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Article ; Online: Quantitative analysis of urinary cytokines in food-allergic and healthy individuals.

Lee, Alexandra S / Parsons, Ella S / Chang, Iris / Dunham, Diane / Chinthrajah, R Sharon / Nadeau, Kari C

2023 Volume 78, Issue 9, Page(s) 2523–2526

MeSH term(s)	Humans ; Cytokines ; Hypersensitivity ; Allergens ; Food
Chemical Substances	Cytokines ; Allergens
Language	English
Publishing date	2023-03-16
Publishing country	Denmark
Document type	Letter ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	391933-x
ISSN	1398-9995 ; 0105-4538
ISSN (online)	1398-9995
ISSN	0105-4538
DOI	10.1111/all.15707
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Article ; Online: A novel mass cytometry protocol optimized for immunophenotyping of low-frequency antigen-specific T cells.

Balz, Kathrin / Grange, Magali / Pegel, Uta / Karamya, Zain A / Mello, Marielle / Zhou, Xiaoying / Berger, Thilo / Bloch, Konstantin / Dunham, Diane / Chinthrajah, Sharon / Nadeau, Kari / Luche, Hervé / Skevaki, Chrysanthi

Frontiers in cellular and infection microbiology

2024 Volume 13, Page(s) 1336489

Abstract: Understanding antigen-specific T-cell responses, for example, following virus infections or allergen exposure, is of high relevance for the development of vaccines and therapeutics. We aimed on optimizing immunophenotyping of T cells after antigen ... ...

Abstract	Understanding antigen-specific T-cell responses, for example, following virus infections or allergen exposure, is of high relevance for the development of vaccines and therapeutics. We aimed on optimizing immunophenotyping of T cells after antigen stimulation by improving staining procedures for flow and mass cytometry. Our method can be used for primary cells of both mouse and human origin for the detection of low-frequency T-cell response using a dual-barcoding system for individual samples and conditions. First, live-cell barcoding was performed using anti-CD45 antibodies prior to an
MeSH term(s)	Humans ; Animals ; Mice ; Flow Cytometry/methods ; Immunophenotyping ; Antigens ; T-Lymphocytes ; Staining and Labeling ; CD8-Positive T-Lymphocytes
Chemical Substances	Antigens
Language	English
Publishing date	2024-01-15
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2023.1336489
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Article ; Online: Cytometric analysis reveals an association between allergen-responsive natural killer cells and human peanut allergy.

Zhou, Xiaoying / Yu, Wong / Dunham, Diane M / Schuetz, Jackson P / Blish, Catherine A / DeKruyff, Rosemarie H / Nadeau, Kari C

The Journal of clinical investigation

2022 Volume 132, Issue 20

Abstract: Food allergies are a leading cause of anaphylaxis, and allergen-specific immune responses in both the innate and the adaptive immune system play key roles in its pathogenesis. We conducted a comprehensive phenotypic and functional investigation of immune ...

Abstract	Food allergies are a leading cause of anaphylaxis, and allergen-specific immune responses in both the innate and the adaptive immune system play key roles in its pathogenesis. We conducted a comprehensive phenotypic and functional investigation of immune cell responses from nonallergic (NA) and peanut allergic (PA) participants cultured with media alone or peanut protein and found, surprisingly, that NK cell activation was strongly associated with the immune response to allergen in PA participants. Peanut-responsive NK cells manifested a distinct expression pattern in PA participants compared with NA participants. Allergen-activated NK cells expressed both Th2 and immune regulatory cytokines, hinting at a potential functional role in mediating and regulating the Th2 allergic response. Depletion of CD3+ T cells attenuated the response of NK cells to peanut-allergen stimulation, suggesting that peanut-responsive NK cells are T cell dependent. We also showed that oral immune therapy was associated with decreased NK responses to peanut allergen stimulation in vitro. These results demonstrate that NK cells are associated with the food-allergic immune response, and the magnitude of this mobilized cell population suggests that they play a functional role in allergic immunity.
MeSH term(s)	Allergens ; Arachis ; Cytokines/metabolism ; Food Hypersensitivity ; Humans ; Killer Cells, Natural ; Peanut Hypersensitivity/therapy
Chemical Substances	Allergens ; Cytokines
Language	English
Publishing date	2022-10-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	3067-3
ISSN	1558-8238 ; 0021-9738
ISSN (online)	1558-8238
ISSN	0021-9738
DOI	10.1172/JCI157962
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Article ; Online: Identification of a Candidate Gene in Solanum habrochaites for Resistance to a Race 1 Strain of Pseudomonas syringae pv. tomato.

