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  1. Article ; Online: An information theoretic approach to detecting spatially varying genes.

    Jones, Daniel C / Danaher, Patrick / Kim, Youngmi / Beechem, Joseph M / Gottardo, Raphael / Newell, Evan W

    Cell reports methods

    2023  Volume 3, Issue 6, Page(s) 100507

    Abstract: A key step in spatial transcriptomics is identifying genes with spatially varying expression patterns. We adopt an information theoretic perspective to this problem by equating the degree of spatial coherence with the Jensen-Shannon divergence between ... ...

    Abstract A key step in spatial transcriptomics is identifying genes with spatially varying expression patterns. We adopt an information theoretic perspective to this problem by equating the degree of spatial coherence with the Jensen-Shannon divergence between pairs of nearby cells and pairs of distant cells. To avoid the notoriously difficult problem of estimating information theoretic divergences, we use modern approximation techniques to implement a computationally efficient algorithm designed to scale with
    MeSH term(s) Humans ; Algorithms ; Carcinoma, Renal Cell/genetics ; Gene Expression Profiling ; Technology ; Kidney Neoplasms/genetics
    Language English
    Publishing date 2023-06-16
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2667-2375
    ISSN (online) 2667-2375
    DOI 10.1016/j.crmeth.2023.100507
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: High-Dimensional Profiling of Tumor-Specific Immune Responses: Asking T Cells about What They "See" in Cancer.

    Newell, Evan W / Becht, Etienne

    Cancer immunology research

    2018  Volume 6, Issue 1, Page(s) 2–9

    Abstract: The foundations of basic T-cell immunology and an understanding of the roles for T cells in controlling cancer have led to the remarkable yet inconsistent success of cancer immunotherapy. Because of these advances in cancer treatment, the need is urgent ... ...

    Abstract The foundations of basic T-cell immunology and an understanding of the roles for T cells in controlling cancer have led to the remarkable yet inconsistent success of cancer immunotherapy. Because of these advances in cancer treatment, the need is urgent for biomarkers that can predict the efficacy of these treatments and for new therapeutic strategies for cases where currently available approaches are ineffective. Although our ability to profile heterogeneous cell populations in human blood or tissue samples has vastly improved in the past decade, identifying the cell subsets relevant to diseases, and to cancer particularly, remains a challenge. Given strong evidence for the implication of T cells specific for tumor-expressed antigens in various forms of effective immunotherapy, here, we focus on the utility, challenges, and techniques for the identification and profiling of these important cells. We review recent techniques that allow identifying and profiling of tumor-specific T cells. As these methods improve, we can expect more rapid progress in the rational design of novel cancer biomarkers and therapies based on antigen-specific T cells.
    MeSH term(s) Animals ; Antigens, Neoplasm/immunology ; Biomarkers ; Humans ; Immunity, Cellular ; Lymphocyte Activation ; Neoplasms/immunology ; Neoplasms/pathology ; T-Cell Antigen Receptor Specificity/immunology ; T-Lymphocytes/immunology ; T-Lymphocytes/metabolism ; Tumor Microenvironment/immunology
    Chemical Substances Antigens, Neoplasm ; Biomarkers
    Language English
    Publishing date 2018-01-03
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2732489-8
    ISSN 2326-6074 ; 2326-6066
    ISSN (online) 2326-6074
    ISSN 2326-6066
    DOI 10.1158/2326-6066.CIR-17-0519
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Publisher Correction: Determining T-cell specificity to understand and treat disease.

    Hadrup, Sine Reker / Newell, Evan W

    Nature biomedical engineering

    2018  Volume 2, Issue 1, Page(s) 51

    Abstract: In the version of this Perspective originally published, in Fig. 4, in the schematic for the DNA barcoded multimers, the barcodes were missing; they have now been included and the figure updated in all versions of the Perspective. ...

    Abstract In the version of this Perspective originally published, in Fig. 4, in the schematic for the DNA barcoded multimers, the barcodes were missing; they have now been included and the figure updated in all versions of the Perspective.
    Language English
    Publishing date 2018-01-01
    Publishing country England
    Document type Journal Article ; Published Erratum
    ISSN 2157-846X
    ISSN (online) 2157-846X
    DOI 10.1038/s41551-017-0176-8
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  4. Article: Higher throughput methods of identifying T cell epitopes for studying outcomes of altered antigen processing and presentation.

    Newell, Evan W

    Frontiers in immunology

    2013  Volume 4, Page(s) 430

    Abstract: Variation in the mechanisms that mediate antigen processing, MHC-loading, and presentation of peptides allows cells to significantly modulate the repertoire of peptides presented by both MHC class I or class II. To more quickly determine how these ... ...

