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Abidin MR, Alpan O, Plassmeyer M, Kozhaya L, Loizou D, Dogan M, Upchurch Z, Manes NP, Nita-Lazar A, Unutmaz D, Sønder SU. STAT4 Phosphorylation of T-helper Cells predicts surgical outcomes in Refractory Chronic Rhinosinusitis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.11.23299743. [PMID: 38168423 PMCID: PMC10760250 DOI: 10.1101/2023.12.11.23299743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Objective Chronic rhinosinusitis (CRS) impacts an estimated 5% to 15% of people worldwide, incurring significant economic healthcare burden. There is a urgent need for the discovery of predictive biomarkers to improve treatment strategies and outcomes for CRS patients. Study design Cohort study of CRS patients and healthy controls using blood samples. Setting Out-patient clinics. Methods Whole blood samples were collected for flow cytometric analysis. Mechanistic studies involved the transfection of human primary T cells and Jurkat cells. Results Our analysis began with a 63-69 year-old female patient diagnosed with refractory CRS,. Despite undergoing multiple surgeries, she continually faced sinus infections. Whole exome sequencing pinpointed a heterozygous IL-12Rb1 mutation situated in the linker region adjacent to the cytokine binding domain. When subjected to IL-12 stimulation, the patient's CD4 T-cells exhibited diminished STAT4 phosphorylation. However, computer modeling or T-cell lines harboring the same IL-12 receptor mutation did not corroborate the hypothesis that IL-12Rb could be responsible for the reduced phosphorylation of STAT4 by IL-12 stimulation. Upon expanding our investigation to a broader CRS patient group using the pSTAT4 assay, we discerned a subset of refractory CRS patients with abnormally low STAT4 phosphorylation. The deficiency showed improvement both in-vitro and in-vivo after exposure to Latilactobacillus sakei (aka Lactobacillus sakei), an effect at least partially dependent on IL-12. Conclusion In refractory CRS patients, an identified STAT4 defect correlates with poor clinical outcomes after sinus surgery, which can be therapeutically targeted by Latilactobacillus sakei treatment. Prospective double-blind placebo-controlled trials are needed to validate our findings.
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Affiliation(s)
| | - Oral Alpan
- Amerimmune LLC, 8260 Greensboro Dr VA-22102 McLean, USA
| | | | - Lina Kozhaya
- The Jackson Laboratory, Farmington, CT, 06032 USA
| | - Denise Loizou
- Amerimmune LLC, 8260 Greensboro Dr VA-22102 McLean, USA
| | - Mikail Dogan
- The Jackson Laboratory, Farmington, CT, 06032 USA
| | | | - Nathan P Manes
- Functional Cellular Networks Section, Laboratory of Immune System Biology, NIAID, NIH, USA
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, NIAID, NIH, USA
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Sonder SU, Plassmeyer M, Loizou D, Alpan O. Towards standardizing basophil identification by flow cytometry. FRONTIERS IN ALLERGY 2023; 4:1133378. [PMID: 36938328 PMCID: PMC10020589 DOI: 10.3389/falgy.2023.1133378] [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: 12/28/2022] [Accepted: 01/27/2023] [Indexed: 03/06/2023] Open
Abstract
Background Basophils normally make up <2% of the white blood cells (WBC). There is no clear consensus for basophil identification by flow cytometry. The increased demand for basophil activation test (BAT) to identifying and monitoring allergic patients highlights the need for a standardized approach to identify basophils. Methods Using flow cytometry we analyzed whole blood stained with antibodies against: IgE, CD123, CD193, CD203c, CD3, HLADR, FcɛRI, CRTH2 and CD45. We examined unstimulated blood as well as blood stimulated with Anti-IgE and fMLP. Finally, we compared the results to a complete blood count (CBC) from an FDA approved hematological analyzer. Results Basophil identification relying on just one surface marker performed worse than approaches utilizing two identification markers. The percentage of basophils from WBC determined by flow cytometry results had a good correlation with the CBC results even though the CBC results were generally higher. Stimulating whole blood with the basophil activators did not interfere with the basophil identification markers. Conclusion In flow cytometry assays, two surface markers should be used for identifying basophils and if a very pure basophil fraction is desired a third marker can be considered. In our hands the approaches that included CD123 in combination with either CD193, HLADRnegative or FcɛRI performed the best.
