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  1. Article ; Online: Lysophosphatidic Acid Is an Inflammatory Lipid Exploited by Cancers for Immune Evasion

    Mathew, Divij / Torres, Raul M

    Frontiers in immunology

    2021  Volume 11, Page(s) 531910

    Abstract: Immunological tolerance has evolved to curtail immune responses against self-antigens and prevent autoimmunity. One mechanism that contributes to immunological tolerance is the expression of inhibitory receptors by lymphocytes that signal to dampen ... ...

    Abstract Immunological tolerance has evolved to curtail immune responses against self-antigens and prevent autoimmunity. One mechanism that contributes to immunological tolerance is the expression of inhibitory receptors by lymphocytes that signal to dampen immune responses during the course of an infection and to prevent immune-mediated collateral damage to the host. The understanding that tumors exploit these physiological mechanisms to avoid elimination has led to remarkable, but limited, success in the treatment of cancer through the use of biologics that interfere with the ability of cancers to suppress immune function. This therapy, based on the understanding of how T lymphocytes are normally activated and suppressed, has led to the development of therapeutic blocking antibodies, referred to as immune checkpoint blockade, which either directly or indirectly promote the activation of CD8 T cells to eradicate cancer. Here, we highlight the distinct signaling mechanisms, timing and location of inhibition used by the CTLA-4 and PD-1 inhibitory receptors compared to a novel inhibitory signaling axis comprised of the bioactive lipid, lysophosphatidic acid (LPA), signaling via the LPA5 receptor expressed by CD8 T cells. Importantly, abundant evidence indicates that an LPA-LPA5 signaling axis is also exploited by diverse cancers to suppress T cell activation and function. Clearly, a thorough molecular and biochemical understanding of how diverse T cell inhibitory receptors signal to suppress T cell antigen receptor signaling and function will be important to inform the choice of which complimentary checkpoint blockade modalities might be used for a given cancer.
    MeSH term(s) Animals ; CD8-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/pathology ; CTLA-4 Antigen/immunology ; Humans ; Inflammation/immunology ; Inflammation/pathology ; Lysophospholipids/immunology ; Neoplasm Proteins/immunology ; Neoplasms/immunology ; Neoplasms/pathology ; Programmed Cell Death 1 Receptor/immunology ; Receptors, Lysophosphatidic Acid/immunology ; Signal Transduction/immunology ; Tumor Escape
    Chemical Substances CTLA-4 Antigen ; CTLA4 protein, human ; LPAR5 protein, human ; Lysophospholipids ; Neoplasm Proteins ; PDCD1 protein, human ; Programmed Cell Death 1 Receptor ; Receptors, Lysophosphatidic Acid ; lysophosphatidic acid (PG6M3969SG)
    Language English
    Publishing date 2021-01-27
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2020.531910
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Multi-ethnic Investigation of Risk and Immune Determinants of COVID-19 Outcomes.

    Jun, Tomi / Mathew, Divij / Sharma, Navya / Nirenberg, Sharon / Huang, Hsin-Hui / Kovatch, Patricia / Wherry, E John / Huang, Kuan-Lin

    Research square

    2022  

    Abstract: Background: ...

    Abstract Background:
    Language English
    Publishing date 2022-03-22
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-1055587/v1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: ARHGEF1 deficiency reveals Gα13-associated GPCRs are critical regulators of human lymphocyte function.

    Mathew, Divij / Kremer, Kimberly N / Torres, Raul M

    The Journal of clinical investigation

    2019  Volume 129, Issue 3, Page(s) 965–968

    Abstract: Primary antibody deficiencies are the most common immunodeficiencies in humans; however, identification of the underlying genetic and biochemical basis for these diseases is often difficult, given that these deficiencies typically involve complex genetic ...

