203 results on '"Immunophenotyping methods"'
Search Results
2. Lymphocyte Immunophenotyping methods from Vaccination with Irradiated Autologous Tumor Cells Mixed with Irradiated GM-K562 Cells Stimulates Antitumor Immunity and T Lymphocyte Activation in Patients with Recurrent Malignant Glioma
- Author
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Glenn Dranoff, Martin C. Mihm, Patrick Y. Wen, Tracy T. Batchelor, Alexandra J. Golby, Elizabeth R. Gerstner, Pamela S. Jones, Pankaj Agarwalla, Tetsuro Sasada, Matthias Piesche, Ramana Gorrepati, and William T. Curry
- Abstract
Extended methods for flow cytometry for lymphocyte phenotyping.
- Published
- 2023
3. Human innate lymphoid cells (ILCs): Toward a uniform immune-phenotyping
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Trabanelli, S., Gomez-Cadena, A., Salomé, B., Michaud, K., Mavilio, D., Landis, B.N., Jandus, P., and Jandus, C.
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body regions ,skin and connective tissue diseases ,Animals ,Flow Cytometry/methods ,Humans ,Immunity, Innate/immunology ,Immunologic Factors/immunology ,Immunophenotyping/methods ,Lymphocytes/immunology ,allergy ,flow cytometry ,immune monitoring ,innate lymphoid cells ,leukemia ,phenotype - Abstract
Helper innate lymphoid cells (ILCs), the most recently identified population of the ILC family, play a fundamental role in the restoration of tissue integrity, in the protection against infiltrating pathogens as well as in tumor immune-surveillance. ILCs have been divided into three main subsets, ILC1, ILC2, and ILC3, that can be specifically activated by different signals coming either indirectly from pathogens or from other cell populations, including cancer cells. Following activation, ILCs are in turn able to promptly secrete a wide range of soluble mediators that modulate effector cell functions. The discovery and the study of these immune cells is now offering important opportunities for innovative therapies of allergic airway diseases, inflammatory disorders and might be crucial for the discovery of new targets for the therapy of cancer. It is therefore fundamental that the scientific community establishes harmonized guidelines to obtain a consensus in the identification and phenotypical and functional characterization of ILCs. © 2018 International Clinical Cytometry Society.
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- 2018
4. Human innate lymphoid cells (ILCs): Toward a uniform immune-phenotyping
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Sara, Trabanelli, Alejandra, Gomez-Cadena, Bérengère, Salomé, Katarzyna, Michaud, Domenico, Mavilio, Basile Nicolas, Landis, Peter, Jandus, and Camilla, Jandus
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ddc:616 ,Immunity ,Lymphocytes/immunology ,Flow Cytometry ,Flow Cytometry/methods ,Immunity, Innate ,Immunophenotyping ,ddc:616.8 ,body regions ,Innate/immunology ,Immunologic Factors ,Animals ,Humans ,Immunologic Factors/immunology ,Lymphocytes ,skin and connective tissue diseases ,Immunophenotyping/methods - Abstract
Helper innate lymphoid cells (ILCs), the most recently identified population of the ILC family, play a fundamental role in the restoration of tissue integrity, in the protection against infiltrating pathogens as well as in tumor immune-surveillance. ILCs have been divided into three main subsets, ILC1, ILC2, and ILC3, that can be specifically activated by different signals coming either indirectly from pathogens or from other cell populations, including cancer cells. Following activation, ILCs are in turn able to promptly secrete a wide range of soluble mediators that modulate effector cell functions. The discovery and the study of these immune cells is now offering important opportunities for innovative therapies of allergic airway diseases, inflammatory disorders and might be crucial for the discovery of new targets for the therapy of cancer. It is therefore fundamental that the scientific community establishes harmonized guidelines to obtain a consensus in the identification and phenotypical and functional characterization of ILCs. © 2018 International Clinical Cytometry Society.
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- 2018
5. Semi-automated and standardized cytometric procedures for multi-panel and multi-parametric whole blood immunophenotyping
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Hasan, Milena, Beitz, Benoit, Rouilly, Vincent, Libri, Valentina, Urrutia, Alejandra, Duffy, Darragh, Cassard, Lydie, Di Santo, James P., Mottez, Estelle, Quintana-Murci, Lluis, Albert, Matthew L., Rogge, Lars, The Milieu Interieur, Consortium, Centre d'Immunologie Humaine (CIH), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Institut Pasteur [Paris] (IP), Immunobiologie des Cellules Dendritiques, Immunité Innée - Innate Immunity, Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Immunorégulation, This work benefited from support of the French government's Invest in the Future Program, managed by the Agence Nationale de la Recherche (ANR, reference 10-LABX-69-01), The Milieu Intérieur Consortium is composed of the following team leaders: Laurent Abel (Hôpital Necker), Andres Alcover, Philippe Bousso, Pierre Bruhns, Ana Cumano, Marc Daëron, Cécile Delval, Caroline Demangel, Ludovic Deriano, James Di Santo, Françoise Dromer, Gérard Eberl, Jost Enninga, Antonio Freitas, Odile Gelpi, Ivo Gomperts-Boneca, Serge Hercberg (Université Paris 13), Olivier Lantz (Institut Curie), Claude Leclerc, Hugo Mouquet, Sandra Pellegrini, Stanislas Pol (Hôpital Côchin), Lars Rogge, Anavaj Sakuntabhai, Olivier Schwartz, Benno Schwikowski, Spencer Shorte, Vassili Soumelis (Institut Curie), Frédéric Tangy, Eric Tartour (Hôpital Européen George Pompidou), Antoine Toubert (Hôpital Saint-Louis), Marie-Noëlle Ungeheuer, Lluis Quintana-Murci, and Matthew L. Albert., ANR-10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE(2010), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris], Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Vougny, Marie-Christine, and Laboratoires d'excellence - GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE - - MILIEU INTERIEUR2010 - ANR-10-LABX-0069 - LABX - VALID
- Subjects
MESH: Killer Cells, Natural ,[SDV.IMM] Life Sciences [q-bio]/Immunology ,MESH: Flow Cytometry/methods ,Neutrophils ,T-Lymphocytes ,Immunology ,Population ,Context (language use) ,MESH: Neutrophils ,MESH: Monocytes ,Monocytes ,Specimen Handling ,Immunophenotyping ,Automation ,Antigens, CD ,MESH: B-Lymphocytes ,Humans ,Immunology and Allergy ,Medicine ,education ,MESH: Automation, Laboratory/methods ,Whole blood ,Automation, Laboratory ,B-Lymphocytes ,education.field_of_study ,MESH: Humans ,Multi parametric ,MESH: Dendritic Cells ,business.industry ,MESH: Immunophenotyping/methods ,MESH: Antigens, CD/immunology ,Dendritic Cells ,Flow Cytometry ,MESH: Specimen Handling/methods ,Standardization ,3. Good health ,Killer Cells, Natural ,MESH: T-Lymphocytes ,Robotic systems ,Reference values ,[SDV.IMM]Life Sciences [q-bio]/Immunology ,business ,Cytometry - Abstract
International audience; Immunophenotyping by multi-parametric flow cytometry is the cornerstone technology for enumeration and characterization of immune cell populations in health and disease. Standardized procedures are essential to allow for inter-individual comparisons in the context of population based or clinical studies. Herein we report the approach taken by the Milieu Intérieur Consortium, highlighting the standardized and automated procedures used for immunophenotyping of human whole blood samples. We optimized eight-color antibody panels and procedures for staining and lysis of whole blood samples, and implemented pre-analytic steps with a semi-automated workflow using a robotic system. We report on four panels that were designed to enumerate and phenotype major immune cell populations (PMN, T, B, NK cells, monocytes and DC). This work establishes a foundation for defining reference values in healthy donors. Our approach provides robust protocols for affordable, semi-automated eight-color cytometric immunophenotyping that can be used in population-based studies and clinical trial settings.
- Published
- 2015
6. Immunophenotypic Shifts in Primary Cutaneous γδ T-Cell Lymphoma Suggest Antigenic Modulation: A Study of Sequential Biopsy Specimens
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Sanam Loghavi, Shaoying Li, Carlos Torres-Cabala, Michael T. Tetzlaff, L. Jeffrey Medeiros, Roberto N. Miranda, Eric D. Merril, Victor G. Prieto, Andrés E. Quesada, Ken H. Young, Shimin Hu, Madeleine Duvic, Phyu P. Aung, Rose Lou Marie C. Agbay, Maria C. Ferrufino-Schmidt, and Keyur P. Patel
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0301 basic medicine ,Male ,Pathology ,Skin Neoplasms ,Time Factors ,Biopsy ,T-Lymphocytes ,Polymerase Chain Reaction ,0302 clinical medicine ,Neoplasm ,T-cell lymphoma ,In Situ Hybridization ,Immunophenotyping/methods ,Aged, 80 and over ,medicine.diagnostic_test ,Skin Neoplasms/genetics/immunology/pathology/therapy ,Receptors, Antigen, T-Cell, gamma-delta/genetics/immunology ,T-Lymphocytes/immunology/pathology ,Receptors, Antigen, T-Cell, gamma-delta ,Middle Aged ,Immunohistochemistry ,Lymphoma, T-Cell, Cutaneous ,Phenotype ,Treatment Outcome ,030220 oncology & carcinogenesis ,Child, Preschool ,Monoclonal ,purl.org/pe-repo/ocde/ford#3.02.11 [https] ,Female ,Anatomy ,Clone (B-cell biology) ,Adult ,medicine.medical_specialty ,Lymphoma, T-Cell, Cutaneous/genetics/immunology/pathology/therapy ,Biology ,Pathology and Forensic Medicine ,Immunophenotyping ,03 medical and health sciences ,Young Adult ,Antigen ,Antigens, Neoplasm ,medicine ,Biomarkers, Tumor ,Humans ,Aged ,Biomarkers, Tumor/genetics/immunology ,medicine.disease ,Antigens, Neoplasm/genetics/immunology ,Survival Analysis ,Lymphoma ,purl.org/pe-repo/ocde/ford#3.01.09 [https] ,030104 developmental biology ,Immunology ,Surgery - Abstract
Primary cutaneous gammadelta T-cell lymphoma (PCGD TCL), an aggressive type of lymphoma, accounts for approximately 1% of all primary cutaneous lymphomas. We have occasionally observed changes in T-cell antigen expression (immunophenotypic [IP] shift) over time, a phenomenon that is considered rare in T-cell lymphoma including cutaneous T-cell lymphoma. Therefore, we assessed sequential biopsies of PCGD TCL for possible IP shifts of the lymphoma cells. We searched for cases of PCGD TCL with consecutive biopsies to perform a comprehensive immunohistochemical analysis of paired specimens. A median of 12 markers per case was tested. We evaluated the percentage of neoplastic lymphocytes and determined the differential expression of antigens (gain, loss, increase or decrease). We identified 9 patients with PCGD TCL with consecutive biopsies. All (100%) cases had IP shifts of at least 1 antigen, whereas overall 22 pairs of markers were shifted: gain of reactivity occurred in 7 (31.8%) and loss in 3 (13.6%); increased reactivity in 4 (18.2%) and decreased in 8 (36.4%). Molecular analysis of TCRgamma showed identically sized monoclonal rearrangements between biopsy pairs in 4/4 (100%) patients. There was no correlation between IP shifts and the clinical appearance of lesions, histopathologic or cytologic features, or molecular rearrangements. IP shifts are common in PCGD TCL, occurring in all patients in this study and involving a variety of antigens. IP shifts do not seem to be linked to changes in the T-cell clone and are without obvious clinical or morphologic correlates. The occurrence of IP shifts in PCGD TCL suggests that antigen modulation may be involved in pathogenesis. IP shifts are somewhat frequent in T-cell lymphoma; however, it does not suggest a second neoplasm, and molecular studies can be used to determine clonal identity.