    Abstract Variation in the mechanisms that mediate antigen processing, MHC-loading, and presentation of peptides allows cells to significantly modulate the repertoire of peptides presented by both MHC class I or class II. To more quickly determine how these different modes or modulations of presentation translate into altered immune responses, higher throughput methods for identifying T cell epitopes are needed. Proteomics-based comprehensive cataloging of peptides eluted from MHC is a challenging but ideal way of identifying peptide sequences influenced by variable modes of processing and presentation. Several groups have already been successful with this approach and ongoing technical improvements will broaden its applicability. Subsequently, high content combinatorial peptide-MHC tetramer staining using mass cytometry, as we have recently described, should enable the broad assessment of how these changes are perceived by T cells and translated into an altered immune response. The importance of this analysis is highlighted by evidence that physiologically relevant variation in antigen processing and presentation as well as other factors can give rise to unpredictably different T cell responses.
    Language English
    Publishing date 2013-12-05
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2606827-8
    ISSN 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2013.00430
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  5. Article ; Online: Toward Meaningful Definitions of Innate-Lymphoid-Cell Subsets.

    Simoni, Yannick / Newell, Evan W

    Immunity

    2017  Volume 46, Issue 5, Page(s) 760–761

    Language English
    Publishing date 2017-05-16
    Publishing country United States
    Document type Letter
    ZDB-ID 1217235-2
    ISSN 1097-4180 ; 1074-7613
    ISSN (online) 1097-4180
    ISSN 1074-7613
    DOI 10.1016/j.immuni.2017.04.026
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  6. Article ; Online: Determining T-cell specificity to understand and treat disease.

    Hadrup, Sine Reker / Newell, Evan W

    Nature biomedical engineering

    2017  Volume 1, Issue 10, Page(s) 784–795

    Abstract: Adaptive immune responses and immunopathogeneses are based on the ability of T cells to respond to specific antigens. Consequently, understanding T-cell recognition patterns in health and disease involves studying the complexity and genetic heterogeneity ...

    Abstract Adaptive immune responses and immunopathogeneses are based on the ability of T cells to respond to specific antigens. Consequently, understanding T-cell recognition patterns in health and disease involves studying the complexity and genetic heterogeneity of the antigen recognition pathway, which includes both T-cell receptors and the antigen-presentation machinery. In this Perspective, we overview the development and use of technologies for assessing T-cell recognition in a clinical context, and discuss how knowledge of T-cell recognition pathways can be critical before, during and after disease treatment. The ability to assess T-cell-mediated immunity in individual patients during disease progression might enable the identification of patient-specific biomarkers that predict therapeutic efficacy and response. Effective strategies for the complex analysis of T-cell specificity in clinical settings are highly desirable and could complement current approaches for the monitoring of therapy responses.
    Language English
    Publishing date 2017-10-10
    Publishing country England
    Document type Journal Article ; Review
    ISSN 2157-846X
    ISSN (online) 2157-846X
    DOI 10.1038/s41551-017-0143-4
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  7. Article ; Online: Dissecting human ILC heterogeneity: more than just three subsets.

    Simoni, Yannick / Newell, Evan W

    Immunology

    2017  Volume 153, Issue 3, Page(s) 297–303

    Abstract: Innate lymphoid cells (ILCs) have been divided into three distinct groups based on functional capacities, cytokine profiles and transcription factor expression. Studies performed mainly in mice have demonstrated the importance of ILCs in chronic ... ...

    Abstract Innate lymphoid cells (ILCs) have been divided into three distinct groups based on functional capacities, cytokine profiles and transcription factor expression. Studies performed mainly in mice have demonstrated the importance of ILCs in chronic inflammation, infection, allergy and cancer. In this review, we discuss the heterogeneity of human ILC and focus primarily on the taxonomy of human ILC cell subsets and their phenotypical and functional diversity. We summarize recent findings concerning the diversity of ILCs between and within the major subsets [natural killer (NK), ILC1, intra-epithelial ILC1 (ieILC1), ILC2, ILC3, lymphoid tissues inducer (LTi) and ILC progenitor (ILCP)], as well as the abundance of each in human tissues. We also discuss the similarities observed between groups of cells in term of receptors expressed and cytokines produced, and how these relate to the pleiotropic properties of each subset.
    MeSH term(s) Animals ; Cytokines/immunology ; Cytokines/metabolism ; Humans ; Inflammation/immunology ; Inflammation/metabolism ; Lymphocyte Subsets/immunology ; Lymphocytes/immunology ; Lymphocytes/metabolism ; Neoplasms/immunology ; Neoplasms/metabolism
    Chemical Substances Cytokines
    Language English
    Publishing date 2017-12-26
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 80124-0
    ISSN 1365-2567 ; 0019-2805 ; 0953-4954
    ISSN (online) 1365-2567
    ISSN 0019-2805 ; 0953-4954
    DOI 10.1111/imm.12862
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    Ud II Zs.181: Show issues Location:
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  8. Article ; Online: Multiplex MHC Class I Tetramer Combined with Intranuclear Staining by Mass Cytometry.