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Santos AF, Alpan O, Hoffmann H. Basophil activation test: Mechanisms and considerations for use in clinical trials and clinical practice. Allergy 2021; 76:2420-2432. [PMID: 33475181 DOI: 10.1111/all.14747] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022]
Abstract
The basophil activation test (BAT) is a functional assay that measures the degree of degranulation following stimulation with allergen or controls by flow cytometry. It correlates directly with histamine release. From the dose-response curve resulting from BAT in allergic patients, basophil reactivity (%CD63+ basophils) and basophil sensitivity (EC50 or similar) are the main outcomes of the test. BAT takes into account all characteristics of IgE and allergen and thus can be more specific than sensitization tests in the diagnosis of allergic disease. BAT reduces the need for in vivo procedures, such as intradermal tests and allergen challenges, which can cause allergic reactions of unpredictable severity. As it closely reflects the patients' phenotype in most cases, it may be used to support the diagnosis of food, venom and drug allergies and chronic urticaria, to monitor the natural resolution of food allergies and to predict and monitor clinical the response to immunomodulatory treatments, such as allergen-specific immunotherapy and biologicals. Clinical application of BAT requires analytical validation, clinical validation, standardization of procedures and quality assurance to ensure reproducibility and reliability of results. Currently, efforts are ongoing to establish a platform that could be used by laboratories in Europe and in the USA for quality assurance and certification.
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Affiliation(s)
- Alexandra F. Santos
- Department of Women and Children's Health (Pediatric Allergy) School of Life Course Sciences Faculty of Life Sciences and Medicine King's College London London UK
- Peter Gorer Department of Immunobiology School of Immunology and Microbial Sciences King's College London London UK
- Asthma UK Centre in Allergic Mechanisms of Asthma London UK
- Children's Allergy ServiceEvelina London Children's HospitalGuy's and St Thomas' Hospital London UK
| | | | - Hans‐Jürgen Hoffmann
- Department of Clinical Medicine Aarhus University Aarhus Denmark
- Department of Respiratory Diseases and Allergy Aarhus University Hospital Aarhus Denmark
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Kim T, Yu J, Li H, Scarupa M, Wasserman RL, Economides A, White M, Ward C, Shah A, Jones D, Rathkopf M, Frye K, Aybar A, Shayegan S, Enav B, Ispas L, Loizou D, Fitzhugh D, Tracy J, Friedlander J, Jacobs Z, Matz J, Golden D, McNeil D, McCann W, Copenhaver C, Factor J, Gupta R, Alpan O, Plassmeyer M, Sønder SU. Validation of inducible basophil biomarkers: Time, temperature and transportation. CYTOMETRY PART B-CLINICAL CYTOMETRY 2021; 100:632-644. [PMID: 33539657 PMCID: PMC9291082 DOI: 10.1002/cyto.b.21991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/26/2020] [Accepted: 12/31/2020] [Indexed: 12/23/2022]
Abstract
Background The short stability window of several hours from blood collection to measuring basophil activation has limited the use of flow cytometry‐based basophil activation assays in clinical settings. We examine if it is possible to extend this window to 1 day allowing for shipment of samples between laboratories. Several options exist for reporting the results including reporting all the measured values directly, calculating ratios and reporting a single value covering all measured results. Each of these options have different stability and value to the physician. Methods Whole blood samples from peanut allergic patients were stimulated with four different peanut concentrations at Day 0, Day 1, and Day 2. Samples were stored under temperature‐controlled conditions. Flow cytometry was used to analyze the samples. The basophil activation and degranulation were measured as percentage of positive CD63 basophils and CD203c MFI fold change. Shipped samples were transported under ambient conditions. Results The results show that CD63 is a stable marker at Day 1. The CD203c ratio decreases significantly at Day 1. Calculating the CD63/IgE ratio proves to be more stable than CD63 alone. The most stable readouts are the semi‐quantitative results and the trajectory of the dose response curve. Finally, we confirmed that the stability can be extended to samples shipped overnight to the laboratory. Conclusions It is possible to extend the stability of the basophil activation assay to 1 day for samples stored at 18–25°C as well as samples shipped under ambient conditions as long as the temperature is within the 2–37°C range.
