesda, MD, USA
| | - Kieren S J Allinson
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Panagiotis Mastorakos
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institute of Health (NIH), Bethesda, MD, USA
- Department of Surgical Neurology, NINDS, NIH, Bethesda, MD, USA
| | | | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, NINDS, NIH, Bethesda, MD, USA
| | | | - Adel Helmy
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Tamara Tajsic
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - John R Ferdinand
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Anais Portet
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ana Peñalver
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Eleanor Gillman
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Zhengping Zhuang
- Neuro-Oncology Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK.
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK.
| | - Dorian B McGavern
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institute of Health (NIH), Bethesda, MD, USA.
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He S, Liu SQ, Teng XY, He JY, Liu Y, Gao JH, Wu Y, Hu W, Dong ZJ, Bei JX, Xu JH. Comparative single-cell RNA sequencing analysis of immune response to inactivated vaccine and natural SARS-CoV-2 infection. J Med Virol 2024; 96:e29577. [PMID: 38572977 DOI: 10.1002/jmv.29577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 03/02/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Uncovering the immune response to an inactivated SARS-CoV-2 vaccine (In-Vac) and natural infection is crucial for comprehending COVID-19 immunology. Here we conducted an integrated analysis of single-cell RNA sequencing (scRNA-seq) data from serial peripheral blood mononuclear cell (PBMC) samples derived from 12 individuals receiving In-Vac compared with those from COVID-19 patients. Our study reveals that In-Vac induces subtle immunological changes in PBMC, including cell proportions and transcriptomes, compared with profound changes for natural infection. In-Vac modestly upregulates IFN-α but downregulates NF-κB pathways, while natural infection triggers hyperactive IFN-α and NF-κB pathways. Both In-Vac and natural infection alter T/B cell receptor repertoires, but COVID-19 has more significant change in preferential VJ gene, indicating a vigorous immune response. Our study reveals distinct patterns of cellular communications, including a selective activation of IL-15RA/IL-15 receptor pathway after In-Vac boost, suggesting its potential role in enhancing In-Vac-induced immunity. Collectively, our study illuminates multifaceted immune responses to In-Vac and natural infection, providing insights for optimizing SARS-CoV-2 vaccine efficacy.
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Affiliation(s)
- Shuai He
- Medical Laboratory Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shu-Qiang Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiang-Yun Teng
- Medical Laboratory Center, Maoming Hospital of Guangzhou University of Chinese Medicine, Maoming, China
| | - Jin-Yong He
- Medical Laboratory Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Yang Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jia-Hui Gao
- Medical Laboratory Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Yue Wu
- Medical Laboratory Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Wei Hu
- Medical Laboratory Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Zhong-Jun Dong
- School of Medicine and Institute for Immunology, Tsinghua University, Beijing, China
| | - Jin-Xin Bei
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jian-Hua Xu
- Medical Laboratory Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
- Medical Laboratory Center, Maoming Hospital of Guangzhou University of Chinese Medicine, Maoming, China
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40
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Beaulaurier J, Ly L, Duty JA, Tyer C, Stevens C, Hung CT, Sookdeo A, Drong AW, Kowdle S, Turner DJ, Juul S, Hickey S, Lee B. De novo antibody discovery in human blood from full-length single B cell transcriptomics and matching haplotyped-resolved germline assemblies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586834. [PMID: 38585716 PMCID: PMC10996687 DOI: 10.1101/2024.03.26.586834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Immunoglobulin (IGH, IGK, IGL) loci in the human genome are highly polymorphic regions that encode the building blocks of the light and heavy chain IG proteins that dimerize to form antibodies. The processes of V(D)J recombination and somatic hypermutation in B cells are responsible for creating an enormous reservoir of highly specific antibodies capable of binding a vast array of possible antigens. However, the antibody repertoire is fundamentally limited by the set of variable (V), diversity (D), and joining (J) alleles present in the germline IG loci. To better understand how the germline IG haplotypes contribute to the expressed antibody repertoire, we combined genome sequencing of the germline IG loci with single-cell transcriptome sequencing of B cells from the same donor. Sequencing and assembly of the germline IG loci captured the IGH locus in a single fully-phased contig where the maternal and paternal contributions to the germline V, D, and J repertoire can be fully resolved. The B cells were collected following a measles, mumps, and rubella (MMR) vaccination, resulting in a population of cells that were activated in response to this specific immune challenge. Single-cell, full-length transcriptome sequencing of these B cells resulted in whole transcriptome characterization of each cell, as well as highly-accurate consensus sequences for the somatically rearranged and hypermutated light and heavy chain IG transcripts. A subset of antibodies synthesized based on their consensus heavy and light chain transcript sequences demonstrated binding to measles antigens and neutralization of measles live virus.
