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Eicher T, Kelly RS, Braisted J, Siddiqui JK, Celedón J, Clish C, Gerszten R, Weiss ST, McGeachie M, Machiraju R, Lasky-Su J, Mathé EA. Consistent Multi-Omic Relationships Uncover Molecular Basis of Pediatric Asthma IgE Regulation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.05.24308502. [PMID: 38883716 PMCID: PMC11178010 DOI: 10.1101/2024.06.05.24308502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Serum total immunoglobulin E levels (total IgE) capture the state of the immune system in relation to allergic sensitization. High levels are associated with airway obstruction and poor clinical outcomes in pediatric asthma. Inconsistent patient response to anti-IgE therapies motivates discovery of molecular mechanisms underlying serum IgE level differences in children with asthma. To uncover these mechanisms using complementary metabolomic and transcriptomic data, abundance levels of 529 named metabolites and expression levels of 22,772 genes were measured among children with asthma in the Childhood Asthma Management Program (CAMP, N=564) and the Genetic Epidemiology of Asthma in Costa Rica Study (GACRS, N=309) via the TOPMed initiative. Gene-metabolite associations dependent on IgE were identified within each cohort using multivariate linear models and were interpreted in a biochemical context using network topology, pathway and chemical enrichment, and representation within reactions. A total of 1,617 total IgE-dependent gene-metabolite associations from GACRS and 29,885 from CAMP met significance cutoffs. Of these, glycine and guanidinoacetic acid (GAA) were associated with the most genes in both cohorts, and the associations represented reactions central to glycine, serine, and threonine metabolism and arginine and proline metabolism. Pathway and chemical enrichment analysis further highlighted additional related pathways of interest. The results of this study suggest that GAA may modulate total IgE levels in two independent pediatric asthma cohorts with different characteristics, supporting the use of L-Arginine as a potential therapeutic for asthma exacerbation. Other potentially new targetable pathways are also uncovered.
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Affiliation(s)
- Tara Eicher
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD USA
- Department of Computer Science and Engineering, College of Engineering, The Ohio State University, Columbus, OH USA
| | - Rachel S. Kelly
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA USA
- Harvard Medical School, Boston, MA USA
| | - John Braisted
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD USA
| | - Jalal K. Siddiqui
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH USA
| | - Juan Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA USA
| | | | - Robert Gerszten
- Harvard Medical School, Boston, MA USA
- Broad Institute, Cambridge, MA USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA USA
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA USA
- Harvard Medical School, Boston, MA USA
| | - Michael McGeachie
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA USA
- Harvard Medical School, Boston, MA USA
| | - Raghu Machiraju
- Department of Computer Science and Engineering, College of Engineering, The Ohio State University, Columbus, OH USA
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH USA
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA USA
- Harvard Medical School, Boston, MA USA
| | - Ewy A. Mathé
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD USA
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Portacci A, Iorillo I, Maselli L, Amendolara M, Quaranta VN, Dragonieri S, Carpagnano GE. The Role of Galectins in Asthma Pathophysiology: A Comprehensive Review. Curr Issues Mol Biol 2024; 46:4271-4285. [PMID: 38785528 PMCID: PMC11119966 DOI: 10.3390/cimb46050260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
Galectins are a group of β-galactoside-binding proteins with several roles in immune response, cellular adhesion, and inflammation development. Current evidence suggest that these proteins could play a crucial role in many respiratory diseases such as pulmonary fibrosis, lung cancer, and respiratory infections. From this standpoint, an increasing body of evidence have recognized galectins as potential biomarkers involved in several aspects of asthma pathophysiology. Among them, galectin-3 (Gal-3), galectin-9 (Gal-9), and galectin-10 (Gal-10) are the most extensively studied in human and animal asthma models. These galectins can affect T helper 2 (Th2) and non-Th2 inflammation, mucus production, airway responsiveness, and bronchial remodeling. Nevertheless, while higher Gal-3 and Gal-9 concentrations are associated with a stronger degree of Th-2 phlogosis, Gal-10, which forms Charcot-Leyden Crystals (CLCs), correlates with sputum eosinophilic count, interleukin-5 (IL-5) production, and immunoglobulin E (IgE) secretion. Finally, several galectins have shown potential in clinical response monitoring after inhaled corticosteroids (ICS) and biologic therapies, confirming their potential role as reliable biomarkers in patients with asthma.
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Affiliation(s)
- Andrea Portacci
- Institute of Respiratory Disease, Department of Translational Biomedicine and Neuroscience, University “Aldo Moro”, 70121 Bari, Italy; (I.I.); (L.M.); (M.A.); (S.D.); (G.E.C.)
| | - Ilaria Iorillo
- Institute of Respiratory Disease, Department of Translational Biomedicine and Neuroscience, University “Aldo Moro”, 70121 Bari, Italy; (I.I.); (L.M.); (M.A.); (S.D.); (G.E.C.)
| | - Leonardo Maselli
- Institute of Respiratory Disease, Department of Translational Biomedicine and Neuroscience, University “Aldo Moro”, 70121 Bari, Italy; (I.I.); (L.M.); (M.A.); (S.D.); (G.E.C.)
| | - Monica Amendolara
- Institute of Respiratory Disease, Department of Translational Biomedicine and Neuroscience, University “Aldo Moro”, 70121 Bari, Italy; (I.I.); (L.M.); (M.A.); (S.D.); (G.E.C.)
| | | | - Silvano Dragonieri
- Institute of Respiratory Disease, Department of Translational Biomedicine and Neuroscience, University “Aldo Moro”, 70121 Bari, Italy; (I.I.); (L.M.); (M.A.); (S.D.); (G.E.C.)
| | - Giovanna Elisiana Carpagnano
- Institute of Respiratory Disease, Department of Translational Biomedicine and Neuroscience, University “Aldo Moro”, 70121 Bari, Italy; (I.I.); (L.M.); (M.A.); (S.D.); (G.E.C.)
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Kim S, Qin Y, Park HJ, Yue M, Xu Z, Forno E, Chen W, Celedón JC. Methyl-TWAS: A powerful method for in silico transcriptome-wide association studies (TWAS) using long-range DNA methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566586. [PMID: 38014125 PMCID: PMC10680683 DOI: 10.1101/2023.11.10.566586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
In silico transcriptome-wide association studies (TWAS) are commonly used to test whether expression of specific genes is linked to a complex trait. However, genotype-based in silico TWAS such as PrediXcan, exhibit low prediction accuracy for a majority of genes because genotypic data lack tissue- and disease-specificity and are not affected by the environment. Because methylation is tissue-specific and, like gene expression, can be modified by environment or disease status, methylation should predict gene expression with more accuracy than SNPs. Therefore, we propose Methyl-TWAS, the first approach that utilizes long-range methylation markers to impute gene expression for in silico TWAS through penalized regression. Methyl-TWAS 1) predicts epigenetically regulated/associated expression (eGReX), which incorporates tissue-specific expression and both genetically- (GReX) and environmentally-regulated expression to identify differentially expressed genes (DEGs) that could not be identified by genotype-based methods; and 2) incorporates both cis- and trans- CpGs, including various regulatory regions to identify DEGs that would be missed using cis- methylation only. Methyl-TWAS outperforms PrediXcan and two other methods in imputing gene expression in the nasal epithelium, particularly for immunity-related genes and DEGs in atopic asthma. Methyl-TWAS identified 3,681 (85.2%) of the 4,316 DEGs identified in a previous TWAS of atopic asthma using measured expression, while PrediXcan could not identify any gene. Methyl-TWAS also outperforms PrediXcan for expression imputation as well as in silico TWAS in white blood cells. Methyl-TWAS is a valuable tool for in silico TWAS, leveraging a growing body of publicly available genome-wide DNA methylation data for a variety of human tissues.