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- 2017
7. Quantification methods for human and large animal leukocytes using DNA dyes by flow cytometry
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Pieper, Ina Laura, Radley, Gemma, Chan, Chris H H, Friedmann, Yasmin, Foster, Graham, and Thornton, Catherine A
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Cell Survival ,Anthraquinones/chemistry ,Gene Expression ,Flow Cytometry ,Leukocytes/classification ,Leukocyte Common Antigens/genetics ,Leukocyte Count ,Animals ,Humans ,Cattle ,Fluorescent Dyes/chemistry ,Anthracyclines/chemistry ,DNA/chemistry ,Sheep, Domestic ,Staining and Labeling/methods ,Immunophenotyping/methods - Abstract
Ovine and bovine blood is used heavily within the development of blood-handling medical devices, such as heart pumps (left ventricular assist devices, LVADs), for which blood cell damage needs to be monitored during in vitro testing. Hematology analyzers provide cell counts but no information about cell viability. The anthraquinone DNA dyes CyTRAK Orange™ and DRAQ7™ have practical and spectral properties rendering them suitable for multicolor assays. Compared to other DNA dyes such as Vybrant Dyecycle, CyTRAK Orange enables a faster staining protocol and does not require incubation at +37°C. Compared to traditional viability dyes such as propidium iodide and 7AAD, DRAQ7's unique spectral profile of excitation in both blue and red lasers and far-red emission enables identification of dual positive dead cell events and frees up detectors for use with other reagents. CyTRAK Orange and DRAQ7 could be used in combination with absolute counting bead standards to provide cell counts and viability but the combination of these dyes has previously only been used for microscopy on rodent cells. The purpose of this study was to evaluate the use of these dyes in combination in large animal blood samples for flow cytometry. A viability and cell counting protocol for bovine, ovine, and human leukocytes using CyTRAK Orange and DRAQ7 was prepared. Four different counting bead standards were evaluated using the Navios and FACSAria cytometers and compared to counts obtained from hematology analyzers. CyTRAK Orange successfully detected CD45(+) leukocytes in all species. The DRAQ7 single-stained dead cell counts correlated well with the CyTRAK Orange/DRAQ7 double-stained dead cell counts in human and bovine blood, but not in ovine blood, which could be related to the blood source. In conclusion, for human and bovine blood, this method works well for viability counts using different flow cytometers and bead standards. © 2016 International Society for Advancement of Cytometry.
- Published
- 2016
8. Chemoattractant Signals and Adhesion Molecules Promoting Human Regulatory T Cell Recruitment to Porcine Endothelium
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Rachel Chicheportiche, Jorg Dieter Seebach, Yannick D. Muller, Driss Ehirchiou, Natacha Madelon, Ruhollah Heyrani Nobari, and Mårten K J Schneider
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0301 basic medicine ,Cytotoxicity, Immunologic ,Swine ,Cytotoxicity ,T-Lymphocytes ,Cell Communication ,T-Lymphocytes, Regulatory ,Cell Degranulation ,Immune tolerance ,Regulatory/immunology/metabolism ,Chemokine receptor ,0302 clinical medicine ,Immunologic ,Killer Cells ,IL-2 receptor ,Cells, Cultured ,Immunophenotyping/methods ,ddc:616 ,Cultured ,biology ,Cell adhesion molecule ,Chemotaxis ,Intercellular adhesion molecule ,Flow Cytometry ,Cell biology ,Killer Cells, Natural ,Chemotaxis, Leukocyte ,Phenotype ,Heterografts ,Endothelial Cells/immunology/metabolism ,Signal Transduction ,Natural/immunology/metabolism ,Cells ,Integrin ,Immunophenotyping ,03 medical and health sciences ,Cell Adhesion ,Immune Tolerance ,Animals ,Humans ,Cell adhesion ,Cell Adhesion Molecules/immunology/metabolism ,Transplantation ,Transendothelial and Transepithelial Migration ,Endothelial Cells ,Leukocyte ,Chemokine CCL17/immunology/metabolism ,Coculture Techniques ,030104 developmental biology ,biology.protein ,Chemokine CCL17 ,Cell Adhesion Molecules ,030215 immunology - Abstract
Background Human CD4+CD25+Foxp3+ T regulatory cells (huTreg) suppress CD4+ T cell-mediated antipig xenogeneic responses in vitro and might therefore be used to induce xenograft tolerance. The present study investigated the role of the adhesion molecules, their porcine ligands, and the chemoattractant factors that may promote the recruitment of huTreg to porcine aortic endothelial cells (PAEC) and their capacity to regulate antiporcine natural killer (NK) cell responses. Methods Interactions between ex vivo expanded huTreg and PAEC were studied by static chemotaxis assays and flow-based adhesion and transmigration assays. In addition, the suppressive function of huTreg on human antiporcine NK cell responses was analyzed. Results The TNFα-activated PAEC released factors that induce huTreg chemotaxis, partially inhibited by antihuman CXCR3 blocking antibodies. Coating of PAEC with human CCL17 significantly increased the transmigration of CCR4+ huTreg under physiological shear stress. Under static conditions, transendothelial Treg migration was inhibited by blocking integrin sub-units (CD18, CD49d) on huTreg, or their respective porcine ligands intercellular adhesion molecule 2 (CD102) and vascular cell adhesion molecule 1 (CD106). Finally, huTreg partially suppressed xenogeneic human NK cell adhesion, NK cytotoxicity and degranulation (CD107 expression) against PAEC; however, this inhibition was modest, and there was no significant change in the production of IFNγ. Conclusions Recruitment of huTreg to porcine endothelium depends on particular chemokine receptors (CXCR3, CCR4) and integrins (CD18 and CD49d) and was increased by CCL17 coating. These results will help to develop new strategies to enhance the recruitment of host huTreg to xenogeneic grafts to regulate cell-mediated xenograft rejection including NK cell responses.
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- 2016
9. Identification of Neoantigens and Construction of Immune Subtypes in Prostate Adenocarcinoma.
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Gao, Yukui, Wang, Guixin, Chen, Yanzhuo, Zhang, Mingpeng, Gao, Wenlong, Shang, Zhiqun, and Niu, Yuanjie
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TUMOR antigens ,PROSTATE ,GENE expression profiling ,ADENOCARCINOMA ,VACCINE development ,TARGETED drug delivery - Abstract
Background: Messenger ribonucleic acid (mRNA) vaccine has been considered as a potential therapeutic strategy and the next research hotspot, but their efficacy against prostate adenocarcinoma (PRAD) remains undefined. This study aimed to find potential antigens of PRAD for mRNA vaccine development and identify suitable patients for vaccination through immunophenotyping. Methods: Gene expression profiles and clinical information were obtained from TCGA and ICGC. GEPIA2 was used to calculate the prognostic index of the selected antigens. The genetic alterations were compared on cBioPortal and the correlation between potential antigen and immune infiltrating cells was explored by TIMER. ConsensusClusterPlus was used to construct a consistency matrix, and identify the immune subtypes. Graph learning-based dimensional reduction was performed to depict immune landscape. Boruta algorithm and LASSO logistic analysis were used to screen PRAD patients who may benefit from mRNA vaccine. Results: Seven potential tumor antigens selected were significantly positively associated with poor prognosis and the antigen-presenting immune cells (APCs) in PRAD, including ADA, FYN, HDC, NFKBIZ, RASSF4, SLC6A3, and UPP1. Five immune subtypes of PRAD were identified by differential molecular, cellular, and clinical characteristics in both cohorts. C3 and C5 had immune "hot" and immunosuppressive phenotype, On the contrary, C1&C2 had immune "cold" phenotype. Finally, the immune landscape characterization showed the immune heterogeneity among patients with PRAD. Conclusions: ADA, FYN, HDC, NFKBIZ, RASSF4, SLC6A3, and UPP1 are potential antigens for mRNA vaccine development against PRAD, and patients in type C1 and C2 are suitable for vaccination. [ABSTRACT FROM AUTHOR]
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- 2022
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10. NBAS Variants Are Associated with Quantitative and Qualitative NK and B Cell Deficiency.
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Lenz, Dominic, Pahl, Jens, Hauck, Fabian, Alameer, Seham, Balasubramanian, Meena, Baric, Ivo, Boy, Nikolas, Church, Joseph A., Crushell, Ellen, Dick, Anke, Distelmaier, Felix, Gujar, Jidnyasa, Indolfi, Giuseppe, Lurz, Eberhard, Peters, Bianca, Schwerd, Tobias, Serranti, Daniele, Kölker, Stefan, Klein, Christoph, and Hoffmann, Georg F.
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KILLER cells ,B cells ,CELL populations ,HUMORAL immunity ,IMMUNE system - Abstract
Purpose: Biallelic pathogenic NBAS variants manifest as a multisystem disorder with heterogeneous clinical phenotypes such as recurrent acute liver failure, growth retardation, and susceptibility to infections. This study explores how NBAS-associated disease affects cells of the innate and adaptive immune system. Methods: Clinical and laboratory parameters were combined with functional multi-parametric immunophenotyping methods in fifteen NBAS-deficient patients to discover possible alterations in their immune system. Results: Our study revealed reduced absolute numbers of mature CD56
dim natural killer (NK) cells. Notably, the residual NK cell population in NBAS-deficient patients exerted a lower potential for activation and degranulation in response to K562 target cells, suggesting an NK cell–intrinsic role for NBAS in the release of cytotoxic granules. NBAS-deficient NK cell activation and degranulation was normalized upon pre-activation by IL-2 in vitro, suggesting that functional impairment was reversible. In addition, we observed a reduced number of naïve B cells in the peripheral blood associated with hypogammaglobulinemia. Conclusion: In summary, we demonstrate that pathogenic biallelic variants in NBAS are associated with dysfunctional NK cells as well as impaired adaptive humoral immunity. [ABSTRACT FROM AUTHOR]- Published
- 2021
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11. Peripheral B-Cell Immunophenotyping Identifies Heterogeneity in IgG4-Related Disease.