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41
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Peres A, Klein V, Frankel B, Lees W, Polak P, Meehan M, Rocha A, Correia Lopes J, Yaari G. Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data. Brief Bioinform 2024; 25:bbae221. [PMID: 38752856 PMCID: PMC11097599 DOI: 10.1093/bib/bbae221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 03/06/2024] [Accepted: 04/18/2024] [Indexed: 05/19/2024] Open
Abstract
Enhancing the reproducibility and comprehension of adaptive immune receptor repertoire sequencing (AIRR-seq) data analysis is critical for scientific progress. This study presents guidelines for reproducible AIRR-seq data analysis, and a collection of ready-to-use pipelines with comprehensive documentation. To this end, ten common pipelines were implemented using ViaFoundry, a user-friendly interface for pipeline management and automation. This is accompanied by versioned containers, documentation and archiving capabilities. The automation of pre-processing analysis steps and the ability to modify pipeline parameters according to specific research needs are emphasized. AIRR-seq data analysis is highly sensitive to varying parameters and setups; using the guidelines presented here, the ability to reproduce previously published results is demonstrated. This work promotes transparency, reproducibility, and collaboration in AIRR-seq data analysis, serving as a model for handling and documenting bioinformatics pipelines in other research domains.
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Affiliation(s)
- Ayelet Peres
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university, 5290002 Ramat Gan, Israel
| | - Vered Klein
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university, 5290002 Ramat Gan, Israel
| | - Boaz Frankel
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university, 5290002 Ramat Gan, Israel
| | - William Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
- INESC TEC – Institute for Systems and Computer Engineering, Technology and Science Porto, Portugal
| | - Pazit Polak
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university, 5290002 Ramat Gan, Israel
| | - Mark Meehan
- INESC TEC – Institute for Systems and Computer Engineering, Technology and Science Porto, Portugal
| | - Artur Rocha
- INESC TEC – Institute for Systems and Computer Engineering, Technology and Science Porto, Portugal
| | - João Correia Lopes
- INESC TEC – Institute for Systems and Computer Engineering, Technology and Science Porto, Portugal
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan institute of nanotechnology and advanced materials, Bar Ilan university, 5290002 Ramat Gan, Israel
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Abdullah L, Emiliani FE, Vaidya CM, Stuart H, Kolling FW, Ackerman ME, Song L, McKenna A, Huang YH. Hierarchal single-cell lineage tracing reveals differential fate commitment of CD8 T-cell clones in response to acute infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586160. [PMID: 38585810 PMCID: PMC10996474 DOI: 10.1101/2024.03.21.586160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Generating balanced populations of CD8 effector and memory T cells is necessary for immediate and durable immunity to infections and cancer. Yet, a definitive understanding of CD8 differentiation remains unclear. We used CARLIN, a processive lineage recording mouse model with single-cell RNA-seq and TCR-seq to track endogenous antigen-specific CD8 T cells during acute viral infection. We identified a diverse repertoire of expanded T-cell clones represented by seven transcriptional states. TCR enrichment analysis revealed differential memory- or effector-fate biases within clonal populations. Shared Vb segments and amino acid motifs were found within biased categories despite high TCR diversity. Using single-cell CARLIN barcode-seq we tracked multi-generational clones and found that unlike unbiased or memory-biased clones, which stably retain their fate profiles, effector-biased clones could adopt memory- or effector-bias within subclones. Collectively, our study demonstrates that a heterogenous T-cell repertoire specific for a shared antigen is composed of clones with distinct TCR-intrinsic fate-biases.