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Affiliation(s)
- Soyeon Kim
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yidi Qin
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hyun Jung Park
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Molin Yue
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhongli Xu
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Erick Forno
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Chen
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Juan C. Celedón
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
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Shoda T, Rochman M, Collins MH, Caldwell JM, Mack LE, Osswald GA, Mukkada VA, Putnam PE, Rothenberg ME. Molecular analysis of duodenal eosinophilia. J Allergy Clin Immunol 2023; 151:1027-1039. [PMID: 36592704 PMCID: PMC10102870 DOI: 10.1016/j.jaci.2022.12.814] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/18/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND Eosinophilic duodenitis (EoD), characterized by nonspecific gastrointestinal symptoms and increased numbers of duodenal eosinophils, may be in the eosinophilic gastrointestinal disease spectrum. However, diagnostic thresholds and pathogenic processes of duodenal tissue eosinophilia are inadequately characterized. OBJECTIVE We aimed to define an EoD transcriptome and pathologic pathways. METHODS RNA sequencing and histologic features of human duodenal biopsy samples were analyzed as a function of duodenal eosinophils levels. For analyses, we defined EoD as more than 52 peak eosinophils/hpf (n = 8), duodenal eosinophilia as 30 to 52 eosinophils/hpf (n = 11), and normal controls as fewer than 30 eosinophils/hpf (n = 8). Associations between gene expression and histologic features were analyzed with Spearman correlation. RESULTS We identified 382 differentially expressed genes (EoD transcriptome) between EoD and normal controls (>2-fold change [adjusted P < .05]). The EoD transcriptome distinguished EoD from controls (duodenal eosinophilia and normal controls). The duodenal eosinophil count was correlated with a distinct EoD transcriptome when 50 to 60 peak eosinophils/hpf were present. The EoD transcriptome was enriched in genes involved in IL-4/IL-13 signaling, mast cells, and myeloid progenitor cells. Among duodenal histologic features, lamina propria eosinophil sheets was the most associated with transcriptomic changes (r = 0.66; P < .01). EoD gene signatures were shared with eosinophilic esophagitis and eosinophilic gastritis but not with eosinophilic colitis or celiac disease. CONCLUSION We have identified an EoD transcriptomic signature that emerges at 50 to 60 peak eosinophils/hpf and established EoD as part of a spectrum of upper eosinophilic gastrointestinal disorder associated with type 2 immunity and distinct from eosinophilic colitis and celiac disease. These findings provide a basis for improving diagnosis and treatment.
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Affiliation(s)
- Tetsuo Shoda
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Mark Rochman
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Margaret H Collins
- Division of Pathology and Laboratory Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Julie M Caldwell
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Lydia E Mack
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Garrett A Osswald
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Vincent A Mukkada
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Philip E Putnam
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio.
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Recto KA, Huan T, Lee DH, Lee GY, Gereige J, Yao C, Hwang SJ, Joehanes R, Kelly RS, Lasky-Su J, O’Connor G, Levy D. Transcriptome-wide association study of circulating IgE levels identifies novel targets for asthma and allergic diseases. Front Immunol 2023; 14:1080071. [PMID: 36793728 PMCID: PMC9922991 DOI: 10.3389/fimmu.2023.1080071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/13/2023] [Indexed: 01/31/2023] Open
Abstract
Measurement of circulating immunoglobulin E (IgE) concentration is helpful for diagnosing and treating asthma and allergic diseases. Identifying gene expression signatures associated with IgE might elucidate novel pathways for IgE regulation. To this end, we performed a discovery transcriptome-wide association study to identify differentially expressed genes associated with circulating IgE levels in whole-blood derived RNA from 5,345 participants in the Framingham Heart Study across 17,873 mRNA gene-level transcripts. We identified 216 significant transcripts at a false discovery rate <0.05. We conducted replication using the meta-analysis of two independent external studies: the Childhood Asthma Management Program (n=610) and the Genetic Epidemiology of Asthma in Costa Rica Study (n=326); we then reversed the discovery and replication cohorts, which revealed 59 significant genes that replicated in both directions. Gene ontology analysis revealed that many of these genes were implicated in immune function pathways, including defense response, inflammatory response, and cytokine production. Mendelian randomization (MR) analysis revealed four genes (CLC, CCDC21, S100A13, and GCNT1) as putatively causal (p<0.05) regulators of IgE levels. GCNT1 (beta=1.5, p=0.01)-which is a top result in the MR analysis of expression in relation to asthma and allergic diseases-plays a role in regulating T helper type 1 cell homing, lymphocyte trafficking, and B cell differentiation. Our findings build upon prior knowledge of IgE regulation and provide a deeper understanding of underlying molecular mechanisms. The IgE-associated genes that we identified-particularly those implicated in MR analysis-can be explored as promising therapeutic targets for asthma and IgE-related diseases.
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Affiliation(s)
- Kathryn A. Recto
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- The Framingham Heart Study, Framingham, MA, United States
| | - Tianxiao Huan
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- The Framingham Heart Study, Framingham, MA, United States
| | - Dong Heon Lee
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- The Framingham Heart Study, Framingham, MA, United States
| | - Gha Young Lee
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- The Framingham Heart Study, Framingham, MA, United States
| | - Jessica Gereige
- Pulmonary Center, Boston University School of Medicine, Boston, MA, United States
| | - Chen Yao
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- The Framingham Heart Study, Framingham, MA, United States
| | - Shih-Jen Hwang
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- The Framingham Heart Study, Framingham, MA, United States
| | - Roby Joehanes
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- The Framingham Heart Study, Framingham, MA, United States
| | - Rachel S. Kelly
- Brigham and Women’s Hospital, Channing Division of Network Medicine, Boston, MA, United States
| | - Jessica Lasky-Su
- Brigham and Women’s Hospital, Channing Division of Network Medicine, Boston, MA, United States
| | - George O’Connor
- Pulmonary Center, Boston University School of Medicine, Boston, MA, United States
| | - Daniel Levy
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- The Framingham Heart Study, Framingham, MA, United States
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Lee HW, Baek MG, Choi S, Ahn YH, Bang JY, Sohn KH, Kang MG, Jung JW, Choi JH, Cho SH, Yi H, Kang HR. Peripheral blood transcriptomic clusters uncovered immune phenotypes of asthma. Respir Res 2022; 23:237. [PMID: 36076228 PMCID: PMC9461267 DOI: 10.1186/s12931-022-02156-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 08/01/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcriptomic analysis has been used to elucidate the complex pathogenesis of heterogeneous disease and may also contribute to identify potential therapeutic targets by delineating the hub genes. This study aimed to investigate whether blood transcriptomic clustering can distinguish clinical and immune phenotypes of asthmatics, and microbiome in asthmatics. METHODS Transcriptomic expression of peripheral blood mononuclear cells (PBMCs) from 47 asthmatics and 21 non-asthmatics was measured using RNA sequencing. A hierarchical clustering algorithm was used to classify asthmatics. Differentially expressed genes, clinical phenotypes, immune phenotypes, and microbiome of each transcriptomic cluster were assessed. RESULTS In asthmatics, three distinct transcriptomic clusters with numerously different transcriptomic expressions were identified. The proportion of severe asthmatics was highest in cluster 3 as 73.3%, followed by cluster 2 (45.5%) and cluster 1 (28.6%). While cluster 1 represented clinically non-severe T2 asthma, cluster 3 tended to include severe non-T2 asthma. Cluster 2 had features of both T2 and non-T2 asthmatics characterized by the highest serum IgE level and neutrophil-dominant sputum cell population. Compared to non-asthmatics, cluster 1 showed higher CCL23 and IL1RL1 expression while the expression of TREML4 was suppressed in cluster 3. CTSD and ALDH2 showed a significant positive linear relationship across three clusters in the order of cluster 1 to 3. No significant differences in the diversities of lung and gut microbiomes were observed among transcriptomic clusters of asthmatics and non-asthmatics. However, our study has limitations in that small sample size data were analyzed with unmeasured confounding factors and causal relationships or function pathways were not verified. CONCLUSIONS Genetic clustering based on the blood transcriptome may provide novel immunological insight, which can be biomarkers of asthma immune phenotypes. Trial registration Retrospectively registered.