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Li, Jieqiong, Liu, Zheng, Zhang, Panpan, Lin, Wei, Lu, Hui, Peng, Yu, Peng, Linyi, Zhou, Jiaxin, Wang, Mu, Chen, Hua, Zhao, Lidan, Wang, Li, Qin, Chenman, Hu, Chaojun, Zeng, Xiaofeng, Zhao, Yan, Fei, Yunyun, and Zhang, Wen
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IMMUNOPHENOTYPING ,B cells ,PRINCIPAL components analysis ,HETEROGENEITY ,CLUSTER analysis (Statistics) - Abstract
Objectives: To elucidate heterogeneity of IgG4-related disease (IgG4-RD) based on B cell immunophenotyping. Methods: Immunophenotyping of 4 B-cell subsets in peripheral blood from patients with active IgG4-RD (aIgG4-RD, n=105) was performed using flow cytometry to get preliminary B-cell heterogeneity spectrum. Then 10 B-cell subsets were characterized in aIgG4-RD (n = 49), remissive IgG4-RD (rIgG4-RD, n = 49), and healthy controls (HCs, n = 47), followed by principal components analysis (PCA) and cluster analysis to distinguish B-cell immunophenotypes and classify IgG4-RD patients into subgroups. Results: Cluster analysis identified two endotypes in 105 aIgG4-RD patients based on 4 B-cell subsets: Group1 with higher Breg and naive B cells (n = 48), and Group2 with higher plasmablasts and memory B cells (MBCs) (n = 57). PCA indicated that aIgG4-RD consisted of plasmablast-naive B cell and MBCs-Breg axes abnormalities. There was a negative relationship between naive B cells and disease activity. Both plasmablasts and MBCs were positively associated with serological biomarkers. Cluster analysis stratified aIgG4-RD patients into 3 subgroups based on 10 B-cell subsets: subgroup1 with low MBCs and normal Breg, subgroup2 with high MBCs and low Breg, and subgroup3 with high plasmablasts and low naive B cells. Patients in subroup2 and subgroup3 were more likely to be resistant to treatment. Conclusion: Patients with aIgG4-RD can be divided into 3 subgroups based on B cell heterogeneity. The B cell immunophenotyping could help elucidate the pathogenesis of IgG4-RD, identify patients with potential refractory IgG4-RD, and provide important information for the development of new therapies. [ABSTRACT FROM AUTHOR]
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- 2021
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12. Dysplasia and PNH-type cells in bone marrow aspirates of myelodysplastic syndromes
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Westers, Theresia M., Alhan, Canan, Visser-Wisselaar, Heleen A., Chitu, Dana A., van de Loosdrecht, Arjan A., Westers, Theresia M., Alhan, Canan, Visser-Wisselaar, Heleen A., Chitu, Dana A., and van de Loosdrecht, Arjan A.
- Abstract
Background: Flow cytometry is increasingly applied in cytopenic patients suspected for myelodysplastic syndromes (MDS). Analysis includes evaluation of antigen expression patterns in granulocytes of which, for example, partial lack of CD16 may indicate dysplasia, but presence of paroxysmal nocturnal hemoglobinuria (PNH)-type cells should be considered. However, diagnostic bone marrow (BM) samples hamper PNH analysis because immature stages in the granulo-/monocytic compartment lack expression of certain glycophosphatidyl-inositol-anchored proteins. In this prospective study, we evaluated the presence of PNH-type cells in BM next to aberrancies from routine MDS immunophenotyping. Methods: We combined antibodies defining maturation trajectories with FLAER. Validation of the designed method against routine PNH analysis and parallel analysis of BM and blood samples revealed similar results (granulocytes: Wilcoxon p = 0.25 and p = 0.82, respectively). We analyzed BM samples from 134 MDS, 17 chronic myelomonocytic leukemia, 15 aplastic anemia (AA), 1 PNH, 51 non-clonal cytopenic controls, and 12 normal controls. Results: Most AA/PNH-BM samples showed clear PNH clones: median 1.1% (0%–35%); CD16 loss on mature neutrophils paralleled PNH-clone sizes. In MDS-BM, only 3.7% of cases showed ≥0.1% PNH-type cells, whereas partial CD16 loss was more frequent and abundant. Conclusions: Our findings confirm that dysplastic features in MDS-BM may point to presence of PNH-type cells, though only few cases displayed FLAER-negative cells. We showed that identification of these cells in the granulocyte compartment of BM specimen is feasible, but—according to international guidelines—results need to be confirmed in peripheral blood.
- Published
- 2023
13. Validation of a hybrid approach to standardize immunophenotyping analysis in large population studies: The Health and Retirement Study.
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Hunter-Schlichting, DeVon, Lane, John, Cole, Benjamin, Flaten, Zachary, Barcelo, Helene, Ramasubramanian, Ramya, Cassidy, Erin, Faul, Jessica, Crimmins, Eileen, Pankratz, Nathan, and Thyagarajan, Bharat
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IMMUNOPHENOTYPING ,DENDRITIC cells ,MONOCYTES ,STANDARDIZATION ,CANCER cells - Abstract
Traditional manual gating strategies are often time-intensive, place a high burden on the analyzer, and are susceptible to bias between analyzers. Several automated gating methods have shown to exceed performance of manual gating for a limited number of cell subsets. However, many of the automated algorithms still require significant manual interventions or have yet to demonstrate their utility in large datasets. Therefore, we developed an approach that utilizes a previously published automated algorithm (OpenCyto framework) with a manually created hierarchically cell gating template implemented, along with a custom developed visualization software (FlowAnnotator) to rapidly and efficiently analyze immunophenotyping data in large population studies. This approach allows pre-defining populations that can be analyzed solely by automated analysis and incorporating manual refinement for smaller downstream populations. We validated this method with traditional manual gating strategies for 24 subsets of T cells, B cells, NK cells, monocytes and dendritic cells in 931 participants from the Health and Retirement Study (HRS). Our results show a high degree of correlation (r ≥ 0.80) for 18 (78%) of the 24 cell subsets. For the remaining subsets, the correlation was low (<0.80) primarily because of the low numbers of events recorded in these subsets. The mean difference in the absolute counts between the hybrid method and manual gating strategy of these cell subsets showed results that were very similar to the traditional manual gating method. We describe a practical method for standardization of immunophenotyping methods in large scale population studies that provides a rapid, accurate and reproducible alternative to labor intensive manual gating strategies. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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14. Systematic profiling of mitochondria-related transcriptome in tumorigenesis, prognosis, and tumor immune microenvironment of intrahepatic cholangiocarcinoma: a multi-center cohort study.
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Bo Chen, Mengmeng Lu, Qiwen Chen, Enguang Zou, Zhiyuan Bo, Jiacheng Li, Rui Zhao, Jungang Zhao, Zhengping Yu, Gang Chen, and Lijun Wu
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KILLER cells ,TUMOR microenvironment ,OXIDATIVE phosphorylation ,RNA sequencing ,BIOLOGY - Abstract
Background: Mitochondrial dysfunction has been shown to play a critical role in cancer biology. However, its involvement in intrahepatic cholangiocarcinoma (iCCA) remains significantly understudied. Methods: RNA sequencing data of 30 pairs of iCCA and paracancerous tissues were collected from the First Affiliated Hospital of Wenzhou Medical University (WMU). The WMU cohort (n = 30) was integrated with public TCGA (n = 30) and GSE107943 (n = 30) datasets to establish a multi-center iCCA cohort. We merged the TCGA and GSE107943 cohorts into an exploration cohort to develop a mitochondria signature for prognosis assessment, and utilized the WMU cohort for external validation. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Hallmarker analyses were used for functional interpretation of iCCA associated mitochondria-related genes (MRGs). In addition, unsupervised clustering was performed to identify mitochondria-based iCCA subtypes with the data of three institutions. Further investigations were conducted to examine the impact of mitochondrial dysfunction on drug responses, alteration of the tumor immune microenvironment, and immune responses. Results: Two hundred and sixty-three iCCA-related MRGs were identified to be related to fatty acid metabolism, oxidative phosphorylation, and apoptosis. Through univariate and multivariate Cox, and LASSO analyses, a mitochondria signature with five optimal MRGs was established to evaluate the prognosis of iCCA patients with the AUC values ranged from 0.785 to 0.928 in the exploration cohort. The signature also exhibited satisfactory performance in the WMU cohort with AUC values of 0.817-0.871, and was identified as an independent risk predictor in both cohorts. Additionally, we found that patients with higher mitochondria score with poor prognosis presented lower infiltration levels of CD4
+ T-cell, NK cells, and monocytes, and demonstrated higher sensitivity to targeted therapies, including sorafenib. Furthermore, two distant mitochondria-based subtypes were determined, and subtype 2 was associated with shorter survival time and immunosuppressive tumor microenvironment. Finally, the differential protein expression of five key MRGs was verified by Immunohistochemistry. Conclusion: We found mitochondrial dysfunction modulates aberrant metabolism, oxidative stress, immune responses, apoptosis, and drug sensitivity in iCCA. A mitochondria signature and two mitochondria-based iCCA subtypes were identified for clinical risk stratification and immunophenotyping. [ABSTRACT FROM AUTHOR]- Published
- 2024
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15. Modulation of Host Immunity by the Gut Microbiome and Cytomegalovirus
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Chin, Ning, Hartigan-O'Connor, Dennis J.1, Chin, Ning, Chin, Ning, Hartigan-O'Connor, Dennis J.1, and Chin, Ning
- Abstract
Host immune responses and the host immune system itself are shaped by interactions with environmental factors including diet, commensal microbiota, and pathogens. The microbiome, defined as a community of microorganisms and their interactions with their surrounding environmental conditions, further interacts with structural elements, metabolites, and signaling molecules from other microorganisms and the host. These networks of interactions result in heterogeneous immune responses and affect our ability to develop immunotherapies or vaccines that are universally applicable to the entire population. Untangling these interactions between environmental factors and the host immune system in the presence of many covariates has been difficult but has been increasingly aided by advances in technologies and our ability to process multi-dimensional data sets. Understanding the extent of environmental influence on the host immune system is important to further identify the important factors to drive desired immune responses, especially for developing cancer therapies and vaccines. In this dissertation, we used metagenomics, transcriptomics, and single-cell immunophenotyping methods to understand important influences on the immune system, including diet, microbiome, latent viral infections, and viral vector-based vaccination. We found that dietary intervention can lead to transient changes in the gut microbiome without causing dramatic changes to the infant immune system, suggesting limited effects of host-microbe interactions over a short time period. Latent viral infections have much greater impacts on the host immune system and can additionally subvert or supplant relationships between the host and other microbes. Latent viral infections also resulted in different vaccine responses that can be observed at the transcriptomic level. Overall, we identified latent infection with cytomegalovirus (CMV) as one of the major contributors to different immune responses in different ind
- Published
- 2022
16. Peripheral Immunophenotyping Identifies Three Subgroups Based on T Cell Heterogeneity in Lupus Patients.
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Kubo, Satoshi, Nakayamada, Shingo, Yoshikawa, Maiko, Miyazaki, Yusuke, Sakata, Kei, Nakano, Kazuhisa, Hanami, Kentaro, Iwata, Shigeru, Miyagawa, Ippei, Saito, Kazuyoshi, and Tanaka, Yoshiya
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CLUSTER analysis (Statistics) ,FACTOR analysis ,FLOW cytometry ,SYSTEMIC lupus erythematosus ,T cells ,PHENOTYPES ,MONONUCLEAR leukocytes - Abstract
Objective To elucidate the diversity of systemic lupus erythematosus (SLE) based on immunophenotyping. Methods Peripheral blood mononuclear cells were obtained from 143 SLE patients and 49 healthy individuals. Circulating B, T, and dendritic cells were defined using flow cytometric analysis as recommended by the Human Immunology Project Consortium. Based on these results, immunophenotypes were distinguished by principal components analysis (PCA), and cluster analysis was used to classify SLE patients into subgroups. Results The proportions of Treg and follicular helper T (Tfh) cells were higher in SLE patients than in healthy controls, whereas Th1 and Th17 cell proportions did not differ. Proportions of class-switched memory B cells and IgD-CD27- B cells were increased in SLE patients as well. The largest difference compared to the control group was observed in the proportion of plasmablasts, which was higher in SLE patients and correlated with disease activity as assessed with the British Isles Lupus Assessment Group index. PCA indicated that the immunophenotype of SLE patients consisted of abnormalities of the T and B cell axes. Cluster analysis showed that the SLE patients could be stratified into 3 subgroups (with high proportions of plasmablasts in all groups): patients who did not show the characteristic features (T cell-independent group), patients with a high percentage of Tfh cells (Tfh-dominant group), and patients with a high percentage of memory Treg cells (Treg-dominant group). The percentage of patients whose SLE was resistant to treatment was highest among the Tfh-dominant group. Conclusion Our study indicates that patients with active SLE can be divided into 3 subgroups based on T cell heterogeneity. Further immunophenotyping studies should help elucidate the pathogenesis of SLE and provide important information for the development of new therapies. [ABSTRACT FROM AUTHOR]
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- 2017
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17. Immune cell phenotypes and mortality in the Framingham Heart Study.