Bao, Zhilong / Meng, Fanhong / Strickler, Susan R / Dunham, Diane M / Munkvold, Kathy R / Martin, Gregory B

The plant genome

2020 Volume 8, Issue 3, Page(s) eplantgenome2015.02.0006

Abstract: Bacterial speck disease caused by Pseudomonas syringae pv. tomato (Pst) is a persistent problem on tomato (Solanum lycopersicum L.). Resistance against race 0 Pst strains is conferred by the Pto protein, which recognizes either of two pathogen effectors: ...

Abstract	Bacterial speck disease caused by Pseudomonas syringae pv. tomato (Pst) is a persistent problem on tomato (Solanum lycopersicum L.). Resistance against race 0 Pst strains is conferred by the Pto protein, which recognizes either of two pathogen effectors: AvrPto or AvrPtoB. However, current tomato varieties do not have resistance to the increasingly common race 1 strains, which lack these effectors. We identified accessions of Solanum habrochaites S. Knapp & D. M. Spooner that are resistant to the race 1 strain T1. Genome sequence comparisons of T1 and two Pst strains that are virulent on these accessions suggested that known microbe-associated molecular patterns (MAMPs) or effectors are not involved in the resistance. We developed an F
Language	English
Publishing date	2020-11-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	2375444-8
ISSN	1940-3372 ; 0011-183X
ISSN (online)	1940-3372
ISSN	0011-183X
DOI	10.3835/plantgenome2015.02.0006
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Article ; Online: CyAnno: a semi-automated approach for cell type annotation of mass cytometry datasets.

Kaushik, Abhinav / Dunham, Diane / He, Ziyuan / Manohar, Monali / Desai, Manisha / Nadeau, Kari C / Andorf, Sandra

Bioinformatics (Oxford, England)

2021 Volume 37, Issue 22, Page(s) 4164–4171

Abstract: Motivation: For immune system monitoring in large-scale studies at the single-cell resolution using CyTOF, (semi-)automated computational methods are applied for annotating live cells of mixed cell types. Here, we show that the live cell pool can be ... ...

Abstract	Motivation: For immune system monitoring in large-scale studies at the single-cell resolution using CyTOF, (semi-)automated computational methods are applied for annotating live cells of mixed cell types. Here, we show that the live cell pool can be highly enriched with undefined heterogeneous cells, i.e. 'ungated' cells, and that current semi-automated approaches ignore their modeling resulting in misclassified annotations. Result: We introduce 'CyAnno', a novel semi-automated approach for deconvoluting the unlabeled cytometry dataset based on a machine learning framework utilizing manually gated training data that allows the integrative modeling of 'gated' cell types and the 'ungated' cells. By applying this framework on several CyTOF datasets, we demonstrated that including the 'ungated' cells can lead to a significant increase in the precision of the 'gated' cell types prediction. CyAnno can be used to identify even a single cell type, including rare cells, with higher efficacy than current state-of-the-art semi-automated approaches. Availability and implementation: The CyAnno is available as a python script with a user-manual and sample dataset at https://github.com/abbioinfo/CyAnno. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Machine Learning ; Computational Biology ; Single-Cell Analysis ; Cells
Language	English
Publishing date	2021-05-24
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btab409
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Article ; Online: Proinflammatory polarization of monocytes by particulate air pollutants is mediated by induction of trained immunity in pediatric asthma.

Movassagh, Hesam / Prunicki, Mary / Kaushik, Abhinav / Zhou, Xiaoying / Dunham, Diane / Smith, Eric M / He, Ziyuan / Aleman Muench, German R / Shi, Minyi / Weimer, Annika K / Cao, Shu / Andorf, Sandra / Feizi, Amir / Snyder, Michael P / Soroosh, Pejman / Mellins, Elizabeth D / Nadeau, Kari C

Allergy

2023 Volume 78, Issue 7, Page(s) 1922–1933

Abstract: Background: The impact of exposure to air pollutants, such as fine particulate matter (PM), on the immune system and its consequences on pediatric asthma, are not well understood. We investigated whether ambient levels of fine PM with aerodynamic ... ...