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Affiliation(s)
- Hyun Woo Lee
- Department of Internal Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Min-Gyung Baek
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, Korea
| | - Sungmi Choi
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, Korea
| | - Yoon Hae Ahn
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-Gu, Seoul, 110-744, Korea
| | - Ji-Young Bang
- Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Kyoung-Hee Sohn
- Department of Internal Medicine, Kyung Hee University Hospital, Seoul, Korea
| | - Min-Gyu Kang
- Department of Internal Medicine, Chungbuk National University College of Medicine, Chungbuk National University Hospital, Cheongju, Korea
| | - Jae-Woo Jung
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Korea
| | - Jeong-Hee Choi
- Department of Pulmonology and Allergy, Allergy and Clinical Immunology Research Center, Hallym University College of Medicine, Chuncheon, Korea
| | - Sang-Heon Cho
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-Gu, Seoul, 110-744, Korea.,Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
| | - Hana Yi
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, Korea. .,School of Biosystems and Biomedical Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Korea.
| | - Hye-Ryun Kang
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-Gu, Seoul, 110-744, Korea. .,Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Korea. .,Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Korea.
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Shen Y, Zhang N, Yang Y, Hong S, Bachert C. Local Immunoglobulin E in nasal polyps: Role and modulation. Front Immunol 2022; 13:961503. [PMID: 36159836 PMCID: PMC9492990 DOI: 10.3389/fimmu.2022.961503] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/19/2022] [Indexed: 11/29/2022] Open
Abstract
In the airway, IgE is traditionally regarded as a key mediator in allergic diseases, such as AR and allergic asthma. However, growing evidence demonstrates the importance of local IgE in airway inflammatory diseases, irrespective of the presence of allergy. In this review, we discuss the most recent evidence for IgE in chronic rhinosinusitis with nasal polyps(CRSwNP), including the local IgE’s characteristics, the modulation of its synthesis, and its function. The levels of local IgE are significantly elevated in polyps independently of IgE serum levels and atopic status. Local IgE, which is correlated with type 2 inflammation, is polyclonal and functional. IgE is produced by active B cells and is dependent on the class switch recombination(CSR). In NPs, this process is triggered by not only allergens but also microbial colonization, especially the superantigen- Staphylococcus aureus. The production of local IgE is modulated by lymphocytes(such as Tfh, ILC2s, iTreg), cytokines(such as IL-4, IL-13, IFN-γ, TGF-β, IL-2, IL-21), transcription factors, and B cell-intrinsic factor. Due to the central role of IgE in NPs, it is regarded as an ideal target for therapy and has been proved to be clinically successful. Based on this knowledge, we believe that exploring the trigger and regulatory factors for the activation of local B cells and CSR to IgE will provide more valuable information for us to recognize the pathological mechanisms of local IgE and offer the possible option for new therapeutic targets of nasal polyps.
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Affiliation(s)
- Yang Shen
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Nan Zhang
- Upper Airways Research Laboratory, Department of Otorhinolaryngology, Ghent University, Ghent, Belgium
| | - Yucheng Yang
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Suling Hong
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Claus Bachert
- Upper Airways Research Laboratory, Department of Otorhinolaryngology, Ghent University, Ghent, Belgium
- Division of Otorhinolaryngology Diseases, Department of Clinical Sciences, Intervention and Technology (CLINTEC), Karolinska Institute, Stockholm, Sweden
- *Correspondence: Claus Bachert,
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Munemura R, Maehara T, Murakami Y, Koga R, Aoyagi R, Kaneko N, Doi A, Perugino CA, Della-Torre E, Saeki T, Sato Y, Yamamoto H, Kiyoshima T, Stone JH, Pillai S, Nakamura S. Distinct disease-specific Tfh cell populations in two different fibrotic diseases: IgG4-related disease and Kimura's disease. J Allergy Clin Immunol 2022; 150:440-455.e17. [PMID: 35568079 PMCID: PMC10369367 DOI: 10.1016/j.jaci.2022.03.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 03/01/2022] [Accepted: 03/21/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND How T follicular (Tfh) cells contribute to many different B-cell class-switching events during T cell-dependent immune responses has been unclear. Diseases with polarized isotype switching offer a unique opportunity for the exploration of Tfh subsets. Secondary and tertiary lymphoid organs (SLOs and TLOs) in patients with elevated tissue expression levels of IgE (Kimura's disease, KD) and those of IgG4 (IgG4-related disease, IgG4-RD) can provide important insights regarding cytokine expression by Tfh cells. OBJECTIVE To identify disease-specific Tfh cell subsets in SLOs and TLOs expressing IL-10 or IL-13 and thus identify different cellular drivers of class switching in two distinct types of fibrotic disorders: allergic fibrosis (driven by type 2 immune cells) and inflammatory fibrosis (driven by cytotoxic T lymphocytes). METHODS Single-cell RNA-sequencing, in situ sequencing, and multi-color immunofluorescence analysis was used to investigate B cells, Tfh cells and infiltrating type 2 cells in lesion tissues from patients with KD or IgG4-RD. RESULTS Infiltrating Tfh cells in TLOs from IgG4-RD were divided into six main clusters. We encountered abundant infiltrating IL-10-expressing LAG3+ Tfh cells in patients with IgG4-RD. Furthermore, we found that infiltrating AID+CD19+B cells expressing IL-4, IL-10, and IL-21 receptors correlated with IgG4 expression. In contrast, we found that infiltrating IL-13-expressing Tfh cells were abundant in affected tissues from patients with KD. Moreover, we observed few infiltrating IL-13-expressing Tfh cells in tissues from patients with IgG4-RD, despite high serum levels of IgE (but low IgE in the disease lesions). Cytotoxic T cells were abundant in IgG4-RD, and in contrast Type 2 immune cells were abundant in KD. CONCLUSIONS This single-cell dataset revealed a novel subset of IL10+LAG3+Tfh cells infiltrating the affected organs of IgG4-RD patients. In contrast, IL13+Tfh cells and type 2 immune cells infiltrated those of KD patients.
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Affiliation(s)
- Ryusuke Munemura
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Takashi Maehara
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan; Dento-craniofacial Development and Regeneration Research Center, Faculty of Dental Science, Kyushu University, Fukuoka, Japan.