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Affiliation(s)
- Leena Abdullah
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Francesco E. Emiliani
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Chinmay M. Vaidya
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | - Hannah Stuart
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | | | - Margaret E. Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
| | - Li Song
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
| | - Aaron McKenna
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
| | - Yina H. Huang
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
- Department of Pathology and Laboratory Medicine, Dartmouth Health, Lebanon, NH 03756, USA
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Nguyen A, Zhao H, Myagmarsuren D, Srinivasan S, Wu D, Chen J, Piszczek G, Schuck P. Modulation of Biophysical Properties of Nucleocapsid Protein in the Mutant Spectrum of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.21.568093. [PMID: 38045241 PMCID: PMC10690151 DOI: 10.1101/2023.11.21.568093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage of the uniquely large genomic database of SARS-CoV-2, we examine the impact of mutations across the spectrum of viable amino acid sequences on the biophysical phenotypes of the highly expressed and multifunctional nucleocapsid protein. We find variation in the physicochemical parameters of its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also exhibiting functional constraints that similarly occur in related coronaviruses. In biophysical experiments with several N-protein species carrying mutations associated with major variants, we find that point mutations in the IDRs can have nonlocal impact and modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, and liquid-liquid phase separation. In the Omicron variant, distant mutations in different IDRs have compensatory effects in shifting a delicate balance of interactions controlling protein assembly properties, and include the creation of a new protein-protein interaction interface in the N-terminal IDR through the defining P13L mutation. A picture emerges where genetic diversity is accompanied by significant variation in biophysical characteristics of functional N-protein species, in particular in the IDRs.
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Affiliation(s)
- Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dulguun Myagmarsuren
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sanjana Srinivasan
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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Lee H, Shin K, Lee Y, Lee S, Lee S, Lee E, Kim SW, Shin HY, Kim JH, Chung J, Kwon S. Identification of B cell subsets based on antigen receptor sequences using deep learning. Front Immunol 2024; 15:1342285. [PMID: 38576618 PMCID: PMC10991714 DOI: 10.3389/fimmu.2024.1342285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/07/2024] [Indexed: 04/06/2024] Open
Abstract
B cell receptors (BCRs) denote antigen specificity, while corresponding cell subsets indicate B cell functionality. Since each B cell uniquely encodes this combination, physical isolation and subsequent processing of individual B cells become indispensable to identify both attributes. However, this approach accompanies high costs and inevitable information loss, hindering high-throughput investigation of B cell populations. Here, we present BCR-SORT, a deep learning model that predicts cell subsets from their corresponding BCR sequences by leveraging B cell activation and maturation signatures encoded within BCR sequences. Subsequently, BCR-SORT is demonstrated to improve reconstruction of BCR phylogenetic trees, and reproduce results consistent with those verified using physical isolation-based methods or prior knowledge. Notably, when applied to BCR sequences from COVID-19 vaccine recipients, it revealed inter-individual heterogeneity of evolutionary trajectories towards Omicron-binding memory B cells. Overall, BCR-SORT offers great potential to improve our understanding of B cell responses.
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Affiliation(s)
- Hyunho Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Kyoungseob Shin
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Yongju Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Soobin Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Seungyoun Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eunjae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung Woo Kim
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ha Young Shin
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Hoon Kim
- Department of Dermatology and Cutaneous Biology Research Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
- Inter-University Semiconductor Research Center, Seoul National University, Seoul, Republic of Korea
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Pollastro S, Musters A, Balzaretti G, Niewold I, van Schaik B, Hässler S, Verhoef CM, Pallardy M, van Kampen A, Mariette X, de Vries N. Sensitive B-cell receptor repertoire analysis shows repopulation correlates with clinical response to rituximab in rheumatoid arthritis. Arthritis Res Ther 2024; 26:70. [PMID: 38493208 PMCID: PMC10943808 DOI: 10.1186/s13075-024-03297-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Although B-cell depleting therapy in rheumatoid arthritis (RA) is clearly effective, response is variable and does not correlate with B cell depletion itself. METHODS The B-cell receptor (BCR) repertoire was prospectively analyzed in peripheral blood samples of twenty-eight RA patients undergoing rituximab therapy. Timepoints of achieved BCR-depletion and -repopulation were defined based on the percentage of unmutated BCRs in the repertoire. The predictive value of early BCR-depletion (within one-month post-treatment) and early BCR-repopulation (within 6 months post-treatment) on clinical response was assessed. RESULTS We observed changes in the peripheral blood BCR repertoire after rituximab treatment, i.e., increased clonal expansion, decreased clonal diversification and increased mutation load which persisted up to 12 months after treatment, but started to revert at month 6. Early BCR depletion was not associated with early clinical response but late depleters did show early response. Patients with early repopulation with unmutated BCRs showed a significant decrease in disease activity in the interval 6 to 12 months. Development of anti-drug antibodies non-significantly correlated with more BCR repopulation. CONCLUSION Our findings indicate that rather than BCR-depletion it is repopulation with unmutated BCRs, possibly from naïve B cells, which induces remission. This suggests that (pre-existing) differences in B-cell turnover between patients explain the interindividual differences in early clinical effect.