Abstract	Background: The impact of exposure to air pollutants, such as fine particulate matter (PM), on the immune system and its consequences on pediatric asthma, are not well understood. We investigated whether ambient levels of fine PM with aerodynamic diameter ≤2.5 microns (PM Methods: Monocyte phenotyping was performed by cytometry time-of-flight (CyTOF). Cytokines were measured using cytometric bead array and Luminex assay. ChIP-Seq was utilized to address histone modifications in monocytes. Results: Increased exposure to ambient PM Conclusion: The specific alterations of monocytes after ambient pollution exposure suggest a possible prognostic immune signature for pediatric asthma, and pollution-induced trained immunity may provide a potential therapeutic target for asthmatic children living in areas with increased air pollution.
MeSH term(s)	Humans ; Particulate Matter/adverse effects ; Monocytes ; Trained Immunity ; Air Pollutants/adverse effects ; Air Pollutants/analysis ; Asthma/etiology ; Asthma/chemically induced ; Air Pollution/adverse effects
Chemical Substances	Particulate Matter ; Air Pollutants
Language	English
Publishing date	2023-03-16
Publishing country	Denmark
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	391933-x
ISSN	1398-9995 ; 0105-4538
ISSN (online)	1398-9995
ISSN	0105-4538
DOI	10.1111/all.15692
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Article ; Online: Mass cytometry analysis of blood from peanut-sensitized tolerant and clinically allergic infants.

Tursi, Amanda R / Saba, Nicholas K / Dunham, Diane / Manohar, Monali / Peters, Rachel L / Saffery, Richard / Koplin, Jennifer J / Nadeau, Kari C / Neeland, Melanie R / Andorf, Sandra

Scientific data

2022 Volume 9, Issue 1, Page(s) 738

Abstract: IgE-mediated food allergies in infants are a significant health concern, with peanut allergy being of particular interest due to its prevalence and severity. Among individuals who produce peanut-specific IgE some experience no adverse reaction on peanut ... ...

Abstract	IgE-mediated food allergies in infants are a significant health concern, with peanut allergy being of particular interest due to its prevalence and severity. Among individuals who produce peanut-specific IgE some experience no adverse reaction on peanut consumption. This asymptomatic phenotype is known as sensitized tolerance. To elucidate the immune environment of peanut sensitized tolerant and clinically allergic one-year-olds, high-dimensional mass cytometry was conducted as part of the HealthNuts study. The resulting data includes peripheral blood mononuclear cells from 36 participants encompassing non-allergic, peanut sensitized with tolerance, and clinically peanut allergic infants. The raw mass cytometry data is described here and freely available for reuse through the Immunology Database and Analysis Portal (ImmPort). Additional allergy information and serum vitamin D levels of the participants were measured and are also included in the data upload. These high-dimensional mass cytometry data, when combined with clinical information, offer a broad immune profile of peanut allergic and sensitized tolerant infants.
MeSH term(s)	Arachis ; Immunoglobulin E ; Leukocytes ; Leukocytes, Mononuclear ; Peanut Hypersensitivity/blood ; Cytophotometry ; Humans ; Infant
Chemical Substances	Immunoglobulin E (37341-29-0)
Language	English
Publishing date	2022-12-01
Publishing country	England
Document type	Dataset ; Journal Article
ZDB-ID	2775191-0
ISSN	2052-4463 ; 2052-4463
ISSN (online)	2052-4463
ISSN	2052-4463
DOI	10.1038/s41597-022-01861-x
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Article ; Online: Selenomethionine attenuates allergic effector responses in human primary mast cells.