| | - Yuka Murakami
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Risako Koga
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Ryuichi Aoyagi
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Naoki Kaneko
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | | | - Cory A Perugino
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Harvard Medical School, Boston, Mass; Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| | - Emanuel Della-Torre
- Unit of Immunology, Rheumatology, Allergy, and Rare Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Takako Saeki
- Department of Internal Medicine, Nagaoka Red Cross Hospital, Nagaoka, Japan
| | - Yasuharu Sato
- Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
| | - Hidetaka Yamamoto
- Division of Diagnostic Pathology, Kyushu University Hospital, Fukuoka, Japan
| | - Tamotsu Kiyoshima
- Laboratory of Oral Pathology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - John H Stone
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| | - Shiv Pillai
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| | - Seiji Nakamura
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
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9
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Hong Y, Tian X, Wang M, Chen C, Sun A. Bioinformatics-based identification of SPNS3 (Spinster homolog 3) as a prognostic biomarker of apoptosis resistance in acute myeloid leukemia. Bioengineered 2021; 12:7837-7848. [PMID: 34608834 PMCID: PMC8806827 DOI: 10.1080/21655979.2021.1982303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Spinster homolog 3 (SPNS3) belongs to the Spinster (SPNS) family which participates in sphingolipid transportation through the cell membrane. However, the functions of SPNS3 in acute myeloid leukemia (AML) are unknown. This study obtained SPNS3 from a gene set that was related to AML relapse and evaluate whether high SPNS3 expression induced apoptosis resistance in an AML cell line, which is consistent with the role of SPNS3 as a marker of poor prognosis in the clinic. Moreover, internal tandem duplication of FMS-like tyrosine kinase 3 (FLT3-ITD) mutation and the AC127521.1/ MIR-139/SPNS3 competing endogenous RNA axis were found to regulate SPNS3 expression. In addition, we noted that SPNS3 may play an important role in the Sphingosine-1-phosphate signal pathway that is involved in the maintenance of the AML microenvironment. These results highlight the anti-apoptosis effect of SPNS3 in AML, and the potential mechanism mediating this effect was explored through bioinformatics. Abbreviations: AML: acute myeloid leukemia; FLT3-ITD: internal tandem duplication of FMS-like tyrosine kinase 3; SPNS3: spinster homolog 3; SPNS1: spinster homolog 1; SPNS2: spinster homolog 2; GO: gene ontology; S1P: sphingosine-1-phosphate; ceRNA: competing endogenous RNA; dAML: acute myeloid leukemia at diagnosis; iAML: acute myeloid leukemia after induction chemotherapy; rAML: acute myeloid leukemia at relapse; DEGs: differentially expressed genes; BP: biological processes; CC: cellular components; MF: molecular functions; MRD: minimal residual disease; EFS: event-free survival; OS: overall survival; KEGG: Kyoto Encyclopedia of Genes and Genomes; SPHK: Sphingosine kinase.
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Affiliation(s)
- Yang Hong
- Department of Hematology, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, National Clinical Research Center for Hematologic Diseases, Suzhou, China
| | - Xiaopeng Tian
- Department of Hematology, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, National Clinical Research Center for Hematologic Diseases, Suzhou, China
| | - Mengmiao Wang
- Department of Hematology, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, National Clinical Research Center for Hematologic Diseases, Suzhou, China
| | - Cheng Chen
- Department of Hematology, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, National Clinical Research Center for Hematologic Diseases, Suzhou, China
| | - Aining Sun
- Institute of Blood and Marrow Transplantation, Medical College of Soochow University, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Collaborative Innovation Center of Hematology, National Clinical Research Center for Hematologic Diseases, Soochow University, Suzhou, China
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10
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Ditz B, Sarma A, Kerstjens HA, Liesker JJ, Bathoorn E, Vonk JM, Bernal V, Horvatovich P, Guryev V, Caldera S, Langelier C, Faiz A, Christenson SA, van den Berge M. The sputum transcriptome better predicts COPD exacerbations after the withdrawal of inhaled corticosteroids than sputum eosinophils. ERJ Open Res 2021; 7:00097-2021. [PMID: 34235210 PMCID: PMC8255541 DOI: 10.1183/23120541.00097-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/26/2021] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Continuing inhaled corticosteroid (ICS) use does not benefit all patients with COPD, yet it is difficult to determine which patients may safely sustain ICS withdrawal. Although eosinophil levels can facilitate this decision, better biomarkers could improve personalised treatment decisions. METHODS We performed transcriptional profiling of sputum to explore the molecular biology and compared the predictive value of an unbiased gene signature versus sputum eosinophils for exacerbations after ICS withdrawal in COPD patients. RNA-sequencing data of induced sputum samples from 43 COPD patients were associated with the time to exacerbation after ICS withdrawal. Expression profiles of differentially expressed genes were summarised to create gene signatures. In addition, we built a Bayesian network model to determine coregulatory networks related to the onset of COPD exacerbations after ICS withdrawal. RESULTS In multivariate analyses, we identified a gene signature (LGALS12, ALOX15, CLC, IL1RL1, CD24, EMR4P) associated with the time to first exacerbation after ICS withdrawal. The addition of this gene signature to a multiple Cox regression model explained more variance of time to exacerbations compared to a model using sputum eosinophils. The gene signature correlated with sputum eosinophil as well as macrophage cell counts. The Bayesian network model identified three coregulatory gene networks as well as sex to be related to an early versus late/nonexacerbation phenotype. CONCLUSION We identified a sputum gene expression signature that exhibited a higher predictive value for predicting COPD exacerbations after ICS withdrawal than sputum eosinophilia. Future studies should investigate the utility of this signature, which might enhance personalised ICS treatment in COPD patients.
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Affiliation(s)
- Benedikt Ditz
- Dept of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Aartik Sarma
- University of California, San Francisco, CA, USA
| | - Huib A.M. Kerstjens
- Dept of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Jeroen J.W. Liesker
- Dept of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Erik Bathoorn
- Dept of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Judith M. Vonk
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
- Dept of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Victor Bernal
- Dept of Analytical Biochemistry, Groningen Research Institute of Pharmacy, Groningen, The Netherlands
| | - Peter Horvatovich
- Dept of Analytical Biochemistry, Groningen Research Institute of Pharmacy, Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Saharai Caldera
- Division of Infectious Diseases, Dept of Medicine, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Chaz Langelier
- Division of Infectious Diseases, Dept of Medicine, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Alen Faiz
- Dept of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life Sciences, Sydney, Australia
- These authors contributed equally
| | | | - Maarten van den Berge
- Dept of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
- These authors contributed equally
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11
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Ferrante G, Licari A, Fasola S, Marseglia GL, La Grutta S. Artificial intelligence in the diagnosis of pediatric allergic diseases. Pediatr Allergy Immunol 2021; 32:405-413. [PMID: 33220121 DOI: 10.1111/pai.13419] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 11/09/2020] [Accepted: 11/16/2020] [Indexed: 12/18/2022]
Abstract
Artificial intelligence (AI) is a field of data science pertaining to advanced computing machines capable of learning from data and interacting with the human world. Early diagnosis and diagnostics, self-care, prevention and wellness, clinical decision support, care delivery, and chronic care management have been identified within the healthcare areas that could benefit from introducing AI. In pediatric allergy research, the recent developments in AI approach provided new perspectives for characterizing the heterogeneity of allergic diseases among patients. Moreover, the increasing use of electronic health records and personal healthcare records highlighted the relevance of AI in improving data quality and processing and setting-up advanced algorithms to interpret the data. This review aimed to summarize current knowledge about AI and discuss its impact on the diagnostic framework of pediatric allergic diseases such as eczema, food allergy, and respiratory allergy, along with the future opportunities that AI research can offer in this medical area.
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Affiliation(s)
- Giuliana Ferrante
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Amelia Licari
- Department of Pediatrics, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
| | - Salvatore Fasola
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR), Palermo, Italy
| | - Gian Luigi Marseglia
- Department of Pediatrics, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
| | - Stefania La Grutta
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR), Palermo, Italy
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12
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Du X, Li F, Zhang C, Li N, Huang H, Shao Z, Zhang M, Zhan X, He Y, Ju Z, Li W, Chen Z, Ying S, Shen H. Eosinophil-derived chemokine (hCCL15/23, mCCL6) interacts with CCR1 to promote eosinophilic airway inflammation. Signal Transduct Target Ther 2021; 6:91. [PMID: 33640900 PMCID: PMC7914252 DOI: 10.1038/s41392-021-00482-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/18/2020] [Accepted: 12/21/2020] [Indexed: 01/21/2023] Open
Abstract
Eosinophils are terminally differentiated cells derived from hematopoietic stem cells (HSCs) in the bone marrow. Several studies have confirmed the effective roles of eosinophils in asthmatic airway pathogenesis. However, their regulatory functions have not been well elucidated. Here, increased C-C chemokine ligand 6 (CCL6) in asthmatic mice and the human orthologs CCL15 and CCL23 that are highly expressed in asthma patients are described, which are mainly derived from eosinophils. Using Ccl6 knockout mice, further studies revealed CCL6-dependent allergic airway inflammation and committed eosinophilia in the bone marrow following ovalbumin (OVA) challenge and identified a CCL6-CCR1 regulatory axis in hematopoietic stem cells (HSCs). Eosinophil differentiation and airway inflammation were remarkably decreased by the specific CCR1 antagonist BX471. Thus, the study identifies that the CCL6-CCR1 axis is involved in the crosstalk between eosinophils and HSCs during the development of allergic airway inflammation, which also reveals a potential therapeutic strategy for targeting G protein-coupled receptors (GPCRs) for future clinical treatment of asthma.