    Abstract Primary antibody deficiencies are the most common immunodeficiencies in humans; however, identification of the underlying genetic and biochemical basis for these diseases is often difficult, given that these deficiencies typically involve complex genetic etiologies. In this issue of the JCI, Bouafia et al. performed whole-exome sequencing on a pair of siblings with primary antibody deficiencies and identified genetic mutations that result in a deficiency of ARHGEF1, a hematopoietic intracellular signaling molecule that transmits signals from GPCRs. ARHGEF1-deficient lymphocytes from the affected siblings exhibited important functional deficits that indicate that loss of ARHGEF1 accounts for the observed primary antibody deficiency, which manifests in an inability to mount antibody responses to vaccines and pathogens. Thus, this report demonstrates an important role for ARHGEF1 in GPCR signal transduction required for appropriate adaptive immune responses in humans.
    MeSH term(s) GTP-Binding Protein alpha Subunits, G12-G13 ; Humans ; Lymphocytes ; Primary Immunodeficiency Diseases ; Rho Guanine Nucleotide Exchange Factors ; Signal Transduction
    Chemical Substances ARHGEF1 protein, human ; Rho Guanine Nucleotide Exchange Factors ; GTP-Binding Protein alpha Subunits, G12-G13 (EC 3.6.5.1)
    Language English
    Publishing date 2019-02-04
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 3067-3
    ISSN 1558-8238 ; 0021-9738
    ISSN (online) 1558-8238
    ISSN 0021-9738
    DOI 10.1172/JCI125893
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: High-throughput interrogation of immune responses using the Human Immune Profiling Pipeline.

    Wang, Guanning / Lyudovyk, Olga / Kim, Justin Y / Lin, Ya-Hui / Elhanati, Yuval / Mathew, Divij / Wherry, E John / Herati, Ramin S / Greenplate, Allison R / Greenbaum, Benjamin / Vardhana, Santosha A / Huang, Alexander C

    STAR protocols

    2023  Volume 4, Issue 2, Page(s) 102289

    Abstract: The current abundance of immunotherapy clinical trials presents an opportunity to learn about the underlying mechanisms and pharmacodynamic effects of novel drugs on the human immune system. Here, we present a protocol to study how these immune responses ...

    Abstract The current abundance of immunotherapy clinical trials presents an opportunity to learn about the underlying mechanisms and pharmacodynamic effects of novel drugs on the human immune system. Here, we present a protocol to study how these immune responses impact clinical outcomes using large-scale high-throughput immune profiling of clinical cohorts. We describe the Human Immune Profiling Pipeline, which comprises an end-to-end solution from flow cytometry results to computational approaches and unsupervised patient clustering based on lymphocyte landscape. For complete details on the use and execution of this protocol, please refer to Lyudovyk et al. (2022).
    Language English
    Publishing date 2023-05-08
    Publishing country United States
    Document type Journal Article
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2023.102289
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Multiethnic Investigation of Risk and Immune Determinants of COVID-19 Outcomes.

    Jun, Tomi / Mathew, Divij / Sharma, Navya / Nirenberg, Sharon / Huang, Hsin-Hui / Kovatch, Patricia / Wherry, Edward John / Huang, Kuan-Lin

    Frontiers in cellular and infection microbiology

    2022  Volume 12, Page(s) 933190

    Abstract: Background: Disparate COVID-19 outcomes have been observed between Hispanic, non-Hispanic Black, and White patients. The underlying causes for these disparities are not fully understood.: Methods: This was a retrospective study utilizing electronic ... ...