    Simoni, Yannick / Fehlings, Michael / Newell, Evan W

    Methods in molecular biology (Clifton, N.J.)

    2019  Volume 1989, Page(s) 147–158

    Abstract: Antigen-specific ... ...

    Abstract Antigen-specific CD8
    MeSH term(s) CD8-Positive T-Lymphocytes/immunology ; Cell Nucleus/immunology ; Cell Nucleus/metabolism ; Flow Cytometry/methods ; Histocompatibility Antigens Class I/analysis ; Histocompatibility Antigens Class I/immunology ; Histocompatibility Antigens Class I/metabolism ; Humans ; Mass Spectrometry/methods ; Neoplasms/immunology ; Neoplasms/metabolism ; Single-Cell Analysis/methods ; Staining and Labeling/methods
    Chemical Substances Histocompatibility Antigens Class I
    Language English
    Publishing date 2019-05-10
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-9454-0_11
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Un marqueur de surface pour identifier les lymphocytes T CD8 spécifiques de tumeurs.

    Becht, Étienne / Newell, Evan W / Simoni, Yannick

    Medecine sciences : M/S

    2019  Volume 34, Issue 12, Page(s) 1032–1034

    Title translation Identification of tumor-specific CD8 T cells with a surface marker.
    MeSH term(s) Animals ; Antigens, Surface/metabolism ; Biomarkers/metabolism ; CD8-Positive T-Lymphocytes/cytology ; CD8-Positive T-Lymphocytes/metabolism ; Cell Separation/methods ; Histocompatibility Antigens Class I/metabolism ; Humans ; Lymphocytes, Tumor-Infiltrating/cytology ; Lymphocytes, Tumor-Infiltrating/metabolism ; Mice ; Neoplasms/immunology ; Neoplasms/pathology
    Chemical Substances Antigens, Surface ; Biomarkers ; Histocompatibility Antigens Class I
    Language French
    Publishing date 2019-01-09
    Publishing country France
    Document type News
    ZDB-ID 632733-3
    ISSN 1958-5381 ; 0767-0974
    ISSN (online) 1958-5381
    ISSN 0767-0974
    DOI 10.1051/medsci/2018286
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    Zs.B 2872: Show issues Location:
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  10. Article ; Online: Multi-omic profiling reveals the endogenous and neoplastic responses to immunotherapies in cutaneous T cell lymphoma.

    Glass, David R / Mayer-Blackwell, Koshlan / Ramchurren, Nirasha / Parks, K Rachael / Duran, George E / Wright, Anna K / Bastidas Torres, Armando N / Islas, Laura / Kim, Youn H / Fling, Steven P / Khodadoust, Michael S / Newell, Evan W

    Cell reports. Medicine

    2024  , Page(s) 101527

    Abstract: Cutaneous T cell lymphomas (CTCLs) are skin cancers with poor survival rates and limited treatments. While immunotherapies have shown some efficacy, the immunological consequences of administering immune-activating agents to CTCL patients have not been ... ...

    Abstract Cutaneous T cell lymphomas (CTCLs) are skin cancers with poor survival rates and limited treatments. While immunotherapies have shown some efficacy, the immunological consequences of administering immune-activating agents to CTCL patients have not been systematically characterized. We apply a suite of high-dimensional technologies to investigate the local, cellular, and systemic responses in CTCL patients receiving either mono- or combination anti-PD-1 plus interferon-gamma (IFN-γ) therapy. Neoplastic T cells display no evidence of activation after immunotherapy. IFN-γ induces muted endogenous immunological responses, while anti-PD-1 elicits broader changes, including increased abundance of CLA
    Language English
    Publishing date 2024-04-22
    Publishing country United States
    Document type Journal Article
    ISSN 2666-3791
    ISSN (online) 2666-3791
    DOI 10.1016/j.xcrm.2024.101527
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