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Affiliation(s)
- Xufei Du
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Fei Li
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Chao Zhang
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China.,Department of Anatomy, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Na Li
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Huaqiong Huang
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Zhehua Shao
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Min Zhang
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Xueqin Zhan
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Yicheng He
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Zhenyu Ju
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Wen Li
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Zhihua Chen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Songmin Ying
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China. .,International Institutes of Medicine, Zhejiang University School of Medicine, Yiwu, 322000, China. .,Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Huahao Shen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China. .,State Key Lab of Respiratory Disease, Guangzhou, 510120, China.
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13
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Katz-Kiriakos E, Steinberg DF, Kluender CE, Osorio OA, Newsom-Stewart C, Baronia A, Byers DE, Holtzman MJ, Katafiasz D, Bailey KL, Brody SL, Miller MJ, Alexander-Brett J. Epithelial IL-33 appropriates exosome trafficking for secretion in chronic airway disease. JCI Insight 2021; 6:136166. [PMID: 33507882 PMCID: PMC7934940 DOI: 10.1172/jci.insight.136166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 01/15/2021] [Indexed: 02/06/2023] Open
Abstract
IL-33 is a key mediator of chronic airway disease driven by type 2 immune pathways, yet the nonclassical secretory mechanism for this cytokine remains undefined. We performed a comprehensive analysis in human airway epithelial cells, which revealed that tonic IL-33 secretion is dependent on the ceramide biosynthetic enzyme neutral sphingomyelinase 2 (nSMase2). IL-33 is cosecreted with exosomes by the nSMase2-regulated multivesicular endosome (MVE) pathway as surface-bound cargo. In support of these findings, human chronic obstructive pulmonary disease (COPD) specimens exhibited increased epithelial expression of the abundantly secreted IL33Δ34 isoform and augmented nSMase2 expression compared with non-COPD specimens. Using an Alternaria-induced airway disease model, we found that the nSMase2 inhibitor GW4869 abrogated both IL-33 and exosome secretion as well as downstream inflammatory pathways. This work elucidates a potentially novel aspect of IL-33 biology that may be targeted for therapeutic benefit in chronic airway diseases driven by type 2 inflammation.
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Affiliation(s)
- Ella Katz-Kiriakos
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, and
| | - Deborah F Steinberg
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, and
| | - Colin E Kluender
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, and
| | - Omar A Osorio
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, and
| | | | - Arjun Baronia
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, and
| | - Derek E Byers
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, and
| | - Michael J Holtzman
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, and.,Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Dawn Katafiasz
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep and Allergy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Kristina L Bailey
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep and Allergy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Steven L Brody
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, and
| | - Mark J Miller
- Department of Medicine, Division of Infectious Diseases, and
| | - Jennifer Alexander-Brett
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, and.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
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14
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Elena-Pérez S, Heredero-Jung DH, García-Sánchez A, Estravís M, Martin MJ, Ramos-González J, Triviño JC, Isidoro-García M, Sanz C, Dávila I. Molecular Analysis of IL-5 Receptor Subunit Alpha as a Possible Pharmacogenetic Biomarker in Asthma. Front Med (Lausanne) 2021; 7:624576. [PMID: 33644088 PMCID: PMC7904892 DOI: 10.3389/fmed.2020.624576] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/30/2020] [Indexed: 01/17/2023] Open
Abstract
Background: Asthma is a heterogeneous syndrome with a broad clinical spectrum and high drug response variability. The inflammatory response in asthma involves multiple effector cells and mediator molecules. Based on asthma immunopathogenesis, precision medicine can be a promising strategy for identifying biomarkers. Biologic therapies acting on the IL-5/IL-5 receptor axis have been developed. IL-5 promotes proliferation, differentiation and activation of eosinophils by binding to the IL-5 receptor, located on the surface of eosinophils and basophils. This study aimed to investigate the expression of IL5RA in patients with several types of asthma and its expression after treatment with benralizumab, a biologic directed against IL-5 receptor subunit alpha. Methods: Sixty peripheral blood samples, 30 from healthy controls and 30 from asthmatic patients, were selected for a transcriptomic RNAseq study. Differential expression analysis was performed by statistical assessment of fold changes and P-values. A validation study of IL5RA expression was developed using qPCR in 100 controls and 187 asthmatic patients. The effect of benralizumab on IL5RA expression was evaluated in five patients by comparing expression levels between pretreatment and after 3 months of treatment. The IL5RA mRNA levels were normalized to GAPDH and TBP expression values for each sample. Calculations were made by the comparative ΔΔCt method. All procedures followed the MIQE guidelines. Results:IL5RA was one of the most differentially overexpressed coding transcripts in the peripheral blood of asthmatic patients (P = 8.63E-08 and fold change of 2.22). In the qPCR validation study, IL5RA expression levels were significantly higher in asthmatic patients than in controls (P < 0.001). Significant expression differences were present in different asthmatic types. In the biological drug study, patients treated with benralizumab showed a significant decrease in IL5RA expression and blood eosinophil counts. A notable improvement in ACT and lung function was also observed in these patients. Conclusions: These results indicate that IL5RA is overexpressed in patients with different types of asthma. It could help identify which asthmatic patients will respond more efficiently to benralizumab, moving toward a more personalized asthma management. Although further studies are required, IL5RA could play a role as a biomarker and pharmacogenetic factor in asthma.