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Ragab, Ahmed A. Y., Doyle, Margaret F., Chen, Jiachen, Fang, Yuan, Lunetta, Kathryn L., and Murabito, Joanne M.
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PHENOTYPES ,MORTALITY ,AGE groups ,SURVIVAL rate ,CARDIOVASCULAR diseases risk factors - Abstract
Background: Global life expectancy is rising, with the 60 + age group projected to hit 2 billion by 2050. Aging impacts the immune system. A notable marker of immune system aging is the presence of Aging-Related Immune Cell Phenotypes (ARIPs). Despite their importance, links between immune cell phenotypes including ARIPs and mortality are underexplored. We prospectively investigated 16 different immune cell phenotypes using flow cytometry and IL-6 in relation to survival outcome among dementia-free Framingham Heart Study (FHS) offspring cohort participants who attended the seventh exam (1998–2001). Results: Among 996 participants (mean age 62 years, range 40 to 88 years, 52% female), the 19-year survival rate was 65%. Adjusting for age, sex, and cytomegalovirus (CMV) serostatus, higher CD4/CD8 and Tc17/CD8 + Treg ratios were significantly associated with lower all-cause mortality (HR: 0.86 [0.76–0.96], 0.84 [0.74–0.94], respectively), while higher CD8 regulatory cell levels (CD8 + CD25 + FoxP3 +) were associated with increased all-cause mortality risk (HR = 1.17, [1.03–1.32]). Elevated IL-6 levels correlated with higher all-cause, cardiovascular, and non-cardiovascular mortality (HR = 1.43 [1.26–1.62], 1.70 [1.31–2.21], and 1.36 [1.18–1.57], respectively). However, after adjusting for cardiovascular risk factors and prevalent cancer alongside age, sex, and CMV, immune cell phenotypes were no longer associated with mortality in our cohort. Nonetheless, IL-6 remained significantly associated with all-cause and cardiovascular mortality (HRs: 1.3 [1.13–1.49], 1.5 [1.12–1.99], respectively). Conclusions: In 19-year follow-up, higher Tc17/CD8 + Treg and CD4/CD8 ratios were associated with lower all-cause mortality, while the CD8 + CD25 + FoxP3 + (CD8 + Treg) phenotype showed increased risk. Elevated IL-6 levels consistently correlated with amplified mortality risks. These findings highlight the links between immune phenotypes and mortality, suggesting implications for future research and clinical considerations. [ABSTRACT FROM AUTHOR]
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- 2024
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18. TRPA1 Covalent Ligand JT010 Modifies T Lymphocyte Activation.
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Szabó, Katalin, Makkai, Géza, Konkoly, János, Kormos, Viktória, Gaszner, Balázs, Berki, Tímea, and Pintér, Erika
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LYMPHOCYTE transformation ,CELL analysis ,T cells ,B cells ,NEURON analysis ,MONOCYTES ,B cell receptors ,TRP channels - Abstract
Transient Receptor Potential Ankyrin 1 (TRPA1) is a non-selective cation channel involved in sensitivity to a plethora of irritating agents and endogenous mediators of oxidative stress. TRPA1 influences neuroinflammation and macrophage and lymphocyte functions, but its role is controversial in immune cells. We reported earlier a detectable, but orders-of-magnitude-lower level of Trpa1 mRNA in monocytes and lymphocytes than in sensory neurons by qRT-PCR analyses of cells from lymphoid organs of mice. Our present goals were to (a) further elucidate the expression of Trpa1 mRNA in immune cells by RNAscope in situ hybridization (ISH) and (b) test the role of TRPA1 in lymphocyte activation. RNAscope ISH confirmed that Trpa1 transcripts were detectable in CD14
+ and CD4+ cells from the peritoneal cavity of mice. A selective TRPA1 agonist JT010 elevated Ca2+ levels in these cells only at high concentrations. However, a concentration-dependent inhibitory effect of JT010 was observed on T-cell receptor (TcR)-induced Ca2+ signals in CD4+ T lymphocytes, while JT010 neither modified B cell activation nor ionomycin-stimulated Ca2+ level. Based on our present and past findings, TRPA1 activation negatively modulates T lymphocyte activation, but it does not appear to be a key regulator of TcR-stimulated calcium signaling. [ABSTRACT FROM AUTHOR]- Published
- 2024
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19. Lingering Effects of Early Institutional Rearing and Cytomegalovirus Infection on the Natural Killer Cell Repertoire of Adopted Adolescents.
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Wood, Elizabeth K., Reid, Brie M., Sheerar, Dagna S., Donzella, Bonny, Gunnar, Megan R., and Coe, Christopher L.
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KILLER cells ,CYTOMEGALOVIRUS diseases ,TUMOR necrosis factors ,ADOLESCENCE ,TEENAGERS ,POOR families ,CELL populations - Abstract
Adversity during infancy can affect neurobehavioral development and perturb the maturation of physiological systems. Dysregulated immune and inflammatory responses contribute to many of the later effects on health. Whether normalization can occur following a transition to more nurturing, benevolent conditions is unclear. To assess the potential for recovery, blood samples were obtained from 45 adolescents adopted by supportive families after impoverished infancies in institutional settings (post-institutionalized, PI). Their immune profiles were compared to 39 age-matched controls raised by their biological parents (non-adopted, NA). Leukocytes were immunophenotyped, and this analysis focuses on natural killer (NK) cell populations in circulation. Cytomegalovirus (CMV) seropositivity was evaluated to determine if early infection contributed to the impact of an atypical rearing. Associations with tumor necrosis factor-alpha (TNF-α) and interferon-gamma (IFN-γ), two cytokines released by activated NK cells, were examined. Compared to the NA controls, PI adolescents had a lower percent of CD56
bright NK cells in circulation, higher TNF-α levels, and were more likely to be infected with CMV. PI adolescents who were latent carriers of CMV expressed NKG2C and CD57 surface markers on more NK cells, including CD56dim lineages. The NK cell repertoire revealed lingering immune effects of early rearing while still maintaining an overall integrity and resilience. [ABSTRACT FROM AUTHOR]- Published
- 2024
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20. Cost-effective approach to the diagnostic workup of B cell lymphoproliferative disorders via optimal integration of flow cytometric data.
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Mason, E. F., Morgan, E. A., Pinkus, G. S., and Pozdnyakova, O.
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B cells ,BIOMARKERS ,CHI-squared test ,COST effectiveness ,ORGAN donation ,FLOW cytometry ,IMMUNOHISTOCHEMISTRY ,IMMUNOPHENOTYPING ,DISEASE relapse ,LYMPHOPROLIFERATIVE disorders ,CYTOMETRY ,ACQUISITION of data ,RETROSPECTIVE studies ,DATA analysis software ,MANN Whitney U Test ,DIAGNOSIS - Abstract
Introduction The workup of lymphoproliferative disorders ( LPDs) involves the combined use of flow cytometry ( FC) and immunohistochemistry ( IHC). This often results in duplicate immunophenotypic testing and adds costs that may not be eligible for reimbursement based on the Medicare National Correct Coding Initiative. We aimed to establish a cost-effective diagnostic algorithm based on initial FC categorization to reduce repetitive immunophenotyping. Methods We retrospectively reviewed 242 cases of suspected LPDs with concurrent FC and IHC testing over a 12-month period. We correlated FC with surgical diagnoses and evaluated the frequency of repeat IHC testing. Results Repetitive immunophenotyping was common; overall, 85% of cases had at least one marker repeated. Concordant cases were significantly less likely to have markers repeated than discordant cases. Of concordant B cell malignancies, 57% represented recurrent disease; however, repeat marker usage was not decreased as compared to new diagnoses. The most frequently repeated markers were CD3, CD5, CD10, and CD20. Conclusions We propose that in concordant cases, CD5 and CD10 should not be repeated by IHC; this would decrease the use of these markers by 80% and 76%, respectively. We developed an algorithmic approach to IHC usage that has improved incorporation of FC data at our institution and may reduce healthcare costs. [ABSTRACT FROM AUTHOR]
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- 2017
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21. American College of Toxicology.
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WEIGHT loss ,DOPAMINE receptors ,CENTRAL nervous system physiology ,MONOCLONAL antibodies ,ANIMAL tracks ,FETAL brain ,LYSOSOMES ,HEALTH facilities - Abstract
This document is a collection of abstracts from the 44th Annual Meeting of the American College of Toxicology, covering a range of topics related to toxicology research. The abstracts discuss various studies, including the protective effect of an antioxidant on kidney fibrosis in mice, sex differences in the lung-brain axis transcriptome in response to exposure to indoor fungi, and the evaluation of respiratory sensitizers using an in vitro model. Other studies explore the role of asparagine synthetase in colorectal cancer tumor metabolism, the induction of platinum resistance in ovarian cancer by certain substances, and the modulation of lung injury and inflammation by an RNA-binding protein. Additionally, the frequency of potential drug interactions in pediatric patients and the rescue role of myricetin in testicular oxidative stress, inflammation, and apoptosis in a rat model of Parkinson's disease are examined. The document also includes studies on the effects of nicotine products on gingival tissue, the safety evaluation of a novel sweetener alternative, the cardiovascular effects of a specific drug in monkeys, the use of an in silico system for drug development assessments, the release of cardiac troponin I from cardiomyocytes, the Membrane Proteome Array platform for assessing biotherapeutics, the translational and in silico assessment of liver injury for a specific compound, a modified method for collecting cerebrospinal fluid in rodents and monkeys, and different methods of delivering gene therapies to the central nervous system in non-human primates. These abstracts provide [Extracted from the article]
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- 2024
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22. Validation of a flow cytometry-based method to quantify viable lymphocyte subtypes in fresh and cryopreserved hematopoietic cellular products.