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Affiliation(s)
- Sabrina Pollastro
- Department of Clinical Immunology & Rheumatology | Amsterdam Rheumatology & Immunology Centre (ARC), Amsterdam UMC location AMC, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute | Program Inflammatory Diseases, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Anne Musters
- Department of Clinical Immunology & Rheumatology | Amsterdam Rheumatology & Immunology Centre (ARC), Amsterdam UMC location AMC, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Giulia Balzaretti
- Department of Clinical Immunology & Rheumatology | Amsterdam Rheumatology & Immunology Centre (ARC), Amsterdam UMC location AMC, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute | Program Inflammatory Diseases, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ilse Niewold
- Department of Clinical Immunology & Rheumatology | Amsterdam Rheumatology & Immunology Centre (ARC), Amsterdam UMC location AMC, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Barbera van Schaik
- Epidemiology and Data Science, Amsterdam Public Health research institute, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Signe Hässler
- Université Paris Saclay, INSERM U1018, CESP, Villejuif, France
- INSERM UMR 959, Immunology-Immunopathology-Immunotherapy (i3), Sorbonne Université, Paris, France
- Publique Hôpitaux de Paris, Hôpital Pitié Salpêtrière, Biotherapy (CIC-BTi), Paris, France
| | | | - Marc Pallardy
- Université Paris-Saclay, INSERM, Inflammation, Microbiome, Immunosurveillance, Châtenay-Malabry, France
| | - Antoine van Kampen
- Epidemiology and Data Science, Amsterdam Public Health research institute, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Xavier Mariette
- Université Paris-Saclay, INSERM UMR1184: Center for immunology of viral infections and autoimmune diseases, Le Kremlin Bicêtre, France
- Department of Rheumatology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Bicêtre, Le Kremlin Bicêtre, France
| | - Niek de Vries
- Department of Clinical Immunology & Rheumatology | Amsterdam Rheumatology & Immunology Centre (ARC), Amsterdam UMC location AMC, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute | Program Inflammatory Diseases, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, The Netherlands.
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Li S, Hu X, Wang M, Yu L, Zhang Q, Xiao J, Hong Z, Zhou D, Li J. Single-cell RNA sequencing reveals diverse B cell phenotypes in patients with anti-NMDAR encephalitis. Psychiatry Clin Neurosci 2024; 78:197-208. [PMID: 38063052 DOI: 10.1111/pcn.13627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUNDS Anti-N-methyl-D-aspartate receptor encephalitis (NMDAR-E) is a severe autoimmune disorder characterized by prominent psychiatric symptoms. Although the role of NMDAR antibodies in the disease has been extensively studied, the phenotype of B cell subsets is still not fully understood. METHODS We utilized single-cell RNA sequencing, single-cell B cell receptor sequencing (scBCR-seq), bulk BCR sequencing, flow cytometry, and enzyme-linked immunosorbent assay to analyze samples from both NMDAR-E patients and control individuals. RESULTS The cerebrospinal fluid (CSF) of NMDAR-E patients showed significantly increased B cell counts, predominantly memory B (Bm) cells. CSF Bm cells in NMDAR-E patients exhibited upregulated expression of differential expression genes (DEGs) associated with immune regulatory function (TNFRSF13B and ITGB1), whereas peripheral B cells upregulated DEGs related to antigen presentation. Additionally, NMDAR-E patients displayed higher levels of IgD- CD27- double negative (DN) cells and DN3 cells in peripheral blood (PB). In vitro, DN1 cell subsets from NMDAR-E patients differentiated into DN2 and DN3 cells, while CD27+ and/or IgD+ B cells (non-DN) differentiated into antibody-secreting cells (ASCs) and DN cells. NR1-IgG antibodies were found in B cell culture supernatants from patients. Differential expression of B cell IGHV genes in CSF and PB of NMDAR-E patients suggests potential antigen class switching. CONCLUSION B cell subpopulations in the CSF and PB of NMDAR-E patients exhibit distinct compositions and transcriptomic features. In vitro, non-DN cells from NMDAR-E can differentiate into DN cells and ASCs, potentially producing NR1-IgG antibodies. Further research is necessary to investigate the potential contribution of DN cell subpopulations to NR1-IgG antibody production.