Zhao, Xiaoli / Blokhuis, Bart R J / Redegeld, Frank A / Chang, Iris / Dunham, Diane / Chen, Hongbing / Nadeau, Kari / Garssen, Johan / Knippels, Leon M J / Hogenkamp, Astrid

Allergy

2022 Volume 77, Issue 8, Page(s) 2552–2555

MeSH term(s)	Food Hypersensitivity ; Humans ; Mast Cells/physiology ; Selenomethionine
Chemical Substances	Selenomethionine (964MRK2PEL)
Language	English
Publishing date	2022-05-05
Publishing country	Denmark
Document type	Letter
ZDB-ID	391933-x
ISSN	1398-9995 ; 0105-4538
ISSN (online)	1398-9995
ISSN	0105-4538
DOI	10.1111/all.15320
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Article ; Online: Allergen-specific CD8

Yu, Wong / Zhou, Xiaoying / Dunham, Diane / Lyu, Shu Chen / Manohar, Monali / Zhang, Wenming / Zhao, Fan / Davis, Mark M / Nadeau, Kari

The Journal of allergy and clinical immunology

2019 Volume 143, Issue 5, Page(s) 1948–1952

MeSH term(s)	Adolescent ; Adult ; Allergens/immunology ; Arachis/immunology ; CD8-Positive T-Lymphocytes/immunology ; Child ; Child, Preschool ; Female ; Humans ; Immunoglobulin E/immunology ; Male ; Middle Aged ; Peanut Hypersensitivity/immunology ; Peptides/immunology ; Plant Proteins/immunology ; Young Adult
Chemical Substances	Allergens ; Peptides ; Plant Proteins ; Immunoglobulin E (37341-29-0)
Language	English
Publishing date	2019-01-22
Publishing country	United States
Document type	Letter ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	121011-7
ISSN	1097-6825 ; 1085-8725 ; 0091-6749
ISSN (online)	1097-6825 ; 1085-8725
ISSN	0091-6749
DOI	10.1016/j.jaci.2019.01.011
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Article ; Online: Combining avidin with CD63 improves basophil activation test accuracy in classifying peanut allergy.

Castaño, Nicolas / Chua, Kaiser / Kaushik, Abhinav / Kim, Sungu / Cordts, Seth C / Nafarzadegan, Ceena D / Hofmann, Grady H / Seastedt, Hana / Schuetz, Jackson P / Dunham, Diane / Parsons, Ella S / Tsai, Mindy / Cao, Shu / Desai, Manisha / Sindher, Sayantani B / Chinthrajah, R Sharon / Galli, Stephen J / Nadeau, Kari C / Tang, Sindy K Y

Allergy

2023 Volume 79, Issue 2, Page(s) 445–455

Abstract: Background: Conventional basophil activation tests (BATs) measure basophil activation by the increased expression of CD63. Previously, fluorophore-labeled avidin, a positively-charged molecule, was found to bind to activated basophils, which tend to ... ...

Abstract	Background: Conventional basophil activation tests (BATs) measure basophil activation by the increased expression of CD63. Previously, fluorophore-labeled avidin, a positively-charged molecule, was found to bind to activated basophils, which tend to expose negatively charged granule constituents during degranulation. This study further compares avidin versus CD63 as basophil activation biomarkers in classifying peanut allergy. Methods: Seventy subjects with either a peanut allergy (N = 47), a food allergy other than peanut (N = 6), or no food allergy (N = 17) were evaluated. We conducted BATs in response to seven peanut extract (PE) concentrations (0.01-10,000 ng/mL) and four control conditions (no stimulant, anti-IgE, fMLP (N-formylmethionine-leucyl-phenylalanine), and anti-FcεRI). We measured avidin binding and CD63 expression on basophils with flow cytometry. We evaluated logistic regression and XGBoost models for peanut allergy classification and feature identification. Results: Avidin binding was correlated with CD63 expression. Both markers discriminated between subjects with and without a peanut allergy. Although small by percentage, an avidin Conclusions: Avidin and CD63 are reliable BAT activation markers associated with degranulation. Their combination enhances the identification of activated basophils and improves the classification accuracy of peanut allergy.
MeSH term(s)	Humans ; Basophil Degranulation Test ; Peanut Hypersensitivity/diagnosis ; Peanut Hypersensitivity/metabolism ; Avidin/metabolism ; Immunoglobulin E/metabolism ; Basophils/metabolism ; Flow Cytometry ; Arachis ; Tetraspanin 30/metabolism
Chemical Substances	Avidin (1405-69-2) ; Immunoglobulin E (37341-29-0) ; Tetraspanin 30 ; CD63 protein, human
Language	English
Publishing date	2023-11-02
Publishing country	Denmark
Document type	Journal Article
ZDB-ID	391933-x
ISSN	1398-9995 ; 0105-4538
ISSN (online)	1398-9995
ISSN	0105-4538
DOI	10.1111/all.15930
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