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Mfarrej, Bechara, Gaude, Julie, Couquiaud, Jerome, Calmels, Boris, Chabannon, Christian, and Lemarie, Claude
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CRYOPRESERVATION of cells , *LYMPHOCYTES , *MANUFACTURING cells , *KILLER cells , *BLOOD products , *BINDING site assay , *CELL survival - Abstract
Adoptive cellular therapy with immune effector cells (IECs) has shown promising efficacy against some neoplastic diseases as well as potential in immune regulation. Both inherent variability in starting material and variations in cell composition produced by the manufacturing process must be thoroughly evaluated with a validated method established to quantify viable lymphocyte subtypes. Currently, commercialized immunophenotyping methods determine cell viability with significant errors in thawed products since they do not include any viability staining. We hereby report on the validation of a flow cytometry-based method for quantifying viable lymphocyte immunophenotypes in fresh and cryopreserved hematopoietic cellular products. Using fresh or frozen cellular products and stabilized blood, we report on the validation parameters accuracy, uncertainty, precision, sensitivity, robustness and contamination between samples for quantification of viable CD3+, CD4+ T cells, CD8+ T cells, CD3–CD56+CD16+/– NK cells, CD19+ B cells and CD14+ monocytes of relevance to fresh and cryopreserved hematopoietic cellular products using the Cytomics FC500 cytometer (Beckman Coulter). The acceptance criteria set in the validation plan were all met. The method is able to accommodate the variability in absolute numbers of cells in starting materials collected or cryopreserved from patients or healthy donors (uncertainty of ≤20% at three different concentrations), stability over time (compliance over 3 years during regular inter-laboratory comparisons) and confidence in meaningful changes during cell processing and manufacturing (intra-assay and intermediate precision of 10% coefficient of variation). Furthermore, the method can accurately report on the efficacy of cell depletion since the lower limit of quantification was established (CD3+, CD4+ and CD8+ cells at 9, 8 and 8 cells/µL, respectively). The method complies with Foundation for the Accreditation of Cellular Therapy (FACT) standards for IEC, FACT-Joint Accreditation Committee of ISCT-EBMT (JACIE) hematopoietic cell therapy standards, International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use Q2(R1) and International Organization for Standardization 15189 standards. Furthermore, it complies with Ligand Binding Assay Bioanalytical Focus Group/American Association of Pharmaceutical Scientists, International Council for Standardization of Hematology/International Clinical Cytometry Society and European Bioanalysis Forum recommendations for validating such methods. The implications of this effort include standardization of viable cell immunophenotyping of starting material for cell manufacturing, cell selection and in-process quality controls or dosing of IECs. This method also complies with all relevant standards, particularly FACT-JACIE standards, in terms of enumerating and reporting on the viability of the "clinically relevant cell populations." [ABSTRACT FROM AUTHOR]
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- 2021
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23. Non-cell-autonomous suppression of tumor growth by RECK in immunocompetent mice.
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Matsuzaki T, Inoue J, Minato N, and Noda M
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RECK is a candidate tumor suppressor gene isolated as a gene that induces flat reversion in a cell line transformed by the KRAS oncogene. Since RECK knockout mice die in utero, they are not suitable for studying the effects of RECK on tumor formation. In this study, we found an increased incidence of spontaneous pulmonary adenomas in mice with reduced RECK expression (RECK-Hypo mice). To evaluate the effects of RECK expressed by either tumor cells or host cells on tumor growth, we established a tumorigenic cell line (MKER) from the kidney of a C57BL/6 mouse and performed syngeneic transplantation experiments. Our results indicate that when RECK expression is low in host cells, transplanted MKER cells grow faster and kill the animal more rapidly. Since RECK is required for the formation of proper fibrillin fibers that serve as a tissue reservoir for precursors of TGFβ-family cytokines, we assessed the levels of TGFβ1 in the peripheral blood. We found a significant increase in TGFβ1 in RECK-Hypo mice compared to wild-type mice. We also found that the proportion of FOXP3-positive regulatory T (Treg) cells among splenocytes was higher in RECK-Hypo mice compared to the control mice. Furthermore, the number of FOXP3-positive cells in spontaneous hematopoietic neoplasms in the lungs as well as tumors that formed after MKER transplantation was significantly higher in RECK-Hypo mice compared to the control mice. These findings indicate that RECK-mediated tumor suppression involves a non-cell-autonomous mechanism and that possible roles of TGFβ1 and Treg cells in such a mechanism warrant further study., (© 2024 The Author(s). Journal of Cellular Physiology published by Wiley Periodicals LLC.)
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- 2024
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24. PIWIL1 gene polymorphism and pediatric acute lymphoblastic leukemia relapse susceptibility among Chinese children: a five-center case-control study.
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Wenjiao Ding, Dao Wang, Mansi Cai, Yaping Yan, Shanshan Liu, Xiaodan Liu, Ailing Luo, Decheng Deng, Xiaoping Liu, and Hua Jiang
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LYMPHOBLASTIC leukemia ,CHINESE people ,ACUTE leukemia ,GENETIC polymorphisms ,SINGLE nucleotide polymorphisms ,Y chromosome - Abstract
Objective: PIWIL1 polymorphisms' role in pediatric acute lymphoblastic leukemia (ALL) relapse susceptibility remains undiscovered. Methods: A case-control designed and multiple logistic regression model was performed to evaluate the overall risk of pediatric ALL and five single-nucleotide polymorphisms (SNPs) of PIWIL1 gene (rs35997018 C>T, rs1106042 A>G, rs7957349 C>G, rs10773771 C>T, and rs10848087 A>G) in 785 cases and 1,323 controls, which were genotyped by TaqMan assay. The odds ratio (OR) and its 95% confidence interval (CI) were used to estimate the relationship. Stratified analysis was used to investigate the correlation of rs1106042 and rs10773771 genotypes and pediatric ALL relapse susceptibility in terms of age, sex, number of white blood cells (WBC), immunophenotyping, gene fusion type, karyotype, primitive/naïve lymphocytes, and minimal residual disease (MRD) in bone marrow. Finally, the haplotype analysis was performed to appraise the relationship between inferred haplotypes of PIWIL1 and pediatric ALL risk. Results: Among the five analyzed SNPs, rs1106042 A>G was related to increased ALL risk, and rs10773771 C>T was related to decreased ALL risk. Compared to the GG genotype, the rs1106042 GA/AA had a deleterious effect on children of age <120 months, who were female and male, had high or average number of WBC, pro-B ALL, pre-B ALL, T-ALL, low- and middle-risk ALL, E2A-PBX fusion gene, non-gene fusion, abnormal diploid, high hyperdiploid, hypodiploid, and normal diploid. Moreover, rs1106042 A>G harmfully affected primitive/naïve lymphocytes and MRD on days 15-19, day 33, and week 12. On the contrary, rs10773771 TC/CC exhibited a protective effect on ALL children with the TEL- AML fusion gene. Haplotype analysis demonstrated that haplotypes CAGT, TACC, TACT, and TAGT were significantly associated with increased pediatric ALL relapse susceptibility. Conclusion: PIWIL1 rs1106042 A>G was related to increased ALL risk, and rs10773771 C>T was linked to decreased ALL risk in eastern Chinese children. Rs1106042 GA/AA may predict poor prognosis. [ABSTRACT FROM AUTHOR]
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- 2023
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25. Genomic and Phenotypic Biomarkers for Precision Medicine Guidance in Advanced Prostate Cancer.
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Davoudi, Fatemeh, Moradi, Afshin, Becker, Therese M., Lock, John G., Abbey, Brian, Fontanarosa, Davide, Haworth, Annette, Clements, Judith, Ecker, Rupert C., and Batra, Jyotsna
- Abstract
Opinion statement: Prostate cancer (PCa) is the second most diagnosed malignant neoplasm and is one of the leading causes of cancer-related death in men worldwide. Despite significant advances in screening and treatment of PCa, given the heterogeneity of this disease, optimal personalized therapeutic strategies remain limited. However, emerging predictive and prognostic biomarkers based on individual patient profiles in combination with computer-assisted diagnostics have the potential to guide precision medicine, where patients may benefit from therapeutic approaches optimally suited to their disease. Also, the integration of genotypic and phenotypic diagnostic methods is supporting better informed treatment decisions. Focusing on advanced PCa, this review discusses polygenic risk scores for screening of PCa and common genomic aberrations in androgen receptor (AR), PTEN-PI3K-AKT, and DNA damage response (DDR) pathways, considering clinical implications for diagnosis, prognosis, and treatment prediction. Furthermore, we evaluate liquid biopsy, protein biomarkers such as serum testosterone levels, SLFN11 expression, total alkaline phosphatase (tALP), neutrophil-to-lymphocyte ratio (NLR), tissue biopsy, and advanced imaging tools, summarizing current phenotypic biomarkers and envisaging more effective utilization of diagnostic and prognostic biomarkers in advanced PCa. We conclude that prognostic and treatment predictive biomarker discovery can improve the management of patients, especially in metastatic stages of advanced PCa. This will result in decreased mortality and enhanced quality of life and help design a personalized treatment regimen. [ABSTRACT FROM AUTHOR]
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- 2023
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26. Joint Conference of the Société Française d'Immunologie (SFI) and the Deutsche Gesellschaft für Immunologie (DGfI), 26–29 September, 2023, Strasbourg, France.
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CONFERENCES & conventions - Published
- 2023
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27. Obesity in Severe COVID-19 Patients Has a Distinct Innate Immune Phenotype.
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Resende, Ayane de Sá, de Oliveira, Yrna Lorena Matos, de Franca, Mariana Nobre Farias, Magalhães, Lucas Sousa, Correa, Cristiane Bani, Fukutani, Kiyoshi Ferreira, Lipscomb, Michael Wheeler, and de Moura, Tatiana Rodrigues
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COVID-19 ,COVID-19 pandemic ,PHENOTYPES ,KILLER cells ,BIOMARKERS ,OBESITY - Abstract
Obesity alters the capacity of effective immune responses in infections. To further address this phenomenon in the context of COVID-19, this study investigated how the immunophenotype of leukocytes was altered in individuals with obesity in severe COVID-19. This cross-sectional study enrolled 27 ICU COVID-19 patients (67% women, 56.33 ± 19.55 years) that were assigned to obese (BMI ≥ 30 kg/m
2 , n = 9) or non-obese (BMI < 30kg/m2 , n = 18) groups. Monocytes, NK, and both Low-Density (LD) and High-Density (HD) neutrophils were isolated from peripheral blood samples, and surface receptors' frequency and expression patterns were analyzed by flow cytometry. Clinical status and biochemical data were additionally evaluated. The frequency of monocytes was negatively correlated with BMI, while NK cells and HD neutrophils were positively associated (p < 0.05). Patients with obesity showed a significant reduction of monocytes, and these cells expressed high levels of PD-L1 (p < 0.05). A higher frequency of NK cells and increased expression of TREM-1+ on HD neutrophils were detected in obese patients (p < 0.05). The expression of receptors related to antigen-presentation, phagocytosis, chemotaxis, inflammation and suppression were strongly correlated with clinical markers only in obese patients (p < 0.05). Collectively, these outcomes revealed that obesity differentially affected, and largely depressed, innate immune response in severe COVID-19. [ABSTRACT FROM AUTHOR]- Published
- 2023
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28. Principal component analysis yields results comparable to those of an elaborate Boolean strategy: simplifying the assessment of measurable residual disease in chronic lymphocytic leukemia patients.
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Brett, Victor-Emmanuel, Dilhuydy, Marie-Sarah, Lechevalier, Nicolas, Adjibabi, And-nan, Gros, François-Xavier, Forcade, Édouard, Letestu, Rémi, and Vial, Jean-Philippe
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- 2023
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29. Evaluation of Flow Cytometric Methods Used in Analysis of Immune Cells in Patients with Malignant Lymphoma.
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Mutema Jonsson, Carla and Mutema Jonsson, Carla
- Abstract
Malignant lymphomas are a group of cancerous diseases that develop from lymphocytes and primarily affect lymph nodes. Being the sixth most common cancer type in Sweden, lymphoma is a societal problem that needs to be tackled by improving care and treatment of patients. This study was designed to examine the blood cell composition in lymphoma patients and well as determine whether the use of cryopreserved cells affected the analysis outcome. An evaluation of the methods used was also performed. Frozen peripheral blood from lymphoma patients as well as fresh and frozen blood from healthy controls was used. The cells of interest were monocytes, granulocytes, Treg, NKT, iNKT, B and T cells plus the dendritic cell activation protein CCR7. Three immunophenotyping methods were used. Method one was used in staining surface cell markers while the other two were for both surface and intracellular staining using two distinctive kits. The results showed no significant difference in immune cell composition between patients and blood donors. Limited patient samples and the lack of female blood donors could explain the unexpected result. A substantial difference in Treg cells was observed in fresh and frozen tested samples as well as T cell outcomes in method one compared to the other two methods. There were fewer Treg cells in frozen samples, which probably was due to cryopreservation while the lack of fixation in method one led to the loss of CD4+ T cells. Overall, the methods used were adequate but definitely require some improvements.