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Affiliation(s)
- Sisi Li
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Department of Breast Cancer, Chongqing University Cancer Hospital, Chongqing, China
| | - Xiang Hu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Minjin Wang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Luoting Yu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Qi Zhang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Xiao
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
| | - Zhen Hong
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
| | - Dong Zhou
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
| | - Jinmei Li
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
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Guo S, Mohan GS, Wang B, Li T, Daver N, Zhao Y, Reville PK, Hao D, Abbas HA. Paired single-B-cell transcriptomics and receptor sequencing reveal activation states and clonal signatures that characterize B cells in acute myeloid leukemia. J Immunother Cancer 2024; 12:e008318. [PMID: 38418394 PMCID: PMC10910691 DOI: 10.1136/jitc-2023-008318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2024] [Indexed: 03/01/2024] Open
Abstract
BACKGROUND Acute myeloid leukemia (AML) is associated with a dismal prognosis. Immune checkpoint blockade (ICB) to induce antitumor activity in AML patients has yielded mixed results. Despite the pivotal role of B cells in antitumor immunity, a comprehensive assessment of B lymphocytes within AML's immunological microenvironment along with their interaction with ICB remains rather constrained. METHODS We performed an extensive analysis that involved paired single-cell RNA and B-cell receptor (BCR) sequencing on 52 bone marrow aspirate samples. These samples included 6 from healthy bone marrow donors (normal), 24 from newly diagnosed AML patients (NewlyDx), and 22 from 8 relapsed or refractory AML patients (RelRef), who underwent assessment both before and after azacitidine/nivolumab treatment. RESULTS We delineated nine distinct subtypes of B cell lineage in the bone marrow. AML patients exhibited reduced nascent B cell subgroups but increased differentiated B cells compared with healthy controls. The limited diversity of BCR profiles and extensive somatic hypermutation indicated antigen-driven affinity maturation within the tumor microenvironment of RelRef patients. We established a strong connection between the activation or stress status of naïve and memory B cells, as indicated by AP-1 activity, and their differentiation state. Remarkably, atypical memory B cells functioned as specialized antigen-presenting cells closely interacting with AML malignant cells, correlating with AML stemness and worse clinical outcomes. In the AML microenvironment, plasma cells demonstrated advanced differentiation and heightened activity. Notably, the clinical response to ICB was associated with B cell clonal expansion and plasma cell function. CONCLUSIONS Our findings establish a comprehensive framework for profiling the phenotypic diversity of the B cell lineage in AML patients, while also assessing the implications of immunotherapy. This will serve as a valuable guide for future inquiries into AML treatment strategies.