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Affiliation(s)
- Theodore Kim
- Allergy Partners of Northern Virginia, Chantilly, Virginia, USA
| | - Jing Yu
- Institute for Asthma and Allergy, Wheaton, Maryland, SA
| | - Henry Li
- Institute for Asthma and Allergy, Wheaton, Maryland, SA
| | - Mark Scarupa
- Institute for Asthma and Allergy, Wheaton, Maryland, SA
| | | | | | - Martha White
- Institute for Asthma and Allergy, Wheaton, Maryland, SA
| | - Carla Ward
- Institute for Asthma and Allergy, Wheaton, Maryland, SA
| | - Atul Shah
- New York Food Allergy and Wellness Center, Centereach, New York, USA
| | | | - Melinda Rathkopf
- Allergy Asthma and Immunology Center of Alaska, Anchorage, Alaska, USA
| | | | - Ahmet Aybar
- Annapolis Pediatric Gastroenterology and Nutrition, Annapolis, Maryland, USA
| | | | - Benjamin Enav
- Pediatric Gastroenterology of Northern Virginia, Fairfax, Virginia, USA
| | - Laura Ispas
- Allergy, Asthma and Immunology Institute, Leesburg, Virginia, USA
| | | | - David Fitzhugh
- Allergy Partners of Chapel Hill, Chapel Hill, North Carolina, USA
| | - James Tracy
- Allergy, Asthma and Immunology Associates, Omaha, Nebraska, USA
| | | | - Zachary Jacobs
- The Center for Allergy and Immunology, Kansas City, Missouri, USA
| | - Jonathan Matz
- Allergy and Asthma Specialists of Maryland, Baltimore, Maryland, USA
| | - David Golden
- Allergy and Asthma Specialists of Maryland, Baltimore, Maryland, USA
| | | | - William McCann
- Allergy Partners of Western North Carolina, Asheville, North Carolina, USA
| | | | - Jeffrey Factor
- New England Food Allergy Treatment Center, Farmington, Connecticut, USA
| | - Raavi Gupta
- Amerimmune, Fairfax, Virginia, USA.,Department of Pathology, SUNY, New York, New York, USA
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Meichner K, Stokol T, Tarigo J, Avery A, Burkhard MJ, Comazzi S, Fogle J, Stowe DM, Rütgen B, Seelig D, Wasserkrug-Naor A, Vernau W, Bienzle D. Multicenter flow cytometry proficiency testing of canine blood and lymph node samples. Vet Clin Pathol 2020; 49:249-257. [PMID: 32246538 DOI: 10.1111/vcp.12843] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/22/2019] [Accepted: 09/20/2019] [Indexed: 12/28/2022]
Abstract
BACKGROUND Flow cytometry (FC) is used increasingly in veterinary medicine for further characterization of hematolymphoid cells. Guidelines for optimizing assay performance and interpretation of results are limited, and concordance of results across laboratories is unknown. OBJECTIVES This study aimed to determine inter-investigator agreement on the interpretation of FC results from split samples analyzed in different laboratories using various protocols, cytometers, and software; and on the interpretation of archived FC standard (FCS) data files contributed by the different investigators. METHODS This was a multicenter observational cross-sectional study. Anticoagulated blood or lymph node aspirate samples from nine client-owned dogs were aliquoted and shipped to participating laboratories. Samples were analyzed with individual laboratory-developed protocols. In addition, FCS files from a set of separate samples from 11 client-owned dogs were analyzed by participating investigators. A person not associated with the study tabulated the results and interpretations. Agreement of interpretations was assessed with Fleiss' kappa statistic. RESULTS Prolonged transit times affected sample quality for some laboratories. Overall agreement among investigators regarding the FC sample interpretation was strong (κ = 0.86 ± 0.19, P < .001), and for specific categories, ranged from moderate to perfect. Agreement of the lymphoproliferation or other leukocyte sample category from the analysis of the FCS files was weak (κ = 0.58 ± 0.05, P < .001). CONCLUSIONS Lymphoproliferations were readily identified by FC, but identification of the categories of hematolymphoid neoplasia in fresh samples or archived files was variable. There is a need for a more standardized approach to maximize the enormous potential of FC in veterinary medicine.
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Affiliation(s)
- Kristina Meichner
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Tracy Stokol
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY, USA
| | - Jaime Tarigo
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Anne Avery
- Department of Microbiology, Immunology & Pathology, University of Colorado, Fort Collins, CO, USA
| | - Mary J Burkhard
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Stefano Comazzi
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Jonathan Fogle
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
| | - Devorah Marks Stowe
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
| | | | - Davis Seelig
- Department of Veterinary Clinical Sciences, University of Minnesota, St Paul, MN, USA
| | - Adi Wasserkrug-Naor
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - William Vernau
- Department of Pathology, Microbiology & Immunology, University of California, Davis, Davis, CA, USA
| | - Dorothee Bienzle
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
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Rybakowska P, Alarcón-Riquelme ME, Marañón C. Key steps and methods in the experimental design and data analysis of highly multi-parametric flow and mass cytometry. Comput Struct Biotechnol J 2020; 18:874-886. [PMID: 32322369 PMCID: PMC7163213 DOI: 10.1016/j.csbj.2020.03.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 01/05/2023] Open
Abstract
High-dimensional, single-cell cell technologies revolutionized the way to study biological systems, and polychromatic flow cytometry (FC) and mass cytometry (MC) are two of the drivers of this revolution. As up to 30-50 dimensions respectively can be measured per single-cell, they allow deep phenotyping combined with cellular functions studies, like cytokine production or protein phosphorylation. In parallel, the bioinformatics field develops algorithms that are able to process incoming data and extract the most useful and meaningful biological information. However, the success of automated analysis tools depends on the generation of high-quality data. In this review we present the most recent FC and MC computational approaches that are used to prepare, process and interpret high-content cytometry data. We also underscore proper experimental design as a key step for obtaining good quality data.
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Affiliation(s)
- Paulina Rybakowska
- GENYO, Centre for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Spain
| | - Marta E. Alarcón-Riquelme
- GENYO, Centre for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Spain
- Institute for Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Concepción Marañón
- GENYO, Centre for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Spain
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