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- 2017
30. Genomic Evidence for the Nonpathogenic State in HIV-1–Infected Northern Pig-Tailed Macaques.
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Pang, Wei, Shao, Yong, Zhuang, Xiao-Lin, Lu, Ying, He, Wen-Qiang, Zheng, Hong-Yi, Xin, Rong, Zhang, Ming-Xu, Zhang, Xiao-Liang, Song, Jia-Hao, Tian, Ren-Rong, Shen, Fan, Li, Yi-Hui, Zhao, Zu-Jiang, Wu, Dong-Dong, and Zheng, Yong-Tang
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MACAQUES ,GENOMICS ,ANIMAL models in research ,TOLL-like receptors ,SWINE breeding ,HIV ,INTERFERON alpha - Abstract
HIV-1 is a highly host-specific retrovirus that infects humans but not most nonhuman primates. Thus, the lack of a suitable primate model that can be directly infected with HIV-1 hinders HIV-1/AIDS research. In the previous study, we have found that the northern pig-tailed macaques (NPMs) are susceptible to HIV-1 infection but show a nonpathogenic state. In this study, to understand this macaque–HIV-1 interaction, we assembled a de novo genome and longitudinal transcriptome for this species during the course of HIV-1 infection. Using comparative genomic analysis, a positively selected gene, Toll-like receptor 8, was identified with a weak ability to induce an inflammatory response in this macaque. In addition, an interferon-stimulated gene, interferon alpha inducible protein 27, was upregulated in acute HIV-1 infection and acquired an enhanced ability to inhibit HIV-1 replication compared with its human ortholog. These findings coincide with the observation of persistently downregulated immune activation and low viral replication and can partially explain the AIDS-free state in this macaque following HIV-1 infection. This study identified a number of unexplored host genes that may hamper HIV-1 replication and pathogenicity in NPMs and provided new insights into the host defense mechanisms in cross-species infection of HIV-1. This work will facilitate the adoption of NPM as a feasible animal model for HIV-1/AIDS research. [ABSTRACT FROM AUTHOR]
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- 2023
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31. Concurrent chronic lymphocytic leukemia and primary hyperparathyroidism in a mule.
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Townsend, Kile S., Johnson, Philip J., Donnelly, Lindsay L., LaCarrubba, Alison M., Lattimer, James C., Havis, Brett, Springer, Nora L., and Kim, Dae Y.
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CHRONIC lymphocytic leukemia ,HYPERPARATHYROIDISM ,ANTIGEN receptors ,PARATHYROID glands ,BLOOD plasma ,WEIGHT loss - Abstract
A 26‐year‐old mule gelding was evaluated for chronic weight loss and decreased appetite. The mule had been losing weight and intermittently hypophagic for approximately 7 months. Laboratory analysis of whole blood and plasma identified severe total hypercalcemia, marked hypophosphatemia, markedly increased parathyroid hormone concentration, and marked lymphocytosis. A sestimibi scan intended to identify parathyroid gland tissue was nondiagnostic. Results of flow cytometry and PCR for antigen receptor rearrangement (PARR) were consistent with a B cell lymphoproliferative disorder, likely chronic lymphocytic leukemia (CLL). Although not previously described concurrently, these conditions may sometimes arise together, complicating definition of the underlying mechanism for weight loss and hypercalcemia in aged equids. [ABSTRACT FROM AUTHOR]
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- 2023
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32. New association between splicing factor‐coding gene polymorphisms and the risk of acute lymphoblastic leukemia in southern Chinese children: A five‐center case–control study.
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Deng, Decheng, Luo, Ailing, Li, Ming, Yan, Yaping, Cai, Mansi, Liu, Shanshan, Liu, Xiaodan, Wang, Xueliang, Zhang, Xiaohong, Jiang, Hua, and Liu, Xiaoping
- Abstract
Background: The role of splicing factor‐coding gene polymorphisms in pediatric acute lymphoblastic leukemia (ALL) susceptibility is still unclear. Methods: A case–control designed model was used to estimate the overall risk of pediatric ALL and five single nucleotide polymorphisms (SNPs) of splicing factor‐coding genes in 808 cases and 1,340 controls, which were genotyped using a TaqMan assay. Stratified analysis was performed to explore the association of rs2233911 genotype and pediatric ALL susceptibility. The influence of splicing factor arginine/serine‐rich 1 (SFRS1) polymorphisms on the sensitivity to different chemotherapeutic regimens based on minimal residual disease (MRD) levels was analyzed. The haplotype analysis was adopted to evaluate the association between inferred haplotypes of the splicing factor‐coding genes and pediatric ALL risk. Results: Among the five analyzed SNPs, SFRS1 rs2233911 AG/GG exhibited a significant association with increased pediatric ALL risk. The stratified analysis further identified the harmful effect of SFRS1 rs2233911 AG/GG in specific subgroups. Moreover, rs2233911 AG/GG had a protective effect on MRD in marrow of ≥0.01% 12 weeks of Chinese Children Cancer Group chemotherapeutics, but provided a harmful effect on MRD in the marrow of ≥0.01% at days 15–19 of the South China Children Leukemia Group chemotherapeutics. Haplotype analysis of these five SNPs yielded haplotypes ACGCC and ACGTC significantly correlating with increased pediatric ALL susceptibility. On the contrary, haplotypes GCATG and GTACC were linked with remarkably decreased pediatric ALL risk. Conclusion: SFRS1 gene polymorphism was associated with increased pediatric ALL risk and indicated that rs2233911 AG/GG might be a potential biomarker for choosing chemotherapeutics. [ABSTRACT FROM AUTHOR]
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- 2023
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33. scAnnotate: an automated cell-type annotation tool for single-cell RNA-sequencing data.
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Ji, Xiangling, Tsao, Danielle, Bai, Kailun, Tsao, Min, Xing, Li, and Zhang, Xuekui
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RNA sequencing ,DATA distribution ,AUTOMATION ,MACHINE learning ,CELL differentiation - Abstract
Motivation Single-cell RNA-sequencing (scRNA-seq) technology enables researchers to investigate a genome at the cellular level with unprecedented resolution. An organism consists of a heterogeneous collection of cell types, each of which plays a distinct role in various biological processes. Hence, the first step of scRNA-seq data analysis is often to distinguish cell types so they can be investigated separately. Researchers have recently developed several automated cell-type annotation tools, requiring neither biological knowledge nor subjective human decisions. Dropout is a crucial characteristic of scRNA-seq data widely used in differential expression analysis. However, no current cell annotation method explicitly utilizes dropout information. Fully utilizing dropout information motivated this work. Results We present scAnnotate, a cell annotation tool that fully utilizes dropout information. We model every gene's marginal distribution using a mixture model, which describes both the dropout proportion and the distribution of the non-dropout expression levels. Then, using an ensemble machine learning approach, we combine the mixture models of all genes into a single model for cell-type annotation. This combining approach can avoid estimating numerous parameters in the high-dimensional joint distribution of all genes. Using 14 real scRNA-seq datasets, we demonstrate that scAnnotate is competitive against nine existing annotation methods. Furthermore, because of its distinct modelling strategy, scAnnotate's misclassified cells differ greatly from competitor methods. This suggests using scAnnotate together with other methods could further improve annotation accuracy. Availability and implementation We implemented scAnnotate as an R package and made it publicly available from CRAN: https://cran.r-project.org/package=scAnnotate. Supplementary information Supplementary data are available at Bioinformatics Advances online. [ABSTRACT FROM AUTHOR]
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- 2023
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34. An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation.
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Bhat, Khalid H., Priyadarshi, Saurabh, Naiyer, Sarah, Qu, Xinyan, Farooq, Hammad, Kleiman, Eden, Xu, Jeffery, Lei, Xue, Cantillo, Jose F., Wuerffel, Robert, Baumgarth, Nicole, Liang, Jie, Feeney, Ann J., and Kenter, Amy L.
- Subjects
GENE rearrangement ,LOCUS (Genetics) ,ARCHITECTURAL details ,B cells ,GENE clusters - Abstract
The mouse Igh locus is organized into a developmentally regulated topologically associated domain (TAD) that is divided into subTADs. Here we identify a series of distal V
H enhancers (EVH s) that collaborate to configure the locus. EVH s engage in a network of long-range interactions that interconnect the subTADs and the recombination center at the DH JH gene cluster. Deletion of EVH 1 reduces V gene rearrangement in its vicinity and alters discrete chromatin loops and higher order locus conformation. Reduction in the rearrangement of the VH 11 gene used in anti-PtC responses is a likely cause of the observed reduced splenic B1 B cell compartment. EVH 1 appears to block long-range loop extrusion that in turn contributes to locus contraction and determines the proximity of distant VH genes to the recombination center. EVH 1 is a critical architectural and regulatory element that coordinates chromatin conformational states that favor V(D)J rearrangement. Here the authors show enhancers in the Igh locus play a major role in configuring locus architecture and in V(D)J recombination, and identify a link between enhancer hub formation, locus contraction and cohesin-mediated loop extrusion. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
- View/download PDF
35. Biomarker-driven development of new therapies for autoimmune diseases: current status and future promises.
- Author
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Laigle, Laurence, Chadli, Loubna, and Moingeon, Philippe
- Subjects
AUTOIMMUNE diseases ,SJOGREN'S syndrome ,SYSTEMIC lupus erythematosus ,RHEUMATOID arthritis ,INDIVIDUALIZED medicine - Abstract
Auto-immune diseases are complex and heterogeneous. Various types of biomarkers can be used to support precision medicine approaches to autoimmune diseases, ensuring that the right patient receives the most appropriate therapy to improve treatment outcomes. We review the recent progress made in modeling several autoimmune diseases such as Systemic Lupus Erythematosus, primary Sjogren Syndrome, and Rheumatoid Arthritis following extensive molecular profiling of large cohorts of patients. From this knowledge, BMKs are being identified which support diagnostic as well as patient stratification and prediction of response to treatment. The identification of biomarkers should be initiated early in drug development and properly validated during subsequent clinical trials. To ensure the robustness and reproducibility of biomarkers, the PERMIT Consortium recently established recommendations highlighting the importance of relevant study design, sample size, and appropriate validation of analytical methods. The integration by AI-powered analytics of massive data provided by multi-omics technologies, high-resolution medical imaging and sensors borne by patients will eventually allow the identification of clinically relevant BMKs, likely in the form of combinatorial predictive algorithms, to support future drug development for autoimmune diseases. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