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Affiliation(s)
- Shengnan Guo
- School of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang, China
| | - Gopi S Mohan
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Bofei Wang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tianhao Li
- School of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang, China
| | - Naval Daver
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yuting Zhao
- School of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang, China
| | - Patrick K Reville
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dapeng Hao
- School of Basic Medical Sciences, Harbin Medical University, Harbin, Heilongjiang, China
| | - Hussein A Abbas
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Kumar S, Bajpai P, Joyce C, Kabra SK, Lodha R, Burton DR, Briney B, Luthra K. B cell repertoire sequencing of HIV-1 pediatric elite-neutralizers identifies multiple broadly neutralizing antibody clonotypes. Front Immunol 2024; 15:1272493. [PMID: 38433846 PMCID: PMC10905035 DOI: 10.3389/fimmu.2024.1272493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/02/2024] [Indexed: 03/05/2024] Open
Abstract
Introduction A limited subset of HIV-1 infected adult individuals typically after at least 2-3 years of chronic infection, develop broadly neutralizing antibodies (bnAbs), suggesting that highly conserved neutralizing epitopes on the HIV-1 envelope glycoprotein are difficult for B cell receptors to effectively target, during natural infection. Recent studies have shown the evolution of bnAbs in HIV-1 infected infants. Methods We used bulk BCR sequencing (BCR-seq) to profile the B cell receptors from longitudinal samples (3 time points) collected from a rare pair of antiretroviralnaïve, HIV-1 infected pediatric monozygotic twins (AIIMS_329 and AIIMS_330) who displayed elite plasma neutralizing activity against HIV-1. Results BCR-seq of both twins revealed convergent antibody characteristics including V-gene use, CDRH3 lengths and somatic hypermutation (SHM). Further, antibody clonotypes with genetic features similar to highly potent bnAbs isolated from adults showed ongoing development in donor AIIMS_330 but not in AIIMS_329, corroborating our earlier findings based on plasma bnAbs responses. An increase in SHM was observed in sequences of the IgA isotype from AIIMS_330. Discussion This study suggests that children living with chronic HIV-1 can develop clonotypes of HIV-1 bnAbs against multiple envelope epitopes similar to those isolated from adults, highlighting that such B cells could be steered to elicit bnAbs responses through vaccines aimed to induce bnAbs against HIV-1 in a broad range of people including children.
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Affiliation(s)
- Sanjeev Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA, United States
- International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Prashant Bajpai
- International Centre for Genetic Engineering and Biotechnology (ICGEB)-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Collin Joyce
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA, United States
- International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Sushil Kumar Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA, United States
- International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA, United States
- Multi-omics Vaccine Evaluation Consortium, The Scripps Research Institute, La Jolla, CA, United States
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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Sutton HJ, Gao X, Kelly HG, Parker BJ, Lofgren M, Dacon C, Chatterjee D, Seder RA, Tan J, Idris AH, Neeman T, Cockburn IA. Lack of affinity signature for germinal center cells that have initiated plasma cell differentiation. Immunity 2024; 57:245-255.e5. [PMID: 38228150 PMCID: PMC10922795 DOI: 10.1016/j.immuni.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 09/08/2023] [Accepted: 12/13/2023] [Indexed: 01/18/2024]
Abstract
Long-lived plasma cells (PCs) secrete antibodies that can provide sustained immunity against infection. High-affinity cells are proposed to preferentially select into this compartment, potentiating the immune response. We used single-cell RNA-seq to track the germinal center (GC) development of Ighg2A10 B cells, specific for the Plasmodium falciparum circumsporozoite protein (PfCSP). Following immunization with Plasmodium sporozoites, we identified 3 populations of cells in the GC light zone (LZ). One LZ population expressed a gene signature associated with the initiation of PC differentiation and readily formed PCs in vitro. The estimated affinity of these pre-PC B cells was indistinguishable from that of LZ cells that remained in the GC. This remained true when high- or low-avidity recombinant PfCSP proteins were used as immunogens. These findings suggest that the initiation of PC development occurs via an affinity-independent process.
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Affiliation(s)
- Henry J Sutton
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Xin Gao
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Hannah G Kelly
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Brian J Parker
- Biological Data Science Institute, The Australian National University, Canberra, ACT 2601, Australia; School of Computing, ANU College of Engineering, Computing & Cybernetics, The Australian National University, Canberra, ACT 2601, Australia
| | - Mariah Lofgren
- Malaria Unit, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cherrelle Dacon
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Deepyan Chatterjee
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Robert A Seder
- Malaria Unit, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joshua Tan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Azza H Idris
- Malaria Unit, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Teresa Neeman
- Biological Data Science Institute, The Australian National University, Canberra, ACT 2601, Australia
| | - Ian A Cockburn
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia.