    Abstract Background: Disparate COVID-19 outcomes have been observed between Hispanic, non-Hispanic Black, and White patients. The underlying causes for these disparities are not fully understood.
    Methods: This was a retrospective study utilizing electronic medical record data from five hospitals within a single academic health system based in New York City. Multivariable logistic regression models were used to identify demographic, clinical, and lab values associated with in-hospital mortality.
    Results: A total of 3,086 adult patients with self-reported race/ethnicity information presenting to the emergency department and hospitalized with COVID-19 up to April 13, 2020, were included in this study. While older age (multivariable odds ratio (OR) 1.06, 95% CI 1.05-1.07) and baseline hypoxia (multivariable OR 2.71, 95% CI 2.17-3.36) were associated with increased mortality overall and across all races/ethnicities, non-Hispanic Black (median age 67, interquartile range (IQR) 58-76) and Hispanic (median age 63, IQR 50-74) patients were younger and had different comorbidity profiles as compared to non-Hispanic White patients (median age 73, IQR 62-84; p < 0.05 for both comparisons). Among inflammatory markers associated with COVID-19 mortality, there was a significant interaction between the non-Hispanic Black population and interleukin-1-beta (interaction p-value 0.04).
    Conclusions: This analysis of a multiethnic cohort highlights the need for inclusion and consideration of diverse populations in ongoing COVID-19 trials targeting inflammatory cytokines.
    MeSH term(s) Adult ; Black or African American ; Aged ; COVID-19 ; Humans ; Middle Aged ; Retrospective Studies ; SARS-CoV-2 ; White People
    Language English
    Publishing date 2022-07-22
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2022.933190
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Signal recovery in single cell batch integration.

    Zhang, Zhaojun / Mathew, Divij / Lim, Tristan / Mason, Kaishu / Martinez, Clara Morral / Huang, Sijia / Wherry, E John / Susztak, Katalin / Minn, Andy J / Ma, Zongming / Zhang, Nancy R

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Data integration to align cells across batches has become a cornerstone of single cell data analysis, critically affecting downstream results. Yet, how much biological signal is erased during integration? Currently, there are no guidelines for when the ... ...

    Abstract Data integration to align cells across batches has become a cornerstone of single cell data analysis, critically affecting downstream results. Yet, how much biological signal is erased during integration? Currently, there are no guidelines for when the biological differences between samples are separable from batch effects, and thus, data integration usually involve a lot of guesswork: Cells across batches should be aligned to be "appropriately" mixed, while preserving "main cell type clusters". We show evidence that current paradigms for single cell data integration are unnecessarily aggressive, removing biologically meaningful variation. To remedy this, we present a novel statistical model and computationally scalable algorithm, CellANOVA, to recover biological signal that is lost during single cell data integration. CellANOVA utilizes a "pool-of-controls" design concept, applicable across diverse settings, to separate unwanted variation from biological variation of interest. When applied with existing integration methods, CellANOVA allows the recovery of subtle biological signals and corrects, to a large extent, the data distortion introduced by integration. Further, CellANOVA explicitly estimates cell- and gene-specific batch effect terms which can be used to identify the cell types and pathways exhibiting the largest batch variations, providing clarity as to which biological signals can be recovered. These concepts are illustrated on studies of diverse designs, where the biological signals that are recovered by CellANOVA are shown to be validated by orthogonal assays. In particular, we show that CellANOVA is effective in the challenging case of single-cell and single-nuclei data integration, where the recovered biological signals are replicated in an independent study.
    Language English
    Publishing date 2023-09-23
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.05.05.539614
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Anti-CD8 monoclonal antibody-mediated depletion alters the phenotype and behavior of surviving CD8+ T cells.

    Cross, Eric W / Blain, Trevor J / Mathew, Divij / Kedl, Ross M

    PloS one

    2019  Volume 14, Issue 2, Page(s) e0211446

    Abstract: It is common practice for researchers to use antibodies to remove a specific cell type to infer its function. However, it is difficult to completely eliminate a cell type and there is often limited or no information as to how the cells which survive ... ...