36. COVID‐19: Using high‐throughput flow cytometry to dissect clinical heterogeneity.
- Author
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del Molino del Barrio, Irene, Hayday, Thomas S., Laing, Adam G., Hayday, Adrian C., and Di Rosa, Francesca
- Abstract
Here we consider how high‐content flow cytometric methodology at appropriate scale and throughput rapidly provided meaningful biological data in our recent studies of COVID‐19, which we discuss in the context of other similar investigations. In our work, high‐throughput flow cytometry was instrumental to identify a consensus immune signature in COVID‐19 patients, and to investigate the impact of SARS‐CoV‐2 exposure on patients with either solid or hematological cancers. We provide here some examples of our 'holistic' approach, in which flow cytometry data generated by lymphocyte and myelomonocyte panels were integrated with other analytical metrics, including SARS‐CoV‐2‐specific serum antibody titers, plasma cytokine/chemokine levels, and in‐depth clinical annotation. We report how selective differences between T cell subsets were revealed by a newly described flow cytometric TDS assay to distinguish actively cycling T cells in the peripheral blood. By such approaches, our and others' high‐content flow cytometry studies collectively identified overt abnormalities and subtle but critical changes that discriminate the immuno‐signature of COVID‐19 patients from those of healthy donors and patients with non‐COVID respiratory infections. Thereby, these studies offered several meaningful biomarkers of COVID‐19 severity that have the potential to improve the management of patients and of hospital resources. In sum, flow cytometry provides an important means for rapidly obtaining data that can guide clinical decision‐making without requiring highly expensive, sophisticated equipment, and/or "‐omics" capabilities. We consider how this approach might be further developed. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
37. Current understanding of the immune potential of B-cell subsets in malarial pathogenesis.
- Author
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Kalkal, Meenu and Das, Jyoti
- Abstract
In the past several decades, our understanding of how B cells are generated and what function they perform has continued to advance. It is widely accepted that Bcell subsets play a critical role in mediating immune response. Surprisingly, human and murine malarial infections cause major alterations in the composition of B-cell subsets in both the spleen and periphery. Multiple B-cell subsets are well characterized in murine models following primary and secondary infection, although in human malarial infection, these subsets are not well defined. Furthermore, a rare known function of B cells includes the potential role of regulating the activities of other cells in the body as regulatory cells. Plasmodium infection strongly alters the frequency of these regulatory B cells indicating the immunoregulatory function of B cells in malarial. It is important to note that these subsets, taken together, form the cellular basis of humoral immune responses, allowing protection against a wide array of Plasmodium antigens to be achieved. However, it remains a challenge and an important area of investigation to understand how these B-cell subsets work together to provide protection against Plasmodium infection. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
38. Exposed seronegative: Cellular immune responses to SARS-CoV-2 in the absence of seroconversion.
- Author
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Jay, Cecilia, Ratcliff, Jeremy, Turtle, Lance, Goulder, Philip, and Klenerman, Paul
- Abstract
The factors determining whether infection will occur following exposure to SARSCoV-2 remain elusive. Certain SARS-CoV-2-exposed individuals mount a specific T-cell response but fail to seroconvert, representing a population that may provide further clarity on the nature of infection susceptibility and correlates of protection against SARS-CoV-2. Exposed seronegative individuals have been reported in patients exposed to the blood-borne pathogens Human Immunodeficiency virus and Hepatitis C virus and the sexually transmitted viruses Hepatitis B virus and Herpes Simplex virus. By comparing the quality of seronegative T-cell responses to SARS-CoV-2 with seronegative cellular immunity to these highly divergent viruses, common patterns emerge that offer insights on the role of cellular immunity against infection. For both SARS-CoV-2 and Hepatitis C, T-cell responses in exposed seronegatives are consistently higher than in unexposed individuals, but lower than in infected, seropositive patients. Durability of T-cell responses to Hepatitis C is dependent upon repeated exposure to antigen – single exposures do not generate long-lived memory T-cells. Finally, exposure to SARS-CoV-2 induces varying degrees of immune activation, suggesting that exposed seronegative individuals represent points on a spectrum rather than a discrete group. Together, these findings paint a complex landscape of the nature of infection but provide clues as to what may be protective early on in SARS-CoV-2 disease course. Further research on this phenomenon, particularly through cohort studies, is warranted. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
39. Silver Nanoparticles Modified by Carbosilane Dendrons and PEG as Delivery Vectors of Small Interfering RNA.
- Author
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Abashkin, Viktar, Pędziwiatr-Werbicka, Elżbieta, Horodecka, Katarzyna, Zhogla, Victoriya, Ulashchik, Egor, Shmanai, Vadim, Shcharbin, Dzmitry, and Bryszewska, Maria
- Subjects
SMALL interfering RNA ,SILVER nanoparticles ,MUTANT proteins ,POLYETHYLENE glycol ,CELL populations ,GENE transfection ,LIGHT scattering ,MAGNETIC nanoparticle hyperthermia - Abstract
The fact that cancer is one of the leading causes of death requires researchers to create new systems of effective treatment for malignant tumors. One promising area is genetic therapy that uses small interfering RNA (siRNA). These molecules are capable of blocking mutant proteins in cells, but require specific systems that will deliver RNA to target cells and successfully release them into the cytoplasm. Dendronized and PEGylated silver nanoparticles as potential vectors for proapoptotic siRNA (siMCL-1) were used here. Using the methods of one-dimensional gel electrophoresis, the zeta potential, dynamic light scattering, and circular dichroism, stable siRNA and AgNP complexes were obtained. Data gathered using multicolor flow cytometry showed that AgNPs are able to deliver (up to 90%) siRNAs efficiently to some types of tumor cells, depending on the degree of PEGylation. Analysis of cell death showed that complexes of some AgNP variations with siMCL-1 lead to ~70% cell death in the populations that uptake these complexes due to apoptosis. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
40. Adult acute lymphoblastic leukemia in a resource-constrained setting: outcomes after expansion of genetic evaluation.
- Author
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Silva, Wellington F., Amano, Mariane T., Perruso, Luiza L., Cordeiro, Maria Gabriella, Kishimoto, Renata Kiyomi, de Medeiros Leal, Aline, Nardinelli, Luciana, Bendit, Israel, Velloso, Elvira DRP, Rego, Eduardo M., and Rocha, Vanderson
- Subjects
LYMPHOBLASTIC leukemia ,ACUTE leukemia ,PHILADELPHIA chromosome ,EXTRAMEDULLARY diseases ,ADULTS - Abstract
Acute lymphoblastic leukemia (ALL) is a challenging disease with a growing genetic landscape, even though there is substantial gap between developed and non-developed countries when it comes to availability of such new technologies. This manuscript reports a 5-year retrospective cohort of newly diagnosed ALL patients and their genetic findings and outcomes. An expanded genetic evaluation by using FISH and RT–PCR was implemented, aiming to identify Ph-like alterations. Patients were treated according to our local protocol, which allocated patients according to age and Philadelphia-chromosome status. A total of 104 patients was included, with median age of 37.5 years. Philadelphia chromosome was detected in 33 cases of B-lineage. Among 45 Ph-negative B-lineage, after excluding KMT2A or TCF3-PBX1 cases, we identified 9 cases with Ph-like fusion. Ph-positive and Ph-like patients had higher initial WBC (p = 0.06). Out of 104 cases, two cases did not start chemotherapy and an early death rate of 10.8% was found. Allogeneic transplantation was performed in 18 cases, being ten performed in first CR. Three-year overall survival (OS) and 3-year event-free survival were 42.8% and 30.8%, respectively. For patients treated with a pediatric regimen, 3-year OS was 52.5%. Extramedullary disease (HR 0.42) and platelet counts (HR 0.9) were independently associated with OS. We still face excessive non-relapse mortality that compromises our results. Alternative strategies implementing FISH and RT–PCR are feasible and able to identify Ph-like fusions. Delays in allogeneic transplantation, as well as the unavailability of new agents, impact long-term survival. Measures to decrease early infection are desirable. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
41. Barcoding of live peripheral blood mononuclear cells to assess immune cell phenotypes using full spectrum flow cytometry.
- Author
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Junker, Fabian and Camillo Teixeira, Priscila
- Abstract
Barcoded flow cytometry is a multiplexing technique allowing for the simultaneous acquisition of cells from different donors or experimental conditions in a high‐throughput manner. This approach allows to synchronize acquisition of samples and reduce variance introduced through the operator or technical platform. However, to date, only very few flow cytometry barcoding protocols have been developed, which often suffer from technical limitations. Here, we developed a novel barcoding protocol for a full‐spectrum flow cytometry platform. We developed a 21‐color immunophenotyping assay for up to 20 different samples analyzed simultaneously with comparable variance between repeated single‐tube acquisition and postde‐multiplexing. Barcoding offers great potential in parallelizing the analysis of complex cell populations such as peripheral blood mononuclear cells (PBMCs). Consequently, we assessed the performance of our method in situations where PBMCs were challenged with phytohaemagglutinin (PHA), a strong mitogen and broad activator of B cells and T cells, and superantigen Staphylococcus enterotoxin B (SEB) that has been reported to induce polyclonal T cell activation. PBMCs were either barcoded before pooled challenge or challenged individually pre‐barcoding. Our final workflow included pooled immunophenotyping followed by machine learning aided single‐cell data analysis and enabled us to identify robust PHA and SEB mode of action related phenotypic changes in PBMC immune cell lineages. Conclusively, we present a novel technique allowing the barcoded acquisition and analysis of PBMCs from up to 20 different donors and present a valid basis for the future development of complex immunophenotyping protocols. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
42. Clinicopathologic and immunophenotypic features in dogs with presumptive large granular lymphocyte leukaemia.
- Author
-
Jaensch, SM, Hayward, DA, and Boyd, SP
- Subjects
LEUKEMIA ,LYMPHOCYTES ,LYMPHOCYTIC leukemia ,CLINICAL pathology ,DOGS ,CD8 antigen - Abstract
Large granular lymphocytic leukaemia (LGLL) has been described in a range of species but has been most commonly reported in humans and dogs. In both species, this neoplasia exhibits diversity in both phenotype and biological behaviour with phenotype only partially predicting behaviour. There is currently little knowledge of concurrent haematological and serum biochemistry features or concurrent occurrence of distinct neoplasia in canine LGLL cases. This study presents a canine case series and defines haematological parameters, novel serum biochemistry findings and phenotype of the large granular lymphocytes in an Australian case series. Neutrophilia was the most common haematological abnormality, identified in 43% of dogs, and 84% of dogs with biochemistry data available had elevated serum gamma‐glutamyl transferase. Five of the 40 dogs in this study exhibited concurrent neoplasia during the period of the study, demonstrating this is a relatively common clinical outcome in canine LGLL cases. In agreement with previous canine and human studies, the most common LGLL phenotype in dogs is CD3+, CD4− and CD8+. Further work is needed to define the variables predictive of the biological behaviour of LGLL in dogs. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
43. EPIDEMIOLOGY, CLINICAL ASPECTS AND MODERN METHODS OF THE TREATMENT OF CHRONIC LYMPHOCYTIC LEUKEMIA.
- Author
-
V., Tcaci and V., Musteață
- Subjects
EPIDEMIOLOGY ,CHRONIC lymphocytic leukemia ,IMMUNE system ,HEMATOLOGY ,LYMPHOCYTES - Abstract
Chronic lymphocytic leukemia is the most common type of leukemia in Western Europe and North America. It is mainly a disease of the elderly [9]. Average age of incidence - 72 years [5]. The pathological substrate is cells of the immune system - predominantly mature lymphocytes with a B-phenotype [1]. The clinical picture is variable, the rate of development of the disease is characterized by a wide range both in objective data and in hematological analyzes. The disease can be asymptomatic for many years, and is detected only during routine examination as an incidental finding. In such cases, a strategy of observation and waiting is chosen, without applying specific treatment. The main goals of treatment are to achieve complete or partial remission with improvement and stabilization of the clinical and hematological picture. [10]. To study the features of the epidemiology, clinical course and modern methods of treating CLL, a study was conducted on the basis of a database of 50 patients registered at the Consultative and Diagnostic Center of the Oncological Institute, Chisinau, Republic of Moldova. It was found that the main group with this diagnosis is people 55-75 years old (62%). The mean age of diagnosis among the selected group is 63 years. The incidence of CLL among men (58%) is slightly higher than among women (42%). The use of bio immunotherapy allows you to establish a positive trend in the course of the disease, as well as improve the quality of life of patients [4]. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