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Affiliation(s)
- Sandra Elena-Pérez
- Department of Clinical Biochemistry, University Hospital of Salamanca, Salamanca, Spain
| | | | - Asunción García-Sánchez
- Allergic Disease Research Group IIMD-01, Institute for Biomedical Research of Salamanca, Salamanca, Spain.,Department of Biomedical Sciences and Diagnostics, University of Salamanca, Salamanca, Spain.,Network for Cooperative Research in Health - RETICS ARADyAL, Carlos III Health Institute, Madrid, Spain
| | - Miguel Estravís
- Allergic Disease Research Group IIMD-01, Institute for Biomedical Research of Salamanca, Salamanca, Spain.,Department of Biomedical Sciences and Diagnostics, University of Salamanca, Salamanca, Spain.,Network for Cooperative Research in Health - RETICS ARADyAL, Carlos III Health Institute, Madrid, Spain
| | - Maria J Martin
- Allergic Disease Research Group IIMD-01, Institute for Biomedical Research of Salamanca, Salamanca, Spain.,Network for Cooperative Research in Health - RETICS ARADyAL, Carlos III Health Institute, Madrid, Spain
| | | | | | - María Isidoro-García
- Department of Clinical Biochemistry, University Hospital of Salamanca, Salamanca, Spain.,Allergic Disease Research Group IIMD-01, Institute for Biomedical Research of Salamanca, Salamanca, Spain.,Network for Cooperative Research in Health - RETICS ARADyAL, Carlos III Health Institute, Madrid, Spain.,Department of Medicine, University of Salamanca, Salamanca, Spain
| | - Catalina Sanz
- Allergic Disease Research Group IIMD-01, Institute for Biomedical Research of Salamanca, Salamanca, Spain.,Network for Cooperative Research in Health - RETICS ARADyAL, Carlos III Health Institute, Madrid, Spain.,Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Ignacio Dávila
- Allergic Disease Research Group IIMD-01, Institute for Biomedical Research of Salamanca, Salamanca, Spain.,Department of Biomedical Sciences and Diagnostics, University of Salamanca, Salamanca, Spain.,Network for Cooperative Research in Health - RETICS ARADyAL, Carlos III Health Institute, Madrid, Spain.,Department of Allergy, University Hospital of Salamanca, Salamanca, Spain
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15
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Singh D, Bassi M, Balzano D, Lucci G, Emirova A, Anna Nandeuil M, Jellema G, Afolabi EK, Leaker B, Kornmann O, Michael Beeh K, Watz H, Govoni M. COPD patients with chronic bronchitis and higher sputum eosinophil counts show increased type-2 and PDE4 gene expression in sputum. J Cell Mol Med 2020; 25:905-918. [PMID: 33295083 PMCID: PMC7812250 DOI: 10.1111/jcmm.16146] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 11/22/2020] [Indexed: 12/18/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) patients with higher eosinophil counts are associated with increased clinical response to phosphodiesterase‐4‐inhibitors (PDE4i). However, the underlying inflammatory mechanisms associated with this increased response is not yet elucidated. This post hoc analysis focused on sputum gene expression in patients with chronic bronchitis who underwent 32‐day treatment with two doses of the inhaled PDE4i CHF6001 (tanimilast) or placebo on top of triple therapy. Biological characterization and treatment effects were assessed between patients with different sputum eosinophil levels (eosinophilhigh ≥ 3%; eosinophillow < 3%) at baseline (primary samples) or at the end of the treatment of the placebo arm (validation samples). Forty‐one genes were differentially expressed in primary samples (p‐adjusted for false discovery rate < 0.05); all up‐regulated in eosinophilhigh patients and functionally enriched for type‐2 and PDE4 inflammatory processes. Eleven out of nineteen genes having immune system biological processes annotations including IL5RA, ALOX15, IL1RL1, CLC, GATA1 and PDE4D were replicated using validation samples. The expression of a number of these inflammatory mediators was reduced by tanimilast treatment, with greater effects observed in eosinophilhigh patients. These findings suggest that type‐2 and PDE4 overexpression in COPD patients with higher sputum eosinophil counts contribute to the differential clinical response to PDE4i observed in previous clinical trials.
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Affiliation(s)
- Dave Singh
- Medicines Evaluation Unit, The University of Manchester, Manchester University NHS Foundation Hospital Trust, Manchester, UK
| | | | | | | | - Aida Emirova
- Global Clinical Development, Chiesi, Parma, Italy
| | | | | | | | | | - Oliver Kornmann
- IKF Pneumologie Frankfurt, Clinical Research Centre Respiratory Diseases, Frankfurt, Germany
| | | | - Henrik Watz
- Pulmonary Research Institute at Lung Clinic Grosshansdorf, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Mirco Govoni
- Global Clinical Development, Chiesi, Parma, Italy
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16
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Predictive significance of arachidonate 15-lipoxygenase for eosinophilic chronic rhinosinusitis with nasal polyps. Allergy Asthma Clin Immunol 2020; 16:82. [PMID: 32973910 PMCID: PMC7493848 DOI: 10.1186/s13223-020-00480-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/04/2020] [Indexed: 12/20/2022] Open
Abstract
Background Eosinophilic chronic rhinosinusitis with nasal polyps (ECRSwNP) exhibits a poorer outcome compared with non-eosinophilic chronic rhinosinusitis with nasal polyps (nonECRSwNP), so it is significant to identify effective markers to differentiate ECRSwNP in guiding the treatment strategies of these patients. Although arachidonate 15-lipoxygenase (ALOX15) is positioned as a marker of eosinophilic inflammation, its study in differentiating ECRSwNP has not been reported. The aim of this study is to assess the potential of ALOX15 in distinguishing and predicting ECRSwNP. Methods Forty-eight patients with chronic rhinosinusitis with nasal polyps (CRSwNP), including 30 ECRSwNP and 18 nonECRSwNP patients, were enrolled. ALOX15 mRNA level was determined in polyps by real-time polymerase chain reaction (RT-PCR). The patients’ baseline characteristics were evaluated and analyzed for correlations with ALOX15. Receiver operating characteristic (ROC) curve was used to assess the predictive significance of the potential predictors for ECRSwNP. Results ALOX15 mRNA level was significantly higher in ECRSwNP patients than in nonECRSwNP patients (P < 0.001). ALOX15 mRNA was significantly correlated with tissue and blood eosinophil percentages (r = 0.565, P < 0.001 and r = 0.395, P = 0.006), olfaction scores (r = 0.400, P = 0.005), total visual analogue scale (VAS) symptom scores (r = 0.383, P = 0.007), ethmoid/maxillary sinus (E/M) ratio (r = 0.463, P = 0.001), and endoscopy scores (r = 0.409, P = 0.004). Logistic regression analysis showed ALOX15 mRNA level and percentage of blood eosinophils to be predictive factors for ECRSwNP (P = 0.004 and P = 0.036, respectively). ROC curve indicated ALOX15 to have high predictive accuracy for ECRSwNP (area under the curve (AUC) = 0.909), which was further improved by combination of ALOX15 with percentage of blood eosinophils (AUC = 0.933). Conclusions The relative ALOX15 mRNA level alone or in combination with blood eosinophils might be a reliable biomarker for predicting a diagnosis of ECRSwNP.
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17
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Huang W, Qian T, Cheng Z, Zeng T, Si C, Liu C, Deng C, Ye X, Liu Y, Cui L, Fu L. Prognostic significance of Spinster homolog gene family in acute myeloid leukemia. J Cancer 2020; 11:4581-4588. [PMID: 32489475 PMCID: PMC7255376 DOI: 10.7150/jca.44766] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/02/2020] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) is a clonal and heterogeneous disease characterized by proliferation of immature myeloid cells, with impaired differentiation and maturation. Spinster homolog (SPNS) is a widely distributed transmembrane transporter, which assists sphingolipids in playing their roles through the cell membrane. However, the expression and clinical implication of the SPNS family has not been investigated in AML. From the Cancer Genome Atlas database, a total of 155 AML patients with complete clinical characteristics and SPNS1-3 expression data were contained in our study. In patients who received chemotherapy only, high expressions of SPNS2 and SPNS3 had adverse effects on event-free survival (EFS) and overall survival (OS) (all P<0.05). However, in the allogeneic hematopoietic stem cell transplantation (allo-HSCT) group, we only found a significant difference in OS between the high and low SPNS3 expression groups (P=0.001), while other SPNS members showed no effect on survival. Multivariate analysis indicated that high SPNS2 expression was an independent risk factor for both EFS and OS in chemotherapy patients. The results confirmed that high expression of SPNS2 and SPNS3 were poor prognostic factors, and the effect of SPNS2 can be neutralized by allo-HSCT.