    Abstract It is common practice for researchers to use antibodies to remove a specific cell type to infer its function. However, it is difficult to completely eliminate a cell type and there is often limited or no information as to how the cells which survive depletion are affected. This is particularly important for CD8+ T cells for two reasons. First, they are more resistant to mAb-mediated depletion than other lymphocytes. Second, targeting either the CD8α or CD8β chain could induce differential effects. We show here that two commonly used mAbs, against either the CD8α or CD8β subunit, can differentially affect cellular metabolism. Further, in vivo treatment leaves behind a population of CD8+ T cells with different phenotypic and functional attributes relative to each other or control CD8+ T cells. The impact of anti-CD8 antibodies on CD8+ T cell phenotype and function indicates the need to carefully consider the use of these, and possibly other "depleting" antibodies, as they could significantly complicate the interpretation of results or change the outcome of an experiment. These observations could impact how immunotherapy and modulation of CD8+ T cell activation is pursued.
    MeSH term(s) Adoptive Transfer ; Animals ; Antibodies, Monoclonal ; CD8 Antigens/immunology ; CD8 Antigens/metabolism ; CD8-Positive T-Lymphocytes/classification ; CD8-Positive T-Lymphocytes/cytology ; CD8-Positive T-Lymphocytes/immunology ; Cell Differentiation/immunology ; Cytotoxicity, Immunologic ; Female ; Immunologic Memory ; Immunophenotyping ; Lymphocyte Activation ; Lymphocyte Depletion/methods ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic
    Chemical Substances Antibodies, Monoclonal ; CD8 Antigens ; CD8 antigen, alpha chain ; Cd8b1 protein, mouse
    Language English
    Publishing date 2019-02-08
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0211446
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Deep Phenotyping of the Lipidomic Response in COVID and non-COVID Sepsis.

    Meng, Hu / Sengupta, Arjun / Ricciotti, Emanuela / Mrčela, Antonijo / Mathew, Divij / Mazaleuskaya, Liudmila L / Ghosh, Soumita / Brooks, Thomas G / Turner, Alexandra P / Schanoski, Alessa Soares / Lahens, Nicholas F / Tan, Ai Wen / Woolfork, Ashley / Grant, Greg / Susztak, Katalin / Letizia, Andrew G / Sealfon, Stuart C / Wherry, E John / Laudanski, Krzysztof /
    Weljie, Aalim M / Meyer, Nuala B / FitzGerald, Garret A

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Lipids may influence cellular penetrance by pathogens and the immune response that they evoke. Here we find a broad based lipidomic storm driven predominantly by secretory (s) phospholipase ... ...

    Abstract Lipids may influence cellular penetrance by pathogens and the immune response that they evoke. Here we find a broad based lipidomic storm driven predominantly by secretory (s) phospholipase A
    Language English
    Publishing date 2023-06-02
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.06.02.543298
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Stat5 opposes the transcription factor Tox and rewires exhausted CD8

    Beltra, Jean-Christophe / Abdel-Hakeem, Mohamed S / Manne, Sasikanth / Zhang, Zhen / Huang, Hua / Kurachi, Makoto / Su, Leon / Picton, Lora / Ngiow, Shin Foong / Muroyama, Yuki / Casella, Valentina / Huang, Yinghui J / Giles, Josephine R / Mathew, Divij / Belman, Jonathan / Klapholz, Max / Decaluwe, Hélène / Huang, Alexander C / Berger, Shelley L /
    Garcia, K Christopher / Wherry, E John

    Immunity

    2023  Volume 56, Issue 12, Page(s) 2699–2718.e11

    Abstract: Rewiring exhausted ... ...

    Abstract Rewiring exhausted CD8
    MeSH term(s) CD8-Positive T-Lymphocytes ; Transcription Factors/genetics ; Interleukin-2 ; Gene Expression Regulation ; Programmed Cell Death 1 Receptor/metabolism
    Chemical Substances Transcription Factors ; Interleukin-2 ; Programmed Cell Death 1 Receptor
    Language English
    Publishing date 2023-12-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1217235-2
    ISSN 1097-4180 ; 1074-7613
    ISSN (online) 1097-4180
    ISSN 1074-7613
    DOI 10.1016/j.immuni.2023.11.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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