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      H3K27M neoepitope vaccination in diffuse midline glioma induces B and T cell responses across diverse HLA loci of a recovered patient

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          Abstract

          H3K27M, a driver mutation with T and B cell neoepitope characteristics, defines an aggressive subtype of diffuse glioma with poor survival. We functionally dissect the immune response of one patient treated with an H3K27M peptide vaccine who subsequently entered complete remission. The vaccine robustly expanded class II human leukocyte antigen (HLA)–restricted peripheral H3K27M-specific T cells. Using functional assays, we characterized 34 clonally unique H3K27M-reactive T cell receptors and identified critical, conserved motifs in their complementarity-determining region 3 regions. Using detailed HLA mapping, we further demonstrate that diverse HLA-DQ and HLA-DR alleles present immunogenic H3K27M epitopes. Furthermore, we identified and profiled H3K27M-reactive B cell receptors from activated B cells in the cerebrospinal fluid. Our results uncover the breadth of the adaptive immune response against a shared clonal neoantigen across multiple HLA allelotypes and support the use of class II–restricted peptide vaccines to stimulate tumor-specific T and B cells harboring receptors with therapeutic potential.

          Abstract

          Adaptive immune responses are functionally characterized in a diffuse midline glioma patient in remission upon H3vac treatment.

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          Comprehensive Integration of Single-Cell Data

          Single-cell transcriptomics has transformed our ability to characterize cell states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise to measure distinct cellular modalities, a key analytical challenge is to integrate these datasets to better understand cellular identity and function. Here, we develop a strategy to "anchor" diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities. After demonstrating improvement over existing methods for integrating scRNA-seq data, we anchor scRNA-seq experiments with scATAC-seq to explore chromatin differences in closely related interneuron subsets and project protein expression measurements onto a bone marrow atlas to characterize lymphocyte populations. Lastly, we harmonize in situ gene expression and scRNA-seq datasets, allowing transcriptome-wide imputation of spatial gene expression patterns. Our work presents a strategy for the assembly of harmonized references and transfer of information across datasets.
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            Integrated analysis of multimodal single-cell data

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

              Checkpoint blockade therapies that reactivate tumour-associated T cells can induce durable tumour control and result in the long-term survival of patients with advanced cancers1. Current predictive biomarkers for therapy response include high levels of intratumour immunological activity, a high tumour mutational burden and specific characteristics of the gut microbiota2,3. Although the role of T cells in antitumour responses has thoroughly been studied, other immune cells remain insufficiently explored. Here we use clinical samples of metastatic melanomas to investigate the role of B cells in antitumour responses, and find that the co-occurrence of tumour-associated CD8+ T cells and CD20+ B cells is associated with improved survival, independently of other clinical variables. Immunofluorescence staining of CXCR5 and CXCL13 in combination with CD20 reveals the formation of tertiary lymphoid structures in these CD8+CD20+ tumours. We derived a gene signature associated with tertiary lymphoid structures, which predicted clinical outcomes in cohorts of patients treated with immune checkpoint blockade. Furthermore, B-cell-rich tumours were accompanied by increased levels of TCF7+ naive and/or memory T cells. This was corroborated by digital spatial-profiling data, in which T cells in tumours without tertiary lymphoid structures had a dysfunctional molecular phenotype. Our results indicate that tertiary lymphoid structures have a key role in the immune microenvironment in melanoma, by conferring distinct T cell phenotypes. Therapeutic strategies to induce the formation of tertiary lymphoid structures should be explored to improve responses to cancer immunotherapy.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: SoftwareRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: ValidationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: ValidationRole: VisualizationRole: Writing - original draft
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ValidationRole: Visualization
                Role: InvestigationRole: MethodologyRole: Validation
                Role: Data curationRole: InvestigationRole: Software
                Role: Methodology
                Role: ConceptualizationRole: Data curationRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing - review & editing
                Role: Funding acquisitionRole: MethodologyRole: Resources
                Role: ConceptualizationRole: ResourcesRole: ValidationRole: VisualizationRole: Writing - review & editing
                Role: InvestigationRole: ResourcesRole: VisualizationRole: Writing - review & editing
                Role: Resources
                Role: Funding acquisitionRole: ResourcesRole: Writing - review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: Writing - review & editing
                Journal
                Sci Adv
                Sci Adv
                sciadv
                advances
                Science Advances
                American Association for the Advancement of Science
                2375-2548
                02 February 2024
                02 February 2024
                : 10
                : 5
                : eadi9091
                Affiliations
                [ 1 ]CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
                [ 2 ]Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.
                [ 3 ]Helmholtz Institute for Translational Oncology (HI-TRON Mainz) - A Helmholtz Institute of the DKFZ, Mainz, Germany.
                [ 4 ]BioMed X GmbH, Heidelberg, Germany.
                [ 5 ]Immune Monitoring Unit, DKFZ and National Center for Tumour Diseases (NCT), Heidelberg, Germany.
                [ 6 ]Department of Neurology, Medical Faculty Mannheim, MCTN Heidelberg University, Mannheim, Germany.
                [ 7 ]DKFZ Hector Cancer Institute at the University Medical Center Mannheim, Mannheim Germany.
                Author notes
                [* ]Corresponding author. Email: e.green@ 123456dkfz.de (E.W.G.); lindner@ 123456bio.mx (J.M.L.)
                [†]