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Affiliation(s)
- Wenhui Huang
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.,Translational Medicine Center, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China.,Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumor Microenvironment, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Tingting Qian
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.,Translational Medicine Center, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China.,Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumor Microenvironment, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Zhiheng Cheng
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Tiansheng Zeng
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.,Translational Medicine Center, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China.,Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumor Microenvironment, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Chaozeng Si
- Information Center, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Chaojun Liu
- Yinfeng Gene Technology Co., Ltd.; No.1109, Gangxing 3 Rd,New and High-tech Zone, Jinan City, Shandong Province, 250102, China
| | - Cong Deng
- Department of Clinical laboratory, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Xu Ye
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Yan Liu
- Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, 475000, China
| | - Longzhen Cui
- Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, 475000, China.,Department of Hematology, Huaihe Hospital of Henan University, Kaifeng, 475000, China
| | - Lin Fu
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.,Translational Medicine Center, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China.,Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumor Microenvironment, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.,Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, 475000, China.,Department of Hematology, Huaihe Hospital of Henan University, Kaifeng, 475000, China
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18
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Persson EK, Verstraete K, Heyndrickx I, Gevaert E, Aegerter H, Percier JM, Deswarte K, Verschueren KHG, Dansercoer A, Gras D, Chanez P, Bachert C, Gonçalves A, Van Gorp H, De Haard H, Blanchetot C, Saunders M, Hammad H, Savvides SN, Lambrecht BN. Protein crystallization promotes type 2 immunity and is reversible by antibody treatment. Science 2019; 364:364/6442/eaaw4295. [PMID: 31123109 DOI: 10.1126/science.aaw4295] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/05/2019] [Indexed: 01/05/2023]
Abstract
Although spontaneous protein crystallization is a rare event in vivo, Charcot-Leyden crystals (CLCs) consisting of galectin-10 (Gal10) protein are frequently observed in eosinophilic diseases, such as asthma. We found that CLCs derived from patients showed crystal packing and Gal10 structure identical to those of Gal10 crystals grown in vitro. When administered to the airways, crystalline Gal10 stimulated innate and adaptive immunity and acted as a type 2 adjuvant. By contrast, a soluble Gal10 mutein was inert. Antibodies directed against key epitopes of the CLC crystallization interface dissolved preexisting CLCs in patient-derived mucus within hours and reversed crystal-driven inflammation, goblet-cell metaplasia, immunoglobulin E (IgE) synthesis, and bronchial hyperreactivity (BHR) in a humanized mouse model of asthma. Thus, protein crystals may promote hallmark features of asthma and are targetable by crystal-dissolving antibodies.
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Affiliation(s)
- Emma K Persson
- Immunoregulation Unit, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Kenneth Verstraete
- Unit for Structural Biology, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Ines Heyndrickx
- Immunoregulation Unit, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Elien Gevaert
- Upper Airways Research Laboratory, ENT Department, Ghent University Hospital, Ghent, Belgium
| | - Helena Aegerter
- Immunoregulation Unit, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | | | - Kim Deswarte
- Immunoregulation Unit, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Koen H G Verschueren
- Unit for Structural Biology, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Ann Dansercoer
- Unit for Structural Biology, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Delphine Gras
- Aix Marseille University, INSERM, INRA, C2VN, Marseille, France
| | - Pascal Chanez
- Aix Marseille University, INSERM, INRA, C2VN, Marseille, France.,Clinique des Bronches, Allergies et Sommeil, Hôpital Nord, AP-HM, Marseille, France
| | - Claus Bachert
- Upper Airways Research Laboratory, ENT Department, Ghent University Hospital, Ghent, Belgium.,Division of ENT Diseases, CLINTEC, Karolinska Institute, Stockholm, Sweden
| | - Amanda Gonçalves
- BioImaging Core, VIB Inflammation Research Center, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Hanne Van Gorp
- Immunoregulation Unit, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | | | | | | | - Hamida Hammad
- Immunoregulation Unit, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Savvas N Savvides
- Unit for Structural Biology, VIB Center for Inflammation Research, Ghent, Belgium. .,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Bart N Lambrecht
- Immunoregulation Unit, VIB Center for Inflammation Research, Ghent, Belgium. .,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Department of Pulmonary Medicine, ErasmusMC, Rotterdam, Netherlands
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19
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Klös M, Thürmann L, Bauer M, Heinrich J, Standl M, von Berg A, Schaaf B, Weichenhan D, Mücke O, Plass C, Röder S, Herberth G, Sack U, Borte M, Stangl GI, Eils R, Trump S, Lehmann I. Longitudinal trends of serum IgE and IL5RA expression throughout childhood are associated with asthma but not with persistent wheeze. Allergy 2019; 74:2002-2006. [PMID: 31012487 DOI: 10.1111/all.13837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/11/2019] [Accepted: 03/21/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Matthias Klös
- Molecular Epidemiology Unit Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, associated partner of the German Center for Lung Research (DZL) Berlin Germany
- Department of Environmental Immunology Helmholtz Centre for EnvironmentalResearch – UFZ Leipzig Germany
| | - Loreen Thürmann
- Molecular Epidemiology Unit Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, associated partner of the German Center for Lung Research (DZL) Berlin Germany
- Department of Environmental Immunology Helmholtz Centre for EnvironmentalResearch – UFZ Leipzig Germany
| | - Mario Bauer
- Department of Environmental Immunology Helmholtz Centre for EnvironmentalResearch – UFZ Leipzig Germany
| | - Joachim Heinrich
- Institute and Clinic for Occupational, Social and Environmental Medicine University HospitalLMU Munich Germany
- Institute of Epidemiology Helmholtz Zentrum München ‐ German ResearchCenter for Environmental Health Neuherberg Germany
| | - Marie Standl
- Institute of Epidemiology Helmholtz Zentrum München ‐ German ResearchCenter for Environmental Health Neuherberg Germany
| | - Andrea von Berg
- Department of Pediatrics Research Institute Marien‐Hospital Wesel Wesel Germany
| | - Beate Schaaf
- Pediatric Outpatient Department Bad Honnef Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics German Cancer Research Center (DKFZ)Heidelberg Germany
| | - Oliver Mücke
- Division of Cancer Epigenomics German Cancer Research Center (DKFZ)Heidelberg Germany
| | - Christoph Plass
- Division of Cancer Epigenomics German Cancer Research Center (DKFZ)Heidelberg Germany
| | - Stefan Röder
- Department of Environmental Immunology Helmholtz Centre for EnvironmentalResearch – UFZ Leipzig Germany
| | - Gunda Herberth
- Department of Environmental Immunology Helmholtz Centre for EnvironmentalResearch – UFZ Leipzig Germany
| | - Ulrich Sack
- Medical Faculty Institute for Clinical Immunology University of Leipzig Leipzig Germany
| | - Michael Borte
- Children's HospitalMunicipal Hospital “St. Georg” Leipzig Germany
| | - Gabriele I. Stangl
- Institute of Agricultural and Nutritional Sciences Martin Luther University Halle‐Wittenberg Halle Germany
| | - Roland Eils
- Center for Digital Health Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, associated partner of the German Center for Lung Research (DZL) Berlin Germany
- Heidelberg University HospitalHealth Data Science Unit Heidelberg Germany
| | - Saskia Trump
- Molecular Epidemiology Unit Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, associated partner of the German Center for Lung Research (DZL) Berlin Germany
- Department of Environmental Immunology Helmholtz Centre for EnvironmentalResearch – UFZ Leipzig Germany
| | - Irina Lehmann
- Molecular Epidemiology Unit Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, associated partner of the German Center for Lung Research (DZL) Berlin Germany
- Department of Environmental Immunology Helmholtz Centre for EnvironmentalResearch – UFZ Leipzig Germany
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20
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Virkud YV, Kelly RS, Wood C, Lasky-Su JA. The nuts and bolts of omics for the clinical allergist. Ann Allergy Asthma Immunol 2019; 123:558-563. [PMID: 31562939 DOI: 10.1016/j.anai.2019.09.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/17/2019] [Accepted: 09/17/2019] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Omics, aka multi-omics, is an emerging area of research that is advancing the use of personalized medicine in clinical practice and is therefore relevant for the practicing allergist. DATA SOURCES We performed a literature search of a selection of scientific findings in omics and allergy, including variants that may be important to allergy outcomes in the genome, transcriptome, metabolome, microbiome, epigenome, and exposome, among others. STUDY SELECTIONS Basic science papers and review articles. RESULTS The use of multi-omic data in clinical practice is changing how clinicians treat their patients whereby more personalized approaches are becoming standard in medical practice and has the potential to transform the treatment of allergies. CONCLUSION Multi-omic data are relevant and will become increasingly important for the clinical allergist.