44. Multiparametric Flow Cytometry-Based Immunophenotyping of Mouse Liver Immune Cells.
- Author
-
Vanekova, Lenka, Pimkova Polidarova, Marketa, Veverka, Vaclav, Birkus, Gabriel, and Brazdova, Andrea
- Subjects
LIVER cells ,CYTOTOXIC T cells ,IMMUNOPHENOTYPING ,KUPFFER cells ,KILLER cells ,BLOOD cells ,CELL suspensions ,T helper cells - Abstract
The liver is a complex organ that governs many types of metabolisms, including energy metabolism and other cellular processes. The liver also plays a crucial role in important functions in immunity, and the activity of liver tissue-associated immunity affects the outcome of many liver pathologies. A thorough characterization of the liver immune microenvironment may contribute to a better understanding of immune signaling, the mechanisms of specific immune responses, and even to improved predictions about therapy outcomes. In this paper, we present an optimized, simple, and rapid protocol to characterize the liver-associated immune cell milieu. We believe that the most suitable technique for obtaining a complex immune cell suspension and for removing contaminating blood cells is to perform mouse liver perfusion, using only phosphate buffer saline. Combining an enzymatic digestion and a mechanical dissociation of liver tissue, followed by cell purification, improves downstream applications. This combination is an essential prerequisite for immune cell determination and characterization. We then demonstrate a flow cytometry-based multiparametric immunophenotyping along with a gating strategy to detect and quantify liver endothelial cells, T cells (helper and cytotoxic), B cells, NK cells, NKT cells, neutrophils, monocytes (subsets included), dendritic cells (subsets included), macrophages and Kupffer cells. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
45. Gastrointestinal Tract Metastases of Invasive Lobular Carcinoma of the Breast: An Immunohistochemical Survey Algorithm.
- Author
-
Zengel, Baha, Çavdar, Demet, Özdemir, Özlem, Taşlı, Funda, Karataş, Murat, Şimşek, Cenk, and Uslu, Adam
- Abstract
Invasive lobular carcinoma (ILC) accounts for almost 15% of all breast carcinomas. The potential of ILC to metastasize to the gastointestinal system is significantly greater than that of invasive ductal carcinoma. Gastric metastasis occurred in the ninth year of the follow-up in a patient who was operated on the right breast due to ILC. The patient was investigated for simultaneous masses in the stomach and colon, and a random mass was found in her right breast. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
46. Novel approach to analysis of the immune system using an ungated model of immune surface marker abundance to predict health outcomes.
- Author
-
Provost, G., Lavoie, F. B., Larbi, A., Ng, TP., Ying, C. Tan Tze, Chua, M., Fulop, T., and Cohen, A. A.
- Subjects
BIOMARKERS ,IMMUNE system ,LONGITUDINAL method ,CYTOMETRY ,FORECASTING - Abstract
Traditionally, the immune system is understood to be divided into discrete cell types that are identified via surface markers. While some cell type distinctions are no doubt discrete, others may in fact vary on a continum, and even within discrete types, differences in surface marker abundance could have functional implications. Here we propose a new way of looking at immune data, which is by looking directly at the values of the surface markers without dividing the cells into different subtypes. To assess the merit of this approach, we compared it with manual gating using cytometry data from the Singapore Longitudinal Aging Study (SLAS) database. We used two different neural networks (one for each method) to predict the presence of several health conditions. We found that the model built using raw surface marker abundance outperformed the manual gating one and we were able to identify some markers that contributed more to the predictions. This study is intended as a brief proof-of-concept and was not designed to predict health outcomes in an applied setting; nonetheless, it demonstrates that alternative methods to understand the structure of immune variation hold substantial progress. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
47. Role of microRNAs in B-Cell Compartment: Development, Proliferation and Hematological Diseases.
- Author
-
Souza, Olívia Fonseca and Popi, Ana Flavia
- Subjects
BLOOD diseases ,MICRORNA ,NON-coding RNA ,EXTRACELLULAR vesicles ,HEMATOLOGIC malignancies - Abstract
B-cell development is a very orchestrated pathway that involves several molecules, such as transcription factors, cytokines, microRNAs, and also different cells. All these components maintain the ideal microenvironment and control B-cell differentiation. MicroRNAs are small non-coding RNAs that bind to target mRNA to control gene expression. These molecules could circulate in the body in a free form, protein-bounded, or encapsulated into extracellular vesicles, such as exosomes. The comprehension of the role of microRNAs in the B-cell development was possible based on microRNA profile of each B-cell stage and functional studies. Herein, we report the knowledge about microRNAs in the B-cell the differentiation, proliferation, and also in hematological malignancies. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
48. Evaluation of T-cell aging-related immune phenotypes in the context of biological aging and multimorbidity in the Health and Retirement Study.
- Author
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Ramasubramanian, Ramya, Meier, Helen C. S., Vivek, Sithara, Klopack, Eric, Crimmins, Eileen M., Faul, Jessica, Nikolich-Žugich, Janko, and Thyagarajan, Bharat
- Subjects
COMORBIDITY ,AGE ,T cells ,CD4 antigen ,AGING ,PSYCHONEUROIMMUNOLOGY - Abstract
Background: Cellular changes in adaptive immune system accompany the process of aging and contribute to an aging-related immune phenotype (ARIP) characterized by decrease in naïve T-cells (T
N ) and increase in memory T-cells (TM ). A population-representative marker of ARIP and its associations with biological aging and age-related chronic conditions have not been studied previously. Methods: We developed two ARIP indicators based on well understood age-related changes in T cell distribution: TN /(TCM (Central Memory) + TEM (Effector Memory) + TEFF (Effector)) (referred as TN /TM ) in CD4 + and CD8 + T-cells. We compared them with existing ARIP measures including CD4/CD8 ratio and CD8 + TN cells by evaluating associations with chronological age and the Klemera Doubal measure of biological age (measured in years) using linear regression, multimorbidity using multinomial logistic regression and two-year mortality using logistic regression. Results: CD8 + TN and CD8 + TN /TM had the strongest inverse association with chronological age (beta estimates: -3.41 and -3.61 respectively; p-value < 0.0001) after adjustment for sex, race/ethnicity and CMV status. CD4 + TN /TM and CD4 + TN had the strongest inverse association with biological age (β = -0.23; p = 0.003 and β = -0.24; p = 0.004 respectively) after adjustment for age, sex, race/ethnicity and CMV serostatus. CD4/CD8 ratio was not associated with chronological age or biological age. CD4 + TN /TM and CD4 + TN was inversely associated with multimorbidity. For CD4 + TN /TM , people with 2 chronic conditions had an odds ratio of for 0.74 (95%CI: 0.63–0.86 p = 0.0003) compared to those without any chronic conditions while those with 3 chronic conditions had an odds ratio of 0.75 (95% CI: 0.63–0.90; p = 0.003) after adjustment for age, sex, race/ethnicity, CMV serostatus, smoking, and BMI. The results for the CD4 + TN subset were very similar to the associations seen with the CD4 + TN /TM . CD4 + TN /TM and CD4 + TN were both associated with two-year mortality (OR = 0.80 (95% CI: 0.67–0.95; p = 0.01) and 0.81 (0.70–0.94; p = 0.01), respectively). Conclusion: CD4 + TN /TM and CD4 + TN had a stronger association with biological age, age-related morbidity and mortality compared to other ARIP measures. Future longitudinal studies are needed to evaluate the utility of the CD4 + subsets in predicting the risk of aging-related outcomes. [ABSTRACT FROM AUTHOR]- Published
- 2022
- Full Text
- View/download PDF
49. Lenalidomide enhances CD23.CAR T cell therapy in chronic lymphocytic leukemia.
- Author
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Tettamanti, Sarah, Rotiroti, Maria Caterina, Giordano Attianese, Greta Maria Paola, Arcangeli, Silvia, Zhang, Ronghua, Banerjee, Priyanka, Galletti, Giovanni, McManus, Sheighlah, Mazza, Massimiliano, Nicolini, Fabio, Martinelli, Giovanni, Ivan, Cristina, Veliz Rodriguez, Tania, Barbaglio, Federica, Scarfò, Lydia, Ponzoni, Maurilio, Wierda, William, Gandhi, Varsha, Keating, Michael, and Biondi, Andrea
- Subjects
CHRONIC lymphocytic leukemia ,T cells ,LENALIDOMIDE ,CELLULAR therapy ,CHIMERIC antigen receptors - Abstract
Chimeric antigen receptors (CAR)-modified T cells are an emerging therapeutic tool for chronic lymphocytic leukemia (CLL). However, in patients with CLL, well-known T-cell defects and the inhibitory properties of the tumor microenvironment (TME) hinder the efficacy of CAR T cells. We explored a novel approach combining CARs with lenalidomide, an immunomodulatory drug that tempers the immunosuppressive activity of the CLL TME. T cells from patients with CLL were engineered to express a CAR specific for CD23, a promising target antigen. Lenalidomide maintained the in vitro effector functions of CD23.CAR
+ T cells effector functions in terms of antigen-specific cytotoxicity, cytokine release and proliferation. Overall, lenalidomide preserved functional CAR T-CLL cell immune synapses. In a Rag2−/− γc −/− -based xenograft model of CLL, we demonstrated that, when combined with low-dose lenalidomide, CD23.CAR+ T cells efficiently migrated to leukemic sites and delayed disease progression when compared to CD23.CAR+ T cells given with rhIL-2. These observations underline the therapeutic potential of this novel CAR-based combination strategy in CLL. [ABSTRACT FROM AUTHOR]- Published
- 2022
- Full Text
- View/download PDF
50. Cancer Stem Cell-Associated Immune Microenvironment in Recurrent Glioblastomas.
- Author
-
Murota, Yoshitaka, Tabu, Kouichi, and Taga, Tetsuya
- Subjects
GLIOBLASTOMA multiforme ,CANCER stem cells ,CANCER relapse ,SURGICAL excision ,TUMOR microenvironment - Abstract
Glioblastoma multiforme (GBM) is the most incurable tumor (due to the difficulty in complete surgical resection and the resistance to conventional chemo/radiotherapies) that displays a high relapse frequency. Cancer stem cells (CSCs) have been considered as a promising target responsible for therapy resistance and cancer recurrence. CSCs are known to organize a self-advantageous microenvironment (niche) for their maintenance and expansion. Therefore, understanding how the microenvironment is reconstructed by the remaining CSCs after conventional treatments and how it eventually causes recurrence should be essential to inhibit cancer recurrence. However, the number of studies focusing on recurrence is limited, particularly those related to tumor immune microenvironment, while numerous data have been obtained from primary resected samples. Here, we summarize recent investigations on the immune microenvironment from the viewpoint of recurrent GBM (rGBM). Based on the recurrence-associated immune cell composition reported so far, we will discuss how CSCs manipulate host immunity and create the special microenvironment for themselves to regrow. An integrated understanding of the interactions between CSCs and host immune cells at the recurrent phase will lead us to develop innovative therapies and diagnoses to achieve GBM eradication. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
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