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Theorell J, Harrison R, Williams R, Raybould MIJ, Zhao M, Fox H, Fower A, Miller G, Wu Z, Browne E, Mgbachi V, Sun B, Mopuri R, Li Y, Waters P, Deane CM, Handel A, Makuch M, Irani SR. Ultrahigh frequencies of peripherally matured LGI1- and CASPR2-reactive B cells characterize the cerebrospinal fluid in autoimmune encephalitis. Proc Natl Acad Sci U S A 2024; 121:e2311049121. [PMID: 38319973 PMCID: PMC10873633 DOI: 10.1073/pnas.2311049121] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 12/22/2023] [Indexed: 02/08/2024] Open
Abstract
Intrathecal synthesis of central nervous system (CNS)-reactive autoantibodies is observed across patients with autoimmune encephalitis (AE), who show multiple residual neurobehavioral deficits and relapses despite immunotherapies. We leveraged two common forms of AE, mediated by leucine-rich glioma inactivated-1 (LGI1) and contactin-associated protein-like 2 (CASPR2) antibodies, as human models to comprehensively reconstruct and profile cerebrospinal fluid (CSF) B cell receptor (BCR) characteristics. We hypothesized that the resultant observations would both inform the observed therapeutic gap and determine the contribution of intrathecal maturation to pathogenic B cell lineages. From the CSF of three patients, 381 cognate-paired IgG BCRs were isolated by cell sorting and scRNA-seq, and 166 expressed as monoclonal antibodies (mAbs). Sixty-two percent of mAbs from singleton BCRs reacted with either LGI1 or CASPR2 and, strikingly, this rose to 100% of cells in clonal groups with ≥4 members. These autoantigen-reactivities were more concentrated within antibody-secreting cells (ASCs) versus B cells (P < 0.0001), and both these cell types were more differentiated than LGI1- and CASPR2-unreactive counterparts. Despite greater differentiation, autoantigen-reactive cells had acquired few mutations intrathecally and showed minimal variation in autoantigen affinities within clonal expansions. Also, limited CSF T cell receptor clonality was observed. In contrast, a comparison of germline-encoded BCRs versus the founder intrathecal clone revealed marked gains in both affinity and mutational distances (P = 0.004 and P < 0.0001, respectively). Taken together, in patients with LGI1 and CASPR2 antibody encephalitis, our results identify CSF as a compartment with a remarkably high frequency of clonally expanded autoantigen-reactive ASCs whose BCR maturity appears dominantly acquired outside the CNS.
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Affiliation(s)
- Jakob Theorell
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, OxfordOX3 9DU, United Kingdom
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm17177, Sweden
- Department of Neurology, Karolinska University Hospital, Stockholm17176, Sweden
| | - Ruby Harrison
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Robyn Williams
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, OxfordOX3 9DU, United Kingdom
- Department of Neurology, John Radcliffe Hospital, Oxford University Hospitals, OxfordOX3 9DU, United Kingdom
| | - Matthew I. J. Raybould
- Department of Statistics, Oxford Protein Informatics Group, University of Oxford, OxfordOX1 3LB, United Kingdom
| | - Meng Zhao
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Hannah Fox
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Andrew Fower
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Georgina Miller
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Zoe Wu
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Eleanor Browne
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Victor Mgbachi
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Bo Sun
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Rohini Mopuri
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL32224
| | - Ying Li
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL32224
| | - Patrick Waters
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Charlotte M. Deane
- Department of Statistics, Oxford Protein Informatics Group, University of Oxford, OxfordOX1 3LB, United Kingdom
| | - Adam Handel
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, OxfordOX3 9DU, United Kingdom
- Department of Neurology, John Radcliffe Hospital, Oxford University Hospitals, OxfordOX3 9DU, United Kingdom
| | - Mateusz Makuch
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Sarosh R. Irani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, OxfordOX3 9DU, United Kingdom
- Department of Neurology, John Radcliffe Hospital, Oxford University Hospitals, OxfordOX3 9DU, United Kingdom
- Departments of Neurology and Neuroscience, Mayo Clinic, Jacksonville, FL32224
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