                These authors contributed equally to this work.

                [‡]

                These authors contributed equally to this work.

                Author information
                https://orcid.org/0009-0007-8957-5319
                https://orcid.org/0009-0005-5617-7635
                https://orcid.org/0000-0002-2735-3266
                https://orcid.org/0000-0002-2529-1030
                https://orcid.org/0000-0002-4387-5566
                https://orcid.org/0000-0002-4490-7574
                https://orcid.org/0000-0001-6831-4282
                https://orcid.org/0000-0001-7987-0444
                https://orcid.org/0009-0008-8825-4908
                https://orcid.org/0000-0001-7694-0988
                https://orcid.org/0000-0002-4746-887X
                https://orcid.org/0000-0002-4940-5354
                https://orcid.org/0000-0003-1922-2298
                Article
                adi9091
                10.1126/sciadv.adi9091
                10836722
                38306431
                045c47a8-1701-4f95-b323-ffbbcc668001
                Copyright © 2024 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).

                This is an open-access article distributed under the terms of the Creative Commons Attribution license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 25 May 2023
                : 03 January 2024
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100008316, Baden-Württemberg Stiftung;
                Award ID: BWST_ISF2018-046
                Funded by: FundRef http://dx.doi.org/10.13039/501100002347, Bundesministerium für Bildung und Forschung;
                Funded by: FundRef http://dx.doi.org/10.13039/501100003493, Gemeinnützige Hertie-Stiftung;
                Funded by: German Cancer Aid;
                Award ID: INTERCEPT-H3
                Funded by: German Cancer Aid;
                Award ID: INTERCEPT-H3
                Funded by: BioMed X;
                Award ID: Janssen_IAA
                Funded by: Dr Rolf M. Schwiete Foundation;
                Award ID: 2021-009
                Funded by: Dr Rolf M. Schwiete Foundation;
                Award ID: 2021-009
                Funded by: Helmholtz International Graduate School;
                Funded by: Helmholtz-Institute for Translational Oncology Mainz;
                Funded by: German Ministry of Education;
                Funded by: Hertie Network of Excellence in Clinical Neuroscience;
                Funded by: Helmholtz-Institute for Translational Oncology Mainz;
                Funded by: Helmholtz-Institute for Translational Oncology Mainz;
                Funded by: Helmholtz-Institute for Translational Oncology Mainz;
                Funded by: German Ministry of Education;
                Categories
                Research Article
                Biomedicine and Life Sciences
                SciAdv r-articles
                Cell Biology
                Immunology
                Immunology
                Custom metadata
                CC BY

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