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Affiliation(s)
- Yamini V Virkud
- Department of Pediatrics, Massachusetts General Hospital for Children and Harvard Medical School, Boston, Massachusetts; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Rachel S Kelly
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Caleb Wood
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jessica A Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.
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21
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O'Shea MK, Fletcher TE, Muller J, Tanner R, Matsumiya M, Bailey JW, Jones J, Smith SG, Koh G, Horsnell WG, Beeching NJ, Dunbar J, Wilson D, Cunningham AF, McShane H. Human Hookworm Infection Enhances Mycobacterial Growth Inhibition and Associates With Reduced Risk of Tuberculosis Infection. Front Immunol 2018; 9:2893. [PMID: 30619265 PMCID: PMC6302045 DOI: 10.3389/fimmu.2018.02893] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 11/26/2018] [Indexed: 12/22/2022] Open
Abstract
Soil-transmitted helminths and Mycobacterium tuberculosis frequently coincide geographically and it is hypothesized that gastrointestinal helminth infection may exacerbate tuberculosis (TB) disease by suppression of Th1 and Th17 responses. However, few studies have focused on latent TB infection (LTBI), which predominates globally. We performed a large observational study of healthy adults migrating from Nepal to the UK (n = 645). Individuals were screened for LTBI and gastrointestinal parasite infections. A significant negative association between hookworm and LTBI-positivity was seen (OR = 0.221; p = 0.039). Hookworm infection treatment did not affect LTBI conversions. Blood from individuals with hookworm had a significantly greater ability to control virulent mycobacterial growth in vitro than from those without, which was lost following hookworm treatment. There was a significant negative relationship between mycobacterial growth and eosinophil counts. Eosinophil-associated differential gene expression characterized the whole blood transcriptome of hookworm infection and correlated with improved mycobacterial control. These data provide a potential alternative explanation for the reduced prevalence of LTBI among individuals with hookworm infection, and possibly an anti-mycobacterial role for helminth-induced eosinophils.
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Affiliation(s)
- Matthew K. O'Shea
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
- Royal Centre for Defence Medicine, Joint Medical Command, Birmingham, United Kingdom
| | - Thomas E. Fletcher
- Royal Centre for Defence Medicine, Joint Medical Command, Birmingham, United Kingdom
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Julius Muller
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Rachel Tanner
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Magali Matsumiya
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - J. Wendi Bailey
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Jayne Jones
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Steven G. Smith
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Gavin Koh
- Department of Infectious Diseases, Northwick Park Hospital, London, United Kingdom
| | - William G. Horsnell
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
- Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Nicholas J. Beeching
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - James Dunbar
- Royal Centre for Defence Medicine, Joint Medical Command, Birmingham, United Kingdom
- Department of Infectious Diseases, The Friarage Hospital, Northallerton, United Kingdom
| | - Duncan Wilson
- Royal Centre for Defence Medicine, Joint Medical Command, Birmingham, United Kingdom
| | - Adam F. Cunningham
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Helen McShane
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
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22
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Croteau-Chonka DC, Chen Z, Barnes KC, Barraza-Villarreal A, Celedón JC, Gauderman WJ, Gilliland FD, Krishnan JA, Liu AH, London SJ, Martinez FD, Millstein J, Naureckas ET, Nicolae DL, White SR, Ober C, Weiss ST, Raby BA. Gene Coexpression Networks in Whole Blood Implicate Multiple Interrelated Molecular Pathways in Obesity in People with Asthma. Obesity (Silver Spring) 2018; 26:1938-1948. [PMID: 30358166 PMCID: PMC6262830 DOI: 10.1002/oby.22341] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/06/2018] [Accepted: 09/11/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Asthmatic children who develop obesity through adolescence have poorer disease outcomes compared with those who do not. This study aimed to characterize the biology of childhood asthma complicated by adult obesity. METHODS Gene expression networks are powerful statistical tools for characterizing human disease that leverage the putative coregulatory relationships of genes to infer relevant biological pathways. Weighted gene coexpression network analysis of gene expression data was performed in whole blood from 514 adult asthmatic subjects. Then, module preservation and association replication analyses were performed in 418 subjects from two independent asthma cohorts (one pediatric and one adult). RESULTS A multivariate model was identified in which three gene coexpression network modules were associated with incident obesity in the discovery cohort (each P < 0.05). Two module memberships were enriched for genes in pathways related to platelets, integrins, extracellular matrix, smooth muscle, NF-κB signaling, and Hedgehog signaling. The network structures of each of the obesity modules were significantly preserved in both replication cohorts (permutation P = 9.999E-05). The corresponding module gene sets were significantly enriched for differential expression in subjects with obesity in both replication cohorts (each P < 0.05). CONCLUSIONS The gene coexpression network profiles thus implicate multiple interrelated pathways in the biology of an important endotype of asthma with obesity.
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Affiliation(s)
- Damien C. Croteau-Chonka
- Channing Division of Network Medicine, Department of
Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston,
MA, USA
| | - Zhanghua Chen
- Division of Environmental Health, Department of Preventive
Medicine, Keck School of Medicine, University of Southern California, Los Angeles,
CA, USA
| | - Kathleen C. Barnes
- Division of Biomedical Informatics and Personalized
Medicine, Department of Medicine, University of Colorado School of Medicine,
Anschutz Medical Campus, Aurora, CO, USA
| | | | - Juan C. Celedón
- Division of Pulmonary Medicine, Allergy and Immunology,
Children’s Hospital of Pittsburgh of the University of Pittsburgh Medical
Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - W. James Gauderman
- Division of Biostatistics, Department of Preventive
Medicine, Keck School of Medicine, University of Southern California, Los Angeles,
CA, USA
| | - Frank D. Gilliland
- Division of Environmental Health, Department of Preventive
Medicine, Keck School of Medicine, University of Southern California, Los Angeles,
CA, USA
| | - Jerry A. Krishnan
- Division of Pulmonary, Critical Care, Sleep, and Allergy,
Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Andrew H. Liu
- Division of Allergy and Clinical Immunology, Department of
Pediatrics, National Jewish Health and University of Colorado School of Medicine,
Denver, CO, USA
| | - Stephanie J. London
- Division of Intramural Research, Department of Health and
Human Services, National Institute of Environmental Health Sciences, National
Institutes of Health, Research Triangle Park, NC, USA
| | - Fernando D. Martinez
- Arizona Respiratory Center and BIO5 Institute, University
of Arizona, Tucson, AZ, USA
| | - Joshua Millstein
- Division of Biostatistics, Department of Preventive
Medicine, Keck School of Medicine, University of Southern California, Los Angeles,
CA, USA
| | - Edward T. Naureckas
- Section of Pulmonary and Critical Care Medicine,
Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Dan L. Nicolae
- Department of Human Genetics, University of Chicago,
Chicago, IL, USA
- Section of Genetic Medicine, Department of Medicine,
University of Chicago, Chicago, IL, USA
- Department of Statistics, University of Chicago, Chicago,
IL, USA
| | - Steven R. White
- Section of Pulmonary and Critical Care Medicine,
Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago,
Chicago, IL, USA
| | - Scott T. Weiss
- Channing Division of Network Medicine, Department of
Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston,
MA, USA
- Partners HealthCare Personalized Medicine, Partners
Health Care, Boston, MA, USA
| | - Benjamin A. Raby
- Channing Division of Network Medicine, Department of
Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston,
MA, USA
- BWH Pulmonary Genetics Center, Division of Pulmonary and
Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital
and Harvard Medical School, Boston, MA, USA
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